diff --git a/firebase.json b/firebase.json index 340ed5b..51a7f62 100644 --- a/firebase.json +++ b/firebase.json @@ -12,5 +12,21 @@ "destination": "/index.html" } ] - } + }, + "functions": [ + { + "source": "functions", + "codebase": "default", + "ignore": [ + "node_modules", + ".git", + "firebase-debug.log", + "firebase-debug.*.log" + ], + "predeploy": [ + "npm --prefix \"$RESOURCE_DIR\" run lint", + "npm --prefix \"$RESOURCE_DIR\" run build" + ] + } + ] } diff --git a/functions/.eslintrc.js b/functions/.eslintrc.js new file mode 100644 index 0000000..3dfe6ca --- /dev/null +++ b/functions/.eslintrc.js @@ -0,0 +1,29 @@ +module.exports = { + root: true, + env: { + es6: true, + node: true, + }, + extends: [ + 'eslint:recommended', + 'plugin:import/errors', + 'plugin:import/warnings', + 'plugin:import/typescript', + 'google', + 'plugin:@typescript-eslint/recommended', + ], + parser: '@typescript-eslint/parser', + parserOptions: { + project: ['tsconfig.json', 'tsconfig.dev.json'], + sourceType: 'module', + }, + ignorePatterns: [ + '/lib/**/*', // Ignore built files. + ], + plugins: ['@typescript-eslint', 'import'], + rules: { + quotes: ['error', 'double'], + 'import/no-unresolved': 0, + indent: ['error', 2], + }, +}; diff --git a/functions/.gitignore b/functions/.gitignore new file mode 100644 index 0000000..65b4c06 --- /dev/null +++ b/functions/.gitignore @@ -0,0 +1,9 @@ +# Compiled JavaScript files +lib/**/*.js +lib/**/*.js.map + +# TypeScript v1 declaration files +typings/ + +# Node.js dependency directory +node_modules/ diff --git a/functions/.tool-versions b/functions/.tool-versions new file mode 100644 index 0000000..31dbaf6 --- /dev/null +++ b/functions/.tool-versions @@ -0,0 +1 @@ +nodejs 18.20.3 \ No newline at end of file diff --git a/functions/package-lock.json b/functions/package-lock.json new file mode 100644 index 0000000..89981e1 --- /dev/null +++ b/functions/package-lock.json @@ -0,0 +1,8385 @@ +{ + "name": "functions", + "lockfileVersion": 3, + 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"firebase-functions": "^4.3.1", + "stopwords-en": "^0.3.0" + }, + "devDependencies": { + "@typescript-eslint/eslint-plugin": "^5.12.0", + "@typescript-eslint/parser": "^5.12.0", + "eslint": "^8.9.0", + "eslint-config-google": "^0.14.0", + "eslint-plugin-import": "^2.25.4", + "firebase-functions-test": "^3.1.0", + "typescript": "^4.9.0" + }, + "private": true +} diff --git a/functions/src/index.ts b/functions/src/index.ts new file mode 100644 index 0000000..9ebe7cf --- /dev/null +++ b/functions/src/index.ts @@ -0,0 +1,37 @@ +/** + * Import function triggers from their respective submodules: + * + * import {onCall} from "firebase-functions/v2/https"; + * import {onDocumentWritten} from "firebase-functions/v2/firestore"; + * + * See a full list of supported triggers at https://firebase.google.com/docs/functions + */ + +import { onDocumentUpdated } from 'firebase-functions/v2/firestore'; + +import { nGramsPipeline } from './ngrams'; + +// Start writing functions +// https://firebase.google.com/docs/functions/typescript + +// TODO: Change to onDocumentCreated +exports.generateKeywords = onDocumentUpdated('publications/{publicationId}', (event) => { + // Get object representing the document + const data = event.data?.after.data(); + const previousData = event.data?.before.data(); + + const abstract: string | undefined = data?.abstract; + + if ( + // No abstract + !abstract || + // Abstract is the same as before + abstract == previousData?.abstract + ) { + return null; + } + + return data?.after.ref.set({ + keywords: nGramsPipeline(abstract), + }); +}); diff --git a/functions/src/ngrams.ts b/functions/src/ngrams.ts new file mode 100644 index 0000000..05ca5fd --- /dev/null +++ b/functions/src/ngrams.ts @@ -0,0 +1,88 @@ +import stopwords from 'stopwords-en'; + +const cleanText = (text: string): string => { + return ( + text + // Remove HTML tags + .replaceAll(/<\/?[^>]+(>|$)/g, '') + // Remove punctuation except periods + .replaceAll(/[^\w\s.]/g, '') + // Replace multiple new lines with one space + .replaceAll(/\n+/g, ' ') + // Remove 'abstract' from the beginning of the text + .replaceAll(/^\s*abstract\s*/i, '') + // Replace multiple spaces with one space + .replaceAll(/\s+/g, ' ') + // Trim white space + .trim() + ); +}; + +const nGrams = (tokens: string[], n: number): string[] => { + const nGrams = []; + + for (let i = 0; i < tokens.length - (n - 1); i++) { + const gram = tokens + .slice(i, i + n) + .join(' ') + // Remove ending periods + .replace(/\.+$/, ''); + + // don't push any that has a period + if (!gram.includes('.')) { + nGrams.push(gram); + } + } + + return nGrams; +}; + +const calcFreqMap = (arr: string[]): { [key: string]: number } => { + const result: { [key: string]: number } = {}; + arr.forEach((item) => { + result[item] = (result[item] ?? 0) + 1; + }); + return result; +}; + +// Remove n-grams that contain stopwords in the first or last position +const filterOutStopwords = (str: string) => { + const words = str.split(' '); + + const first = words[0]; + const last = words[words.length - 1]; + + return !(stopwords.includes(first.toLowerCase()) || stopwords.includes(last.toLowerCase())); +}; + +export const nGramsPipeline = (abstract: string) => { + const tokenized = cleanText(abstract).split(' '); + const monograms = nGrams(tokenized, 1); + + const biGrams = nGrams(tokenized, 2); + const triGrams = nGrams(tokenized, 3); + + const entries = [ + ...Object.entries(calcFreqMap(monograms)), + ...Object.entries(calcFreqMap(biGrams)), + ...Object.entries(calcFreqMap(triGrams)), + ]; + + const filtered = entries.filter(([gram, frequency]) => + // Filter out stopwords + filterOutStopwords(gram) + ); + + // Combine grams + // TODO: Singularize + // TODO: Deal with uppercase/lowercase for titles and beginning of sentences? + + // Sort by frequency and then by gram + return filtered.sort(([gramA, frequencyA], [gramB, frequencyB]) => { + if (frequencyA === frequencyB) { + return gramA.localeCompare(gramB); + } + + return frequencyA - frequencyB; + }); +}; diff --git a/functions/tsconfig.dev.json b/functions/tsconfig.dev.json new file mode 100644 index 0000000..c0f990d --- /dev/null +++ b/functions/tsconfig.dev.json @@ -0,0 +1,3 @@ +{ + "include": [".eslintrc.js"] +} diff --git a/functions/tsconfig.json b/functions/tsconfig.json new file mode 100644 index 0000000..5b2bad4 --- /dev/null +++ b/functions/tsconfig.json @@ -0,0 +1,13 @@ +{ + "compilerOptions": { + "module": "commonjs", + "noImplicitReturns": true, + "noUnusedLocals": true, + "outDir": "lib", + "sourceMap": true, + "strict": true, + "target": "es2021", + }, + "compileOnSave": true, + "include": ["src", "types"], +} diff --git a/functions/types/index.d.ts b/functions/types/index.d.ts new file mode 100644 index 0000000..794d1f4 --- /dev/null +++ b/functions/types/index.d.ts @@ -0,0 +1 @@ +declare module 'stopwords-en'; diff --git a/scripts/sortedPublications/completed.json b/scripts/sortedPublications/completed.json new file mode 100644 index 0000000..6e7528e --- /dev/null +++ b/scripts/sortedPublications/completed.json @@ -0,0 +1,3033 @@ +[ + { + "title": "Stable genetic structure and connectivity in pollution-adapted and nearby pollution-sensitive populations ofFundulus heteroclitus", + "author": "Joaquin C. B. Nunez, Leann M. Biancani, Patrick A. Flight, Diane E. Nacci, David M. Rand, Douglas L. Crawford, Marjorie F. Oleksiak", + "publisher": "The Royal Society", + "url": "http://dx.doi.org/10.1098/rsos.171532", + "doi": "10.1098/rsos.171532", + "year": 2018, + "month": 5, + "abstract": "Populations of the non-migratory estuarine fishFundulus heteroclitusinhabiting the heavily polluted New Bedford Harbour (NBH) estuary have shown inherited tolerance to local pollutants introduced to their habitats in the past 100 years. Here we examine two questions: (i) Is there pollution-driven selection on the mitochondrial genome across a fine geographical scale? and (ii) What is the pattern of migration among sites spanning a strong pollution gradient? Whole mitochondrial genomes were analysed for 133F. heteroclitusfrom seven nearby collection sites: four sites along the NBH pollution cline (approx. 5 km distance), which had pollution-adapted fish, as well as one site adjacent to the pollution cline and two relatively unpolluted sites about 30 km away, which had pollution-sensitive fish. Additionally, we used microsatellite analyses to quantify genetic variation over threeF. heteroclitusgenerations in both pollution-adapted and sensitive individuals collected from two sites at two different time points (1999/2000 and 2007/2008). Our results show no evidence for a selective sweep of mtDNA in the polluted sites. Moreover, mtDNA analyses revealed that both pollution-adapted and sensitive populations harbour similar levels of genetic diversity. We observed a high level of non-synonymous mutations in the most polluted site. This is probably associated with a reduction inNeand concomitant weakening of purifying selection, a demographic expansion following a pollution-related bottleneck or increased mutation rates. Our demographic analyses suggest that isolation by distance influences the distribution of mtDNA genetic variation between the pollution cline and the clean populations at broad spatial scales. At finer scales, population structure is patchy, and neither spatial distance, pollution concentration or pollution tolerance is a good predictor of mtDNA variation. Lastly, microsatellite analyses revealed stable population structure over the last decade.", + "subject": [], + "keywords": [] + }, + { + "title": "Hemispheric sea ice distribution sets the glacial tempo", + "author": "Jung‐Eun Lee, Aaron Shen, Baylor Fox‐Kemper, Yi Ming", + "publisher": "American Geophysical Union (AGU)", + "url": "http://dx.doi.org/10.1002/2016gl071307", + "doi": "10.1002/2016gl071307", + "year": 2017, + "month": 1, + "abstract": "AbstractThe proxy record of global temperature shows that the dominant periodicity of the glacial cycle shifts from 40 kyr (obliquity) to 100 kyr (eccentricity) about a million years ago. Using climate model simulations, here we show that the pace of the glacial cycle depends on the pattern of hemispheric sea ice growth. In a cold climate the sea ice grows asymmetrically between two hemispheres under changes to Earth's orbital precession, because sea ice growth potential outside of the Arctic Circle is limited. This difference in hemispheric sea ice growth leads to an asymmetry in absorbed solar energy for the two hemispheres, particularly when eccentricity is high, even if the annual average insolation is similar. In a warmer climate, the hemispheric asymmetry of the sea ice decreases as mean Arctic and Antarctic sea ice decreases, diminishing the precession and eccentricity signals and explaining the dominant obliquity signal (40 kyr) before the mid‐Pleistocene transition.", + "subject": [], + "keywords": [] + }, + { + "title": "A numerical study of shock waves generated through laser ablation of explosives", + "author": "Wenyu Bai, Gerald J. Diebold, Charles M. Wynn, Robert W. Haupt, John H. Doherty", + "publisher": "AIP Publishing", + "url": "http://dx.doi.org/10.1063/1.4967825", + "doi": "10.1063/1.4967825", + "year": 2016, + "month": 11, + "abstract": "Shock waves resulting from irradiation of energetic materials with a pulsed ultraviolet laser source have been shown to be an effective indicator for explosives detection. Here, the features of shock wave propagation are explored theoretically. The initial stage of the shock motion is simulated as a one-dimensional process. As the nonlinear wave expands to form a blast wave, a system of conservation equations, simplified to the Euler equations, is employed to model wave propagation. The Euler equations are solved numerically by the 5th order weighted essentially non-oscillatory finite difference scheme with the time integration carried out using the 3rd order total variation diminishing Runge Kutta method. The numerical results for the shock wave evolution are compared with those obtained from experiments with a meltcast 2,6-dinitrotoluene sample. The calculations lay a theoretical foundation for a recently investigated technique for photoacoustically sensing explosives using a vibrometer.", + "subject": [], + "keywords": [] + }, + { + "title": "Patient-specific blood rheology in sickle-cell anaemia", + "author": "Xuejin Li, E. Du, Huan Lei, Yu-Hang Tang, Ming Dao, Subra Suresh, George Em Karniadakis", + "publisher": "The Royal Society", + "url": "http://dx.doi.org/10.1098/rsfs.2015.0065", + "doi": "10.1098/rsfs.2015.0065", + "year": 2016, + "month": 2, + "abstract": "Sickle-cell anaemia (SCA) is an inherited blood disorder exhibiting heterogeneous cell morphology and abnormal rheology, especially under hypoxic conditions. By using a multiscale red blood cell (RBC) model with parameters derived from patient-specific data, we present a mesoscopic computational study of the haemodynamic and rheological characteristics of blood from SCA patients with hydroxyurea (HU) treatment (on-HU) and those without HU treatment (off-HU). We determine the shear viscosity of blood in health as well as in different states of disease. Our results suggest that treatment with HU improves or worsens the rheological characteristics of blood in SCA depending on the degree of hypoxia. However, on-HU groups always have higher levels of haematocrit-to-viscosity ratio (HVR) than off-HU groups, indicating that HU can indeed improve the oxygen transport potential of blood. Our patient-specific computational simulations suggest that the HVR level, rather than the shear viscosity of sickle RBC suspensions, may be a more reliable indicator in assessing the response to HU treatment.", + "subject": [], + "keywords": [] + }, + { + "title": "Acceleration of saddle-point searches with machine learning", + "author": "Andrew A. Peterson", + "publisher": "AIP Publishing", + "url": "http://dx.doi.org/10.1063/1.4960708", + "doi": "10.1063/1.4960708", + "year": 2016, + "month": 8, + "abstract": "In atomistic simulations, the location of the saddle point on the potential-energy surface (PES) gives important information on transitions between local minima, for example, via transition-state theory. However, the search for saddle points often involves hundreds or thousands of ab initio force calls, which are typically all done at full accuracy. This results in the vast majority of the computational effort being spent calculating the electronic structure of states not important to the researcher, and very little time performing the calculation of the saddle point state itself. In this work, we describe how machine learning (ML) can reduce the number of intermediate ab initio calculations needed to locate saddle points. Since machine-learning models can learn from, and thus mimic, atomistic simulations, the saddle-point search can be conducted rapidly in the machine-learning representation. The saddle-point prediction can then be verified by an ab initio calculation; if it is incorrect, this strategically has identified regions of the PES where the machine-learning representation has insufficient training data. When these training data are used to improve the machine-learning model, the estimates greatly improve. This approach can be systematized, and in two simple example problems we demonstrate a dramatic reduction in the number of ab initio force calls. We expect that this approach and future refinements will greatly accelerate searches for saddle points, as well as other searches on the potential energy surface, as machine-learning methods see greater adoption by the atomistics community.", + "subject": [], + "keywords": [] + }, + { + "title": "The Influence of Elastic Strain on Catalytic Activity in the Hydrogen Evolution Reaction", + "author": "Kai Yan, Tuhina Adit Maark, Alireza Khorshidi, Vijay A. Sethuraman, Andrew A. Peterson, Pradeep R. Guduru", + "publisher": "Wiley", + "url": "http://dx.doi.org/10.1002/anie.201508613", + "doi": "10.1002/anie.201508613", + "year": 2016, + "month": 4, + "abstract": "AbstractUnderstanding the role of elastic strain in modifying catalytic reaction rates is crucial for catalyst design, but experimentally, this effect is often coupled with a ligand effect. To isolate the strain effect, we have investigated the influence of externally applied elastic strain on the catalytic activity of metal films in the hydrogen evolution reaction (HER). We show that elastic strain tunes the catalytic activity in a controlled and predictable way. Both theory and experiment show strain controls reactivity in a controlled manner consistent with the qualitative predictions of the HER volcano plot and the d‐band theory: Ni and Pt's activities were accelerated by compression, while Cu's activity was accelerated by tension. By isolating the elastic strain effect from the ligand effect, this study provides a greater insight into the role of elastic strain in controlling electrocatalytic activity.", + "subject": [], + "keywords": [] + }, + { + "title": "Computer vision cracks the leaf code", + "author": "Peter Wilf, Shengping Zhang, Sharat Chikkerur, Stefan A. Little, Scott L. Wing, Thomas Serre", + "publisher": "Proceedings of the National Academy of Sciences", + "url": "http://dx.doi.org/10.1073/pnas.1524473113", + "doi": "10.1073/pnas.1524473113", + "year": 2016, + "month": 3, + "abstract": "SignificanceThe botanical value of angiosperm leaf shape and venation (“leaf architecture”) is well known, but the astounding complexity and variation of leaves have thwarted efforts to access this underused resource. This challenge is central for paleobotany because most angiosperm fossils are isolated, unidentified leaves. We here demonstrate that a computer vision algorithm trained on several thousand images of diverse cleared leaves successfully learns leaf-architectural features, then categorizes novel specimens into natural botanical groups above the species level. The system also produces heat maps to display the locations of numerous novel, informative leaf characters in a visually intuitive way. With assistance from computer vision, the systematic and paleobotanical value of leaves is ready to increase significantly.", + "subject": [], + "keywords": [] + }, + { + "title": "Assessing the mineralogy of the watershed and fan deposits of the Jezero crater paleolake system, Mars", + "author": "Timothy A. Goudge, John F. Mustard, James W. Head, Caleb I. Fassett, Sandra M. Wiseman", + "publisher": "American Geophysical Union (AGU)", + "url": "http://dx.doi.org/10.1002/2014je004782", + "doi": "10.1002/2014je004782", + "year": 2015, + "month": 4, + "abstract": "AbstractWe present results from geomorphic mapping and visible to near‐infrared spectral analyses of the Jezero crater paleolake basin and its associated watershed. The goal of this study is to understand the provenance of the sedimentary deposits within this open‐basin lake using a source‐to‐sink approach. Two fan deposits located within the basin have distinct visible to near‐infrared mineralogic signatures measured by the Compact Reconnaissance Imaging Spectrometer for Mars (CRISM). The northern fan is spectrally characterized by a mixture of Mg‐rich carbonate and olivine, while the western fan is characterized by Fe/Mg‐smectite (e.g., saponite or nontronite) with variable amounts of Mg‐rich carbonate and olivine in isolated exposures. The watersheds of these deposits contain a variety of geomorphic units that are likely to have supplied sediment to the Jezero crater paleolake, as the fluvial valleys that fed the basin incise these units. The geomorphic units include exposures of Fe/Mg‐smectite‐, olivine‐, and Mg‐rich carbonate‐bearing terrain. We show that the difference in fan deposit mineralogy is a function of the areal exposure of the major geomorphic units within their watersheds. This indicates that the spectrally dominant aqueous alteration minerals in the fan deposits are primarily detrital, or transported, in nature and did not form in situ. We conclude that the aqueous alteration of the units in the watershed occurred prior to the fluvial activity that carved the valleys of the Jezero crater paleolake system, and that the two periods of aqueous activity are not genetically related.", + "subject": [], + "keywords": [] + }, + { + "title": "Ultrafast structural dynamics in Rydberg excited N,N,N′,N′-tetramethylethylenediamine: conformation dependent electron lone pair interaction and charge delocalization", + "author": "Xinxin Cheng, Yao Zhang, Sanghamitra Deb, Michael P. Minitti, Yan Gao, Hannes Jónsson, Peter M. Weber", + "publisher": "Royal Society of Chemistry (RSC)", + "url": "http://dx.doi.org/10.1039/c4sc01646g", + "doi": "10.1039/c4sc01646g", + "year": 2014, + "month": -1, + "abstract": "Time-resolved Rydberg fingerprint spectroscopy and quantum calculations reveal the structure dependent electron lone pair interaction and charge delocalization in real time.", + "subject": [], + "keywords": [] + }, + { + "title": "Phylogenomic analyses of deep gastropod relationships reject Orthogastropoda", + "author": "Felipe Zapata, Nerida G. Wilson, Mark Howison, Sónia C. S. Andrade, Katharina M. Jörger, Michael Schrödl, Freya E. Goetz, Gonzalo Giribet, Casey W. Dunn", + "publisher": "The Royal Society", + "url": "http://dx.doi.org/10.1098/rspb.2014.1739", + "doi": "10.1098/rspb.2014.1739", + "year": 2014, + "month": 11, + "abstract": "Gastropods are a highly diverse clade of molluscs that includes many familiar animals, such as limpets, snails, slugs and sea slugs. It is one of the most abundant groups of animals in the sea and the only molluscan lineage that has successfully colonized land. Yet the relationships among and within its constituent clades have remained in flux for over a century of morphological, anatomical and molecular study. Here, we re-evaluate gastropod phylogenetic relationships by collecting new transcriptome data for 40 species and analysing them in combination with publicly available genomes and transcriptomes. Our datasets include all five main gastropod clades: Patellogastropoda, Vetigastropoda, Neritimorpha, Caenogastropoda and Heterobranchia. We use two different methods to assign orthology, subsample each of these matrices into three increasingly dense subsets, and analyse all six of these supermatrices with two different models of molecular evolution. All 12 analyses yield the same unrooted network connecting the five major gastropod lineages. This reduces deep gastropod phylogeny to three alternative rooting hypotheses. These results reject the prevalent hypothesis of gastropod phylogeny, Orthogastropoda. Our dated tree is congruent with a possible end-Permian recovery of some gastropod clades, namely Caenogastropoda and some Heterobranchia subclades.", + "subject": [], + "keywords": [] + }, + { + "title": "A chloroplast tree for Viburnum (Adoxaceae) and its implications for phylogenetic classification and character evolution", + "author": "Wendy L. Clement, Mónica Arakaki, Patrick W. Sweeney, Erika J. Edwards, Michael J. Donoghue", + "publisher": "Wiley", + "url": "http://dx.doi.org/10.3732/ajb.1400015", + "doi": "10.3732/ajb.1400015", + "year": 2014, + "month": 6, + "abstract": "• Premise of the study: Despite recent progress, significant uncertainties remain concerning relationships among early‐branching lineages within Viburnum (Adoxaceae), prohibiting a new classification and hindering studies of character evolution and the increasing use of Viburnum in addressing a wide range of ecological and evolutionary questions. We hoped to resolve these issues by sequencing whole plastid genomes for representative species and combining these with molecular data previously obtained from an expanded taxon sample.• Methods: We performed paired‐end Illumina sequencing of plastid genomes of 22 Viburnum species and combined these data with a 10‐gene data set to infer phylogenetic relationships for 113 species. We used the results to devise a comprehensive phylogenetic classification and to analyze the evolution of eight morphological characters that vary among early‐branching lineages.• Key results: With greatly increased levels of confidence in most of the early branches, we propose a phylogenetic classification of Viburnum, providing formal phylogenetic definitions for 30 clades, including 13 with names recognized under the International Code of Nomenclature for Algae, Fungi, and Plants, eight with previously proposed informal names, and nine newly proposed names for major branches. Our parsimony reconstructions of bud structure, leaf margins, inflorescence form, ruminate endosperm, extrafloral nectaries, glandular trichomes, palisade anatomy, and pollen exine showed varying levels of homoplasy, but collectively provided morphological support for some, though not all, of the major clades.• Conclusions: Our study demonstrates the value of next‐generation plastid sequencing, the ease of creating a formal phylogenetic classification, and the utility of such a system in describing patterns of character evolution.", + "subject": [], + "keywords": [] + }, + { + "title": "Selective accumulation of germ‐line associated gene products in early development of the sea star and distinct differences from germ‐line development in the sea urchin", + "author": "Tara Fresques, Vanesa Zazueta‐Novoa, Adrian Reich, Gary M. Wessel", + "publisher": "Wiley", + "url": "http://dx.doi.org/10.1002/dvdy.24038", + "doi": "10.1002/dvdy.24038", + "year": 2013, + "month": 12, + "abstract": "Background: Echinodermata is a diverse phylum, a sister group to chordates, and contains diverse organisms that may be useful to understand varied mechanisms of germ‐line specification. Results: We tested 23 genes in development of the sea star Patiria miniata that fall into five categories: (1) Conserved germ‐line factors; (2) Genes involved in the inductive mechanism of germ‐line specification; (3) Germ‐line associated genes; (4) Molecules involved in left–right asymmetry; and (5) Genes involved in regulation and maintenance of the genome during early embryogenesis. Overall, our results support the contention that the posterior enterocoel is a source of the germ line in the sea star P. miniata. Conclusions: The germ line in this organism appears to be specified late in embryogenesis, and in a pattern more consistent with inductive interactions amongst cells. This is distinct from the mechanism seen in sea urchins, a close relative of the sea star clad. We propose that P. miniata may serve as a valuable model to study inductive mechanisms of germ‐cell specification and when compared with germ‐line formation in the sea urchin S. purpuratus may reveal developmental transitions that occur in the evolution of inherited and inductive mechanisms of germ‐line specification. Developmental Dynamics 243:568–587, 2014. © 2013 Wiley Periodicals, Inc.", + "subject": [], + "keywords": [] + }, + { + "title": "Comparing Spatial and Multilevel Regression Models for Binary Outcomes in Neighborhood Studies", + "author": "Hongwei Xu", + "publisher": "SAGE Publications", + "url": "http://dx.doi.org/10.1177/0081175013490188", + "doi": "10.1177/0081175013490188", + "year": 2014, + "month": 4, + "abstract": "The standard multilevel regressions that are widely used in neighborhood research typically ignore potential between-neighborhood correlations due to underlying spatial processes, and hence they produce inappropriate inferences about neighborhood effects. In contrast, spatial models make estimations and predictions across areas by explicitly modeling the spatial correlations among observations in different locations. A better understanding of the strengths and limitations of spatial models as compared with the standard multilevel model is needed to improve the research on neighborhood and spatial effects. This research systematically compares model estimations and predictions for binary outcomes between (distance- and lattice-based) spatial and the standard multilevel models in the presence of both within- and between-neighborhood correlations, through simulations. Results from simulation analysis reveal that the standard multilevel and spatial models produce similar estimates of fixed effects but different estimates of random effects variances. Both the standard multilevel and pure spatial models tend to overestimate the corresponding random effects variances compared with hybrid models when both nonspatial within-neighborhood and spatial between-neighborhood effects exist. Spatial models also outperform the standard multilevel model by a narrow margin in case of fully out-of-sample predictions. Distance-based spatial models provide additional spatial information and have stronger predictive power than lattice-based models under certain circumstances. These merits of spatial modeling are exhibited in an empirical analysis of the child mortality data from 1880 Newark, New Jersey.", + "subject": [], + "keywords": [] + }, + { + "title": "Piwi regulates Vasa accumulation during embryogenesis in the sea urchin", + "author": "Mamiko Yajima, Eric A. Gustafson, Jia L. Song, Gary M. Wessel", + "publisher": "Wiley", + "url": "http://dx.doi.org/10.1002/dvdy.24096", + "doi": "10.1002/dvdy.24096", + "year": 2013, + "month": 12, + "abstract": "Background: Piwi proteins are essential for germ line development, stem cell maintenance, and more recently found to function in epigenetic and somatic gene regulation. In the sea urchin Strongylocentrotus purpuratus, two Piwi proteins, Seawi and Piwi‐like1, have been identified, yet their functional contributions have not been reported. Results: Here we found that Seawi protein was localized uniformly in the early embryo and then became enriched in the primordial germ cells (PGCs) (the small micromere lineage) from blastula stage and thereafter. Morpholino knockdown of Sp‐seawi diminished PGC‐specific localization of Seawi proteins, and altered expression of other germ line markers such as Vasa and Gustavus, but had no effect on Nanos. Furthermore, Seawi knockdown transiently resulted in Vasa positive cell proliferation in the right coelomic pouch that appear to be derived from the small micromere lineage, yet they quickly disappeared with an indication of apoptosis by larval stage. Severe Seawi knockdown resulted in an increased number of apoptotic cells in the entire gut area. Conclusion: Piwi proteins appear to regulate PGC proliferation perhaps through control of Vasa accumulation. In this organism, Piwi is likely regulating mRNAs, not just transposons, and is potentially functioning both inside and outside of the germ line during embryogenesis. Developmental Dynamics 243:451–458, 2014. © 2013 Wiley Periodicals, Inc.", + "subject": [], + "keywords": [] + }, + { + "title": "The Neural Dynamics of Face Detection in the Wild Revealed by MVPA", + "author": "Maxime Cauchoix, Gladys Barragan-Jason, Thomas Serre, Emmanuel J. Barbeau", + "publisher": "Society for Neuroscience", + "url": "http://dx.doi.org/10.1523/jneurosci.3030-13.2014", + "doi": "10.1523/jneurosci.3030-13.2014", + "year": 2014, + "month": 1, + "abstract": "Previous magnetoencephalography/electroencephalography (M/EEG) studies have suggested that face processing is extremely rapid, indeed faster than any other object category. Most studies, however, have been performed using centered, cropped stimuli presented on a blank background resulting in artificially low interstimulus variability. In contrast, the aim of the present study was to assess the underlying temporal dynamics of face detection presented in complex natural scenes.We recorded EEG activity while participants performed a rapid go/no-go categorization task in which they had to detect the presence of a human face. Subjects performed at ceiling (94.8% accuracy), and traditional event-related potential analyses revealed only modest modulations of the two main components classically associated with face processing (P100 and N170). A multivariate pattern analysis conducted across all EEG channels revealed that face category could, however, be readout very early, under 100 ms poststimulus onset. Decoding was linked to reaction time as early as 125 ms. Decoding accuracy did not increase monotonically; we report an increase during an initial 95–140 ms period followed by a plateau ∼140–185 ms–perhaps reflecting a transitory stabilization of the face information available–and a strong increase afterward. Further analyses conducted on individual images confirmed these phases, further suggesting that decoding accuracy may be initially driven by low-level stimulus properties. Such latencies appear to be surprisingly short given the complexity of the natural scenes and the large intraclass variability of the face stimuli used, suggesting that the visual system is highly optimized for the processing of natural scenes.", + "subject": [], + "keywords": [] + }, + { + "title": "PIWI proteins and PIWI-interacting RNAs function in\n Hydra\n somatic stem cells", + "author": "Celina E. Juliano, Adrian Reich, Na Liu, Jessica Götzfried, Mei Zhong, Selen Uman, Robert A. Reenan, Gary M. Wessel, Robert E. Steele, Haifan Lin", + "publisher": "Proceedings of the National Academy of Sciences", + "url": "http://dx.doi.org/10.1073/pnas.1320965111", + "doi": "10.1073/pnas.1320965111", + "year": 2013, + "month": 12, + "abstract": "Significance\n \n The P-element–induced wimpy testis (PIWI) proteins and their bound small RNAs (PIWI-interacting RNAs, piRNAs) are known to repress transposon expression in the germline, yet they likely have broader regulatory functions. We show that the PIWI–piRNA pathway functions in the stem cells of an early diverging animal. We demonstrate that\n Hydra\n has two PIWI proteins that are localized in the cytoplasm of all adult stem/progenitor cell types. We identified putative targets of the pathway, both transposon and nontransposon, by sequencing piRNAs and mapping them to a newly assembled\n Hydra\n transcriptome. Finally we demonstrate that\n Hydra\n PIWI is essential in the somatic lineages. This study supports the existence of a common regulatory pathway ancestral to both stem and germ cells.", + "subject": [], + "keywords": [] + }, + { + "title": "The potential for machine learning in hybrid QM/MM calculations", + "author": "Yin-Jia Zhang, Alireza Khorshidi, Georg Kastlunger, Andrew A. Peterson", + "publisher": "AIP Publishing", + "url": "http://dx.doi.org/10.1063/1.5029879", + "doi": "10.1063/1.5029879", + "year": 2018, + "month": 6, + "abstract": "Hybrid quantum-mechanics/molecular-mechanics (QM/MM) simulations are popular tools for the simulation of extended atomistic systems, in which the atoms in a core region of interest are treated with a QM calculator and the surrounding atoms are treated with an empirical potential. Recently, a number of atomistic machine-learning (ML) tools have emerged that provide functional forms capable of reproducing the output of more expensive electronic-structure calculations; such ML tools are intriguing candidates for the MM calculator in QM/MM schemes. Here, we suggest that these ML potentials provide several natural advantages when employed in such a scheme. In particular, they may allow for newer, simpler QM/MM frameworks while also avoiding the need for extensive training sets to produce the ML potential. The drawbacks of employing ML potentials in QM/MM schemes are also outlined, which are primarily based on the added complexity to the algorithm of training and re-training ML models. Finally, two simple illustrative examples are provided which show the power of adding a retraining step to such “QM/ML” algorithms.", + "subject": [], + "keywords": [] + }, + { + "title": "The role of oxygen vacancies in biomass deoxygenation by reducible zinc/zinc oxide catalysts", + "author": "Xiao Xiao, Helen Bergstrom, Ryan Saenger, Benjamin Johnson, Runcang Sun, Andrew Peterson", + "publisher": "Royal Society of Chemistry (RSC)", + "url": "http://dx.doi.org/10.1039/c7cy02535a", + "doi": "10.1039/c7cy02535a", + "year": 2018, + "month": -1, + "abstract": "Selective removal of oxygen is the key challenge in the upgrading of biomass-derived molecules, and reducible metal oxides have shown the ability to catalytically remove oxygen even at low exogenous H2 pressures.", + "subject": [], + "keywords": [] + }, + { + "title": "Validation of XMALab software for marker-based XROMM", + "author": "Benjamin J. Knörlein, David B. Baier, Stephen M. Gatesy, J. D. Laurence-Chasen, Elizabeth L. Brainerd", + "publisher": "The Company of Biologists", + "url": "http://dx.doi.org/10.1242/jeb.145383", + "doi": "10.1242/jeb.145383", + "year": 2016, + "month": 1, + "abstract": "Marker-based XROMM requires software tools for: 1) correcting fluoroscope distortion; 2) calibrating X-ray cameras; 3) tracking radio-opaque markers; and 4) calculating rigid body motion. In this paper we describe and validate XMALab, a new open-source software package for marker-based XROMM (C++ source and compiled versions on Bitbucket). Most marker-based XROMM studies to date have used XrayProject in MATLAB. XrayProject can produce results with excellent accuracy and precision, but it is somewhat cumbersome to use and requires a MATLAB license. We have designed XMALab to accelerate the XROMM process and to make it more accessible to new users. Features include the four XROMM steps (listed above) in one cohesive user interface, real-time plot windows for detecting errors, and integration with an online data management system, XMAPortal. Accuracy and precision of XMALab when tracking markers in a machined object are ±0.010 and ±0.043 mm, respectively. Mean precision for nine users tracking markers in a tutorial dataset of minipig feeding was ±0.062 mm in XMALab and ±0.14 mm in XrayProject. Reproducibility of 3D point locations across nine users was tenfold greater in XMALab than in XrayProject, and six degree-of-freedom bone motions calculated with a joint coordinate system were three- to sixfold more reproducible in XMALab. XMALab is also suitable for tracking white or black markers in standard light videos with optional checkerboard calibration. We expect XMALab to increase both the quality and quantity of animal motion data available for comparative biomechanics research.", + "subject": [], + "keywords": [] + }, + { + "title": "Universal and domain-specific sequences in 23S–28S ribosomal RNA identified by computational phylogenetics", + "author": "Stephen M. Doris, Deborah R. Smith, Julia N. Beamesderfer, Benjamin J. Raphael, Judith A. Nathanson, Susan A. Gerbi", + "publisher": "Cold Spring Harbor Laboratory", + "url": "http://dx.doi.org/10.1261/rna.051144.115", + "doi": "10.1261/rna.051144.115", + "year": 2015, + "month": 8, + "abstract": "Comparative analysis of ribosomal RNA (rRNA) sequences has elucidated phylogenetic relationships. However, this powerful approach has not been fully exploited to address ribosome function. Here we identify stretches of evolutionarily conserved sequences, which correspond with regions of high functional importance. For this, we developed a structurally aligned database, FLORA (full-lengthorganismalrRNAalignment) to identify highly conserved nucleotide elements (CNEs) in 23S–28S rRNA from each phylogenetic domain (Eukarya, Bacteria, and Archaea). Universal CNEs (uCNEs) are conserved in sequence and structural position in all three domains. Those in regions known to be essential for translation validate our approach. Importantly, some uCNEs reside in areas of unknown function, thus identifying novel sequences of likely great importance. In contrast to uCNEs, domain-specific CNEs (dsCNEs) are conserved in just one phylogenetic domain. This is the first report of conserved sequence elements in rRNA that are domain-specific; they are largely a eukaryotic phenomenon. The locations of the eukaryotic dsCNEs within the structure of the ribosome suggest they may function in nascent polypeptide transit through the ribosome tunnel and in tRNA exit from the ribosome. Our findings provide insights and a resource for ribosome function studies.", + "subject": [], + "keywords": [] + }, + { + "title": "Characterizing and controlling intrinsic biases of lambda exonuclease in nascent strand sequencing reveals phasing between nucleosomes and G-quadruplex motifs around a subset of human replication origins", + "author": "Michael S. Foulk, John M. Urban, Cinzia Casella, Susan A. Gerbi", + "publisher": "Cold Spring Harbor Laboratory", + "url": "http://dx.doi.org/10.1101/gr.183848.114", + "doi": "10.1101/gr.183848.114", + "year": 2015, + "month": 2, + "abstract": "Nascent strand sequencing (NS-seq) is used to discover DNA replication origins genome-wide, allowing identification of features for their specification. NS-seq depends on the ability of lambda exonuclease (λ-exo) to efficiently digest parental DNA while leaving RNA-primer protected nascent strands intact. We used genomics and biochemical approaches to determine if λ-exo digests all parental DNA sequences equally. We report that λ-exo does not efficiently digest G-quadruplex (G4) structures in a plasmid. Moreover, λ-exo digestion of nonreplicating genomic DNA (LexoG0) enriches GC-rich DNA and G4 motifs genome-wide. We used LexoG0 data to control for nascent strand–independent λ-exo biases in NS-seq and validated this approach at the rDNA locus. The λ-exo–controlled NS-seq peaks are not GC-rich, and only 35.5% overlap with 6.8% of all G4s, suggesting that G4s are not general determinants for origin specification but may play a role for a subset. Interestingly, we observed a periodic spacing of G4 motifs and nucleosomes around the peak summits, suggesting that G4s may position nucleosomes at this subset of origins. Finally, we demonstrate that use of Na+ instead of K+ in the λ-exo digestion buffer reduced the effect of G4s on λ-exo digestion and discuss ways to increase both the sensitivity and specificity of NS-seq.", + "subject": [], + "keywords": [] + }, + { + "title": "(Invited) Optimizing Electrocatalyst Selectivity for CO2 Reduction over H2 Evolution", + "author": "Andrew A. Peterson", + "publisher": "The Electrochemical Society", + "url": "http://dx.doi.org/10.1149/06603.0041ecst", + "doi": "10.1149/06603.0041ecst", + "year": 2015, + "month": 4, + "abstract": "The electrocatalytic reduction of CO2 to fuels or chemicals is an attractive alternative to fossil- or biomass-based feedstocks. However, since the reduction typically requires protons in the reaction pathway, the evolution of H2 is a common side reaction; in practice H2 often dominates the observed products. In the current work, ways in which the selectivity between these two reactions can be understood and optimized are presented. First, it is shown that the identification and optimization of the expression of active edge sites in nanostructured Au catalysts for CO evolution results in catalysts with extremely high selectivities and mass activities at low overpotentials. Second, it is shown that the reactive state of the catalyst surface can have a strong steering effect on the selectivity. Fundamental adsorbate–adsorbate interactions drive the reactivity and selectivity across more reactive catalyst surfaces, and it is shown that in the example cases of Cu and Mo catalysts, the interaction can have opposite qualitative trends.", + "subject": [], + "keywords": [] + }, + { + "title": "The opercular mouth-opening mechanism of largemouth bass functions as a 3D four-bar linkage with three degrees of freedom", + "author": "Aaron M. Olsen, Ariel L. Camp, Elizabeth L. Brainerd", + "publisher": "The Company of Biologists", + "url": "http://dx.doi.org/10.1242/jeb.159079", + "doi": "10.1242/jeb.159079", + "year": 2017, + "month": 12, + "abstract": "ABSTRACT\n The planar, one degree of freedom (1-DoF) four-bar linkage is an important model for understanding the function, performance and evolution of numerous biomechanical systems. One such system is the opercular mechanism in fishes, which is thought to function like a four-bar linkage to depress the lower jaw. While anatomical and behavioral observations suggest some form of mechanical coupling, previous attempts to model the opercular mechanism as a planar four-bar have consistently produced poor model fits relative to observed kinematics. Using newly developed, open source mechanism fitting software, we fitted multiple three-dimensional (3D) four-bar models with varying DoF to in vivo kinematics in largemouth bass to test whether the opercular mechanism functions instead as a 3D four-bar with one or more DoF. We examined link position error, link rotation error and the ratio of output to input link rotation to identify a best-fit model at two different levels of variation: for each feeding strike and across all strikes from the same individual. A 3D, 3-DoF four-bar linkage was the best-fit model for the opercular mechanism, achieving link rotational errors of less than 5%. We also found that the opercular mechanism moves with multiple degrees of freedom at the level of each strike and across multiple strikes. These results suggest that active motor control may be needed to direct the force input to the mechanism by the axial muscles and achieve a particular mouth-opening trajectory. Our results also expand the versatility of four-bar models in simulating biomechanical systems and extend their utility beyond planar or single-DoF systems.", + "subject": [], + "keywords": [] + }, + { + "title": "Rib kinematics during lung ventilation in the American alligator (Alligator mississippiensis): an XROMM analysis", + "author": "Robert J. Brocklehurst, Sabine Moritz, Jonathan Codd, William I. Sellers, Elizabeth L. Brainerd", + "publisher": "The Company of Biologists", + "url": "http://dx.doi.org/10.1242/jeb.156166", + "doi": "10.1242/jeb.156166", + "year": 2017, + "month": 9, + "abstract": "ABSTRACT\n The current hypothesis regarding the mechanics of breathing in crocodylians is that the double-headed ribs, with both a capitulum and tuberculum, rotate about a constrained axis passing through the two articulations; moreover, this axis shifts in the caudal thoracic ribs, as the vertebral parapophysis moves from the centrum to the transverse process. Additionally, the ventral ribcage in crocodylians is thought to possess additional degrees of freedom through mobile intermediate ribs. In this study, X-ray reconstruction of moving morphology (XROMM) was used to quantify rib rotation during breathing in American alligators. Whilst costovertebral joint anatomy predicted overall patterns of motion across the ribcage (decreased bucket handle motion and increased calliper motion), there were significant deviations: anatomical axes overestimated pump handle motion and, generally, ribs in vivo rotate about all three body axes more equally than predicted. The intermediate ribs are mobile, with a high degree of rotation measured about the dorsal intracostal joints, especially in the more caudal ribs. Motion of the sternal ribs became increasingly complex caudally, owing to a combination of the movements of the vertebral and intermediate segments. As the crocodylian ribcage is sometimes used as a model for the ancestral archosaur, these results have important implications for how rib motion is reconstructed in fossil taxa, and illustrate the difficulties in reconstructing rib movement based on osteology alone.", + "subject": [], + "keywords": [] + }, + { + "title": "Dual function of the pectoral girdle for feeding and locomotion in white-spotted bamboo sharks", + "author": "Ariel L. Camp, Bradley Scott, Elizabeth L. Brainerd, Cheryl D. Wilga", + "publisher": "The Royal Society", + "url": "http://dx.doi.org/10.1098/rspb.2017.0847", + "doi": "10.1098/rspb.2017.0847", + "year": 2017, + "month": 7, + "abstract": "Positioned at the intersection of the head, body and forelimb, the pectoral girdle has the potential to function in both feeding and locomotor behaviours—although the latter has been studied far more. In ray-finned fishes, the pectoral girdle attaches directly to the skull and is retracted during suction feeding, enabling the ventral body muscles to power rapid mouth expansion. However, in sharks, the pectoral girdle is displaced caudally and entirely separate from the skull (as in tetrapods), raising the question of whether it is mobile during suction feeding and contributing to suction expansion. We measured three-dimensional kinematics of the pectoral girdle in white-spotted bamboo sharks during suction feeding with X-ray reconstruction of moving morphology, and found the pectoral girdle consistently retracted about 11° by rotating caudoventrally about the dorsal scapular processes. This motion occurred mostly after peak gape, so it likely contributed more to accelerating captured prey through the oral cavity and pharynx, than to prey capture as in ray-finned fishes. Our results emphasize the multiple roles of the pectoral girdle in feeding and locomotion, both of which should be considered in studying the functional and evolutionary morphology of this structure.", + "subject": [], + "keywords": [] + }, + { + "title": "van der Waals-corrected density functional study of electric field noise heating in ion traps caused by electrode surface adsorbates", + "author": "Keith G Ray, Brenda M Rubenstein, Wenze Gu, Vincenzo Lordi", + "publisher": "IOP Publishing", + "url": "http://dx.doi.org/10.1088/1367-2630/ab1875", + "doi": "10.1088/1367-2630/ab1875", + "year": 2019, + "month": 5, + "abstract": "Abstract\n In order to realize the full potential of ion trap quantum computers, an improved understanding is required of the motional heating that trapped ions experience. Experimental studies of the temperature-, frequency-, and ion–electrode distance-dependence of the electric field noise responsible for motional heating, as well as the noise before and after ion bombardment cleaning of trap electrodes, suggest that fluctuations of adsorbate dipoles are a likely source of so-called ‘anomalous heating,’ or motional heating of the trapped ions at a rate much higher than the Johnson noise limit. Previous computational studies have investigated how the fluctuation of model adsorbate dipoles affects anomalous heating. However, the way in which specific adsorbates affect the electric field noise has not yet been examined, and an electric dipole model employed in previous studies is only accurate for a small subset of possible adsorbates. Here, we analyze the behavior of both in-plane and out-of-plane vibrational modes of twenty-one adsorbate–electrode combinations within the independent fluctuating dipole model, utilizing accurate first principles computational methods to determine the surface-induced dipole moments. We find the chemical specificity of the adsorbate can change the electric field noise by seven orders of magnitude and specifically that soft in-plane modes of weakly-adsorbed hydrocarbons produce the greatest noise and ion heating. We discuss the dynamics captured by the fluctuating dipole model, namely the adsorbate-dependent turn-on temperature and electric field noise magnitude, and also discuss the model’s failure to reproduce the measured 1/ω noise frequency scaling with a single adsorbate species. We suggest future research directions for improved, quantitatively predictive models based on extensions of the present framework to multiple interacting adsorbates.", + "subject": [], + "keywords": [] + }, + { + "title": "Charge localization in a diamine cation provides a test of energy functionals and self-interaction correction", + "author": "Xinxin Cheng, Yao Zhang, Elvar Jónsson, Hannes Jónsson, Peter M. Weber", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1038/ncomms11013", + "doi": "10.1038/ncomms11013", + "year": 2016, + "month": 3, + "abstract": "AbstractDensity functional theory (DFT) is widely applied in calculations of molecules and materials. Yet, it suffers from a well-known over-emphasis on charge delocalization arising from self-interaction error that destabilizes localized states. Here, using the symmetric diamine N,N′-dimethylpiperazine as a model, we have experimentally determined the relative energy of a state with positive charge localized on one of the two nitrogen atoms, and a state with positive charge delocalized over both nitrogen atoms. The charge-localized state was found to be 0.33 (0.04) eV higher in energy than the charge-delocalized state. This provides an important test of theoretical approaches to electronic structure calculations. Calculations with all DFT functionals commonly used today, including hybrid functionals with exact exchange, fail to predict a stable charge-localized state. However, the application of an explicit self-interaction correction to a semi-local functional identifies both states and gives relative energy in excellent agreement with both experiment and CCSD(T) calculations.", + "subject": [], + "keywords": [] + }, + { + "title": "Charge transfer and ultrafast nuclear motions: the complex structural dynamics of an electronically excited triamine", + "author": "Xinxin Cheng, Yan Gao, Fedor Rudakov, Peter M. Weber", + "publisher": "Royal Society of Chemistry (RSC)", + "url": "http://dx.doi.org/10.1039/c5sc03042k", + "doi": "10.1039/c5sc03042k", + "year": 2016, + "month": -1, + "abstract": "Time-resolved Rydberg fingerprint spectroscopy combined with quantum chemical calculations reveals the complex structural dynamics and charge transfer in real time.", + "subject": [], + "keywords": [] + }, + { + "title": "Oxygen-induced changes to selectivity-determining steps in electrocatalytic CO2 reduction", + "author": "Yin-Jia Zhang, Andrew A. Peterson", + "publisher": "Royal Society of Chemistry (RSC)", + "url": "http://dx.doi.org/10.1039/c4cp03783a", + "doi": "10.1039/c4cp03783a", + "year": 2015, + "month": -1, + "abstract": "The state of the electrocatalyst surface—including the oxidation state of the catalyst and the presence of spectator species—is investigated on Cu surfaces with density functional theory in order to understand predicted ramifications on the selectivity of CO2 reduction between CH4 and CH3OH.", + "subject": [], + "keywords": [] + }, + { + "title": "Chemical looping of metal nitride catalysts: low-pressure ammonia synthesis for energy storage", + "author": "R. Michalsky, A. M. Avram, B. A. Peterson, P. H. Pfromm, A. A. Peterson", + "publisher": "Royal Society of Chemistry (RSC)", + "url": "http://dx.doi.org/10.1039/c5sc00789e", + "doi": "10.1039/c5sc00789e", + "year": 2015, + "month": -1, + "abstract": "Design principles for reducible metal nitride catalysts are developed and demonstrated for ambient-pressure solar-driven N2 reduction into NH3.", + "subject": [], + "keywords": [] + }, + { + "title": "Abstract IA20: Reduced expression of MYC increases longevity and enhances healthspan", + "author": "John M. Sedivy", + "publisher": "American Association for Cancer Research (AACR)", + "url": "http://dx.doi.org/10.1158/1557-3125.myc15-ia20", + "doi": "10.1158/1557-3125.myc15-ia20", + "year": 2015, + "month": 10, + "abstract": "Abstract\n MYC is a highly pleiotropic transcription factor whose deregulation promotes cancer. We find that Myc haploinsufficient (Myc+/–) mice exhibit increased lifespan. They show resistance to several age-associated pathologies, including osteoporosis, cardiac fibrosis and immunosenescence. They also appear to be more active, with a higher metabolic rate and healthier lipid metabolism. Transcriptomic analysis reveals a gene expression signature enriched for metabolic and immune processes. The ancestral role of MYC as a regulator of ribosome biogenesis is reflected in reduced protein translation, which is inversely correlated with longevity. We also observe changes in nutrient and energy sensing pathways, including reduced serum IGF-1, increased AMPK activity, and decreased AKT, TOR and S6K activities. In contrast to observations in other longevity models, Myc+/– mice do not show improvements in stress management pathways. Our findings indicate that MYC activity has a significant impact on longevity and multiple aspects of mammalian healthspan.\n Citation Format: John M. Sedivy. Reduced expression of MYC increases longevity and enhances healthspan. [abstract]. In: Proceedings of the AACR Special Conference on Myc: From Biology to Therapy; Jan 7-10, 2015; La Jolla, CA. Philadelphia (PA): AACR; Mol Cancer Res 2015;13(10 Suppl):Abstract nr IA20.", + "subject": [], + "keywords": [] + }, + { + "title": "The free energy of mechanically unstable phases", + "author": "A. van de Walle, Q. Hong, S. Kadkhodaei, R. Sun", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1038/ncomms8559", + "doi": "10.1038/ncomms8559", + "year": 2015, + "month": 7, + "abstract": "AbstractPhase diagrams provide ‘roadmaps’ to the possible states of matter. Their determination traditionally rests on the assumption that all phases, even unstable ones, have well-defined free energies under all conditions. However, this assumption is commonly violated in condensed phases due to mechanical instabilities. This long-standing problem impedes thermodynamic database development, as pragmatic attempts at solving this problem involve delicate extrapolations that are highly nonunique and that lack an underlying theoretical justification. Here we propose an efficient computational solution to this problem that has a simple interpretation, both as a topological partitioning of atomic configuration space and as a minimally constrained physical system. Our natural scheme smoothly extends the free energy of stable phases, without relying on extrapolation, thus enabling a formal assessment of widely used extrapolation schemes.", + "subject": [], + "keywords": [] + }, + { + "title": "Within- and across-trial dynamics of human EEG reveal cooperative interplay between reinforcement learning and working memory", + "author": "Anne G. E. Collins, Michael J. Frank", + "publisher": "Proceedings of the National Academy of Sciences", + "url": "http://dx.doi.org/10.1073/pnas.1720963115", + "doi": "10.1073/pnas.1720963115", + "year": 2018, + "month": 2, + "abstract": "Significance\n A major factor that improves learning in artificial agents is the use of multiple algorithms in parallel to benefit from their complementary strengths across different environments. The human brain performs a similar optimization, balancing the use of resource-intensive but immediately accessible information in working memory and a more reliable slow but steady reinforcement learning to build habits. These parallel computations are evident in neural signal dynamics that unfold across both short- and long-term time scales, which reveal that the two processes compete for decisions but cooperate for learning. These findings further our understanding of human learning and may inspire better artificial learners.", + "subject": [], + "keywords": [] + }, + { + "title": "Not-So-CLEVR: learning same–different relations strains feedforward neural networks", + "author": "Junkyung Kim, Matthew Ricci, Thomas Serre", + "publisher": "The Royal Society", + "url": "http://dx.doi.org/10.1098/rsfs.2018.0011", + "doi": "10.1098/rsfs.2018.0011", + "year": 2018, + "month": 6, + "abstract": "The advent of deep learning has recently led to great successes in various engineering applications. As a prime example, convolutional neural networks, a type of feedforward neural network, now approach human accuracy on visual recognition tasks like image classification and face recognition. However, here we will show that feedforward neural networks struggle to learn abstract visual relations that are effortlessly recognized by non-human primates, birds, rodents and even insects. We systematically study the ability of feedforward neural networks to learn to recognize a variety of visual relations and demonstrate that same–different visual relations pose a particular strain on these networks. Networks fail to learn same–different visual relations when stimulus variability makes rote memorization difficult. Further, we show that learning same–different problems becomes trivial for a feedforward network that is fed with perceptually grouped stimuli. This demonstration and the comparative success of biological vision in learning visual relations suggests that feedback mechanisms such as attention, working memory and perceptual grouping may be the key components underlying human-level abstract visual reasoning.", + "subject": [], + "keywords": [] + }, + { + "title": "Opponent surrounds explain diversity of contextual phenomena across visual modalities", + "author": "David A. Mély, Thomas Serre", + "publisher": "Cold Spring Harbor Laboratory", + "url": "http://dx.doi.org/10.1101/070821", + "doi": "10.1101/070821", + "year": 2016, + "month": 8, + "abstract": "AsbtractContext is known to affect how a stimulus is perceived. A variety of illusions have been attributed to contextual processing — from orientation tilt effects to chromatic induction phenomena, but their neural underpinnings remain poorly understood. Here, we present a recurrent network model of classical and extra-classical receptive fields that is constrained by the anatomy and physiology of the visual cortex. A key feature of the model is the postulated existence of two spatially disjoint near-vs. far-extra-classical regions with complementary facilitatory and suppressive contributions to the classical receptive field. The model accounts for a variety of contextual illusions, reveals commonalities between seemingly disparate phenomena, and helps organize them into a novel taxonomy. It explains how center-surround interactions may shift from attraction to repulsion in tilt effects, and from contrast to assimilation in induction phenomena. The model further explains enhanced perceptual shifts generated by a class of patterned background stimuli that activate the two opponent extra-classical regions cooperatively. Overall, the ability of the model to account for the variety and complexity of contextual illusions provides computational evidence for a novel canonical circuit that is shared across visual modalities.", + "subject": [], + "keywords": [] + }, + { + "title": "Predicting the spatiotemporal diversity of seizure propagation and termination in human focal epilepsy", + "author": "Timothée Proix, Viktor K. Jirsa, Fabrice Bartolomei, Maxime Guye, Wilson Truccolo", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1038/s41467-018-02973-y", + "doi": "10.1038/s41467-018-02973-y", + "year": 2018, + "month": 3, + "abstract": "AbstractRecent studies have shown that seizures can spread and terminate across brain areas via a rich diversity of spatiotemporal patterns. In particular, while the location of the seizure onset area is usually invariant across seizures in an individual patient, the source of traveling (2–3 Hz) spike-and-wave discharges during seizures can either move with the slower propagating ictal wavefront or remain stationary at the seizure onset area. Furthermore, although many focal seizures terminate synchronously across brain areas, some evolve into distinct ictal clusters and terminate asynchronously. Here, we introduce a unifying perspective based on a new neural field model of epileptic seizure dynamics. Two main mechanisms, the co-existence of wave propagation in excitable media and coupled-oscillator dynamics, together with the interaction of multiple time scales, account for the reported diversity. We confirm our predictions in seizures and tractography data obtained from patients with pharmacologically resistant epilepsy. Our results contribute toward patient-specific seizure modeling.", + "subject": [], + "keywords": [] + }, + { + "title": "Phase reorganization leads to transient β-LFP spatial wave patterns in motor cortex during steady-state movement preparation", + "author": "Michael E. Rule, Carlos Vargas-Irwin, John P. Donoghue, Wilson Truccolo", + "publisher": "American Physiological Society", + "url": "http://dx.doi.org/10.1152/jn.00525.2017", + "doi": "10.1152/jn.00525.2017", + "year": 2018, + "month": 6, + "abstract": "Previous studies on the origin and properties of spatial patterns in motor cortex β-local field potential (β-LFP) oscillations have focused on planar traveling waves. However, it is unclear 1) whether β-LFP waves are limited to plane waves, or even 2) whether they are propagating waves of excito-excitatory activity, i.e., primarily traveling waves in excitable media; they could reflect, instead, reorganization in the relative phases of transient oscillations at different spatial sites. We addressed these two problems in β-LFPs recorded via microelectrode arrays implanted in three adjacent motor cortex areas of nonhuman primates during steady-state movement preparation. Our findings are fourfold: 1) β-LFP wave patterns emerged as transient events, despite stable firing rates of single neurons concurrently recorded during the same periods. 2) β-LFP waves showed a richer variety of spatial dynamics, including rotating and complex waves. 3) β-LFP wave patterns showed no characteristic wavelength, presenting instead a range of scales with global zero-lag phase synchrony as a limiting case, features surprising for purely excito-excitatory waves but consistent with waves in coupled oscillator systems. 4) Furthermore, excito-excitatory traveling waves induced by optogenetic stimulation in motor cortex showed, in contrast, a characteristic wavelength and reduced phase synchrony. Overall, β-LFP wave statistics differed from those of induced traveling waves in excitable media recorded under the same microelectrode array setup. Our findings suggest phase reorganization in neural coupled oscillators contribute significantly to the origin of transient β-LFP spatial dynamics during preparatory steady states and outline important constraints for spatially extended models of β-LFP dynamics in motor cortex. NEW & NOTEWORTHY We show that a rich variety of transient β-local field potential (β-LFP) wave patterns emerge in motor cortex during preparatory steady states, despite stable neuronal firing rates. Furthermore, unlike optogenetically induced traveling waves, β-LFP waves showed no characteristic wavelength, presenting instead a range of scales with global phase synchrony as a limiting case. Overall, our statistical analyses suggest that transient phase reorganization in neural coupled oscillators, beyond purely excito-excitatory traveling waves, contribute significantly to the origin of motor cortex β-LFP wave patterns.", + "subject": [], + "keywords": [] + }, + { + "title": "Dissociation between sustained single-neuron spiking and transient β-LFP oscillations in primate motor cortex", + "author": "Michael E. Rule, Carlos E. Vargas-Irwin, John P. Donoghue, Wilson Truccolo", + "publisher": "American Physiological Society", + "url": "http://dx.doi.org/10.1152/jn.00651.2016", + "doi": "10.1152/jn.00651.2016", + "year": 2017, + "month": 4, + "abstract": "Determining the relationship between single-neuron spiking and transient (20 Hz) β-local field potential (β-LFP) oscillations is an important step for understanding the role of these oscillations in motor cortex. We show that whereas motor cortex firing rates and beta spiking rhythmicity remain sustained during steady-state movement preparation periods, β-LFP oscillations emerge, in contrast, as short transient events. Single-neuron mean firing rates within and outside transient β-LFP events showed no differences, and no consistent correlation was found between the beta oscillation amplitude and firing rates, as was the case for movement- and visual cue-related β-LFP suppression. Importantly, well-isolated single units featuring beta-rhythmic spiking (43%, 125/292) showed no apparent or only weak phase coupling with the transient β-LFP oscillations. Similar results were obtained for the population spiking. These findings were common in triple microelectrode array recordings from primary motor (M1), ventral (PMv), and dorsal premotor (PMd) cortices in nonhuman primates during movement preparation. Although beta spiking rhythmicity indicates strong membrane potential fluctuations in the beta band, it does not imply strong phase coupling with β-LFP oscillations. The observed dissociation points to two different sources of variation in motor cortex β-LFPs: one that impacts single-neuron spiking dynamics and another related to the generation of mesoscopic β-LFP signals. Furthermore, our findings indicate that rhythmic spiking and diverse neuronal firing rates, which encode planned actions during movement preparation, may naturally limit the ability of different neuronal populations to strongly phase-couple to a single dominant oscillation frequency, leading to the observed spiking and β-LFP dissociation. NEW & NOTEWORTHY We show that whereas motor cortex spiking rates and beta (~20 Hz) spiking rhythmicity remain sustained during steady-state movement preparation periods, β-local field potential (β-LFP) oscillations emerge, in contrast, as transient events. Furthermore, the β-LFP phase at which neurons spike drifts: phase coupling is typically weak or absent. This dissociation points to two sources of variation in the level of motor cortex beta: one that impacts single-neuron spiking and another related to the generation of measured mesoscopic β-LFPs.", + "subject": [], + "keywords": [] + }, + { + "title": "A point‐process response model for spike trains from single neurons in neural circuits under optogenetic stimulation", + "author": "X. Luo, S. Gee, V. Sohal, D. Small", + "publisher": "Wiley", + "url": "http://dx.doi.org/10.1002/sim.6742", + "doi": "10.1002/sim.6742", + "year": 2015, + "month": 9, + "abstract": "Optogenetics is a new tool to study neuronal circuits that have been genetically modified to allow stimulation by flashes of light. We study recordings from single neurons within neural circuits under optogenetic stimulation. The data from these experiments present a statistical challenge of modeling a high‐frequency point process (neuronal spikes) while the input is another high‐frequency point process (light flashes). We further develop a generalized linear model approach to model the relationships between two point processes, employing additive point‐process response functions. The resulting model, point‐process responses for optogenetics (PRO), provides explicit nonlinear transformations to link the input point process with the output one. Such response functions may provide important and interpretable scientific insights into the properties of the biophysical process that governs neural spiking in response to optogenetic stimulation. We validate and compare the PRO model using a real dataset and simulations, and our model yields a superior area‐under‐the‐curve value as high as 93% for predicting every future spike. For our experiment on the recurrent layer V circuit in the prefrontal cortex, the PRO model provides evidence that neurons integrate their inputs in a sophisticated manner. Another use of the model is that it enables understanding how neural circuits are altered under various disease conditions and/or experimental conditions by comparing the PRO parameters. Copyright © 2015 John Wiley & Sons, Ltd.", + "subject": [], + "keywords": [] + }, + { + "title": "fMRI and EEG Predictors of Dynamic Decision Parameters during Human Reinforcement Learning", + "author": "Michael J. Frank, Chris Gagne, Erika Nyhus, Sean Masters, Thomas V. Wiecki, James F. Cavanagh, David Badre", + "publisher": "Society for Neuroscience", + "url": "http://dx.doi.org/10.1523/jneurosci.2036-14.2015", + "doi": "10.1523/jneurosci.2036-14.2015", + "year": 2015, + "month": 1, + "abstract": "What are the neural dynamics of choice processes during reinforcement learning? Two largely separate literatures have examined dynamics of reinforcement learning (RL) as a function of experience but assuming a static choice process, or conversely, the dynamics of choice processes in decision making but based on static decision values. Here we show that human choice processes during RL are well described by a drift diffusion model (DDM) of decision making in which the learned trial-by-trial reward values are sequentially sampled, with a choice made when the value signal crosses a decision threshold. Moreover, simultaneous fMRI and EEG recordings revealed that this decision threshold is not fixed across trials but varies as a function of activity in the subthalamic nucleus (STN) and is further modulated by trial-by-trial measures of decision conflict and activity in the dorsomedial frontal cortex (pre-SMA BOLD and mediofrontal theta in EEG). These findings provide converging multimodal evidence for a model in which decision threshold in reward-based tasks is adjusted as a function of communication from pre-SMA to STN when choices differ subtly in reward values, allowing more time to choose the statistically more rewarding option.", + "subject": [], + "keywords": [] + }, + { + "title": "A cholinergic feedback circuit to regulate striatal population uncertainty and optimize reinforcement learning", + "author": "Nicholas T Franklin, Michael J Frank", + "publisher": "eLife Sciences Publications, Ltd", + "url": "http://dx.doi.org/10.7554/elife.12029", + "doi": "10.7554/elife.12029", + "year": 2015, + "month": 12, + "abstract": "Convergent evidence suggests that the basal ganglia support reinforcement learning by adjusting action values according to reward prediction errors. However, adaptive behavior in stochastic environments requires the consideration of uncertainty to dynamically adjust the learning rate. We consider how cholinergic tonically active interneurons (TANs) may endow the striatum with such a mechanism in computational models spanning three Marr's levels of analysis. In the neural model, TANs modulate the excitability of spiny neurons, their population response to reinforcement, and hence the effective learning rate. Long TAN pauses facilitated robustness to spurious outcomes by increasing divergence in synaptic weights between neurons coding for alternative action values, whereas short TAN pauses facilitated stochastic behavior but increased responsiveness to change-points in outcome contingencies. A feedback control system allowed TAN pauses to be dynamically modulated by uncertainty across the spiny neuron population, allowing the system to self-tune and optimize performance across stochastic environments.", + "subject": [], + "keywords": [] + }, + { + "title": "Spatiotemporal Conditional Inference and Hypothesis Tests for Neural Ensemble Spiking Precision", + "author": "Matthew T. Harrison, Asohan Amarasingham, Wilson Truccolo", + "publisher": "MIT Press - Journals", + "url": "http://dx.doi.org/10.1162/neco_a_00681", + "doi": "10.1162/neco_a_00681", + "year": 2015, + "month": 1, + "abstract": "The collective dynamics of neural ensembles create complex spike patterns with many spatial and temporal scales. Understanding the statistical structure of these patterns can help resolve fundamental questions about neural computation and neural dynamics. Spatiotemporal conditional inference (STCI) is introduced here as a semiparametric statistical framework for investigating the nature of precise spiking patterns from collections of neurons that is robust to arbitrarily complex and nonstationary coarse spiking dynamics. The main idea is to focus statistical modeling and inference not on the full distribution of the data, but rather on families of conditional distributions of precise spiking given different types of coarse spiking. The framework is then used to develop families of hypothesis tests for probing the spatiotemporal precision of spiking patterns. Relationships among different conditional distributions are used to improve multiple hypothesis-testing adjustments and design novel Monte Carlo spike resampling algorithms. Of special note are algorithms that can locally jitter spike times while still preserving the instantaneous peristimulus time histogram or the instantaneous total spike count from a group of recorded neurons. The framework can also be used to test whether first-order maximum entropy models with possibly random and time-varying parameters can account for observed patterns of spiking. STCI provides a detailed example of the generic principle of conditional inference, which may be applicable to other areas of neurostatistical analysis.", + "subject": [], + "keywords": [] + }, + { + "title": "Spatiotemporal dynamics of optogenetically induced and spontaneous seizure transitions in primary generalized epilepsy", + "author": "Fabien B. Wagner, Wilson Truccolo, Jing Wang, Arto V. Nurmikko", + "publisher": "American Physiological Society", + "url": "http://dx.doi.org/10.1152/jn.01040.2014", + "doi": "10.1152/jn.01040.2014", + "year": 2015, + "month": 4, + "abstract": "Transitions into primary generalized epileptic seizures occur abruptly and synchronously across the brain. Their potential triggers remain unknown. We used optogenetics to causally test the hypothesis that rhythmic population bursting of excitatory neurons in a local neocortical region can rapidly trigger absence seizures. Most previous studies have been purely correlational, and it remains unclear whether epileptiform events induced by rhythmic stimulation (e.g., sensory/electrical) mimic actual spontaneous seizures, especially regarding their spatiotemporal dynamics. In this study, we used a novel combination of intracortical optogenetic stimulation and microelectrode array recordings in freely moving WAG/Rij rats, a model of absence epilepsy with a cortical focus in the somatosensory cortex (SI). We report three main findings: 1) Brief rhythmic bursting, evoked by optical stimulation of neocortical excitatory neurons at frequencies around 10 Hz, induced seizures consisting of self-sustained spike-wave discharges (SWDs) for about 10% of stimulation trials. The probability of inducing seizures was frequency-dependent, reaching a maximum at 10 Hz. 2) Local field potential power before stimulation and response amplitudes during stimulation both predicted seizure induction, demonstrating a modulatory effect of brain states and neural excitation levels. 3) Evoked responses during stimulation propagated as cortical waves, likely reaching the cortical focus, which in turn generated self-sustained SWDs after stimulation was terminated. Importantly, SWDs during induced and spontaneous seizures propagated with the same spatiotemporal dynamics. Our findings demonstrate that local rhythmic bursting of excitatory neurons in neocortex at particular frequencies, under susceptible ongoing brain states, is sufficient to trigger primary generalized seizures with stereotypical spatiotemporal dynamics.", + "subject": [], + "keywords": [] + }, + { + "title": "Model-Based Cognitive Neuroscience Approaches to Computational Psychiatry", + "author": "Thomas V. Wiecki, Jeffrey Poland, Michael J. Frank", + "publisher": "SAGE Publications", + "url": "http://dx.doi.org/10.1177/2167702614565359", + "doi": "10.1177/2167702614565359", + "year": 2015, + "month": 3, + "abstract": "Psychiatric research is in crisis. We highlight efforts to overcome current challenges by focusing on the emerging field of computational psychiatry, which might enable the field to move from a symptom-based description of mental illness to descriptors based on objective computational multidimensional functional variables. We survey recent efforts toward this goal and describe a set of methods that together form a toolbox to aid this research program. We identify four levels in computational psychiatry: (a) behavioral tasks that index various psychological processes, (b) computational models that identify the generative psychological processes, (c) parameter-estimation methods concerned with quantitatively fitting these models to subject behavior by focusing on hierarchical Bayesian estimation as a rich framework with many desirable properties, and (d) machine-learning clustering methods that identify clinically significant conditions and subgroups of individuals. As a proof of principle, we apply these methods to two different data sets. Finally, we highlight challenges for future research.", + "subject": [], + "keywords": [] + }, + { + "title": "Human EEG Uncovers Latent Generalizable Rule Structure during Learning", + "author": "Anne G. E. Collins, James F. Cavanagh, Michael J. Frank", + "publisher": "Society for Neuroscience", + "url": "http://dx.doi.org/10.1523/jneurosci.3900-13.2014", + "doi": "10.1523/jneurosci.3900-13.2014", + "year": 2014, + "month": 3, + "abstract": "Human cognition is flexible and adaptive, affording the ability to detect and leverage complex structure inherent in the environment and generalize this structure to novel situations. Behavioral studies show that humans impute structure into simple learning problems, even when this tendency affords no behavioral advantage. Here we used electroencephalography to investigate the neural dynamics indicative of such incidental latent structure. Event-related potentials over lateral prefrontal cortex, typically observed for instructed task rules, were stratified according to individual participants' constructed rule sets. Moreover, this individualized latent rule structure could be independently decoded from multielectrode pattern classification. Both neural markers were predictive of participants' ability to subsequently generalize rule structure to new contexts. These EEG dynamics reveal that the human brain spontaneously constructs hierarchically structured representations during learning of simple task rules.", + "subject": [], + "keywords": [] + }, + { + "title": "Assessing the Effects of Langmuir Turbulence on the Entrainment Buoyancy Flux in the Ocean Surface Boundary Layer", + "author": "Qing Li, Baylor Fox-Kemper", + "publisher": "American Meteorological Society", + "url": "http://dx.doi.org/10.1175/jpo-d-17-0085.1", + "doi": "10.1175/jpo-d-17-0085.1", + "year": 2017, + "month": 12, + "abstract": "AbstractLarge-eddy simulations (LESs) with various constant wind, wave, and surface destabilizing surface buoyancy flux forcing are conducted, with a focus on assessing the impact of Langmuir turbulence on the entrainment buoyancy flux at the base of the ocean surface boundary layer. An estimate of the entrainment buoyancy flux scaling is made to best fit the LES results. The presence of Stokes drift forcing and the resulting Langmuir turbulence enhances the entrainment rate significantly under weak surface destabilizing buoyancy flux conditions, that is, weakly convective turbulence. In contrast, Langmuir turbulence effects are moderate when convective turbulence is dominant and appear to be additive rather than multiplicative to the convection-induced mixing. The parameterized unresolved velocity scale in the K-profile parameterization (KPP) is modified to adhere to the new scaling law of the entrainment buoyancy flux and account for the effects of Langmuir turbulence. This modification is targeted on common situations in a climate model where either Langmuir turbulence or convection is important and may overestimate the entrainment when both are weak. Nevertheless, the modified KPP is tested in a global climate model and generally outperforms those tested in previous studies. Improvements in the simulated mixed layer depth are found, especially in the Southern Ocean in austral summer.", + "subject": [], + "keywords": [] + }, + { + "title": "Bluegill sunfish use high power outputs from axial muscles to generate powerful suction-feeding strikes", + "author": "Ariel L. Camp, Thomas J. Roberts, Elizabeth L. Brainerd", + "publisher": "The Company of Biologists", + "url": "http://dx.doi.org/10.1242/jeb.178160", + "doi": "10.1242/jeb.178160", + "year": 2018, + "month": 6, + "abstract": "ABSTRACT\n Suction-feeding fish rapidly expand the mouth cavity to generate high-velocity fluid flows that accelerate food into the mouth. Such fast and forceful suction expansion poses a challenge, as muscle power is limited by muscle mass and the muscles in fish heads are relatively small. The largemouth bass powers expansion with its large body muscles, with negligible power produced by the head muscles (including the sternohyoideus). However, bluegill sunfish – with powerful strikes but different morphology and feeding behavior – may use a different balance of cranial and axial musculature to power feeding and different power outputs from these muscles. We estimated the power required for suction expansion in sunfish from measurements of intraoral pressure and rate of volume change, and measured muscle length and velocity. Unlike largemouth bass, the sternohyoideus did shorten to generate power, but it and other head muscles were too small to contribute more than 5–10% of peak expansion power in sunfish. We found no evidence of catapult-style power amplification. Instead, sunfish powered suction feeding by generating high power outputs (up to 438 W kg−1) from their axial muscles. These muscles shortened across the cranial half of the body as in bass, but at faster speeds that may be nearer the optimum for power production. Sunfish were able to generate strikes of the same absolute power as bass, but with 30–40% of the axial muscle mass. Thus, species may use the body and head muscles differently to meet the requirements of suction feeding, depending on their morphology and behavior.", + "subject": [], + "keywords": [] + }, + { + "title": "Stable long-term BCI-enabled communication in ALS and locked-in syndrome using LFP signals", + "author": "Tomislav Milekovic, Anish A. Sarma, Daniel Bacher, John D. Simeral, Jad Saab, Chethan Pandarinath, Brittany L. Sorice, Christine Blabe, Erin M. Oakley, Kathryn R. Tringale, Emad Eskandar, Sydney S. Cash, Jaimie M. Henderson, Krishna V. Shenoy, John P. Donoghue, Leigh R. Hochberg", + "publisher": "American Physiological Society", + "url": "http://dx.doi.org/10.1152/jn.00493.2017", + "doi": "10.1152/jn.00493.2017", + "year": 2018, + "month": 7, + "abstract": "Restoring communication for people with locked-in syndrome remains a challenging clinical problem without a reliable solution. Recent studies have shown that people with paralysis can use brain-computer interfaces (BCIs) based on intracortical spiking activity to efficiently type messages. However, due to neuronal signal instability, most intracortical BCIs have required frequent calibration and continuous assistance of skilled engineers to maintain performance. Here, an individual with locked-in syndrome due to brain stem stroke and an individual with tetraplegia secondary to amyotrophic lateral sclerosis (ALS) used a simple communication BCI based on intracortical local field potentials (LFPs) for 76 and 138 days, respectively, without recalibration and without significant loss of performance. BCI spelling rates of 3.07 and 6.88 correct characters/minute allowed the participants to type messages and write emails. Our results indicate that people with locked-in syndrome could soon use a slow but reliable LFP-based BCI for everyday communication without ongoing intervention from a technician or caregiver. NEW & NOTEWORTHY This study demonstrates, for the first time, stable repeated use of an intracortical brain-computer interface by people with tetraplegia over up to four and a half months. The approach uses local field potentials (LFPs), signals that may be more stable than neuronal action potentials, to decode participants’ commands. Throughout the several months of evaluation, the decoder remained unchanged; thus no technical interventions were required to maintain consistent brain-computer interface operation.", + "subject": [], + "keywords": [] + }, + { + "title": "Three-dimensional kinematics of the equine metacarpophalangeal joint using x-ray reconstruction of moving morphology – a pilot study", + "author": "Bronwen Childs, Brenna Pugliese, Cristina Carballo, Daniel Miranda, Elizabeth Brainerd, Carl Kirker-Head", + "publisher": "Georg Thieme Verlag KG", + "url": "http://dx.doi.org/10.3415/vcot-16-06-0095", + "doi": "10.3415/vcot-16-06-0095", + "year": 2017, + "month": -1, + "abstract": "SummaryX-ray reconstruction of moving morphology (XROMM) uses biplanar videoradiography and computed tomography (CT) scanning to capture three-dimensional (3D) bone motion. In XROMM, morphologically accurate 3D bone models derived from CT are animated with motion from videoradiography, yielding a highly accurate and precise reconstruction of skeletal kinematics. We employ this motion analysis technique to characterize metacarpophalangeal joint (MCPJ) motion in the absence and presence of protective legwear in a healthy pony. Our in vivo marker tracking precision was 0.09 mm for walk and trot, and 0.10 mm during jump down exercises. We report MCPJ maximum extension (walk: –27.70 ± 2.78° [standard deviation]; trot: –33.84 ± 4.94°), abduction/adduction (walk: 0.04 ± 0.24°; trot: –0.23 ± 0.35°) and external/internal rotations (walk: 0.30 ± 0.32°; trot: –0.49 ± 1.05°) indicating that the MCPJ in this pony is a stable hinge joint with negligible extra-sagittal rotations. No substantial change in MCPJ maximum extension angles or vertical ground reaction forces (GRFv) were observed upon application of legwear during jump down exercise. Neoprene boot application yielded –65.20 ± 2.06° extension (GRFv = 11.97 ± 0.67 N/kg) and fleece polo wrap application yielded –64.23 ± 1.68° extension (GRFv = 11.36 ± 1.66 N/kg), when compared to naked control (-66.11 ± 0.96°; GRFv = 12.02 ± 0.53 N/kg). Collectively, this proof of concept study illustrates the benefits and practical limitations of using XROMM to document equine MCPJ kinematics in the presence and absence of legwear.Supplementary Material to this article is available online at https://doi.org/10.3415/VCOT-16-06-0095.", + "subject": [], + "keywords": [] + }, + { + "title": "In situ vocal fold properties and pitch prediction by dynamic actuation of the songbird syrinx", + "author": "Daniel N. Düring, Benjamin J. Knörlein, Coen P. H. Elemans", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1038/s41598-017-11258-1", + "doi": "10.1038/s41598-017-11258-1", + "year": 2017, + "month": 9, + "abstract": "AbstractThe biomechanics of sound production forms an integral part of the neuromechanical control loop of avian vocal motor control. However, we critically lack quantification of basic biomechanical parameters describing the vocal organ, the syrinx, such as material properties of syringeal elements, forces and torques exerted on, and motion of the syringeal skeleton during song. Here, we present a novel marker-based 3D stereoscopic imaging technique to reconstruct 3D motion of servo-controlled actuation of syringeal muscle insertions sites in vitro and focus on two muscles controlling sound pitch. We furthermore combine kinematic analysis with force measurements to quantify elastic properties of sound producing medial labia (ML). The elastic modulus of the zebra finch ML is 18 kPa at 5% strain, which is comparable to elastic moduli of mammalian vocal folds. Additionally ML lengthening due to musculus syringealis ventralis (VS) shortening is intrinsically constraint at maximally 12% strain. Using these values we predict sound pitch to range from 350–800 Hz by VS modulation, corresponding well to previous observations. The presented methodology allows for quantification of syringeal skeleton motion and forces, acoustic effects of muscle recruitment, and calibration of computational birdsong models, enabling experimental access to the entire neuromechanical control loop of vocal motor control.", + "subject": [], + "keywords": [] + }, + { + "title": "Paleoenvironments, taphonomy, and stable isotopic content of the terrestrial, fossil-vertebrate–bearing sequence of the El Disecado Member, El Gallo Formation, Upper Cretaceous, Baja California, México", + "author": "David E. Fastovsky, Marisol Montellano-Ballesteros, Henry C. Fricke, Jahandar Ramezani, Kaori Tsukui, Gregory P. Wilson, Paul Hall, Rene Hernandez-Rivera, Geraldo Alvarez", + "publisher": "Geological Society of America", + "url": "http://dx.doi.org/10.1130/ges02207.1", + "doi": "10.1130/ges02207.1", + "year": 2020, + "month": 6, + "abstract": "Abstract\n The Late Campanian (Late Cretaceous), upper part of the El Disecado Member, El Gallo Formation, Baja California, México, preserves a rich fossil assemblage of microvertebrates and macrovertebrates, silicified logs, macroscopic plant remains, and pollen that was likely deposited as the distal part of a subaerial fan. The unit was episodic and high energy, with its salient features deriving from active river channels and sheet, debris-flow deposits. Landscape stability is indicated by the presence of compound paleosol horizons, containing Fe2O3 mottling in B horizons, cutans, and calcium carbonate concretions. All of these features indicate wet/dry cyclicity in subsurface horizons, likely attributable to such cyclicity in the climate. Drainage was largely to the north and to a lesser extent, the west; however, some current flow to the south and east is preserved which, in conjunction with the proximal location of marginal marine deposits, suggest the influence of tides in this setting.\n The fossil vertebrates preserved in this part of the El Disecado Member are almost exclusively allochthonous, preserved as disarticulated isolated clasts in hydraulic equivalence in the braided fluvial system. A relatively diverse microvertebrate assemblage is preserved, the largest components of which are first, dinosaurs, and second, turtles. Non-tetrapod fossils are relatively uncommon, perhaps reflecting an absence of permanent standing water in this depositional setting.\n Here we report a high-precision U-Pb date of 74.706 + 0.028 Ma (2σ internal uncertainty), obtained from zircons in an airfall tuff. The tuff is located low within the sequence studied; therefore, most of the sedimentology and fossils reported here are slightly younger. This date, which improves upon previously published 40Ar/39Ar geochronology, ultimately allows for comparison of these El Gallo faunas and environments with coeval ones globally.\n Primary stable isotopic nodules associated with roots in the paleosols of the terrestrial portion of the El Disecado Member are compared with ratios from similar sources from coeval northern and eastern localities in North America. Distinctive latitudinal gradients are observed in both δ13C and δ18O, reflecting the unique southern and western, coastal geographic position of this locality. These differences are best explained by differences in the floras that populated the northern and eastern localities, relative to the southern and western floras reported here.", + "subject": [], + "keywords": [] + }, + { + "title": "The step-like evolution of Arctic open water", + "author": "Michael A. Goldstein, Amanda H. Lynch, Andras Zsom, Todd Arbetter, Andres Chang, Florence Fetterer", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1038/s41598-018-35064-5", + "doi": "10.1038/s41598-018-35064-5", + "year": 2018, + "month": 11, + "abstract": "AbstractSeptember open water fraction in the Arctic is analyzed using the satellite era record of ice concentration (1979–2017). Evidence is presented that three breakpoints (shifts in the mean) occurred in the Pacific sector, with higher amounts of open water starting in 1989, 2002, and 2007. Breakpoints in the Atlantic sector record of open water are evident in 1971 in longer records, and around 2000 and 2011. Multiple breakpoints are also evident in the Canadian and Russian halves. Statistical models that use detected breakpoints of the Pacific and Atlantic sectors, as well as models with breakpoints in the Canadian and Russian halves and the Arctic as a whole, outperform linear trend models in fitting the data. From a physical standpoint, the results support the thesis that Arctic sea ice may have critical points beyond which a return to the previous state is less likely. From an analysis standpoint, the findings imply that de-meaning the data using the breakpoint means is less likely to cause spurious signals than employing a linear detrend.", + "subject": [], + "keywords": [] + }, + { + "title": "VarStack: a Web Tool for Data Retrieval to Interpret Somatic Variants in Cancer", + "author": "Morgan Howard, Bruce Kane, Mary Lepry, Paul Stey, Ashok Ragavendran, Ece D. Gamsiz Uzun", + "publisher": "Cold Spring Harbor Laboratory", + "url": "http://dx.doi.org/10.1101/2020.03.10.985952", + "doi": "10.1101/2020.03.10.985952", + "year": 2020, + "month": 3, + "abstract": "AbstractBackground and objectiveAdvances in tumor genome sequencing created an urgent need for bioinformatics tools to support the interpretation of the clinical significance of the variants detected. VarStack is a web tool which is a base to retrieve somatic variant data in cancer from existing databases.MethodsVarStack incorporates data from several publicly available databases and presents them with an easy-to-navigate user-interface. It currently supports data from the Catalogue of Somatic Mutations in Cancer (COSMIC), gnomAD, cBioPortal, ClinVar, OncoKB and UCSC Genome browser. It retrieves the data from these databases and returns back to the user in a fraction of the time it would take to manually navigate each site independently.ResultsUsers submit a variant with gene symbol, peptide change, and coding sequence change. They may select a variety of tumor specific studies in cBioportal to search through in addition to their original query. The results from the databases are presented in tabs. Users can export the results as a CSV file. VarStack also has the batch search feature in which user submits a list of variants and download a CSV file with the data from the databases. With the batch search and data download options users can easily incorporate VarStack into their workflow or tools. VarStack saves time by providing variant data to the user from multiple databases in an easy-to-export and interpretable format.AvailabilityVarStack is freely available under https://varstack.brown.edu.", + "subject": [], + "keywords": [] + }, + { + "title": "VIVA (VIsualization of VAriants): A VCF File Visualization Tool", + "author": "G. A. Tollefson, J. Schuster, F. Gelin, A. Agudelo, A. Ragavendran, I. Restrepo, P. Stey, J. Padbury, A. Uzun", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1038/s41598-019-49114-z", + "doi": "10.1038/s41598-019-49114-z", + "year": 2019, + "month": 9, + "abstract": "AbstractHigh-throughput sequencing produces an extraordinary amount of genomic data that is organized into a number of high-dimension datasets. Accordingly, visualization of genomic data has become essential for quality control, exploration, and data interpretation. The Variant Call Format (VCF) is a text file format generated during the variant calling process that contains genomic information and locations of variants in a group of sequenced samples. The current workflow for visualization of genomic variant data from VCF files requires use of a combination of existing tools. Here, we describe VIVA (VIsualization of VAriants), a command line utility and Jupyter Notebook based tool for evaluating and sharing genomic data for variant analysis and quality control of sequencing experiments from VCF files. VIVA combines the functionality of existing tools into a single command to interactively evaluate and share genomic data, as well as create publication quality graphics.", + "subject": [], + "keywords": [] + }, + { + "title": "Machine learning approach to literature mining for the genetics of complex diseases", + "author": "Jessica Schuster, Michael Superdock, Anthony Agudelo, Paul Stey, James Padbury, Indra Neil Sarkar, Alper Uzun", + "publisher": "Oxford University Press (OUP)", + "url": "http://dx.doi.org/10.1093/database/baz124", + "doi": "10.1093/database/baz124", + "year": 2019, + "month": 1, + "abstract": "AbstractTo generate a parsimonious gene set for understanding the mechanisms underlying complex diseases, we reasoned it was necessary to combine the curation of public literature, review of experimental databases and interpolation of pathway-associated genes. Using this strategy, we previously built the following two databases for reproductive disorders: The Database for Preterm Birth (dbPTB) and The Database for Preeclampsia (dbPEC). The completeness and accuracy of these databases is essential for supporting our understanding of these complex conditions. Given the exponential increase in biomedical literature, it is becoming increasingly difficult to manually maintain these databases. Using our curated databases as reference data sets, we implemented a machine learning-based approach to optimize article selection for manual curation. We used logistic regression, random forests and neural networks as our machine learning algorithms to classify articles. We examined features derived from abstract text, annotations and metadata that we hypothesized would best classify articles with genetically relevant content associated to the disorder of interest. Combinations of these features were used build the classifiers and the performance of these feature sets were compared to a standard ‘Bag-of-Words’. Several combinations of these genetic based feature sets outperformed ‘Bag-of-Words’ at a threshold such that 95% of the curated gene set obtained from the original manual curation of all articles were extracted from the articles classified by machine learning as ‘considered’. The performance was superior in terms of the reduction of required manual curation and two measures of the harmonic mean of precision and recall. The reduction in workload ranged from 0.814 to 0.846 for the dbPTB and 0.301 to 0.371 for the dbPEC. Additionally, a database of metadata and annotations is generated which allows for rapid query of individual features. Our results demonstrate that machine learning algorithms can identify articles with relevant data for databases of genes associated with complex diseases.", + "subject": [], + "keywords": [] + }, + { + "title": "Cell‐free DNA as a biomarker of aging", + "author": "Yee Voan Teo, Miriam Capri, Cristina Morsiani, Grazia Pizza, Ana Maria Caetano Faria, Claudio Franceschi, Nicola Neretti", + "publisher": "Wiley", + "url": "http://dx.doi.org/10.1111/acel.12890", + "doi": "10.1111/acel.12890", + "year": 2018, + "month": 12, + "abstract": "AbstractCell‐free DNA (cfDNA) is present in the circulating plasma and other body fluids and is known to originate mainly from apoptotic cells. Here, we provide the first in vivo evidence of global and local chromatin changes in human aging by analyzing cfDNA from the blood of individuals of different age groups. Our results show that nucleosome signals inferred from cfDNA are consistent with the redistribution of heterochromatin observed in cellular senescence and aging in other model systems. In addition, we detected a relative cfDNA loss at several genomic locations, such as transcription start and termination sites, 5′UTR of L1HS retrotransposons and dimeric AluY elements with age. Our results also revealed age and deteriorating health status correlate with increased enrichment of signals from cells in different tissues. In conclusion, our results show that the sequencing of circulating cfDNA from human blood plasma can be used as a noninvasive methodology to study age‐associated changes to the epigenome in vivo.", + "subject": [], + "keywords": [] + }, + { + "title": "Assessment of holographic microscopy for quantifying marine particle size and concentration", + "author": "Noah L. Walcutt, Benjamin Knörlein, Ivona Cetinić, Zrinka Ljubesic, Suncica Bosak, Tom Sgouros, Amanda L. Montalbano, Aimee Neeley, Susanne Menden‐Deuer, Melissa M. Omand", + "publisher": "Wiley", + "url": "http://dx.doi.org/10.1002/lom3.10379", + "doi": "10.1002/lom3.10379", + "year": 2020, + "month": 8, + "abstract": "AbstractHolographic microscopy has emerged as a tool for in situ imaging of microscopic organisms and other particles in the marine environment: appealing because of the relatively larger sampling volume and simpler optical configuration compared to other imaging systems. However, its quantitative capabilities have so far remained uncertain, in part because hologram reconstruction and image recognition have required manual operation. Here, we assess the quantitative skill of our automated hologram processing pipeline (CCV Pipeline), to evaluate the size and concentration measurements of environmental and cultured assemblages of marine plankton particles, and microspheres. Over 1 million particles, ranging from 10 to 200 μm in equivalent spherical diameter, imaged by the 4‐Deep HoloSea digital inline holographic microscope (DIHM) are analyzed. These measurements were collected in parallel with a FlowCam (FC), Imaging FlowCytobot (IFCB), and manual microscope identification. Once corrections for particle location and nonuniform illumination were developed and applied, the DIHM showed an underestimate in ESD of about 3% to 10%, but successfully reproduced the size spectral slope from environmental samples, and the size distribution of cultures (Dunaliella tertiolecta, Heterosigma akashiwo, and Prorocentrum micans) and microspheres. DIHM concentrations (order 1 to 1000 particles ml−1) showed a linear agreement (r2 = 0.73) with the other instruments, but individual comparisons at times had large uncertainty. Overall, we found the DIHM and the CCV Pipeline required extensive manual correction, but once corrected, provided concentration and size estimates comparable to the other imaging systems assessed in this study. Holographic cameras are mechanically simple, autonomous, can operate at very high pressures, and provide a larger sampling volume than comparable lens‐based tools. Thus, we anticipate that these characterization efforts will be rewarded with novel discovery in new oceanic environments.", + "subject": [], + "keywords": [] + }, + { + "title": "Global and Regional Implications of Biome Evolution on the Hydrologic Cycle and Climate in the NCAR Dynamic Vegetation Model", + "author": "Jessica Levey, Jung-Eun Lee", + "publisher": "MDPI AG", + "url": "http://dx.doi.org/10.3390/land9100342", + "doi": "10.3390/land9100342", + "year": 2020, + "month": 9, + "abstract": "Vegetation influences climate by altering water and energy budgets. With intensifying threats from anthropogenic activities, both terrestrial biomes and climate are expected to change, and the need to understand land–atmosphere interactions will become increasingly crucial. We ran a climate model coupled with a Dynamic Global Vegetation Model (DGVM) to investigate the establishment of terrestrial biomes starting from a bareground scenario and how these biomes influence the climate throughout their evolution. Vegetation reaches quasi-equilibrium after ~350 years, and the vegetation establishment results in global increases in temperature (~2.5 °C), precipitation (~5.5%) and evapotranspiration as well as declines in albedo and sea ice volumes. In high latitude regions, vegetation establishment decreases albedo, causing an increase in global temperatures as well as a northward shift of the Intertropical Convergence Zone (ITCZ). Low latitude tropical afforestation results in greater evapotranspiration and precipitation, and an initial decrease in temperatures due to evaporative cooling.", + "subject": [], + "keywords": [] + }, + { + "title": "Reinforcement learning for bluff body active flow control in experiments and simulations", + "author": "Dixia Fan, Liu Yang, Zhicheng Wang, Michael S. Triantafyllou, George Em Karniadakis", + "publisher": "Proceedings of the National Academy of Sciences", + "url": "http://dx.doi.org/10.1073/pnas.2004939117", + "doi": "10.1073/pnas.2004939117", + "year": 2020, + "month": 10, + "abstract": "Significance\n \n Reinforcement learning (RL) has been applied effectively in games and robotic manipulation. We demonstrate the effectiveness of RL in experimental fluid mechanics by applying it to reduce the drag of circular cylinders in turbulent flow, a canonical fluid–structure interaction problem. Although physics agnostic, RL managed to reduce the drag by\n \n \n 30\n %\n \n \n or reach another specified optimum point very quickly. Following this discovery, we used high-fidelity simulations to probe the underlying physical mechanisms so that the discovered control techniques can be generalized to other similar flow problems. More broadly, RL-guided active control can lead to efficient exploration of additional flow-control strategies in experimental fluid mechanics, potentially paving the way for accelerating scientific discovery and different designs in flow-related engineering problems.", + "subject": [], + "keywords": [] + }, + { + "title": "The effects of monovalent metal cations on the crystal and electronic structures of Cs2MBiCl6 (M = Ag, Cu, Na, K, Rb, and Cs) perovskites", + "author": "Wenwu Shi, Tong Cai, Zhiguo Wang, Ou Chen", + "publisher": "AIP Publishing", + "url": "http://dx.doi.org/10.1063/5.0021238", + "doi": "10.1063/5.0021238", + "year": 2020, + "month": 10, + "abstract": "Lead-halide perovskites have attracted much attention over the past decade, while two main issues, i.e., the lead-induced toxicity and materials’ instability, limit their further practice in widespread applications. To overcome these limitations, an effective alternative is to design lead-free perovskite materials with the substitution of two divalent lead ions with a pair of monovalent and trivalent metal ions. However, fundamental physics and chemistry about how tuning material’s composition affects the crystal phase, electronic band structures, and optoelectronic properties of the material have yet to be fully understood. In this work, we conducted a series of density functional theory calculations to explore the mechanism that how various monovalent metal ions influence the crystal and electronic structures of lead-free Cs2MBiCl6 perovskites. We found that the Cs2MBiCl6 (M = Ag, Cu, and Na) perovskites preferred a cubic double perovskite phase with low carrier effective masses, while the Cs2MBiCl6 (M = K, Rb, and Cs) perovskites favored a monoclinic phase with relatively high carrier effective masses. The different crystal phase preferences were attributed to the different radii of monovalent metal cations and the orbital hybridization between the metal and Cl ions. The calculation showed that all Cs2MBiCl6 perovskites studied here exhibited indirect bandgaps. Smaller bandgap energies for the perovskites with a cubic phase were calculated than those of the monoclinic phase counterparts. Charge density difference calculation and electron localization functional analysis were also conducted and revealed that the carrier mobility can be improved via changing the characteristics of metal-halide bonds through compositional and, thus, crystal structure tuning. Our study shown here sheds light on the future design and fabrication of various lead-free perovskite materials for optoelectronic applications.", + "subject": [], + "keywords": [] + }, + { + "title": "High‐Resolution Photoelectron Imaging of IrB3−: Observation of a π‐Aromatic B3+ Ring Coordinated to a Transition Metal", + "author": "Joseph Czekner, Ling Fung Cheung, G. Stephen Kocheril, Maksim Kulichenko, Alexander I. Boldyrev, Lai‐Sheng Wang", + "publisher": "Wiley", + "url": "http://dx.doi.org/10.1002/anie.201902406", + "doi": "10.1002/anie.201902406", + "year": 2019, + "month": 5, + "abstract": "AbstractIn a high‐resolution photoelectron imaging and theoretical study of the IrB3− cluster, two isomers were observed experimentally with electron affinities (EAs) of 1.3147(8) and 1.937(4) eV. Quantum calculations revealed two nearly degenerate isomers competing for the global minimum, both with a B3 ring coordinated with the Ir atom. The isomer with the higher EA consists of a B3 ring with a bridge‐bonded Ir atom (Cs , 2A′), and the second isomer features a tetrahedral structure (C3v , 2A1). The neutral tetrahedral structure was predicted to be considerably more stable than all other isomers. Chemical bonding analysis showed that the neutral C3v isomer involves significant covalent Ir−B bonding and weak ionic bonding with charge transfer from B3 to Ir, and can be viewed as an Ir–(η3‐B3+) complex. This study provides the first example of a boron‐to‐metal charge‐transfer complex and evidence of a π‐aromatic B3+ ring coordinated to a transition metal.", + "subject": [], + "keywords": [] + }, + { + "title": "Observation of Transition‐Metal–Boron Triple Bonds in IrB2O− and ReB2O−", + "author": "Teng‐Teng Chen, Ling Fung Cheung, Wei‐Jia Chen, Joseph Cavanagh, Lai‐Sheng Wang", + "publisher": "Wiley", + "url": "http://dx.doi.org/10.1002/ange.202006652", + "doi": "10.1002/ange.202006652", + "year": 2020, + "month": 6, + "abstract": "AbstractMultiple bonds between boron and transition metals are known in many borylene (:BR) complexes via metal dπ→BR back‐donation, despite the electron deficiency of boron. An electron‐precise metal–boron triple bond was first observed in BiB2O− [Bi≡B−B≡O]− in which both boron atoms can be viewed as sp‐hybridized and the [B−BO]− fragment is isoelectronic to a carbyne (CR). To search for the first electron‐precise transition‐metal‐boron triple‐bond species, we have produced IrB2O− and ReB2O− and investigated them by photoelectron spectroscopy and quantum‐chemical calculations. The results allow to elucidate the structures and bonding in the two clusters. We find IrB2O− has a closed‐shell bent structure (Cs, 1A′) with BO− coordinated to an Ir≡B unit, (−OB)Ir≡B, whereas ReB2O− is linear (C∞v, 3Σ−) with an electron‐precise Re≡B triple bond, [Re≡B−B≡O]−. The results suggest the intriguing possibility of synthesizing compounds with electron‐precise M≡B triple bonds analogous to classical carbyne systems.", + "subject": [], + "keywords": [] + }, + { + "title": "Spatial patterns of recent US summertime heat trends: Implications for heat sensitivity and health adaptations", + "author": "Keith R Spangler, Gregory A Wellenius", + "publisher": "IOP Publishing", + "url": "http://dx.doi.org/10.1088/2515-7620/ab7abb", + "doi": "10.1088/2515-7620/ab7abb", + "year": 2020, + "month": 3, + "abstract": "Abstract\n Heat is known to cause illness and death not only at extreme temperatures, but also at moderate levels. Although substantial research has shown how summertime temperature distributions have changed over recent decades in the United States, less is known about how the heat index—a potentially more health-applicable metric of heat—has similarly evolved over this period. Moreover, the extent to which these distributional changes have overlapped with indicators of social vulnerability has not been established, despite the applicability of co-varying climatic and sociodemographic characteristics to heat-related health adaptations. Presented here is an analysis of trends in the median, 95th percentile, and ‘warm-tail spread’ (i.e., intra-seasonal range between the upper extreme and median) of warm-season (May-September) maximum heat index between 1979 and 2018 across the conterminous US. Using 40 years of data from the North American Regional Reanalysis dataset, it is shown that most of the US has experienced statistically significant positive trends in summertime heat, and that both the magnitude of trends and the shape of the frequency distributions of these measures vary regionally. Comparisons with data from the Social Vulnerability Index show that the most socially vulnerable counties appear to be warming faster than the least vulnerable, but that opposite patterns hold for trends in warm-tail spread. These findings may be applicable to further studies on climate change, heat adaptations, and environmental justice in the US.", + "subject": [], + "keywords": [] + }, + { + "title": "Predictive modelling of thrombus formation in diabetic retinal microaneurysms", + "author": "He Li, Konstantina Sampani, Xiaoning Zheng, Dimitrios P. Papageorgiou, Alireza Yazdani, Miguel O. Bernabeu, George E. Karniadakis, Jennifer K. Sun", + "publisher": "The Royal Society", + "url": "http://dx.doi.org/10.1098/rsos.201102", + "doi": "10.1098/rsos.201102", + "year": 2020, + "month": 8, + "abstract": "Microaneurysms (MAs) are one of the earliest clinically visible signs of diabetic retinopathy (DR). Vision can be reduced at any stage of DR by MAs, which may enlarge, rupture and leak fluid into the neural retina. Recent advances in ophthalmic imaging techniques enable reconstruction of the geometries of MAs and quantification of the corresponding haemodynamic metrics, such as shear rate and wall shear stress, but there is lack of computational models that can predict thrombus formation in individual MAs. In this study, we couple a particle model to a continuum model to simulate the platelet aggregation in MAs with different shapes. Our simulation results show that under a physiologically relevant blood flow rate, thrombosis is more pronounced in saccular-shaped MAs than fusiform-shaped MAs, in agreement with recent clinical findings. Our model predictions of the size and shape of the thrombi in MAs are consistent with experimental observations, suggesting that our model is capable of predicting the formation of thrombus for newly detected MAs. This is the first quantitative study of thrombosis in MAs through simulating platelet aggregation, and our results suggest that computational models can be used to predict initiation and development of intraluminal thrombus in MAs as well as provide insights into their role in the pathophysiology of DR.", + "subject": [], + "keywords": [] + }, + { + "title": "A simple local expression for the prefactor in transition state theory", + "author": "S. Kadkhodaei, A. van de Walle", + "publisher": "AIP Publishing", + "url": "http://dx.doi.org/10.1063/1.5086746", + "doi": "10.1063/1.5086746", + "year": 2019, + "month": 4, + "abstract": "We present a simple and accurate computational technique to determine the frequency prefactor in harmonic transition state theory without necessitating full phonon density of states (DOS) calculations. The atoms in the system are partitioned into an “active region,” where the kinetic process takes place, and an “environment” surrounding the active region. It is shown that the prefactor can be obtained by a partial phonon DOS calculation of the active region with a simple correction term accounting for the environment, under reasonable assumptions regarding atomic interactions. Convergence with respect to the size of the active region is investigated for different systems, as well as the reduction in computational costs when compared to full phonon DOS calculation. Additionally, we provide an open source implementation of the algorithm that can be added as an extension to Large-scale Atomic/Molecular Massively Parallel Simulator software.", + "subject": [], + "keywords": [] + }, + { + "title": "A single cell RNA sequencing resource for early sea urchin development", + "author": "Stephany Foster, Nathalie Oulhen, Gary Wessel", + "publisher": "The Company of Biologists", + "url": "http://dx.doi.org/10.1242/dev.191528", + "doi": "10.1242/dev.191528", + "year": 2020, + "month": 9, + "abstract": "ABSTRACT\n Identifying cell states during development from their mRNA profiles provides insight into their gene regulatory network. Here, we leverage the sea urchin embryo for its well-established gene regulatory network to interrogate the embryo using single cell RNA sequencing. We tested eight developmental stages in Strongylocentrotus purpuratus, from the eight-cell stage to late in gastrulation. We used these datasets to parse out 22 major cell states of the embryo, focusing on key transition stages for cell type specification of each germ layer. Subclustering of these major embryonic domains revealed over 50 cell states with distinct transcript profiles. Furthermore, we identified the transcript profile of two cell states expressing germ cell factors, one we conclude represents the primordial germ cells and the other state is transiently present during gastrulation. We hypothesize that these cells of the Veg2 tier of the early embryo represent a lineage that converts to the germ line when the primordial germ cells are deleted. This broad resource will hopefully enable the community to identify other cell states and genes of interest to expose the underpinning of developmental mechanisms.", + "subject": [], + "keywords": [] + }, + { + "title": "High-throughput calculations in the context of alloy design", + "author": "Axel van de Walle, Mark Asta", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1557/mrs.2019.71", + "doi": "10.1557/mrs.2019.71", + "year": 2019, + "month": 4, + "abstract": "Abstract", + "subject": [], + "keywords": [] + }, + { + "title": "Identifying rhenium substitute candidate multiprincipal-element alloys from electronic structure and thermodynamic criteria", + "author": "Axel van de Walle, Julian E.C. Sabisch, Andrew M. Minor, Mark Asta", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1557/jmr.2019.179", + "doi": "10.1557/jmr.2019.179", + "year": 2019, + "month": 6, + "abstract": "Abstract", + "subject": [], + "keywords": [] + }, + { + "title": "An independent derivation and verification of the voids nucleation failure mechanism: significance for materials failure", + "author": "Richard Christensen, Zhi Li, Huajian Gao", + "publisher": "The Royal Society", + "url": "http://dx.doi.org/10.1098/rspa.2018.0755", + "doi": "10.1098/rspa.2018.0755", + "year": 2019, + "month": 2, + "abstract": "Independent derivations are given for the failure criteria of the purely dilatational stress state involving voids nucleation failure as well as for the purely distortional stress state involving shear bands failure. The results are consistent with those from a recently derived failure theory and they further substantiate the failure theory. The voids nucleation mechanism is compared with the ideal theoretical strength of isotropic materials as derived by density functional theory and two other atomic-scale methods. It is found that a cross-over occurs from the voids nucleation failure mechanism to the ideal strength limitation as the tensile to compressive strengths ratio,\n T\n /\n C\n , increases toward a value of unity. All the results are consistent with the failure modes transition results from the general failure theory.", + "subject": [], + "keywords": [] + }, + { + "title": "A Statistical Pipeline for Identifying Physical Features that Differentiate Classes of 3D Shapes", + "author": "Bruce Wang, Timothy Sudijono, Henry Kirveslahti, Tingran Gao, Douglas M. Boyer, Sayan Mukherjee, Lorin Crawford", + "publisher": "Cold Spring Harbor Laboratory", + "url": "http://dx.doi.org/10.1101/701391", + "doi": "10.1101/701391", + "year": 2019, + "month": 7, + "abstract": "AbstractThe recent curation of large-scale databases with 3D surface scans of shapes has motivated the development of tools that better detect global patterns in morphological variation. Studies which focus on identifying differences between shapes have been limited to simple pairwise comparisons and rely on pre-specified landmarks (that are often known). We present SINATRA: the first statistical pipeline for analyzing collections of shapes without requiring any correspondences. Our novel algorithm takes in two classes of shapes and highlights the physical features that best describe the variation between them. We use a rigorous simulation framework to assess our approach. Lastly, as a case study, we use SINATRA to analyze mandibular molars from four different suborders of primates and demonstrate its ability recover known morphometric variation across phylogenies.", + "subject": [], + "keywords": [] + }, + { + "title": "Concurrent coupling of atomistic simulation and mesoscopic hydrodynamics for flows over soft multi-functional surfaces", + "author": "Yuying Wang, Zhen Li, Junbo Xu, Chao Yang, George Em Karniadakis", + "publisher": "Royal Society of Chemistry (RSC)", + "url": "http://dx.doi.org/10.1039/c8sm02170h", + "doi": "10.1039/c8sm02170h", + "year": 2019, + "month": -1, + "abstract": "We develop an efficient parallel multiscale method that bridges the atomistic and mesoscale regimes, from nanometers to microns and beyond,viaconcurrent coupling of atomistic simulation and mesoscopic dynamics.", + "subject": [], + "keywords": [] + }, + { + "title": "Transition from source- to stress-controlled plasticity in nanotwinned materials below a softening temperature", + "author": "Seyedeh Mohadeseh Taheri Mousavi, Haofei Zhou, Guijin Zou, Huajian Gao", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1038/s41524-018-0140-5", + "doi": "10.1038/s41524-018-0140-5", + "year": 2019, + "month": 1, + "abstract": "AbstractNanotwinned materials have been widely studied as a promising class of nanostructured materials that exhibit an exceptional combination of high strength, good ductility, large fracture toughness, remarkable fatigue resistance, and creep stability. Recently, an apparent controversy has emerged with respect to how the strength of nanotwinned materials varies as the twin thickness is reduced. While a transition from hardening to softening was observed in nanotwinned Cu when the twin thickness is reduced below a critical value, continuous hardening was reported in nanotwinned ceramics and nanotwinned diamond. Here, by conducting atomistic simulations and developing a theoretical modeling of nanotwinned Pd and Cu systems, we discovered that there exists a softening temperature, below which the material hardens continuously as the twin thickness is reduced (as in nanotwinned ceramics and diamond), while above which the strength first increases and then decreases, exhibiting a maximum strength and a hardening to softening transition at a critical twin thickness (as in nanotwinned Cu). This important phenomenon has been attributed to a transition from source- to stress-controlled plasticity below the softening temperature, and suggests that different hardening behaviors may exist even in the same nanotwinned material depending on the temperature and that at a given temperature, different materials could exhibit different hardening behaviors depending on their softening temperature.", + "subject": [], + "keywords": [] + }, + { + "title": "A massively scalable distributed multigrid framework for nonlinear marine hydrodynamics", + "author": "Stefan Lemvig Glimberg, Allan Peter Engsig-Karup, Luke N Olson", + "publisher": "SAGE Publications", + "url": "http://dx.doi.org/10.1177/1094342019826662", + "doi": "10.1177/1094342019826662", + "year": 2019, + "month": 2, + "abstract": "The focus of this article is on the parallel scalability of a distributed multigrid framework, known as the DTU Compute GPUlab Library, for execution on graphics processing unit (GPU)-accelerated supercomputers. We demonstrate near-ideal weak scalability for a high-order fully nonlinear potential flow (FNPF) time domain model on the Oak Ridge Titan supercomputer, which is equipped with a large number of many-core CPU-GPU nodes. The high-order finite difference scheme for the solver is implemented to expose data locality and scalability, and the linear Laplace solver is based on an iterative multilevel preconditioned defect correction method designed for high-throughput processing and massive parallelism. In this work, the FNPF discretization is based on a multi-block discretization that allows for large-scale simulations. In this setup, each grid block is based on a logically structured mesh with support for curvilinear representation of horizontal block boundaries to allow for an accurate representation of geometric features such as surface-piercing bottom-mounted structures—for example, mono-pile foundations as demonstrated. Unprecedented performance and scalability results are presented for a system of equations that is historically known as being too expensive to solve in practical applications. A novel feature of the potential flow model is demonstrated, being that a modest number of multigrid restrictions is sufficient for fast convergence, improving overall parallel scalability as the coarse grid problem diminishes. In the numerical benchmarks presented, we demonstrate using 8192 modern Nvidia GPUs enabling large-scale and high-resolution nonlinear marine hydrodynamics applications.", + "subject": [], + "keywords": [] + }, + { + "title": "Adinkra foundation of component decomposition and the scan for superconformal multiplets in 11D, $$ \\mathcal{N} $$ = 1 superspace", + "author": "S. James Gates, Yangrui Hu, S.-N. Hazel Mak", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1007/jhep09(2020)089", + "doi": "10.1007/jhep09(2020)089", + "year": 2020, + "month": 9, + "abstract": "Abstract\n For the first time in the physics literature, the Lorentz representations of all 2,147,483,648 bosonic degrees of freedom and 2,147,483,648 fermionic degrees of freedom in an unconstrained eleven dimensional scalar superfield are presented. Comparisons of the conceptual bases for this advance in terms of component field, superfield, and adinkra arguments, respectively, are made. These highlight the computational efficiency of the adinkra-based approach over the others. It is noted at level sixteen in the 11D, $$ \\mathcal{N} $$\n N\n = 1 scalar superfield, the {65} representation of SO(1,10), the conformal graviton, is present. Thus, adinkra-based arguments suggest the surprising possibility that the 11D, $$ \\mathcal{N} $$\n N\n = 1 scalar superfield alone might describe a Poincaré supergravity prepotential or semi-prepotential in analogy to one of the off-shell versions of 4D, $$ \\mathcal{N} $$\n N\n = 1 superfield supergravity. We find the 11D, $$ \\mathcal{N} $$\n N\n = 1 scalar superfield contains 1,494 bosonic fields, 1,186 fermionic fields, and a maximum number of 29,334 links connecting them via orbits of the supercharges.", + "subject": [], + "keywords": [] + }, + { + "title": "Small RNAs in Rat Sperm Are a Predictive and Sensitive Biomarker of Exposure to the Testicular Toxicant Ethylene Glycol Monomethyl Ether", + "author": "Angela R Stermer, Gerardo Reyes, Susan J Hall, Kim Boekelheide", + "publisher": "Oxford University Press (OUP)", + "url": "http://dx.doi.org/10.1093/toxsci/kfz041", + "doi": "10.1093/toxsci/kfz041", + "year": 2019, + "month": 2, + "abstract": "Abstract\n Testicular histology and semen parameters are considered the gold standards when determining male reproductive toxicity. Ethylene glycol monomethyl ether (EGME) is a testicular toxicant with well-described effects on histopathology and sperm parameters. To compare the predictivity and sensitivity of molecular biomarkers of testicular toxicity to the traditional endpoints, small RNAs in the sperm were analyzed by next generation RNA-sequencing (RNA-seq). Adult rats were exposed to 0, 50, 60, or 75 mg/kg EGME by oral gavage for 5 consecutive days. Testis histology, epididymal sperm motility, and sperm small RNAs, including microRNAs (miRNAs), mRNA fragments, piwi-interacting RNAs (piRNAs), and tRNA fragments (tRFs), were analyzed 5 weeks after cessation of exposure. Testicular histology showed a significant dose-dependent increase in retained spermatid heads (RSH), while sperm motility declined with increasing dose. RNA-sequencing of sperm small RNAs was used to identify significant dose-dependent changes in percent mRNA fragments (of total reads), percent miRNAs (of total reads), average tRF length, average piRNA length, and piRNA and tRF length-distributions. Discriminant analysis showed relatively low predictivity of exposure based on RSH or motility compared to the average read length of all assigned RNAs. Benchmark dose (BMD) modeling resulted in a BMD of 62 mg/kg using RSH, whereas average read length of all assigned RNAs resulted in a BMD of 47 mg/kg. These results showed that sperm small RNAs are sensitive and predictive biomarkers of EGME-induced male reproductive toxicity.", + "subject": [], + "keywords": [] + }, + { + "title": "Dissipative particle dynamics simulation of critical pore size in a lipid bilayer membrane", + "author": "Clark Bowman, Mark Chaplain, Anastasios Matzavinos", + "publisher": "The Royal Society", + "url": "http://dx.doi.org/10.1098/rsos.181657", + "doi": "10.1098/rsos.181657", + "year": 2019, + "month": 3, + "abstract": "We investigate with computer simulations the critical radius of pores in a lipid bilayer membrane. Ilton\n et al.\n (Ilton\n et al.\n 2016\n Phys. Rev. Lett.\n 117\n , 257801 (\n doi:10.1103/PhysRevLett.117.257801\n )) recently showed that nucleated pores in a homopolymer film can increase or decrease in size, depending on whether they are larger or smaller than a critical size which scales linearly with film thickness. Using dissipative particle dynamics, a particle-based simulation method, we investigate the same scenario for a lipid bilayer membrane whose structure is determined by lipid–water interactions. We simulate a perforated membrane in which holes larger than a critical radius grow, while holes smaller than the critical radius close, as in the experiment of Ilton\n et al.\n (Ilton\n et al.\n 2016\n Phys. Rev. Lett.\n 117\n , 257801 (\n doi:10.1103/PhysRevLett.117.257801\n )). By altering key system parameters such as the number of particles per lipid and the periodicity, we also describe scenarios in which pores of any initial size can seal or even remain stable, showing a fundamental difference in the behaviour of lipid membranes from polymer films.", + "subject": [], + "keywords": [] + }, + { + "title": "Decoding task engagement from distributed network electrophysiology in humans", + "author": "Nicole R Provenza, Angelique C Paulk, Noam Peled, Maria I Restrepo, Sydney S Cash, Darin D Dougherty, Emad N Eskandar, David A Borton, Alik S Widge", + "publisher": "IOP Publishing", + "url": "http://dx.doi.org/10.1088/1741-2552/ab2c58", + "doi": "10.1088/1741-2552/ab2c58", + "year": 2019, + "month": 8, + "abstract": "Abstract\n \n Objective. Here, our objective was to develop a binary decoder to detect task engagement in humans during two distinct, conflict-based behavioral tasks. Effortful, goal-directed decision-making requires the coordinated action of multiple cognitive processes, including attention, working memory and action selection. That type of mental effort is often dysfunctional in mental disorders, e.g. when a patient attempts to overcome a depression or anxiety-driven habit but feels unable. If the onset of engagement in this type of focused mental activity could be reliably detected, decisional function might be augmented, e.g. through neurostimulation. However, there are no known algorithms for detecting task engagement with rapid time resolution. Approach. We defined a new network measure, fixed canonical correlation (FCCA), specifically suited for neural decoding applications. We extracted FCCA features from local field potential recordings in human volunteers to give a temporally continuous estimate of mental effort, defined by engagement in experimental conflict tasks. Main results. Using a small number of features per participant, we accurately decoded and distinguished task engagement from other mental activities. Further, the decoder distinguished between engagement in two different conflict-based tasks within seconds of their onset. Significance. These results demonstrate that network-level brain activity can detect specific types of mental efforts. This could form the basis of a responsive intervention strategy for decision-making deficits.", + "subject": [], + "keywords": [] + }, + { + "title": "Double- and multi-slit interference in photodetachment from nanometer organic molecular anions", + "author": "Yuan Liu, Chuan-Gang Ning, Lai-Sheng Wang", + "publisher": "AIP Publishing", + "url": "http://dx.doi.org/10.1063/1.5100799", + "doi": "10.1063/1.5100799", + "year": 2019, + "month": 6, + "abstract": "We present the predictions of double-slit and multislit interference of photoelectrons from a nanometer-size molecular negative ion. The interference clearly appears in both photoelectron angular distributions and photodetachment cross sections. In contrast to the diatomic photoelectron interference via the X-ray photon, the interference in the nanometer-size negative ions can be readily observed via a visible or extreme ultraviolet laser. Therefore, the phenomenon can be realized on a table-top setup, instead of a large accelerator.", + "subject": [], + "keywords": [] + }, + { + "title": "Rapid motor fluctuations reveal short-timescale neurophysiological biomarkers of Parkinson’s disease", + "author": "Minkyu Ahn, Shane Lee, Peter M Lauro, Erin L Schaeffer, Umer Akbar, Wael F Asaad", + "publisher": "IOP Publishing", + "url": "http://dx.doi.org/10.1088/1741-2552/abaca3", + "doi": "10.1088/1741-2552/abaca3", + "year": 2020, + "month": 8, + "abstract": "Abstract\n \n Objective. Identifying neural activity biomarkers of brain disease is essential to provide objective estimates of disease burden, obtain reliable feedback regarding therapeutic efficacy, and potentially to serve as a source of control for closed-loop neuromodulation. In Parkinson’s disease (PD), microelectrode recordings (MER) are routinely performed in the basal ganglia to guide electrode implantation for deep brain stimulation (DBS). While pathologically-excessive oscillatory activity has been observed and linked to PD motor dysfunction broadly, the extent to which these signals provide quantitative information about disease expression and fluctuations, particularly at short timescales, is unknown. Furthermore, the degree to which informative signal features are similar or different across patients has not been rigorously investigated. We sought to determine the extent to which motor error in PD across patients can be decoded on a rapid timescale using spectral features of neural activity. Approach. Here, we recorded neural activity from the subthalamic nucleus (STN) of subjects with PD undergoing awake DBS surgery while they performed an objective, continuous behavioral assessment that synthesized heterogenous PD motor manifestations to generate a scalar measure of motor dysfunction at short timescales. We then leveraged natural motor performance variations as a ‘ground truth’ to identify corresponding neurophysiological biomarkers. Main results. Support vector machines using multi-spectral decoding of neural signals from the STN succeeded in tracking the degree of motor impairment at short timescales (as short as one second). Spectral power across a wide range of frequencies, beyond the classic ‘β’ oscillations, contributed to this decoding, and multi-spectral models consistently outperformed those generated using more isolated frequency bands. While generalized decoding models derived across subjects were able to estimate motor impairment, patient-specific models typically performed better. Significance. These results demonstrate that quantitative information about short-timescale PD motor dysfunction is available in STN neural activity, distributed across various patient-specific spectral components, such that an individualized approach will be critical to fully harness this information for optimal disease tracking and closed-loop neuromodulation.", + "subject": [], + "keywords": [] + }, + { + "title": "Characterizing Spatial Variability of Climate‐Relevant Hazards and Vulnerabilities in the New England Region of the United States", + "author": "K. R. Spangler, J. Manjourides, A. H. Lynch, G. A. Wellenius", + "publisher": "American Geophysical Union (AGU)", + "url": "http://dx.doi.org/10.1029/2018gh000179", + "doi": "10.1029/2018gh000179", + "year": 2019, + "month": 4, + "abstract": "AbstractWeather and climate have substantial effects on human health. While much is known about how morbidity and mortality are affected by moderate‐to‐extreme heat, poor air quality, and heavy precipitation individually, less is known about the cumulative occurrence of these climatic hazards, and the extent to which they spatially overlap with community‐scale vulnerabilities. Specifically, there is interest in determining whether individuals living in places with the highest exposure to multiple health hazardous climatic conditions are also more vulnerable to having negative health outcomes. Presented here is a spatial analysis of the distribution of health‐relevant climatic hazards and social vulnerabilities across the New England region of the northeastern United States. We show that the frequency of excessive heat days, heavy precipitation days, and ozone (O3) and fine particulate matter (PM2.5) exceedances during the warm seasons (May–September) from 2009 to 2014 have distinct spatial distributions and are statistically significantly correlated across space with indicators of social vulnerability. We further quantify an integrated measure of the hazards and vulnerabilities to illustrate the spatial heterogeneity of overall risk, as well as to demonstrate how the choice of spatial scale influences the identification of high‐risk areas. These methods are transferrable to other locations and contexts, which could be of utility not only to geographers and epidemiologists, but also to policymakers tasked with allocating public health resources to populations at greatest risk of weather‐ and climate‐related health effects.", + "subject": [], + "keywords": [] + }, + { + "title": "Footprints of natural selection at the mannose-6-phosphate isomerase locus in barnacles", + "author": "Joaquin C. B. Nunez, Patrick A. Flight, Kimberly B. Neil, Stephen Rong, Leif A. Eriksson, David A. Ferranti, Magnus Alm Rosenblad, Anders Blomberg, David M. Rand", + "publisher": "Proceedings of the National Academy of Sciences", + "url": "http://dx.doi.org/10.1073/pnas.1918232117", + "doi": "10.1073/pnas.1918232117", + "year": 2020, + "month": 2, + "abstract": "The mannose-6-phosphate isomerase (\n Mpi\n ) locus in\n Semibalanus balanoides\n has been studied as a candidate gene for balancing selection for more than two decades. Previous work has shown that\n Mpi\n allozyme genotypes (fast and slow) have different frequencies across Atlantic intertidal zones due to selection on postsettlement survival (i.e., allele zonation). We present the complete gene sequence of the\n Mpi\n locus and quantify nucleotide polymorphism in\n S. balanoides\n , as well as divergence to its sister taxon\n Semibalanus cariosus\n . We show that the slow allozyme contains a derived charge-altering amino acid polymorphism, and both allozyme classes correspond to two haplogroups with multiple internal haplotypes. The locus shows several footprints of balancing selection around the fast/slow site: an enrichment of positive Tajima’s D for nonsynonymous mutations, an excess of polymorphism, and a spike in the levels of silent polymorphism relative to silent divergence, as well as a site frequency spectrum enriched for midfrequency mutations. We observe other departures from neutrality across the locus in both coding and noncoding regions. These include a nonsynonymous trans-species polymorphism and a recent mutation under selection within the fast haplogroup. The latter suggests ongoing allelic replacement of functionally relevant amino acid variants. Moreover, predicted models of\n Mpi\n protein structure provide insight into the functional significance of the putatively selected amino acid polymorphisms. While footprints of selection are widespread across the range of\n S. balanoides\n , our data show that intertidal zonation patterns are variable across both spatial and temporal scales. These data provide further evidence for heterogeneous selection on\n Mpi\n .", + "subject": [], + "keywords": [] + }, + { + "title": "Metabarcoding Reveals Temporal Patterns of Community Composition and Realized Thermal Niches of Thalassiosira Spp. (Bacillariophyceae) from the Narragansett Bay Long-Term Plankton Time Series", + "author": "Tatiana A. Rynearson, Sarah A. Flickinger, Diana N. Fontaine", + "publisher": "MDPI AG", + "url": "http://dx.doi.org/10.3390/biology9010019", + "doi": "10.3390/biology9010019", + "year": 2020, + "month": 1, + "abstract": "Diatoms generate nearly half of marine primary production and are comprised of a diverse array of species that are often morphologically cryptic or difficult to identify using light microscopy. Here, species composition and realized thermal niches of species in the diatom genus Thalassiosira were examined at the site of the Narragansett Bay (NBay) Long-Term Plankton Time Series using a combination of light microscopy (LM), high-throughput sequencing (HTS) of the 18S rDNA V4 region and historical records. Thalassiosira species were identified over 6 years using a combination of LM and DNA sequences. Sixteen Thalassiosira taxa were identified using HTS: nine were newly identified in NBay. Several newly identified species have small cell diameters and are difficult to identify using LM. However, they appeared frequently and thus may play a significant ecological role in NBay, particularly since their realized niches suggest they are eurythermal and able to tolerate the >25 °C temperature range of NBay. Four distinct species assemblages that grouped by season were best explained by surface water temperature. When compared to historical records, we found that the cold-water species Thalassiosira nordenskioeldii has decreased in persistence over time, suggesting that increasing surface water temperature has influenced the ecology of phytoplankton in NBay.", + "subject": [], + "keywords": [] + }, + { + "title": "Testing for calibration systematics in the EDGES low-band data using Bayesian model selection", + "author": "Peter H Sims, Jonathan C Pober", + "publisher": "Oxford University Press (OUP)", + "url": "http://dx.doi.org/10.1093/mnras/stz3388", + "doi": "10.1093/mnras/stz3388", + "year": 2019, + "month": 12, + "abstract": "ABSTRACT\n Cosmic Dawn (CD), when the first stars and proto-galaxies began to form, is commonly expected to be accompanied by an absorption signature at radio frequencies. This feature arises as Lyman α photons emitted by these first luminous objects couple the 21 cm excitation temperature of intergalactic hydrogen gas to its kinetic temperature, driving it into absorption relative to the cosmic microwave background. The detailed properties of this absorption profile encode powerful information about the physics of CD. Recently, Bowman et al. analysed data from the EDGES low-band radio antenna and found an unexpectedly deep absorption profile centred at 78 MHz, which could be a detection of this signature. Their specific analysis fit their measurements using a polynomial foreground model, a flattened Gaussian absorption profile, and a white noise model; we argue that a more accurate model, that includes a detailed noise model and accounting for the effects of plausible calibration errors, is essential for describing the EDGES data set. We perform a Bayesian evidence-based comparison of models of the EDGES low-band data set and find that those incorporating these additional components are decisively preferred. The subset of the best-fitting models of the data that include a global signal favours an amplitude consistent with standard cosmological assumptions (A &lt; 209 mK). However, there is not strong evidence to favour models of the data including a global 21 cm signal over those without one. Ultimately, we find that the derivation of robust constraints on astrophysics from the data is limited by the presence of systematics.", + "subject": [], + "keywords": [] + }, + { + "title": "Waves at a fluid-solid interface: Explicit versus implicit formulation of boundary conditions using a discontinuous Galerkin method", + "author": "Khemraj Shukla, José M. Carcione, Jan S. Hesthaven, Elizabeth L'heureux", + "publisher": "Acoustical Society of America (ASA)", + "url": "http://dx.doi.org/10.1121/10.0001170", + "doi": "10.1121/10.0001170", + "year": 2020, + "month": 5, + "abstract": "An accurate solution of the wave equation at a fluid-solid interface requires a correct implementation of the boundary condition. Boundary conditions at fluid-solid interface require continuity of the normal component of particle velocity and traction, whereas the tangential components vanish. A main challenge is to model interface waves, namely, the Scholte and leaky Rayleigh waves. This study uses a nodal discontinuous Galerkin (dG) finite-element method with the medium discretized using an unstructured uniform triangular meshes. The natural boundary conditions in the dG method are implemented by (1) using an explicit upwind numerical flux and (2) by using an implicit penalty flux and setting the modulus of rigidity of the acoustic medium to zero. The accuracy of these methods is evaluated by comparing the numerical solutions with analytical ones, with source and receiver at and away from the interface. The study shows that the solutions obtained from the explicit and implicit boundary conditions provide the correct results. The stability of the dG scheme is determined by the numerical flux, which also implements the boundary conditions by unifying the numerical solution at shared edges of the elements in an energy stable manner.", + "subject": [], + "keywords": [] + }, + { + "title": "Controlled release of entrapped nanoparticles from thermoresponsive hydrogels with tunable network characteristics", + "author": "Yi Wang, Zhen Li, Jie Ouyang, George Em Karniadakis", + "publisher": "Royal Society of Chemistry (RSC)", + "url": "http://dx.doi.org/10.1039/d0sm00207k", + "doi": "10.1039/d0sm00207k", + "year": 2020, + "month": -1, + "abstract": "Thermoresponsive hydrogels have been studied intensively for creating smart drug carriers and controlled drug delivery.", + "subject": [], + "keywords": [] + }, + { + "title": "Sequential Control Underlies Robust Ramping Dynamics in the Rostrolateral Prefrontal Cortex", + "author": "Theresa M. Desrochers, Anne G.E. Collins, David Badre", + "publisher": "Society for Neuroscience", + "url": "http://dx.doi.org/10.1523/jneurosci.1060-18.2018", + "doi": "10.1523/jneurosci.1060-18.2018", + "year": 2018, + "month": 12, + "abstract": "An essential human skill is our capacity to monitor and execute a sequence of tasks in the service of an overarching goal. Such a sequence can be as mundane as making a cup of coffee or as complex as flying a fighter plane. Previously, we showed that, during sequential control, the rostrolateral prefrontal cortex (RLPFC) exhibits activation that ramps steadily through the sequence and is necessary for sequential task execution using fMRI in humans (Desrochers et al., 2015). It remains unknown what computations may underlie this ramping dynamic. Across two independent fMRI experiments, we manipulated three features that were unique to the sequential control task to determine whether and how they modulated ramping activity in the RLPFC: (1) sequence position uncertainty, (2) sequential monitoring without external position cues (i.e., from memory), and (3) sequential monitoring without multilevel decision making (i.e., task execution). We replicated the ramping activation in RLPFC and found it to be remarkably robust regardless of the level of task abstraction or engagement of memory functions. Therefore, these results both replicate and extend previous findings regarding the function of the RLPFC. They suggest that sequential control processes are integral to the dynamics of RLPFC activity. Advancing knowledge of the neural bases of sequential control is crucial for our understanding of the sequential processes that are necessary for daily living.SIGNIFICANCE STATEMENTWe perform sequences of tasks every day, but little is known about how they are controlled in the brain. Previously we found that ramping activity in the rostrolateral prefrontal cortex (RLPFC) was necessary to perform a sequence of tasks. We designed two independent fMRI experiments in human participants to determine which features of the previous sequential task potentially engaged ramping in the RLPFC. We found that any demand to monitor a sequence of state transitions consistently elicited ramping in the RLPFC, regardless of the level of the decisions made at each step in the sequence or engagement of memory functions. These results provide a framework for understanding RLPFC function during sequential control, and consequently, daily life.", + "subject": [], + "keywords": [] + }, + { + "title": "Detecting Shared Genetic Architecture Among Multiple Phenotypes by Hierarchical Clustering of Gene-Level Association Statistics", + "author": "Melissa R McGuirl, Samuel Pattillo Smith, Björn Sandstede, Sohini Ramachandran", + "publisher": "Oxford University Press (OUP)", + "url": "http://dx.doi.org/10.1534/genetics.120.303096", + "doi": "10.1534/genetics.120.303096", + "year": 2020, + "month": 6, + "abstract": "AbstractMcGuirl et al. present a new method, Ward clustering to identify Internal Node branch length outliers using Gene Scores (WINGS), for identifying shared genetic architecture among multiple phenotypes. Past research...Emerging large-scale biobanks pairing genotype data with phenotype data present new opportunities to prioritize shared genetic associations across multiple phenotypes for molecular validation. Past research, by our group and others, has shown gene-level tests of association produce biologically interpretable characterization of the genetic architecture of a given phenotype. Here, we present a new method, Ward clustering to identify Internal Node branch length outliers using Gene Scores (WINGS), for identifying shared genetic architecture among multiple phenotypes. The objective of WINGS is to identify groups of phenotypes, or “clusters,” sharing a core set of genes enriched for mutations in cases. We validate WINGS using extensive simulation studies and then combine gene-level association tests with WINGS to identify shared genetic architecture among 81 case-control and seven quantitative phenotypes in 349,468 European-ancestry individuals from the UK Biobank. We identify eight prioritized phenotype clusters and recover multiple published gene-level associations within prioritized clusters.", + "subject": [], + "keywords": [] + }, + { + "title": "Transcriptional consequences of MBD5 disruption in mouse brain and CRISPR-derived neurons", + "author": "Catarina M. Seabra, Tatsiana Aneichyk, Serkan Erdin, Derek J. C. Tai, Celine E. F. De Esch, Parisa Razaz, Yu An, Poornima Manavalan, Ashok Ragavendran, Alexei Stortchevoi, Clemer Abad, Juan I. Young, Patricia Maciel, Michael E. Talkowski, James F. Gusella", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1186/s13229-020-00354-1", + "doi": "10.1186/s13229-020-00354-1", + "year": 2020, + "month": 6, + "abstract": "Abstract\n Background\n MBD5, encoding the methyl-CpG-binding domain 5 protein, has been proposed as a necessary and sufficient driver of the 2q23.1 microdeletion syndrome. De novo missense and protein-truncating variants from exome sequencing studies have directly implicated MBD5 in the etiology of autism spectrum disorder (ASD) and related neurodevelopmental disorders (NDDs). However, little is known concerning the specific function(s) of MBD5.\n \n Methods\n To gain insight into the complex interactions associated with alteration of MBD5 in individuals with ASD and related NDDs, we explored the transcriptional landscape of MBD5 haploinsufficiency across multiple mouse brain regions of a heterozygous hypomorphic Mbd5+/GT mouse model, and compared these results to CRISPR-mediated mutations of MBD5 in human iPSC-derived neuronal models.\n \n Results\n Gene expression analyses across three brain regions from Mbd5+/GT mice showed subtle transcriptional changes, with cortex displaying the most widespread changes following Mbd5 reduction, indicating context-dependent effects. Comparison with MBD5 reduction in human neuronal cells reinforced the context-dependence of gene expression changes due to MBD5 deficiency. Gene co-expression network analyses revealed gene clusters that were associated with reduced MBD5 expression and enriched for terms related to ciliary function.\n \n Limitations\n These analyses included a limited number of mouse brain regions and neuronal models, and the effects of the gene knockdown are subtle. As such, these results will not reflect the full extent of MBD5 disruption across human brain regions during early neurodevelopment in ASD, or capture the diverse spectrum of cell-type-specific changes associated with MBD5 alterations.\n \n Conclusions\n Our study points to modest and context-dependent transcriptional consequences of Mbd5 disruption in the brain. It also suggests a possible link between MBD5 and perturbations in ciliary function, which is an established pathogenic mechanism in developmental disorders and syndromes.", + "subject": [], + "keywords": [] + }, + { + "title": "First Season MWA Phase II Epoch of Reionization Power Spectrum Results at Redshift 7", + "author": "W. Li, J. C. Pober, N. Barry, B. J. Hazelton, M. F. Morales, C. M. Trott, A. Lanman, M. Wilensky, I. Sullivan, A. P. Beardsley, T. Booler, J. D. Bowman, R. Byrne, B. Crosse, D. Emrich, T. M. O. Franzen, K. Hasegawa, L. Horsley, M. Johnston-Hollitt, D. C. Jacobs, C. H. Jordan, R. C. Joseph, T. Kaneuji, D. L. Kaplan, D. Kenney, K. Kubota, J. Line, C. Lynch, B. McKinley, D. A. Mitchell, S. Murray, D. Pallot, B. Pindor, M. Rahimi, J. Riding, G. Sleap, K. Steele, K. Takahashi, S. J. Tingay, M. Walker, R. B. Wayth, R. L. Webster, A. Williams, C. Wu, J. S. B. Wyithe, S. Yoshiura, Q. Zheng", + "publisher": "American Astronomical Society", + "url": "http://dx.doi.org/10.3847/1538-4357/ab55e4", + "doi": "10.3847/1538-4357/ab55e4", + "year": 2019, + "month": 12, + "abstract": "Abstract\n The compact configuration of Phase II of the Murchison Widefield Array (MWA) consists of both a redundant subarray and pseudo-random baselines, offering unique opportunities to perform sky-model and redundant interferometric calibration. The highly redundant hexagonal cores give improved power spectrum sensitivity. In this paper, we present the analysis of nearly 40 hr of data targeting one of the MWA’s epoch of reionization (EoR) fields observed in 2016. We use both improved analysis techniques presented in Barry et al. and several additional techniques developed for this work, including data quality control methods and interferometric calibration approaches. We show the EoR power spectrum limits at redshift 6.5, 6.8, and 7.1 based on our deep analysis on this 40 hr data set. These limits span a range in k-space of 0.18 h Mpc−1 < k < 1.6 h Mpc−1, with a lowest measurement of Δ2 ≤ 2.39 × 103 mK2 at k = 0.59 h Mpc−1 and z = 6.5.", + "subject": [], + "keywords": [] + }, + { + "title": "Joint estimation of the Epoch of Reionization power spectrum and foregrounds", + "author": "Peter H Sims, Jonathan C Pober", + "publisher": "Oxford University Press (OUP)", + "url": "http://dx.doi.org/10.1093/mnras/stz1888", + "doi": "10.1093/mnras/stz1888", + "year": 2019, + "month": 7, + "abstract": "ABSTRACTThe power spectrum of redshifted 21 cm emission brightness temperature fluctuations is a powerful probe of the Epoch of Reionization (EoR). However, bright foreground emission presents a significant impediment to its unbiased recovery from interferometric data. We estimate the power spectrum within a Bayesian framework and demonstrate that incorporating a priori knowledge of the spectral structure of foregrounds in the large spectral scale component of the data model enables significantly improved modelling of the foregrounds without increasing the model complexity. We explore two astrophysically motivated parametrizations of the large spectral scale model: (i) a constant plus power-law model of the form $q_{0}+q_{1}(\\nu /\\nu _{0})^{b_{1}}$ for two values of b1: b1 = 〈β〉GDSE and b1 = 〈β〉EGS, the mean spectral indices of the Galactic diffuse synchrotron emission and extragalactic source foreground emission, respectively; and (ii) a constant plus double power-law model of the form $q_{0}+q_{1}(\\nu /\\nu _{0})^{b_{1}}+q_{2}(\\nu /\\nu _{0})^{b_{2}}$ with b1 = 〈β〉GDSE and b2 = 〈β〉EGS. We estimate the EoR power spectrum from simulated interferometric data consisting of an EoR signal, Galactic diffuse synchrotron emission, extragalactic sources, and diffuse free–free emission from the Galaxy. We show that, by jointly estimating a model of the EoR signal with the constant plus double power-law parametrization of the large spectral scale model, unbiased estimates of the EoR power spectrum are recoverable on all spatial scales accessible in the data set, including on the large spatial scales that were found to be contaminated in earlier work.", + "subject": [], + "keywords": [] + }, + { + "title": "Imaging with pre-stack migration based on Sp scattering kernels", + "author": "Junlin Hua, Karen M Fischer, Nicholas J Mancinelli, Tiezhao Bao", + "publisher": "Oxford University Press (OUP)", + "url": "http://dx.doi.org/10.1093/gji/ggz459", + "doi": "10.1093/gji/ggz459", + "year": 2019, + "month": 10, + "abstract": "SUMMARYSp receiver functions have been widely used to detect the lithosphere–asthenosphere boundary (LAB) and other mantle discontinuities. However, traditional common conversion point (CCP) stacking can be biased by the assumption of horizontal layers and this method typically underestimates scattering amplitudes from velocity boundaries with significant dips. A new pre-stack migration method based on recently developed Sp scattering kernels offers an alternative that more accurately captures the timing and amplitude of scattering. When calculating kernels, Sp-S times are estimated with the fast-marching method, and scattering amplitude versus direction, geometrical spreading and phase shifts are accounted for. To minimize imaging artefacts with larger station spacing, Sp receiver functions are interpolated to more closely spaced pseudo-stations using either compressive sampling or spatial averaging algorithms. To test the kernel-based stacking method, synthetic Sp phases were predicted using SPECFEM2D for velocity models with a flat Moho and a negative mantle velocity gradient with a ramp structure. The kernel-based stacking method resolves horizontal interfaces equally well as CCP stacking and outperforms CCP stacking when imaging boundaries with dips of more than 8°, although dip resolution is still limited. Use of more vertically incident phases such as SKSp improves retrieval of dipping discontinuity segments. A second approach is to down-weight the portions of the kernels that have the greatest positive interference among neighbouring stations, thus enhancing scattering from dipping structures where positive interference is lower. With this downweighting, the kernel-based stacking method applied to Sp data is able to continuously resolve LAB discontinuities with dips up to 15° and to partially resolve continuous LAB discontinuities with dips of ∼20°. The intrinsic properties of teleseismic Sp phase kernels limit their ability to resolve LAB structures with dips of ∼20–35°, but still larger dips of ∼40–50° are resolvable with dense and appropriately placed stations. Analysis of Sp scattering kernels also explains the effectiveness of CCP stacking for quasi-horizontal interfaces.", + "subject": [], + "keywords": [] + }, + { + "title": "A Parameterization with a Constrained Potential Energy Conversion Rate of Vertical Mixing Due to Langmuir Turbulence", + "author": "Brandon G. Reichl, Qing Li", + "publisher": "American Meteorological Society", + "url": "http://dx.doi.org/10.1175/jpo-d-18-0258.1", + "doi": "10.1175/jpo-d-18-0258.1", + "year": 2019, + "month": 11, + "abstract": "AbstractIn this study we develop a new parameterization for turbulent mixing in the ocean surface boundary layer (OSBL), including the effect of Langmuir turbulence. This new parameterization builds on a recent study (Reichl and Hallberg 2018, hereafter RH18), which predicts the available energy for turbulent mixing against stable stratification driven by shear and convective turbulence. To investigate the role of Langmuir turbulence in the framework of RH18, we utilize data from a suite of previously published large-eddy simulation (LES) experiments (Li and Fox-Kemper 2017, hereafter LF17) with and without Langmuir turbulence under different idealized forcing conditions. We find that the parameterization of RH18 is able to reproduce the mixing simulated by the LES in the non-Langmuir cases, but not the Langmuir cases. We therefore investigate the enhancement of the integrated vertical buoyancy flux within the entrainment layer in the presence of Langmuir turbulence using the LES data. An additional factor is introduced in the RH18 framework to capture the enhanced mixing due to Langmuir turbulence. This additional factor depends on the surface-layer averaged Langmuir number with a reduction in the presence of destabilizing surface buoyancy fluxes. It is demonstrated that including this factor within the RH18 OSBL turbulent mixing parameterization framework captures the simulated effect of Langmuir turbulence in the LES, which can be used for simulating the effect of Langmuir turbulence in climate simulations. This new parameterization is compared to the KPP-based Langmuir entrainment parameterization introduced by LF17, and differences are explored in detail.", + "subject": [], + "keywords": [] + }, + { + "title": "Mitochondrial DNA Fitness Depends on Nuclear Genetic Background inDrosophila", + "author": "Jim A Mossman, Jennifer Y Ge, Freddy Navarro, David M Rand", + "publisher": "Oxford University Press (OUP)", + "url": "http://dx.doi.org/10.1534/g3.119.400067", + "doi": "10.1534/g3.119.400067", + "year": 2019, + "month": 4, + "abstract": "AbstractMitochondrial DNA (mtDNA) has been one of the most extensively studied molecules in ecological, evolutionary and clinical genetics. In its early application in evolutionary genetics, mtDNA was assumed to be a selectively neutral marker conferring negligible fitness consequences for its host. However, this dogma has been overturned in recent years due to now extensive evidence for non-neutral evolutionary dynamics. Since mtDNA proteins physically interact with nuclear proteins to provide the mitochondrial machinery for aerobic ATP production, among other cell functions, co-variation of the respective genes is predicted to affect organismal fitness. To test this hypothesis we used an mtDNA-nuclear DNA introgression model in Drosophila melanogaster to test the fitness of genotypes in perturbation-reperturbation population cages and in a non-competitive assay for female fecundity. Genotypes consisted of both conspecific and heterospecific mtDNA-nDNA constructs, with either D. melanogaster or D. simulans mtDNAs on two alternative D. melanogaster nuclear backgrounds, to investigate mitonuclear genetic interactions (G x G effects). We found considerable variation between nuclear genetic backgrounds on the selection of mtDNA haplotypes. In addition, there was variation in the selection on mtDNAs pre- and post- reperturbation, demonstrating overall poor repeatability of selection. There was a strong influence of nuclear background on non-competitive fecundity across all the mtDNA species types. In only one of the four cage types did we see a significant fecundity effect between genotypes that could help explain the respective change in genotype frequency over generational time. We discuss these results in the context of G x G interactions and the possible influence of stochastic environments on mtDNA-nDNA selection.", + "subject": [], + "keywords": [] + }, + { + "title": "A selective membrane-targeting repurposed antibiotic with activity against persistent methicillin-resistant\n Staphylococcus aureus", + "author": "Wooseong Kim, Guijin Zou, Taylor P. A. Hari, Ingrid K. Wilt, Wenpeng Zhu, Nicolas Galle, Hammad A. Faizi, Gabriel L. Hendricks, Katerina Tori, Wen Pan, Xiaowen Huang, Andrew D. Steele, Erika E. Csatary, Madeline M. Dekarske, Jake L. Rosen, Noelly de Queiroz Ribeiro, Kiho Lee, Jenna Port, Beth Burgwyn Fuchs, Petia M. Vlahovska, William M. Wuest, Huajian Gao, Frederick M. Ausubel, Eleftherios Mylonakis", + "publisher": "Proceedings of the National Academy of Sciences", + "url": "http://dx.doi.org/10.1073/pnas.1904700116", + "doi": "10.1073/pnas.1904700116", + "year": 2019, + "month": 7, + "abstract": "Significance\n \n There is a critical lack of therapeutic agents to treat infections caused by nongrowing persister forms of methicillin-resistant\n Staphylococcus aureus\n (MRSA). Although membrane-disrupting agents can kill persister cells, their therapeutic potential has been mostly overlooked because of low selectivity for bacterial versus mammalian membranes. We report that the clinically approved anthelmintic drug bithionol kills MRSA persisters by disrupting membrane lipid bilayers at concentrations that exhibit low levels of toxicity to mammalian cells. The selectivity of bithionol results from the presence of cholesterol in mammalian but not in bacterial membranes. We also show that the antipersister potency of membrane-active antimicrobial agents correlates with their ability to increase membrane fluidity. Our results significantly enhance our understanding of bacterial membrane disruption and membrane selectivity.", + "subject": [], + "keywords": [] + }, + { + "title": "Combined computational and experimental investigation of high temperature thermodynamics and structure of cubic ZrO2 and HfO2", + "author": "Qi-Jun Hong, Sergey V. Ushakov, Denys Kapush, Chris J. Benmore, Richard J. K. Weber, Axel van de Walle, Alexandra Navrotsky", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1038/s41598-018-32848-7", + "doi": "10.1038/s41598-018-32848-7", + "year": 2018, + "month": 10, + "abstract": "AbstractStructure and thermodynamics of pure cubic ZrO2 and HfO2 were studied computationally and experimentally from their tetragonal to cubic transition temperatures (2311 and 2530 °C) to their melting points (2710 and 2800 °C). Computations were performed using automated ab initio molecular dynamics techniques. High temperature synchrotron X-ray diffraction on laser heated aerodynamically levitated samples provided experimental data on volume change during tetragonal-to-cubic phase transformation (0.55 ± 0.09% for ZrO2 and 0.87 ± 0.08% for HfO2), density and thermal expansion. Fusion enthalpies were measured using drop and catch calorimetry on laser heated levitated samples as 55 ± 7 kJ/mol for ZrO2 and 61 ± 10 kJ/mol for HfO2, compared with 54 ± 2 and 52 ± 2 kJ/mol from computation. Volumetric thermal expansion for cubic ZrO2 and HfO2 are similar and reach (4 ± 1)·10−5/K from experiment and (5 ± 1)·10−5/K from computation. An agreement with experiment renders confidence in values obtained exclusively from computation: namely heat capacity of cubic HfO2 and ZrO2, volume change on melting, and thermal expansion of the liquid to 3127 °C. Computed oxygen diffusion coefficients indicate that above 2400 °C pure ZrO2 is an excellent oxygen conductor, perhaps even better than YSZ.", + "subject": [], + "keywords": [] + }, + { + "title": "S‐to‐Rayleigh Wave Scattering From the Continental Margin Observed at USArray", + "author": "J. S. Buehler, N. J. Mancinelli, P. M. Shearer", + "publisher": "American Geophysical Union (AGU)", + "url": "http://dx.doi.org/10.1029/2017gl076812", + "doi": "10.1029/2017gl076812", + "year": 2018, + "month": 5, + "abstract": "AbstractWe show examples of teleseismic S waves from western Pacific earthquakes converting to surface waves near the western U.S. coastline. Many of these events originate in the Tonga‐Samoa region. We observe these surface wave conversions at USArray stations at relatively long periods (>10 s). The amplitudes vary considerably from station to station and appear highly amplified in the Yellowstone region. Two‐dimensional spectral element simulations successfully generate scattered Rayleigh waves from incident SV waves and models with surface topography at the coastline and crustal thickness variations across the margin, although simple models cannot explain the large Rayleigh wave amplitudes (greater than the direct S wave amplitude) observed in some regions, suggesting that the wave train is amplified by local structure or 3‐D focusing effects.", + "subject": [], + "keywords": [] + }, + { + "title": "Mitonuclear epistasis, genotype‐by‐environment interactions, and personalized genomics of complex traits in Drosophila", + "author": "David M. Rand, Jim A. Mossman, Lei Zhu, Leann M. Biancani, Jennifer Y. Ge", + "publisher": "Wiley", + "url": "http://dx.doi.org/10.1002/iub.1954", + "doi": "10.1002/iub.1954", + "year": 2018, + "month": 11, + "abstract": "AbstractMitochondrial function requires the coordinated expression of dozens of gene products from the mitochondrial genome and hundreds from the nuclear genomes. The systems that emerge from these interactions convert the food we eat and the oxygen we breathe into energy for life, while regulating a wide range of other cellular processes. These facts beg the question of whether the gene‐by‐gene interactions (G x G) that enable mitochondrial function are distinct from the gene‐by‐environment interactions (G x E) that fuel mitochondrial activity. We examine this question using a Drosophila model of mitonuclear interactions in which experimental combinations of mtDNA and nuclear chromosomes generate pairs of mitonuclear genotypes to test for epistatic interactions (G x G). These mitonuclear genotypes are then exposed to altered dietary or oxygen environments to test for G x E interactions. We use development time to assess dietary effects, and genome wide RNAseq analyses to assess hypoxic effects on transcription, which can be partitioned in to mito, nuclear, and environmental (G x G x E) contributions to these complex traits. We find that mitonuclear epistasis is universal, and that dietary and hypoxic treatments alter the epistatic interactions. We further show that the transcriptional response to alternative mitonuclear interactions has significant overlap with the transcriptional response to alternative oxygen environments. Gene coexpression analyses suggest that these shared genes are more central in networks of gene interactions, implying some functional overlap between epistasis and genotype by environment interactions. These results are discussed in the context of evolutionary fitness, the genetic basis of complex traits, and the challenge of achieving precision in personalized medicine. © 2018 The Authors. IUBMB Life published by Wiley Periodicals, Inc. on behalf of International Union of Biochemistry and Molecular Biology, 70(12):1275–1288, 2018", + "subject": [], + "keywords": [] + }, + { + "title": "[(Cp2M)2B9H11] (M = Zr or Hf): early transition metal ‘guarded’ heptaborane with strong covalent and electrostatic bonding", + "author": "Anangsha De, Qian-Fan Zhang, Bijan Mondal, Ling Fung Cheung, Sourav Kar, Koushik Saha, Babu Varghese, Lai-Sheng Wang, Sundargopal Ghosh", + "publisher": "Royal Society of Chemistry (RSC)", + "url": "http://dx.doi.org/10.1039/c7sc05014c", + "doi": "10.1039/c7sc05014c", + "year": 2018, + "month": -1, + "abstract": "We have isolated and structurally characterized two new transition metal complexes of the heptaborane, [(Cp2M)2B9H11] (Cp = η5-C5H5; M = Zr or Hf).", + "subject": [], + "keywords": [] + }, + { + "title": "An evaluation of the failure modes transition and the Christensen ductile/brittle failure theory using molecular dynamics", + "author": "Richard Christensen, Zhi Li, Huajian Gao", + "publisher": "The Royal Society", + "url": "http://dx.doi.org/10.1098/rspa.2018.0361", + "doi": "10.1098/rspa.2018.0361", + "year": 2018, + "month": 11, + "abstract": "The Christensen ductile/brittle failure theory can be interpreted in terms of the associated failure modes, those of shear bands and voids nucleation. Their conjunction is then termed as the failure modes transition and it is studied here using molecular dynamics. The test material is taken as a particular metallic glass, CuZr. First the theoretical failure criteria are evaluated and then the theoretical failure modes transition is evaluated. Both are found to perform extremely well. The overall failure theory contains three modes of failure, the two already mentioned plus a fracture criterion. A general conclusion from the work is that the voids nucleation criterion is of unusually broad relevance. Voids nucleation leads to voids growth and then further deteriorating mechanisms and ultimately failure. But the voids nucleation is the precipitating event of all that subsequently occurs in this process. Access to these capabilities is gained through the failure theory for all homogeneous, full density, isotropic materials. Only two standard testing measurements are needed to calibrate the entire failure theory, including the transitions.", + "subject": [], + "keywords": [] + }, + { + "title": "The role of oxygen vacancies in biomass deoxygenation by reducible zinc/zinc oxide catalysts", + "author": "Xiao Xiao, Helen Bergstrom, Ryan Saenger, Benjamin Johnson, Runcang Sun, Andrew Peterson", + "publisher": "Royal Society of Chemistry (RSC)", + "url": "http://dx.doi.org/10.1039/c7cy02535a", + "doi": "10.1039/c7cy02535a", + "year": 2018, + "month": -1, + "abstract": "Selective removal of oxygen is the key challenge in the upgrading of biomass-derived molecules, and reducible metal oxides have shown the ability to catalytically remove oxygen even at low exogenous H2 pressures.", + "subject": [], + "keywords": [] + }, + { + "title": "Explaining the ocean's richest biodiversity hotspot and global patterns of fish diversity", + "author": "Elizabeth Christina Miller, Kenji T. Hayashi, Dongyuan Song, John J. Wiens", + "publisher": "The Royal Society", + "url": "http://dx.doi.org/10.1098/rspb.2018.1314", + "doi": "10.1098/rspb.2018.1314", + "year": 2018, + "month": 10, + "abstract": "For most marine organisms, species richness peaks in the Central Indo-Pacific region and declines longitudinally, a striking pattern that remains poorly understood. Here, we used phylogenetic approaches to address the causes of richness patterns among global marine regions, comparing the relative importance of colonization time, number of colonization events, and diversification rates (speciation minus extinction). We estimated regional richness using distributional data for almost all percomorph fishes (17 435 species total, including approximately 72% of all marine fishes and approximately 33% of all freshwater fishes). The high diversity of the Central Indo-Pacific was explained by its colonization by many lineages 5.3–34 million years ago. These relatively old colonizations allowed more time for richness to build up through\n in situ\n diversification compared to other warm-marine regions. Surprisingly, diversification rates were decoupled from marine richness patterns, with clades in low-richness cold-marine habitats having the highest rates. Unlike marine richness, freshwater diversity was largely derived from a few ancient colonizations, coupled with high diversification rates. Our results are congruent with the geological history of the marine tropics, and thus may apply to many other organisms. Beyond marine biogeography, we add to the growing number of cases where colonization and time-for-speciation explain large-scale richness patterns instead of diversification rates.", + "subject": [], + "keywords": [] + }, + { + "title": "Comparing Redundant and Sky-model-based Interferometric Calibration: A First Look with Phase II of the MWA", + "author": "W. Li, J. C. Pober, B. J. Hazelton, N. Barry, M. F. Morales, I. Sullivan, A. R. Parsons, Z. S. Ali, J. S. Dillon, A. P. Beardsley, J. D. Bowman, F. Briggs, R. Byrne, P. Carroll, B. Crosse, D. Emrich, A. Ewall-Wice, L. Feng, T. M. O. Franzen, J. N. Hewitt, L. Horsley, D. C. Jacobs, M. Johnston-Hollitt, C. Jordan, R. C. Joseph, D. L. Kaplan, D. Kenney, H. Kim, P. Kittiwisit, A. Lanman, J. Line, B. McKinley, D. A. Mitchell, S. Murray, A. Neben, A. R. Offringa, D. Pallot, S. Paul, B. Pindor, P. Procopio, M. Rahimi, J. Riding, S. K. Sethi, N. Udaya Shankar, K. Steele, R. Subrahmanian, M. Tegmark, N. Thyagarajan, S. J. Tingay, C. Trott, M. Walker, R. B. Wayth, R. L. Webster, A. Williams, C. Wu, S. Wyithe", + "publisher": "American Astronomical Society", + "url": "http://dx.doi.org/10.3847/1538-4357/aad3c3", + "doi": "10.3847/1538-4357/aad3c3", + "year": 2018, + "month": 8, + "abstract": "Abstract\n Interferometric arrays seeking to measure the 21 cm signal from the epoch of reionization (EOR) must contend with overwhelmingly bright emission from foreground sources. Accurate recovery of the 21 cm signal will require precise calibration of the array, and several new avenues for calibration have been pursued in recent years, including methods using redundancy in the antenna configuration. The newly upgraded Phase II of Murchison Widefield Array (MWA) is the first interferometer that has large numbers of redundant baselines while retaining good instantaneous UV coverage. This array therefore provides a unique opportunity to compare redundant calibration with sky-model-based algorithms. In this paper, we present the first results from comparing both calibration approaches with MWA Phase II observations. For redundant calibration, we use the package OMNICAL and produce sky-based calibration solutions with the analysis package Fast Holographic Deconvolution (FHD). There are three principal results: (1) We report the success of OMNICAL on observations of ORBComm satellites, showing substantial agreement between redundant visibility measurements after calibration. (2) We directly compare OMNICAL calibration solutions with those from FHD and demonstrate that these two different calibration schemes give extremely similar results. (3) We explore improved calibration by combining OMNICAL and FHD. We evaluate these combined methods using power spectrum techniques developed for EOR analysis and find evidence for marginal improvements mitigating artifacts in the power spectrum. These results are likely limited by the signal-to-noise ratio in the 6 hr of data used, but they suggest future directions for combining these two calibration schemes.", + "subject": [], + "keywords": [] + }, + { + "title": "Mechanics of cellular packing of nanorods with finite and non-uniform diameters", + "author": "Xin Yi, Guijin Zou, Huajian Gao", + "publisher": "Royal Society of Chemistry (RSC)", + "url": "http://dx.doi.org/10.1039/c8nr04110e", + "doi": "10.1039/c8nr04110e", + "year": 2018, + "month": -1, + "abstract": "Theoretical modeling and MD simulations demonstrate that the diameter, length, and shape of an encapsulated nanorod together play key roles in regulating its mechanical interplay with the confining vesicle, shedding light on the cellular packing of microtubule bundles, filopodial protrusion, mitotic cell division, and cytotoxicity.", + "subject": [], + "keywords": [] + }, + { + "title": "Improved 21 cm Epoch of Reionization Power Spectrum Measurements with a Hybrid Foreground Subtraction and Avoidance Technique", + "author": "Joshua R. Kerrigan, Jonathan C. Pober, Zaki S. Ali, Carina Cheng, Adam P. Beardsley, Aaron R. Parsons, James E. Aguirre, Nichole Barry, Richard F. Bradley, Gianni Bernardi, Chris L. Carilli, David R. DeBoer, Joshua S. Dillon, Daniel C. Jacobs, Saul A. Kohn, Matthew Kolopanis, Adam Lanman, Wenyang Li, Adrian Liu, Ian Sullivan", + "publisher": "American Astronomical Society", + "url": "http://dx.doi.org/10.3847/1538-4357/aad8bb", + "doi": "10.3847/1538-4357/aad8bb", + "year": 2018, + "month": 9, + "abstract": "Abstract\n Observations of the 21 cm Epoch of Reionization signal are dominated by Galactic and extragalactic foregrounds. The need for foreground removal has led to the development of two main techniques, often referred to as “foreground avoidance” and “foreground subtraction.” Avoidance is associated with filtering foregrounds in Fourier space, while subtraction uses an explicit foreground model that is removed. Using 1088 hr of data from the 64-element PAPER array, we demonstrate that subtraction of a foreground model prior to delay-space foreground filtering results in a modest but measurable improvement of the performance of the filter. This proof-of-concept result shows that improvement stems from the reduced dynamic range requirements needed for the foreground filter: subtraction of a foreground model reduces the total foreground power, so for a fixed dynamic range, the filter can push toward fainter limits. We also find that the choice of window function used in the foreground filter can have an appreciable affect on the performance near the edges of the observing band. We demonstrate these effects using a smaller 3 hr sampling of data from the MWA, and find that the hybrid filtering and subtraction removal approach provides similar improvements across the band as seen in the case with PAPER-64.", + "subject": [], + "keywords": [] + }, + { + "title": "Data-driven Modeling of Hemodynamics and its Role on Thrombus Size and Shape in Aortic Dissections", + "author": "Alireza Yazdani, He Li, Matthew R. Bersi, Paolo Di Achille, Joseph Insley, Jay D. Humphrey, George Em Karniadakis", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1038/s41598-018-20603-x", + "doi": "10.1038/s41598-018-20603-x", + "year": 2018, + "month": 2, + "abstract": "AbstractAortic dissection is a pathology that manifests due to microstructural defects in the aortic wall. Blood enters the damaged wall through an intimal tear, thereby creating a so-called false lumen and exposing the blood to thrombogenic intramural constituents such as collagen. The natural history of this acute vascular injury thus depends, in part, on thrombus formation, maturation, and possible healing within the false lumen. A key question is: Why do some false lumens thrombose completely while others thrombose partially or little at all? An ability to predict the location and extent of thrombus in subjects with dissection could contribute significantly to clinical decision-making, including interventional design. We develop, for the first time, a data-driven particle-continuum model for thrombus formation in a murine model of aortic dissection. In the proposed model, we simulate a final-value problem in lieu of the original initial-value problem with significantly fewer particles that may grow in size upon activation, thus representing the local concentration of blood-borne species. Numerical results confirm that geometry and local hemodynamics play significant roles in the acute progression of thrombus. Despite geometrical differences between murine and human dissections, mouse models can provide considerable insight and have gained popularity owing to their reproducibility. Our results for three classes of geometrically different false lumens show that thrombus forms and extends to a greater extent in regions with lower bulk shear rates. Dense thrombi are less likely to form in high-shear zones and in the presence of strong vortices. The present data-driven study suggests that the proposed model is robust and can be employed to assess thrombus formation in human aortic dissections.", + "subject": [], + "keywords": [] + }, + { + "title": "Study of low temperature chlorine atom initiated oxidation of methyl and ethyl butyrate using synchrotron photoionization TOF-mass spectrometry", + "author": "Joseph Czekner, Craig A. Taatjes, David L. Osborn, Giovanni Meloni", + "publisher": "Royal Society of Chemistry (RSC)", + "url": "http://dx.doi.org/10.1039/c7cp08221e", + "doi": "10.1039/c7cp08221e", + "year": 2018, + "month": -1, + "abstract": "The initial oxidation products of methyl butyrate (MB) and ethyl butyrate (EB) are studied using a time- and energy-resolved photoionization mass spectrometer.", + "subject": [], + "keywords": [] + }, + { + "title": "Bismuth–Boron Multiple Bonding in BiB2O− and Bi2B−", + "author": "Tian Jian, Ling Fung Cheung, Teng‐Teng Chen, Lai‐Sheng Wang", + "publisher": "Wiley", + "url": "http://dx.doi.org/10.1002/ange.201705209", + "doi": "10.1002/ange.201705209", + "year": 2017, + "month": 6, + "abstract": "AbstractDespite its electron deficiency, boron is versatile in forming multiple bonds. Transition‐metal–boron double bonding is known, but boron–metal triple bonds have been elusive. Two bismuth boron cluster anions, BiB2O− and Bi2B−, containing triple and double B−Bi bonds are presented. The BiB2O− and Bi2B− clusters are produced by laser vaporization of a mixed B/Bi target and characterized by photoelectron spectroscopy and ab initio calculations. Well‐resolved photoelectron spectra are obtained and interpreted with the help of ab initio calculations, which show that both species are linear. Chemical bonding analyses reveal that Bi forms triple and double bonds with boron in BiB2O− ([Bi≡B−B≡O]−) and Bi2B− ([Bi=B=Bi]−), respectively. The Bi−B double and triple bond strengths are calculated to be 3.21 and 4.70 eV, respectively. This is the first experimental observation of Bi−B double and triple bonds, opening the door to design main‐group metal–boron complexes with multiple bonding.", + "subject": [], + "keywords": [] + }, + { + "title": "Revising transcriptome assemblies with phylogenetic information in Agalma1.0", + "author": "August Guang, Mark Howison, Felipe Zapata, Charles Lawrence, Casey Dunn", + "publisher": "Cold Spring Harbor Laboratory", + "url": "http://dx.doi.org/10.1101/202416", + "doi": "10.1101/202416", + "year": 2017, + "month": 10, + "abstract": "AbstractMotivationOne of the most common transcriptome assembly errors is to mistake different transcripts of the same gene as transcripts from multiple closely related genes. It is difficult to identify these errors during assembly, but in a phylogenetic analysis these errors can be diagnosed from gene trees containing clades of tips from the same species with improbably short branch lengths.Resultstreeinform is a module implemented in Agalma1.0 that uses phylogenetic analyses across species to refine transcriptome assemblies. It identifies transcripts of the same gene that were incorrectly assigned to multiple genes and reassign them as transcripts of the same gene.Availability and Implementationtreeinform is implemented in Agalma1.0, available at https://bitbucket.org/caseywdunn/agalma.Contactaugust_guang@brown.eduSupplementary informationSupplementary information is available at bioRxiv.", + "subject": [], + "keywords": [] + }, + { + "title": "The effect of ilmenite viscosity on the dynamics and evolution of an overturned lunar cumulate mantle", + "author": "Nan Zhang, Nick Dygert, Yan Liang, E. M. Parmentier", + "publisher": "American Geophysical Union (AGU)", + "url": "http://dx.doi.org/10.1002/2017gl073702", + "doi": "10.1002/2017gl073702", + "year": 2017, + "month": 7, + "abstract": "AbstractLunar cumulate mantle overturn and the subsequent upwelling of overturned mantle cumulates provide a potential framework for understanding the first‐order thermochemical evolution of the Moon. Upwelling of ilmenite‐bearing cumulates (IBCs) after the overturn has a dominant influence on the dynamics and long‐term thermal evolution of the lunar mantle. An important parameter determining the stability and convective behavior of the IBC is its viscosity, which was recently constrained through rock deformation experiments. To examine the effect of IBC viscosity on the upwelling of overturned lunar cumulate mantle, here we conduct three‐dimensional mantle convection models with an evolving core superposed by an IBC‐rich layer, which resulted from mantle overturn after magma ocean solidification. Our modeling shows that a reduction of mantle viscosity by 1 order of magnitude, due to the presence of ilmenite, can dramatically change convective planform and long‐term lunar mantle evolution. Our model results suggest a relatively stable partially molten IBC layer that has surrounded the lunar core to the present day.", + "subject": [], + "keywords": [] + }, + { + "title": "Addressing uncertainty in atomistic machine learning", + "author": "Andrew A. Peterson, Rune Christensen, Alireza Khorshidi", + "publisher": "Royal Society of Chemistry (RSC)", + "url": "http://dx.doi.org/10.1039/c7cp00375g", + "doi": "10.1039/c7cp00375g", + "year": 2017, + "month": -1, + "abstract": "Machine-learning regression can precisely emulate the potential energy and forces of more expensive electronic-structure calculations, but to make useful predictions an assessment must be made of the prediction's credibility.", + "subject": [], + "keywords": [] + }, + { + "title": "Large-scale analysis of branchpoint usage across species and cell lines", + "author": "Allison J. Taggart, Chien-Ling Lin, Barsha Shrestha, Claire Heintzelman, Seongwon Kim, William G. Fairbrother", + "publisher": "Cold Spring Harbor Laboratory", + "url": "http://dx.doi.org/10.1101/gr.202820.115", + "doi": "10.1101/gr.202820.115", + "year": 2017, + "month": 1, + "abstract": "The coding sequence of each human pre-mRNA is interrupted, on average, by 11 introns that must be spliced out for proper gene expression. Each intron contains three obligate signals: a 5′ splice site, a branch site, and a 3′ splice site. Splice site usage has been mapped exhaustively across different species, cell types, and cellular states. In contrast, only a small fraction of branch sites have been identified even once. The few reported annotations of branch site are imprecise as reverse transcriptase skips several nucleotides while traversing a 2–5 linkage. Here, we report large-scale mapping of the branchpoints from deep sequencing data in three different species and in the SF3B1 K700E oncogenic mutant background. We have developed a novel method whereby raw lariat reads are refined by U2snRNP/pre-mRNA base-pairing models to return the largest current data set of branchpoint sequences with quality metrics. This analysis discovers novel modes of U2snRNA:pre-mRNA base-pairing conserved in yeast and provides insight into the biogenesis of intron circles. Finally, matching branch site usage with isoform selection across the extensive panel of ENCODE RNA-seq data sets offers insight into the mechanisms by which branchpoint usage drives alternative splicing.", + "subject": [], + "keywords": [] + }, + { + "title": "Coherence in nonradiative transitions: internal conversion in Rydberg-excited N-methyl and N-ethyl morpholine", + "author": "Yao Zhang, Hannes Jónsson, Peter M. Weber", + "publisher": "Royal Society of Chemistry (RSC)", + "url": "http://dx.doi.org/10.1039/c7cp05244h", + "doi": "10.1039/c7cp05244h", + "year": 2017, + "month": -1, + "abstract": "The survival of coherent wavepacket motion during internal conversions is observed in relatively large molecules,N-methyl morpholine andN-ethyl morpholine, where standard models imply fast decoherence in a statistical limit.", + "subject": [], + "keywords": [] + }, + { + "title": "Nb2©Au6: a molecular wheel with a short NbNb triple bond coordinated by an Au6 ring and reinforced by σ aromaticity", + "author": "Tian Jian, Ling Fung Cheung, Joseph Czekner, Teng-Teng Chen, Gary V. Lopez, Wei-Li Li, Lai-Sheng Wang", + "publisher": "Royal Society of Chemistry (RSC)", + "url": "http://dx.doi.org/10.1039/c7sc02881d", + "doi": "10.1039/c7sc02881d", + "year": 2017, + "month": -1, + "abstract": "Vibrationally-resolved photoelectron spectroscopy and theoretical calculations reveal that Nb2Au6−/0 possess a Au6 ring coordinated equatorially to a triply-bonded NbNb.", + "subject": [], + "keywords": [] + }, + { + "title": "Nb2©Au6: a molecular wheel with a short NbNb triple bond coordinated by an Au6 ring and reinforced by σ aromaticity", + "author": "Tian Jian, Ling Fung Cheung, Joseph Czekner, Teng-Teng Chen, Gary V. Lopez, Wei-Li Li, Lai-Sheng Wang", + "publisher": "Royal Society of Chemistry (RSC)", + "url": "http://dx.doi.org/10.1039/c7sc02881d", + "doi": "10.1039/c7sc02881d", + "year": 2017, + "month": -1, + "abstract": "Vibrationally-resolved photoelectron spectroscopy and theoretical calculations reveal that Nb2Au6−/0 possess a Au6 ring coordinated equatorially to a triply-bonded NbNb.", + "subject": [], + "keywords": [] + }, + { + "title": "Characterizing the cirri and gut microbiomes of the intertidal barnacle Semibalanus balanoides", + "author": "Bianca R. P. Brown, Joaquin C. B. Nunez, David M. Rand", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1186/s42523-020-00058-0", + "doi": "10.1186/s42523-020-00058-0", + "year": 2020, + "month": 11, + "abstract": "Abstract\nBackground\nNatural populations inhabiting the rocky intertidal experience multiple ecological stressors and provide an opportunity to investigate how environmental differences influence microbiomes over small geographical scales. However, very few microbiome studies focus on animals that inhabit the intertidal. In this study, we investigate the microbiome of the intertidal barnacle Semibalanus balanoides. We first describe the microbiome of two body tissues: the feeding appendages, or cirri, and the gut. Next, we examine whether there are differences between the microbiome of each body tissue of barnacles collected from the thermally extreme microhabitats of the rocky shores’ upper and lower tidal zones.\n\nResults\nOverall, the microbiome of S. balanoides consisted of 18 phyla from 408 genera. Our results showed that although cirri and gut microbiomes shared a portion of their amplicon sequence variants (ASVs), the microbiome of each body tissue was distinct. Over 80% of the ASVs found in the cirri were also found in the gut, and 44% of the ASVs found in the gut were also found in the cirri. Notably, the gut microbiome was not a subset of the cirri microbiome. Additionally, we identified that the cirri microbiome was responsive to microhabitat differences.\n\nConclusion\nResults from this study indicate that S. balanoides maintains distinct microbiomes in its cirri and gut tissues, and that the gut microbiome is more stable than the cirri microbiome between the extremes of the intertidal.", + "subject": [], + "keywords": [] + }, + { + "title": "Theoretical prediction of high melting temperature for a Mo–Ru–Ta–W HCP multiprincipal element alloy", + "author": "Qi-Jun Hong, Jan Schroers, Douglas Hofmann, Stefano Curtarolo, Mark Asta, Axel van de Walle", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1038/s41524-020-00473-6", + "doi": "10.1038/s41524-020-00473-6", + "year": 2021, + "month": 1, + "abstract": "AbstractWhile rhenium is an ideal material for rapid thermal cycling applications under high temperatures, such as rocket engine nozzles, its high cost limits its widespread use and prompts an exploration of viable cost-effective substitutes. In prior work, we identified a promising pool of candidate substitute alloys consisting of Mo, Ru, Ta, and W. In this work we demonstrate, based on density functional theory melting temperature calculations, that one of the candidates, Mo0.292Ru0.555Ta0.031W0.122, exhibits a high melting temperature (around 2626 K), thus supporting its use in high-temperature applications.", + "subject": [], + "keywords": [] + }, + { + "title": "Toward a statistically explicit understanding of de novo sequence assembly", + "author": "Mark Howison, Felipe Zapata, Casey W. Dunn", + "publisher": "Oxford University Press (OUP)", + "url": "http://dx.doi.org/10.1093/bioinformatics/btt525", + "doi": "10.1093/bioinformatics/btt525", + "year": 2013, + "month": 9, + "abstract": "Abstract\n Motivation: Draft de novo genome assemblies are now available for many organisms. These assemblies are point estimates of the true genome sequences. Each is a specific hypothesis, drawn from among many alternative hypotheses, of the sequence of a genome. Assembly uncertainty, the inability to distinguish between multiple alternative assembly hypotheses, can be due to real variation between copies of the genome in the sample, errors and ambiguities in the sequenced data and assumptions and heuristics of the assemblers. Most assemblers select a single assembly according to ad hoc criteria, and do not yet report and quantify the uncertainty of their outputs. Those assemblers that do report uncertainty take different approaches to describing multiple assembly hypotheses and the support for each.\n Results: Here we review and examine the problem of representing and measuring uncertainty in assemblies. A promising recent development is the implementation of assemblers that are built according to explicit statistical models. Some new assembly methods, for example, estimate and maximize assembly likelihood. These advances, combined with technical advances in the representation of alternative assembly hypotheses, will lead to a more complete and biologically relevant understanding of assembly uncertainty. This will in turn facilitate the interpretation of downstream analyses and tests of specific biological hypotheses.\n Contact:  mhowison@brown.edu", + "subject": [], + "keywords": [] + }, + { + "title": "A 3‐D numerical study of the thermal evolution of the Moon after cumulate mantle overturn: The importance of rheology and core solidification", + "author": "Nan Zhang, E. M. Parmentier, Yan Liang", + "publisher": "American Geophysical Union (AGU)", + "url": "http://dx.doi.org/10.1002/jgre.20121", + "doi": "10.1002/jgre.20121", + "year": 2013, + "month": 9, + "abstract": "AbstractModels in which the mantle of the Moon evolves from an initially stratified state following magma ocean solidification and overturn have been applied to address important features of long‐term thermal evolution of the Moon, including convective instability of overturned ilmenite‐bearing cumulates (IBC) at the lunar core‐mantle boundary, generation of mare basalts, core sulfur content and inner core radius, paleomagnetism, and the present‐day mantle structure. Whether a dense overturned IBC‐rich layer at the bottom of the mantle can become thermally unstable to generate a single upwelling is controlled largely by the temperature‐dependence of viscosity (the activation energy). Convective instability of the IBC‐rich layer controls the heat flux out the core and the presence of an internally generated magnetic field. A long period of (~700 Ma) high positive core‐mantle‐boundary (CMB) heat flux after the instability of the IBC‐rich layer is expected from our models. Present‐day deep mantle temperatures inferred from seismic and gravitational inversion constrain the magnitude of mantle viscosity from 5 × 1019 to 1 × 1021 Pa s. The CMB temperature and solidified inner core radius inferred from seismic reflection constrain the core sulfur content. Our evolution models with 5–10 wt % sulfur content can produce the observed 240 km radius inner core at the present day. The asymmetrical distribution of the deep moonquakes only in the nearside mantle could be explained as the remnant structure of the single chemical upwelling generated from IBC‐rich layer. Our evolution model after the overturn results in an early ~0.55 km expansion in radius for ~1000 Ma due to the radiogenic heating associated with IBC in the deep mantle and may provide a simple explanation for the early expansion inferred from the Gravity Recovery and Interior Laboratory mission.", + "subject": [], + "keywords": [] + }, + { + "title": "A combined photoelectron spectroscopy and ab initio study of the quasi-planar B24− cluster", + "author": "Ivan A. Popov, Zachary A. Piazza, Wei-Li Li, Lai-Sheng Wang, Alexander I. Boldyrev", + "publisher": "AIP Publishing", + "url": "http://dx.doi.org/10.1063/1.4824156", + "doi": "10.1063/1.4824156", + "year": 2013, + "month": 10, + "abstract": "The structure and chemical bonding of the 24-atom boron cluster are investigated using photoelectron spectroscopy and ab initio calculations. The joint experimental and theoretical investigation shows that B24− possesses a quasi-planar structure containing fifteen outer and nine inner atoms with six of the inner atoms forming a filled pentagonal moiety. The central atom of the pentagonal moiety is puckered out of plane by 0.9 Å, reminiscent of the six-atom pentagonal caps of the well-known B12 icosahedral unit. The next closest isomer at the ROCCSD(T) level of theory has a tubular double-ring structure. Comparison of the simulated spectra with the experimental data shows that the global minimum quasi-planar B24− isomer is the major contributor to the observed photoelectron spectrum, while the tubular isomer has no contribution to the experiment. Chemical bonding analyses reveal that the periphery of the quasi-planar B24 constitutes 15 classical 2c-2e B-B σ-bonds, whereas delocalized σ- and π-bonds are found in the interior of the cluster with one unique 6c-2e π-bond responsible for bonding in the B-centered pentagon. The current work suggests that the 24-atom boron cluster continues to be quasi-2D, albeit the tendency to form filled pentagonal units, characteristic of 3D cage-like structures of bulk boron, is observed.", + "subject": [], + "keywords": [] + }, + { + "title": "Enhanced Spontaneous Oscillations in the Supplementary Motor Area Are Associated with Sleep-Dependent Offline Learning of Finger-Tapping Motor-Sequence Task", + "author": "Masako Tamaki, Tsung-Ren Huang, Yuko Yotsumoto, Matti Hämäläinen, Fa-Hsuan Lin, José E. Náñez, Takeo Watanabe, Yuka Sasaki", + "publisher": "Society for Neuroscience", + "url": "http://dx.doi.org/10.1523/jneurosci.1198-13.2013", + "doi": "10.1523/jneurosci.1198-13.2013", + "year": 2013, + "month": 8, + "abstract": "Sleep is beneficial for various types of learning and memory, including a finger-tapping motor-sequence task. However, methodological issues hinder clarification of the crucial cortical regions for sleep-dependent consolidation in motor-sequence learning. Here, to investigate the core cortical region for sleep-dependent consolidation of finger-tapping motor-sequence learning, while human subjects were asleep, we measured spontaneous cortical oscillations by magnetoencephalography together with polysomnography, and source-localized the origins of oscillations using individual anatomical brain information from MRI. First, we confirmed that performance of the task at a retest session after sleep significantly increased compared with performance at the training session before sleep. Second, spontaneous δ and fast-σ oscillations significantly increased in the supplementary motor area (SMA) during post-training compared with pretraining sleep, showing significant and high correlation with the performance increase. Third, the increased spontaneous oscillations in the SMA correlated with performance improvement were specific to slow-wave sleep. We also found that correlations of δ oscillation between the SMA and the prefrontal and between the SMA and the parietal regions tended to decrease after training. These results suggest that a core brain region for sleep-dependent consolidation of the finger-tapping motor-sequence learning resides in the SMA contralateral to the trained hand and is mediated by spontaneous δ and fast-σ oscillations, especially during slow-wave sleep. The consolidation may arise along with possible reorganization of a larger-scale cortical network that involves the SMA and cortical regions outside the motor regions, including prefrontal and parietal regions.", + "subject": [], + "keywords": [] + }, + { + "title": "Multinephron dynamics on the renal vascular network", + "author": "Donald J. Marsh, Anthony S. Wexler, Alexey Brazhe, Dmitri E. Postnov, Olga V. Sosnovtseva, Niels-Henrik Holstein-Rathlou", + "publisher": "American Physiological Society", + "url": "http://dx.doi.org/10.1152/ajprenal.00237.2012", + "doi": "10.1152/ajprenal.00237.2012", + "year": 2013, + "month": 1, + "abstract": "Tubuloglomerular feedback (TGF) and the myogenic mechanism combine in each nephron to regulate blood flow and glomerular filtration rate. Both mechanisms are nonlinear, generate self-sustained oscillations, and interact as their signals converge on arteriolar smooth muscle, forming a regulatory ensemble. Ensembles may synchronize. Smooth muscle cells in the ensemble depolarize periodically, generating electrical signals that propagate along the vascular network. We developed a mathematical model of a nephron-vascular network, with 16 versions of a single nephron model containing representations of both mechanisms in the regulatory ensemble, to examine the effects of network structure on nephron synchronization. Symmetry, as a property of a network, facilitates synchronization. Nephrons received blood from a symmetric electrically conductive vascular tree. Symmetry was created by using identical nephron models at each of the 16 sites and symmetry breaking by varying nephron length. The symmetric model achieved synchronization of all elements in the network. As little as 1% variation in nephron length caused extensive desynchronization, although synchronization was maintained in small nephron clusters. In-phase synchronization predominated among nephrons separated by one or three vascular nodes and antiphase synchronization for five or seven nodes of separation. Nephron dynamics were irregular and contained low-frequency fluctuations. Results are consistent with simultaneous blood flow measurements in multiple nephrons. An interaction between electrical signals propagated through the network to cause synchronization; variation in vascular pressure at vessel bifurcations was a principal cause of desynchronization. The results suggest that the vasculature supplies blood to nephrons but also engages in robust information transfer.", + "subject": [], + "keywords": [] + }, + { + "title": "Revising transcriptome assemblies with phylogenetic information", + "author": "August Guang, Mark Howison, Felipe Zapata, Charles Lawrence, Casey W. Dunn", + "publisher": "Public Library of Science (PLoS)", + "url": "http://dx.doi.org/10.1371/journal.pone.0244202", + "doi": "10.1371/journal.pone.0244202", + "year": 2021, + "month": 1, + "abstract": "A common transcriptome assembly error is to mistake different transcripts of the same gene as transcripts from multiple closely related genes. This error is difficult to identify during assembly, but in a phylogenetic analysis such errors can be diagnosed from gene phylogenies where they appear as clades of tips from the same species with improbably short branch lengths.treeinformis a method that uses phylogenetic information across species to refine transcriptome assemblies within species. It identifies transcripts of the same gene that were incorrectly assigned to multiple genes and reassign them as transcripts of the same gene. Thetreeinformmethod is implemented in Agalma, available athttps://bitbucket.org/caseywdunn/agalma, and the general approach is relevant in a variety of other contexts.", + "subject": [], + "keywords": [] + }, + { + "title": "Preexposure prophylaxis strategies for African–American women affected by mass incarceration", + "author": "Joëlla W. Adams, Maria R. Khan, S.E. Bessey, Samuel R. Friedman, James M. McMahon, Mark N. Lurie, Sandro Galea, Brandon D.L. Marshall", + "publisher": "Ovid Technologies (Wolters Kluwer Health)", + "url": "http://dx.doi.org/10.1097/qad.0000000000002749", + "doi": "10.1097/qad.0000000000002749", + "year": 2020, + "month": 11, + "abstract": "Objective:\n We aimed to determine the effectiveness of various preexposure prophylaxis (PrEP) prescription strategies for African–American women impacted by mass incarceration within an urban setting.\n \n \n Design:\n An agent-based model was utilized to evaluate prevention strategies in an efficient, ethical manner. By defining agents, their characteristics and relationships, we assessed population-level effects of PrEP on HIV incidence.\n \n \n Methods:\n We tested hypothetical PrEP prescription strategies within a simulation representing the African–American population of Philadelphia, Pennsylvania. Four strategies were evaluated: PrEP for women meeting CDC indicators regarding partner characteristics, PrEP for women with a recently incarcerated male partner, PrEP for women with a recently released male partner and couples-based PrEP at time of release. Interventions occurred alongside scale-up of HAART. We evaluated reductions in HIV transmissions, the number of persons on PrEP needed to avert one HIV transmission (NNT) and the resulting proportions of people on PrEP.\n \n \n Results:\n Scenarios prescribing PrEP based on criminal justice system involvement reduced HIV transmissions. The NNT ranged from 147 (couples-based scenario) to 300 (recently released scenario). The percentage of the female population covered by PrEP at any one time ranged from 0.14% (couples-based) to 10.8% (CDC-based). CDC-guideline scenarios were consistently less efficient compared to the justice-involved interventions.\n \n \n Conclusion:\n Expanding PrEP for African–American women and their male partners affected by incarceration should be considered in national HIV prevention goals and correctional facilities leveraged as intervention sites. Partner characteristics in the current CDC indications may be more effective and efficient if guidelines considered criminal justice involvement.", + "subject": [], + "keywords": [] + }, + { + "title": "Transcription Profiles Associated with Inducible Adhesion in Candida parapsilosis", + "author": "Joseph M. Bliss, George A. Tollefson, Abigail Cuevas, Sarah J. Longley, Matthew N. Neale, Alper Uzun, Sunil K. Shaw", + "publisher": "American Society for Microbiology", + "url": "http://dx.doi.org/10.1128/msphere.01071-20", + "doi": "10.1128/msphere.01071-20", + "year": 2021, + "month": 2, + "abstract": "Invasive\n Candida\n infections are frequent complications of the immunocompromised and are associated with substantive morbidity and mortality. Although\n C. albicans\n is the best-studied species, emerging infections by non-\n albicans Candida\n species have led to increased efforts to understand aspects of their pathogenesis that are unique from\n C. albicans\n .\n C. parapsilosis\n is a frequent cause of invasive infections, particularly among premature infants.", + "subject": [], + "keywords": [] + }, + { + "title": "Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans", + "author": "Eric D. Salomaki, Kristina X. Terpis, Sonja Rueckert, Michael Kotyk, Zuzana Kotyková Varadínová, Ivan Čepička, Christopher E. Lane, Martin Kolisko", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1186/s12915-021-01007-2", + "doi": "10.1186/s12915-021-01007-2", + "year": 2021, + "month": 4, + "abstract": "Abstract\n Background\n Apicomplexa is a diverse phylum comprising unicellular endobiotic animal parasites and contains some of the most well-studied microbial eukaryotes including the devastating human pathogens Plasmodium falciparum and Cryptosporidium hominis. In contrast, data on the invertebrate-infecting gregarines remains sparse and their evolutionary relationship to other apicomplexans remains obscure. Most apicomplexans retain a highly modified plastid, while their mitochondria remain metabolically conserved. Cryptosporidium spp. inhabit an anaerobic host-gut environment and represent the known exception, having completely lost their plastid while retaining an extremely reduced mitochondrion that has lost its genome. Recent advances in single-cell sequencing have enabled the first broad genome-scale explorations of gregarines, providing evidence of differential plastid retention throughout the group. However, little is known about the retention and metabolic capacity of gregarine mitochondria.\n \n Results\n Here, we sequenced transcriptomes from five species of gregarines isolated from cockroaches. We combined these data with those from other apicomplexans, performed detailed phylogenomic analyses, and characterized their mitochondrial metabolism. Our results support the placement of Cryptosporidium as the earliest diverging lineage of apicomplexans, which impacts our interpretation of evolutionary events within the phylum. By mapping in silico predictions of core mitochondrial pathways onto our phylogeny, we identified convergently reduced mitochondria. These data show that the electron transport chain has been independently lost three times across the phylum, twice within gregarines.\n \n Conclusions\n Apicomplexan lineages show variable functional restructuring of mitochondrial metabolism that appears to have been driven by adaptations to parasitism and anaerobiosis. Our findings indicate that apicomplexans are rife with convergent adaptations, with shared features including morphology, energy metabolism, and intracellularity.", + "subject": [], + "keywords": [] + }, + { + "title": "Bayesian versus Empirical Calibration of Microsimulation Models: A Comparative Analysis", + "author": "Stavroula A. Chrysanthopoulou, Carolyn M. Rutter, Constantine A. Gatsonis", + "publisher": "SAGE Publications", + "url": "http://dx.doi.org/10.1177/0272989x211009161", + "doi": "10.1177/0272989x211009161", + "year": 2021, + "month": 5, + "abstract": "Calibration of a microsimulation model (MSM) is a challenging but crucial step for the development of a valid model. Numerous calibration methods for MSMs have been suggested in the literature, most of which are usually adjusted to the specific needs of the model and based on subjective criteria for the selection of optimal parameter values. This article compares 2 general approaches for calibrating MSMs used in medical decision making, a Bayesian and an empirical approach. We use as a tool the MIcrosimulation Lung Cancer (MILC) model, a streamlined, continuous-time, dynamic MSM that describes the natural history of lung cancer and predicts individual trajectories accounting for age, sex, and smoking habits. We apply both methods to calibrate MILC to observed lung cancer incidence rates from the Surveillance, Epidemiology and End Results (SEER) database. We compare the results from the 2 methods in terms of the resulting parameter distributions, model predictions, and efficiency. Although the empirical method proves more practical, producing similar results with smaller computational effort, the Bayesian method resulted in a calibrated model that produced more accurate outputs for rare events and is based on a well-defined theoretical framework for the evaluation and interpretation of the calibration outcomes. A combination of the 2 approaches is an alternative worth considering for calibrating complex predictive models, such as microsimulation models.", + "subject": [], + "keywords": [] + }, + { + "title": "From tides to nucleotides: Genomic signatures of adaptation to environmental heterogeneity in barnacles", + "author": "Joaquin C. B. Nunez, Stephen Rong, David A. Ferranti, Alejandro Damian‐Serrano, Kimberly B. Neil, Henrik Glenner, Rebecca G. Elyanow, Bianca R. P. Brown, Magnus Alm Rosenblad, Anders Blomberg, Kerstin Johannesson, David M. Rand", + "publisher": "Wiley", + "url": "http://dx.doi.org/10.1111/mec.15949", + "doi": "10.1111/mec.15949", + "year": 2021, + "month": 5, + "abstract": "AbstractThe northern acorn barnacle (Semibalanus balanoides) is a robust system to study the genetic basis of adaptations to highly heterogeneous environments. Adult barnacles may be exposed to highly dissimilar levels of thermal stress depending on where they settle in the intertidal (i.e., closer to the upper or lower tidal boundary). For instance, barnacles near the upper tidal limit experience episodic summer temperatures above recorded heat coma levels. This differential stress at the microhabitat level is also dependent on the aspect of sun exposure. In the present study, we used pool‐seq approaches to conduct a genome wide screen for loci responding to intertidal zonation across the North Atlantic basin (Maine, Rhode Island, and Norway). Our analysis discovered 382 genomic regions containing SNPs which are consistently zonated (i.e., SNPs whose frequencies vary depending on their position in the rocky intertidal) across all surveyed habitats. Notably, most zonated SNPs are young and private to the North Atlantic. These regions show high levels of genetic differentiation across ecologically extreme microhabitats concomitant with elevated levels of genetic variation and Tajima's D, suggesting the action of non‐neutral processes. Overall, these findings support the hypothesis that spatially heterogeneous selection is a general and repeatable feature for this species, and that natural selection can maintain functional genetic variation in heterogeneous environments.", + "subject": [], + "keywords": [] + }, + { + "title": "Spillway preheating", + "author": "JiJi Fan, Kaloian D. Lozanov, Qianshu Lu", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1007/jhep05(2021)069", + "doi": "10.1007/jhep05(2021)069", + "year": 2021, + "month": 5, + "abstract": "Abstract\n In traditional models only an order one fraction of energy is transferred from the inflaton to radiation through nonperturbative resonance production in preheating immediately after inflation, due to backreaction effects. We propose a particle production mechanism that could improve the depletion of the inflaton energy density by up to four orders of magnitude. The improvement comes from the fast perturbative decays of resonantly produced daughter particles. They act as a “spillway” to drain these daughter particles, reducing their backreaction on the inflaton and keeping the resonant production effective for a longer period. Thus we dub the scenario “spillway preheating”. We also show that the fraction of energy density remaining in the inflaton has a simple inverse power-law scaling in the scenario. In general, spillway preheating is a much more efficient energy dissipation mechanism, which may have other applications in model building for particle physics.", + "subject": [], + "keywords": [] + }, + { + "title": "Knowledge extraction and transfer in data-driven fracture mechanics", + "author": "Xing Liu, Christos E. Athanasiou, Nitin P. Padture, Brian W. Sheldon, Huajian Gao", + "publisher": "Proceedings of the National Academy of Sciences", + "url": "http://dx.doi.org/10.1073/pnas.2104765118", + "doi": "10.1073/pnas.2104765118", + "year": 2021, + "month": 6, + "abstract": "Significance\n Data-driven approaches have launched a new paradigm in scientific research that is bound to have an impact on all disciplines of science and engineering. However, at this juncture, the exploration of data-driven techniques in the century-old field of fracture mechanics is highly limited, and there are key challenges including accurate and intelligent knowledge extraction and transfer in a data-limited regime. Here, we propose a framework for data-driven knowledge extraction in fracture mechanics with rigorous accuracy assessment which employs active learning for optimizing data usage and for data-driven knowledge transfer that allows efficient treatment of three-dimensional fracture problems based on two-dimensional solutions.", + "subject": [], + "keywords": [] + }, + { + "title": "Feature extraction and machine learning techniques for identifying historic urban environmental hazards: New methods to locate lost fossil fuel infrastructure in US cities", + "author": "Jonathan Tollefson, Scott Frickel, Maria I. Restrepo", + "publisher": "Public Library of Science (PLoS)", + "url": "http://dx.doi.org/10.1371/journal.pone.0255507", + "doi": "10.1371/journal.pone.0255507", + "year": 2021, + "month": 8, + "abstract": "U.S. cities contain unknown numbers of undocumented “manufactured gas” sites, legacies of an industry that dominated energy production during the late-19th and early-20th centuries. While many of these unidentified sites likely contain significant levels of highly toxic and biologically persistent contamination, locating them remains a significant challenge. We propose a new method to identify manufactured gas production, storage, and distribution infrastructure in bulk by applying feature extraction and machine learning techniques to digitized historic Sanborn fire insurance maps. Our approach, which relies on a two-part neural network to classify candidate map regions, increases the rate of site identification 20-fold compared to unaided visual coding.", + "subject": [], + "keywords": [] + }, + { + "title": "Lipopolysaccharide-induced neuroinflammation disrupts functional connectivity and community structure in primary cortical microtissues", + "author": "Elaina Atherton, Sophie Brown, Emily Papiez, Maria I. Restrepo, David A. Borton", + "publisher": "Cold Spring Harbor Laboratory", + "url": "http://dx.doi.org/10.1101/2021.07.08.451705", + "doi": "10.1101/2021.07.08.451705", + "year": 2021, + "month": 7, + "abstract": "AbstractThree-dimensional (3D) neural microtissues are a powerful in vitro paradigm for studying brain development and disease under controlled conditions, while maintaining many key attributes of the in vivo environment. Here, we used primary cortical microtissues to study the effects of neuroinflammation on neural microcircuits. We demonstrated the use of a genetically encoded calcium indicator combined with a novel live-imaging platform to record spontaneous calcium transients in microtissues from day 14-34 in vitro. We implemented graph theory analysis of calcium activity to characterize underlying functional connectivity and community structure of microcircuits, which are capable of capturing subtle changes in network dynamics during early diseases states. We found that microtissues cultured for 34 days displayed functional remodeling of microcircuits and that community structure strengthened over time. Lipopolysaccharide, a neuroinflammatory agent, significantly increased functional connectivity and disrupted community structure 5-9 days after exposure. These microcircuit-level changes have broad implications for the role of neuroinflammation in functional dysregulation of neural networks.", + "subject": [], + "keywords": [] + }, + { + "title": "Novel use of FDA-approved drugs identified by cluster analysis of behavioral profiles", + "author": "Sara Tucker Edmister, Thaís Del Rosario Hernández, Rahma Ibrahim, Cameron A. Brown, Sayali V. Gore, Rohit Kakodkar, Jill A. Kreiling, Robbert Creton", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1038/s41598-022-10133-y", + "doi": "10.1038/s41598-022-10133-y", + "year": 2022, + "month": 4, + "abstract": "AbstractRepurposing FDA-approved drugs is an efficient and cost-effective approach in the development of therapeutics for a broad range of diseases. However, prediction of function can be challenging, especially in the brain. We screened a small-molecule library with FDA-approved drugs for effects on behavior. The studies were carried out using zebrafish larvae, imaged in a 384-well format. We found that various drugs affect activity, habituation, startle responses, excitability, and optomotor responses. The changes in behavior were organized in behavioral profiles, which were examined by hierarchical cluster analysis. One of the identified clusters includes the calcineurin inhibitors cyclosporine (CsA) and tacrolimus (FK506), which are immunosuppressants and potential therapeutics in the prevention of Alzheimer’s disease. The calcineurin inhibitors form a functional cluster with seemingly unrelated drugs, including bromocriptine, tetrabenazine, rosiglitazone, nebivolol, sorafenib, cabozantinib, tamoxifen, meclizine, and salmeterol. We propose that drugs with ‘CsA-type’ behavioral profiles are promising candidates for the prevention and treatment of Alzheimer’s disease.", + "subject": [], + "keywords": [] + }, + { + "title": "Intramolecular tetrazine-acryloyl cycloaddition: chemistry and applications", + "author": "Akil Hamsath, Oren L. Lederberg, Qi Cui, Meg Shieh, Yannie Lam, Brock J. Brummett, Shi Xu, Jerome R. Robinson, Ming Xian", + "publisher": "Royal Society of Chemistry (RSC)", + "url": "http://dx.doi.org/10.1039/d2sc04331a", + "doi": "10.1039/d2sc04331a", + "year": 2022, + "month": -1, + "abstract": "Tetrazines rapidly react with tethered acrylates/acrylamides to produce fused coumarin derivatives. This template can be used in prodrug designs by depleting toxic α,β-unsaturated byproducts while also producing an imaging agent.", + "subject": [], + "keywords": [] + }, + { + "title": "Simulations of flow over a bio-inspired undulated cylinder with dynamically morphing topography", + "author": "Mikihisa Yuasa, Kathleen Lyons, Jennifer A. Franck", + "publisher": "Cold Spring Harbor Laboratory", + "url": "http://dx.doi.org/10.1101/2021.09.30.462620", + "doi": "10.1101/2021.09.30.462620", + "year": 2021, + "month": 10, + "abstract": "AbstractInspired by the geometric properties of seal whiskers, the addition of spanwise undulations on a cylinder have been shown to lower the mean and oscillatory forces and modify the frequency of flow-induced vibration when compared to smooth cylinders. Previously, computational fluid dynamics (CFD) has been used to characterize the hydrodynamic response with respect to specific geometric features. However simulations are time intensive due to complex three-dimensional meshing and computation time, limiting the number of geometric perturbations explored. A method is proposed in which the specific geometric features of this complex topography can be modified during a simulation thereby decreasing the time per geometric modification and removing the need for manual meshing of the complex structure. The surface of the seal whisker inspired geometry is parameterized into seven defining parameters, each of which is directly controlled in order to morph the surface into any realization within the defined parameter space. Once validated, the algorithm is used to explore the undulation amplitudes in the chord and thickness directions, by varying each independently from 0 to 0.3 thicknesses in increments of 0.05 at a Reynolds number of 500. The force and frequency response are examined for this matrix of geometric parameters, yielding detailed force trends not previously investigated. The impact of the bio-inspired morphing algorithm will allow for further optimization and development of force-mitigating underwater devices and other engineering applications in need of vibration suppression, frequency tuning, or force reduction.", + "subject": [], + "keywords": [] + }, + { + "title": "Understanding the Computational Demands Underlying Visual Reasoning", + "author": "Mohit Vaishnav, Remi Cadene, Andrea Alamia, Drew Linsley, Rufin VanRullen, Thomas Serre", + "publisher": "MIT Press - Journals", + "url": "http://dx.doi.org/10.1162/neco_a_01485", + "doi": "10.1162/neco_a_01485", + "year": 2022, + "month": 4, + "abstract": "Abstract\n Visual understanding requires comprehending complex visual relations between objects within a scene. Here, we seek to characterize the computational demands for abstract visual reasoning. We do this by systematically assessing the ability of modern deep convolutional neural networks (CNNs) to learn to solve the synthetic visual reasoning test (SVRT) challenge, a collection of 23 visual reasoning problems. Our analysis reveals a novel taxonomy of visual reasoning tasks, which can be primarily explained by both the type of relations (same-different versus spatial-relation judgments) and the number of relations used to compose the underlying rules. Prior cognitive neuroscience work suggests that attention plays a key role in humans' visual reasoning ability. To test this hypothesis, we extended the CNNs with spatial and feature-based attention mechanisms. In a second series of experiments, we evaluated the ability of these attention networks to learn to solve the SVRT challenge and found the resulting architectures to be much more efficient at solving the hardest of these visual reasoning tasks. Most important, the corresponding improvements on individual tasks partially explained our novel taxonomy. Overall, this work provides a granular computational account of visual reasoning and yields testable neuroscience predictions regarding the differential need for feature-based versus spatial attention depending on the type of visual reasoning problem.", + "subject": [], + "keywords": [] + }, + { + "title": "Arctic Maritime Cyclone Distribution and Trends in the ERA5 Reanalysis", + "author": "Zihan Chen, Amanda H. Lynch", + "publisher": "American Meteorological Society", + "url": "http://dx.doi.org/10.1175/jamc-d-21-0016.1", + "doi": "10.1175/jamc-d-21-0016.1", + "year": 2022, + "month": 4, + "abstract": "Abstract\nWe present a tracking algorithm for synoptic to meso-α-scale Arctic cyclones that differentiates between cold- and warm-core systems. The algorithm is applied to the ERA5 reanalysis north of 60°N from 1950 to 2019. In this dataset, over one-half of the cyclones that meet minimum intensity and duration thresholds can be classified as cold-core systems. Systems that undergo transition, typically from cold to warm core, make up 27.2% of cyclones and are longer lived. The relatively infrequent warm-core cyclones are more intense and are most common in winter. The Arctic-wide occurrence of maritime cyclones has increased from 1979 to 2019 when compared with the period from 1950 to 1978, but the trends have high interannual variability. This shift has ramifications for transportation, fisheries, and extractive industries, as well as impacts on communities across the Arctic.", + "subject": [], + "keywords": [] + }, + { + "title": "Beyond HIV outbreaks: protocol, rationale and implementation of a prospective study quantifying the benefit of incorporating viral sequence clustering analysis into routine public health interventions", + "author": "Jon A Steingrimsson, John Fulton, Mark Howison, Vlad Novitsky, Fizza S Gillani, Thomas Bertrand, Anna Civitarese, Katharine Howe, Guillermo Ronquillo, Benjamin Lafazia, Zoanne Parillo, Theodore Marak, Philip A Chan, Lila Bhattarai, Casey Dunn, Utpala Bandy, Nicole Alexander Scott, Joseph W Hogan, Rami Kantor", + "publisher": "BMJ", + "url": "http://dx.doi.org/10.1136/bmjopen-2021-060184", + "doi": "10.1136/bmjopen-2021-060184", + "year": 2022, + "month": 4, + "abstract": "IntroductionHIV continues to have great impact on millions of lives. Novel methods are needed to disrupt HIV transmission networks. In the USA, public health departments routinely conduct contact tracing and partner services and interview newly HIV-diagnosed index cases to obtain information on social networks and guide prevention interventions. Sequence clustering methods able to infer HIV networks have been used to investigate and halt outbreaks. Incorporation of such methods into routine, not only outbreak-driven, contact tracing and partner services holds promise for further disruption of HIV transmissions.Methods and analysisBuilding on a strong academic–public health collaboration in Rhode Island, we designed and have implemented a state-wide prospective study to evaluate an intervention that incorporates real-time HIV molecular clustering information with routine contact tracing and partner services. We present the rationale and study design of our approach to integrate sequence clustering methods into routine public health interventions as well as related important ethical considerations. This prospective study addresses key questions about the benefit of incorporating a clustering analysis triggered intervention into the routine workflow of public health departments, going beyond outbreak-only circumstances. By developing an intervention triggered by, and incorporating information from, viral sequence clustering analysis, and evaluating it with a novel design that avoids randomisation while allowing for methods comparison, we are confident that this study will inform how viral sequence clustering analysis can be routinely integrated into public health to support the ending of the HIV pandemic in the USA and beyond.Ethics and disseminationThe study was approved by both the Lifespan and Rhode Island Department of Health Human Subjects Research Institutional Review Boards and study results will be published in peer-reviewed journals.", + "subject": [], + "keywords": [] + }, + { + "title": "A probabilistic map of emotional experiences during competitive social interactions", + "author": "Joseph Heffner, Oriel FeldmanHall", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1038/s41467-022-29372-8", + "doi": "10.1038/s41467-022-29372-8", + "year": 2022, + "month": 3, + "abstract": "AbstractTheories of emotion and decision-making argue that negative, high arousing emotions—such as anger—motivate competitive social choice (e.g., punishing and defecting). However, given the long-standing challenge of quantifying emotion and the narrow framework in which emotion is traditionally examined, it remains unclear which emotions are actually associated with motivating these types of choices. To address this gap, we combine machine learning algorithms with a measure of affect that is agnostic to any specific emotion label. The result is a probabilistic map of emotion that is used to classify the specific emotions experienced by participants in a variety of social interactions (Ultimatum Game, Prisoner’s Dilemma, and Public Goods Game). Our results reveal that punitive and uncooperative choices are linked to a diverse array of negative, neutrally arousing emotions, such as sadness and disappointment, while only weakly linked to anger. These findings stand in contrast to the commonly held assumption that anger drives decisions to punish, defect, and freeride—thus, offering new insight into the role of emotion in motiving social choice.", + "subject": [], + "keywords": [] + }, + { + "title": "Validation Solutions to the Full-sky Radio Interferometry Measurement Equation for Diffuse Emission", + "author": "Adam E. Lanman, Steven G. Murray, Daniel C. Jacobs", + "publisher": "American Astronomical Society", + "url": "http://dx.doi.org/10.3847/1538-4365/ac45fd", + "doi": "10.3847/1538-4365/ac45fd", + "year": 2022, + "month": 3, + "abstract": "Abstract\n Low-frequency radio observatories are reaching unprecedented levels of sensitivity in an effort to detect the 21 cm signal from the Cosmic Dawn. High precision is needed because the expected signal is overwhelmed by foreground contamination, largely from so-called diffuse emission—a nonlocalized glow comprising Galactic synchrotron emission and radio galaxies. The impact of this diffuse emission on observations may be better understood through detailed simulations, which evaluate the Radio Interferometry Measurement Equation (RIME) for a given instrument and sky model. Evaluating the RIME involves carrying out an integral over the full sky, which is naturally discretized for point sources but must be approximated for diffuse emission. The choice of integration scheme can introduce errors that must be understood and isolated from the instrumental effects under study. In this paper, we present several analytically defined patterns of unpolarized diffuse sky emission for which the RIME integral is manageable, yielding closed-form or series visibility functions. We demonstrate the usefulness of these RIME solutions for validation by comparing them to simulated data and show that the remaining differences behave as expected with varied sky resolution and baseline orientation and length.", + "subject": [], + "keywords": [] + }, + { + "title": "A nearsighted force-training approach to systematically generate training data for the machine learning of large atomic structures", + "author": "Cheng Zeng, Xi Chen, Andrew A. Peterson", + "publisher": "AIP Publishing", + "url": "http://dx.doi.org/10.1063/5.0079314", + "doi": "10.1063/5.0079314", + "year": 2022, + "month": 2, + "abstract": "A challenge of atomistic machine-learning (ML) methods is ensuring that the training data are suitable for the system being simulated, which is particularly challenging for systems with large numbers of atoms. Most atomistic ML approaches rely on the nearsightedness principle (“all chemistry is local”), using information about the position of an atom’s neighbors to predict a per-atom energy. In this work, we develop a framework that exploits the nearsighted nature of ML models to systematically produce an appropriate training set for large structures. We use a per-atom uncertainty estimate to identify the most uncertain atoms and extract chunks centered around these atoms. It is crucial that these small chunks are both large enough to satisfy the ML’s nearsighted principle (that is, filling the cutoff radius) and are large enough to be converged with respect to the electronic structure calculation. We present data indicating when the electronic structure calculations are converged with respect to the structure size, which fundamentally limits the accuracy of any nearsighted ML calculator. These new atomic chunks are calculated in electronic structures, and crucially, only a single force—that of the central atom—is added to the growing training set, preventing the noisy and irrelevant information from the piece’s boundary from interfering with ML training. The resulting ML potentials are robust, despite requiring single-point calculations on only small reference structures and never seeing large training structures. We demonstrated our approach via structure optimization of a 260-atom structure and extended the approach to clusters with up to 1415 atoms.", + "subject": [], + "keywords": [] + }, + { + "title": "Evolution of Gene Expression across Species and Specialized Zooids in Siphonophora", + "author": "Catriona Munro, Felipe Zapata, Mark Howison, Stefan Siebert, Casey W Dunn", + "publisher": "Oxford University Press (OUP)", + "url": "http://dx.doi.org/10.1093/molbev/msac027", + "doi": "10.1093/molbev/msac027", + "year": 2022, + "month": 2, + "abstract": "Abstract\n Siphonophores are complex colonial animals, consisting of asexually produced bodies (zooids) that are functionally specialized for specific tasks, including feeding, swimming, and sexual reproduction. Though this extreme functional specialization has captivated biologists for generations, its genomic underpinnings remain unknown. We use RNA-seq to investigate gene expression patterns in five zooids and one specialized tissue across seven siphonophore species. Analyses of gene expression across species present several challenges, including identification of comparable expression changes on gene trees with complex histories of speciation, duplication, and loss. We examine gene expression within species, conduct classical analyses examining expression patterns between species, and introduce species branch filtering, which allows us to examine the evolution of expression across species in a phylogenetic framework. Within and across species, we identified hundreds of zooid-specific and species-specific genes, as well as a number of putative transcription factors showing differential expression in particular zooids and developmental stages. We found that gene expression patterns tended to be largely consistent in zooids with the same function across species, but also some large lineage-specific shifts in gene expression. Our findings show that patterns of gene expression have the potential to define zooids in colonial organisms. Traditional analyses of the evolution of gene expression focus on the tips of gene phylogenies, identifying large-scale expression patterns that are zooid or species variable. The new explicit phylogenetic approach we propose here focuses on branches (not tips) offering a deeper evolutionary perspective into specific changes in gene expression within zooids along all branches of the gene (and species) trees.", + "subject": [], + "keywords": [] + }, + { + "title": "A combined first principles study of the structural, magnetic, and phonon properties of monolayer CrI3", + "author": "Daniel Staros, Guoxiang Hu, Juha Tiihonen, Ravindra Nanguneri, Jaron Krogel, M. Chandler Bennett, Olle Heinonen, Panchapakesan Ganesh, Brenda Rubenstein", + "publisher": "AIP Publishing", + "url": "http://dx.doi.org/10.1063/5.0074848", + "doi": "10.1063/5.0074848", + "year": 2022, + "month": 1, + "abstract": "The first magnetic 2D material discovered, monolayer (ML) CrI3, is particularly fascinating due to its ground state ferromagnetism. However, because ML materials are difficult to probe experimentally, much remains unresolved about ML CrI3’s structural, electronic, and magnetic properties. Here, we leverage Density Functional Theory (DFT) and high-accuracy Diffusion Monte Carlo (DMC) simulations to predict lattice parameters, magnetic moments, and spin–phonon and spin–lattice coupling of ML CrI3. We exploit a recently developed surrogate Hessian DMC line search technique to determine CrI3’s ML geometry with DMC accuracy, yielding lattice parameters in good agreement with recently published STM measurements—an accomplishment given the ∼10% variability in previous DFT-derived estimates depending upon the functional. Strikingly, we find that previous DFT predictions of ML CrI3’s magnetic spin moments are correct on average across a unit cell but miss critical local spatial fluctuations in the spin density revealed by more accurate DMC. DMC predicts that magnetic moments in ML CrI3 are 3.62 μB per chromium and −0.145 μB per iodine, both larger than previous DFT predictions. The large disparate moments together with the large spin–orbit coupling of CrI3’s I-p orbital suggest a ligand superexchange-dominated magnetic anisotropy in ML CrI3, corroborating recent observations of magnons in its 2D limit. We also find that ML CrI3 exhibits a substantial spin–phonon coupling of ∼3.32 cm−1. Our work, thus, establishes many of ML CrI3’s key properties, while also continuing to demonstrate the pivotal role that DMC can assume in the study of magnetic and other 2D materials.", + "subject": [], + "keywords": [] + }, + { + "title": "Subthalamic–Cortical Network Reorganization during Parkinson's Tremor", + "author": "Peter M. Lauro, Shane Lee, Umer Akbar, Wael F. Asaad", + "publisher": "Society for Neuroscience", + "url": "http://dx.doi.org/10.1523/jneurosci.0854-21.2021", + "doi": "10.1523/jneurosci.0854-21.2021", + "year": 2021, + "month": 10, + "abstract": "Tremor, a common and often primary symptom of Parkinson's disease, has been modeled with distinct onset and maintenance dynamics. To identify the neurophysiologic correlates of each state, we acquired intraoperative cortical and subthalamic nucleus recordings from 10 patients (9 male, 1 female) performing a naturalistic visual–motor task. From this task, we isolated short epochs of tremor onset and sustained tremor. Comparing these epochs, we found that the subthalamic nucleus was central to tremor onset, as it drove both motor cortical activity and tremor output. Once tremor became sustained, control of tremor shifted to cortex. At the same time, changes in directed functional connectivity across sensorimotor cortex further distinguished the sustained tremor state.SIGNIFICANCE STATEMENTTremor is a common symptom of Parkinson's disease (PD). While tremor pathophysiology is thought to involve both basal ganglia and cerebello–thalamic–cortical circuits, it is unknown how these structures functionally interact to produce tremor. In this article, we analyzed intracranial recordings from the subthalamic nucleus and sensorimotor cortex in patients with PD undergoing deep brain stimulation surgery. Using an intraoperative task, we examined tremor in two separate dynamic contexts: when tremor first emerged, and when tremor was sustained. We believe that these findings reconcile several models of Parkinson's tremor, while describing the short-timescale dynamics of subcortical–cortical interactions during tremor for the first time. These findings may describe a framework for developing proactive and responsive neurostimulation models for specifically treating tremor.", + "subject": [], + "keywords": [] + }, + { + "title": "Cognitive maps of social features enable flexible inference in social networks", + "author": "Jae-Young Son, Apoorva Bhandari, Oriel FeldmanHall", + "publisher": "Proceedings of the National Academy of Sciences", + "url": "http://dx.doi.org/10.1073/pnas.2021699118", + "doi": "10.1073/pnas.2021699118", + "year": 2021, + "month": 9, + "abstract": "Significance\n How do people learn the large, complex web of social relations around them? We test how people use information about social features (such as being part of the same club or sharing hobbies) to fill in gaps in their knowledge of friendships and to make inferences about unobserved friendships in the social network. We find the ability to infer friendships depends on a simple but inflexible heuristic that infers friendship when two people share the same features, and a more complex but flexible cognitive map that encodes relationships between features rather than between people. Our results reveal that cognitive maps play a powerful role in shaping how people represent and reason about relationships in a social network.", + "subject": [], + "keywords": [] + }, + { + "title": "Boron Nitride Nanosheets Can Induce Water Channels Across Lipid Bilayers Leading to Lysosomal Permeabilization", + "author": "Matteo Andrea Lucherelli, Xuliang Qian, Paula Weston, Matilde Eredia, Wenpeng Zhu, Paolo Samorì, Huajian Gao, Alberto Bianco, Annette von dem Bussche", + "publisher": "Wiley", + "url": "http://dx.doi.org/10.1002/adma.202103137", + "doi": "10.1002/adma.202103137", + "year": 2021, + "month": 9, + "abstract": "AbstractWhile the interaction between 2D materials and cells is of key importance to the development of nanomedicines and safe applications of nanotechnology, still little is known about the biological interactions of many emerging 2D materials. Here, an investigation of how hexagonal boron nitride (hBN) interacts with the cell membrane is carried out by combining molecular dynamics (MD), liquid‐phase exfoliation, and in vitro imaging methods. MD simulations reveal that a sharp hBN wedge can penetrate a lipid bilayer and form a cross‐membrane water channel along its exposed polar edges, while a round hBN sheet does not exhibit this behavior. It is hypothesized that such water channels can facilitate cross‐membrane transport, with important consequences including lysosomal membrane permeabilization, an emerging mechanism of cellular toxicity that involves the release of cathepsin B and generation of radical oxygen species leading to cell apoptosis. To test this hypothesis, two types of hBN nanosheets, one with a rhomboidal, cornered morphology and one with a round morphology, are prepared, and human lung epithelial cells are exposed to both materials. The cornered hBN with lateral polar edges results in a dose‐dependent cytotoxic effect, whereas round hBN does not cause significant toxicity, thus confirming our premise.", + "subject": [], + "keywords": [] + }, + { + "title": "Two‐trajectory laser amygdalohippocampotomy: Anatomic modeling and initial seizure outcomes", + "author": "David D. Liu, Peter M. Lauro, Ronald K. Phillips, Owen P. Leary, Bryan Zheng, Julie L. Roth, Andrew S. Blum, David J. Segar, Wael F. Asaad", + "publisher": "Wiley", + "url": "http://dx.doi.org/10.1111/epi.17019", + "doi": "10.1111/epi.17019", + "year": 2021, + "month": 8, + "abstract": "AbstractObjectiveLaser interstitial thermal therapy (LITT) for mesial temporal lobe epilepsy (mTLE) is typically performed with one trajectory to target the medial temporal lobe (MTL). MTL structures such as piriform and entorhinal cortex are epileptogenic, but due to their relative geometry, they are difficult to target with one trajectory while simultaneously maintaining adequate ablation of the amygdala and hippocampus. We hypothesized that a two‐trajectory approach could improve ablation of all relevant MTL structures. First, we created large‐scale computer simulations to compare idealized one‐ vs two‐trajectory approaches. A two‐trajectory approach was then validated in an initial cohort of patients.MethodsWe used magnetic resonance imaging (MRI) from the Human Connectome Project (HCP) to create subject‐specific target structures consisting of hippocampus, amygdala, and piriform/entorhinal/perirhinal cortex. An algorithm searched for safe potential trajectories along the hippocampal axis (catheter one) and along the amygdala‐piriform axis (catheter two) and compared this to a single trajectory optimized over all structures. The proportion of each structure ablated at various burn radii was evaluated. A cohort of 11 consecutive patients with mTLE received two‐trajectory LITT; demographic, operative, and outcome data were collected.ResultsThe two‐trajectory approach was superior to the one‐trajectory approach at nearly all burn radii for all hippocampal subfields and amygdala nuclei (p < .05). Two‐laser trajectories achieved full ablation of MTL cortical structures at physiologically realistic burn radii, whereas one‐laser trajectories could not. Five patients with at least 1 year of follow‐up (mean = 21.8 months) experienced Engel class I outcomes; 6 patients with less than 1 year of follow‐up (mean = 6.6 months) are on track for Engel class I outcomes.SignificanceOur anatomic analyses and initial clinical results suggest that LITT amygdalohippocampotomy performed via two‐laser trajectories may promote excellent seizure outcomes. Future studies are required to validate the long‐term clinical efficacy and safety of this approach.", + "subject": [], + "keywords": [] + }, + { + "title": "Suppressed Daytime Convection Over the Amazon River", + "author": "M. Wu, J.‐E. Lee, D. Wang, M. Salameh", + "publisher": "American Geophysical Union (AGU)", + "url": "http://dx.doi.org/10.1029/2020jd033627", + "doi": "10.1029/2020jd033627", + "year": 2021, + "month": 7, + "abstract": "AbstractWe investigated the interaction between surface conditions and precipitating convection by comparing the Amazon River against the surrounding forest. Despite similar synoptic conditions within a few tens of kilometers, the river surface is substantially cooler than the surrounding forest during the day and warmer at night. We analyzed 20 years of high‐resolution satellite precipitation data and confirmed previous findings of daytime rainfall reduction over the river for the whole Amazon Basin. The percentage reduction is strongest during the dry‐to‐wet transition season. In addition, the percentage reduction of individual tributary is significantly correlated with the Laplacian of surface temperature, which causes thermally driven surface divergence and suppresses local convection. Additionally, nighttime rainfall is enhanced over tributaries near the Atlantic coast during the wet season. A regional climate model then simulates the local rainfall anomalies associated with the river. Above the river, moisture diverges near the surface and converges above the surface before the daytime rainfall, partially driven by the horizontal gradient of humidity. Unlike the river, moisture convergence within the boundary layer is more critical for the rainfall above the forest region. Our studies suggest that strong thermal contrast can be important in deriving heterogeneous convection in moist tropical regions.", + "subject": [], + "keywords": [] + }, + { + "title": "Consistent Predictability of the Ocean State Ocean Model Using Information Theory and Flushing Timescales", + "author": "Aakash Sane, Baylor Fox‐Kemper, David S. Ullman, Christopher Kincaid, Lewis Rothstein", + "publisher": "American Geophysical Union (AGU)", + "url": "http://dx.doi.org/10.1029/2020jc016875", + "doi": "10.1029/2020jc016875", + "year": 2021, + "month": 7, + "abstract": "AbstractThe Ocean State Ocean Model (OSOM) is an application of the Regional Ocean Modeling System spanning the Rhode Island waterways, including Narragansett Bay, Mt. Hope Bay, larger rivers, and the Block Island Shelf circulation from Long Island to Nantucket. This study discusses the physical aspects of the estuary (Narragansett and Mount Hope Bays and larger rivers) to evaluate physical circulation predictability. This estimate is intended to help decide if a forecast and prediction system is warranted, to prepare for coupling with biogeochemistry and fisheries models with widely disparate timescales, and to find the spin‐up time needed to establish the climatological circulation of the region. Perturbed initial condition ensemble simulations are combined with metrics from information theory to quantify the predictability of the OSOM forecast system–i.e., how long anomalies from different initial conditions persist. The predictability timescale in this model agrees with readily estimable timescales such as the freshwater flushing timescale evaluated using the total exchange flow (TEF) framework, indicating that the estuarine dynamics rather than chaotic transport is the dominant model behavior limiting predictions. The predictability of the OSOM is ∼7–40 days, varying with parameters, region, and season.", + "subject": [], + "keywords": [] + }, + { + "title": "Computational Assessment of Novel Predicted Compounds in Ni-Re Alloy System", + "author": "Siya Zhu, Axel van de Walle", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1007/s11669-021-00884-y", + "doi": "10.1007/s11669-021-00884-y", + "year": 2021, + "month": 4, + "abstract": "AbstractAb initio high-throughput efforts are continuously identifying new intermetallic compounds in a wide range of alloy systems that were previously thought to be well-characterized. While such predictions are likely valid near absolute zero, they carry the risk that such phases become unstable at the higher temperature relevant to typical synthesis conditions. We illustrate how this possibility can be rapidly tested by integrating Calphad modeling into the high-throughput loop. As an example, we investigate the Ni-Re system, in which D019 and D1a phases were predicted as possible intermetallic compounds. We confirm that these phases are indeed stable at practical synthesis temperatures and explain how they could have been overlooked in prior assessments.", + "subject": [], + "keywords": [] + }, + { + "title": "Temperature-Dependent Configurational Entropy Calculations for Refractory High-Entropy Alloys", + "author": "Chiraag M Nataraj, Axel van de Walle, Amit Samanta", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1007/s11669-021-00879-9", + "doi": "10.1007/s11669-021-00879-9", + "year": 2021, + "month": 4, + "abstract": "AbstractThe cluster expansion formalism for alloys is used to construct surrogate models for three refractory high-entropy alloys (NbTiVZr, HfNbTaTiZr, and AlHfNbTaTiZr). These cluster expansion models are then used along with Monte Carlo methods and thermodynamic integration to calculate the configurational entropy of these refractory high-entropy alloys as a function of temperature. Many solid solution alloy design guidelines are based on the ideal entropy of mixing, which increases monotonically with $$N$$\n N\n , the number of elements in the alloy. However, our results show that at low temperatures, the configurational entropy of these materials is largely independent of $$N$$\n N\n , and the assumption described above only holds in the high-temperature limit. This suggests that alloy design guidelines based on the ideal entropy of mixing require further examination.", + "subject": [], + "keywords": [] + }, + { + "title": "Topological data analysis of collective and individual epithelial cells using persistent homology of loops", + "author": "Dhananjay Bhaskar, William Y. Zhang, Ian Y. Wong", + "publisher": "Royal Society of Chemistry (RSC)", + "url": "http://dx.doi.org/10.1039/d1sm00072a", + "doi": "10.1039/d1sm00072a", + "year": 2021, + "month": -1, + "abstract": "Topology-based machine learning classifies complex spatial patterns of epithelial cells into distinct phases. The presence and stability of spatially-connected loops is an effective measure of topological similarity, even when population size varies significantly due to proliferation.", + "subject": [], + "keywords": [] + }, + { + "title": "Transition-metal-mediated reduction and reversible double-cyclization of cyanuric triazide to an asymmetric bitetrazolate involving cleavage of the six-membered aromatic ring", + "author": "Shivaiah Vaddypally, Vitaly G. Kiselev, Alex N. Byrne, C. Franklin Goldsmith, Michael J. Zdilla", + "publisher": "Royal Society of Chemistry (RSC)", + "url": "http://dx.doi.org/10.1039/d0sc04949b", + "doi": "10.1039/d0sc04949b", + "year": 2021, + "month": -1, + "abstract": "Cyanuric triazide reacts with transition metal precursors, extruding N2 and reducing the ligand by two electrons, which breaks an aromatic ring and rearranges to a bitetrazolylmethanediiminate (biTzI2−) ligand, forming two new aromatic rings.", + "subject": [], + "keywords": [] + }, + { + "title": "Ecological Load and Balancing Selection in Circumboreal Barnacles", + "author": "Joaquin C B Nunez, Stephen Rong, Alejandro Damian-Serrano, John T Burley, Rebecca G Elyanow, David A Ferranti, Kimberly B Neil, Henrik Glenner, Magnus Alm Rosenblad, Anders Blomberg, Kerstin Johannesson, David M Rand", + "publisher": "Oxford University Press (OUP)", + "url": "http://dx.doi.org/10.1093/molbev/msaa227", + "doi": "10.1093/molbev/msaa227", + "year": 2020, + "month": 9, + "abstract": "AbstractAcorn barnacle adults experience environmental heterogeneity at various spatial scales of their circumboreal habitat, raising the question of how adaptation to high environmental variability is maintained in the face of strong juvenile dispersal and mortality. Here, we show that 4% of genes in the barnacle genome experience balancing selection across the entire range of the species. Many of these genes harbor mutations maintained across 2 My of evolution between the Pacific and Atlantic oceans. These genes are involved in ion regulation, pain reception, and heat tolerance, functions which are essential in highly variable ecosystems. The data also reveal complex population structure within and between basins, driven by the trans-Arctic interchange and the last glaciation. Divergence between Atlantic and Pacific populations is high, foreshadowing the onset of allopatric speciation, and suggesting that balancing selection is strong enough to maintain functional variation for millions of years in the face of complex demography.", + "subject": [], + "keywords": [] + }, + { + "title": "Synthesis of lead-free Cs4(Cd1−xMnx)Bi2Cl12 (0 ≤ x ≤ 1) layered double perovskite nanocrystals with controlled Mn–Mn coupling interaction", + "author": "Hanjun Yang, Wenwu Shi, Tong Cai, Katie Hills-Kimball, Zhenyang Liu, Lacie Dube, Ou Chen", + "publisher": "Royal Society of Chemistry (RSC)", + "url": "http://dx.doi.org/10.1039/d0nr06771g", + "doi": "10.1039/d0nr06771g", + "year": 2020, + "month": -1, + "abstract": "Lead-free perovskites and their analogues have been extensively studied as a class of next-generation luminescent and optoelectronic materials.", + "subject": [], + "keywords": [] + }, + { + "title": "Finite temperature auxiliary field quantum Monte Carlo in the canonical ensemble", + "author": "Tong Shen, Yuan Liu, Yang Yu, Brenda M. Rubenstein", + "publisher": "AIP Publishing", + "url": "http://dx.doi.org/10.1063/5.0026606", + "doi": "10.1063/5.0026606", + "year": 2020, + "month": 11, + "abstract": "Finite temperature auxiliary field-based quantum Monte Carlo methods, including determinant quantum Monte Carlo and Auxiliary Field Quantum Monte Carlo (AFQMC), have historically assumed pivotal roles in the investigation of the finite temperature phase diagrams of a wide variety of multidimensional lattice models and materials. Despite their utility, however, these techniques are typically formulated in the grand canonical ensemble, which makes them difficult to apply to condensates such as superfluids and difficult to benchmark against alternative methods that are formulated in the canonical ensemble. Working in the grand canonical ensemble is furthermore accompanied by the increased overhead associated with having to determine the chemical potentials that produce desired fillings. Given this backdrop, in this work, we present a new recursive approach for performing AFQMC simulations in the canonical ensemble that does not require knowledge of chemical potentials. To derive this approach, we exploit the convenient fact that AFQMC solves the many-body problem by decoupling many-body propagators into integrals over one-body problems to which non-interacting theories can be applied. We benchmark the accuracy of our technique on illustrative Bose and Fermi–Hubbard models and demonstrate that it can converge more quickly to the ground state than grand canonical AFQMC simulations. We believe that our novel use of HS-transformed operators to implement algorithms originally derived for non-interacting systems will motivate the development of a variety of other methods and anticipate that our technique will enable direct performance comparisons against other many-body approaches formulated in the canonical ensemble.", + "subject": [], + "keywords": [] + }, + { + "title": "Observation of Transition‐Metal–Boron Triple Bonds in IrB2O− and ReB2O−", + "author": "Teng‐Teng Chen, Ling Fung Cheung, Wei‐Jia Chen, Joseph Cavanagh, Lai‐Sheng Wang", + "publisher": "Wiley", + "url": "http://dx.doi.org/10.1002/anie.202006652", + "doi": "10.1002/anie.202006652", + "year": 2020, + "month": 6, + "abstract": "AbstractMultiple bonds between boron and transition metals are known in many borylene (:BR) complexes via metal dπ→BR back‐donation, despite the electron deficiency of boron. An electron‐precise metal–boron triple bond was first observed in BiB2O− [Bi≡B−B≡O]− in which both boron atoms can be viewed as sp‐hybridized and the [B−BO]− fragment is isoelectronic to a carbyne (CR). To search for the first electron‐precise transition‐metal‐boron triple‐bond species, we have produced IrB2O− and ReB2O− and investigated them by photoelectron spectroscopy and quantum‐chemical calculations. The results allow to elucidate the structures and bonding in the two clusters. We find IrB2O− has a closed‐shell bent structure (Cs, 1A′) with BO− coordinated to an Ir≡B unit, (−OB)Ir≡B, whereas ReB2O− is linear (C∞v, 3Σ−) with an electron‐precise Re≡B triple bond, [Re≡B−B≡O]−. The results suggest the intriguing possibility of synthesizing compounds with electron‐precise M≡B triple bonds analogous to classical carbyne systems.", + "subject": [], + "keywords": [] + }, + { + "title": "Validation of a Monte Carlo model for multi leaf collimator based electron delivery", + "author": "Maduka M. Kaluarachchi, Ziad H. Saleh, Michelle L. Schwer, Eric E. Klein", + "publisher": "Wiley", + "url": "http://dx.doi.org/10.1002/mp.14194", + "doi": "10.1002/mp.14194", + "year": 2020, + "month": 5, + "abstract": "PurposeTo develop and validate a Monte Carlo model of the Varian TrueBeam to study electron collimation using the existing photon multi‐leaf collimators (pMLC), instead of conventional electron applicators and apertures.Materials and MethodsA complete Monte Carlo model of the Varian TrueBeam was developed using Tool for particle simulation (TOPAS) (version 3.1.p3). Vendor‐supplied information was used to model the treatment head components and the source parameters. A phase space plane was setup above the collimating jaws and captured particles were reused until a statistical uncertainty of 1% was achieved in the central axis. Electron energies 6, 9, 12, 16, and 20 MeV with a jaw‐defined field of 20 × 20 cm2 at iso‐center, pMLC‐defined fields of 6.8 × 6.8 cm2 and 11.4 × 11.4 cm2 at 80 cm source‐to‐surface distance (SSD) and an applicator‐defined field of 10 × 10 cm2 at iso‐center were evaluated. All the measurements except the applicator‐defined fields were measured using an ionization chamber in a water tank using 80 cm SSD. The dose difference, distance‐to‐agreement and gamma index were used to evaluate the agreement between the Monte Carlo calculations and measurements. Contributions of electron scattering off pMLC leaves and inter‐leaf leakage on dose profiles were evaluated and compared with Monte Carlo calculations. Electron transport through a heterogeneous phantom was simulated and the resulting dose distributions were compared with film measurements. The validated Monte Carlo model was used to simulate several clinically motivated cases to demonstrate the benefit of pMLC‐based electron delivery compared to applicator‐based electron delivery.ResultsCalculated and measured percentage depth‐dose (PDD) curves agree within 2% after normalization. The agreement between normalized percentage depth dose curves were evaluated using one‐dimensional gamma analysis with a local tolerance of 2%/1 mm and the %points passing gamma criteria was 100% for all energies. For jaw‐defined fields, calculated profiles agree with measurements with pass rates of >97% for 2%/2 mm gamma criteria. Calculated FWHM and penumbra width agree with measurements within 0.4 cm. For fields with tertiary collimation using an pMLC or applicator, the average gamma pass rate of compared profiles was 98% with 2%/2 mm gamma criteria. The profiles measured to evaluate the pMLC leaf scattering agreed with Monte Carlo calculations with an average gamma pass rate of 96.5% with 3%/2 mm gamma criteria. Measured dose profiles below the heterogenous phantom agreed well with calculated profiles and matched within 2.5% for most points. The calculated clinically applicable cases using TOPAS MC and Eclipse TPS for single enface electron beam, electron‐photon mixed beam and a matched electron‐electron beam exhibited a reasonable agreement in PDDs, profiles and dose volume histograms.ConclusionWe present a validation of a Monte Carlo model of Varian TrueBeam for pMLC‐based electron delivery. Monte Carlo calculations agreed with measurements satisfying gamma criterion of 1%/1 mm for depth dose curves and 2%/1 mm for dose profiles. The simulation of clinically applicable cases demonstrated the clinical utility of pMLC‐based electrons and the use of MC simulations for development of advanced radiation therapy techniques.", + "subject": [], + "keywords": [] + }, + { + "title": "Quantifying EoR delay spectrum contamination from diffuse radio emission", + "author": "Adam E Lanman, Jonathan C Pober, Nicholas S Kern, Eloy de Lera Acedo, David R DeBoer, Nicolas Fagnoni", + "publisher": "Oxford University Press (OUP)", + "url": "http://dx.doi.org/10.1093/mnras/staa987", + "doi": "10.1093/mnras/staa987", + "year": 2020, + "month": 4, + "abstract": "ABSTRACT\n The 21 cm hyperfine transition of neutral hydrogen offers a promising probe of the large-scale structure of the universe before and during the Epoch of Reionization (EoR), when the first ionizing sources formed. Bright radio emission from foreground sources remains the biggest obstacle to detecting the faint 21 cm signal. However, the expected smoothness of foreground power leaves a clean window in Fourier space where the EoR signal can potentially be seen over thermal noise. Though the boundary of this window is well defined in principle, spectral structure in foreground sources, instrumental chromaticity, and choice of spectral weighting in analysis all affect how much foreground power spills over into the EoR window. In this paper, we run a suite of numerical simulations of wide-field visibility measurements, with a variety of diffuse foreground models and instrument configurations, and measure the extent of contaminated Fourier modes in the EoR window using a delay-transform approach to estimate power spectra. We also test these effects with a model of the Hydrogen Epoch of Reionization Array (HERA) antenna beam generated from electromagnetic simulations, to take into account further chromatic effects in the real instrument. We find that foreground power spillover is dominated by the so-called pitchfork effect, in which diffuse foreground power is brightened near the horizon due to the shortening of baselines. As a result, the extent of contaminated modes in the EoR window is largely constant over time, except when the Galaxy is near the pointing centre.", + "subject": [], + "keywords": [] + }, + { + "title": "The impact of tandem redundant/sky-based calibration in MWA Phase II data analysis", + "author": "Zheng Zhang, Jonathan C. Pober, Wenyang Li, Bryna J. Hazelton, Miguel F. Morales, Cathryn M. Trott, Christopher H. Jordan, Ronniy C. Joseph, Adam Beardsley, Nichole Barry, Ruby Byrne, Steven J. Tingay, Aman Chokshi, Kenji Hasegawa, Daniel C. Jacobs, Adam Lanman, Jack L. B. Line, Christene Lynch, Benjamin McKinley, Daniel A. Mitchell, Steven Murray, Bart Pindor, Mahsa Rahimi, Keitaro Takahashi, Randall B. Wayth, Rachel L. Webster, Michael Wilensky, Shintaro Yoshiura, Qian Zheng", + "publisher": "Cambridge University Press (CUP)", + "url": "http://dx.doi.org/10.1017/pasa.2020.37", + "doi": "10.1017/pasa.2020.37", + "year": 2020, + "month": -1, + "abstract": "AbstractPrecise instrumental calibration is of crucial importance to 21-cm cosmology experiments. The Murchison Widefield Array’s (MWA) Phase II compact configuration offers us opportunities for both redundant calibration and sky-based calibration algorithms; using the two in tandem is a potential approach to mitigate calibration errors caused by inaccurate sky models. The MWA Epoch of Reionization (EoR) experiment targets three patches of the sky (dubbed EoR0, EoR1, and EoR2) with deep observations. Previous work in Li et al. (2018) and (2019) studied the effect of tandem calibration on the EoR0 field and found that it yielded no significant improvement in the power spectrum (PS) over sky-based calibration alone. In this work, we apply similar techniques to the EoR1 field and find a distinct result: the improvements in the PS from tandem calibration are significant. To understand this result, we analyse both the calibration solutions themselves and the effects on the PS over three nights of EoR1 observations. We conclude that the presence of the bright radio galaxy Fornax A in EoR1 degrades the performance of sky-based calibration, which in turn enables redundant calibration to have a larger impact. These results suggest that redundant calibration can indeed mitigate some level of model incompleteness error.", + "subject": [], + "keywords": [] + }, + { + "title": "Mitochondrial-Nuclear Interactions Mediate Sex-Specific Transcriptional Profiles inDrosophila", + "author": "Jim A Mossman, Jennifer G Tross, Nan Li, Zhijin Wu, David M Rand", + "publisher": "Oxford University Press (OUP)", + "url": "http://dx.doi.org/10.1534/genetics.116.192328", + "doi": "10.1534/genetics.116.192328", + "year": 2016, + "month": 10, + "abstract": "AbstractThe assembly and function of mitochondria require coordinated expression from two distinct genomes, the mitochondrial DNA (mtDNA) and nuclear DNA (nDNA). Mutations in either genome can be a source of phenotypic variation, yet their coexpression has been largely overlooked as a source of variation, particularly in the emerging paradigm of mitochondrial replacement therapy. Here we tested how the transcriptome responds to mtDNA and nDNA variation, along with mitonuclear interactions (mtDNA × nDNA) in Drosophila melanogaster. We used two mtDNA haplotypes that differ in a substantial number of single nucleotide polymorphisms, with &gt;100 amino acid differences. We placed each haplotype on each of two D. melanogaster nuclear backgrounds and tested for transcription differences in both sexes. We found that large numbers of transcripts were differentially expressed between nuclear backgrounds, and that mtDNA type altered the expression of nDNA genes, suggesting a retrograde, trans effect of mitochondrial genotype. Females were generally more sensitive to genetic perturbation than males, and males demonstrated an asymmetrical effect of mtDNA in each nuclear background; mtDNA effects were nuclear-background specific. mtDNA-sensitive genes were not enriched in male- or female-limited expression space in either sex. Using a variety of differential expression analyses, we show the responses to mitonuclear covariation to be substantially different between the sexes, yet the mtDNA genes were consistently differentially expressed across nuclear backgrounds and sexes. Our results provide evidence that the main mtDNA effects can be consistent across nuclear backgrounds, but the interactions between mtDNA and nDNA can lead to sex-specific global transcript responses.", + "subject": [], + "keywords": [] + }, + { + "title": "The Primary Bilayer Ruga-Phase Diagram II: Irreversibility in Ruga Evolution", + "author": "R. Zhao, M. Diab, K.-S. Kim", + "publisher": "ASME International", + "url": "http://dx.doi.org/10.1115/1.4033722", + "doi": "10.1115/1.4033722", + "year": 2016, + "month": 6, + "abstract": "When an elastic thin-film/substrate bilayer is cyclically compressed with a large plane-strain stroke, various surface morphologies develop either reversibly or irreversibly with cyclic hysteresis. Here, we examine the cyclic morphology evolution with extensive finite-element analyses and present a generic irreversibility map on the primary bilayer Ruga-phase diagram (PB-RPD). The term “PB” refers to a system of a film on a substrate, both of which are incompressible neo-Hookean, while the term “Ruga-phase” refers to the classification of corrugated surface morphologies. Our generic map reveals two configurational irreversibility types of Ruga-phases during a loading and unloading cycle. One, localization irreversibility, is caused by unstable crease localization and the other, modal irreversibility, by unstable mode transitions of wrinkle-Ruga configurations. While the instability of crease localization depends mainly on smoothness of the creasing surface or interface, the instability of Ruga-mode transition is sensitive to film/substrate stiffness ratio, film/substrate strain mismatch (εps), and material viscosity of the bilayer. For small strain mismatches (εps ≲ 0.5), PB Ruga structures are ordered; otherwise, for large strain mismatches, the Ruga structures can evolve to ridge configurations. For evolution of ordered Ruga phases, the configurational irreversibility leads to shake-down or divergence of cyclic hysteresis. Underlying mechanisms of the cyclic hysteresis are found to be the unstable Ruga-phase transitions of mode-period multiplications in the loading cycle, followed by either mode “locking” or primary-period “switching” in the unloading cycle. In addition, we found that the primary-period switching is promoted by the strain mismatch and material viscosity. These results indicate that various Ruga configurations can be excited, and thus, diverse Ruga-phases can coexist, under cyclic loading. Our irreversibility map will be useful in controlling reversibility as well as uniformity of Ruga configurations in many practical applications.", + "subject": [], + "keywords": [] + }, + { + "title": "A discrete mesoscopic particle model of the mechanics of a multi-constituent arterial wall", + "author": "Alexandra Witthoft, Alireza Yazdani, Zhangli Peng, Chiara Bellini, Jay D. Humphrey, George Em Karniadakis", + "publisher": "The Royal Society", + "url": "http://dx.doi.org/10.1098/rsif.2015.0964", + "doi": "10.1098/rsif.2015.0964", + "year": 2016, + "month": 1, + "abstract": "Blood vessels have unique properties that allow them to function together within a complex, self-regulating network. The contractile capacity of the wall combined with complex mechanical properties of the extracellular matrix enables vessels to adapt to changes in haemodynamic loading. Homogenized phenomenological and multi-constituent, structurally motivated continuum models have successfully captured these mechanical properties, but truly describing intricate microstructural details of the arterial wall may require a discrete framework. Such an approach would facilitate modelling interactions between or the separation of layers of the wall and would offer the advantage of seamless integration with discrete models of complex blood flow. We present a discrete particle model of a multi-constituent, nonlinearly elastic, anisotropic arterial wall, which we develop using the dissipative particle dynamics method. Mimicking basic features of the microstructure of the arterial wall, the model comprises an elastin matrix having isotropic nonlinear elastic properties plus anisotropic fibre reinforcement that represents the stiffer collagen fibres of the wall. These collagen fibres are distributed evenly and are oriented in four directions, symmetric to the vessel axis. Experimental results from biaxial mechanical tests of an artery are used for model validation, and a delamination test is simulated to demonstrate the new capabilities of the model.", + "subject": [], + "keywords": [] + }, + { + "title": "Surface hydrogenation regulated wrinkling and torque capability of hydrogenated graphene annulus under circular shearing", + "author": "Yinfeng Li, Silin Liu, Dibakar Datta, Zhonghua Li", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1038/srep16556", + "doi": "10.1038/srep16556", + "year": 2015, + "month": 11, + "abstract": "AbstractWrinkles as intrinsic topological feature have been expected to affect the electrical and mechanical properties of atomically thin graphene. Molecular dynamics simulations are adopted to investigate the wrinkling characteristics in hydrogenated graphene annulus under circular shearing at the inner edge. The amplitude of wrinkles induced by in-plane rotation around the inner edge is sensitive to hydrogenation and increases quadratically with hydrogen coverage. The effect of hydrogenation on mechanical properties is investigated by calculating the torque capability of annular graphene with varying hydrogen coverage and inner radius. Hydrogenation-enhanced wrinkles cause the aggregation of carbon atoms towards the inner edge and contribute to the critical torque strength of annulus. Based on detailed stress distribution contours, a shear-to-tension conversion mechanism is proposed for the contribution of wrinkles on torque capacity. As a result, the graphane annulus anomalously has similar torque capacity to pristine graphene annulus. The competition between hydrogenation caused bond strength deterioration and wrinkling induced local stress state conversion leads to a U-shaped evolution of torque strength relative to the increase of hydrogen coverage from 0 to 100%. Such hydrogenation tailored topological and mechanical characteristics provides an innovative mean to develop novel graphene-based devices.", + "subject": [], + "keywords": [] + }, + { + "title": "Design Principles for Metal Oxide Redox Materials for Solar‐Driven Isothermal Fuel Production", + "author": "Ronald Michalsky, Venkatesh Botu, Cory M. Hargus, Andrew A. Peterson, Aldo Steinfeld", + "publisher": "Wiley", + "url": "http://dx.doi.org/10.1002/aenm.201401082", + "doi": "10.1002/aenm.201401082", + "year": 2014, + "month": 12, + "abstract": "The performance of metal oxides as redox materials is limited by their oxygen conductivity and thermochemical stability. Predicting these properties from the electronic structure can support the screening of advanced metal oxides and accelerate their development for clean energy applications. Specifically, reducible metal oxide catalysts and potential redox materials for the solar‐thermochemical splitting of CO2 and H2O via an isothermal redox cycle are examined. A volcano‐type correlation is developed from available experimental data and density functional theory. It is found that the energy of the oxygen‐vacancy formation at the most stable surfaces of TiO2, Ti2O3, Cu2O, ZnO, ZrO2, MoO3, Ag2O, CeO2, yttria‐stabilized zirconia, and three perovskites scales with the Gibbs free energy of formation of the bulk oxides. Analogously, the experimental oxygen self‐diffusion constants correlate with the transition‐state energy of oxygen conduction. A simple descriptor is derived for rapid screening of oxygen‐diffusion trends across a large set of metal oxide compositions. These general trends are rationalized with the electronic charge localized at the lattice oxygen and can be utilized to predict the surface activity, the free energy of complex bulk metal oxides, and their oxygen conductivity.", + "subject": [], + "keywords": [] + }, + { + "title": "Probing the electronic and vibrational structure of Au2Al2− and Au2Al2 using photoelectron spectroscopy and high resolution photoelectron imaging", + "author": "Gary V. Lopez, Joseph Czekner, Tian Jian, Wei-Li Li, Zheng Yang, Lai-Sheng Wang", + "publisher": "AIP Publishing", + "url": "http://dx.doi.org/10.1063/1.4903784", + "doi": "10.1063/1.4903784", + "year": 2014, + "month": 12, + "abstract": "The electronic and vibrational structures of Au2Al2− and Au2Al2 have been investigated using photoelectron spectroscopy (PES), high-resolution photoelectron imaging, and theoretical calculations. Photoelectron spectra taken at high photon energies with a magnetic-bottle apparatus reveal numerous detachment transitions and a large energy gap for the neutral Au2Al2. Vibrationally resolved PE spectra are obtained using high-resolution photoelectron imaging for the ground state detachment transition of Au2Al2− at various photon energies (670.55−843.03 nm). An accurate electron affinity of 1.4438(8) eV is obtained for the Au2Al2 neutral cluster, as well as two vibrational frequencies at 57 ± 8 and 305 ± 13 cm−1. Hot bands transitions yield two vibrational frequencies for Au2Al2− at 57 ± 10 and 144 ± 12 cm−1. The obtained vibrational and electronic structure information is compared with density functional calculations, unequivocally confirming that both Au2Al2− and Au2Al2 possess C2v tetrahedral structures.", + "subject": [], + "keywords": [] + }, + { + "title": "Recent Ice Ages on Mars: The role of radiatively active clouds and cloud microphysics", + "author": "J.‐B. Madeleine, J. W. Head, F. Forget, T. Navarro, E. Millour, A. Spiga, A. Colaïtis, A. Määttänen, F. Montmessin, J. L. Dickson", + "publisher": "American Geophysical Union (AGU)", + "url": "http://dx.doi.org/10.1002/2014gl059861", + "doi": "10.1002/2014gl059861", + "year": 2014, + "month": 7, + "abstract": "AbstractGlobal climate models (GCMs) have been successfully employed to explain the origin of many glacial deposits on Mars. However, the latitude‐dependent mantle (LDM), a dust‐ice mantling deposit that is thought to represent a recent “Ice Age,” remains poorly explained by GCMs. We reexamine this question by considering the effect of radiatively active water‐ice clouds (RACs) and cloud microphysics. We find that when obliquity is set to 35°, as often occurred in the past 2 million years, warming of the atmosphere and polar caps by clouds modifies the water cycle and leads to the formation of a several centimeter‐thick ice mantle poleward of 30° in each hemisphere during winter. This mantle can be preserved over the summer if increased atmospheric dust content obscures the surface and provides dust nuclei to low‐altitude clouds. We outline a scenario for its deposition and preservation that compares favorably with the characteristics of the LDM.", + "subject": [], + "keywords": [] + }, + { + "title": "A photoelectron spectroscopy and ab initio study of the structures and chemical bonding of the B25− cluster", + "author": "Zachary A. Piazza, Ivan A. Popov, Wei-Li Li, Rhitankar Pal, Xiao Cheng Zeng, Alexander I. Boldyrev, Lai-Sheng Wang", + "publisher": "AIP Publishing", + "url": "http://dx.doi.org/10.1063/1.4879551", + "doi": "10.1063/1.4879551", + "year": 2014, + "month": 7, + "abstract": "Photoelectron spectroscopy and ab initio calculations are used to investigate the structures and chemical bonding of the B25− cluster. Global minimum searches reveal a dense potential energy landscape with 13 quasi-planar structures within 10 kcal/mol at the CCSD(T)/6-311+G(d) level of theory. Three quasi-planar isomers (I, II, and III) are lowest in energy and nearly degenerate at the CCSD(T) level of theory, with II and III being 0.8 and 0.9 kcal/mol higher, respectively, whereas at two density functional levels of theory isomer III is the lowest in energy (8.4 kcal/mol more stable than I at PBE0/6-311+G(2df) level). Comparison with experimental photoelectron spectroscopic data shows isomer II to be the major contributor while isomers I and III cannot be ruled out as minor contributors to the observed spectrum. Theoretical analyses reveal similar chemical bonding in I and II, both involving peripheral 2c-2e B−B σ-bonding and delocalized interior σ- and π-bonding. Isomer III has an interesting elongated ribbon-like structure with a π-bonding pattern analogous to those of dibenzopentalene. The high density of low-lying isomers indicates the complexity of the medium-sized boron clusters; the method dependency of predicting relative energies of the low-lying structures for B25− suggests the importance of comparison with experiment in determining the global minima of boron clusters at this size range. The appearance of many low-lying quasi-planar structures containing a hexagonal hole in B25− suggests the importance of this structural feature in maintaining planarity of larger boron clusters.", + "subject": [], + "keywords": [] + }, + { + "title": "Multi-core and many-core shared-memory parallel raycasting volume rendering optimization and tuning", + "author": "E Wes Bethel, Mark Howison", + "publisher": "SAGE Publications", + "url": "http://dx.doi.org/10.1177/1094342012440466", + "doi": "10.1177/1094342012440466", + "year": 2012, + "month": 4, + "abstract": "Given the computing industry trend of increasing processing capacity by adding more cores to a chip, the focus of this work is tuning the performance of a staple visualization algorithm, raycasting volume rendering, for shared-memory parallelism on multi-core CPUs and many-core GPUs. Our approach is to vary tunable algorithmic settings, along with known algorithmic optimizations and two different memory layouts, and measure performance in terms of absolute runtime and L2 memory cache misses. Our results indicate there is a wide variation in runtime performance on all platforms, as much as 254% for the tunable parameters we test on multi-core CPUs and 265% on many-core GPUs, and the optimal configurations vary across platforms, often in a non-obvious way. For example, our results indicate the optimal configurations on the GPU occur at a crossover point between those that maintain good cache utilization and those that saturate computational throughput. This result is likely to be extremely difficult to predict with an empirical performance model for this particular algorithm because it has an unstructured memory access pattern that varies locally for individual rays and globally for the selected viewpoint. Our results also show that optimal parameters on modern architectures are markedly different from those in previous studies run on older architectures. In addition, given the dramatic performance variation across platforms for both optimal algorithm settings and performance results, there is a clear benefit for production visualization and analysis codes to adopt a strategy for performance optimization through auto-tuning. These benefits will likely become more pronounced in the future as the number of cores per chip and the cost of moving data through the memory hierarchy both increase.", + "subject": [], + "keywords": [] + }, + { + "title": "A photoelectron spectroscopy and ab initio study of B21−: Negatively charged boron clusters continue to be planar at 21", + "author": "Zachary A. Piazza, Wei-Li Li, Constantin Romanescu, Alina P. Sergeeva, Lai-Sheng Wang, Alexander I. Boldyrev", + "publisher": "AIP Publishing", + "url": "http://dx.doi.org/10.1063/1.3692967", + "doi": "10.1063/1.3692967", + "year": 2012, + "month": 3, + "abstract": "The structures and chemical bonding of the B21− cluster have been investigated by a combined photoelectron spectroscopy and ab initio study. The photoelectron spectrum at 193 nm revealed a very high adiabatic electron binding energy of 4.38 eV for B21− and a congested spectral pattern. Extensive global minimum searches were conducted using two different methods, followed by high-level calculations of the low-lying isomers. The global minimum of B21− was found to be a quasiplanar structure with the next low-lying planar isomer only 1.9 kcal/mol higher in energy at the CCSD(T)/6-311-G* level of theory. The calculated vertical detachment energies for the two isomers were found to be in good agreement with the experimental spectrum, suggesting that they were both present experimentally and contributed to the observed spectrum. Chemical bonding analyses showed that both isomers consist of a 14-atom periphery, which is bonded by classical two-center two-electron bonds, and seven interior atoms in the planar structures. A localized two-center two-electron bond is found in the interior of the two planar isomers, in addition to delocalized multi-center σ and π bonds. The structures and the delocalized bonding of the two lowest lying isomers of B21− were found to be similar to those in the two lowest energy isomers in B19−.", + "subject": [], + "keywords": [] + }, + { + "title": "Anomalous Strength Characteristics of Tilt Grain Boundaries in Graphene", + "author": "Rassin Grantab, Vivek B. Shenoy, Rodney S. Ruoff", + "publisher": "American Association for the Advancement of Science (AAAS)", + "url": "http://dx.doi.org/10.1126/science.1196893", + "doi": "10.1126/science.1196893", + "year": 2010, + "month": 11, + "abstract": "Perfect Imperfections\n \n Graphene is composed of six-atom rings, but will include a number of five- and seven-atom rings as defects. Using simulations,\n \n Grantab\n et al.\n \n (p.\n 946\n ) show that more defects do not necessarily lead to greater deterioration of mechanical properties. Mismatches caused by differences in the orientation of neighboring crystals are divided into low- and high-angle grain boundaries, and typically it is the lower-angle boundaries that are stronger. In graphene, by contrast, the larger-angle boundaries, which consist of higher-defect densities, are better able to accommodate the strain and prevent failure that originates in the breakup of the seven-member graphene rings. This suggests ways for synthesizing imperfect graphene sheets that will have mechanical properties that are close to those of perfect graphene.", + "subject": [], + "keywords": [] + }, + { + "title": "A Size Threshold Limits Prion Transmission and Establishes Phenotypic Diversity", + "author": "Aaron Derdowski, Suzanne S. Sindi, Courtney L. Klaips, Susanne DiSalvo, Tricia R. Serio", + "publisher": "American Association for the Advancement of Science (AAAS)", + "url": "http://dx.doi.org/10.1126/science.1197785", + "doi": "10.1126/science.1197785", + "year": 2010, + "month": 10, + "abstract": "Processing Prion Phenotype\n \n How misfolding of a prion protein translates into transmissible changes in cellular physiology is unclear.\n \n Derdowski\n et al.\n \n (p.\n 680\n ) integrated a computational model of prion aggregate dynamics with an empirical analysis of the physical and functional dynamics of prion protein in yeast cells. Remarkably, they found that prion phenotypes resulted from fluctuations in the accumulation of aggregates and suggested that it is the process rather than the product of protein misfolding that is crucial in establishing the severity or stability of the resulting phenotype.", + "subject": [], + "keywords": [] + }, + { + "title": "Decimative Multiplication of Entropy Arrays, with Application to Influenza", + "author": "William A. Thompson, Andy Martwick, Joel K. Weltman", + "publisher": "MDPI AG", + "url": "http://dx.doi.org/10.3390/e11030351", + "doi": "10.3390/e11030351", + "year": 2009, + "month": 7, + "abstract": "The use of the digital signal processing procedure of decimation is introduced as a tool to detect patterns of information entropy distribution and is applied to information entropy in influenza A segment 7. Decimation was able to reveal patterns of entropy accumulation in archival and emerging segment 7 sequences that were not apparent in the complete, undecimated data. The low entropy accumulation along the first 25% of segment 7, revealed by the three frames of decimation, may be a sign of regulation at both protein and RNA levels to conserve important viral functions. Low segment 7 entropy values from the 2009 H1N1 swine flu pandemic suggests either that: (1) the viruses causing the current outbreak have convergently evolved to their low entropy state or (2) more likely, not enough time has yet passed for the entropy to accumulate. Because of its dependence upon the periodicity of the codon, the decimative procedure should be generalizable to any biological system.", + "subject": [], + "keywords": [] + }, + { + "title": "Information Entropy of Influenza A Segment 7", + "author": "William A. Thompson, Shaohua Fan, Joel K. Weltman", + "publisher": "MDPI AG", + "url": "http://dx.doi.org/10.3390/e10040736", + "doi": "10.3390/e10040736", + "year": 2008, + "month": 11, + "abstract": "Information entropy (H) is a measure of uncertainty at each position within in a sequence of nucleotides.H was used to characterize a set of influenza A segment 7 nucleotide sequences. Nucleotide locations of high entropy were identified near the 5’ start of all of the sequences and the sequences were assigned to subsets according to synonymous nucleotide variants at those positions: either uracil at position six (U6), cytosine at position six (C6), adenine (A12) at position 12, guanine at position 12 (G12), adenine at position 15 (A15) or cytosine (C15) at position 15. H values were found to be correlated/corresponding (Kendall tau) along the lengths of the nucleotide segments of the subset pairs at each position. However, the H values of each subset of sequences were statistically distinguishable from those of the other member of the pair (Kolmogorov-Smirnov test). The joint probability of uncorrelated distributions of U6 and C6 sequences to viral subtypes and to viral host species was 34 times greater than for the A12:G12 subset pair and 214 times greater than for the A15:C15 pair. This result indicates that the high entropy position six of segment 7 is either a reporter or a sentinel location. The fact that not one of the H5N1 sequences in the dataset was a member of the C6 subset, but all 125 H5N1 sequences are members of the U6 subset suggests a non-random sentinel function.", + "subject": [], + "keywords": [] + }, + { + "title": "TIMEOR: a web-based tool to uncover temporal regulatory mechanisms from multi-omics data", + "author": "Ashley Mae Conard, Nathaniel Goodman, Yanhui Hu, Norbert Perrimon, Ritambhara Singh, Charles Lawrence, Erica Larschan", + "publisher": "Oxford University Press (OUP)", + "url": "http://dx.doi.org/10.1093/nar/gkab384", + "doi": "10.1093/nar/gkab384", + "year": 2021, + "month": 6, + "abstract": "Abstract\n Uncovering how transcription factors regulate their targets at DNA, RNA and protein levels over time is critical to define gene regulatory networks (GRNs) and assign mechanisms in normal and diseased states. RNA-seq is a standard method measuring gene regulation using an established set of analysis stages. However, none of the currently available pipeline methods for interpreting ordered genomic data (in time or space) use time-series models to assign cause and effect relationships within GRNs, are adaptive to diverse experimental designs, or enable user interpretation through a web-based platform. Furthermore, methods integrating ordered RNA-seq data with protein–DNA binding data to distinguish direct from indirect interactions are urgently needed. We present TIMEOR (Trajectory Inference and Mechanism Exploration with Omics data in R), the first web-based and adaptive time-series multi-omics pipeline method which infers the relationship between gene regulatory events across time. TIMEOR addresses the critical need for methods to determine causal regulatory mechanism networks by leveraging time-series RNA-seq, motif analysis, protein–DNA binding data, and protein-protein interaction networks. TIMEOR’s user-catered approach helps non-coders generate new hypotheses and validate known mechanisms. We used TIMEOR to identify a novel link between insulin stimulation and the circadian rhythm cycle. TIMEOR is available at https://github.com/ashleymaeconard/TIMEOR.git and http://timeor.brown.edu.", + "subject": [], + "keywords": [] + }, + { + "title": "Urogenital schistosomiasis is associated with signatures of microbiome dysbiosis in Nigerian adolescents", + "author": "Olumide Ajibola, Aislinn D. Rowan, Clement O. Ogedengbe, Mari B. Mshelia, Damien J. Cabral, Anthonius A. Eze, Stephen Obaro, Peter Belenky", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1038/s41598-018-36709-1", + "doi": "10.1038/s41598-018-36709-1", + "year": 2019, + "month": 1, + "abstract": "AbstractUrogenital schistosomiasis is a neglected tropical disease caused by the parasiteSchistosoma haematobium, which resides in the vasculature surrounding the urogenital system. Previous work has suggested that helminthic infections can affect the intestinal microbiome, and we hypothesized thatS.haematobiuminfection could result in an alteration of immune system-microbiota homeostasis and impact the composition of the gut microbiota. To address this question, we compared the fecal microbiomes of infected and uninfected schoolchildren from the Argungu Local Government Area of Kebbi State, Nigeria, detecting significant differences in community composition between the two groups. Most remarkably, we observed a decreased abundance of Firmicutes and increased abundance of Proteobacteria – a shift in community structure which has been previously associated with dysbiosis. More specifically, we detected a number of changes in lower taxa reminiscent of inflammation-associated dysbiosis, including decreases in Clostridiales and increases in Moraxellaceae, Veillonellaceae, Pasteurellaceae, and Desulfovibrionaceae. Functional potential analysis also revealed an enrichment in orthologs of urease, which has been linked to dysbiosis and inflammation. Overall, our analysis indicates thatS.haematobiuminfection is associated with perturbations in the gut microbiota and may point to microbiome disruption as an additional consequence of schistosome infection.", + "subject": [], + "keywords": [] + }, + { + "title": "Prey size is more representative than prey taxa when measuring dietary overlap in sympatric forest bats", + "author": "Timothy J. Divoll, Veronica A. Brown, Gary F. McCracken, Joy M. O'Keefe", + "publisher": "Wiley", + "url": "http://dx.doi.org/10.1002/edn3.354", + "doi": "10.1002/edn3.354", + "year": 2022, + "month": 8, + "abstract": "AbstractIn temperate forests, insectivorous bats need to use variable hunting strategies as prey availability fluctuates during the growing season. At sites with variable amounts of forested habitat, sympatric bat species may exhibit high dietary overlap, but mechanisms of coexistence are unknown. We analyzed the diets of sympatric Myotis septentrionalis and Myotis sodalis in two different landscapes in central Indiana, USA: a riparian agricultural site and a managed forest site, aiming to assess interspecific dietary overlap. We collected fecal samples from 166 Myotis over four maternity seasons and used DNA metabarcoding to assess niche overlap by operational taxonomic units (OTUs, n = 708) and prey‐size taxa (n = 79). Analyzing diets by prey‐size classes, as opposed to only species, provided an alternative interpretation of dietary richness and overlap that may more accurately represent predator perceptions of prey. With overall prey sizes ranging from 2–36 mm, M. septentrionalis (n = 88) consumed larger prey (10.0 ± 5.5 mm, μ ± σ) than M. sodalis (n = 78; 8.9 ± 5.0 mm). Myotis sodalis had a more diverse diet (547 OTUs) compared to M. septentrionalis (453 OTUs) despite the smaller sample size. Of the 708 OTUs detected, 41% (292) were common across bat species. We found greater dietary overlap between species within each site than within either species across sites, suggesting both species mostly consume whatever insects are available on the landscape. Flexible hunting strategies may allow these species to coexist by consuming different sizes of prey at different rates in the tradeoff between travel cost and profitability. Prey size is an important measure for dietary overlap and resource partitioning in bats that few studies have yet considered, with implications for linking predators, prey, and habitats.", + "subject": [], + "keywords": [] + }, + { + "title": "The impact of syringe services program closure on the risk of rebound HIV outbreaks among people who inject drugs: a modeling study", + "author": "Xiao Zang, Williams C. Goedel, Sam E. Bessey, Mark N. Lurie, Sandro Galea, Alison P. Galvani, Samuel R. Friedman, Bohdan Nosyk, Brandon D.L. Marshall", + "publisher": "Ovid Technologies (Wolters Kluwer Health)", + "url": "http://dx.doi.org/10.1097/qad.0000000000003199", + "doi": "10.1097/qad.0000000000003199", + "year": 2022, + "month": 2, + "abstract": "Objective:\n Despite their effectiveness in preventing the transmission of HIV among people who inject drugs (PWID), syringe services programs (SSPs) in many settings are hampered by social and political opposition. We aimed to estimate the impact of closure and temporary interruption of SSP on the HIV epidemic in a rural United States setting.\n \n \n Methods:\n Using an agent-based model (ABM) calibrated to observed surveillance data, we simulated HIV risk behaviors and transmission in adult populations who inject and do not inject drugs in Scott County, Indiana. We projected HIV incidence and prevalence between 2020 and 2025 for scenarios with permanent closure, delayed closure (one additional renewal for 24 months before closure), and temporary closure (lasting 12 months) of an SSP in comparison to persistent SSP operation.\n \n \n Results:\n With sustained SSP operation, we projected an incidence rate of 0.15 per 100 person-years among the overall population (95% simulation interval: 0.06–0.28). Permanently closing the SSP would cause an average of 58.4% increase in the overall incidence rate during 2021–2025, resulting in a higher prevalence of 60.8% (50.9–70.6%) (18.7% increase) among PWID by 2025. A delayed closure would increase the incidence rate by 38.9%. A temporary closure would cause 12 (35.3%) more infections during 2020–2021.\n \n \n Conclusion:\n Our analysis suggests that temporary interruption and permanent closure of existing SSPs operating in rural United States may lead to ‘rebound’ HIV outbreaks among PWID. To reach and sustain HIV epidemic control, it will be necessary to maintain existing and implement new SSPs in combination with other prevention interventions.", + "subject": [], + "keywords": [] + }, + { + "title": "Disseminated Effects in Agent-Based Models: A Potential Outcomes Framework and Application to Inform Preexposure Prophylaxis Coverage Levels for HIV Prevention", + "author": "Ashley L Buchanan, S Bessey, William C Goedel, Maximilian King, Eleanor J Murray, Samuel R Friedman, M Elizabeth Halloran, Brandon D L Marshall", + "publisher": "Oxford University Press (OUP)", + "url": "http://dx.doi.org/10.1093/aje/kwaa239", + "doi": "10.1093/aje/kwaa239", + "year": 2020, + "month": 10, + "abstract": "Abstract\n Preexposure prophylaxis (PrEP) for prevention of human immunodeficiency virus (HIV) infection may benefit not only the person who uses it but also their uninfected sexual risk contacts. We developed an agent-based model using a novel trial emulation approach to quantify disseminated effects of PrEP use among men who have sex with men in Atlanta, Georgia, from 2015 to 2017. Model components (subsets of agents connected through partnerships in a sexual network but not sharing partnerships with any other agents) were first randomized to an intervention coverage level or the control group; then, within intervention components, eligible agents were randomized to receive or not receive PrEP. We calculated direct and disseminated (indirect) effects using randomization-based estimators and report corresponding 95% simulation intervals across scenarios ranging from 10% coverage in the intervention components to 90% coverage. A population of 11,245 agents was simulated, with an average of 1,551 components identified. When comparing agents randomized to no PrEP in 70% coverage components with control agents, there was a 15% disseminated risk reduction in HIV incidence (risk ratio = 0.85, 95% simulation interval: 0.65, 1.05). Persons not on PrEP may receive a protective benefit by being in a sexual network with higher PrEP coverage. Agent-based models are useful for evaluating possible direct and disseminated effects of HIV prevention modalities in sexual networks.", + "subject": [], + "keywords": [] + }, + { + "title": "Genome assembly of the chemosynthetic endosymbiont of the hydrothermal vent snailAlviniconcha adamantisfrom the Mariana Arc", + "author": "Corinna Breusing, Nathan Hagen Klobusnik, Michelle A Hauer, Roxanne A Beinart", + "publisher": "Oxford University Press (OUP)", + "url": "http://dx.doi.org/10.1093/g3journal/jkac220", + "doi": "10.1093/g3journal/jkac220", + "year": 2022, + "month": 8, + "abstract": "AbstractChemosynthetic animal-microbe symbioses sustain hydrothermal vent communities in the global deep sea. In the Indo-Pacific Ocean, hydrothermal ecosystems are often dominated by gastropod species of the genus Alviniconcha, which live in association with chemosynthetic Gammaproteobacteria or Campylobacteria. While the symbiont genomes of most extant Alviniconcha species have been sequenced, no genome information is currently available for the gammaproteobacterial endosymbiont of Alviniconcha adamantis—a comparatively shallow living species that is thought to be the ancestor to all other present Alviniconcha lineages. Here, we report the first genome sequence for the symbiont of A. adamantis from the Chamorro Seamount at the Mariana Arc. Our phylogenomic analyses show that the A. adamantis symbiont is most closely related to Chromatiaceae endosymbionts of the hydrothermal vent snails Alviniconcha strummeri and Chrysomallon squamiferum, but represents a distinct bacterial species or possibly genus. Overall, the functional capacity of the A. adamantis symbiont appeared to be similar to other chemosynthetic Gammaproteobacteria, though several flagella and chemotaxis genes were detected, which are absent in other gammaproteobacterial Alviniconcha symbionts. These differences might suggest potential contrasts in symbiont transmission dynamics, host recognition, or nutrient transfer. Furthermore, an abundance of genes for ammonia transport and urea usage could indicate adaptations to the oligotrophic waters of the Mariana region, possibly via recycling of host- and environment-derived nitrogenous waste products. This genome assembly adds to the growing genomic resources for chemosynthetic bacteria from hydrothermal vents and will be valuable for future comparative genomic analyses assessing gene content evolution in relation to environment and symbiotic lifestyles.", + "subject": [], + "keywords": [] + }, + { + "title": "Fast inference of spinal neuromodulation for motor control using amortized neural networks", + "author": "Lakshmi Narasimhan Govindarajan, Jonathan S Calvert, Samuel R Parker, Minju Jung, Radu Darie, Priyanka Miranda, Elias Shaaya, David A Borton, Thomas Serre", + "publisher": "IOP Publishing", + "url": "http://dx.doi.org/10.1088/1741-2552/ac9646", + "doi": "10.1088/1741-2552/ac9646", + "year": 2022, + "month": 10, + "abstract": "Abstract\n \n Objective. Epidural electrical stimulation (EES) has emerged as an approach to restore motor function following spinal cord injury (SCI). However, identifying optimal EES parameters presents a significant challenge due to the complex and stochastic nature of muscle control and the combinatorial explosion of possible parameter configurations. Here, we describe a machine-learning approach that leverages modern deep neural networks to learn bidirectional mappings between the space of permissible EES parameters and target motor outputs. Approach. We collected data from four sheep implanted with two 24-contact EES electrode arrays on the lumbosacral spinal cord. Muscle activity was recorded from four bilateral hindlimb electromyography (EMG) sensors. We introduce a general learning framework to identify EES parameters capable of generating desired patterns of EMG activity. Specifically, we first amortize spinal sensorimotor computations in a forward neural network model that learns to predict motor outputs based on EES parameters. Then, we employ a second neural network as an inverse model, which reuses the amortized knowledge learned by the forward model to guide the selection of EES parameters. Main results. We found that neural networks can functionally approximate spinal sensorimotor computations by accurately predicting EMG outputs based on EES parameters. The generalization capability of the forward model critically benefited our inverse model. We successfully identified novel EES parameters, in under 20 min, capable of producing desired target EMG recruitment during in vivo testing. Furthermore, we discovered potential functional redundancies within the spinal sensorimotor networks by identifying unique EES parameters that result in similar motor outcomes. Together, these results suggest that our framework is well-suited to probe spinal circuitry and control muscle recruitment in a completely data-driven manner. Significance. We successfully identify novel EES parameters within minutes, capable of producing desired EMG recruitment. Our approach is data-driven, subject-agnostic, automated, and orders of magnitude faster than manual approaches.", + "subject": [], + "keywords": [] + }, + { + "title": "Rapid Geometric Screening of Low-Energy Surfaces in Crystals", + "author": "Helena Liu, Axel van de Walle", + "publisher": "MDPI AG", + "url": "http://dx.doi.org/10.3390/sym14102067", + "doi": "10.3390/sym14102067", + "year": 2022, + "month": 10, + "abstract": "A high-throughput approach to determine the equilibrium shape of a crystal by brute force is impractical due to the vast number of density functional theory (DFT) calculations required along just a single crystallographic direction. We propose a screening method that allows the bypass of performing DFT calculations for each candidate surface. Using a series of physically-motivated simplifications, we are able to consider the relative surface energy of each of the large number of candidate surfaces required to solve the surface energy minimization problem in 3 dimensions. Application of this technique to calculate the surface energy landscapes of a set of well-known crystal structures demonstrates high accuracy in the prediction of stable planes and validates its potential as a valuable tool in ab initio determination of equilibrium crystal shapes.", + "subject": [], + "keywords": [] + }, + { + "title": "Brief Report: Use of Pre-Exposure Prophylaxis to Prevent Rapid HIV Transmission Among People Who Inject Drugs in Rural Counties in the United States: A Modeling Study", + "author": "Brendan P. Jacka, Shayla Nolen, Sam E. Bessey, Xiao Zang, William C. Goedel, Jesse L. Yedinak, Brandon D.L. Marshall", + "publisher": "Ovid Technologies (Wolters Kluwer Health)", + "url": "http://dx.doi.org/10.1097/qai.0000000000003093", + "doi": "10.1097/qai.0000000000003093", + "year": 2022, + "month": 12, + "abstract": "Background:\n Despite recent HIV outbreaks among people who inject drugs (PWID) in nonurban US settings, syringe service programs (SSP) are often inaccessible in these communities. Furthermore, pre-exposure prophylaxis (PrEP) awareness and coverage for PWID is limited. We aimed to model the impact of PrEP on HIV transmission among PWID in a rural setting.\n \n \n Setting:\n Using a calibrated agent-based model, we simulated HIV transmission in an adult population (n = 14,573 agents) in Scott County, Indiana between 2015 and 2024.\n \n \n Methods:\n We modeled PrEP eligibility according to CDC guidelines for PWID. PrEP coverage increased by 15% points in the range 10%–70%. Two counterfactual scenarios were modeled: Unrestricted access for PWID and PrEP for SSP attendees. We calculated the number of new HIV infections and number of person-years on PrEP per averted infection.\n \n \n Results:\n In the status quo scenario, 153 (95% Simulation Interval: 85, 259) new HIV infections occurred among PWID over 10 years. Compared with the status quo, 40% PrEP coverage resulted in 25% fewer HIV infections in the Unrestricted access for PWID scenario and 10% fewer HIV infections in the PrEP for SSP attendees scenario. The PYPAI was 21 and 43 in the Unrestricted access for PWID and PrEP for SSP attendees scenarios, respectively.\n \n \n Conclusion:\n Our modeling suggests that PrEP provides substantial benefit to PWID in rural US communities, with fewer restrictions on access providing the greatest effect. Control of HIV outbreaks will require expansion of public health interventions that meet the needs of all individuals.", + "subject": [], + "keywords": [] + }, + { + "title": "A Bayesian approach to high fidelity interferometric calibration − II: demonstration with simulated data", + "author": "Peter H Sims, Jonathan C Pober, Jonathan L Sievers", + "publisher": "Oxford University Press (OUP)", + "url": "http://dx.doi.org/10.1093/mnras/stac1749", + "doi": "10.1093/mnras/stac1749", + "year": 2022, + "month": 7, + "abstract": "ABSTRACT\n In a companion paper, we presented bayescal, a mathematical formalism for mitigating sky-model incompleteness in interferometric calibration. In this paper, we demonstrate the use of bayescal to calibrate the degenerate gain parameters of full-Stokes simulated observations with a HERA-like hexagonal close-packed redundant array, for three assumed levels of completeness of the a priori known component of the calibration sky model. We compare the bayescal calibration solutions to those recovered by calibrating the degenerate gain parameters with only the a priori known component of the calibration sky model both with and without imposing physically motivated priors on the gain amplitude solutions and for two choices of baseline length range over which to calibrate. We find that bayescal provides calibration solutions with up to 4 orders of magnitude lower power in spurious gain amplitude fluctuations than the calibration solutions derived for the same data set with the alternate approaches, and between ∼107 and ∼1010 times smaller than in the mean degenerate gain amplitude, on the full range of spectral scales accessible in the data. Additionally, we find that in the scenarios modelled only bayescal has sufficiently high fidelity calibration solutions for unbiased recovery of the 21-cm power spectrum on large spectral scales (k∥ ≲ 0.15 hMpc−1). In all other cases, in the completeness regimes studied, those scales are contaminated.", + "subject": [], + "keywords": [] + }, + { + "title": "The requirement of ubiquitin C-terminal hydrolase L1 in mouse ovarian development and fertility", + "author": "Morgan F Woodman, Meghan C H Ozcan, Megan A Gura, Payton De La Cruz, Alexis K Gadson, Kathryn J Grive", + "publisher": "Oxford University Press (OUP)", + "url": "http://dx.doi.org/10.1093/biolre/ioac086", + "doi": "10.1093/biolre/ioac086", + "year": 2022, + "month": 5, + "abstract": "Abstract\n Ubiquitin C-terminal hydrolase L1 (UCHL1) is a de-ubiquitinating enzyme enriched in neuronal and gonadal tissues known to regulate the cellular stores of mono-ubiquitin and protein turnover. While its function in maintaining proper motor neuron function is well established, investigation into its role in the health and function of reproductive processes is only just beginning to be studied. Single-cell-sequencing analysis of all ovarian cells from the murine perinatal period revealed that Uchl1 is very highly expressed in the developing oocyte population, an observation which was corroborated by high levels of oocyte-enriched UCHL1 protein expression in oocytes of all stages throughout the mouse reproductive lifespan. To better understand the role UCHL1 may be playing in oocytes, we utilized a UCHL1-deficient mouse line, finding reduced number of litters, reduced litter sizes, altered folliculogenesis, morphologically abnormal oocytes, disrupted estrous cyclicity and apparent endocrine dysfunction in these animals compared to their wild-type and heterozygous littermates. These data reveal a novel role of UCHL1 in female fertility as well as overall ovarian function, and suggest a potentially essential role for the ubiquitin proteasome pathway in mediating reproductive health.", + "subject": [], + "keywords": [] + }, + { + "title": "Learning two-phase microstructure evolution using neural operators and autoencoder architectures", + "author": "Vivek Oommen, Khemraj Shukla, Somdatta Goswami, Rémi Dingreville, George Em Karniadakis", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1038/s41524-022-00876-7", + "doi": "10.1038/s41524-022-00876-7", + "year": 2022, + "month": 9, + "abstract": "AbstractPhase-field modeling is an effective but computationally expensive method for capturing the mesoscale morphological and microstructure evolution in materials. Hence, fast and generalizable surrogate models are needed to alleviate the cost of computationally taxing processes such as in optimization and design of materials. The intrinsic discontinuous nature of the physical phenomena incurred by the presence of sharp phase boundaries makes the training of the surrogate model cumbersome. We develop a framework that integrates a convolutional autoencoder architecture with a deep neural operator (DeepONet) to learn the dynamic evolution of a two-phase mixture and accelerate time-to-solution in predicting the microstructure evolution. We utilize the convolutional autoencoder to provide a compact representation of the microstructure data in a low-dimensional latent space. After DeepONet is trained in the latent space, it can be used to replace the high-fidelity phase-field numerical solver in interpolation tasks or to accelerate the numerical solver in extrapolation tasks.", + "subject": [], + "keywords": [] + }, + { + "title": "Identification of Heme Oxygenase-1 as a Putative DNA-Binding Protein", + "author": "Alejandro Scaffa, George A. Tollefson, Hongwei Yao, Salu Rizal, Joselynn Wallace, Nathalie Oulhen, Jennifer F. Carr, Katy Hegarty, Alper Uzun, Phyllis A. Dennery", + "publisher": "MDPI AG", + "url": "http://dx.doi.org/10.3390/antiox11112135", + "doi": "10.3390/antiox11112135", + "year": 2022, + "month": 10, + "abstract": "Heme oxygenase-1 (HO-1) is a rate-limiting enzyme in degrading heme into biliverdin and iron. HO-1 can also enter the nucleus and regulate gene transcription independent of its enzymatic activity. Whether HO-1 can alter gene expression through direct binding to target DNA remains unclear. Here, we performed HO-1 CHIP-seq and then employed 3D structural modeling to reveal putative HO-1 DNA binding domains. We identified three probable DNA binding domains on HO-1. Using the Proteinarium, we identified several genes as the most highly connected nodes in the interactome among the HO-1 gene binding targets. We further demonstrated that HO-1 modulates the expression of these key genes using Hmox1 deficient cells. Finally, mutation of four conserved amino acids (E215, I211, E201, and Q27) within HO-1 DNA binding domain 1 significantly increased expression of Gtpbp3 and Eif1 genes that were identified within the top 10 binding hits normalized by gene length predicted to bind this domain. Based on these data, we conclude that HO-1 protein is a putative DNA binding protein, and regulates targeted gene expression. This provides the foundation for developing specific inhibitors or activators targeting HO-1 DNA binding domains to modulate targeted gene expression and corresponding cellular function.", + "subject": [], + "keywords": [] + }, + { + "title": "A South Pole–Aitken impact origin of the lunar compositional asymmetry", + "author": "Matt J. Jones, Alexander J. Evans, Brandon C. Johnson, Matthew B. Weller, Jeffrey C. Andrews-Hanna, Sonia M. Tikoo, James T. Keane", + "publisher": "American Association for the Advancement of Science (AAAS)", + "url": "http://dx.doi.org/10.1126/sciadv.abm8475", + "doi": "10.1126/sciadv.abm8475", + "year": 2022, + "month": 4, + "abstract": "The formation of the largest and most ancient lunar impact basin, South Pole–Aitken (SPA), was a defining event in the Moon’s evolution. Using numerical simulations, we show that widespread mantle heating from the SPA impact can catalyze the formation of the long-lived nearside-farside lunar asymmetry in incompatible elements and surface volcanic deposits, which has remained unexplained since its discovery in the Apollo era. The impact-induced heat drives hemisphere-scale mantle convection, which would sequester Th- and Ti-rich lunar magma ocean cumulates in the nearside hemisphere within a few hundred million years if they remain immediately beneath the lunar crust at the time of the SPA impact. A warm initial upper mantle facilitates generation of a pronounced compositional asymmetry consistent with the observed lunar asymmetry.", + "subject": [], + "keywords": [] + }, + { + "title": "A South Pole–Aitken impact origin of the lunar compositional asymmetry", + "author": "Matt J. Jones, Alexander J. Evans, Brandon C. Johnson, Matthew B. Weller, Jeffrey C. Andrews-Hanna, Sonia M. Tikoo, James T. Keane", + "publisher": "American Association for the Advancement of Science (AAAS)", + "url": "http://dx.doi.org/10.1126/sciadv.abm8475", + "doi": "10.1126/sciadv.abm8475", + "year": 2022, + "month": 4, + "abstract": "The formation of the largest and most ancient lunar impact basin, South Pole–Aitken (SPA), was a defining event in the Moon’s evolution. Using numerical simulations, we show that widespread mantle heating from the SPA impact can catalyze the formation of the long-lived nearside-farside lunar asymmetry in incompatible elements and surface volcanic deposits, which has remained unexplained since its discovery in the Apollo era. The impact-induced heat drives hemisphere-scale mantle convection, which would sequester Th- and Ti-rich lunar magma ocean cumulates in the nearside hemisphere within a few hundred million years if they remain immediately beneath the lunar crust at the time of the SPA impact. A warm initial upper mantle facilitates generation of a pronounced compositional asymmetry consistent with the observed lunar asymmetry.", + "subject": [], + "keywords": [] + }, + { + "title": "Machine Learning to Classify Vortex Wakes of Energy Harvesting Oscillating Foils", + "author": "Bernardo Luiz R. Ribeiro, Jennifer A. Franck", + "publisher": "American Institute of Aeronautics and Astronautics (AIAA)", + "url": "http://dx.doi.org/10.2514/1.j062091", + "doi": "10.2514/1.j062091", + "year": 2022, + "month": 12, + "abstract": "A machine learning model is developed to establish wake patterns behind oscillating foils for energy harvesting. The role of the wake structure is particularly important for array deployments of oscillating foils since the unsteady wake highly influences the performance of downstream foils. This work explores 46 oscillating foil kinematics, with the goal of parameterizing the wake based on the input kinematic variables and grouping vortex wakes through image analysis of vorticity fields. A combination of a convolutional neural network with long short-term memory units is developed to classify the wakes into three classes. To fully verify the physical wake differences among foil kinematics, a convolutional autoencoder combined with [Formula: see text]-means++ clustering is used to reveal four wake patterns via an unsupervised method. Future work can use these patterns to predict the performance of foils placed in the wake and build optimal foil arrangements for tidal energy harvesting.", + "subject": [], + "keywords": [] + }, + { + "title": "Multilayer Shells Interacting Through Friction", + "author": "Mert D. Alaydin, Yuri Bazilevs", + "publisher": "ASME International", + "url": "http://dx.doi.org/10.1115/1.4062139", + "doi": "10.1115/1.4062139", + "year": 2023, + "month": 9, + "abstract": "Abstract\n The corresponding author had the pleasure of attending an excellent symposium titled “Experimental and Theoretical Micro- and Nano-Mechanics: Honoring the Contributions of Prof. Kyung-Suk Kim” organized by Professors Ashraf Bastawros, Wendy Crone, Yanfei Gao, and Ruike (Renee) Zhao as part of the 2022 Society of Engineering Sciences Annual Technical Meeting held in College Station, TX on October 16–19, 2022. The symposium was held in honor of Prof. Kim’s 70th Birthday and celebrated over 40 years of Prof. Kim’s independent research achievements across several areas of Applied Mechanics. The present paper is dedicated to Prof. Kim, a great colleague at Brown University.We present a new formulation for the multilayer isogeometric Kirchhoff–Love (KL) shells, where the individual layers are assumed to interact through no-penetration and frictional contact. This work is largely motivated by the experiments and analysis presented in Poincloux et al. (2021, “Bending Response of a Book With Internal Friction,” Phys. Rev. Lett., 126(21), p. 218004). We utilize a regularized version of Coulomb’s friction law to model the tangential traction between the contacting shell surfaces. To ensure objectivity (i.e., reference-frame invariance) in the frictional model, we propose two different strategies to extrapolate the velocity vectors of the contact pair at the contact interface: (i) using the underlying KL kinematics of the individual shell layers and (ii) using the Taylor series-based extension from Kamensky et al. (2019, “Peridynamic Modeling of Frictional Contact,” J. Peridyn. Nonlocal Model., 1(2), pp. 107–121). We compare the performance of both approaches through a numerical benchmark example. We then validate our multilayer shell formulation using the “bending response of a book with internal friction” experiments of Poincloux et al. (2021, “Bending Response of a Book With Internal Friction,” Phys. Rev. Lett., 126(21), p. 218004).", + "subject": [], + "keywords": [] + }, + { + "title": "GenBank as a source to monitor and analyze Host-Microbiome data", + "author": "Vivek Ramanan, Shanti Mechery, Indra Neil Sarkar", + "publisher": "Oxford University Press (OUP)", + "url": "http://dx.doi.org/10.1093/bioinformatics/btac487", + "doi": "10.1093/bioinformatics/btac487", + "year": 2022, + "month": 7, + "abstract": "AbstractMotivationMicrobiome datasets are often constrained by sequencing limitations. GenBank is the largest collection of publicly available DNA sequences, which is maintained by the National Center of Biotechnology Information (NCBI). The metadata of GenBank records are a largely understudied resource and may be uniquely leveraged to access the sum of prior studies focused on microbiome composition. Here, we developed a computational pipeline to analyze GenBank metadata, containing data on hosts, microorganisms and their place of origin. This work provides the first opportunity to leverage the totality of GenBank to shed light on compositional data practices that shape how microbiome datasets are formed as well as examine host–microbiome relationships.ResultsThe collected dataset contains multiple kingdoms of microorganisms, consisting of bacteria, viruses, archaea, protozoa, fungi, and invertebrate parasites, and hosts of multiple taxonomical classes, including mammals, birds and fish. A human data subset of this dataset provides insights to gaps in current microbiome data collection, which is biased towards clinically relevant pathogens. Clustering and phylogenic analysis reveals the potential to use these data to model host taxonomy and evolution, revealing groupings formed by host diet, environment and coevolution.Availability and implementationGenBank Host-Microbiome Pipeline is available at https://github.com/bcbi/genbank_holobiome. The GenBank loader is available at https://github.com/bcbi/genbank_loader.Supplementary informationSupplementary data are available at Bioinformatics online.", + "subject": [], + "keywords": [] + }, + { + "title": "Optimistic Initialization for Exploration in Continuous Control", + "author": "Sam Lobel, Omer Gottesman, Cameron Allen, Akhil Bagaria, George Konidaris", + "publisher": "Association for the Advancement of Artificial Intelligence (AAAI)", + "url": "http://dx.doi.org/10.1609/aaai.v36i7.20727", + "doi": "10.1609/aaai.v36i7.20727", + "year": 2022, + "month": 6, + "abstract": "Optimistic initialization underpins many theoretically sound exploration schemes in tabular domains; however, in the deep function approximation setting, optimism can quickly disappear if initialized naively. We propose a framework for more effectively incorporating optimistic initialization into reinforcement learning for continuous control. Our approach uses metric information about the state-action space to estimate which transitions are still unexplored, and explicitly maintains the initial Q-value optimism for the corresponding state-action pairs. We also develop methods for efficiently approximating these training objectives, and for incorporating domain knowledge into the optimistic envelope to improve sample efficiency. We empirically evaluate these approaches on a variety of hard exploration problems in continuous control, where our method outperforms existing exploration techniques.", + "subject": [], + "keywords": [] + }, + { + "title": "Incorporating Within-Host Diversity in Phylogenetic Analyses for Detecting Clusters of New HIV Diagnoses", + "author": "August Guang, Mark Howison, Lauren Ledingham, Matthew D’Antuono, Philip A. Chan, Charles Lawrence, Casey W. Dunn, Rami Kantor", + "publisher": "Frontiers Media SA", + "url": "http://dx.doi.org/10.3389/fmicb.2021.803190", + "doi": "10.3389/fmicb.2021.803190", + "year": 2022, + "month": 2, + "abstract": "BackgroundPhylogenetic analyses of HIV sequences are used to detect clusters and inform public health interventions. Conventional approaches summarize within-host HIV diversity with a single consensus sequence per host of the pol gene, obtained from Sanger or next-generation sequencing (NGS). There is growing recognition that this approach discards potentially important information about within-host sequence variation, which can impact phylogenetic inference. However, whether alternative summary methods that incorporate intra-host variation impact phylogenetic inference of transmission network features is unknown.MethodsWe introduce profile sampling, a method to incorporate within-host NGS sequence diversity into phylogenetic HIV cluster inference. We compare this approach to Sanger- and NGS-derived pol and near-whole-genome consensus sequences and evaluate its potential benefits in identifying molecular clusters among all newly-HIV-diagnosed individuals over six months at the largest HIV center in Rhode Island.ResultsProfile sampling cluster inference demonstrated that within-host viral diversity impacts phylogenetic inference across individuals, and that consensus sequence approaches can obscure both magnitude and effect of these impacts. Clustering differed between Sanger- and NGS-derived consensus and profile sampling sequences, and across gene regions.DiscussionProfile sampling can incorporate within-host HIV diversity captured by NGS into phylogenetic analyses. This additional information can improve robustness of cluster detection.", + "subject": [], + "keywords": [] + }, + { + "title": "An Automated Bioinformatics Pipeline Informing Near-Real-Time Public Health Responses to New HIV Diagnoses in a Statewide HIV Epidemic", + "author": "Mark Howison, Fizza S. Gillani, Vlad Novitsky, Jon A. Steingrimsson, John Fulton, Thomas Bertrand, Katharine Howe, Anna Civitarese, Lila Bhattarai, Meghan MacAskill, Guillermo Ronquillo, Joel Hague, Casey W. Dunn, Utpala Bandy, Joseph W. Hogan, Rami Kantor", + "publisher": "MDPI AG", + "url": "http://dx.doi.org/10.3390/v15030737", + "doi": "10.3390/v15030737", + "year": 2023, + "month": 3, + "abstract": "Molecular HIV cluster data can guide public health responses towards ending the HIV epidemic. Currently, real-time data integration, analysis, and interpretation are challenging, leading to a delayed public health response. We present a comprehensive methodology for addressing these challenges through data integration, analysis, and reporting. We integrated heterogeneous data sources across systems and developed an open-source, automatic bioinformatics pipeline that provides molecular HIV cluster data to inform public health responses to new statewide HIV-1 diagnoses, overcoming data management, computational, and analytical challenges. We demonstrate implementation of this pipeline in a statewide HIV epidemic and use it to compare the impact of specific phylogenetic and distance-only methods and datasets on molecular HIV cluster analyses. The pipeline was applied to 18 monthly datasets generated between January 2020 and June 2022 in Rhode Island, USA, that provide statewide molecular HIV data to support routine public health case management by a multi-disciplinary team. The resulting cluster analyses and near-real-time reporting guided public health actions in 37 phylogenetically clustered cases out of 57 new HIV-1 diagnoses. Of the 37, only 21 (57%) clustered by distance-only methods. Through a unique academic-public health partnership, an automated open-source pipeline was developed and applied to prospective, routine analysis of statewide molecular HIV data in near-real-time. This collaboration informed public health actions to optimize disruption of HIV transmission.", + "subject": [], + "keywords": [] + }, + { + "title": "Chemical degradation kinetics for two-dimensional materials in natural and biological environments – a data-driven review", + "author": "Vidushi Shukla, Aidan Stone, Mary McGrath, Agnes Kane, Robert Hurt", + "publisher": "Royal Society of Chemistry (RSC)", + "url": "http://dx.doi.org/10.1039/d1en01171e", + "doi": "10.1039/d1en01171e", + "year": 2022, + "month": -1, + "abstract": "Many 2D materials undergo chemical degradation in the environment or living systems. This review converts raw literature data into standard kinetic parameters for meta-analysis, and discusses implications for 2D technologies and risk assessment.", + "subject": [], + "keywords": [] + }, + { + "title": "Single-cell analysis of the aging female mouse hypothalamus", + "author": "Kaitlyn H. Hajdarovic, Doudou Yu, Lexi-Amber Hassell, Shane A. Evans, Sarah Packer, Nicola Neretti, Ashley E. Webb", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1038/s43587-022-00246-4", + "doi": "10.1038/s43587-022-00246-4", + "year": 2022, + "month": 7, + "abstract": "AbstractAlterations in metabolism, sleep patterns, body composition and hormone status are all key features of aging. While the hypothalamus is a well-conserved brain region that controls these homeostatic and survival-related behaviors, little is known about the intrinsic features of hypothalamic aging. Here, we perform single-nuclei RNA sequencing of 40,064 hypothalamic nuclei from young and aged female mice. We identify cell type-specific signatures of aging in neuronal subtypes as well as astrocytes and microglia. We uncover changes in cell types critical for metabolic regulation and body composition and in an area of the hypothalamus linked to cognition. Our analysis also reveals an unexpected female-specific feature of hypothalamic aging: the master regulator of X inactivation, Xist, is elevated with age, particularly in hypothalamic neurons. Moreover, using machine learning, we show that levels of X chromosome genes and Xist itself, can accurately predict cellular age. This study identifies critical cell-specific changes of the aging hypothalamus in mammals and uncovers a potential marker of neuronal aging in females.", + "subject": [], + "keywords": [] + }, + { + "title": "Projected Effects of Disruptions to Human Immunodeficiency Virus (HIV) Prevention Services During the Coronavirus Disease 2019 Pandemic Among Black/African American Men Who Have Sex With Men in an Ending the HIV Epidemic Priority Jurisdiction", + "author": "Jennifer Labs, Amy S Nunn, Philip A Chan, S Bessey, Carolyn J Park, Brandon D L Marshall, Rupa R Patel, Leandro A Mena, William C Goedel", + "publisher": "Oxford University Press (OUP)", + "url": "http://dx.doi.org/10.1093/ofid/ofac274", + "doi": "10.1093/ofid/ofac274", + "year": 2022, + "month": 6, + "abstract": "Abstract\n \n Background\n Disruptions in access to in-person human immunodeficiency virus (HIV) preventive care during the coronavirus disease 2019 (COVID-19) pandemic may have a negative impact on our progress towards the Ending the HIV Epidemic goals in the United States.\n \n \n Methods\n We used an agent-based model to simulate HIV transmission among Black/African American men who have sex with men in Mississippi over 5 years to estimate how different reductions in access affected the number of undiagnosed HIV cases, new pre-exposure prophylaxis (PrEP) starts, and HIV incidence.\n \n \n Results\n We found that each additional 25% decrease in HIV testing and PrEP initiation was associated with decrease of 20% in the number of cases diagnosed and 23% in the number of new PrEP starts, leading to a 15% increase in HIV incidence from 2020 to 2022.\n \n \n Conclusions\n Unmet need for HIV testing and PrEP prescriptions during the COVID-19 pandemic may temporarily increase HIV incidence in the years immediately after the disruption period.", + "subject": [], + "keywords": [] + }, + { + "title": "Unit Testing for Concepts in Neural Networks", + "author": "Charles Lovering, Ellie Pavlick", + "publisher": "MIT Press", + "url": "http://dx.doi.org/10.1162/tacl_a_00514", + "doi": "10.1162/tacl_a_00514", + "year": 2022, + "month": -1, + "abstract": "Abstract\n Many complex problems are naturally understood in terms of symbolic concepts. For example, our concept of “cat” is related to our concepts of “ears” and “whiskers” in a non-arbitrary way. Fodor (1998) proposes one theory of concepts, which emphasizes symbolic representations related via constituency structures. Whether neural networks are consistent with such a theory is open for debate. We propose unit tests for evaluating whether a system’s behavior is consistent with several key aspects of Fodor’s criteria. Using a simple visual concept learning task, we evaluate several modern neural architectures against this specification. We find that models succeed on tests of groundedness, modularity, and reusability of concepts, but that important questions about causality remain open. Resolving these will require new methods for analyzing models’ internal states.", + "subject": [], + "keywords": [] + }, + { + "title": "Single-cell RNA-sequencing analysis of early sea star development", + "author": "Stephany Foster, Nathalie Oulhen, Tara Fresques, Hossam Zaki, Gary Wessel", + "publisher": "The Company of Biologists", + "url": "http://dx.doi.org/10.1242/dev.200982", + "doi": "10.1242/dev.200982", + "year": 2022, + "month": 11, + "abstract": "ABSTRACT\n Echinoderms represent a broad phylum with many tractable features to test evolutionary changes and constraints. Here, we present a single-cell RNA-sequencing analysis of early development in the sea star Patiria miniata, to complement the recent analysis of two sea urchin species. We identified 20 cell states across six developmental stages from 8 hpf to mid-gastrula stage, using the analysis of 25,703 cells. The clusters were assigned cell states based on known marker gene expression and by in situ RNA hybridization. We found that early (morula, 8-14 hpf) and late (blastula-to-mid-gastrula) cell states are transcriptionally distinct. Cells surrounding the blastopore undergo rapid cell state changes that include endomesoderm diversification. Of particular import to understanding germ cell specification is that we never see Nodal pathway members within Nanos/Vasa-positive cells in the region known to give rise to the primordial germ cells (PGCs). The results from this work contrast the results of PGC specification in the sea urchin, and the dataset presented here enables deeper comparative studies in tractable developmental models for testing a variety of developmental mechanisms.", + "subject": [], + "keywords": [] + }, + { + "title": "TAF4b Transcriptional Regulation During Cellular Quiescence of Developing Prospermatogonia", + "author": "Megan A. Gura, Myles A. Bartholomew, Kimberly M. Abt, Soňa Relovská, Kimberly A. Seymour, Richard N. Freiman", + "publisher": "Cold Spring Harbor Laboratory", + "url": "http://dx.doi.org/10.1101/2022.04.20.488869", + "doi": "10.1101/2022.04.20.488869", + "year": 2022, + "month": 4, + "abstract": "ABSTRACTProspermatogonia (ProSpg) link the embryonic development of male primordial germ cells to the healthy establishment of postnatal spermatogonia and long-term mammalian spermatogenesis. While these spermatogenic precursor cells undergo the characteristic transitions of cycling and quiescence, the transcriptional events underlying these developmental hallmarks remain unknown. Here we investigated the expression and function of TAF4b in the timely development of mouse ProSpg using an integration of gene expression profiling and chromatin mapping. We find that Taf4b mRNA expression is elevated during the transition of M-to-T1 ProSpg and Taf4b-deficient ProSpg are delayed in their entry into quiescence. Gene ontology, protein network analysis, and chromatin mapping demonstrate that TAF4b is both a direct and indirect regulator of cell cycle-related gene expression programs during ProSpg quiescence. By comparing the transcriptome changes in male and female Taf4b-deficient embryonic germ cells, we revealed that TAF4b promotes sex-independent and -dependent gene expression pathways, highlighting its unique and critical role in the fertility of both sexes.", + "subject": [], + "keywords": [] + }, + { + "title": "Learning two-phase microstructure evolution using neural operators and autoencoder architectures", + "author": "George Karniadakis, Vivek Oommen, Khemraj Shukla, Somdatta Goswami, Remi Dingreville", + "publisher": "Research Square Platform LLC", + "url": "http://dx.doi.org/10.21203/rs.3.rs-1578287/v1", + "doi": "10.21203/rs.3.rs-1578287/v1", + "year": 2022, + "month": 4, + "abstract": "Abstract\n Phase-field modeling is an effective but computationally expensive method for capturing the mesoscale morphological and microstructure evolution in materials. Hence, fast and generalizable surrogate models are needed to alleviate the cost in computationally taxing processes such as in optimization and design of materials. The intrinsic discontinuous nature of the physical phenomena incurred by the presence of sharp phase boundaries makes the training of the surrogate model cumbersome. We develop a framework that integrates a convolutional autoencoder architecture with a deep neural operator (DeepONet) to learn the dynamic evolution of a two-phase mixture. We utilize the convolutional autoencoder to provide a compact representation of the microstructure data in a low-dimensional latent space. DeepONet, which consists of two sub-networks, one for encoding the input function at a fixed number of sensors locations (branch net) and another for encoding the locations for the output functions (trunk net), learns the mesoscale dynamics of the microstructure evolution from the autoencoder latent space. The decoder part of the convolutional autoencoder then reconstructs the time-evolved microstructure from the DeepONet predictions. The result is an efficient and accurate accelerated phase-field framework that is robust to noisy inputs.", + "subject": [], + "keywords": [] + }, + { + "title": "Accurate prediction of oxygen vacancy concentration with disordered A-site cations in high-entropy perovskite oxides", + "author": "Jiyun Park, Boyuan Xu, Jie Pan, Dawei Zhang, Stephan Lany, Xingbo Liu, Jian Luo, Yue Qi", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1038/s41524-023-00981-1", + "doi": "10.1038/s41524-023-00981-1", + "year": 2023, + "month": 2, + "abstract": "AbstractEntropic stabilized ABO3 perovskite oxides promise many applications, including the two-step solar thermochemical hydrogen (STCH) production. Using binary and quaternary A-site mixed {A}FeO3 as a model system, we reveal that as more cation types, especially above four, are mixed on the A-site, the cell lattice becomes more cubic-like but the local Fe–O octahedrons are more distorted. By comparing four different Density Functional Theory-informed statistical models with experiments, we show that the oxygen vacancy formation energies ($${E}_{V}^{f}$$\n \n \n E\n \n \n V\n \n \n f\n \n \n ) distribution and the vacancy interactions must be considered to predict the oxygen non-stoichiometry (δ) accurately. For STCH applications, the $${E}_{V}^{f}$$\n \n \n E\n \n \n V\n \n \n f\n \n \n distribution, including both the average and the spread, can be optimized jointly to improve Δδ (difference of δ between the two-step conditions) in some hydrogen production levels. This model can be used to predict the range of water splitting that can be thermodynamically improved by mixing cations in {A}FeO3 perovskites.", + "subject": [], + "keywords": [] + }, + { + "title": "Comparing Projected Fatal Overdose Outcomes and Costs of Strategies to Expand Community-Based Distribution of Naloxone in Rhode Island", + "author": "Xiao Zang, Sam E. Bessey, Maxwell S. Krieger, Benjamin D. Hallowell, Jennifer A. Koziol, Shayla Nolen, Czarina N. Behrends, Sean M. Murphy, Alexander Y. Walley, Benjamin P. Linas, Bruce R. Schackman, Brandon D. L. Marshall", + "publisher": "American Medical Association (AMA)", + "url": "http://dx.doi.org/10.1001/jamanetworkopen.2022.41174", + "doi": "10.1001/jamanetworkopen.2022.41174", + "year": 2022, + "month": 11, + "abstract": "ImportanceIn 2021, the state of Rhode Island distributed 10 000 additional naloxone kits compared with the prior year through partnerships with community-based organizations.ObjectiveTo compare various strategies to increase naloxone distribution through community-based programs in Rhode Island to identify one most effective and efficient strategy in preventing opioid overdose deaths (OODs).Design, Setting, and ParticipantsIn this decision analytical model study conducted from January 2016 to December 2022, a spatial microsimulation model with an integrated decision tree was developed and calibrated to compare the outcomes of alternative strategies for distributing 10 000 additional naloxone kits annually among all individuals at risk for opioid overdose in Rhode Island.InterventionsDistribution of 10 000 additional naloxone kits annually, focusing on people who inject drugs, people who use illicit opioids and stimulants, individuals at various levels of risk for opioid overdose, or people who misuse prescription opioids vs no additional kits (status quo). Two expanded distribution implementation approaches were considered: one consistent with the current spatial distribution patterns for each distribution program type (supply-based approach) and one consistent with the current spatial distribution of individuals in each of the risk groups, assuming that programs could direct the additional kits to new geographic areas if required (demand-based approach).Main Outcomes and MeasuresWitnessed OODs, cost per OOD averted (efficiency), geospatial health inequality measured by the Theil index, and between-group variance for OOD rates.ResultsA total of 63 131 simulated individuals were estimated to be at risk for opioid overdose in Rhode Island based on current population data. With the supply-based approach, prioritizing additional naloxone kits to people who use illicit drugs averted more witnessed OODs by an estimated mean of 18.9% (95% simulation interval [SI], 13.1%-30.7%) annually. Expanded naloxone distribution using the demand-based approach and focusing on people who inject drugs had the best outcomes across all scenarios, averting an estimated mean of 25.3% (95% SI, 13.1%-37.6%) of witnessed OODs annually, at the lowest mean incremental cost of $27 312 per OOD averted. Other strategies were associated with fewer OODs averted at higher costs but showed similar patterns of improved outcomes and lower unit costs if kits could be reallocated to areas with greater need. The demand-based approach reduced geospatial inequality in OOD rates in all scenarios compared with the supply-based approach and status quo.Conclusions and RelevanceIn this decision analytical model study, variations in the effectiveness, efficiency, and health inequality of the different naloxone distribution expansion strategies and approaches were identified. Future efforts should be prioritized for people at highest risk for overdose (those who inject drugs or use illicit drugs) and redirected toward areas with the greatest need. These findings may inform future naloxone distribution priority settings.", + "subject": [], + "keywords": [] + }, + { + "title": "LoVoCCS. I. Survey Introduction, Data Processing Pipeline, and Early Science Results", + "author": "Shenming Fu, Ian Dell’Antonio, Ranga-Ram Chary, Douglas Clowe, M. C. Cooper, Megan Donahue, August Evrard, Mark Lacy, Tod Lauer, Binyang Liu, Jacqueline McCleary, Massimo Meneghetti, Hironao Miyatake, Mireia Montes, Priyamvada Natarajan, Michelle Ntampaka, Elena Pierpaoli, Marc Postman, Jubee Sohn, Keiichi Umetsu, Yousuke Utsumi, Gillian Wilson", + "publisher": "American Astronomical Society", + "url": "http://dx.doi.org/10.3847/1538-4357/ac68e8", + "doi": "10.3847/1538-4357/ac68e8", + "year": 2022, + "month": 7, + "abstract": "Abstract\n We present the Local Volume Complete Cluster Survey (LoVoCCS; we pronounce it as “low-vox” or “law-vox,” with stress on the second syllable), an NSF’s National Optical-Infrared Astronomy Research Laboratory survey program that uses the Dark Energy Camera to map the dark matter distribution and galaxy population in 107 nearby (0.03 < z < 0.12) X-ray luminous ([0.1–2.4 keV] L\n X500 > 1044 erg s−1) galaxy clusters that are not obscured by the Milky Way. The survey will reach Vera C. Rubin Observatory Legacy Survey of Space and Time (LSST) Year 1–2 depth (for galaxies r = 24.5, i = 24.0, signal-to-noise ratio (S/N) > 20; u = 24.7, g = 25.3, z = 23.8, S/N > 10) and conclude in ∼2023 (coincident with the beginning of LSST science operations), and will serve as a zeroth-year template for LSST transient studies. We process the data using the LSST Science Pipelines that include state-of-the-art algorithms and analyze the results using our own pipelines, and therefore the catalogs and analysis tools will be compatible with the LSST. We demonstrate the use and performance of our pipeline using three X-ray luminous and observation-time complete LoVoCCS clusters: A3911, A3921, and A85. A3911 and A3921 have not been well studied previously by weak lensing, and we obtain similar lensing analysis results for A85 to previous studies. (We mainly use A3911 to show our pipeline and give more examples in the Appendix.)", + "subject": [], + "keywords": [] + }, + { + "title": "Critical dynamics in the spread of focal epileptic seizures: Network connectivity, neural excitability and phase transitions", + "author": "S. Amin Moosavi, Viktor K. Jirsa, Wilson Truccolo", + "publisher": "Public Library of Science (PLoS)", + "url": "http://dx.doi.org/10.1371/journal.pone.0272902", + "doi": "10.1371/journal.pone.0272902", + "year": 2022, + "month": 8, + "abstract": "Focal epileptic seizures can remain localized or, alternatively, spread across brain areas, often resulting in impairment of cognitive function and loss of consciousness. Understanding the factors that promote spread is important for developing better therapeutic approaches. Here, we show that: (1) seizure spread undergoes “critical” phase transitions in models (epileptor-networks) that capture the neural dynamics of spontaneous seizures while incorporating patient-specific brain network connectivity, axonal delays and identified epileptogenic zones (EZs). We define a collective variable for the spreading dynamics as the spread size, i.e. the number of areas or nodes in the network to which a seizure has spread. Global connectivity strength and excitability in the surrounding non-epileptic areas work as phase-transition control parameters for this collective variable. (2) Phase diagrams are predicted by stability analysis of the network dynamics. (3) In addition, the components of the Jacobian’s leading eigenvector, which tend to reflect the connectivity strength and path lengths from the EZ to surrounding areas, predict the temporal order of network-node recruitment into seizure. (4) However, stochastic fluctuations in spread size in a near-criticality region make predictability more challenging. Overall, our findings support the view that within-patient seizure-spread variability can be characterized by phase-transition dynamics under transient variations in network connectivity strength and excitability across brain areas. Furthermore, they point to the potential use and limitations of model-based prediction of seizure spread in closed-loop interventions for seizure control.", + "subject": [], + "keywords": [] + }, + { + "title": "Protein Network Analysis of Whole Exome Sequencing of Severe Preeclampsia", + "author": "Jessica Schuster, George A. Tollefson, Valeria Zarate, Anthony Agudelo, Joan Stabila, Ashok Ragavendran, James Padbury, Alper Uzun", + "publisher": "Frontiers Media SA", + "url": "http://dx.doi.org/10.3389/fgene.2021.765985", + "doi": "10.3389/fgene.2021.765985", + "year": 2022, + "month": 6, + "abstract": "Preeclampsia is a hypertensive disorder of pregnancy, which complicates up to 15% of US deliveries. It is an idiopathic disorder associated with several different phenotypes. We sought to determine if the genetic architecture of preeclampsia can be described by clusters of patients with variants in genes in shared protein interaction networks. We performed a case-control study using whole exome sequencing on early onset preeclamptic mothers with severe clinical features and control mothers with uncomplicated pregnancies between 2016 and 2020. A total of 143 patients were enrolled, 61 women with early onset preeclampsia with severe features based on ACOG criteria, and 82 control women at term, matched for race and ethnicity. A network analysis and visualization tool, Proteinarium, was used to confirm there are clusters of patients with shared gene networks associated with severe preeclampsia. The majority of the sequenced patients appear in two significant clusters. We identified one case dominant and one control dominant cluster. Thirteen genes were unique to the case dominated cluster. Among these genes, LAMB2, PTK2, RAC1, QSOX1, FN1, and VCAM1 have known associations with the pathogenic mechanisms of preeclampsia. Using bioinformatic analysis, we were able to identify subsets of patients with shared protein interaction networks, thus confirming our hypothesis about the genetic architecture of preeclampsia.", + "subject": [], + "keywords": [] + }, + { + "title": "The optical depth of foregrounds for the highest redshift 21 cm signals", + "author": "Daniya Seitova, Jonathan Pober", + "publisher": "Oxford University Press (OUP)", + "url": "http://dx.doi.org/10.1093/mnras/stac1237", + "doi": "10.1093/mnras/stac1237", + "year": 2022, + "month": 5, + "abstract": "ABSTRACT\n Foreground emission makes it difficult to detect the highly redshifted cosmological 21 cm signal at any frequency. However, at low frequencies, foregrounds are likely to become optically thick, which would make it completely impossible to see a 21 cm signal behind them. To find out which regions of the sky might be optically thick for the highest redshifts of the 21 cm signal, we fit the measurements from LWA1 and the Haslam 408 MHz map with a two-component spectral model and calculate the frequency-dependent foreground optical depth point-by-point across the sky. Limitations of the current data prevent us from making any strong conclusions at high statistical significance, but there is suggestive evidence (∼1σ) that as much as 25 per cent of the sky could be obscured for the highest redshift 21 cm signals.", + "subject": [], + "keywords": [] + }, + { + "title": "Deceptive learning in histopathology", + "author": "Sahar Shahamatdar, Daryoush Saeed-Vafa, Drew Linsley, Farah Khalil, Katherine Lovinger, Lester Li, Howard McLeod, Sohini Ramachandran, Thomas Serre", + "publisher": "Cold Spring Harbor Laboratory", + "url": "http://dx.doi.org/10.1101/2022.04.21.489110", + "doi": "10.1101/2022.04.21.489110", + "year": 2022, + "month": 4, + "abstract": "AbstractDeep learning holds immense potential for histopathology, automating tasks that are simple for expert pathologists, and revealing novel biology for tasks that were previously considered difficult or impossible to solve by eye alone. However, the extent to which the visual strategies learned by deep learning models in histopathological analysis are trustworthy or not has yet to be systematically analyzed. In this work, we address this problem and discover new limits on the histopathological tasks for which deep learning models learn trustworthy versus deceptive solutions. While tasks that have been extensively studied in the field like tumor detection are reliable and trustworthy, recent advances demonstrating the ability to learn molecular profiling from hematoxylin and eosin (H&E) stained slides do not hold up to closer scrutiny. Our analysis framework represents a new approach in understanding the capabilities of deep learning models, which should be incorporated into the computational pathologists toolkit.", + "subject": [], + "keywords": [] + }, + { + "title": "TAF4b transcription networks regulating early oocyte differentiation", + "author": "Megan A. Gura, Soňa Relovská, Kimberly M. Abt, Kimberly A. Seymour, Tong Wu, Haskan Kaya, James M. A. Turner, Thomas G. Fazzio, Richard N. Freiman", + "publisher": "The Company of Biologists", + "url": "http://dx.doi.org/10.1242/dev.200074", + "doi": "10.1242/dev.200074", + "year": 2022, + "month": 2, + "abstract": "ABSTRACT\n Establishment of a healthy ovarian reserve is contingent upon numerous regulatory pathways during embryogenesis. Previously, mice lacking TBP-associated factor 4b (Taf4b) were shown to exhibit a diminished ovarian reserve. However, potential oocyte-intrinsic functions of TAF4b have not been examined. Here, we use a combination of gene expression profiling and chromatin mapping to characterize TAF4b-dependent gene regulatory networks in mouse oocytes. We find that Taf4b-deficient oocytes display inappropriate expression of meiotic, chromatin modification/organization, and X-linked genes. Furthermore, dysregulated genes in Taf4b-deficient oocytes exhibit an unexpected amount of overlap with dysregulated genes in oocytes from XO female mice, a mouse model of Turner Syndrome. Using Cleavage Under Targets and Release Using Nuclease (CUT&RUN), we observed TAF4b enrichment at genes involved in chromatin remodeling and DNA repair, some of which are differentially expressed in Taf4b-deficient oocytes. Interestingly, TAF4b target genes were enriched for Sp/Klf family and NFY target motifs rather than TATA-box motifs, suggesting an alternative mode of promoter interaction. Together, our data connect several gene regulatory nodes that contribute to the precise development of the mammalian ovarian reserve.", + "subject": [], + "keywords": [] + }, + { + "title": "Zebrafish Larvae Position Tracker (Z-LaP Tracker): a high-throughput deep-learning behavioral approach for the identification of calcineurin pathway-modulating drugs using zebrafish larvae", + "author": "Sayali V. Gore, Rohit Kakodkar, Thaís Del Rosario Hernández, Sara Tucker Edmister, Robbert Creton", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1038/s41598-023-30303-w", + "doi": "10.1038/s41598-023-30303-w", + "year": 2023, + "month": 2, + "abstract": "AbstractBrain function studies greatly depend on quantification and analysis of behavior. While behavior can be imaged efficiently, the quantification of specific aspects of behavior is labor-intensive and may introduce individual biases. Recent advances in deep learning and artificial intelligence-based tools have made it possible to precisely track individual features of freely moving animals in diverse environments without any markers. In the current study, we developed Zebrafish Larvae Position Tracker (Z-LaP Tracker), a modification of the markerless position estimation software DeepLabCut, to quantify zebrafish larval behavior in a high-throughput 384-well setting. We utilized the high-contrast features of our model animal, zebrafish larvae, including the eyes and the yolk for our behavioral analysis. Using this experimental setup, we quantified relevant behaviors with similar accuracy to the analysis performed by humans. The changes in behavior were organized in behavioral profiles, which were examined by K-means and hierarchical cluster analysis. Calcineurin inhibitors exhibited a distinct behavioral profile characterized by increased activity, acoustic hyperexcitability, reduced visually guided behaviors, and reduced habituation to acoustic stimuli. The developed methodologies were used to identify ‘CsA-type’ drugs that might be promising candidates for the prevention and treatment of neurological disorders.", + "subject": [], + "keywords": [] + }, + { + "title": "Physics‐Informed Neural Networks (PINNs) for Wave Propagation and Full Waveform Inversions", + "author": "Majid Rasht‐Behesht, Christian Huber, Khemraj Shukla, George Em Karniadakis", + "publisher": "American Geophysical Union (AGU)", + "url": "http://dx.doi.org/10.1029/2021jb023120", + "doi": "10.1029/2021jb023120", + "year": 2022, + "month": 4, + "abstract": "AbstractWe propose a new approach to the solution of the wave propagation and full waveform inversions (FWIs) based on a recent advance in deep learning called physics‐informed neural networks (PINNs). In this study, we present an algorithm for PINNs applied to the acoustic wave equation and test the method with both forward models and FWI case studies. These synthetic case studies are designed to explore the ability of PINNs to handle varying degrees of structural complexity using both teleseismic plane waves and seismic point sources. PINNs' meshless formalism allows for a flexible implementation of the wave equation and different types of boundary conditions. For instance, our models demonstrate that PINN automatically satisfies absorbing boundary conditions, a serious computational challenge for common wave propagation solvers. Furthermore, a priori knowledge of the subsurface structure can be seamlessly encoded in PINNs' formulation. We find that the current state‐of‐the‐art PINNs provide good results for the forward model, even though spectral element or finite difference methods are more efficient and accurate. More importantly, our results demonstrate that PINNs yield excellent results for inversions on all cases considered and with limited computational complexity. We discuss the current limitations of the method with complex velocity models as well as strategies to overcome these challenges. Using PINNs as a geophysical inversion solver offers exciting perspectives, not only for the full waveform seismic inversions, but also when dealing with other geophysical datasets (e.g., MT, gravity) as well as joint inversions because of its robust framework and simple implementation.", + "subject": [], + "keywords": [] + }, + { + "title": "All-sky modelling requirements for Bayesian 21 cm power spectrum estimation with bayeseor", + "author": "Jacob Burba, Peter H Sims, Jonathan C Pober", + "publisher": "Oxford University Press (OUP)", + "url": "http://dx.doi.org/10.1093/mnras/stad401", + "doi": "10.1093/mnras/stad401", + "year": 2023, + "month": 2, + "abstract": "ABSTRACT\n We present a comprehensive simulation-based study of the bayeseor code for 21 cm power spectrum recovery when analytically marginalizing over foreground parameters. To account for covariance between the 21 cm signal and contaminating foreground emission, bayeseor jointly constructs models for both signals within a Bayesian framework. Due to computational constraints, the forward model is constructed using a restricted field of view (FoV) in the image domain. When the only Epoch of Reionization contaminants are noise and foregrounds, we demonstrate that bayeseor can accurately recover the 21 cm power spectrum when the component of sky emission outside this forward-modelled region is downweighted by the beam at the level of the dynamic range between the foreground and 21 cm signals. However, when all-sky foreground emission is included along with a realistic instrument primary beam with sidelobes above this threshold extending to the horizon, the recovered power spectrum is contaminated by unmodelled sky emission outside the restricted FoV model. Expanding the combined cosmological and foreground model to cover the whole sky is computationally prohibitive. To address this, we present a modified version of bayeseor that allows for an all-sky foreground model, while the modelled 21 cm signal remains only within the primary FoV of the telescope. With this modification, it will be feasible to run an all-sky bayeseor analysis on a sizeable compute cluster. We also discuss several future directions for further reducing the need to model all-sky foregrounds, including wide-field foreground subtraction, an image-domain likelihood utilizing a tapering function, and instrument primary beam design.", + "subject": [], + "keywords": [] + }, + { + "title": "3D Microtissues Mimic the Architecture, Estradiol Synthesis, and Gap Junction Intercellular Communication of the Avascular Granulosa", + "author": "Blanche C Ip, Elizabeth Leary, Benjamin Knorlein, David Reich, Vivian Van, Joshua Manning, Jeffrey R Morgan", + "publisher": "Oxford University Press (OUP)", + "url": "http://dx.doi.org/10.1093/toxsci/kfab153", + "doi": "10.1093/toxsci/kfab153", + "year": 2021, + "month": 12, + "abstract": "Abstract\n Humans are consistently exposed to thousands of untested chemicals that have been detected in the follicular fluid of the ovaries, and can disrupt reproductive health. Human granulosa cells (GCs) are the functional unit of the ovarian follicle with steroidogenic and signaling activities, and play a pivotal role in oocyte development. During follicle progression, GCs multiply to form a 3D avascular structure, and establish gap junction intercellular communication (GJIC) that is critical to maintaining optimal viability and function. We developed a high-throughput in vitro platform of human GCs for the screening of chemicals that can impact GJIC and estradiol (E2) production of human granulosa. Our granulosa 3D microtissues fabricated with human ovarian granulosa-like tumor KGN cells are multicell-layered structures that mimic the avascular granulosa layers surrounding the oocyte. These microtissues robustly expressed the steroidogenic CYP19 aromatase enzyme and GJIC intercellular membrane channel, connexin 43. Granulosa microtissues produced E2 at rates comparable to primary human GCs as previously reported. E2 production was suppressed by the CYP19 inhibitor, letrozole, and induced by CYP19 activators, bisphenol A at 100 µM, and genistein at 100 µM. Granulosa microtissues displayed active GJIC function, as demonstrated by the connexin 43-dependent diffusion of calcein fluorescent dye from microtissue surface to the core using high-throughput confocal microscopy in conjunction with our open-sourced automated image analysis tool. Overall, our 3D human granulosa screening platform is highly promising for predictive and efficient in vitro toxicity testing to screen for chemicals that contaminate follicular fluid and may affect fertility.", + "subject": [], + "keywords": [] + }, + { + "title": "Application of single cell multiomics points to changes in chromatin accessibility near calcitonin receptor like receptor and a possible role for adrenomedullin in the post-shock lung", + "author": "Brandon E. Armstead, Chung Sunny Lee, Yaping Chen, Runping Zhao, Chun-Shiang Chung, Alger M. Fredericks, Sean F. Monaghan, Alfred Ayala", + "publisher": "Frontiers Media SA", + "url": "http://dx.doi.org/10.3389/fmed.2023.1003121", + "doi": "10.3389/fmed.2023.1003121", + "year": 2023, + "month": 4, + "abstract": "IntroductionAcute lung injury (ALI)/acute respiratory distress syndrome (ARDS) is a commonly occurring sequelae of traumatic injury resulting from indirect insults like hypovolemic shock and/or extrapulmonary sepsis. The high lethality rate associated with these pathologies outlines the importance of clarifying the “priming” effects seen in the post-shock lung microenvironment, which are understood to bring about a dysregulated or overt immune response when triggered by a secondary systemic infectious/septic challenge culminating in ALI. In this pilot project, we test the hypothesis that application of a single cell multiomics approach can elucidate novel phenotype specific pathways potentially contributing to shock-induced ALI/ARDS.MethodsHypovolemic shock was induced in C57BL/6 (wild-type), PD-1, PD-L1, or VISTA gene deficient male mice, 8–12 weeks old. Wild-type sham surgeries function as negative controls. A total of 24-h post-shock rodents were sacrificed, their lungs harvested and sectioned, with pools prepared from 2 mice per background, and flash frozen on liquid nitrogen. N = 2 biological replicates (representing 4 mice total) were achieved for all treatment groups across genetic backgrounds. Samples were received by the Boas Center for Genomics and Human Genetics, where single cell multiomics libraries were prepared for RNA/ATAC sequencing. The analysis pipeline Cell Ranger ARC was implemented to attain feature linkage assessments across genes of interest.ResultsSham (pre-shock) results suggest high chromatin accessibility around calcitonin receptor like receptor (CALCRL) across cellular phenotypes with 17 and 18 feature links, exhibiting positive correlation with gene expression between biological replicates. Similarity between both sample chromatin profiles/linkage arcs is evident. Post-shock wild-type accessibility is starkly reduced across replicates where the number of feature links drops to 1 and 3, again presenting similar replicate profiles. Samples from shocked gene deficient backgrounds displayed high accessibility and similar profiles to the pre-shock lung microenvironment.ConclusionHigh pre-shock availability of DNA segments and their positive correlation with CALCRL gene expression suggests an apparent regulatory capacity on transcription. Post-shock gene deficient chromatin profiles presented similar results to that of pre-shock wild-type samples, suggesting an influence on CALCRL accessibility. Key changes illustrated in the pre-ALI context of shock may allow for additional resolution of “priming” and “cellular pre-activation/pre-disposition” processes within the lung microenvironment.", + "subject": [], + "keywords": [] + }, + { + "title": "Characterizing suicidal ideation, suicidal behaviors, and service utilization among unhoused individuals using a health information exchange", + "author": "Zandra V. Ho, Sarah A. Arias, Zachary J. Kunicki, Indra Neil Sarkar, Elizabeth S. Chen", + "publisher": "Wiley", + "url": "http://dx.doi.org/10.1002/jclp.23566", + "doi": "10.1002/jclp.23566", + "year": 2023, + "month": 7, + "abstract": "AbstractIntroductionUnhoused individuals have high rates of suicidal ideation (SI) and suicidal behaviors (SB), but few have studied the relative timing of homelessness and SI/SB. Our study examines the potential to use state‐wide electronic health record data from Rhode Island's health information exchange (HIE) to identify temporal relationships, service utilization, and associations of SI/SB among unhoused individuals.MethodsWe use timestamped HIE data for 5368 unhoused patients to analyze service utilization and the relative timing of homelessness versus SI/SB onset. Multivariable models identified associations of SI/SB, hospitalization, and repeat acute care utilization within 30 days from clinical features representing 10,000+ diagnoses captured within the HIE.ResultsThe onset of SI typically precedes homelessness onset, while the onset of SB typically follows. Weekly rates of suicide‐related service utilization increased over 25 times the baseline rate during the week before and after homelessness onset. Over 50% of encounters involving SI/SB result in hospitalization. Of those engaging in acute care for suicide‐related reasons, we found high rates of repeat acute care encounters.ConclusionHIEs are a particularly valuable resource for understudied populations. Our study demonstrates how longitudinal, multi‐institutional data from an HIE can be used to characterize temporal associations, service utilization, and clinical associations of SI and behaviors among a vulnerable population at scale. Increasing access to services that address co‐occurring SI/SB, mental health, and substance use is needed.", + "subject": [], + "keywords": [] + }, + { + "title": "Increased Biogenic Calcification and Burial Under Elevated pCO2 During the Miocene: A Model‐Data Comparison", + "author": "Weimin Si, Timothy Herbert, Mengxi Wu, Yair Rosenthal", + "publisher": "American Geophysical Union (AGU)", + "url": "http://dx.doi.org/10.1029/2022gb007541", + "doi": "10.1029/2022gb007541", + "year": 2023, + "month": 5, + "abstract": "AbstractOcean acidification due to anthropogenic CO2 emission reduces ocean pH and carbonate saturation, with the projection that marine calcifiers and associated ecosystems will be negatively affected in the future. On longer time scale, however, recent studies of deep‐sea carbonate sediments suggest significantly increased carbonate production and burial in the open ocean during the warm Middle Miocene. Here, we present new model simulations in comparison to published Miocene carbonate accumulation rates to show that global biogenic carbonate production in the pelagic environment was approximately doubled relative to present‐day values when elevated atmospheric pCO2 led to substantial global warming ∼13–15 million years ago. Our analysis also finds that although high carbonate production was associated with high dissolution in the deep‐sea, net pelagic carbonate burial was approximately 30%–45% higher than modern. At the steady state of the long‐term carbon cycle, this requires an equivalent increase in riverine carbonate alkalinity influx during the Middle Miocene, attributable to enhanced chemical weathering under a warmer climate. Elevated biogenic carbonate production resulted in a Miocene ocean that had carbon (dissolved inorganic carbon) and alkalinity (total alkalinity) inventories similar to modern values but was poorly buffered and less saturated in both the surface and the deep ocean relative to modern.", + "subject": [], + "keywords": [] + }, + { + "title": "A combined computational and experimental investigation of the filtration function of splenic macrophages in sickle cell disease", + "author": "Guansheng Li, Yuhao Qiang, He Li, Xuejin Li, Pierre A. Buffet, Ming Dao, George Em Karniadakis", + "publisher": "Cold Spring Harbor Laboratory", + "url": "http://dx.doi.org/10.1101/2023.05.31.543007", + "doi": "10.1101/2023.05.31.543007", + "year": 2023, + "month": 6, + "abstract": "AbstractBeing the largest lymphatic organ in the body, the spleen also constantly controls the quality of red blood cells (RBCs) in circulation through its two major filtration components, namely interendothelial slits (IES) and red pulp macrophages. In contrast to the extensive studies in understanding the filtration function of IES, there are relatively fewer works on investigating how the splenic macrophages retain the aged and diseased RBCs, i.e., RBCs in sickle cell disease (SCD). Herein, we perform a computational study informed by companion experiments to quantify the dynamics of RBCs captured and retained by the macrophages. We first calibrate the parameters in the computational model based on microfluidic experimental measurements for sickle RBCs under normoxia and hypoxia, as those parameters are not available in the literature. Next, we quantify the impact of a set of key factors that are expected to dictate the RBC retention by the macrophages in the spleen, namely, blood flow conditions, RBC aggregation, hematocrit, RBC morphology, and oxygen levels. Our simulation results show that hypoxic conditions could enhance the adhesion between the sickle RBCs and macrophages. This, in turn, increases the retention of RBCs by as much as five-fold, which could be a possible cause of RBC congestion in the spleen of patients with SCD. Our study on the impact of RBC aggregation illustrates a ‘clustering effect’, where multiple RBCs in one aggregate can make contact and adhere to the macrophages, leading to a higher retention rate than that resulting from RBC-macrophage pair interactions. Our simulations of sickle RBCs flowing past macrophages for a range of blood flow velocities indicate that the increased blood velocity could quickly attenuate the function of the red pulp macrophages on detaining aged or diseased RBCs, thereby providing a possible rationale for the slow blood flow in the open circulation of the spleen. Furthermore, we quantify the impact of RBC morphology on their tendency to be retained by the macrophages. We find that the sickle and granular-shaped RBCs are more likely to be filtered by macrophages in the spleen. This finding is consistent with the observation of low percentages of these two forms of sickle RBCs in the blood smear of SCD patients. Taken together, our experimental and simulation results aid in our quantitative understanding of the function of splenic macrophages in retaining the diseased RBCs and provide an opportunity to combine such knowledge with the current knowledge of the interaction between IES and traversing RBCs to apprehend the complete filtration function of the spleen in SCD.", + "subject": [], + "keywords": [] + }, + { + "title": "Multi‐year time series reveals temporally synchronous diatom communities with annual frequency of recurrence in a temperate estuary", + "author": "Diana N. Fontaine, Tatiana A. Rynearson", + "publisher": "Wiley", + "url": "http://dx.doi.org/10.1002/lno.12400", + "doi": "10.1002/lno.12400", + "year": 2023, + "month": 7, + "abstract": "AbstractDiatoms are among the most abundant phytoplankton that inhabit coastal ecosystems, forming large blooms that fuel coastal food webs. Although diatoms are often large and morphologically distinct, many are small or morphologically cryptic making it difficult to understand the temporal dynamics of whole diatom communities and the environmental factors that drive them. Here, we investigated diatom diversity and its environmental correlates using 6 yr of monthly surface water samples from the Narragansett Bay Plankton Time Series to investigate the seasonal and annual variability of diatom species occurrence. High‐throughput amplicon sequencing of filtered biomass yielded 658 diatom amplicon sequence variants (ASVs), of which 347 were identified to species. Of the 49 diatom genera in the sequencing dataset, 33% had never been observed in the time series using microscopy (1959–2014). We observed a weak quadratic relationship between ASV richness and chlorophyll‐a concentrations, suggesting that richness decreases during blooms. There was a significant difference in diatom ASV richness by season and we identified distinct assemblages associated with different seasons. These assemblages were remarkably synchronous, exhibiting a sinewave‐like pattern, over 6 yr with an annual periodicity that correlated significantly with seasonal changes in temperature, light, and dissolved inorganic nitrogen. The annual cycle of diatom assemblages suggests stability in a key component of the estuarine food web known to influence ecosystem resilience and function. Deviations from the annual cycle of recurrence could be used to distinguish between changes in community structure driven by annual fluctuations in the environment and those driven by climate‐change stressors.", + "subject": [], + "keywords": [] + }, + { + "title": "Q-functionals for Value-Based Continuous Control", + "author": "Samuel Lobel, Sreehari Rammohan, Bowen He, Shangqun Yu, George Konidaris", + "publisher": "Association for the Advancement of Artificial Intelligence (AAAI)", + "url": "http://dx.doi.org/10.1609/aaai.v37i7.26073", + "doi": "10.1609/aaai.v37i7.26073", + "year": 2023, + "month": 6, + "abstract": "We present Q-functionals, an alternative architecture for continuous control deep reinforcement learning. Instead of returning a single value for a state-action pair, our network transforms a state into a function that can be rapidly evaluated in parallel for many actions, allowing us to efficiently choose high-value actions through sampling. This contrasts with the typical architecture of off-policy continuous control, where a policy network is trained for the sole purpose of selecting actions from the Q-function. We represent our action-dependent Q-function as a weighted sum of basis functions (Fourier, Polynomial, etc) over the action space, where the weights are state-dependent and output by the Q-functional network. Fast sampling makes practical a variety of techniques that require Monte-Carlo integration over Q-functions, and enables action-selection strategies besides simple value-maximization. We characterize our framework, describe various implementations of Q-functionals, and demonstrate strong performance on a suite of continuous control tasks.", + "subject": [], + "keywords": [] + }, + { + "title": "Brain Glutamate Dynamics Predict Positive Agency in Healthy Women", + "author": "Tara L. White, Meghan A. Gonsalves, Ashley D. Harris, Edward G. Walsh, Hannah E. Joyce", + "publisher": "Research Square Platform LLC", + "url": "http://dx.doi.org/10.21203/rs.3.rs-3021527/v1", + "doi": "10.21203/rs.3.rs-3021527/v1", + "year": 2023, + "month": 6, + "abstract": "Abstract\n Contributions of brain glutamate to conscious emotion are not well understood. Here we evaluate the relationship of experimentally-induced change in neocortical glutamate (△Glu) and subjective states in well individuals. Drug challenge with d-amphetamine (AMP; 20 mg oral), methamphetamine (MA; Desoxyn®, 20 mg oral), and placebo (PBO) was conducted on three separate test days in a within-subjects double blind design. Proton magnetic resonance spectroscopy (MRS) quantified neurometabolites in the right dorsal anterior cingulate cortex (dACC) 140-150 m post-drug and PBO. Subjective states were assessed at half hour intervals over 5.5-hours on each session, yielding 3,792 responses per participant (91,008 responses overall, N=24 participants). Self-reports were reduced by principal components analysis to a single factor score of AMP- and MA-induced Positive Agency (△PA) in each participant. We found drug-induced △Glu related positively with △PA (△GluMA r=+.44, p<.05, N=21), with large effects in females (△GluMA r=+.52, p<.05; △GluAMP r=+.61, p<.05, N=11). States related to △Glu in females included rise in subjective stimulation, vigor, friendliness, elation, positive mood, positive affect (r’s=+.51 to +.74, p<.05), and alleviation of anxiety (r=-.61, p<.05, N=11). Self-reports correlated with DGlu to the extent they loaded on △PA (r=.95 AMP, p=5x10-10; r=.63 MA, p=.0015, N=11), indicating coherence of △Glu effects. Timing data indicated Glu shaped emotion both concurrently and prospectively, with no relationship to pre-MRS emotion (△GluAMP r=+.59 to +.65, p’s<.05; △GluMA r=+.53, p<.05, N=11). Together these findings indicate substantive, mechanistic contributions of neocortical Glu to positive agentic states in healthy individuals, most readily observed in women.", + "subject": [], + "keywords": [] + }, + { + "title": "Short-Term Dietary Intervention with Whole Oats Protects from Antibiotic-Induced Dysbiosis", + "author": "Stephen K. Costa, Katherine Antosca, Chapman N. Beekman, Rachel L. Peterson, Swathi Penumutchu, Peter Belenky", + "publisher": "American Society for Microbiology", + "url": "http://dx.doi.org/10.1128/spectrum.02376-23", + "doi": "10.1128/spectrum.02376-23", + "year": 2023, + "month": 8, + "abstract": "We utilize a multi-omics approach to demonstrate that diets supplemented with oats, a rich source of microbiota-accessible carbohydrates, are able to confer protection against antibiotic-induced dysbiosis (AID). Our findings affirm that not only is host diet important in shaping antibiotics effects on gut microbiome composition and function but also that the timing of these diets may play an even greater role in managing AID.", + "subject": [], + "keywords": [] + }, + { + "title": "Strategic predatory pursuit of the stealthy, highly manoeuvrable, slow flying bat\n Corynorhinus townsendii", + "author": "Alberto Bortoni, Sharon M. Swartz, Hamid Vejdani, Aaron J. Corcoran", + "publisher": "The Royal Society", + "url": "http://dx.doi.org/10.1098/rspb.2023.0138", + "doi": "10.1098/rspb.2023.0138", + "year": 2023, + "month": 6, + "abstract": "A predator's capacity to catch prey depends on its ability to navigate its environment in response to prey movements or escape behaviour. In predator–prey interactions that involve an active chase, pursuit behaviour can be studied as the collection of rules that dictate how a predator should steer to capture prey. It remains unclear how variable this behaviour is within and across species since most studies have detailed the pursuit behaviour of high-speed, open-area foragers. In this study, we analyse the pursuit behaviour in 44 successful captures by\n Corynorhinus townsendii\n , Townsend's big-eared bat (\n n\n = 4). This species forages close to vegetation using slow and highly manoeuvrable flight, which contrasts with the locomotor capabilities and feeding ecologies of other taxa studied to date. Our results indicate that this species relies on an initial stealthy approach, which is generally sufficient to capture prey (32 out of 44 trials). In cases where the initial approach is not sufficient to perform a capture attempt (12 out of 44 trials),\n C. townsendii\n continues its pursuit by reacting to prey movements in a manner best modelled with a combination of pure pursuit, or following prey directly, and proportional navigation, or moving to an interception point.", + "subject": [], + "keywords": [] + }, + { + "title": "Ancient Mongolian aurochs genomes reveal sustained introgression and management in East Asia", + "author": "Katherine Brunson, Kelsey E. Witt, Susan Monge, Sloan Williams, David Peede, Davaakhuu Odsuren, Dashzeveg Bukhchuluun, Asa Cameron, Paul Szpak, Chunag Amartuvshin, William Honeychurch, Joshua Wright, Sarah Pleuger, Myagmar Erdene, Dashtseveg Tumen, Leland Rogers, Dorjpurev Khatanbaatar, Byambatseren Batdalai, Ganbaatar Galdan, Lisa Janz", + "publisher": "Cold Spring Harbor Laboratory", + "url": "http://dx.doi.org/10.1101/2023.08.10.552443", + "doi": "10.1101/2023.08.10.552443", + "year": 2023, + "month": 8, + "abstract": "AbstractSocieties in East Asia have utilized domesticated cattle for over 5000 years, but the genetic history of cattle in East Asia remains understudied. Genome-wide analyses of 23 ancient Mongolian cattle reveal that East Asian aurochs and ancient East Asian taurine cattle are closely related, but neither are closely related to any modern East Asian breeds. We observe binary variation in aurochs diet throughout the early Neolithic, and genomic evidence shows millennia of sustained male-dominated introgression. We identify a unique connection between ancient Mongolian aurochs and the European Hereford breed. These results point to the likelihood of human management of aurochs in Northeast Asia prior to and during the initial adoption of taurine cattle pastoralism.One-Sentence SummaryAncient interbreeding of East Asian aurochs and cattle suggests management, but leaves no signature in modern eastern breeds.", + "subject": [], + "keywords": [] + }, + { + "title": "Modeling high strain-rate microcavitation in soft materials: the role of material behavior in bubble dynamics", + "author": "Anastasia Tzoumaka, Jin Yang, Selda Buyukozturk, Christian Franck, David L. Henann", + "publisher": "Royal Society of Chemistry (RSC)", + "url": "http://dx.doi.org/10.1039/d2sm01212j", + "doi": "10.1039/d2sm01212j", + "year": 2023, + "month": -1, + "abstract": "Inertial Microcavitation Rheometry is a promising tool for characterizing the behavior of soft materials at high strain rates. We develop a simulation capability for spherical bubbles, incorporating compressibility and complex viscoelastic behavior.", + "subject": [], + "keywords": [] + }, + { + "title": "Monkey Dorsolateral Prefrontal Cortex Represents Abstract Visual Sequences during a No-Report Task", + "author": "Nadira Yusif Rodriguez, Theresa H. McKim, Debaleena Basu, Aarit Ahuja, Theresa M. Desrochers", + "publisher": "Society for Neuroscience", + "url": "http://dx.doi.org/10.1523/jneurosci.2058-22.2023", + "doi": "10.1523/jneurosci.2058-22.2023", + "year": 2023, + "month": 3, + "abstract": "Monitoring sequential information is an essential component of our daily lives. Many of these sequences are abstract, in that they do not depend on the individual stimuli, but do depend on an ordered set of rules (e.g., chop then stir when cooking). Despite the ubiquity and utility of abstract sequential monitoring, little is known about its neural mechanisms. Human rostrolateral prefrontal cortex (RLPFC) exhibits specific increases in neural activity (i.e., “ramping”) during abstract sequences. Monkey dorsolateral prefrontal cortex (DLPFC) has been shown to represent sequential information in motor (not abstract) sequence tasks, and contains a subregion, area 46, with homologous functional connectivity to human RLPFC. To test the prediction that area 46 may represent abstract sequence information, and do so with parallel dynamics to those found in humans, we conducted functional magnetic resonance imaging (fMRI) in three male monkeys. When monkeys performed no-report abstract sequence viewing, we found that left and right area 46 responded to abstract sequential changes. Interestingly, responses to rule and number changes overlapped in right area 46 and left area 46 exhibited responses to abstract sequence rules with changes in ramping activation, similar to that observed in humans. Together, these results indicate that monkey DLPFC monitors abstract visual sequential information, potentially with a preference for different dynamics in the two hemispheres. More generally, these results show that abstract sequences are represented in functionally homologous regions across monkeys and humans.SIGNIFICANCE STATEMENTDaily, we complete sequences that are “abstract” because they depend on an ordered set of rules (e.g., chop then stir when cooking) rather than the identity of individual items. Little is known about how the brain tracks, or monitors, this abstract sequential information. Based on previous human work showing abstract sequence related dynamics in an analogous area, we tested whether monkey dorsolateral prefrontal cortex (DLPFC), specifically area 46, represents abstract sequential information using awake monkey functional magnetic resonance imaging (fMRI). We found that area 46 responded to abstract sequence changes, with a preference for more general responses on the right and dynamics similar to humans on the left. These results suggest that abstract sequences are represented in functionally homologous regions across monkeys and humans.", + "subject": [], + "keywords": [] + }, + { + "title": "Brain Glutamate Dynamics Predict Positive Agency in Healthy Women", + "author": "Tara L. White, Meghan A. Gonsalves, Ashley D Harris, Edward Walsh, Hannah Joyce", + "publisher": "Center for Open Science", + "url": "http://dx.doi.org/10.31219/osf.io/u7j6y", + "doi": "10.31219/osf.io/u7j6y", + "year": 2023, + "month": 6, + "abstract": "Contributions of brain glutamate to conscious emotion are not well understood. Here we evaluate the relationship of experimentally-induced change in neocortical glutamate (Delta Glu) and subjective states in well individuals, using combined application of pharmacological challenge, magnetic resonance spectroscopy (MRS), and comprehensive affective assessment. Drug challenge with d-amphetamine (AMP; 20 mg oral), methamphetamine (MA; Desoxyn®, 20 mg oral), and placebo (PBO) was conducted on three separate test days in a within-subjects double blind design. Proton MRS quantified neurometabolites in the right dorsal anterior cingulate cortex (dACC) 140-150 min post-drug and PBO. Subjective states were assessed at half hour intervals over 5.5-hours on each session, yielding 3,792 responses per participant (91,008 responses overall, N=24 participants), with self-reports reduced by principal components analysis (PCA). PCA produced a primary factor score of AMP- and MA-induced Positive Agency (Delta PA). MRS indicated drug-induced Glu related positively to PA (Delta GluMA r=+.44, p&lt;0.05, N=21), with large effects in females (Delta GluMA r=+.52, p&lt;0.05; Delta GluAMP r=+.61, p&lt;0.05, N=11). Subjective states related to Delta Glu included rise in subjective stimulation, vigor, friendliness, elation, positive mood, positive affect (r’s=+.51 to +.74, p&lt;0.05), and alleviation of anxiety in females (r=-.61, p&lt;0.05, N=11). These self-reports correlated with Delta Glu to the extent they loaded on Delta PA (r=0.95 AMP, p=5x10-10; r=0.63 MA, p=0.0015, N=11), indicating coherence of Glu effects on emotional states. Timing data indicated Glu shaped positive emotion both concurrently and prospectively, with no relationship with pre-MRS emotion (Delta GluAMP r=+0.59 to +0.65, p’s&lt;0.05; Delta GluMA r=+0.53, p&lt;0.05, N=11). Together these findings indicate substantive, mechanistic contributions of neocortical Glu to positive agentic states in healthy individuals, most readily observed in women. The findings illustrate the promise of combined application of pharmacological challenge, comprehensive affective assessment, and MRS neuroimaging techniques in basic and clinical studies.", + "subject": [], + "keywords": [] + }, + { + "title": "Extreme image transformations affect humans and machines differently", + "author": "Girik Malik, Dakarai Crowder, Ennio Mingolla", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1007/s00422-023-00968-7", + "doi": "10.1007/s00422-023-00968-7", + "year": 2023, + "month": 6, + "abstract": "AbstractSome recent artificial neural networks (ANNs) claim to model aspects of primate neural and human performance data. Their success in object recognition is, however, dependent on exploiting low-level features for solving visual tasks in a way that humans do not. As a result, out-of-distribution or adversarial input is often challenging for ANNs. Humans instead learn abstract patterns and are mostly unaffected by many extreme image distortions. We introduce a set of novel image transforms inspired by neurophysiological findings and evaluate humans and ANNs on an object recognition task. We show that machines perform better than humans for certain transforms and struggle to perform at par with humans on others that are easy for humans. We quantify the differences in accuracy for humans and machines and find a ranking of difficulty for our transforms for human data. We also suggest how certain characteristics of human visual processing can be adapted to improve the performance of ANNs for our difficult-for-machines transforms.", + "subject": [], + "keywords": [] + }, + { + "title": "Internal vs Forced Variability Metrics for Geophysical Flows Using Information Theory", + "author": "Aakash Sane, Baylor Fox-Kemper, David Ullman, Aakash Sane", + "publisher": "Wiley", + "url": "http://dx.doi.org/10.1002/essoar.10505545.4", + "doi": "10.1002/essoar.10505545.4", + "year": 2023, + "month": 8, + "abstract": "We demonstrate the use of information theory metrics, Shannon entropy\nand mutual information, for measuring internal and forced variability in\ngeneral circulation coastal and global ocean models. These metrics have\nbeen applied on spatially and temporally averaged data. A combined\nmetric reliably delineates intrinsic and extrinsic variability in a\nwider range of circumstances than previous approaches based on variance\nratios that therefore assume Gaussian distributions. Shannon entropy and\nmutual information manage correlated fields, apply to any distribution,\nand are insensitive to outliers and a change of units or scale.\nDifferent metrics are used to quantify internal vs forced variability in\n(1) idealized Gaussian and uniformly distributed data, (2) an initial\ncondition ensemble of a realistic coastal ocean model (OSOM), (3) the\nGFDL-ESM2M climate model large ensemble. A metric based on information\ntheory partly agrees with the traditional variance-based metric and\nidentifies regions where non-linear correlations might exist. Mutual\ninformation and Shannon entropy are used to quantify the impact of\ndifferent boundary forcings in a coastal ocean model ensemble.\nInformation theory enables ranking the potential impacts of improving\nboundary and forcing conditions across multiple predicted variables with\ndifferent dimensions. The climate model ensemble application shows how\ninformation theory metrics are robust even in a highly skewed\nprobability distribution (Arctic sea surface temperature) resulting from\nsharply non-linear behavior (freezing point).", + "subject": [], + "keywords": [] + }, + { + "title": "Criticality in probabilistic models of spreading dynamics in brain networks: Epileptic seizures", + "author": "S Amin Moosavi, Wilson Truccolo", + "publisher": "Public Library of Science (PLoS)", + "url": "http://dx.doi.org/10.1371/journal.pcbi.1010852", + "doi": "10.1371/journal.pcbi.1010852", + "year": 2023, + "month": 2, + "abstract": "The spread of seizures across brain networks is the main impairing factor, often leading to loss-of-consciousness, in people with epilepsy. Despite advances in recording and modeling brain activity, uncovering the nature of seizure spreading dynamics remains an important challenge to understanding and treating pharmacologically resistant epilepsy. To address this challenge, we introduce a new probabilistic model that captures the spreading dynamics in patient-specific complex networks. Network connectivity and interaction time delays between brain areas were estimated from white-matter tractography. The model’s computational tractability allows it to play an important complementary role to more detailed models of seizure dynamics. We illustrate model fitting and predictive performance in the context of patient-specific Epileptor networks. We derive the phase diagram of spread size (order parameter) as a function of brain excitability and global connectivity strength, for different patient-specific networks. Phase diagrams allow the prediction of whether a seizure will spread depending on excitability and connectivity strength. In addition, model simulations predict the temporal order of seizure spread across network nodes. Furthermore, we show that the order parameter can exhibit both discontinuous and continuous (critical) phase transitions as neural excitability and connectivity strength are varied. Existence of a critical point, where response functions and fluctuations in spread size show power-law divergence with respect to control parameters, is supported by mean-field approximations and finite-size scaling analyses. Notably, the critical point separates two distinct regimes of spreading dynamics characterized by unimodal and bimodal spread-size distributions. Our study sheds new light on the nature of phase transitions and fluctuations in seizure spreading dynamics. We expect it to play an important role in the development of closed-loop stimulation approaches for preventing seizure spread in pharmacologically resistant epilepsy. Our findings may also be of interest to related models of spreading dynamics in epidemiology, biology, finance, and statistical physics.", + "subject": [], + "keywords": [] + }, + { + "title": "Attacks on Encrypted Response-Hiding Range Search Schemes in Multiple Dimensions", + "author": "Evangelia Anna Markatou, Francesca Falzon, Zachary Espiritu, Roberto Tamassia", + "publisher": "Privacy Enhancing Technologies Symposium Advisory Board", + "url": "http://dx.doi.org/10.56553/popets-2023-0106", + "doi": "10.56553/popets-2023-0106", + "year": 2023, + "month": 10, + "abstract": "In this work, we present the first database reconstruction attacks against response-hiding private range search schemes on encrypted databases of arbitrary dimensions. Falzon et al. (VLDB 2022) present a number of range-supporting schemes on arbitrary dimensions exhibiting different security and efficiency trade-offs. Additionally, they characterize a form of leakage, structure pattern leakage, also present in many one-dimensional schemes e.g., Demertzis et al. (SIGMOD 2016) and Faber et al. (ESORICS 2015). We present the first systematic study of this leakage and attack a broad collection of schemes, including schemes that allow the responses to contain false-positives (often considered the gold standard in security). We characterize the information theoretic limitations of a passive persistent adversary. Our work shows that for range queries, structure pattern leakage can be as vulnerable to attacks as access pattern leakage. We give a comprehensive evaluation of our attacks with a complexity analysis, a prototype implementation, and an experimental assessment on real-world datasets.", + "subject": [], + "keywords": [] + }, + { + "title": "New EoR power spectrum limits from MWA Phase II using the delay spectrum method and novel systematic rejection", + "author": "Matthew Kolopanis, Jonathan C Pober, Daniel C Jacobs, Samantha McGraw", + "publisher": "Oxford University Press (OUP)", + "url": "http://dx.doi.org/10.1093/mnras/stad845", + "doi": "10.1093/mnras/stad845", + "year": 2023, + "month": 3, + "abstract": "ABSTRACT\n We present an analysis of Epoch of Reionization (EoR) data from Phase II of the Murchison Widefield Array using the simpleds delay spectrum pipeline. Prior work analysed the same observations using the fhd/εppsilon imaging pipeline, and so the present analysis represents the first time that both principal types of 21 cm cosmology power spectrum estimation approaches have been applied to the same data set. Our limits on the 21 cm power spectrum amplitude span a range in k space of $|k| \\lt 1 \\, h_{100}\\, {\\rm Mpc}^{-1}$ with a lowest measurement of Δ2(k) ≤ 4.58 × 103 mK2 at $k = 0.190\\, h_{100}\\, \\rm {Mpc}^{-1}$ and z = 7.14. In order to achieve these limits, we need to mitigate a previously unidentified common mode systematic in the data set. If not accounted for, this systematic introduces an overall negative bias that can make foreground contaminated measurements appear as stringent, noise-limited constraints on the 21 cm signal amplitude. The identification of this systematic highlights the risk in modelling systematics as positive-definite contributions to the power spectrum and in ‘conservatively’ interpreting all measurements as upper limits.", + "subject": [], + "keywords": [] + }, + { + "title": "Multioviz: an interactive platform forin silicoperturbation and interrogation of gene regulatory networks", + "author": "Helen Xie, Lorin Crawford, Ashley Mae Conard", + "publisher": "Cold Spring Harbor Laboratory", + "url": "http://dx.doi.org/10.1101/2023.10.10.561790", + "doi": "10.1101/2023.10.10.561790", + "year": 2023, + "month": 10, + "abstract": "AbstractIn this paper, we aim to build a tool that will help bridge the gap between high-dimensional computation and wet-lab experimentation by allowing users to interrogate genomic signatures at multiple molecular levels and identify best next actionable steps for downstream decision making. We introduceMultioviz: a publicly accessibleRpackage and web application platform to easily performin silicohypothesis testing of generated gene regulatory networks. We demonstrate the utility ofMultiovizby conducting an end-to-end analysis in a statistical genetics application focused on measuring the effect ofin silicoperturbations of complex trait architecture. By using a real data set from the Wellcome Trust Centre for Human Genetics, we both recapitulate previous findings and propose hypotheses about the genes involved in the percentage of immune CD8+ cells found in heterogeneous stocks of mice. Source code for theMultioviz Rpackage is available athttps://github.com/lcrawlab/multio-vizand an interactive version of the platform is available atmultioviz.ccv.brown.edu.", + "subject": [], + "keywords": [] + }, + { + "title": "Multioviz: an interactive platform forin silicoperturbation and interrogation of gene regulatory networks", + "author": "Helen Xie, Lorin Crawford, Ashley Mae Conard", + "publisher": "Cold Spring Harbor Laboratory", + "url": "http://dx.doi.org/10.1101/2023.10.10.561790", + "doi": "10.1101/2023.10.10.561790", + "year": 2023, + "month": 10, + "abstract": "AbstractIn this paper, we aim to build a tool that will help bridge the gap between high-dimensional computation and wet-lab experimentation by allowing users to interrogate genomic signatures at multiple molecular levels and identify best next actionable steps for downstream decision making. We introduceMultioviz: a publicly accessibleRpackage and web application platform to easily performin silicohypothesis testing of generated gene regulatory networks. We demonstrate the utility ofMultiovizby conducting an end-to-end analysis in a statistical genetics application focused on measuring the effect ofin silicoperturbations of complex trait architecture. By using a real data set from the Wellcome Trust Centre for Human Genetics, we both recapitulate previous findings and propose hypotheses about the genes involved in the percentage of immune CD8+ cells found in heterogeneous stocks of mice. Source code for theMultioviz Rpackage is available athttps://github.com/lcrawlab/multio-vizand an interactive version of the platform is available atmultioviz.ccv.brown.edu.", + "subject": [], + "keywords": [] + }, + { + "title": "Extracellular vesicle treatment partially reverts epigenetic alterations in chronically ischemic porcine myocardium", + "author": "Mark Broadwin, Ghazal Aghagoli, Sharif A. Sabe, Dwight D. Harris, Joselynn Wallace, Jordan Lawson, Ashok Ragayendran, Alexey V. Fedulov, Frank W. Sellke", + "publisher": "OAE Publishing Inc.", + "url": "http://dx.doi.org/10.20517/2574-1209.2023.103", + "doi": "10.20517/2574-1209.2023.103", + "year": 2023, + "month": -1, + "abstract": "Introduction: Research has shown epigenetic change via alternation of the methylation profile of human skeletal muscle DNA after Cardio-Pulmonary Bypass (CPB). In this study, we investigated the change in epigenome-wide DNA methylation profiles of porcine myocardium after ischemic insult in the setting of treatment with extracellular vesicle (EV) therapy in normal vs. high-fat diet (HFD) pigs. Methods: Four groups of three pigs underwent ameroid constrictor placement to the left circumflex artery (LCx) and were assigned to the following groups: (1) normal diet saline injection; (2) normal diet EV injection; (3) HFD saline injection; and (4) HFD EV injection. DNA methylation was profiled via reduced-representation bisulfite sequencing (RRBS) and compared using a custom bioinformatic pipeline. Results: After initial analysis, 441 loci had a nominal P value < 0.05 when examining the effect of ischemia vs. normal heart tissue on a normal diet in the absence of treatment. 426 loci at P value threshold < 0.05 were identified when comparing the ischemic vs. normal tissue from high-fat diet animals. When examining the effect of EV treatment in ischemic tissue in subjects on a normal diet, there were 574 loci with nominal P value < 0.05 with two loci Fructosamine 3 kinase related protein [(FN3KRP) (P < 0.001)] and SNTG1 (P = 0.03) significant after Bonferroni correction. When examining the effect of EV treatment in ischemic tissue in HFD, there were 511 loci with nominal P values < 0.05. After Bonferroni correction, two loci had P values less than 0.05, betacellulin [(BTC) (P = 0.008)] and [proprotein convertase subtilisin/kexin type 7 (PCSK7) (P = 0.01)]. Conclusions: Alterations in DNA methylation were identified in pig myocardium after ischemic insult, change in diet, and treatment with EVs. Hundreds of differentially methylated loci were detected, but the magnitude of the effects was low. These changes represent significant alterations in DNA methylation and merit further investigation.", + "subject": [], + "keywords": [] + }, + { + "title": "Public Health Dashboards in Overdose Prevention: The Rhode Island Approach to Public Health Data Literacy, Partnerships, and Action (Preprint)", + "author": "Jesse Yedinak, Maxwell S Krieger, Raynald Joseph, Stacey Levin, Sarah Edwards, Dennis A Bailer, Jonathan Goyer, Colleen Daley Ndoye, Cathy Schultz, Jennifer Koziol, Rachael Elmaleh, Benjamin D Hallowell, Todd Hampson, Ellen Duong, Abdullah Shihipar, William C Goedel, Brandon DL Marshall", + "publisher": "JMIR Publications Inc.", + "url": "http://dx.doi.org/10.2196/preprints.51671", + "doi": "10.2196/preprints.51671", + "year": 2023, + "month": 8, + "abstract": "UNSTRUCTURED\n As the field of public health rises to the demands of real-time surveillance and rapid data-sharing needs in a postpandemic world, it is time to examine our approaches to the dissemination and accessibility of such data. Distinct challenges exist when working to develop a shared public health language and narratives based on data. It requires that we assess our understanding of public health data literacy, revisit our approach to communication and engagement, and continuously evaluate our impact and relevance. Key stakeholders and cocreators are critical to this process and include people with lived experience, community organizations, governmental partners, and research institutions. In this viewpoint paper, we offer an instructive approach to the tools we used, assessed, and adapted across 3 unique overdose data dashboard projects in Rhode Island, United States. We are calling this model the “Rhode Island Approach to Public Health Data Literacy, Partnerships, and Action.” This approach reflects the iterative lessons learned about the improvement of data dashboards through collaboration and strong partnerships across community members, state agencies, and an academic research team. We will highlight key tools and approaches that are accessible and engaging and allow developers and stakeholders to self-assess their goals for their data dashboards and evaluate engagement with these tools by their desired audiences and users.", + "subject": [], + "keywords": [] + }, + { + "title": "Abstract cognitive maps of social network structure aid adaptive inference", + "author": "Jae-Young Son, Apoorva Bhandari, Oriel FeldmanHall", + "publisher": "Proceedings of the National Academy of Sciences", + "url": "http://dx.doi.org/10.1073/pnas.2310801120", + "doi": "10.1073/pnas.2310801120", + "year": 2023, + "month": 11, + "abstract": "Social navigation—such as anticipating where gossip may spread, or identifying which acquaintances can help land a job—relies on knowing how people are connected within their larger social communities. Problematically, for most social networks, the space of possible relationships is too vast to observe and memorize. Indeed, people's knowledge of these social relations is well known to be biased and error-prone. Here, we reveal that these biased representations reflect a fundamental computation that abstracts over individual relationships to enable principled inferences about unseen relationships. We propose a theory of network representation that explains how people learn inferential cognitive maps of social relations from direct observation, what kinds of knowledge structures emerge as a consequence, and why it can be beneficial to encode systematic biases into social cognitive maps. Leveraging simulations, laboratory experiments, and “field data” from a real-world network, we find that people abstract observations of direct relations (e.g., friends) into inferences of multistep relations (e.g., friends-of-friends). This multistep abstraction mechanism enables people to discover and represent complex social network structure, affording adaptive inferences across a variety of contexts, including friendship, trust, and advice-giving. Moreover, this multistep abstraction mechanism unifies a variety of otherwise puzzling empirical observations about social behavior. Our proposal generalizes the theory of cognitive maps to the fundamental computational problem of social inference, presenting a powerful framework for understanding the workings of a predictive mind operating within a complex social world.", + "subject": [], + "keywords": [] + }, + { + "title": "Transcription and chromatin regulation by TAF4b during cellular quiescence of developing prospermatogonia", + "author": "Megan A. Gura, Myles A. Bartholomew, Kimberly M. Abt, Soňa Relovská, Kimberly A. Seymour, Richard N. Freiman", + "publisher": "Frontiers Media SA", + "url": "http://dx.doi.org/10.3389/fcell.2023.1270408", + "doi": "10.3389/fcell.2023.1270408", + "year": 2023, + "month": 10, + "abstract": "Prospermatogonia (ProSpg) link the embryonic development of male primordial germ cells to the healthy establishment of postnatal spermatogonia and spermatogonial stem cells. While these spermatogenic precursor cells undergo the characteristic transitions of cycling and quiescence, the transcriptional events underlying these developmental hallmarks remain unknown. Here, we investigated the expression and function of TBP-associated factor 4b (Taf4b) in the timely development of quiescent mouse ProSpg using an integration of gene expression profiling and chromatin mapping. We find that Taf4b mRNA expression is elevated during the transition of mitotic-to-quiescent ProSpg and Taf4b-deficient ProSpg are delayed in their entry into quiescence. Gene ontology, protein network analysis, and chromatin mapping demonstrate that TAF4b is a direct and indirect regulator of chromatin and cell cycle-related gene expression programs during ProSpg quiescence. Further validation of these cell cycle mRNA changes due to the loss of TAF4b was accomplished via immunostaining for proliferating cell nuclear antigen (PCNA). Together, these data indicate that TAF4b is a key transcriptional regulator of the chromatin and quiescent state of the developing mammalian spermatogenic precursor lineage.", + "subject": [], + "keywords": [] + }, + { + "title": "Targeting NHE6 gene expression identifies lysosome and neurodevelopmental mechanisms in a haploid in vitro cell model", + "author": "Qing Wu, Li Ma, Lena Joesch-Cohen, Michael Schmidt, Ece D. Gamsiz Uzun, Eric M. Morrow", + "publisher": "The Company of Biologists", + "url": "http://dx.doi.org/10.1242/bio.059778", + "doi": "10.1242/bio.059778", + "year": 2023, + "month": 11, + "abstract": "ABSTRACT\n Christianson syndrome (CS) is an X-linked disorder resulting from loss-of-function (LoF) mutations in SLC9A6 encoding the endosomal Na+/H+ exchanger 6 (NHE6). CS presents with developmental delay, seizures, intellectual disability, nonverbal status, postnatal microcephaly, and ataxia. To define transcriptome signatures of NHE6 LoF, we conducted in-depth RNA-sequencing (RNA-seq) analysis on a haploid NHE6 null cell model. CRIPSR/Cas9 genome editing introduced multiple LoF mutations into SLC9A6 in the near haploid human cell line Hap1. Isogenic, paired parental controls were also studied. NHE6 mutant cell lines were confirmed to have intra-endosomal over-acidification as was seen in other NHE6 null cells. RNA-seq analysis was performed by two widely used pipelines: HISAT2-StringTie-DEseq2 and STAR-HTseq-DEseq2. We identified 1056 differentially expressed genes in mutant NHE6 lines, including genes associated with neurodevelopment, synapse function, voltage-dependent calcium channels, and neuronal signaling. Weighted gene co-expression network analysis was then applied and identified a critical module enriched for genes governing lysosome function. By identifying significantly changed gene expression that is associated with lysosomal mechanisms in NHE6-null cells, our analyses suggest that loss of NHE6 function may converge on mechanisms implicated in lysosome-related neurologic disease. Further, this haploid cell model will serve as an important tool for translational science in CS.", + "subject": [], + "keywords": [] + }, + { + "title": "Predicting Relative Populations of Protein Conformations without a Physics Engine Using AlphaFold2", + "author": "Gabriel Monteiro da Silva, Jennifer Y Cui, David C Dalgarno, George P Lisi, Brenda M Rubenstein", + "publisher": "Cold Spring Harbor Laboratory", + "url": "http://dx.doi.org/10.1101/2023.07.25.550545", + "doi": "10.1101/2023.07.25.550545", + "year": 2023, + "month": 7, + "abstract": "This paper presents a novel approach for predicting the relative populations of protein conformations using AlphaFold 2, an AI-powered method that has revolutionized biology by enabling the accurate prediction of protein structures. While AlphaFold 2 has shown exceptional accuracy and speed, it is designed to predict proteins' single ground state conformations and is limited in its ability to predict fold switching and the effects of mutations on conformational landscapes. Here, we demonstrate how AlphaFold 2 can directly predict the relative populations of different conformations of proteins and even accurately predict changes in those populations induced by mutations by subsampling multiple sequence alignments. We tested our method against NMR experiments on two proteins with drastically different amounts of available sequence data, Abl1 kinase and the granulocyte-macrophage colony-stimulating factor, and predicted their relative state populations with accuracies in excess of 80%. Our method offers a fast and cost-effective way to predict protein conformations and their relative populations at even single point mutation resolution, making it a useful tool for pharmacology, analyzing NMR data, and studying the effects of evolution.", + "subject": [], + "keywords": [] + }, + { + "title": "Topological data analysis of spatial patterning in heterogeneous cell populations: clustering and sorting with varying cell-cell adhesion", + "author": "Dhananjay Bhaskar, William Y. Zhang, Alexandria Volkening, Björn Sandstede, Ian Y. Wong", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1038/s41540-023-00302-8", + "doi": "10.1038/s41540-023-00302-8", + "year": 2023, + "month": 9, + "abstract": "AbstractDifferent cell types aggregate and sort into hierarchical architectures during the formation of animal tissues. The resulting spatial organization depends (in part) on the strength of adhesion of one cell type to itself relative to other cell types. However, automated and unsupervised classification of these multicellular spatial patterns remains challenging, particularly given their structural diversity and biological variability. Recent developments based on topological data analysis are intriguing to reveal similarities in tissue architecture, but these methods remain computationally expensive. In this article, we show that multicellular patterns organized from two interacting cell types can be efficiently represented through persistence images. Our optimized combination of dimensionality reduction via autoencoders, combined with hierarchical clustering, achieved high classification accuracy for simulations with constant cell numbers. We further demonstrate that persistence images can be normalized to improve classification for simulations with varying cell numbers due to proliferation. Finally, we systematically consider the importance of incorporating different topological features as well as information about each cell type to improve classification accuracy. We envision that topological machine learning based on persistence images will enable versatile and robust classification of complex tissue architectures that occur in development and disease.", + "subject": [], + "keywords": [] + }, + { + "title": "Categorizing Dog’s Real World Visual Environment", + "author": "Madeline Helmer Pelgrim, Shreyas Sundara Raman, Thomas Serre, Daphna Buchsbaum", + "publisher": "Center for Open Science", + "url": "http://dx.doi.org/10.31219/osf.io/xa3yq", + "doi": "10.31219/osf.io/xa3yq", + "year": 2023, + "month": 9, + "abstract": "Dogs have a unique evolutionary relationship with humans and are relied upon in a variety of working roles, yet little is known about the kinds of visual information available to them, as well as how they direct their visual attention within their environment. The present study, inspired by comparable work in infants, aimed to categorize the items available to be gazed at by dogs during a common event in their daily life, a walk. We then explored the statistics over the availability of those categories and over the dogs’ visual attention. Using a head-mounted eye-tracking apparatus that was custom designed for dogs, 11 dogs walked on a pre-determined route outdoors under naturalistic conditions generating a total of 11,698 gazes for analysis. Image stills from these fixations were then analyzed using computer vision techniques to explore the items present, and how much space within the visual field those items occupied, and which of the items the dog was gazing at. On average, there were few individual differences between dogs both in the items in dogs’ field of view and their gaze to items. Dogs looked proportionally most at people, buses, plants, the pavement, and construction equipment. The results of this project provide a foundational step towards understanding how dogs look at and interact with their physical world, opening up avenues for future research into how they complete tasks, and learn and make decisions, both independently and with a human social partner.", + "subject": [], + "keywords": [] + }, + { + "title": "Ancient Mongolian aurochs genomes reveal sustained introgression and management in East Asia", + "author": "Katherine Brunson, Kelsey E. Witt, Susan Monge, Sloan Williams, David Peede, Davaakhuu Odsuren, Dashzeveg Bukhchuluun, Asa Cameron, Paul Szpak, Chunag Amartuvshin, William Honeychurch, Joshua Wright, Sarah Pleuger, Myagmar Erdene, Dashtseveg Tumen, Leland Rogers, Dorjpurev Khatanbaatar, Byambatseren Batdalai, Ganbaatar Galdan, Lisa Janz", + "publisher": "Cold Spring Harbor Laboratory", + "url": "http://dx.doi.org/10.1101/2023.08.10.552443", + "doi": "10.1101/2023.08.10.552443", + "year": 2023, + "month": 8, + "abstract": "AbstractSocieties in East Asia have utilized domesticated cattle for over 5000 years, but the genetic history of cattle in East Asia remains understudied. Genome-wide analyses of 23 ancient Mongolian cattle reveal that East Asian aurochs and ancient East Asian taurine cattle are closely related, but neither are closely related to any modern East Asian breeds. We observe binary variation in aurochs diet throughout the early Neolithic, and genomic evidence shows millennia of sustained male-dominated introgression. We identify a unique connection between ancient Mongolian aurochs and the European Hereford breed. These results point to the likelihood of human management of aurochs in Northeast Asia prior to and during the initial adoption of taurine cattle pastoralism.One-Sentence SummaryAncient interbreeding of East Asian aurochs and cattle suggests management, but leaves no signature in modern eastern breeds.", + "subject": [], + "keywords": [] + }, + { + "title": "Fiber supplementation protects from antibiotic-induced gut microbiome dysbiosis by modulating gut redox potential", + "author": "Swathi Penumutchu, Benjamin J. Korry, Katharine Hewlett, Peter Belenky", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1038/s41467-023-40553-x", + "doi": "10.1038/s41467-023-40553-x", + "year": 2023, + "month": 8, + "abstract": "AbstractAntibiotic-induced gut dysbiosis (AID) is a frequent and serious side effect of antibiotic use and mitigating this dysbiosis is a critical therapeutic target. We propose that the host diet can modulate the chemical environment of the gut resulting in changes to the structure and function of the microbiome during antibiotic treatment. Gut dysbiosis is typically characterized by increases in aerobic respiratory bacterial metabolism, redox potential, and abundance of Proteobacteria. In this study, we explore dietary fiber supplements as potential modulators of the chemical environment in the gut to reduce this pattern of dysbiosis. Using defined-diets and whole-genome sequencing of female murine microbiomes during diet modulation and antibiotic treatment, we find that fiber prebiotics significantly reduced the impact of antibiotic treatment on microbiome composition and function. We observe reduced abundance of aerobic bacteria as well as metabolic pathways associated with oxidative metabolism. These metatranscriptomic results are corroborated by chemical measurements of eH and pH suggesting that fiber dampens the dysbiotic effects of antibiotics. This work indicates that fiber may act as a potential therapeutic for AID by modulating bacterial metabolism in the gut to prevent an increase in redox potential and protect commensal microbes during antibiotic treatment.", + "subject": [], + "keywords": [] + }, + { + "title": "Abstract cognitive maps of social network structure aid adaptive inference", + "author": "Jae-Young Son, Apoorva Bhandari, Oriel FeldmanHall", + "publisher": "Center for Open Science", + "url": "http://dx.doi.org/10.31234/osf.io/qpa2g", + "doi": "10.31234/osf.io/qpa2g", + "year": 2023, + "month": 5, + "abstract": "Social navigation—such as anticipating where gossip may spread, or identifying which acquaintances can help land a job—relies on knowing how people are connected within their larger social communities. Problematically, for most social networks, the space of possible relationships is too vast to observe and memorize. Indeed, people's knowledge of these social relations is well known to be biased and error-prone. Here we reveal that these biased representations reflect a fundamental computation that abstracts over individual relationships to enable principled inferences about unseen relationships. We propose a theory of network representation that explains how people learn inferential cognitive maps of social relations from direct observation, what kinds of knowledge structures emerge as a consequence, and why it can be beneficial to encode systematic biases into social cognitive maps. Leveraging simulations, laboratory experiments, and ‘field data’ from a real-world network, we find that people abstract observations of direct relations (e.g., friends) into inferences of multistep relations (e.g., friends-of-friends). This multistep abstraction mechanism enables people to discover and represent complex social network structure, affording adaptive inferences across a variety of contexts, including friendship, trust, and advice-giving. Moreover, this multistep abstraction mechanism unifies a variety of otherwise puzzling empirical observations about social behavior. Our proposal generalizes the theory of cognitive maps to the fundamental computational problem of social inference, presenting a powerful framework for understanding the workings of a predictive mind operating within a complex social world.", + "subject": [], + "keywords": [] + }, + { + "title": "Oligotrophic waters of the Northwest Atlantic support taxonomically diverse diatom communities that are distinct from coastal waters", + "author": "Samantha P. Setta, Sarah Lerch, Bethany D. Jenkins, Sonya T. Dyhrman, Tatiana A. Rynearson", + "publisher": "Wiley", + "url": "http://dx.doi.org/10.1111/jpy.13388", + "doi": "10.1111/jpy.13388", + "year": 2023, + "month": 9, + "abstract": "AbstractDiatoms are important components of the marine food web and one of the most species‐rich groups of phytoplankton. The diversity and composition of diatoms in eutrophic nearshore habitats have been well documented due to the outsized influence of diatoms on coastal ecosystem functioning. In contrast, patterns of both diatom diversity and community composition in offshore oligotrophic regions where diatom biomass is low have been poorly resolved. To compare the diatom diversity and community composition in oligotrophic and eutrophic waters, diatom communities were sampled along a 1,250 km transect from the oligotrophic Sargasso Sea to the coastal waters of the northeast US shelf. Diatom community composition was determined by amplifying and sequencing the 18S rDNA V4 region. Of the 301 amplicon sequence variants (ASVs) identified along the transect, the majority (70%) were sampled exclusively from oligotrophic waters of the Gulf Stream and Sargasso Sea and included the genera Bacteriastrum, Haslea, Hemiaulus, Pseudo‐nitzschia, and Nitzschia. Diatom ASV richness did not vary along the transect, indicating that the oligotrophic Sargasso Sea and Gulf Stream are occupied by a diverse diatom community. Although ASV richness was similar between oligotrophic and coastal waters, diatom community composition in these regions differed significantly and was correlated with temperature and phosphate, two environmental variables known to influence diatom metabolism and geographic distribution. In sum, oligotrophic waters of the western North Atlantic harbor diverse diatom assemblages that are distinct from coastal regions, and these open ocean diatoms warrant additional study, as they may play critical roles in oligotrophic ecosystems.", + "subject": [], + "keywords": [] + }, + { + "title": "Brain Glutamate Dynamics Predict Positive Agency in Healthy Women", + "author": "Tara L. White, Meghan A. Gonsalves, Ashley D. Harris, Edward G. Walsh, Hannah E. Joyce", + "publisher": "Research Square Platform LLC", + "url": "http://dx.doi.org/10.21203/rs.3.rs-3021527/v1", + "doi": "10.21203/rs.3.rs-3021527/v1", + "year": 2023, + "month": 6, + "abstract": "Abstract\n Contributions of brain glutamate to conscious emotion are not well understood. Here we evaluate the relationship of experimentally-induced change in neocortical glutamate (△Glu) and subjective states in well individuals. Drug challenge with d-amphetamine (AMP; 20 mg oral), methamphetamine (MA; Desoxyn®, 20 mg oral), and placebo (PBO) was conducted on three separate test days in a within-subjects double blind design. Proton magnetic resonance spectroscopy (MRS) quantified neurometabolites in the right dorsal anterior cingulate cortex (dACC) 140-150 m post-drug and PBO. Subjective states were assessed at half hour intervals over 5.5-hours on each session, yielding 3,792 responses per participant (91,008 responses overall, N=24 participants). Self-reports were reduced by principal components analysis to a single factor score of AMP- and MA-induced Positive Agency (△PA) in each participant. We found drug-induced △Glu related positively with △PA (△GluMA r=+.44, p<.05, N=21), with large effects in females (△GluMA r=+.52, p<.05; △GluAMP r=+.61, p<.05, N=11). States related to △Glu in females included rise in subjective stimulation, vigor, friendliness, elation, positive mood, positive affect (r’s=+.51 to +.74, p<.05), and alleviation of anxiety (r=-.61, p<.05, N=11). Self-reports correlated with DGlu to the extent they loaded on △PA (r=.95 AMP, p=5x10-10; r=.63 MA, p=.0015, N=11), indicating coherence of △Glu effects. Timing data indicated Glu shaped emotion both concurrently and prospectively, with no relationship to pre-MRS emotion (△GluAMP r=+.59 to +.65, p’s<.05; △GluMA r=+.53, p<.05, N=11). Together these findings indicate substantive, mechanistic contributions of neocortical Glu to positive agentic states in healthy individuals, most readily observed in women.", + "subject": [], + "keywords": [] + }, + { + "title": "TheMUC19gene in Denisovans, Neanderthals, and Modern Humans: An Evolutionary History of Recurrent Introgression and Natural Selection", + "author": "Fernando A. Villanea, David Peede, Eli J. Kaufman, Valeria Añorve-Garibay, Kelsey E. Witt, Viridiana Villa-Islas, Roberta Zeloni, Davide Marnetto, Priya Moorjani, Flora Jay, Paul N. Valdmanis, María C. Ávila-Arcos, Emilia Huerta-Sánchez", + "publisher": "Cold Spring Harbor Laboratory", + "url": "http://dx.doi.org/10.1101/2023.09.25.559202", + "doi": "10.1101/2023.09.25.559202", + "year": 2023, + "month": 9, + "abstract": "AbstractAll humans carry a small fraction of archaic ancestry across the genome, the legacy of gene flow from Neanderthals, Denisovans, and other hominids into the ancestors of modern humans. While the effects of Neanderthal ancestry on human fitness and health have been explored more thoroughly, there are fewer examples of adaptive introgression of Denisovan variants. Here, we study the geneMUC19, for which some modern humans carry aDenisovan-likehaplotype.MUC19is a mucin, a glycoprotein that forms gels with various biological functions, from lubrication to immunity. We find the diagnostic variants for theDenisovan-like MUC19haplotype at high frequencies in admixed Latin American individuals among global population, and at highest frequency in 23 ancient Indigenous American individuals, all predating population admixture with Europeans and Africans. We find that some Neanderthals––Vindija and Chagyrskaya––carry theDenisovan-like MUC19haplotype, and that it was likely introgressed into human populations through Neanderthal introgression rather than Denisovan introgression. Finally, we find that theDenisovan-like MUC19haplotype carries a higher copy number of a 30 base-pair variable number tandem repeat relative to theHuman-likehaplotype, and that copy numbers of this repeat are exceedingly high in American populations. Our results suggest that theDenisovan-like MUC19haplotype served as the raw genetic material for positive selection as American populations adapted to novel environments during their movement from Beringia into North and then South America.", + "subject": [], + "keywords": [] + }, + { + "title": "Timing and cell specificity of senescence drives postnatal lung development and injury", + "author": "Hongwei Yao, Joselynn Wallace, Abigail L. Peterson, Alejandro Scaffa, Salu Rizal, Katy Hegarty, Hajime Maeda, Jason L. Chang, Nathalie Oulhen, Jill A. Kreiling, Kelsey E. Huntington, Monique E. De Paepe, Guilherme Barbosa, Phyllis A. Dennery", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1038/s41467-023-35985-4", + "doi": "10.1038/s41467-023-35985-4", + "year": 2023, + "month": 1, + "abstract": "AbstractSenescence causes age-related diseases and stress-related injury. Paradoxically, it is also essential for organismal development. Whether senescence contributes to lung development or injury in early life remains unclear. Here, we show that lung senescence occurred at birth and decreased throughout the saccular stage in mice. Reducing senescent cells at this stage disrupted lung development. In mice (<12 h old) exposed to hyperoxia during the saccular stage followed by air recovery until adulthood, lung senescence increased particularly in type II cells and secondary crest myofibroblasts. This peaked during the alveolar stage and was mediated by the p53/p21 pathway. Decreasing senescent cells during the alveolar stage attenuated hyperoxia-induced alveolar and vascular simplification. Conclusively, early programmed senescence orchestrates postnatal lung development whereas later hyperoxia-induced senescence causes lung injury through different mechanisms. This defines the ontogeny of lung senescence and provides an optimal therapeutic window for mitigating neonatal hyperoxic lung injury by inhibiting senescence.", + "subject": [], + "keywords": [] + }, + { + "title": "Fractional Path Integral Monte Carlo", + "author": "Mamikon Gulian, Haobo Yang, Brenda M. Rubenstein", + "publisher": "arXiv", + "url": "https://arxiv.org/abs/1709.09089", + "doi": "10.48550/ARXIV.1709.09089", + "year": 2018, + "month": 5, + "abstract": "Fractional derivatives are nonlocal differential operators of real order that often appear in models of anomalous diffusion and a variety of nonlocal phenomena. Recently, a version of the Schrödinger Equation containing a fractional Laplacian has been proposed. In this work, we develop a Fractional Path Integral Monte Carlo algorithm that can be used to study the finite temperature behavior of the time-independent Fractional Schrödinger Equation for a variety of potentials. In so doing, we derive an analytic form for the finite temperature fractional free particle density matrix and demonstrate how it can be sampled to acquire new sets of particle positions. We employ this algorithm to simulate both the free particle and $^{4}$He (Aziz) Hamiltonians. We find that the fractional Laplacian strongly encourages particle delocalization, even in the presence of interactions, suggesting that fractional Hamiltonians may manifest atypical forms of condensation. Our work opens the door to studying fractional Hamiltonians with arbitrarily complex potentials that escape analytical solutions.", + "keywords": [] + }, + { + "title": "How Deep is the Feature Analysis underlying Rapid Visual Categorization?", + "author": "Sven Eberhardt, Jonah Cader, Thomas Serre", + "publisher": "arXiv", + "url": "https://arxiv.org/abs/1606.01167", + "doi": "10.48550/ARXIV.1606.01167", + "year": 2016, + "month": 6, + "abstract": "Rapid categorization paradigms have a long history in experimental psychology: Characterized by short presentation times and speedy behavioral responses, these tasks highlight the efficiency with which our visual system processes natural object categories. Previous studies have shown that feed-forward hierarchical models of the visual cortex provide a good fit to human visual decisions. At the same time, recent work in computer vision has demonstrated significant gains in object recognition accuracy with increasingly deep hierarchical architectures. But it is unclear how well these models account for human visual decisions and what they may reveal about the underlying brain processes. We have conducted a large-scale psychophysics study to assess the correlation between computational models and human participants on a rapid animal vs. non-animal categorization task. We considered visual representations of varying complexity by analyzing the output of different stages of processing in three state-of-the-art deep networks. We found that recognition accuracy increases with higher stages of visual processing (higher level stages indeed outperforming human participants on the same task) but that human decisions agree best with predictions from intermediate stages. Overall, these results suggest that human participants may rely on visual features of intermediate complexity and that the complexity of visual representations afforded by modern deep network models may exceed those used by human participants during rapid categorization.", + "keywords": [] + }, + { + "title": "Low-energy (0.7-74 keV) nuclear recoil calibration of the LUX dark matter experiment using D-D neutron scattering kinematics", + "author": "undefined undefined, D. S. Akerib, S. Alsum, H. M. Araújo, X. Bai, A. J. Bailey, J. Balajthy, P. Beltrame, E. P. Bernard, A. Bernstein, T. P. Biesiadzinski, E. M. Boulton, A. Bradley, R. Bramante, P. Brás, D. Byram, S. B. Cahn, M. C. Carmona-Benitez, C. Chan, J. J. Chapman, A. A. Chiller, C. Chiller, A. Currie, J. E. Cutter, T. J. R. Davison, L. de Viveiros, A. Dobi, J. E. Y. Dobson, E. Druszkiewicz, B. N. Edwards, C. H. Faham, S. Fiorucci, R. J. Gaitskell, V. M. Gehman, C. Ghag, K. R. Gibson, M. G. D. Gilchriese, C. R. Hall, M. Hanhardt, S. J. Haselschwardt, S. A. Hertel, D. P. Hogan, M. Horn, D. Q. Huang, C. M. Ignarra, M. Ihm, R. G. Jacobsen, W. Ji, K. Kamdin, K. Kazkaz, D. Khaitan, R. Knoche, N. A. Larsen, C. Lee, B. G. Lenardo, K. T. Lesko, A. Lindote, M. I. Lopes, D. C. Malling, A. Manalaysay, R. L. Mannino, M. F. Marzioni, D. N. McKinsey, D. M. Mei, J. Mock, M. Moongweluwan, J. A. Morad, A. St. J. Murphy, C. Nehrkorn, H. N. Nelson, F. Neves, K. O'Sullivan, K. C. Oliver-Mallory, K. J. Palladino, M. Pangilinan, E. K. Pease, P. Phelps, L. Reichhart, C. A. Rhyne, S. Shaw, T. A. Shutt, C. Silva, M. Solmaz, V. N. Solovov, P. Sorensen, S. Stephenson, T. J. Sumner, M. Szydagis, D. J. Taylor, W. C. Taylor, B. P. Tennyson, P. A. Terman, D. R. Tiedt, W. H. To, M. Tripathi, L. Tvrznikova, S. Uvarov, J. R. Verbus, R. C. Webb, J. T. White, T. J. Whitis, M. S. Witherell, F. L. H. Wolfs, J. Xu, K. Yazdani, S. K. Young, C. Zhang", + "publisher": "arXiv", + "url": "https://arxiv.org/abs/1608.05381", + "doi": "10.48550/ARXIV.1608.05381", + "year": 2016, + "month": 10, + "abstract": "The Large Underground Xenon (LUX) experiment is a dual-phase liquid xenon time projection chamber (TPC) operating at the Sanford Underground Research Facility in Lead, South Dakota. A calibration of nuclear recoils in liquid xenon was performed $\\textit{in situ}$ in the LUX detector using a collimated beam of mono-energetic 2.45 MeV neutrons produced by a deuterium-deuterium (D-D) fusion source. The nuclear recoil energy from the first neutron scatter in the TPC was reconstructed using the measured scattering angle defined by double-scatter neutron events within the active xenon volume. We measured the absolute charge ($Q_{y}$) and light ($L_{y}$) yields at an average electric field of 180 V/cm for nuclear recoil energies spanning 0.7 to 74 keV and 1.1 to 74 keV, respectively. This calibration of the nuclear recoil signal yields will permit the further refinement of liquid xenon nuclear recoil signal models and, importantly for dark matter searches, clearly demonstrates measured ionization and scintillation signals in this medium at recoil energies down to $\\mathcal{O}$(1 keV).", + "keywords": [] + }, + { + "title": "Neuronal Synchrony in Complex-Valued Deep Networks", + "author": "David P. Reichert, Thomas Serre", + "publisher": "arXiv", + "url": "https://arxiv.org/abs/1312.6115", + "doi": "10.48550/ARXIV.1312.6115", + "year": 2014, + "month": 3, + "abstract": "Deep learning has recently led to great successes in tasks such as image recognition (e.g Krizhevsky et al., 2012). However, deep networks are still outmatched by the power and versatility of the brain, perhaps in part due to the richer neuronal computations available to cortical circuits. The challenge is to identify which neuronal mechanisms are relevant, and to find suitable abstractions to model them. Here, we show how aspects of spike timing, long hypothesized to play a crucial role in cortical information processing, could be incorporated into deep networks to build richer, versatile representations. We introduce a neural network formulation based on complex-valued neuronal units that is not only biologically meaningful but also amenable to a variety of deep learning frameworks. Here, units are attributed both a firing rate and a phase, the latter indicating properties of spike timing. We show how this formulation qualitatively captures several aspects thought to be related to neuronal synchrony, including gating of information processing and dynamic binding of distributed object representations. Focusing on the latter, we demonstrate the potential of the approach in several simple experiments. Thus, neuronal synchrony could be a flexible mechanism that fulfills multiple functional roles in deep networks.", + "keywords": [] + }, + { + "title": "Functional Mediation Analysis with an Application to Functional Magnetic Resonance Imaging Data", + "author": "Yi Zhao, Xi Luo, Martin Lindquist, Brian Caffo", + "publisher": "arXiv", + "url": "https://arxiv.org/abs/1805.06923", + "doi": "10.48550/ARXIV.1805.06923", + "year": 2018, + "month": 5, + "abstract": "Causal mediation analysis is widely utilized to separate the causal effect of treatment into its direct effect on the outcome and its indirect effect through an intermediate variable (the mediator). In this study we introduce a functional mediation analysis framework in which the three key variables, the treatment, mediator, and outcome, are all continuous functions. With functional measures, causal assumptions and interpretations are not immediately well-defined. Motivated by a functional magnetic resonance imaging (fMRI) study, we propose two functional mediation models based on the influence of the mediator: (1) a concurrent mediation model and (2) a historical mediation model. We further discuss causal assumptions, and elucidate causal interpretations. Our proposed models enable the estimation of individual causal effect curves, where both the direct and indirect effects vary across time. Applied to a task-based fMRI study, we illustrate how our functional mediation framework provides a new perspective for studying dynamic brain connectivity. The R package cfma is available on CRAN.", + "keywords": [] + } +] diff --git a/scripts/sortedPublications/manuallyFixing.json b/scripts/sortedPublications/manuallyFixing.json new file mode 100644 index 0000000..a2af7da --- /dev/null +++ b/scripts/sortedPublications/manuallyFixing.json @@ -0,0 +1,5009 @@ +[ + { + "title": "Granger Mediation Analysis of Multiple Time Series with an Application to fMRI", + "author": "Xi Luo", + "publisher": "Open Science Framework", + "url": "https://osf.io/9a3xq/", + "doi": "10.17605/OSF.IO/9A3XQ", + "year": 2017, + "month": 9, + "abstract": "It becomes increasingly popular to perform mediation analysis for complex data from sophisticated experimental studies. In this paper, we present Granger Mediation Analysis (GMA), a new framework for causal mediation analysis of multiple time series. This framework is motivated by a functional magnetic resonance imaging(fMRI) experiment where we are interested in estimating the mediation effects between a randomized stimulus timeseries and brain activity time series from two brain regions. The stable unit treatment assumption for causal mediation analysis is thus unrealistic for this type of time series data. To address this challenge, our framework integrates two types of models: causal mediation analysis across the variables and vector autoregressive models across the temporal observations. We further extend this framework to handle multilevel data to address individual variability and correlated errors between the mediator and the outcome variables. These models not only provide valid causal mediation for time series data but also model the causal dynamics across time. We show that the modeling parameters in our models are identifiable, and we develop computationally efficient methods to maximize the likelihood-based optimization criteria. Simulation studies show that our method reduces the estimation bias and improve statistical power, compared to existing approaches. On a real fMRI data set, our approach not only infers the causal effects ofbrain pathways but accurately captures the feedback effect of the outcome region on the mediator region.Key words:Spatiotemporal dependence; Structural equation modeling; Vector autoregressive models.", + "keywords": [] + }, + { + "title": "Pathway Lasso: Estimate and Select Sparse Mediation Pathways with High Dimensional Mediators", + "author": "Xi Luo", + "publisher": "Open Science Framework", + "url": "https://osf.io/vzsr4/", + "doi": "10.17605/OSF.IO/VZSR4", + "year": 2017, + "month": 9, + "abstract": "In many scientific studies, it becomes increasingly important to delineate the causal pathways through a large number of mediators, such as genetic and brain mediators. Structural equation modeling (SEM) is a popular technique to estimate the pathway effects, commonly expressed as products of coefficients. However, it becomes unstable to fit such models with high dimensional mediators, especially for a general setting where all the mediators are causally dependent but the exact causal relationships between them are unknown. This paper proposes a sparse mediation model using a regularized SEM approach, where sparsity here means that a small number of mediators have nonzero mediation effects between a treatment and an outcome. To address the model selection challenge, we innovate by introducing a new penalty calledPathway Lasso.This penalty function is a convex relaxation of the non-convex product function, and it enables a computationally tractable optimization criterion to estimate and select many pathway effects simultaneously. We develop a fast ADMM-type algorithm to compute the model parameters,and we show that the iterative updates can be expressed in closed form. On both simulated data and a real fMRI dataset, the proposed approach yields higher pathway selection accuracy and lower estimation bias than other competing methods.", + "keywords": [] + }, + { + "title": "Minimax Optimal Variable Clustering in G-models via Cord", + "author": "Xi Luo", + "publisher": "Open Science Framework", + "url": "https://osf.io/enc32/", + "doi": "10.17605/OSF.IO/ENC32", + "year": 2017, + "month": 9, + "abstract": "The goal of variable clustering is to partition a random vector X∈R pin sub-groups of similar probabilistic behavior. Popular methods such as hierarchical clustering orK-means are algorith-mic procedures applied to observations onX, while no population level target is defined prior to estimation. We take a different view in this paper, where we propose and investigate model based variable clustering. We consider three models, of increasing level of complex-ity, termed generically G-models, with G standing for the partition to be estimated. Motivated by the potential lack of identifiability of the G-latent models, which are currently used in problems involving variable clustering, we introduce two new classes of models, theG-exchangeable and theG-block covariance models. We show that both classes are identifiable, for any distribution of X.Our focus is on clusters that are invariant with respect to unknown monotone transformations of the data, and that can be estimated ina computationally feasible manner. Both desiderata can be met if the clusters correspond to blocks in the copula correlation matrix ofX, assumed to have a Gaussian copula distribution. This motivates the introduction of a new similarity metric for cluster membership,CORD, and a homonymous method for cluster estimation. Central to our work is the derivation of the minimax value of the CORD cluster separation for exact partition recovery. We obtained the surprising result that this value is of order plog(p)/n, irrespective of the number of clusters, or of the size of the smallest cluster. Our new procedure,CORD, available on CRAN, achieves this bound, is easy to implement and has computational complexity that is polynomial inp.", + "keywords": [] + }, + { + "title": "Estimating Causal Mediation Effects under Correlated Errors", + "author": "Xi Luo", + "publisher": "Open Science Framework", + "url": "https://osf.io/da6uf/", + "doi": "10.17605/OSF.IO/DA6UF", + "year": 2017, + "month": 9, + "abstract": "Causal mediation analysis usually requires strong assumptions, such as ignorability of the mediator, which may not hold in many social and scientific studies.Motivated by a multilevel randomized treatment experiment using functional magnetic resonance imaging (fMRI), this paper proposes a multilevel causal mediation frame-work for data with hierarchically nested structure, and this framework provides valid inference even if structured unmeasured confounding for the mediator and outcome is present. For the first-level data, we propose a linear structural equation model fora continuous mediator and a continuous outcome, both of which may contain correlated additive errors. A likelihood-based approach is proposed to estimate the model coefficients. The analysis of our estimator characterizes the nonidentifiability issue due to the correlation parameter. To address the identifiability issue and model the variability in multilevel data, we propose to incorporate multiple first-level mediation models across different levels in a unified multilevel mediation framework. All the model coefficients are estimated simultaneously by our optimization algorithms, with innovation to estimate the unknown correlation parameter from data, instead of per-forming sensitivity analysis. Our asymptotic analysis shows that the correlation parameter is identifiable, and our estimates for the mediation effects are consistent with the parametric convergence rates. Using extensive simulated data and a real fMRI dataset, we demonstrate the improvement of our approaches over existing methods.", + "keywords": [] + }, + { + "title": "3D modeling of electric fields in the LUX detector", + "author": "D.S. Akerib, S. Alsum, H.M. Araújo, X. Bai, A.J. Bailey, J. Balajthy, P. Beltrame, E.P. Bernard, A. Bernstein, T.P. Biesiadzinski, E.M. Boulton, P. Brás, D. Byram, S.B. Cahn, M.C. Carmona-Benitez, C. Chan, A. Currie, J.E. Cutter, T.J.R. Davison, A. Dobi, E. Druszkiewicz, B.N. Edwards, S.R. Fallon, A. Fan, S. Fiorucci, R.J. Gaitskell, J. Genovesi, C. Ghag, M.G.D. Gilchriese, C.R. Hall, M. Hanhardt, S.J. Haselschwardt, S.A. Hertel, D.P. Hogan, M. Horn, D.Q. Huang, C.M. Ignarra, R.G. Jacobsen, W. Ji, K. Kamdin, K. Kazkaz, D. Khaitan, R. Knoche, N.A. Larsen, B.G. Lenardo, K.T. Lesko, A. Lindote, M.I. Lopes, A. Manalaysay, R.L. Mannino, M.F. Marzioni, D.N. McKinsey, D.-M. Mei, J. Mock, M. Moongweluwan, J.A. Morad, A.St.J. Murphy, C. Nehrkorn, H.N. Nelson, F. Neves, K. O'Sullivan, K.C. Oliver-Mallory, K.J. Palladino, E.K. Pease, C. Rhyne, S. Shaw, T.A. Shutt, C. Silva, M. Solmaz, V.N. Solovov, P. Sorensen, T.J. Sumner, M. Szydagis, D.J. Taylor, W.C. Taylor, B.P. Tennyson, P.A. Terman, D.R. Tiedt, W.H. To, M. Tripathi, L. Tvrznikova, S. Uvarov, V. Velan, J.R. Verbus, R.C. Webb, J.T. White, T.J. Whitis, M.S. Witherell, F.L.H. Wolfs, J. Xu, K. Yazdani, S.K. Young, C. Zhang", + "publisher": "IOP Publishing", + "url": "http://dx.doi.org/10.1088/1748-0221/12/11/P11022", + "doi": "10.1088/1748-0221/12/11/p11022", + "year": 2017, + "month": 11, + "abstract": "This work details the development of a three-dimensional (3D) electric field model for the LUX detector. The detector took data to search for weakly interacting massive particles (WIMPs) during two periods. After the first period completed, a time-varying non-uniform negative charge developed in the polytetrafluoroethylene (PTFE) panels that define the radial boundary of the detector's active volume. This caused electric field variations in the detector in time, depth and azimuth, generating an electrostatic radially-inward force on electrons on their way upward to the liquid surface. To map this behavior, 3D electric field maps of the detector's active volume were generated on a monthly basis. This was done by fitting a model built in COMSOL Multiphysics to the uniformly distributed calibration data that were collected on a regular basis. The modeled average PTFE charge density increased over the course of the exposure from -3.6 to −5.5 μC/m2. From our studies, we deduce that the electric field magnitude varied locally while the mean value of the field of ∼200 V/cm remained constant throughout the exposure. As a result of this work the varying electric fields and their impact on event reconstruction and discrimination were successfully modeled.", + "subject": [], + "keywords": [] + }, + { + "title": "Proposed low-energy absolute calibration of nuclear recoils in a dual-phase noble element TPC using D-D neutron scattering kinematics", + "author": "J.R. Verbus, C.A. Rhyne, D.C. Malling, M. Genecov, S. Ghosh, A.G. Moskowitz, S. Chan, J.J. Chapman, L. de Viveiros, C.H. Faham, S. Fiorucci, D.Q. Huang, M. Pangilinan, W.C. Taylor, R.J. Gaitskell", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.nima.2017.01.053", + "doi": "10.1016/j.nima.2017.01.053", + "year": 2017, + "month": 4, + "abstract": "We propose a new technique for the calibration of nuclear recoils in large noble element dual-phase time projection chambers used to search for WIMP dark matter in the local galactic halo. This technique provides an measurement of the low-energy nuclear recoil response of the target media using the measured scattering angle between multiple neutron interactions within the detector volume. The low-energy reach and reduced systematics of this calibration have particular significance for the low-mass WIMP sensitivity of several leading dark matter experiments. Multiple strategies for improving this calibration technique are discussed, including the creation of a new type of quasi-monoenergetic neutron source with a minimum possible peak energy of 272 keV. We report results from a time-of-flight-based measurement of the neutron energy spectrum produced by an Adelphi Technology, Inc. DD108 neutron generator, confirming its suitability for the proposed nuclear recoil calibration.", + "subject": [], + "keywords": [] + }, + { + "title": "First Results from the LUX Dark Matter Experiment at the Sanford Underground Research Facility", + "author": "D. S. Akerib, H. M. Araújo, X. Bai, A. J. Bailey, J. Balajthy, S. Bedikian, E. Bernard, A. Bernstein, A. Bolozdynya, A. Bradley, D. Byram, S. B. Cahn, M. C. Carmona-Benitez, C. Chan, J. J. Chapman, A. A. Chiller, C. Chiller, K. Clark, T. Coffey, A. Currie, A. Curioni, S. Dazeley, L. de Viveiros, A. Dobi, J. Dobson, E. M. Dragowsky, E. Druszkiewicz, B. Edwards, C. H. Faham, S. Fiorucci, C. Flores, R. J. Gaitskell, V. M. Gehman, C. Ghag, K. R. Gibson, M. G. D. Gilchriese, C. Hall, M. Hanhardt, S. A. Hertel, M. Horn, D. Q. Huang, M. Ihm, R. G. Jacobsen, L. Kastens, K. Kazkaz, R. Knoche, S. Kyre, R. Lander, N. A. Larsen, C. Lee, D. S. Leonard, K. T. Lesko, A. Lindote, M. I. Lopes, A. Lyashenko, D. C. Malling, R. Mannino, D. N. McKinsey, D.-M. Mei, J. Mock, M. Moongweluwan, J. Morad, M. Morii, A. St. J. Murphy, C. Nehrkorn, H. Nelson, F. Neves, J. A. Nikkel, R. A. Ott, M. Pangilinan, P. D. Parker, E. K. Pease, K. Pech, P. Phelps, L. Reichhart, T. Shutt, C. Silva, W. Skulski, C. J. Sofka, V. N. Solovov, P. Sorensen, T. Stiegler, K. O’Sullivan, T. J. Sumner, R. Svoboda, M. Sweany, M. Szydagis, D. Taylor, B. Tennyson, D. R. Tiedt, M. Tripathi, S. Uvarov, J. R. Verbus, N. Walsh, R. Webb, J. T. White, D. White, M. S. Witherell, M. Wlasenko, F. L. H. Wolfs, M. Woods, C. Zhang, undefined undefined", + "publisher": "American Physical Society (APS)", + "url": "http://dx.doi.org/10.1103/PhysRevLett.112.091303", + "doi": "10.1103/physrevlett.112.091303", + "year": 2014, + "month": 3, + "abstract": "The Large Underground Xenon (LUX) experiment is a dual-phase xenon time-projection chamber operating at the Sanford Underground Research Facility (Lead, South Dakota). The LUX cryostat was filled for the first time in the underground laboratory in February 2013. We report results of the first WIMP search data set, taken during the period from April to August 2013, presenting the analysis of 85.3 live days of data with a fiducial volume of 118 kg. A profile-likelihood analysis technique shows our data to be consistent with the background-only hypothesis, allowing 90% confidence limits to be set on spin-independent WIMP-nucleon elastic scattering with a minimum upper limit on the cross section of 7.6×1\u20620−46  cm\u20622 at a WIMP mass of 33  GeV/c\u20622. We find that the LUX data are in disagreement with low-mass WIMP signal interpretations of the results from several recent direct detection experiments.", + "subject": [], + "keywords": [] + }, + { + "title": "Feeding by Antarctic krill Euphausia superba in the West Antarctic Peninsula: differences between fjords and open waters", + "author": "AC Cleary, EG Durbin, MC Casas", + "publisher": "Inter-Research Science Center", + "url": "http://dx.doi.org/10.3354/meps12568", + "doi": "10.3354/meps12568", + "year": 2018, + "month": 5, + "abstract": "Antarctic krill Euphausia superba are key components of Antarctic ecosystems, serving as the major prey item for most of the megafauna in the region. Coastal fjords along the West Antarctic Peninsula have been identified as biological hotspots, areas in which high biomasses of both E. superba and their megafauna predators are consistently observed. We investigated feeding by E. superba in fjords and adjacent open waters of the West Antarctic Peninsula. Next generation sequencing of stomach contents from 174 krill indicated a diverse diet, with broad patterns consistent with previous understanding of E. superba feeding. Diatom sequence reads were frequent and abundant, indicating a largely diatom-based diet, while the occasional presence of high abundances of copepod sequence reads suggests carnivory supplemented the diet. Striking differences were observed between the stomach contents of krill collected in fjords and those of krill collected in adjacent open waters. Chaetoceros spp. diatoms made up 71% of the stomach contents sequences of krill collected in fjords, but less than 10% of the stomach contents sequences of krill collected in open waters. These differences could not be explained by differences in the surface water phytoplankton communities, as in both open waters and fjords Chaetoceros spp. made up less than 10% of the surface water sequence read assemblages. These feeding differences highlight the importance of taking into account regional differences in krill feeding when considering E. superba’s roles in Southern Ocean ecosystems, and suggest krill in fjords may make use of vertical structure in phytoplankton assemblages.", + "subject": [], + "keywords": [] + }, + { + "title": "A Bioinformatic Glimpse of Human-Origin Zika Virus Polyprotein", + "author": "Joel K Weltman", + "publisher": "OMICS Publishing Group", + "url": "http://dx.doi.org/10.4172/2161-0703.1000265", + "doi": "10.4172/2161-0703.1000265", + "year": 2017, + "month": -1, + "abstract": "Zika virus (ZIKV) is a single-stranded, positive sense RNA virus [1]. T he Zika virus polyprotein consists of precursors of three structural proteins (capsid, precursor membrane (prM) and envelope (E) protein) and seven major nonstructural proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B, and NS5) [2]. ZIKV causes microcephaly and other birth defects in a significant fraction of gestationally infected infants and causes Guillain–Barré syndrome in a very small percentage of infected adults [3,4]. The major transmitters of ZIKV to humans are Aedes mosquitos, especially species Aedes aegypti [5]. It was recently reported that the set of mutations in polyproteins obtained from ZIKV isolated from humans can be partitioned into two subsets [6]: Exclusive (x) subset and Common (c) subset. Mutations in the x subset occur exclusively in the human host. In contrast, mutations in the c subset occur in ZIKV isolated both from human hosts and from the Aedes mosquito vectors. The present report is focused on identification and proposed immunological significance of the bioinformatically predominant member of the exclusively human (x) subset. It is proposed that the mutations that occurred only in the x subset but not in the c subset may reflect biological processes occurring only in humans but not in mosquitos. Some of these processes may be metabolic, some may be conformational, and some may be immunologic. In the work reported here, an amino acid position with prominent bioinformatic properties is identified within the Zika virus polyprotein and a biologic function of that amino acid position is proposed.", + "subject": [ + "Zika virus", + "ZIKV", + "Polyprotein", + "nonstructural protein", + "NS1", + "Shannon information entropy H", + "Cumulative mutual information", + "cMI", + "Secondary structure", + "ss3", + "Epitopes" + ], + "keywords": [] + }, + { + "title": "Pathogenic variants that alter protein code often disrupt splicing", + "author": "Rachel Soemedi, Kamil J Cygan, Christy L Rhine, Jing Wang, Charlston Bulacan, John Yang, Pinar Bayrak-Toydemir, Jamie McDonald, William G Fairbrother", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1038/ng.3837", + "doi": "10.1038/ng.3837", + "year": 2017, + "month": 4, + "abstract": "The lack of tools to identify causative variants from sequencing data greatly limits the promise of precision medicine. Previous studies suggest that one-third of disease-associated alleles alter splicing. We discovered that the alleles causing splicing defects cluster in disease-associated genes (for example, haploinsufficient genes). We analyzed 4,964 published disease-causing exonic mutations using a massively parallel splicing assay (MaPSy), which showed an 81% concordance rate with splicing in patient tissue. Approximately 10% of exonic mutations altered splicing, mostly by disrupting multiple stages of spliceosome assembly. We present a large-scale characterization of exonic splicing mutations using a new technology that facilitates variant classification and keeps pace with variant discovery.", + "subject": [], + "keywords": [] + }, + { + "title": "Analysis of Active Transport by Fluorescence Recovery after Photobleaching", + "author": "Maria-Veronica Ciocanel, Jill A. Kreiling, James A. Gagnon, Kimberly L. Mowry, Björn Sandstede", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.bpj.2017.02.042", + "doi": "10.1016/j.bpj.2017.02.042", + "year": 2017, + "month": 4, + "abstract": "Fluorescence recovery after photobleaching (FRAP) is a well-established experimental technique to study binding and diffusion of molecules in cells. Although a large number of analytical and numerical models have been developed to extract binding and diffusion rates from FRAP recovery curves, active transport of molecules is typically not included in the existing models that are used to estimate these rates. Here we present a validated numerical method for estimating diffusion, binding/unbinding rates, and active transport velocities using FRAP data that captures intracellular dynamics through partial differential equation models. We apply these methods to transport and localization of mRNA molecules in Xenopus laevis oocytes, where active transport processes are essential to generate developmental polarity. By providing estimates of the effective velocities and diffusion, as well as expected run times and lengths, this approach can help quantify dynamical properties of localizing and nonlocalizing RNA. Our results confirm the distinct transport dynamics in different regions of the cytoplasm, and suggest that RNA movement in both the animal and vegetal directions may influence the timescale of RNA localization in Xenopus oocytes. We also show that model initial conditions extracted from FRAP postbleach intensities prevent underestimation of diffusion, which can arise from the instantaneous bleaching assumption. The numerical and modeling approach presented here to estimate parameters using FRAP recovery data is a broadly applicable tool for systems where intracellular transport is a key molecular mechanism.", + "subject": [], + "keywords": [] + }, + { + "title": "Task-shifting alcohol interventions for HIV+ persons in Kenya: a cost-benefit analysis", + "author": "Omar Galárraga, Burke Gao, Benson N. Gakinya, Debra A. Klein, Richard G. Wamai, John E. Sidle, Rebecca K. Papas", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1186/s12913-017-2169-4", + "doi": "10.1186/s12913-017-2169-4", + "year": 2017, + "month": 3, + "abstract": "Background\nAmong HIV+ patients, alcohol use is a highly prevalent risk factor for both HIV transmission and poor adherence to HIV treatment. The large-scale implementation of effective interventions for treating alcohol problems remains a challenge in low-income countries with generalized HIV epidemics. It is essential to consider an intervention’s cost-effectiveness in dollars-per-health-outcome, and the long-term economic impact —or 'return on investment' in monetary terms.\n\nMethods\nWe conducted a cost-benefit analysis, measuring economic return on investment, of a task-shifted cognitive-behavioral therapy (CBT) intervention delivered by paraprofessionals to reduce alcohol use in a modeled cohort of 13,440 outpatients in Kenya. In our base-case, we estimated the costs and economic benefits from a societal perspective across a six-year time horizon, with a 3% annual discount rate. Costs included all costs associated with training and administering task-shifted CBT therapy. Benefits included the economic impact of lowered HIV incidence as well as the improvements in household and labor-force productivity. We conducted univariate and multivariate probabilistic sensitivity analyses to test the robustness of our results.\n\nResults\nUnder the base case, total costs for CBT rollout was $554,000, the value of benefits were $628,000, and the benefit-to-cost ratio was 1.13. Sensitivity analyses showed that under most assumptions, the benefit-to-cost ratio remained above unity indicating that the intervention was cost-saving (i.e., had positive return on investment). The duration of the treatment effect most effected the results in sensitivity analyses.\n\nConclusions\nCBT can be effectively and economically task-shifted to paraprofessionals in Kenya. The intervention can generate not only reductions in morbidity and mortality, but also economic savings for the health system in the medium and long term. The findings have implications for other countries with generalized HIV epidemics, high prevalence of alcohol consumption, and shortages of mental health professionals.\n\nTrial registration\nThis paper uses data derived from 'Cognitive Behavioral Treatment to Reduce Alcohol Use Among HIV-Infected Kenyans (KHBS)' with ClinicalTrials.gov registration NCT00792519 on 11/17/2008; and preliminary data from 'A Stage 2 Cognitive-behavioral Trial: Reduce Alcohol First in Kenya Intervention' (NCT01503255, registered on 12/16/2011).", + "subject": [], + "keywords": [] + }, + { + "title": "Giant Acceleration of DNA Diffusion in an Array of Entropic Barriers", + "author": "Daniel Kim, Clark Bowman, Jackson T. Del Bonis-O’Donnell, Anastasios Matzavinos, Derek Stein", + "publisher": "American Physical Society (APS)", + "url": "http://dx.doi.org/10.1103/physrevlett.118.048002", + "doi": "10.1103/physrevlett.118.048002", + "year": 2017, + "month": 1, + "abstract": "We investigate with experiments and computer simulations the nonequilibrium dynamics of DNA polymers crossing arrays of entropic barriers in nanofluidic devices in a pressure-driven flow. With increasing driving pressure, the effective diffusivity of DNA rises and then peaks at a value that is many times higher than the equilibrium diffusivity. This is an entropic manifestation of 'giant acceleration of diffusion.' The phenomenon is sensitive to the effective energy landscape; thus, it offers a unique probe of entropic barriers in a system driven away from equilibrium.", + "subject": [], + "keywords": [] + }, + { + "title": "A combined experimental and theoretical study of enthalpy of phase transition and fusion of yttria above 2000 °C using 'drop-n-catch' calorimetry and first-principles calculation", + "author": "D. Kapush, S.V. Ushakov, A. Navrotsky, Q.-J. Hong, H. Liu, A. van de Walle", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.actamat.2016.11.003", + "doi": "10.1016/j.actamat.2016.11.003", + "year": 2017, + "month": 2, + "abstract": "'Drop-n-catch' calorimetry was performed on Y2O3 spheroids of 2–3 mm in diameter, prepared by laser melting of powders. Samples were aerodynamically levitated in a splittable nozzle levitator in air or argon flow, laser heated from ∼2200 to 3000 °C and dropped into a calorimeter at 25 °C, thus measuring their enthalpy as a function of temperature. The fusion enthalpy of cubic Y2O3 was derived from the step in the temperature–enthalpy curve as 119 ± 10 kJ/mol. Calculations performed using density functional theory and molecular dynamics techniques produced the value 127 ± 3 kJ/mol Y2O3. This combined methodology enables accurate determination of the enthalpies of fusion and phase transition of refractory oxides, including those containing lanthanides and actinides.", + "subject": [], + "keywords": [] + }, + { + "title": "Free energy calculation of mechanically unstable but dynamically stabilized bcc titanium", + "author": "Sara Kadkhodaei, Qi-Jun Hong, Axel van de Walle", + "publisher": "American Physical Society (APS)", + "url": "http://dx.doi.org/10.1103/physrevb.95.064101", + "doi": "10.1103/physrevb.95.064101", + "year": 2017, + "month": 2, + "abstract": "The phase diagram of numerous materials of technological importance features high-symmetry high-temperature phases that exhibit phonon instabilities. Leading examples include shape-memory alloys, as well as ferroelectric, refractory, and structural materials. The thermodynamics of these phases have proven challenging to handle by atomistic computational thermodynamic techniques due to the occurrence of constant anharmonicity-driven hopping between local low-symmetry distortions, while maintaining a high-symmetry time-averaged structure. To compute the free energy in such phases, we propose to explore the system's potential-energy surface by discrete sampling of local minima by means of a lattice gas Monte Carlo approach and by continuous sampling by means of a lattice dynamics approach in the vicinity of each local minimum. Given the proximity of the local minima, it is necessary to carefully partition phase space by using a Voronoi tessellation to constrain the domain of integration of the partition function in order to avoid double counting artifacts and enable an accurate harmonic treatment near each local minima. We consider the bcc phase of titanium as a prototypical example to illustrate our approach.", + "subject": [], + "keywords": [] + }, + { + "title": "Tritium calibration of the LUX dark matter experiment", + "author": "D. S. Akerib, H. M. Araújo, X. Bai, A. J. Bailey, J. Balajthy, P. Beltrame, E. P. Bernard, A. Bernstein, T. P. Biesiadzinski, E. M. Boulton, A. Bradley, R. Bramante, S. B. Cahn, M. C. Carmona-Benitez, C. Chan, J. J. Chapman, A. A. Chiller, C. Chiller, A. Currie, J. E. Cutter, T. J. R. Davison, L. de Viveiros, A. Dobi, J. E. Y. Dobson, E. Druszkiewicz, B. N. Edwards, C. H. Faham, S. Fiorucci, R. J. Gaitskell, V. M. Gehman, C. Ghag, K. R. Gibson, M. G. D. Gilchriese, C. R. Hall, M. Hanhardt, S. J. Haselschwardt, S. A. Hertel, D. P. Hogan, M. Horn, D. Q. Huang, C. M. Ignarra, M. Ihm, R. G. Jacobsen, W. Ji, K. Kazkaz, D. Khaitan, R. Knoche, N. A. Larsen, C. Lee, B. G. Lenardo, K. T. Lesko, A. Lindote, M. I. Lopes, D. C. Malling, A. G. Manalaysay, R. L. Mannino, M. F. Marzioni, D. N. McKinsey, D.-M. Mei, J. Mock, M. Moongweluwan, J. A. Morad, A. St. J. Murphy, C. Nehrkorn, H. N. Nelson, F. Neves, K. O’Sullivan, K. C. Oliver-Mallory, R. A. Ott, K. J. Palladino, M. Pangilinan, E. K. Pease, P. Phelps, L. Reichhart, C. Rhyne, S. Shaw, T. A. Shutt, C. Silva, V. N. Solovov, P. Sorensen, S. Stephenson, T. J. Sumner, M. Szydagis, D. J. Taylor, W. Taylor, B. P. Tennyson, P. A. Terman, D. R. Tiedt, W. H. To, M. Tripathi, L. Tvrznikova, S. Uvarov, J. R. Verbus, R. C. Webb, J. T. White, T. J. Whitis, M. S. Witherell, F. L. H. Wolfs, S. K. Young, C. Zhang, undefined undefined", + "publisher": "American Physical Society (APS)", + "url": "http://dx.doi.org/10.1103/physrevd.93.072009", + "doi": "10.1103/physrevd.93.072009", + "year": 2016, + "month": 4, + "abstract": "We present measurements of the electron-recoil (ER) response of the LUX dark matter detector based upon 170 000 highly pure and spatially uniform tritium decays. We reconstruct the tritium energy spectrum using the combined energy model and find good agreement with expectations. We report the average charge and light yields of ER events in liquid xenon at 180 and 105  V/cm and compare the results to the NEST model. We also measure the mean charge recombination fraction and its fluctuations, and we investigate the location and width of the LUX ER band. These results provide input to a reanalysis of the LUX run 3 weakly interacting massive particle search.", + "subject": [], + "keywords": [] + }, + { + "title": "Improved Limits on Scattering of Weakly Interacting Massive Particles from Reanalysis of 2013 LUX Data", + "author": "D. S. Akerib, H. M. Araújo, X. Bai, A. J. Bailey, J. Balajthy, P. Beltrame, E. P. Bernard, A. Bernstein, T. P. Biesiadzinski, E. M. Boulton, A. Bradley, R. Bramante, S. B. Cahn, M. C. Carmona-Benitez, C. Chan, J. J. Chapman, A. A. Chiller, C. Chiller, A. Currie, J. E. Cutter, T. J. R. Davison, L. de Viveiros, A. Dobi, J. E. Y. Dobson, E. Druszkiewicz, B. N. Edwards, C. H. Faham, S. Fiorucci, R. J. Gaitskell, V. M. Gehman, C. Ghag, K. R. Gibson, M. G. D. Gilchriese, C. R. Hall, M. Hanhardt, S. J. Haselschwardt, S. A. Hertel, D. P. Hogan, M. Horn, D. Q. Huang, C. M. Ignarra, M. Ihm, R. G. Jacobsen, W. Ji, K. Kazkaz, D. Khaitan, R. Knoche, N. A. Larsen, C. Lee, B. G. Lenardo, K. T. Lesko, A. Lindote, M. I. Lopes, D. C. Malling, A. Manalaysay, R. L. Mannino, M. F. Marzioni, D. N. McKinsey, D.-M. Mei, J. Mock, M. Moongweluwan, J. A. Morad, A. St. J. Murphy, C. Nehrkorn, H. N. Nelson, F. Neves, K. O’Sullivan, K. C. Oliver-Mallory, R. A. Ott, K. J. Palladino, M. Pangilinan, E. K. Pease, P. Phelps, L. Reichhart, C. Rhyne, S. Shaw, T. A. Shutt, C. Silva, V. N. Solovov, P. Sorensen, S. Stephenson, T. J. Sumner, M. Szydagis, D. J. Taylor, W. Taylor, B. P. Tennyson, P. A. Terman, D. R. Tiedt, W. H. To, M. Tripathi, L. Tvrznikova, S. Uvarov, J. R. Verbus, R. C. Webb, J. T. White, T. J. Whitis, M. S. Witherell, F. L. H. Wolfs, K. Yazdani, S. K. Young, C. Zhang, undefined undefined", + "publisher": "American Physical Society (APS)", + "url": "http://dx.doi.org/10.1103/physrevlett.116.161301", + "doi": "10.1103/physrevlett.116.161301", + "year": 2016, + "month": 4, + "abstract": "We present constraints on weakly interacting massive particles (WIMP)-nucleus scattering from the 2013 data of the Large Underground Xenon dark matter experiment, including 1.4×104  kg day of search exposure. This new analysis incorporates several advances: single-photon calibration at the scintillation wavelength, improved event-reconstruction algorithms, a revised background model including events originating on the detector walls in an enlarged fiducial volume, and new calibrations from decays of an injected tritium \uD835\uDEFD source and from kinematically constrained nuclear recoils down to 1.1 keV. Sensitivity, especially to low-mass WIMPs, is enhanced compared to our previous results which modeled the signal only above a 3 keV minimum energy. Under standard dark matter halo assumptions and in the mass range above 4  GeV \uD835\uDC50−2, these new results give the most stringent direct limits on the spin-independent WIMP-nucleon cross section. The 90% C.L. upper limit has a minimum of 0.6 zb at 33  GeV \uD835\uDC50−2 WIMP mass.", + "subject": [], + "keywords": [] + }, + { + "title": "Cosmological constraints to dark matter with two- and many-body decays", + "author": "Gordon Blackadder, Savvas M. Koushiappas", + "publisher": "American Physical Society (APS)", + "url": "http://dx.doi.org/10.1103/physrevd.93.023510", + "doi": "10.1103/physrevd.93.023510", + "year": 2016, + "month": 1, + "abstract": "We present a study of cosmological implications of generic dark matter decays. We consider two-body and many-body decaying scenarios. In the two-body case the massive particle has a possibly relativistic kick velocity and thus possesses a dynamical equation of state. This has implications to the expansion history of the Universe. We use recent observational data from the cosmic microwave background, baryon acoustic oscillations and supernovae type Ia to obtain constraints on the lifetime of the dark matter particle. We find that for an energy splitting where more than 40% of the dark matter particle energy is transferred to massless, relativistic particles in the two-body case, or more than 50% in the many-body case, lifetimes less than the age of the Universe are excluded at more than 95% confidence. When the energy splitting falls to 10% the lifetime is constrained to be more than roughly half the age.", + "subject": [], + "keywords": [] + }, + { + "title": "Sets and Subsets of Mutating Amino Acids in Zika Virus Polyprotein", + "author": "Joel K Weltman", + "publisher": "OMICS Publishing Group", + "url": "http://dx.doi.org/10.4172/2161-0703.1000247", + "doi": "10.4172/2161-0703.1000247", + "year": 2017, + "month": 1, + "abstract": "Two subsets of Zika virus (ZIKV) polyprotein amino acid positions are identified. One subset (Exclusive) consists of mutating amino acid positions which were found only in polyproteins isolated from ZIKV of human origin. A second subset (Common) consists of mutating amino acid positions which were found both in ZIKV polyproteins of human origin and in ZIKV polyproteins of Aedes species mosquito origin. The dominance of the Exclusive subset in the polyprotein was found to range from the N-terminus structural proteins until non-structural protein NS3. Although no longer greater than the Common subset, elements of the Exclusive subset existed almost to the C-terminus of non-structural protein NS5. These results are considered in the context of reported epitopic and other biological characteristics of ZIKV.", + "subject": [], + "keywords": [] + }, + { + "title": "Shape-based Image Correspondence", + "author": "Berk Sevilmis, Benjamin Kimia", + "publisher": "British Machine Vision Association", + "url": "http://dx.doi.org/10.5244/c.30.66", + "doi": "10.5244/c.30.66", + "year": 2016, + "month": 1, + "abstract": "Current state-of-the-art dense correspondence algorithms establish correspondences between pair of images by searching for a flow field that minimizes the distance between local signatures (eg, color histogram, SIFT descriptor) of aligned pixels while preserving smoothness. Agnostic to the global signatures (eg, object membership, category of object), these local signatures face difficulties in resolving alignment ambiguities when scene content undergoes type and configuration variation. In this paper, we investigate the effect of adding shape correspondence constraints either in the form of pair of corresponding contour fragments or pair of closed curves. We find the shape does not play a significant role in optical flow and stereo correspondence but it does play a significant role when scene content changes are large. We also explore using object proposals as a way of providing shape constraints with encouraging results.", + "subject": [], + "keywords": [] + }, + { + "title": "Interaction between synaptic inhibition and glial-potassium dynamics leads to diverse seizure transition modes in biophysical models of human focal seizures", + "author": "E. C. Y. Ho, Wilson Truccolo", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1007/s10827-016-0615-7", + "doi": "10.1007/s10827-016-0615-7", + "year": 2016, + "month": 8, + "abstract": "How focal seizures initiate and evolve in human neocortex remains a fundamental problem in neuroscience. Here, we use biophysical neuronal network models of neocortical patches to study how the interaction between inhibition and extracellular potassium ([K +] o ) dynamics may contribute to different types of focal seizures. Three main types of propagated focal seizures observed in recent intracortical microelectrode recordings in humans were modelled: seizures characterized by sustained (∼30−60 Hz) gamma local field potential (LFP) oscillations; seizures where the onset in the propagated site consisted of LFP spikes that later evolved into rhythmic (∼2−3 Hz) spike-wave complexes (SWCs); and seizures where a brief stage of low-amplitude fast-oscillation (∼10−20 Hz) LFPs preceded the SWC activity. Our findings are fourfold: (1) The interaction between elevated [K +] o (due to abnormal potassium buffering by glial cells) and the strength of synaptic inhibition plays a predominant role in shaping these three types of seizures. (2) Strengthening of inhibition leads to the onset of sustained narrowband gamma seizures. (3) Transition into SWC seizures is obtained either by the weakening of inhibitory synapses, or by a transient strengthening followed by an inhibitory breakdown (e.g. GABA depletion). This reduction or breakdown of inhibition among fast-spiking (FS) inhibitory interneurons increases their spiking activity and leads them eventually into depolarization block. Ictal spike-wave discharges in the model are then sustained solely by pyramidal neurons. (4) FS cell dynamics are also critical for seizures where the evolution into SWC activity is preceded by low-amplitude fast oscillations. Different levels of elevated [K +] o were important for transitions into and maintenance of sustained gamma oscillations and SWC discharges. Overall, our modelling study predicts that the interaction between inhibitory interneurons and [K +] o glial buffering under abnormal conditions may explain different types of ictal transitions and dynamics during propagated seizures in human focal epilepsy.", + "subject": [], + "keywords": [] + }, + { + "title": "MD/DPD Multiscale Framework for Predicting Morphology and Stresses of Red Blood Cells in Health and Disease", + "author": "Hung-Yu Chang, Xuejin Li, He Li, George Em Karniadakis", + "publisher": "Public Library of Science (PLoS)", + "url": "http://dx.doi.org/10.1371/journal.pcbi.1005173", + "doi": "10.1371/journal.pcbi.1005173", + "year": 2016, + "month": 10, + "abstract": "Healthy red blood cells (RBCs) have remarkable deformability, squeezing through narrow capillaries as small as 3 microns in diameter without any damage. However, in many hematological disorders the spectrin network and lipid bilayer of diseased RBCs may be significantly altered, leading to impaired functionality including loss of deformability. We employ a two-component whole-cell multiscale model to quantify the biomechanical characteristics of the healthy and diseased RBCs, including Plasmodium falciparum-infected RBCs (Pf-RBCs) and defective RBCs in hereditary disorders, such as spherocytosis and elliptocytosis. In particular, we develop a two-step multiscale framework based on coarse-grained molecular dynamics (CGMD) and dissipative particle dynamics (DPD) to predict the static and dynamic responses of RBCs subject to tensile forcing, using experimental information only on the structural defects in the lipid bilayer, cytoskeleton, and their interaction. We first employ CGMD on a small RBC patch to compute the shear modulus, bending stiffness, and network parameters, which are subsequently used as input to a whole-cell DPD model to predict the RBC shape and corresponding stress field. For Pf-RBCs at trophozoite and schizont stages, the presence of cytoadherent knobs elevates the shear response in the lipid bilayer and stiffens the RBC membrane. For RBCs in spherocytosis and elliptocytosis, the bilayer-cytoskeleton interaction is weakened, resulting in substantial increase of the tensile stress in the lipid bilayer. Furthermore, we investigate the transient behavior of stretching deformation and shape relaxation of the normal and defective RBCs. Different from the normal RBCs possessing high elasticity, our simulations reveal that the defective RBCs respond irreversibly, i.e., they lose their ability to recover the normal biconcave shape in successive loading cycles of stretching and relaxation. Our findings provide fundamental insights into the microstructure and biomechanics of RBCs, and demonstrate that the two-step multiscale framework presented here can be used effectively for in silico studies of hematological disorders based on first principles and patient-specific experimental input at the protein level.", + "subject": [], + "keywords": [] + }, + { + "title": "A systematic comparison between visual cues for boundary detection", + "author": "David A. Mély, Junkyung Kim, Mason McGill, Yuliang Guo, Thomas Serre", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.visres.2015.11.007", + "doi": "10.1016/j.visres.2015.11.007", + "year": 2016, + "month": 3, + "abstract": "The detection of object boundaries is a critical first step for many visual processing tasks. Multiple cues (we consider luminance, color, motion and binocular disparity) available in the early visual system may signal object boundaries but little is known about their relative diagnosticity and how to optimally combine them for boundary detection. This study thus aims at understanding how early visual processes inform boundary detection in natural scenes. We collected color binocular video sequences of natural scenes to construct a video database. Each scene was annotated with two full sets of ground-truth contours (one set limited to object boundaries and another set which included all edges). We implemented an integrated computational model of early vision that spans all considered cues, and then assessed their diagnosticity by training machine learning classifiers on individual channels. Color and luminance were found to be most diagnostic while stereo and motion were least. Combining all cues yielded a significant improvement in accuracy beyond that of any cue in isolation. Furthermore, the accuracy of individual cues was found to be a poor predictor of their unique contribution for the combination. This result suggested a complex interaction between cues, which we further quantified using regularization techniques. Our systematic assessment of the accuracy of early vision models for boundary detection together with the resulting annotated video dataset should provide a useful benchmark towards the development of higher-level models of visual processing.", + "subject": [], + "keywords": [] + }, + { + "title": "Fast ventral stream neural activity enables rapid visual categorization", + "author": "Maxime Cauchoix, Sébastien M. Crouzet, Denis Fize, Thomas Serre", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.neuroimage.2015.10.012", + "doi": "10.1016/j.neuroimage.2015.10.012", + "year": 2016, + "month": 1, + "abstract": "Primates can recognize objects embedded in complex natural scenes in a glimpse. Rapid categorization paradigms have been extensively used to study our core perceptual abilities when the visual system is forced to operate under strong time constraints. However, the neural underpinning of rapid categorization remains to be understood, and the incredible speed of sight has yet to be reconciled with modern ventral stream cortical theories of object recognition.\n\nHere we recorded multichannel subdural electrocorticogram (ECoG) signals from intermediate areas (V4/PIT) of the ventral stream of the visual cortex while monkeys were actively engaged in a rapid animal/non-animal categorization task. A traditional event-related potential (ERP) analysis revealed short visual latencies (< 50–70 ms) followed by a rapidly developing visual selectivity (within ~ 20–30 ms) for most electrodes. A multi-variate pattern analysis (MVPA) technique further confirmed that reliable animal/non-animal category information was possible from this initial ventral stream neural activity (within ~ 90–100 ms). Furthermore, this early category-selective neural activity was (a) unaffected by the presentation of a backward (pattern) mask, (b) generalized to novel (unfamiliar) stimuli and (c) co-varied with behavioral responses (both accuracy and reaction times). Despite the strong prevalence of task-related information on the neural signal, task-irrelevant visual information could still be decoded independently of monkey behavior. Monkey behavioral responses were also found to correlate significantly with human behavioral responses for the same set of stimuli.\n\nTogether, the present study establishes that rapid ventral stream neural activity induces a visually selective signal subsequently used to drive rapid visual categorization and that this visual strategy may be shared between human and non-human primates.", + "subject": [], + "keywords": [] + }, + { + "title": "Results on the Spin-Dependent Scattering of Weakly Interacting Massive Particles on Nucleons from the Run 3 Data of the LUX Experiment", + "author": "D. S. Akerib, H. M. Araújo, X. Bai, A. J. Bailey, J. Balajthy, P. Beltrame, E. P. Bernard, A. Bernstein, T. P. Biesiadzinski, E. M. Boulton, A. Bradley, R. Bramante, S. B. Cahn, M. C. Carmona-Benitez, C. Chan, J. J. Chapman, A. A. Chiller, C. Chiller, A. Currie, J. E. Cutter, T. J. R. Davison, L. de Viveiros, A. Dobi, J. E. Y. Dobson, E. Druszkiewicz, B. N. Edwards, C. H. Faham, S. Fiorucci, R. J. Gaitskell, V. M. Gehman, C. Ghag, K. R. Gibson, M. G. D. Gilchriese, C. R. Hall, M. Hanhardt, S. J. Haselschwardt, S. A. Hertel, D. P. Hogan, M. Horn, D. Q. Huang, C. M. Ignarra, M. Ihm, R. G. Jacobsen, W. Ji, K. Kazkaz, D. Khaitan, R. Knoche, N. A. Larsen, C. Lee, B. G. Lenardo, K. T. Lesko, A. Lindote, M. I. Lopes, D. C. Malling, A. Manalaysay, R. L. Mannino, M. F. Marzioni, D. N. McKinsey, D.-M. Mei, J. Mock, M. Moongweluwan, J. A. Morad, A. St. J. Murphy, C. Nehrkorn, H. N. Nelson, F. Neves, K. O’Sullivan, K. C. Oliver-Mallory, R. A. Ott, K. J. Palladino, M. Pangilinan, E. K. Pease, P. Phelps, L. Reichhart, C. Rhyne, S. Shaw, T. A. Shutt, C. Silva, V. N. Solovov, P. Sorensen, S. Stephenson, T. J. Sumner, M. Szydagis, D. J. Taylor, W. Taylor, B. P. Tennyson, P. A. Terman, D. R. Tiedt, W. H. To, M. Tripathi, L. Tvrznikova, S. Uvarov, J. R. Verbus, R. C. Webb, J. T. White, T. J. Whitis, M. S. Witherell, F. L. H. Wolfs, K. Yazdani, S. K. Young, C. Zhang, undefined undefined", + "publisher": "American Physical Society (APS)", + "url": "http://dx.doi.org/10.1103/physrevlett.116.161302", + "doi": "10.1103/physrevlett.116.161302", + "year": 2016, + "month": 4, + "abstract": "We present experimental constraints on the spin-dependent WIMP (weakly interacting massive particle)-nucleon elastic cross sections from LUX data acquired in 2013. LUX is a dual-phase xenon time projection chamber operating at the Sanford Underground Research Facility (Lead, South Dakota), which is designed to observe the recoil signature of galactic WIMPs scattering from xenon nuclei. A profile likelihood ratio analysis of 1.4×104  kg day of fiducial exposure allows 90% C.L. upper limits to be set on the WIMP-neutron (WIMP-proton) cross section of \uD835\uDF0E\uD835\uDC5B=9.4×10−41  cm2 (\uD835\uDF0E\uD835\uDC5D=2.9×10−39  cm2) at 33  GeV/\uD835\uDC502. The spin-dependent WIMP-neutron limit is the most sensitive constraint to date.", + "subject": [], + "keywords": [] + }, + { + "title": "Signal yields, energy resolution, and recombination fluctuations in liquid xenon", + "author": "D. S. Akerib, S. Alsum, H. M. Araújo, X. Bai, A. J. Bailey, J. Balajthy, P. Beltrame, E. P. Bernard, A. Bernstein, T. P. Biesiadzinski, E. M. Boulton, R. Bramante, P. Brás, D. Byram, S. B. Cahn, M. C. Carmona-Benitez, C. Chan, A. A. Chiller, C. Chiller, A. Currie, J. E. Cutter, T. J. R. Davison, A. Dobi, J. E. Y. Dobson, E. Druszkiewicz, B. N. Edwards, C. H. Faham, S. Fiorucci, R. J. Gaitskell, V. M. Gehman, C. Ghag, K. R. Gibson, M. G. D. Gilchriese, C. R. Hall, M. Hanhardt, S. J. Haselschwardt, S. A. Hertel, D. P. Hogan, M. Horn, D. Q. Huang, C. M. Ignarra, M. Ihm, R. G. Jacobsen, W. Ji, K. Kamdin, K. Kazkaz, D. Khaitan, R. Knoche, N. A. Larsen, C. Lee, B. G. Lenardo, K. T. Lesko, A. Lindote, M. I. Lopes, A. Manalaysay, R. L. Mannino, M. F. Marzioni, D. N. McKinsey, D.-M. Mei, J. Mock, M. Moongweluwan, J. A. Morad, A. St. J. Murphy, C. Nehrkorn, H. N. Nelson, F. Neves, K. O’Sullivan, K. C. Oliver-Mallory, K. J. Palladino, E. K. Pease, P. Phelps, L. Reichhart, C. Rhyne, S. Shaw, T. A. Shutt, C. Silva, M. Solmaz, V. N. Solovov, P. Sorensen, S. Stephenson, T. J. Sumner, M. Szydagis, D. J. Taylor, W. C. Taylor, B. P. Tennyson, P. A. Terman, D. R. Tiedt, W. H. To, M. Tripathi, L. Tvrznikova, S. Uvarov, J. R. Verbus, R. C. Webb, J. T. White, T. J. Whitis, M. S. Witherell, F. L. H. Wolfs, J. Xu, K. Yazdani, S. K. Young, C. Zhang, undefined undefined", + "publisher": "American Physical Society (APS)", + "url": "http://dx.doi.org/10.1103/physrevd.95.012008", + "doi": "10.1103/physrevd.95.012008", + "year": 2017, + "month": 1, + "abstract": "This work presents an analysis of monoenergetic electronic recoil peaks in the dark-matter-search and calibration data from the first underground science run of the Large Underground Xenon (LUX) detector. Liquid xenon charge and light yields for electronic recoil energies between 5.2 and 661.7 keV are measured, as well as the energy resolution for the LUX detector at those same energies. Additionally, there is an interpretation of existing measurements and descriptions of electron-ion recombination fluctuations in liquid xenon as limiting cases of a more general liquid xenon recombination fluctuation model. Measurements of the standard deviation of these fluctuations at monoenergetic electronic recoil peaks exhibit a linear dependence on the number of ions for energy deposits up to 661.7 keV, consistent with previous LUX measurements between 2 and 16 keV with \n3\n H \n . We highlight similarities in liquid xenon recombination for electronic and nuclear recoils with a comparison of recombination fluctuations measured with low-energy calibration data.", + "subject": [], + "keywords": [] + }, + { + "title": "Analysis of hydrodynamic fluctuations in heterogeneous adjacent multidomains in shear flow", + "author": "Xin Bian, Mingge Deng, Yu-Hang Tang, George Em Karniadakis", + "publisher": "American Physical Society (APS)", + "url": "http://dx.doi.org/10.1103/physreve.93.033312", + "doi": "10.1103/physreve.93.033312", + "year": 2016, + "month": 3, + "abstract": "We analyze hydrodynamic fluctuations of a hybrid simulation under shear flow. The hybrid simulation is based on the Navier-Stokes (NS) equations on one domain and dissipative particle dynamics (DPD) on the other. The two domains overlap, and there is an artificial boundary for each one within the overlapping region. To impose the artificial boundary of the NS solver, a simple spatial-temporal averaging is performed on the DPD simulation. In the artificial boundary of the particle simulation, four popular strategies of constraint dynamics are implemented, namely the Maxwell buffer [Hadjiconstantinou and Patera, Int. J. Mod. Phys. C 08, 967 (1997)], the relaxation dynamics [O'Connell and Thompson, Phys. Rev. E 52, R5792 (1995)], the least constraint dynamics [Nie et al., J. Fluid Mech. 500, 55 (2004); Werder et al., J. Comput. Phys. 205, 373 (2005)], and the flux imposition [Flekkøy et al., Europhys. Lett. 52, 271 (2000)], to achieve a target mean value given by the NS solver. Going beyond the mean flow field of the hybrid simulations, we investigate the hydrodynamic fluctuations in the DPD domain. Toward that end, we calculate the transversal autocorrelation functions of the fluctuating variables in \uD835\uDC58 space to evaluate the generation, transport, and dissipation of fluctuations in the presence of a hybrid interface. We quantify the unavoidable errors in the fluctuations, due to both the truncation of the domain and the constraint dynamics performed in the artificial boundary. Furthermore, we compare the four methods of constraint dynamics and demonstrate how to reduce the errors in fluctuations. The analysis and findings of this work are directly applicable to other hybrid simulations of fluid flow with thermal fluctuations.", + "subject": [], + "keywords": [] + }, + { + "title": "Results from a Search for Dark Matter in the Complete LUX Exposure", + "author": "D. S. Akerib, S. Alsum, H. M. Araújo, X. Bai, A. J. Bailey, J. Balajthy, P. Beltrame, E. P. Bernard, A. Bernstein, T. P. Biesiadzinski, E. M. Boulton, R. Bramante, P. Brás, D. Byram, S. B. Cahn, M. C. Carmona-Benitez, C. Chan, A. A. Chiller, C. Chiller, A. Currie, J. E. Cutter, T. J. R. Davison, A. Dobi, J. E. Y. Dobson, E. Druszkiewicz, B. N. Edwards, C. H. Faham, S. Fiorucci, R. J. Gaitskell, V. M. Gehman, C. Ghag, K. R. Gibson, M. G. D. Gilchriese, C. R. Hall, M. Hanhardt, S. J. Haselschwardt, S. A. Hertel, D. P. Hogan, M. Horn, D. Q. Huang, C. M. Ignarra, M. Ihm, R. G. Jacobsen, W. Ji, K. Kamdin, K. Kazkaz, D. Khaitan, R. Knoche, N. A. Larsen, C. Lee, B. G. Lenardo, K. T. Lesko, A. Lindote, M. I. Lopes, A. Manalaysay, R. L. Mannino, M. F. Marzioni, D. N. McKinsey, D.-M. Mei, J. Mock, M. Moongweluwan, J. A. Morad, A. St. J. Murphy, C. Nehrkorn, H. N. Nelson, F. Neves, K. O’Sullivan, K. C. Oliver-Mallory, K. J. Palladino, E. K. Pease, P. Phelps, L. Reichhart, C. Rhyne, S. Shaw, T. A. Shutt, C. Silva, M. Solmaz, V. N. Solovov, P. Sorensen, S. Stephenson, T. J. Sumner, M. Szydagis, D. J. Taylor, W. C. Taylor, B. P. Tennyson, P. A. Terman, D. R. Tiedt, W. H. To, M. Tripathi, L. Tvrznikova, S. Uvarov, J. R. Verbus, R. C. Webb, J. T. White, T. J. Whitis, M. S. Witherell, F. L. H. Wolfs, J. Xu, K. Yazdani, S. K. Young, C. Zhang, undefined undefined", + "publisher": "American Physical Society (APS)", + "url": "http://dx.doi.org/10.1103/physrevlett.118.021303", + "doi": "10.1103/physrevlett.118.021303", + "year": 2017, + "month": 1, + "abstract": "We report constraints on spin-independent weakly interacting massive particle (WIMP)-nucleon scattering using a 3.35×1\u206204  kg day exposure of the Large Underground Xenon (LUX) experiment. A dual-phase xenon time projection chamber with 250 kg of active mass is operated at the Sanford Underground Research Facility under Lead, South Dakota (USA). With roughly fourfold improvement in sensitivity for high WIMP masses relative to our previous results, this search yields no evidence of WIMP nuclear recoils. At a WIMP mass of 50  GeV \uD835\uDC50−2, WIMP-nucleon spin-independent cross sections above 2.2×10−46  cm2 are excluded at the 90% confidence level. When combined with the previously reported LUX exposure, this exclusion strengthens to 1.1×10−46  cm2 at 50  GeV \uD835\uDC50−2.", + "subject": [], + "keywords": [] + }, + { + "title": "Automating impurity-enhanced antiphase boundary energy calculations from ab initio Monte Carlo", + "author": "R. Sun, A. van de Walle", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.calphad.2016.02.005", + "doi": "10.1016/j.calphad.2016.02.005", + "year": 2016, + "month": 6, + "abstract": "The effect of impurities on antiphase boundary (APB) energies is studied using cluster expansion and Monte Carlo (MC) techniques from first-principles total-energy calculations. We present a code that automates the generation of APB structures for MC sampling within the Alloy Theoretic Automated Toolkit software package. The functionalities of the code is demonstrated by a case study on Ni3Al with Ti impurities.", + "subject": [], + "keywords": [] + }, + { + "title": "Amp: A modular approach to machine learning in atomistic simulations", + "author": "Alireza Khorshidi, Andrew A. Peterson", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.cpc.2016.05.010", + "doi": "10.1016/j.cpc.2016.05.010", + "year": 2016, + "month": 10, + "abstract": "Electronic structure calculations, such as those employing Kohn–Sham density functional theory or ab initio wavefunction theories, have allowed for atomistic-level understandings of a wide variety of phenomena and properties of matter at small scales. However, the computational cost of electronic structure methods drastically increases with length and time scales, which makes these methods difficult for long time-scale molecular dynamics simulations or large-sized systems. Machine-learning techniques can provide accurate potentials that can match the quality of electronic structure calculations, provided sufficient training data. These potentials can then be used to rapidly simulate large and long time-scale phenomena at similar quality to the parent electronic structure approach. Machine-learning potentials usually take a bias-free mathematical form and can be readily developed for a wide variety of systems. Electronic structure calculations have favorable properties–namely that they are noiseless and targeted training data can be produced on-demand–that make them particularly well-suited for machine learning. This paper discusses our modular approach to atomistic machine learning through the development of the open-source Atomistic Machine-learning Package (Amp), which allows for representations of both the total and atom-centered potential energy surface, in both periodic and non-periodic systems. Potentials developed through the atom-centered approach are simultaneously applicable for systems with various sizes. Interpolation can be enhanced by introducing custom descriptors of the local environment. We demonstrate this in the current work for Gaussian-type, bispectrum, and Zernike-type descriptors. Amp has an intuitive and modular structure with an interface through the python scripting language yet has parallelizable fortran components for demanding tasks; it is designed to integrate closely with the widely used Atomic Simulation Environment (ASE), which makes it compatible with a wide variety of commercial and open-source electronic structure codes. We finally demonstrate that the neural network model inside Amp can accurately interpolate electronic structure energies as well as forces of thousands of multi-species atomic systems.\n\n", + "subject": [], + "keywords": [] + }, + { + "title": "Understanding the Low-Overpotential Production of CH4 from CO2 on Mo2C Catalysts", + "author": "Seok Ki Kim, Yin-Jia Zhang, Helen Bergstrom, Ronald Michalsky, Andrew Peterson", + "publisher": "American Chemical Society (ACS)", + "url": "http://dx.doi.org/10.1021/acscatal.5b02424", + "doi": "10.1021/acscatal.5b02424", + "year": 2016, + "month": 2, + "abstract": "While Cu is the only electrocatalyst that converts CO2 into meaningful quantities of CH4 fuel, it requires significant overpotentials (onset potential of ∼−0.80 V vs RHE), decreasing energy conversion efficiencies. We report that Mo2C is capable of catalyzing CO2 into CH4 at low potentials (onset potential of ∼−0.55 V vs RHE), where Cu electrocatalysts do not convert CO2. This low-overpotential catalyst was first identified as a candidate by electronic structure calculations, which indicated the free energetics of CO hydrogenation to be more favorable than that on conventional transition metals such as Cu. Despite the low onset potential for CH4, the CH4 has a steep Tafel slope (∼−280 mV/dec), resulting in most of the current passing through the Mo2C electrocatalysts being utilized for the competitive hydrogen evolution reaction. We conducted a detailed theoretical analysis on the basis of density functional theory calculations, microkinetic analysis, and simulated Pourbaix diagrams to suggest the reasons for these characteristics. These analyses suggest that the potential-limiting step in CH4 evolution is the clearing of OH from the surface, while the rate-limiting step is the nonelectrochemical C–O bond scission, resulting in a high OH coverage and a high Tafel slope. Our calculations suggest that this high coverage weakens H binding, causing enhancement of the H2 evolution reaction in comparison to that under CO2-free conditions. This analysis shows that the detailed interaction of theory and experiment can be used to design and analyze operational electrocatalysts for CO2 reduction and other complicated electrocatalytic reactions.", + "subject": [], + "keywords": [] + }, + { + "title": "Multi-species protein similarity clustering reveals novel expanded immune gene families in the eastern oyster Crassostrea virginica", + "author": "Ian C. McDowell, Tejashree H. Modak, Chris E. Lane, Marta Gomez-Chiarri", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.fsi.2016.03.157", + "doi": "10.1016/j.fsi.2016.03.157", + "year": 2016, + "month": 6, + "abstract": "Comparative genomics research in non-model species has highlighted how invertebrate hosts possess complex diversified repertoires of immune molecules. The levels of diversification in particular immune gene families appear to differ between invertebrate lineages and even between species within lineages, reflecting differences not only in evolutionary histories, but also in life histories, environmental niches, and pathogen exposures. The goal of this research was to identify immune-related gene families experiencing high levels of diversification in eastern oysters, Crassostrea virginica. Families containing 1) transcripts differentially expressed in eastern oysters in response to bacterial challenge and 2) a larger number of transcripts compared to other species included those coding for the C1q and C-type lectin domain containing proteins (C1qDC and CTLDC), GTPase of the immune-associated proteins (GIMAP), scavenger receptors (SR), fibrinogen-C domain containing proteins (also known as FREPs), dopamine beta-hydrolase (DBH), interferon-inducible 44 (IFI44), serine protease inhibitors, apextrin, and dermatopontin. Phylogenetic analysis of two of the families significantly expanded in bivalves, IFI44 and GIMAP, showed a patchy distribution within both protostomes and deuterostomes, suggesting multiple independent losses and lineage-specific expansions. Increased availability of genomic information for a broader range of non-model species broadly distributed through vertebrate and invertebrate phyla will likely lead to improved knowledge on mechanisms of immune-gene diversification.", + "subject": [], + "keywords": [] + }, + { + "title": "A user guide for SLUSCHI: Solid and Liquid in Ultra Small Coexistence with Hovering Interfaces", + "author": "Qi-Jun Hong, Axel van de Walle", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.calphad.2015.12.003", + "doi": "10.1016/j.calphad.2015.12.003", + "year": 2016, + "month": 3, + "abstract": "Although various approaches for melting point calculations from first principles have been proposed and employed for years, their practical implementation has hitherto remained a complex and time-consuming process. The SLUSCHI code (Solid and Liquid in Ultra Small Coexistence with Hovering Interfaces) drastically simplifies this procedure into an automated package, by implementing the recently-developed small-size coexistence method and putting together a series of steps that lead to final melting point evaluation. Based on density functional theory, SLUSCHI employs Born–Oppenheimer molecular dynamics techniques under the isobaric–isothermal (NPT) ensemble, with interface to the first-principles code VASP. In order to make this useful code available to a wide community of researchers who could benefit from it, this paper outlines the procedure to perform melting point calculations, and presents a detailed user guide to the code.", + "subject": [], + "keywords": [] + }, + { + "title": "The Secreted Proteins of Achlya hypogyna and Thraustotheca clavata Identify the Ancestral Oomycete Secretome and Reveal Gene Acquisitions by Horizontal Gene Transfer", + "author": "Ian Misner, Nic Blouin, Guy Leonard, Thomas A. Richards, Christopher E. Lane", + "publisher": "Oxford University Press (OUP)", + "url": "http://dx.doi.org/10.1093/gbe/evu276", + "doi": "10.1093/gbe/evu276", + "year": 2014, + "month": 12, + "abstract": "Saprotrophic and parasitic microorganisms secrete proteins into the environment to breakdown macromolecules and obtain nutrients. The molecules secreted are collectively termed the 'secretome' and the composition and function of this set of proteins varies depending on the ecology, life cycle, and environment of an organism. Beyond the function of nutrient acquisition, parasitic lineages must also secrete molecules to manipulate their host. Here, we use a combination of de novo genome and transcriptome sequencing and bioinformatic identification of signal peptides to identify the putative secreted proteome of two oomycetes, the facultative parasite Achlya hypogyna and free-living Thraustotheca clavata. By comparing the secretomes of these saprolegnialean oomycetes with that of eight other oomycetes, we were able to characterize the evolution of this protein set across the oomycete clade. These species span the last common ancestor of the two major oomycete families allowing us to identify the ancestral secretome. This putative ancestral secretome consists of at least 84 gene families. Only 11 of these gene families are conserved across all 10 secretomes analyzed and the two major branches in the oomycete radiation. Notably, we have identified expressed elicitin-like effector genes in the saprotrophic decomposer, T. clavata. Phylogenetic analyses show six novel horizontal gene transfers to the oomycete secretome from bacterial and fungal donor lineages, four of which are specific to the Saprolegnialeans. Comparisons between free-living and pathogenic taxa highlight the functional changes of oomycete secretomes associated with shifts in lifestyle.", + "subject": [ + "oomycete", + "horizontal gene transfer", + "evolution", + "comparative genomics", + "osmotrophy" + ], + "keywords": [] + }, + { + "title": "Ultralow energy calibration of LUX detector using \nXe127\n electron capture", + "author": "D. S. Akerib, S. Alsum, H. M. Araújo, X. Bai, A. J. Bailey, J. Balajthy, P. Beltrame, E. P. Bernard, A. Bernstein, T. P. Biesiadzinski, E. M. Boulton, P. Brás, D. Byram, S. B. Cahn, M. C. Carmona-Benitez, C. Chan, A. Currie, J. E. Cutter, T. J. R. Davison, A. Dobi, E. Druszkiewicz, B. N. Edwards, S. R. Fallon, A. Fan, S. Fiorucci, R. J. Gaitskell, J. Genovesi, C. Ghag, M. G. D. Gilchriese, C. R. Hall, M. Hanhardt, S. J. Haselschwardt, S. A. Hertel, D. P. Hogan, M. Horn, D. Q. Huang, C. M. Ignarra, R. G. Jacobsen, W. Ji, K. Kamdin, K. Kazkaz, D. Khaitan, R. Knoche, N. A. Larsen, B. G. Lenardo, K. T. Lesko, A. Lindote, M. I. Lopes, A. Manalaysay, R. L. Mannino, M. F. Marzioni, D. N. McKinsey, D.-M. Mei, J. Mock, M. Moongweluwan, J. A. Morad, A. St. J. Murphy, C. Nehrkorn, H. N. Nelson, F. Neves, K. O’Sullivan, K. C. Oliver-Mallory, K. J. Palladino, E. K. Pease, C. Rhyne, S. Shaw, T. A. Shutt, C. Silva, M. Solmaz, V. N. Solovov, P. Sorensen, T. J. Sumner, M. Szydagis, D. J. Taylor, W. C. Taylor, B. P. Tennyson, P. A. Terman, D. R. Tiedt, W. H. To, M. Tripathi, L. Tvrznikova, S. Uvarov, V. Velan, J. R. Verbus, R. C. Webb, J. T. White, T. J. Whitis, M. S. Witherell, F. L. H. Wolfs, J. Xu, K. Yazdani, S. K. Young, C. Zhang", + "publisher": "American Physical Society (APS)", + "url": "http://dx.doi.org/10.1103/physrevd.96.112011", + "doi": "10.1103/physrevd.96.112011", + "year": 2017, + "month": 12, + "abstract": "We report an absolute calibration of the ionization yields (\uD835\uDC44\uD835\uDC66) and fluctuations for electronic recoil events in liquid xenon at discrete energies between 186 eV and 33.2 keV. The average electric field applied across the liquid xenon target is 180  V/cm. The data are obtained using low energy \n127\n Xe \n electron capture decay events from the 95.0-day first run from LUX (WS2013) in search of weakly interacting massive particles. The sequence of gamma-ray and x-ray cascades associated with \n127\n I \n deexcitations produces clearly identified two-vertex events in the LUX detector. We observe the K-(binding energy, 33.2 keV), L-(5.2 keV), M-(1.1 keV), and N-(186 eV) shell cascade events and verify that the relative ratio of observed events for each shell agrees with calculations. The N-shell cascade analysis includes single extracted electron (SE) events and represents the lowest-energy electronic recoil in situ measurements that have been explored in liquid xenon.", + "subject": [], + "keywords": [] + }, + { + "title": "Phylogenomic Analyses of Echinodermata Support the Sister Groups of Asterozoa and Echinozoa", + "author": "Adrian Reich, Casey Dunn, Koji Akasaka, Gary Wessel", + "publisher": "Public Library of Science (PLoS)", + "url": "http://dx.doi.org/10.1371/journal.pone.0119627", + "doi": "10.1371/journal.pone.0119627", + "year": 2015, + "month": 3, + "abstract": "Echinoderms (sea urchins, sea stars, brittle stars, sea lilies and sea cucumbers) are a group of diverse organisms, second in number within deuterostome species to only the chordates. Echinoderms serve as excellent model systems for developmental biology due to their diverse developmental mechanisms, tractable laboratory use, and close phylogenetic distance to chordates. In addition, echinoderms are very well represented in the fossil record, including some larval features, making echinoderms a valuable system for studying evolutionary development. The internal relationships of Echinodermata have not been consistently supported across phylogenetic analyses, however, and this has hindered the study of other aspects of their biology. In order to test echinoderm phylogenetic relationships, we sequenced 23 de novo transcriptomes from all five clades of echinoderms. Using multiple phylogenetic methods at a variety of sampling depths we have constructed a well-supported phylogenetic tree of Echinodermata, including support for the sister groups of Asterozoa (sea stars and brittle stars) and Echinozoa (sea urchins and sea cucumbers). These results will help inform developmental and evolutionary studies specifically in echinoderms and deuterostomes in general.", + "subject": [ + "Echinoderms", + "Phylogenetic analysis", + "Starfish", + "Transcriptome analysis", + "Larvae", + "Phylogenetics", + "Sea urchins", + "Sea cucumbers" + ], + "keywords": [] + }, + { + "title": "Ultrafast Structural Pathway of Charge Transfer in N,N,N′,N′-Tetramethylethylenediamine", + "author": "Xinxin Cheng, Yao Zhang, Yan Gao, Hannes Jónsson, Peter M. Weber", + "publisher": "American Chemical Society (ACS)", + "url": "http://dx.doi.org/10.1021/acs.jpca.5b01797", + "doi": "10.1021/acs.jpca.5b01797", + "year": 2015, + "month": 3, + "abstract": "We have explored the ultrafast molecular structural dynamics associated with charge transfer in N,N,N′,N′-tetramethylethylenediamine using Rydberg fingerprint spectroscopy in conjunction with self-interaction corrected density functional theory. Excitation at 239 nm prepares the molecule in the Franck–Condon region of the 3s state with the charge localized on one of the two amine groups. As seen from the time-dependent Rydberg electron binding energies, the pathway of the rapidly ensuing dynamics leads through several structurally distinct conformers with various degrees of charge localization before reaching the fully charge-delocalized structure on a picosecond time scale. At several steps along the reaction path, the transient structures are identified through a comparison of the spectroscopically observed binding energies with computed values. The molecular structure is seen to evolve dynamically from an initially folded conformer to the stretched form that supports charge delocalization before an equilibrium sets in with forward and backward time constants of 1.19 (0.14) and 2.61 (0.31) ps, respectively. A coherent wavepacket motion in the charge-localized state with a period of 270 (17) fs and damping of 430 (260) fs is observed and tentatively assigned to the nitrogen umbrella motion. The damping time constant indicates the rate of the energy flow into other vibrations that are not activated by the optical excitation.", + "subject": ["Electrical energy", "Equilibrium", "Ions", "Molecular structure", "Molecules"], + "keywords": [] + }, + { + "title": "Integrating CRISM and TES hyperspectral data to characterize a halloysite-bearing deposit in Kashira crater, Mars", + "author": "Timothy A. Goudge, John F. Mustard, James W. Head, Mark R. Salvatore, Sandra M. Wiseman", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.icarus.2014.11.034", + "doi": "10.1016/j.icarus.2014.11.034", + "year": 2015, + "month": 4, + "abstract": "We present morphologic observations and spectral modeling results of a large, kaolin-group mineral-bearing deposit within Kashira crater in the southern highlands of Mars. We employ both non-linear unmixing of Compact Reconnaissance Imaging Spectrometer for Mars (CRISM) visible to near-infrared (VNIR) reflectance data and linear unmixing of Thermal Emission Spectrometer (TES) thermal infrared (TIR) emissivity data to quantitatively analyze the kaolin-group mineral within this deposit. We use a novel approach for quantitative analysis of CRISM data through non-linear unmixing with in-scene, orbitally-derived endmembers combined with laboratory measured endmembers. Results from this approach indicate that the deposit within Kashira crater is best modeled as a combination of surrounding spectral units (i.e., in-scene derived endmembers) with the addition of the kaolin-group mineral halloysite. Linear unmixing of TES data suggest that the deposit contains ∼30% halloysite, a result that is supported by a sensitivity analysis. Potential formation mechanisms for this deposit include hydrothermal alteration, arid-environment pedogenic weathering of a basaltic mound deposit, or pedogenic weathering of a volcanic ash deposit. Our modeling results offer a quantitative reconciliation of the CRISM and TES datasets, and provide a consistent mineralogy from spectral unmixing for an aqueous alteration mineral-bearing deposit on Mars using a combined analysis of both VNIR and TIR hyperspectral data.", + "subject": ["Mars", "surface", "Mineralogy", "Spectroscopy", "Geological processes"], + "keywords": [] + }, + { + "title": "Identification of Invariant Peptide Domains within Ebola Virus Glycoprotein GP1, 2", + "author": "Joel Kenneth Weltman", + "publisher": "OMICS Publishing Group", + "url": "http://dx.doi.org/10.4172/2161-0703.1000176", + "doi": "10.4172/2161-0703.1000176", + "year": 2015, + "month": 1, + "abstract": "Six invariant oligopeptide sequences of length 12 amino acids, or greater, were identified in GP1,2 of ZEBOV Zaire and SEBOV Sudan Ebola viruses. Five of these invariant peptides had positive scores for predicted B-cell epitope scores. In contrast, the amino acid positions of the remaining invariant peptide all displayed negative predicted epitope scores. Invariant regions of Ebola GP1,2 oligopeptides may reflect structural, functional and immunological constraints on the virus, and thus, may be useful as immunological and pharmacological targets.", + "subject": [ + "Ebola virus", + "EBOV", + "Glycoprotein", + "Entropy", + "Epitope", + "Bepipred", + "Antibodies", + "B-cell", + "Immunology" + ], + "keywords": [] + }, + { + "title": "The C-Terminal Threonine of Aβ43 Nucleates Toxic Aggregation via Structural and Dynamical Changes in Monomers and Protofibrils", + "author": "Alexander E. Conicella, Nicolas L. Fawzi", + "publisher": "American Chemical Society (ACS)", + "url": "http://dx.doi.org/10.1021/bi500131a", + "doi": "10.1021/bi500131a", + "year": 2014, + "month": 5, + "abstract": "Recent studies suggest that deposition of amyloid β (Aβ) into oligomeric aggregates and fibrils, hallmarks of Alzheimer’s disease, may be initiated by the aggregation of Aβ species other than the well-studied 40- and 42-residue forms, Aβ40 and Aβ42, respectively. Here we report on key structural, dynamic, and aggregation kinetic parameters of Aβ43, extended by a single threonine at the C-terminus relative to Aβ42. Using aggregation time course experiments, electron microscopy, and a combination of nuclear magnetic resonance measurements including backbone relaxation, dark-state exchange saturation transfer, and quantification of chemical shift differences and scalar coupling constants, we demonstrate that the C-terminal threonine in Aβ43 increases the rate and extent of protofibril aggregation and confers slow C-terminal motions in the monomeric and protofibril-bound forms of Aβ43. Relative to the neighboring residues, the hydrophilic Thr43 of Aβ43 favors direct contact with the protofibril surface more so than the C-terminus of Aβ40 or Aβ42. Taken together, these results demonstrate the potential of a small chemical modification to affect the properties of Aβ structure and aggregation, providing a mechanism for the potential role of Aβ43 as a primary nucleator of Aβ aggregates in Alzheimer’s disease.", + "subject": ["Aggregation", "Chemical structure", "Monomers", "Peptides and proteins"], + "keywords": [] + }, + { + "title": "Combined computational and experimental investigation of the refractory properties of La2Zr2O7", + "author": "Qi-Jun Hong, Sergey V. Ushakov, Alexandra Navrotsky, Axel van de Walle", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.actamat.2014.10.026", + "doi": "10.1016/j.actamat.2014.10.026", + "year": 2015, + "month": 2, + "abstract": "We demonstrate how key material properties that provide guidance in the design of refractory materials can be accurately determined via ab initio thermodynamic calculations in conjunction with experimental techniques based on synchrotron X-ray diffraction and thermal analysis under laser-heated aerodynamic levitation. The properties considered include melting point, heat of fusion, heat capacity, thermal expansion coefficients, thermal stability and sublattice disordering, as illustrated in a motivating example of lanthanum zirconate (La2Zr2O7). This work also sheds light on the unresolved controversy of possible phase transition before melting and identifies specific mechanisms responsible for the material’s high melting point. This study benefits from the use of two very recent techniques: (i) a new small-cell coexistence method that enables the accurate and efficient determination of the melting points from ab initio calculations alone; (ii) the experimental determination of solid structure at high temperatures by high-temperature synchrotron X-ray diffraction of laser-heated aerodynamically levitated samples.", + "subject": [ + "Lanthanum zirconate", + "Heat of fusion", + "Melting temperature", + "Disorder", + "Thermal expansion", + "heat capacity" + ], + "keywords": [] + }, + { + "title": "Verbal memory declines more rapidly with age in HIV infected versus uninfected adults", + "author": "Talia R. Seider, Xi Luo, Assawin Gongvatana, Kathryn N. Devlin, Suzanne M. de la Monte, Jesse D. Chasman, Peisi Yan, Karen T. Tashima, Bradford Navia, Ronald A. Cohen", + "publisher": "Informa UK Limited", + "url": "http://dx.doi.org/10.1080/13803395.2014.892061", + "doi": "10.1080/13803395.2014.892061", + "year": 2014, + "month": 3, + "abstract": "In the current era of effective antiretroviral treatment, the number of older adults living with HIV is rapidly increasing. This study investigated the combined influence of age and HIV infection on longitudinal changes in verbal and visuospatial learning and memory. Method: In this longitudinal, case-control design, 54 HIV seropositive and 30 seronegative individuals aged 40–74 years received neurocognitive assessments at baseline visits and again one year later. Assessment included tests of verbal and visuospatial learning and memory. Linear regression was used to predict baseline performance and longitudinal change on each test using HIV serostatus, age, and their interaction as predictors. Multivariate analysis of variance (MANOVA) was used to assess the effects of these predictors on overall baseline performance and overall longitudinal change. Results: The interaction of HIV and age significantly predicted longitudinal change in verbal memory performance, as did HIV status, indicating that although the seropositive group declined more than the seronegative group overall, the rate of decline depended on age such that greater age was associated with a greater decline in this group. The regression models for visuospatial learning and memory were significant at baseline, but did not predict change over time. HIV status significantly predicted overall baseline performance and overall longitudinal change. Conclusions: This is the first longitudinal study focused on the effects of age and HIV on memory. Findings suggest that age and HIV interact to produce larger declines in verbal memory over time. Further research is needed to gain a greater understanding of the effects of HIV on the aging brain.", + "subject": [ + "HIV", + "Memory", + "Cognitive aging", + "Autoimmune diseases", + "HIV-associated neurocognitive disorder" + ], + "keywords": [] + }, + { + "title": "Transcriptome of American Oysters, Crassostrea virginica, in Response to Bacterial Challenge: Insights into Potential Mechanisms of Disease Resistance", + "author": "Ian C. McDowell, Chamilani Nikapitiya, Derek Aguiar, Christopher E. Lane, Sorin Istrail, Marta Gomez-Chiarri", + "publisher": "Public Library of Science (PLoS)", + "url": "http://dx.doi.org/10.1371/journal.pone.0105097", + "doi": "10.1371/journal.pone.0105097", + "year": 2014, + "month": 8, + "abstract": "The American oyster Crassostrea virginica, an ecologically and economically important estuarine organism, can suffer high mortalities in areas in the Northeast United States due to Roseovarius Oyster Disease (ROD), caused by the gram-negative bacterial pathogen Roseovarius crassostreae. The goals of this research were to provide insights into: 1) the responses of American oysters to R. crassostreae, and 2) potential mechanisms of resistance or susceptibility to ROD. The responses of oysters to bacterial challenge were characterized by exposing oysters from ROD-resistant and susceptible families to R. crassostreae, followed by high-throughput sequencing of cDNA samples from various timepoints after disease challenge. Sequence data was assembled into a reference transcriptome and analyzed through differential gene expression and functional enrichment to uncover genes and processes potentially involved in responses to ROD in the American oyster. While susceptible oysters experienced constant levels of mortality when challenged with R. crassostreae, resistant oysters showed levels of mortality similar to non-challenged oysters. Oysters exposed to R. crassostreae showed differential expression of transcripts involved in immune recognition, signaling, protease inhibition, detoxification, and apoptosis. Transcripts involved in metabolism were enriched in susceptible oysters, suggesting that bacterial infection places a large metabolic demand on these oysters. Transcripts differentially expressed in resistant oysters in response to infection included the immune modulators IL-17 and arginase, as well as several genes involved in extracellular matrix remodeling. The identification of potential genes and processes responsible for defense against R. crassostreae in the American oyster provides insights into potential mechanisms of disease resistance.", + "subject": [ + "Oysters", + "Gene expression", + "Bacterial pathogens", + "Gene ontologies", + "Transcriptome analysis", + "Immune response", + "Apoptosis", + "Protein domains" + ], + "keywords": [] + }, + { + "title": "Conservation of sequence and function in fertilization of the cortical granule serine protease in echinoderms", + "author": "Nathalie Oulhen, Dongdong Xu, Gary M. Wessel", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.bbrc.2014.05.098", + "doi": "10.1016/j.bbrc.2014.05.098", + "year": 2014, + "month": 8, + "abstract": "Conservation of the cortical granule serine protease during fertilization in echinoderms was tested both functionally in sea stars, and computationally throughout the echinoderm phylum. We find that the inhibitor of serine protease (soybean trypsin inhibitor) effectively blocks proper transition of the sea star fertilization envelope into a protective sperm repellent, whereas inhibitors of the other main types of proteases had no effect. Scanning the transcriptomes of 15 different echinoderm ovaries revealed sequences of high conservation to the originally identified sea urchin cortical serine protease, CGSP1. These conserved sequences contained the catalytic triad necessary for enzymatic activity, and the tandemly repeated LDLr-like repeats. We conclude that the protease involved in the slow block to polyspermy is an essential and conserved element of fertilization in echinoderms, and may provide an important reagent for identification and testing of the cell surface proteins in eggs necessary for sperm binding.", + "subject": [ + "Cortical granules", + "Fertilization", + "Cortical granule protease", + "Egg receptor for sperm", + "Echinoderms", + "Sea star" + ], + "keywords": [] + }, + { + "title": "MERS-Cov and Immunobioinformatics", + "author": "Joel K Weltman", + "publisher": "OMICS Publishing Group", + "url": "http://dx.doi.org/10.4172/2161-0703.1000e126", + "doi": "10.4172/2161-0703.1000e126", + "year": 2014, + "month": 7, + "abstract": "MERS (Middle East Respiratory Syndrome) is an emerging infectious disease threat, caused by the single-stranded, positive sense (+) RNA MERS-Cov, a highly virulent coronavirus [1,2]. In this editorial report, the immunobioinformatic techniques previously applied to influenza A, described elsewhere in this issue of the Journal of Medical Microbiology and Diagnosis [3] are applied to the spike protein (S) of human MERS-Cov. The S protein is precursor of the S1 and S2 proteins. S1 protein contains a receptor binding domain (RBD; amino acid positions 367–606) which binds to CD26 on the target lymphocyte membrane [4,5]. S2 protein probably facilitates membrane fusion and entry of bound MERS-Cov into the target cell. The dataset of 13 complete MERS-Cov S human protein sequences was downloaded from GenBank [6] on July 4, 2014. Hamming distance (D; [7,8]) and Bepipred Score [9] were determined for each of the 1353 S protein amino acid positions (Figure 1). There were 14 amino acid positions with D>0.0 (Figure 1, top). Three of these 14 amino acid positions were within the RBD in the S1 region of the S protein (positions 400, 506, 520). Amino acid 520 possessed a Bepipred Score of 0.437, which is above the recommended cutoff of 0.350. These results suggest that an A520S mutation at an S1 protein epitope within the RBD domain influences the evolutionary trajectory of MERS-Cov by mechanisms involving host immunological responses. Such a mutation may be a component of a suitable epitope target for a preventive vaccine [10]. The maximum observed value of D was at amino acid position 1020, within the the S2 region of the S protein. The Bepipred Score at this position was only 0.302, below the recommended threshold of 0.350, however position 1020 is located between two epitopic regions beginning at position 1010 and ending at amino acid position 1031. It remains to be determined whether the relatively high D value at position 1020 reflects non-immunological forces or whether amino acid 1020 is a component of one of the closely neighboring epitope regions. The mutations observed at S protein position 1020 were H1020R and H1020Q. Histidine is an essential amino acid, which suggests that host dietary factors may be involved in the mutations at position 1020. All three of the amino acids occurring at position 1020 possess nitrogen-containing side-chains. Thus, these results suggest viral structural influences and constraints on the viral mutational process at S protein position 1020. Contiguous positions 1158 and 1159 each had a positive D value and significant Bepipred Score in a densely epitopic section of the S2 region of the S protein. These results suggest antigenic activity of the S protein in a non-RBD region. Such an epitope may serve as a vaccine antigen target to ameliorate, but not prevent, MERS. It is proposed, and hoped, that the results presented in this editorial demonstrate the potential usefulness of immunobioinformatic analysis of MERS-Cov as a tool to increase our understanding of the pathophysiology of MERS on a level that assists our ability to design protective strategies, treatments and vaccines.", + "subject": [], + "keywords": [] + }, + { + "title": "An Immunobioinformatic Comparison of Influenza A Subtype Hemagglutinins", + "author": "Joel K Weltman", + "publisher": "OMICS Publishing Group", + "url": "http://dx.doi.org/10.4172/2161-0703.1000135", + "doi": "10.4172/2161-0703.1000135", + "year": 2014, + "month": -1, + "abstract": "The purpose of this research is to identify nucleotide and amino acid positions are essential for the function of the HA gene and its protein products. A metric for sequence variability was Hamming distance, determined for all possible inter-subtype HA sequence pairs of H1N1, H3N2 and H6N1 HA sequences in the complete NCBI HA gene datasets. Almost all (97.22%) of nucleotide positions at which the Hamming distance was zero were in the HA2 domain of the HA gene; the invariant nucleotides occupied second and first codon positions except for a tail-region encoded invariant tryptophan. In contrast with the results at the nucleotide level, the patterns of epitope distribution in the encoded HA proteins were similar except for a 25-amino acid sequence (283-307) in the HA1 region of HA H6N1. These results demonstrate the occurrence of similar organization of immunological epitopic biopatterns in influenza A hemagglutinins at the protein level, even in the face of large differences in the sequences of encoding nucleotides and encoded amino acids.", + "subject": [ + "Influenza A", + "Subtypes", + "Hemagglutinin", + "Bioinformatics", + "Hamming distance", + "Bepipred", + "Epitopes" + ], + "keywords": [] + }, + { + "title": "Protein degradation machinery is present broadly during early development in the sea urchin", + "author": "Vanesa Zazueta-Novoa, Gary M. Wessel", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.gep.2014.06.002", + "doi": "10.1016/j.gep.2014.06.002", + "year": 2014, + "month": 7, + "abstract": "Ubiquitin-dependent proteosome-mediated proteolysis is an important pathway of degradation that controls the timed destruction of cellular proteins in all tissues. All intracellular proteins and many extracellular proteins are continually being hydrolyzed to their constituent amino acids as a result of their recognition by E3 ligases for specific targeting of ubiquitination. Gustavus is a member of an ECS-type E3 ligase which interacts with Vasa, a DEAD-box RNA helicase, to regulate its localization during sea urchin embryonic development, and Gustavus mRNA accumulation is highly localized and dynamic during development. We tested if the core complex for Gustavus function was present in the embryo and if other SOCS box proteins also had restricted expression profiles that would inform future research. Expression patterns of the key members of the proteasomal function, such as the E3 core complex which interacts with Gustavus, and other E3-SOCS box proteins, are widely spread and dynamic in early development of the embryo suggesting broad core complex availability in the proteasome degradation pathway and temporal/spatial enrichments of various E3 ligase dependent targeting mechanisms.", + "subject": ["Ubiquitination", "Proteolysis", "E3 ligases", "Proteasome"], + "keywords": [] + }, + { + "title": "Shared origins of a key enzyme during the evolution of C4 and CAM metabolism", + "author": "Pascal-Antoine Christin, Monica Arakaki, Colin P. Osborne, Andrea Bräutigam, Rowan F. Sage, Julian M. Hibberd, Steven Kelly, Sarah Covshoff, Gane Ka-Shu Wong, Lillian Hancock, Erika J. Edwards", + "publisher": "Oxford University Press (OUP)", + "url": "http://dx.doi.org/10.1093/jxb/eru087", + "doi": "10.1093/jxb/eru087", + "year": 2014, + "month": 3, + "abstract": "CAM and C4 photosynthesis are two key plant adaptations that have evolved independently multiple times, and are especially prevalent in particular groups of plants, including the Caryophyllales. We investigate the origin of photosynthetic PEPC, a key enzyme of both the CAM and C4 pathways. We combine phylogenetic analyses of genes encoding PEPC with analyses of RNA sequence data of Portulaca, the only plants known to perform both CAM and C4 photosynthesis. Three distinct gene lineages encoding PEPC exist in eudicots (namely ppc-1E1, ppc-1E2 and ppc-2), one of which (ppc-1E1) was recurrently recruited for use in both CAM and C4 photosynthesis within the Caryophyllales. This gene is present in multiple copies in the cacti and relatives, including Portulaca. The PEPC involved in the CAM and C4 cycles of Portulaca are encoded by closely related yet distinct genes. The CAM-specific gene is similar to genes from related CAM taxa, suggesting that CAM has evolved before C4 in these species. The similar origin of PEPC and other genes involved in the CAM and C4 cycles highlights the shared early steps of evolutionary trajectories towards CAM and C4, which probably diverged irreversibly only during the optimization of CAM and C4 phenotypes.", + "subject": [ + "C4 photosynthesis", + "CAM photosynthesis", + "co-option", + "evolution", + "phosphoenolpyruvate carboxylase", + "PEPC", + "phylogenetics" + ], + "keywords": [] + }, + { + "title": "Phylogeny and the inference of evolutionary trajectories", + "author": "Lillian Hancock, Erika J. Edwards", + "publisher": "Oxford University Press (OUP)", + "url": "http://dx.doi.org/10.1093/jxb/eru118", + "doi": "10.1093/jxb/eru118", + "year": 2014, + "month": 4, + "abstract": "Most important organismal adaptations are not actually single traits, but complex trait syndromes that are evolutionarily integrated into a single emergent phenotype. Two alternative photosynthetic pathways, C4 photosynthesis and crassulacean acid metabolism (CAM), are primary plant adaptations of this sort, each requiring multiple biochemical and anatomical modifications. Phylogenetic methods are a promising approach for teasing apart the order of character acquisition during the evolution of complex traits, and the phylogenetic placement of intermediate phenotypes as sister taxa to fully optimized syndromes has been taken as good evidence of an ‘ordered’ evolutionary trajectory. But how much power does the phylogenetic approach have to detect ordered evolution? This study simulated ordered and unordered character evolution across a diverse set of phylogenetic trees to understand how tree size, models of evolution, and sampling efforts influence the ability to detect an evolutionary trajectory. The simulations show that small trees (15 taxa) do not contain enough information to correctly infer either an ordered or unordered trajectory, although inference improves as tree size and sampling increases. However, even when working with a 1000-taxon tree, the possibility of inferring the incorrect evolutionary model (type I/type II error) remains. Caution is needed when interpreting the phylogenetic placement of intermediate phenotypes, especially in small lineages. Such phylogenetic patterns can provide a line of evidence for the existence of a particular evolutionary trajectory, but they should be coupled with other types of data to infer the stepwise evolution of a complex character trait.", + "subject": [ + "C4 photosynthesis", + "crassulacean acid metabolism", + "evolution", + "intermediate phenotypes", + "phylogenetic approach", + "phylogeny" + ], + "keywords": [] + }, + { + "title": "GPU-accelerated denoising of 3D magnetic resonance images", + "author": "Mark Howison, E. Wes Bethel", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1007/s11554-014-0436-8", + "doi": "10.1007/s11554-014-0436-8", + "year": 2014, + "month": 6, + "abstract": "The raw computational power of GPU accelerators enables fast denoising of 3D MR images using bilateral filtering, anisotropic diffusion, and non-local means. In practice, applying these filtering operations requires setting multiple parameters. This study was designed to provide better guidance to practitioners for choosing the most appropriate parameters by answering two questions: what parameters yield the best denoising results in practice? And what tuning is necessary to achieve optimal performance on a modern GPU? To answer the first question, we use two different metrics, mean squared error (MSE) and mean structural similarity (MSSIM), to compare denoising quality against a reference image. Surprisingly, the best improvement in structural similarity with the bilateral filter is achieved with a small stencil size that lies within the range of real-time execution on an NVIDIA Tesla M2050 GPU. Moreover, inappropriate choices for parameters, especially scaling parameters, can yield very poor denoising performance. To answer the second question, we perform an autotuning study to empirically determine optimal memory tiling on the GPU. The variation in these results suggests that such tuning is an essential step in achieving real-time performance. These results have important implications for the real-time application of denoising to MR images in clinical settings that require fast turn-around times.", + "subject": [], + "keywords": [] + }, + { + "title": "Bayesian Genome Assembly and Assessment by Markov Chain Monte Carlo Sampling", + "author": "Mark Howison, Felipe Zapata, Erika J. Edwards, Casey W. Dunn", + "publisher": "Public Library of Science (PLoS)", + "url": "http://dx.doi.org/10.1371/journal.pone.0099497", + "doi": "10.1371/journal.pone.0099497", + "year": 2014, + "month": 6, + "abstract": "Most genome assemblers construct point estimates, choosing only a single genome sequence from among many alternative hypotheses that are supported by the data. We present a Markov chain Monte Carlo approach to sequence assembly that instead generates distributions of assembly hypotheses with posterior probabilities, providing an explicit statistical framework for evaluating alternative hypotheses and assessing assembly uncertainty. We implement this approach in a prototype assembler, called Genome Assembly by Bayesian Inference (GABI), and illustrate its application to the bacteriophage X174. Our sampling strategy achieves both good mixing and convergence on Illumina test data for X174, demonstrating the feasibility of our approach. We summarize the posterior distribution of assembly hypotheses generated by GABI as a majority-rule consensus assembly. Then we compare the posterior distribution to external assemblies of the same test data, and annotate those assemblies by assigning posterior probabilities to features that are in common with GABI’s assembly graph. GABI is freely available under a GPL license from https://bitbucket.org/mhowison/gabi.", + "subject": [], + "keywords": [] + }, + { + "title": "Departures from the Adsorption Energy Scaling Relations for Metal Carbide Catalysts", + "author": "Ronald Michalsky, Yin-Jia Zhang, Andrew J. Medford, Andrew A. Peterson", + "publisher": "American Chemical Society (ACS)", + "url": "http://dx.doi.org/10.1021/jp503756g", + "doi": "10.1021/jp503756g", + "year": 2014, + "month": 6, + "abstract": "The activity of heterogeneous catalysts is often limited by a strong correlation between the chemisorption energies of reaction intermediates described by the 'scaling relations' among the transition metals. We present electronic structure calculations that suggest that metal carbides do not in general follow the transition-metal scaling relations and tend to exhibit a carbophobic departure relative to the transition metals, meaning they tend to bind carbon-bound species weakly compared to oxygen-bound species. This contrasts with the oxophobic departure exhibited by Pt and Pd. Relative to the parent metals, carbides tend to bind carbon and oxygen more weakly and hydrogen more strongly. The departures are rationalized with the adsorbate–surface valence configuration and the energy of the metal sp-states. We employ these general trends to aid in the understanding of various catalytic properties such as the high activity of iron carbides for Fischer–Tropsch synthesis and Pt-group catalysts for partial oxidation of methane. These conclusions are shown to extend beyond atomic probe adsorbates to molecular fragments of relevance to catalysis, making these concepts generally useful for the theory-based design of catalytic materials.", + "subject": [], + "keywords": [] + }, + { + "title": "The first-night effect suppresses the strength of slow-wave activity originating in the visual areas during sleep", + "author": "Masako Tamaki, Ji Won Bang, Takeo Watanabe, Yuka Sasaki", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.visres.2013.10.023", + "doi": "10.1016/j.visres.2013.10.023", + "year": 2014, + "month": 6, + "abstract": "Our visual system is plastic and adaptive in response to the stimuli and environments we experience. Although visual adaptation and plasticity have been extensively studied while participants are awake, little is known about what happens while they are asleep. It has been documented that sleep structure as measured by sleep stages using polysomnography is altered specifically in the first sleep session due to exposure to a new sleep environment, known as the first-night effect (FNE). However, the impact of the FNE on spontaneous oscillations in the visual system is poorly understood. How does the FNE affect the visual system during sleep? To address this question, the present study examined whether the FNE modifies the strength of slow-wave activity (SWA, 1–4 Hz)—the dominant spontaneous brain oscillation in slow-wave sleep—in the visual areas. We measured the strength of SWA originating in the visual areas during the first and the second sleep sessions. Magnetoencephalography, polysomnography, and magnetic resonance imaging were used to localize the source of SWA to the visual areas. The visual areas were objectively defined using retinotopic mapping and an automated anatomical parcellation technique. The results showed that the strength of SWA was reduced in the first sleep session in comparison to the second sleep session, especially during slow-wave sleep, in the ventral part of the visual areas. These results suggest that environmental novelty may affect the visual system through suppression of SWA. The impact of the FNE may not be negligible in vision research.", + "subject": [], + "keywords": [] + }, + { + "title": "A Lack of Parasitic Reduction in the Obligate Parasitic Green Alga Helicosporidium", + "author": "Jean-François Pombert, Nicolas Achille Blouin, Chris Lane, Drion Boucias, Patrick J. Keeling", + "publisher": "Public Library of Science (PLoS)", + "url": "http://dx.doi.org/10.1371/journal.pgen.1004355", + "doi": "10.1371/journal.pgen.1004355", + "year": 2014, + "month": 5, + "abstract": "The evolution of an obligate parasitic lifestyle is often associated with genomic reduction, in particular with the loss of functions associated with increasing host-dependence. This is evident in many parasites, but perhaps the most extreme transitions are from free-living autotrophic algae to obligate parasites. The best-known examples of this are the apicomplexans such as Plasmodium, which evolved from algae with red secondary plastids. However, an analogous transition also took place independently in the Helicosporidia, where an obligate parasite of animals with an intracellular infection mechanism evolved from algae with green primary plastids. We characterised the nuclear genome of Helicosporidium to compare its transition to parasitism with that of apicomplexans. The Helicosporidium genome is small and compact, even by comparison with the relatively small genomes of the closely related green algae Chlorella and Coccomyxa, but at the functional level we find almost no evidence for reduction. Nearly all ancestral metabolic functions are retained, with the single major exception of photosynthesis, and even here reduction is not complete. The great majority of genes for light-harvesting complexes, photosystems, and pigment biosynthesis have been lost, but those for other photosynthesis-related functions, such as Calvin cycle, are retained. Rather than loss of whole function categories, the predominant reductive force in the Helicosporidium genome is a contraction of gene family complexity, but even here most losses affect families associated with genome maintenance and expression, not functions associated with host-dependence. Other gene families appear to have expanded in response to parasitism, in particular chitinases, including those predicted to digest the chitinous barriers of the insect host or remodel the cell wall of Helicosporidium. Overall, the Helicosporidium genome presents a fascinating picture of the early stages of a transition from free-living autotroph to parasitic heterotroph where host-independence has been unexpectedly preserved.", + "subject": [ + "Invertebrate genomics", + "Genomics", + "Algae", + "Parasite evolution", + "Parasitism", + "Metabolic pathways", + "Transcriptome analysis", + "Malarial parasites" + ], + "keywords": [] + }, + { + "title": "Dysferlin is essential for endocytosis in the sea star oocyte", + "author": "Nathalie Oulhen, Thomas M. Onorato, Isabela Ramos, Gary M. Wessel", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.ydbio.2013.12.018", + "doi": "10.1016/j.ydbio.2013.12.018", + "year": 2014, + "month": 4, + "abstract": "Dysferlin is a calcium-binding transmembrane protein involved in membrane fusion and membrane repair. In humans, mutations in the dysferlin gene are associated with muscular dystrophy. In this study, we isolated plasma membrane-enriched fractions from full-grown immature oocytes of the sea star, and identified dysferlin by mass spectrometry analysis. The full-length dysferlin sequence is highly conserved between human and the sea star. We learned that in the sea star Patiria miniata, dysferlin RNA and protein are expressed from oogenesis to gastrulation. Interestingly, the protein is highly enriched in the plasma membrane of oocytes. Injection of a morpholino against dysferlin leads to a decrease of endocytosis in oocytes, and to a developmental arrest during gastrulation. These results suggest that dysferlin is critical for normal endocytosis during oogenesis and for embryogenesis in the sea star and that this animal may be a useful model for studying the relationship of dysferlin structure as it relates to its function.", + "subject": [ + "Dysferlin", + "Sea star", + "Plasma membrane", + "Oocytes", + "Endocytosis", + "Gastrulation" + ], + "keywords": [] + }, + { + "title": "The design of a retinal resolution fully immersive VR display", + "author": "Anne Kenyon, John van Rosendale, Samuel Fulcomer, David Laidlaw", + "publisher": "IEEE", + "url": "http://dx.doi.org/10.1109/vr.2014.6802065", + "doi": "10.1109/vr.2014.6802065", + "year": 2014, + "month": 3, + "abstract": "We present the design of Brown University's new Cave, which is expected to be fully operational in February 2014. With one arc-minute resolution, 3.8 π steradians of visual surround, head-tracked stereo, and an almost seamless screen, this Cave offers advances to the state-of-the-art virtual reality experience. This improvement is achieved with the installation of 69 high-resolution long throw projectors, a cylindrical screen with conical ceiling, and a 135 square foot rear-projection floor. Though Caves have been around for over 20 years, they have remained impractical for many potential uses due to their limited resolution, brightness, and overall immersion. Brown's new Cave aims to bridge this gap.", + "subject": [], + "keywords": [] + }, + { + "title": "Trends in the Hydrogen Evolution Activity of Metal Carbide Catalysts", + "author": "Ronald Michalsky, Yin-Jia Zhang, Andrew A. Peterson", + "publisher": "American Chemical Society (ACS)", + "url": "http://dx.doi.org/10.1021/cs500056u", + "doi": "10.1021/cs500056u", + "year": 2014, + "month": 3, + "abstract": "Metal carbide catalysts are alternative nonprecious electrode materials for electrochemical energy conversion devices, such as for H2 fuel cells or electrolyzers. In this article, we report the experimental exchange current densities for the hydrogen evolution reaction (HER) on eight mono- and bimetallic carbide electrocatalysts and correlate the current densities to hydrogen binding energies that we have calculated via electronic structure computations. We find these materials to have activities higher than those of their parent metals and intermediate between the catalytic activities of the Pt group and early transition-metal surfaces. Increased HER activities on metal carbides relative to their parent metals can be understood with a 3-fold higher sensitivity of metal carbides to the coverage-induced weakening of hydrogen adsorption relative to metal surfaces. The trends presented here can be useful for the design of bimetallic carbide electrocatalysts.", + "subject": [ + "Adsorption", + "Evolution reactions", + "Hydrogen", + "Inorganic carbon compounds", + "Metals", + "electrocatalysis", + "surfaces", + "Sabatier principle", + "renewable energy", + "sustainable fuels" + ], + "keywords": [] + }, + { + "title": "Prevention And Treatment Produced Large Decreases In HIV Incidence In A Model Of People Who Inject Drugs", + "author": "Brandon D. L. Marshall, Samuel R. Friedman, João F. G. Monteiro, Magdalena Paczkowski, Barbara Tempalski, Enrique R. Pouget, Mark N. Lurie, Sandro Galea", + "publisher": "Health Affairs (Project Hope)", + "url": "http://dx.doi.org/10.1377/hlthaff.2013.0824", + "doi": "10.1377/hlthaff.2013.0824", + "year": 2014, + "month": 3, + "abstract": "In the United States, people who inject drugs continue to be at greatly increased risk of HIV infection. To estimate the effectiveness of various prevention scenarios, we modeled HIV transmission in a dynamic network of drug users and people who did not use drugs that was based on the New York Metropolitan Statistical Area population. We compared the projected HIV incidence in 2020 and 2040 if current approaches continue to be used to the incidence if one or more of the following hypothetical interventions were applied: increased HIV testing, improved access to substance abuse treatment, increased use of needle and syringe programs, scaled-up treatment as prevention, and a 'high impact' combination scenario, consisting of all of the strategies listed above. No strategy completely eliminated HIV transmission. The high-impact combination strategy produced the largest decrease in HIV incidence—a 62 percent reduction compared to the status quo. Our results suggest that increased resources for and investments in multiple HIV prevention approaches will be required to eliminate HIV transmission among people who inject drugs.", + "subject": [ + "HIV", + "AIDS", + "pharmaceuticals", + "drug use", + "access to care", + "HIV testing", + "substance use disorder", + "confidence intervals", + "diseases", + "injections", + "prevention programs" + ], + "keywords": [] + }, + { + "title": "Pan-genome analyses identify lineage- and niche-specific markers of evolution and adaptation in Epsilonproteobacteria", + "author": "Ying Zhang, Stefan M. Sievert", + "publisher": "Frontiers Media SA", + "url": "http://dx.doi.org/10.3389/fmicb.2014.00110", + "doi": "10.3389/fmicb.2014.00110", + "year": 2014, + "month": 3, + "abstract": "The rapidly increasing availability of complete bacterial genomes has created new opportunities for reconstructing bacterial evolution, but it has also highlighted the difficulty to fully understand the genomic and functional variations occurring among different lineages. Using the class Epsilonproteobacteria as a case study, we investigated the composition, flexibility, and function of its pan-genomes. Models were constructed to extrapolate the expansion of pan-genomes at three different taxonomic levels. The results show that, for Epsilonproteobacteria the seemingly large genome variations among strains of the same species are less noticeable when compared with groups at higher taxonomic ranks, indicating that genome stability is imposed by the potential existence of taxonomic boundaries. The analyses of pan-genomes has also defined a set of universally conserved core genes, based on which a phylogenetic tree was constructed to confirm that thermophilic species from deep-sea hydrothermal vents represent the most ancient lineages of Epsilonproteobacteria. Moreover, by comparing the flexible genome of a chemoautotrophic deep-sea vent species to (1) genomes of species belonging to the same genus, but inhabiting different environments, and (2) genomes of other vent species, but belonging to different genera, we were able to delineate the relative importance of lineage-specific versus niche-specific genes. This result not only emphasizes the overall importance of phylogenetic proximity in shaping the variable part of the genome, but also highlights the adaptive functions of niche-specific genes. Overall, by modeling the expansion of pan-genomes and analyzing core and flexible genes, this study provides snapshots on how the complex processes of gene acquisition, conservation, and removal affect the evolution of different species, and contribute to the metabolic diversity and versatility of Epsilonproteobacteria.", + "subject": [], + "keywords": [] + }, + { + "title": "Understanding Boron through Size-Selected Clusters: Structure, Chemical Bonding, and Fluxionality", + "author": "Alina P. Sergeeva, Ivan A. Popov, Zachary A. Piazza, Wei-Li Li, Constantin Romanescu, Lai-Sheng Wang, Alexander I. Boldyrev", + "publisher": "American Chemical Society (ACS)", + "url": "http://dx.doi.org/10.1021/ar400310g", + "doi": "10.1021/ar400310g", + "year": 2014, + "month": 3, + "abstract": "", + "subject": [ + "Aromatic compounds", + "Boron", + "Cluster chemistry", + "Cluster structure", + "Hydrocarbons" + ], + "keywords": [] + }, + { + "title": "Global Optimization of Adsorbate–Surface Structures While Preserving Molecular Identity", + "author": "Andrew A. Peterson", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1007/s11244-013-0161-8", + "doi": "10.1007/s11244-013-0161-8", + "year": 2013, + "month": 10, + "abstract": "As the complexity of atomistic simulations in catalysis and surface science increases, the challenge of manually finding the lowest-energy adsorbate–surface geometries grows significantly. In the current work, a global optimization approach that preserves adsorbate identity is applied to enable the automated search for optimized binding geometries. This technique is based on the minima hopping method developed by Goedecker, but is modified to preserve the molecular identity of adsorbates by the application of a new class of Hookean constraints. These constraints are completely inactive when the adsorbate identity is preserved, but act to restore the adsorbate structure via a Hookean force when the bond length exceeds a threshold distance. Additionally, a related Hookean constraint has been developed to prevent adsorbates (particularly such adsorbates as CO and CH2O that have stable gas-phase forms) from volatilizing during the molecular dynamics portion of the minima hopping technique. This combination, referred to herein as the constrained minima hopping method, was tested for its suitability in finding the minimum-energy binding configuration for a set of 17 C x H y O z adsorbates on a stepped Cu fcc(211) surface and in all cases found the global minima in comparable or fewer steps than the previous brute force methodologies. It is expected that methods such as this will be crucial to finding low-energy states in more complex systems, such as those with high coverages of adsorbed species or in the presence of explicit solvent molecules.\n\n", + "subject": [], + "keywords": [] + }, + { + "title": "Microscale-calibrated modeling of the deformation response of dual-phase steels", + "author": "Peng Chen, Hassan Ghassemi-Armaki, Sharvan Kumar, Allan Bower, Shrikant Bhat, Sriram Sadagopan", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.actamat.2013.11.036", + "doi": "10.1016/j.actamat.2013.11.036", + "year": 2014, + "month": 2, + "abstract": "A combination of micropillar compression tests and microstructure-based numerical simulations were used to determine the flow strength and strain rate partitioning in uniaxial tension in two commercial low-carbon dual-phase sheet steels, DP980 (0.09% C–2.15% Mn–0.60% Si (wt.%)) and DF140T (0.15% C–1.45% Mn–0.30% Si (wt.%)). The two steels have different microstructures, with the martensite volume fraction in DP980 being ∼60%, compared to ∼40% in DF140T. Nevertheless, they exhibit similar uniaxial stress–strain behavior. To determine the microstructural origin of this behavior, micropillar compression specimens from ferrite and martensitic phases in both steels were deformed in uniaxial compression to obtain their individual response. A microstructure-based crystal plasticity model that accounts for non-Schmid behavior in the ferrite phase and contains a detailed description of the hierarchical microstructure of martensite was developed and material parameters were determined by fitting model predictions to the micropillar compression data. The crystal plasticity model was then used to predict the flow stress and strain rate partitioning during uniaxial tensile deformation of the two steels. The ferrite phase in the two steels was found to have similar flow strength. In contrast, the flow stress of martensite in DF140T was found to be approximately twice that in DP980. This strength difference is offset by the difference in martensite volume fraction in the two steels, resulting in nearly identical uniaxial tensile behavior. The strain rate partitioning and interfacial stress distributions in the two steels differ significantly, however, and have important implications on their tensile ductility.", + "subject": [], + "keywords": [] + }, + { + "title": "Understanding Strain and Ligand Effects in Hydrogen Evolution over Pd(111) Surfaces", + "author": "Tuhina Adit Maark, Andrew A. Peterson", + "publisher": "American Chemical Society (ACS)", + "url": "http://dx.doi.org/10.1021/jp4121035", + "doi": "10.1021/jp4121035", + "year": 2014, + "month": 2, + "abstract": "Pseudomorphic catalytic systems can exhibit enhanced or inhibited activity relative to the pure surface parent metal, based on a combination of strain and ligand effects. In contrast, mechanically strained and dealloyed systems can exhibit pure strain effects. Density functional calculations for hydrogen adsorption at different coverages between 0.25 and 1 monolayer on biaxially strained Pd(111) are carried out to illustrate its differing catalytic behavior for the hydrogen evolution reaction (HER) in comparison to selected pseudomorphic Pd overlayers (Pd/M). The separation of the ligand and strain effects present in Pd/M pseudomorphs and the consequent modification of the binding strengths caused by them individually are estimated. The strain exhibits a systematic contribution to binding energy changes while the ligand effect can act to either intensify or weaken the strain effect. In certain systems (e.g., Pd/Ir) the ligand effect is more pronounced than the strain effect while in others (e.g., Pd/Au) the strain effect is larger. The individual contributions of strain and ligand effects to shifts in the d-band center are also calculated and found to correlate well with the observed binding energy changes. We suggest that in the absence of a ligand effect—as would be expected in mechanically strained Pd (111)—H binding is tunable, and a differential free energy of hydrogen adsorption of ∼0 eV (at 0 V vs RHE) is achieved at various combinations of strain and coverage. For pure Pd under compressive strain, this leads to a prediction of a broad region of enhanced activity for the HER which may compare favorably to Pd overlayers supported on more expensive metals such as Pt and PtRu.", + "subject": ["Adsorption", "Evolution reactions", "Ligand effects", "Metals", "Palladium"], + "keywords": [] + }, + { + "title": "Planar hexagonal B36 as a potential basis for extended single-atom layer boron sheets", + "author": "Zachary A. Piazza, Han-Shi Hu, Wei-Li Li, Ya-Fan Zhao, Jun Li, Lai-Sheng Wang", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1038/ncomms4113", + "doi": "10.1038/ncomms4113", + "year": 2014, + "month": 1, + "abstract": "Boron is carbon’s neighbour in the periodic table and has similar valence orbitals. However, boron cannot form graphene-like structures with a honeycomb hexagonal framework because of its electron deficiency. Computational studies suggest that extended boron sheets with partially filled hexagonal holes are stable; however, there has been no experimental evidence for such atom-thin boron nanostructures. Here, we show experimentally and theoretically that B36 is a highly stable quasiplanar boron cluster with a central hexagonal hole, providing the first experimental evidence that single-atom layer boron sheets with hexagonal vacancies are potentially viable. Photoelectron spectroscopy of B36− reveals a relatively simple spectrum, suggesting a symmetric cluster. Global minimum searches for B36− lead to a quasiplanar structure with a central hexagonal hole. Neutral B36 is the smallest boron cluster to have sixfold symmetry and a perfect hexagonal vacancy, and it can be viewed as a potential basis for extended two-dimensional boron sheets.", + "subject": [], + "keywords": [] + }, + { + "title": "Controlled-Potential Simulation of Elementary Electrochemical Reactions: Proton Discharge on Metal Surfaces", + "author": "Georg Kastlunger, Per Lindgren, Andrew A. Peterson", + "publisher": "American Chemical Society (ACS)", + "url": "http://dx.doi.org/10.1021/acs.jpcc.8b02465", + "doi": "10.1021/acs.jpcc.8b02465", + "year": 2018, + "month": 6, + "abstract": "The simulation of electrochemical reaction dynamics from first principles remains challenging, since over the course of an elementary step, an electron is either consumed or produced by the electrode. For example, the hydrogen evolution reaction begins with a simple proton discharge to a metal surface, but with conventional electronic structure methods, the simulated potential, which is manifested as the metal’s workfunction, varies over the course of the simulation as the electron is consumed in the new metal–hydrogen bond. Here, we present a simple approach to allow the direct control of the electrochemical potential via charging of the electrode surface. This is achieved by changing the total number of electrons in the self-consistent cycle, while enforcing charge neutrality through the introduction of a jellium counter charge dispersed in an implicit solvent region above the slab. We observe that the excess electrons localize selectively at the metal’s reactive surface and that the metal workfunction responds nearly linearly to the variation in electronic count. This linear response allows for control of the potential in simulations with a minimal computational penalty compared to standard electronic structure calculations. This scheme can be straightforwardly implemented with common electronic structure calculators (density functional theory in the present work), and we find this method to be compatible with the commonly used computational hydrogen electrode model, which we expect will make it useful in the construction of potential-dependent free-energy diagrams in electrochemistry. We apply this approach to the proton-deposition (Volmer) step on both Au(111) and Pt(111) surfaces and show that we can reliably control the simulated electrode potential and thus assess the potential dependence of the initial, transition, and final states. Our method allows us to directly assess the location along the reaction pathway with the greatest amount of charge transfer, which we find to correspond well with the reaction barrier, indicating this reaction is a concerted proton–electron transfer. Interestingly, we show that the Pt electrode has not only a more favorable equilibrium energy with adsorbed hydrogen but also a lower intrinsic barrier under thermoneutral conditions.", + "subject": ["Electrochemical cells", "Electrodes", "Solvents", "Surface charge", "Vesicles"], + "keywords": [] + }, + { + "title": "Neural-network-enhanced evolutionary algorithm applied to supported metal nanoparticles", + "author": "E. L. Kolsbjerg, A. A. Peterson, B. Hammer", + "publisher": "American Physical Society (APS)", + "url": "http://dx.doi.org/10.1103/physrevb.97.195424", + "doi": "10.1103/physrevb.97.195424", + "year": 2018, + "month": 5, + "abstract": "We show that approximate structural relaxation with a neural network enables orders of magnitude faster global optimization with an evolutionary algorithm in a density functional theory framework. The increased speed facilitates reliable identification of global minimum energy structures, as exemplified by our finding of a hollow Pt13 nanoparticle on an MgO support. We highlight the importance of knowing the correct structure when studying the catalytic reactivity of the different particle shapes. The computational speedup further enables screening of hundreds of different pathways in the search for optimum kinetic transitions between low-energy conformers and hence pushes the limits of the insight into thermal ensembles that can be obtained from theory.", + "subject": [], + "keywords": [] + }, + { + "title": "Nanocomposites of transition-metal carbides on reduced graphite oxide as catalysts for the hydrogen evolution reaction", + "author": "Seok Ki Kim, Yang Qiu, Yin-Jia Zhang, Robert Hurt, Andrew Peterson", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.apcatb.2018.04.032", + "doi": "10.1016/j.apcatb.2018.04.032", + "year": 2018, + "month": 11, + "abstract": "Transition metal carbides (TMC), Mo2C, Fe3C, and WC·W2C, were synthesized as well-dispersed nanoparticles on a reduced graphite oxide (rGO) substrate and each of their hydrogen evolution reaction (HER) activities was compared with that of a bulk TMC powder. Among the TMC/rGO nanocomposites, only Mo2C/rGO exhibited an obvious increase in the capacitance-normalized current density compared to the bulk powder. We performed density functional theory calculations which suggest that the distinctive activity of Mo2C can be attributed to the structure-sensitive binding energies of atomic H, which binds less strongly on the stepped surface than the flat surface of Mo2C, while other TMCs do not exhibit clear structure-sensitivity. The charge transfer resistances were significantly reduced by using rGO as the substrate, but its correlation with the HER activity was not strong. An analysis of the kinetic data suggested that hydrogen evolution on the TMC surface follows the Volmer–Tafel mechanism with the Tafel step (recombination) rate limiting, which is responsible to the weak correlation between the charge transfer properties and HER activity.", + "subject": [], + "keywords": [] + }, + { + "title": "How strain can break the scaling relations of catalysis", + "author": "Alireza Khorshidi, James Violet, Javad Hashemi, Andrew A. Peterson", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1038/s41929-018-0054-0", + "doi": "10.1038/s41929-018-0054-0", + "year": 2018, + "month": 4, + "abstract": "Heterogeneous catalysts control the rates of chemical reactions by changing the energy levels of bound intermediates relative to one another. However, the design flexibility in catalysis is limited by scaling relations: when a catalyst binds one adsorbate more strongly, it tends to bind similar adsorbates more strongly as well. Here we show how strain can break this constraint by employing a mechanics-based eigenstress model to rationalize the effect of strain on adsorbate–catalyst bonding. This model suggests that the sign of the binding-energy response to strain depends on the coupling of the adsorbate-induced eigenstress with the applied strain; thus, tensile strain can make binding either stronger or weaker, depending on the eigenstress characteristics of the adsorbate on the surface. We then suggest how these principles can be used in conjunction with anisotropic strain to engineer opposite responses of adjacent adsorbates to strain; such effects are expected to allow larger changes to reaction rates than predicted by scaling relations.", + "subject": [], + "keywords": [] + }, + { + "title": "Unexpected prevalence of parasite 18S rDNA sequences in winter among Antarctic marine protists", + "author": "Alison C. Cleary, Edward G. Durbin", + "publisher": "Oxford University Press (OUP)", + "url": "http://dx.doi.org/10.1093/plankt/fbw005", + "doi": "10.1093/plankt/fbw005", + "year": 2016, + "month": 2, + "abstract": "Parasites are not typically considered to be important components of polar marine ecosystems. It was therefore surprising when 18S rDNA surveys of protists in the West Antarctic Peninsula in winter revealed high abundances of parasite sequences. Parasite sequences made up, on average, over half (52%) of sequence reads in samples from deep water in winter. Winter surface water and sediment samples contained relatively fewer, but still strikingly high, parasite sequence reads (13 and 9%, respectively), while surface water samples in summer contained fewer parasite sequences (1.8%). A total of 1028 distinct parasite Operational Taxonomic Units were observed in winter, with the largest abundances and diversities within Syndiniales groups I and II, including Amoebophrya. Less abundant parasite sequence groups included Apicomplexa, Blastodinium, Chytriodinium, Cryptocaryon, Paradinium, Perkinsidae, Pirsonia and Ichthyophonae. Parasite sequence distributions suggested interactions with known hosts, such as diatom parasites which were mainly in the sediments, where resting spores of Chaetoceros spp. diatoms were abundant. Syndiniales sequences were correlated with radiolarian sequences, suggesting parasite–host interactions. The abundant proportions of parasite sequences indicate a potentially important role for parasites in the Antarctic marine ecosystem, with implications for plankton population dynamics, the role of the microbial loop, carbon flows and ecosystem responses to ongoing anthropogenic climate change.", + "subject": [], + "keywords": [] + }, + { + "title": "MASS SUBSTRUCTURE IN ABELL 3128", + "author": "J. McCleary, I. dell’Antonio, P. Huwe", + "publisher": "American Astronomical Society", + "url": "http://dx.doi.org/10.1088/0004-637x/805/1/40", + "doi": "10.1088/0004-637x/805/1/40", + "year": 2015, + "month": 5, + "abstract": "We perform a detailed two-dimensional weak gravitational lensing analysis of the nearby (z = 0.058) galaxy cluster Abell 3128 using deep ugrz imaging from the Dark Energy Camera (DECam). We have designed a pipeline to remove instrumental artifacts from DECam images and stack multiple dithered observations without inducing a spurious ellipticity signal. We develop a new technique to characterize the spatial variation of the point-spread function that enables us to circularize the field to better than 0.5% and thereby extract the intrinsic galaxy ellipticities. By fitting photometric redshifts to sources in the observation, we are able to select a sample of background galaxies for weak-lensing analysis free from low-redshift contaminants. Photometric redshifts are also used to select a high-redshift galaxy subsample with which we successfully isolate the signal from an interloping z = 0.44 cluster. We estimate the total mass of Abell 3128 by fitting the tangential ellipticity of background galaxies with the weak-lensing shear profile of a Navarro–Frenk–White (NFW) halo and also perform NFW fits to substructures detected in the 2D mass maps of the cluster. This study yields one of the highest resolution mass maps of a low-z cluster to date and is the first step in a larger effort to characterize the redshift evolution of mass substructures in clusters.", + "subject": [], + "keywords": [] + }, + { + "title": "Advancing quantitative techniques to improve understanding of the skeletal structure-function relationship", + "author": "Frances T. Sheehan, Elizabeth L. Brainerd, Karen L. Troy, Sandra J. Shefelbine, Janet L. Ronsky", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1186/s12984-018-0368-9", + "doi": "10.1186/s12984-018-0368-9", + "year": 2018, + "month": 3, + "abstract": "Although all functional movement arises from the interplay between the neurological, skeletal, and muscular systems, it is the skeletal system that forms the basic framework for functional movement. Central to understanding human neuromuscular development, along with the genesis of musculoskeletal pathologies, is quantifying how the human skeletal system adapts and mal-adapts to its mechanical environment. Advancing this understanding is hampered by an inability to directly and non-invasively measure in vivo strains, stresses, and forces on bone. Thus, we traditionally have turned to animal models to garner such information. These models enable direct in vivo measures that are not available for human subjects, providing information in regards to both skeletal adaptation and the interplay between the skeletal and muscular systems. Recently, there has been an explosion of new imaging and modeling techniques providing non-invasive, in vivo measures and estimates of skeletal form and function that have long been missing. Combining multiple modalities and techniques has proven to be one of our most valuable resources in enhancing our understanding of the form-function relationship of the human skeletal, muscular, and neurological systems. Thus, to continue advancing our knowledge of the structural-functional relationship, validation of current tools is needed, while development is required to limit the deficiencies in these tools and develop new ones.\n\n", + "subject": [], + "keywords": [] + }, + { + "title": "On calibration of the response of liquid argon detectors to nuclear recoils using inelastic neutron scattering on40Ar", + "author": "S. Polosatkin, E. Grishnyaev, A. Dolgov", + "publisher": "IOP Publishing", + "url": "http://dx.doi.org/10.1088/1748-0221/9/10/p10017", + "doi": "10.1088/1748-0221/9/10/p10017", + "year": 2014, + "month": 10, + "abstract": "A method for measuring of ionization and scintillation yields in liquid argon from recoils with particular energy—8.2 keV—is proposed. The method utilizes a process of inelastic scattering of monoenergetic neutrons produced by fusion DD neutron generator. Features of kinematics of inelastic scattering result in a sufficient (fifteen times) increase in count rate of useful events relative to a traditional scheme using elastic scattering with the same recoil energy and comparable energy resolution.", + "subject": [], + "keywords": [] + }, + { + "title": "Fiber bundle length and cognition: a length-based tractography MRI study", + "author": "Ashley M. Behrman-Lay, Christina Usher, Thomas E. Conturo, Stephen Correia, David H. Laidlaw, Elizabeth M. Lane, Jacob Bolzenius, Jodi M. Heaps, Lauren E. Salminen, Laurie M. Baker, Ryan Cabeen, Erbil Akbudak, Xi Luo, Peisi Yan, Robert H. Paul", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1007/s11682-014-9334-8", + "doi": "10.1007/s11682-014-9334-8", + "year": 2014, + "month": 11, + "abstract": "Executive function (EF) and cognitive processing speed (CPS) are two cognitive performance domains that decline with advanced age. Reduced EF and CPS are known to correlate with age-related frontal-lobe volume loss. However, it remains unclear whether white matter microstructure in these regions is associated with age-related decline in EF and/or CPS. We utilized quantitative tractography metrics derived from diffusion-tensor MRI to investigate the relationship between the mean fiber bundle lengths (FBLs) projecting to different lobes, and EF/CPS performance in 73 healthy aging adults. We measured aspects of EF and CPS with the Trail Making Test (TMT), Color-Word Interference Test, Letter-Number Sequencing (L-N Seq), and Symbol Coding. Results revealed that parietal and occipital FBLs explained a significant portion of variance in EF. Frontal, temporal, and occipital FBLs explained a significant portion of variance in CPS. Shorter occipital FBLs were associated with poorer performance on the EF tests TMT-B and CWIT 3. Shorter frontal, parietal, and occipital FBLs were associated with poorer performance on L-N Seq and Symbol Coding. Shorter frontal and temporal FBLs were associated with lower performance on CPS tests TMT-A and CWIT 1. Shorter FBLs were also associated with increased age. Results suggest an age-related FBL shortening in specific brain regions related to poorer EF and CPS performance among older adults. Overall, results support both the frontal aging hypothesis and processing speed theory, suggesting that each mechanism is contributing to age-related cognitive decline.", + "subject": [], + "keywords": [] + }, + { + "title": "Using microkinetic analysis to search for novel anhydrous formaldehyde production catalysts", + "author": "Han-Jung Li, Adam C. Lausche, Andrew A. Peterson, Heine A. Hansen, Felix Studt, Thomas Bligaard", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.susc.2015.04.028", + "doi": "10.1016/j.susc.2015.04.028", + "year": 2015, + "month": 11, + "abstract": "Direct dehydrogenation of methanol to produce anhydrous formaldehyde is investigated using periodic density functional theory (DFT) and combining the microkinetic model to estimate rates and selectivities on stepped (211) surfaces under a desired reaction condition. Binding energies of reaction intermediates and transition state energies for each elementary reaction can be accurately scaled with CHO and OH binding energies as the only descriptors. Based on these two descriptors, a steady-state microkinetic model is constructed with a piecewise adsorbate–adsorbate interaction model that explicitly includes the effects of adsorbate coverage on the rates and selectivities as well as the volcano plots are obtained. Our results show that most of the stepped (211) pure-metallic surfaces such as Au, Pt, Pd, Rh, Ru, Ni, Fe, and Co are located in a region of low activity and selectivity toward CH2O production due to higher rate for CH2O dehydrogenation than CH2O desorption. The selectivities toward CH2O production on Zn, Cu, and Ag surfaces are located on the boundary between the high and low selectivity regions. To find suitable catalysts for anhydrous CH2O production, a large number of A3B-type transition metal alloys are screened based on their predicted rates and selectivities, as well as their estimated stabilities and prices. We finally propose several promising candidates for the dehydrogenation of CH3OH.", + "subject": [], + "keywords": [] + }, + { + "title": "Unsupervised invariance learning of transformation sequences in a model of object recognition yields selectivity for non-accidental properties", + "author": "Sarah M. Parker, Thomas Serre", + "publisher": "Frontiers Media SA", + "url": "http://dx.doi.org/10.3389/fncom.2015.00115", + "doi": "10.3389/fncom.2015.00115", + "year": 2015, + "month": 10, + "abstract": "Non-accidental properties (NAPs) correspond to image properties that are invariant to changes in viewpoint (e.g., straight vs. curved contours) and are distinguished from metric properties (MPs) that can change continuously with in-depth object rotation (e.g., aspect ratio, degree of curvature, etc.). Behavioral and electrophysiological studies of shape processing have demonstrated greater sensitivity to differences in NAPs than in MPs. However, previous work has shown that such sensitivity is lacking in multiple-views models of object recognition such as HMAX. These models typically assume that object processing is based on populations of view-tuned neurons with distributed symmetrical bell-shaped tuning that are modulated at least as much by differences in MPs as in NAPs. Here, we test the hypothesis that unsupervised learning of invariances to object transformations may increase the sensitivity to differences in NAPs vs. MPs in HMAX. We collected a database of video sequences with objects slowly rotating in-depth in an attempt to mimic sequences viewed during object manipulation by young children during early developmental stages. We show that unsupervised learning yields shape-tuning in higher stages with greater sensitivity to differences in NAPs vs. MPs in agreement with monkey IT data. Together, these results suggest that greater NAP sensitivity may arise from experiencing different in-depth rotations of objects.\n\n", + "subject": [], + "keywords": [] + }, + { + "title": "Explaining the Timing of Natural Scene Understanding with a Computational Model of Perceptual Categorization", + "author": "Imri Sofer, Sébastien M. Crouzet, Thomas Serre", + "publisher": "Public Library of Science (PLoS)", + "url": "http://dx.doi.org/10.1371/journal.pcbi.1004456", + "doi": "10.1371/journal.pcbi.1004456", + "year": 2015, + "month": 9, + "abstract": "Observers can rapidly perform a variety of visual tasks such as categorizing a scene as open, as outdoor, or as a beach. Although we know that different tasks are typically associated with systematic differences in behavioral responses, to date, little is known about the underlying mechanisms. Here, we implemented a single integrated paradigm that links perceptual processes with categorization processes. Using a large image database of natural scenes, we trained machine-learning classifiers to derive quantitative measures of task-specific perceptual discriminability based on the distance between individual images and different categorization boundaries. We showed that the resulting discriminability measure accurately predicts variations in behavioral responses across categorization tasks and stimulus sets. We further used the model to design an experiment, which challenged previous interpretations of the so-called 'superordinate advantage.' Overall, our study suggests that observed differences in behavioral responses across rapid categorization tasks reflect natural variations in perceptual discriminability.", + "subject": [ + "vision", + "sensory perception", + "reaction time", + "taxonomy", + "machine learning", + "behavior", + "experimental design", + "birds" + ], + "keywords": [] + }, + { + "title": "Prediction of the material with highest known melting point fromab initiomolecular dynamics calculations", + "author": "Qi-Jun Hong, Axel van de Walle", + "publisher": "American Physical Society (APS)", + "url": "http://dx.doi.org/10.1103/physrevb.92.020104", + "doi": "10.1103/physrevb.92.020104", + "year": 2015, + "month": 7, + "abstract": "Using electronic structure calculations, we conduct an extensive investigation into the Hf-Ta-C system, which includes the compounds that have the highest melting points known to date. We identify three major chemical factors that contribute to the high melting temperatures. Based on these factors, we propose a class of materials that may possess even higher melting temperatures and explore it via efficient ab initio molecular dynamics calculations in order to identify the composition maximizing the melting point. This study demonstrates the feasibility of automated and high-throughput materials screening and discovery via ab initio calculations for the optimization of 'higher-level' properties, such as melting points, whose determination requires extensive sampling of atomic configuration space.", + "subject": [], + "keywords": [] + }, + { + "title": "Competition between CO2 Reduction and H2 Evolution on Transition-Metal Electrocatalysts", + "author": "Yin-Jia Zhang, Vijay Sethuraman, Ronald Michalsky, Andrew A. Peterson", + "publisher": "American Chemical Society (ACS)", + "url": "http://dx.doi.org/10.1021/cs5012298", + "doi": "10.1021/cs5012298", + "year": 2014, + "month": 9, + "abstract": "The well-known hydrogen evolution reaction (HER) volcano plot describes the relationship between H binding energy and the corresponding hydrogen evolution catalytic activity, which depends on the species of metal. Under CO2/CO reduction conditions or in cases where CO impurities enter electrodes, the catalyst may exist under a high coverage of coadsorbed CO. We present DFT calculations that suggest that coadsorbed CO during hydrogen evolution will weaken the binding strength between H and the catalyst surface. For metals on the right-hand side (too weak of hydrogen binding) this should lead to a suppression of the HER, as has been reported for metals such as Cu and Pt. However, for metals on the left-hand side of the volcano (too strong of hydrogen binding), this may actually enhance the kinetics of the hydrogen evolution reaction, although this effect will be countered by a decreased availability of sites for HER, which are blocked by CO. We performed experiments in Ar and CO2 environments of two representative metals that bind CO on the far right- and left-hand side of the volcano, namely, Cu and Mo (respectively). On Cu, we find that the CO2 environment suppresses HER, which is consistent with previous findings. However, on Mo we find that the CO2 environment enhances HER in the kinetically active region. This helps to explain the outstanding performance of copper in CO2 reduction and suggests that searches for high-selectivity CO2/CO reduction catalysts may benefit from focusing on the right-hand side of the HER volcano. This also suggests principles for assessing the activity of catalysts for fuel cell and electrolysis reactions in which impurities such as CO may be present.", + "subject": [ + "Copper", + "Evolution reactions", + "Hydrogen", + "Inorganic carbon compounds", + "Oxides" + ], + "keywords": [] + }, + { + "title": "Learning Sparse Prototypes for Crowd Perception via Ensemble Coding Mechanisms", + "author": "Yanhao Zhang, Shengping Zhang, Qingming Huang, Thomas Serre", + "publisher": "Springer International Publishing", + "url": "http://dx.doi.org/10.1007/978-3-319-11839-0_8", + "doi": "10.1007/978-3-319-11839-0_8", + "year": 2014, + "month": 9, + "abstract": "Recent work in cognitive psychology suggests that crowd perception may be based on pre-attentive ensemble coding mechanisms consistent with feedforward hierarchical models of visual processing. Here, we extend a biological model of motion processing with a new dictionary learning method tailored for crowd perception. Our approach uses a sparse coding model to learn crowd prototypes. Ensemble coding mechanisms are implemented via structural and local coherence constraints. We evaluate the proposed method on multiple crowd perception problems from collective or abnormal crowd detection to tracking individuals in crowded scenes. Experimental results on crowd datasets demonstrate competitive results on par or better than state-of-the-art approaches.", + "subject": [], + "keywords": [] + }, + { + "title": "The Language of Actions: Recovering the Syntax and Semantics of Goal-Directed Human Activities", + "author": "Hilde Kuehne, Ali Arslan, Thomas Serre", + "publisher": "IEEE", + "url": "http://dx.doi.org/10.1109/cvpr.2014.105", + "doi": "10.1109/cvpr.2014.105", + "year": 2014, + "month": 6, + "abstract": "This paper describes a framework for modeling human activities as temporally structured processes. Our approach is motivated by the inherently hierarchical nature of human activities and the close correspondence between human actions and speech: We model action units using Hidden Markov Models, much like words in speech. These action units then form the building blocks to model complex human activities as sentences using an action grammar. To evaluate our approach, we collected a large dataset of daily cooking activities: The dataset includes a total of 52 participants, each performing a total of 10 cooking activities in multiple real-life kitchens, resulting in over 77 hours of video footage. We evaluate the HTK toolkit, a state-of-the-art speech recognition engine, in combination with multiple video feature descriptors, for both the recognition of cooking activities (e.g., making pancakes) as well as the semantic parsing of videos into action units (e.g., cracking eggs). Our results demonstrate the benefits of structured temporal generative approaches over existing discriminative approaches in coping with the complexity of human daily life activities.", + "subject": [ + "Hidden Markov models", + "Dairy products", + "Accuracy", + "Speech recognition", + "Speech", + "Grammar", + "Sugar", + "Human Activities", + "Hidden Markov Model", + "Speech Recognition", + "Temporal Structure", + "Action Recognition", + "Action Units", + "Discriminative Approach", + "Cooking Activities", + "Hierarchical Structure", + "Behavioral Analysis", + "Transition Probabilities", + "Types Of Errors", + "Gaussian Mixture Model", + "Level Of Granularity", + "Starting State", + "Shorter Ones", + "Video Dataset", + "Video Segments", + "Synthetic Minority Oversampling Technique", + "Dynamic Time Warping", + "Chocolate Milk", + "Context-free Grammar", + "Human Activity Recognition", + "Different Types Of Errors", + "Number Of Gaussians", + "Action Recognition Model", + "Level Of Annotation", + "Combination Of Units" + ], + "keywords": [] + }, + { + "title": "A Pilot Study of Neural Correlates of Loss of Control Eating in Children With Overweight/Obesity: Probing Intermittent Access to Food as a Means of Eliciting Disinhibited Eating", + "author": "Andrea B Goldschmidt, Daniel P Dickstein, Annmarie E MacNamara, K Luan Phan, Setareh O’Brien, Daniel Le Grange, Jennifer O Fisher, Sarah Keedy", + "publisher": "Oxford University Press (OUP)", + "url": "http://dx.doi.org/10.1093/jpepsy/jsy009", + "doi": "10.1093/jpepsy/jsy009", + "year": 2018, + "month": 2, + "abstract": "Neural substrates of loss of control (LOC) eating are undercharacterized. We aimed to model intermittent access to food to elicit disinhibited eating in youth undergoing neuroimaging, given evidence that restricted food access may increase subsequent food intake via enhancing reward value of food and diminishing eating-related self-control.", + "subject": [ + "dietary restriction", + "disinhibited eating", + "executive functioning", + "loss of control eating", + "neural activation", + "obesity", + "feeding behaviors", + "food", + "unconsciousness", + "eating", + "overweight" + ], + "keywords": [] + }, + { + "title": "Improved phylogenetic resolution within Siphonophora (Cnidaria) with implications for trait evolution", + "author": "Catriona Munro, Stefan Siebert, Felipe Zapata, Mark Howison, Alejandro Damian-Serrano, Samuel H. Church, Freya E. Goetz, Philip R. Pugh, Steven H.D. Haddock, Casey W. Dunn", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.ympev.2018.06.030", + "doi": "10.1016/j.ympev.2018.06.030", + "year": 2018, + "month": 10, + "abstract": "Siphonophores are a diverse group of hydrozoans (Cnidaria) that are found at most depths of the ocean - from the surface, like the familiar Portuguese man of war, to the deep sea. They play important roles in ocean ecosystems, and are among the most abundant gelatinous predators. A previous phylogenetic study based on two ribosomal RNA genes provided insight into the internal relationships between major siphonophore groups. There was, however, little support for many deep relationships within the clade Codonophora. Here, we present a new siphonophore phylogeny based on new transcriptome data from 29 siphonophore species analyzed in combination with 14 publicly available genomic and transcriptomic datasets. We use this new phylogeny to reconstruct several traits that are central to siphonophore biology, including sexual system (monoecy vs. dioecy), gain and loss of zooid types, life history traits, and habitat. The phylogenetic relationships in this study are largely consistent with the previous phylogeny, but we find strong support for new clades within Codonophora that were previously unresolved. These results have important implications for trait evolution within Siphonophora, including favoring the hypothesis that monoecy arose at least twice.", + "subject": [], + "keywords": [] + }, + { + "title": "First-principles calculations of thermal properties of the mechanically unstable phases of the PtTi and NiTi shape memory alloys", + "author": "Sara Kadkhodaei, Axel van de Walle", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.actamat.2018.01.025", + "doi": "10.1016/j.actamat.2018.01.025", + "year": 2018, + "month": 4, + "abstract": "The design of shape memory alloys (SMA) demands detailed knowledge of their thermodynamic properties and of the underlying atomic-level mechanisms governing their shape-memory behavior. This knowledge is traditionally obtained via atomistic simulations, but these systems have so far resisted such efforts due to the presence of phonon instabilities and associated spontaneous symmetry breaking. In this study, we investigate the thermodynamics of PtTi, a novel and promising SMA (and of the related better-known NiTi SMA, for comparison purposes) using recently developed first-principles computational method specifically designed to tackle this issue. The method efficiently explores the system's potential energy surface by discrete sampling of local minima, combined with a continuous sampling of the vicinity of these local minima via a constrained harmonic lattice dynamic approach. Our calculations provide a complete and atomic-level-based model for these compounds' free energy and shed some light on the ongoing search for the precise structure of dynamically stabilized high temperature phases in SMAs.", + "subject": [], + "keywords": [] + }, + { + "title": "First-principles study on \nNi3Al (111)\n antiphase boundary with Ti and Hf impurities", + "author": "Ruoshi Sun, Christopher Woodward, Axel van de Walle", + "publisher": "American Physical Society (APS)", + "url": "http://dx.doi.org/10.1103/physrevb.95.214121", + "doi": "10.1103/physrevb.95.214121", + "year": 2017, + "month": 6, + "abstract": "The effect of Ti and Hf impurities on the (111) antiphase boundary (APB) energy of Ni3\u2062Al is investigated via ab initio calculations. Cluster expansion is performed to predict supercell total energies sampled in a Monte Carlo approach that accounts for nondilute point defects at finite temperature, obtaining APB energies as a function of impurity concentration and temperature. Of the two ternary elements, Hf is more effective in increasing the APB energy. While the (111) APB energy of a pure L\u206212 material requires at least second-nearest-neighbor interactions, we observe a strong correlation between impurity-induced APB energy enhancement and formation of first-nearest-neighbor Ni-Ni bonds across the APB due to symmetry breaking. Using a linear-chain model and effective bond energies derived from effective cluster interactions, we propose a mechanism that explains why Hf is more effective than Ti.", + "subject": [ + "crystal defects", + "impurities", + "alloys", + "cluster expansion", + "density functional theory", + "Monte Carlo methods" + ], + "keywords": [] + }, + { + "title": "Preliminary mapping of the structural effects of age in pediatric bipolar disorder with multimodal MR imaging", + "author": "Ryan P. Cabeen, David H. Laidlaw, Amanda Ruggieri, Daniel P. Dickstein", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.pscychresns.2017.12.006", + "doi": "10.1016/j.pscychresns.2017.12.006", + "year": 2018, + "month": 3, + "abstract": "This study investigates multimodal structural MR imaging biomarkers of development trajectories in pediatric bipolar disorder. T1-weighted and diffusion-weighted MR imaging was conducted to investigate cross-sectional group differences with age between typically developing controls (N = 26) and youths diagnosed with bipolar disorder (N = 26). Region-based analysis was used to examine cortical thickness of gray matter and diffusion tensor parameters in superficial white matter, and tractography-based analysis was used to examine deep white matter fiber bundles. Patients and controls showed significantly different maturation trajectories across brain areas; however, the magnitude of differences varied by region. The rate of cortical thinning with age was greater in patients than controls in the left frontal pole. While controls showed increasing fractional anisotropy (FA) and axial diffusivity (AD) with age, patients showed an opposite trend of decreasing FA and AD with age in fronto-temporal-striatal regions located in both superficial and deep white matter. The findings support fronto-temporal-striatal alterations in the developmental trajectories of youths diagnosed with bipolar disorder, and further, show the value of multimodal computational techniques in the assessment of neuropsychiatric disorders. These preliminary results warrant further investigation into longitudinal changes and the effects of treatment in the brain areas identified in this study.", + "subject": [], + "keywords": [] + }, + { + "title": "Compositional clustering in task structure learning", + "author": "Nicholas T. Franklin, Michael J. Frank", + "publisher": "Public Library of Science (PLoS)", + "url": "http://dx.doi.org/10.1371/journal.pcbi.1006116", + "doi": "10.1371/journal.pcbi.1006116", + "year": 2018, + "month": 4, + "abstract": "Humans are remarkably adept at generalizing knowledge between experiences in a way that can be difficult for computers. Often, this entails generalizing constituent pieces of experiences that do not fully overlap, but nonetheless share useful similarities with, previously acquired knowledge. However, it is often unclear how knowledge gained in one context should generalize to another. Previous computational models and data suggest that rather than learning about each individual context, humans build latent abstract structures and learn to link these structures to arbitrary contexts, facilitating generalization. In these models, task structures that are more popular across contexts are more likely to be revisited in new contexts. However, these models can only re-use policies as a whole and are unable to transfer knowledge about the transition structure of the environment even if only the goal has changed (or vice-versa). This contrasts with ecological settings, where some aspects of task structure, such as the transition function, will be shared between context separately from other aspects, such as the reward function. Here, we develop a novel non-parametric Bayesian agent that forms independent latent clusters for transition and reward functions, affording separable transfer of their constituent parts across contexts. We show that the relative performance of this agent compared to an agent that jointly clusters reward and transition functions depends environmental task statistics: the mutual information between transition and reward functions and the stochasticity of the observations. We formalize our analysis through an information theoretic account of the priors, and propose a meta learning agent that dynamically arbitrates between strategies across task domains to optimize a statistical tradeoff.", + "subject": [ + "human learning", + "agent-based modeling", + "learning", + "approximation modeling", + "ecological risk", + "cognition", + "hierarchical clustering", + "human performance" + ], + "keywords": [] + }, + { + "title": "Early life stress leads to sex differences in development of depressive-like outcomes in a mouse model", + "author": "Haley L. Goodwill, Gabriela Manzano-Nieves, Meghan Gallo, Hye-In Lee, Esther Oyerinde, Thomas Serre, Kevin G. Bath", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1038/s41386-018-0195-5", + "doi": "10.1038/s41386-018-0195-5", + "year": 2018, + "month": 9, + "abstract": "Childhood trauma and neglect influence emotional development and increase the risk for and severity of mental illness. Women have a heightened susceptibility to the effects of early life stress (ELS) and are twice as likely as men to develop debilitating, stress-associated disorders later in life, such as major depressive disorder (MDD). Until now, mouse models of depression have been largely unsuccessful at replicating the diverse symptomatology of this disease and the sex bias in vulnerability. From P4 to P11, a limited bedding model that leads to fragmented maternal care, was used to induce ELS. Early adolescent and young adult mice were tested on an array of assays to test for depressive-like behavior. This included our newly developed automated home cage behavioral recognition system, where the home cage behavior of ELS and control mice could be monitored over a continuous 5–10 day span. ELS females, but not males, exhibited depressive-like behaviors on traditional assays. These effects emerged during adolescence and became more severe in adulthood. Using the novel home cage video monitoring method, we identified robust and continuous markers of depressive-like pathology in ELS females that phenocopy many of the behavioral characteristics of depression in humans. ELS effects on home cage behavior were rapidly rescued by ketamine, a fast-acting antidepressant. Together, these findings highlight that limited bedding ELS (1) produces an early emerging, female-specific depressive phenotype that responds to a fast-acting antidepressant and (2) this model has the potential to inform sex-selective risk for the development of stress-induced mental illness.", + "subject": [], + "keywords": [] + }, + { + "title": "FPGA implementation of deep-learning recurrent neural networks with sub-millisecond real-time latency for BCI-decoding of large-scale neural sensors (104 nodes)", + "author": "C Heelan, AV Nurmikko, W Truccolo", + "publisher": "IEEE", + "url": "http://dx.doi.org/10.1109/embc.2018.8512415", + "doi": "10.1109/embc.2018.8512415", + "year": 2018, + "month": 7, + "abstract": "Advances in neurotechnology are expected to provide access to thousands of neural channel recordings including neuronal spiking, multiunit activity and local field potentials. In addition, recent studies have shown that deep learning, in particular recurrent neural networks (RNNs), provide promising approaches for decoding of large-scale neural data. These approaches involve computationally intensive algorithms with millions of parameters. In this context, an important challenge in the application of neural decoding to next generation brain-computer interfaces for complex human tasks is the development of low-latency real-time implementations. We demonstrate a Field-Programmable Gate Array (FPGA) implementation of Long Short-Term Memory (LSTM) RNNs for decoding 10,000 channels of neural data on a mobile lowpower embedded system platform called 'NeuroCoder'. We provide a proof of concept in the context of decoding 20dimensional spectrotemporal representation of spoken words from simulated 10,000 neural channels. In this particular case, the LSTM model included 4,042,420 parameters. In addition to providing multiple communication interfaces for the BCI system, the NeuroCoder platform can achieve sub-millisecond real-time latencies.", + "subject": [ + "Decoding", + "Field programmable gate arrays", + "Real-time systems", + "Brain modeling", + "Random access memory", + "Recurrent neural networks", + "Runtime", + "Neural Network", + "Deep Learning", + "Recurrent Neural Network", + "Real-time Latency", + "Short-term Memory", + "Long Short-term Memory", + "Challenge For Applications", + "Word Representations", + "Neural Data", + "Long Short-term Memory Model", + "Neurotechnology", + "Multi-unit Activity", + "Millions Of Parameters", + "Neural Decoding", + "Linear Model", + "Test Data", + "Simulated Data", + "Neural Activity", + "Network Parameters", + "High-level Synthesis", + "Long Short-term Memory Network", + "Auditory Cortex", + "Decoding Step", + "Input Vector", + "Long Short-term Memory Output", + "Long Short-term Memory Cell", + "Speech Features", + "Record Neural Activity", + "On-chip Memory", + "Algorithms", + "Brain-Computer Interfaces", + "Humans", + "Memory", + "Long-Term", + "Neural Networks", + "Computer", + "Neurons" + ], + "keywords": [] + }, + { + "title": "Learning to predict action potentials end-to-end from calcium imaging data", + "author": "Drew Linsley, Jeremy W. Linsley, Tarun Sharma, Nathan Meyers, Thomas Serre", + "publisher": "IEEE", + "url": "http://dx.doi.org/10.1109/ciss.2018.8362319", + "doi": "10.1109/ciss.2018.8362319", + "year": 2018, + "month": 3, + "abstract": "Advances in two-photon calcium (Ca 2+ ) imaging technologies are rapidly increasing the fidelity and scale of in-vivo neural recordings from behaving animals. These methodologies hold great promises for uncovering the neural computations that support behavior. One remaining challenge is the need to estimate the timing of action potentials (APs) from measured cellular Ca 2+ traces revealed by genetically encoded calcium indicators. Current approaches rely on manually pre-processing Ca 2+ imaging data, with routines for cell segmentation and signal normalization preceding deconvolution. Here, we show that by leveraging recent advances in recurrent neural networks it is possible to learn to detect APs end-to-end directly from raw Ca 2+ recordings. Our novel model achieves state-of-the-art performance on this task. We further demonstrate that the relative success of the approach is based in part on the system's ability to learn spatio-temporal features that are typically associated with biophysical events known to contribute to the AP process.", + "subject": [ + "Imaging", + "Computer architecture", + "Logic gates", + "Neurons", + "Training", + "Convolution", + "Deconvolution", + "Action Potential", + "Imaging Data", + "Calcium Imaging", + "Neural Network", + "Deconvolution", + "Recurrent Neural Network", + "Spatiotemporal Characteristics", + "Two-photon Calcium Imaging", + "Cell Bodies", + "Convolutional Layers", + "Computer Vision", + "Version Of Model", + "Visual Features", + "Raw Images", + "Test Sequences", + "Hidden State", + "Spatial Filter", + "Complex Learning", + "Temporal Activity", + "Gated Recurrent Unit", + "Gated Recurrent Unit Model", + "Computer Vision System", + "Activation Gate", + "calcium imaging", + "spike prediction", + "convolutional networks", + "recurrent networks" + ], + "keywords": [] + }, + { + "title": "Supplemental Material for Chunking as a Rational Strategy for Lossy Data Compression in Visual Working Memory", + "author": "", + "publisher": "American Psychological Association (APA)", + "url": "http://dx.doi.org/10.1037/rev0000101.supp", + "doi": "10.1037/rev0000101.supp", + "year": 2018, + "month": 7, + "abstract": "The nature of capacity limits for visual working memory has been the subject of an intense debate that has relied on models that assume items are encoded independently. Here we propose that instead, similar features are jointly encoded through a 'chunking' process to optimize performance on visual working memory tasks. We show that such chunking can: (a) facilitate performance improvements for abstract capacity-limited systems, (b) be optimized through reinforcement, (c) be implemented by center-surround dynamics, and (d) increase effective storage capacity at the expense of recall precision. Human performance on a variant of a canonical working memory task demonstrated performance advantages, precision detriments, interitem dependencies, and trial-to-trial behavioral adjustments diagnostic of performance optimization through center-surround chunking. Models incorporating center-surround chunking provided a better quantitative description of human performance in our study as well as in a meta-analytic dataset, and apparent differences in working memory capacity across individuals were attributable to individual differences in the implementation of chunking. Our results reveal a normative rationale for center-surround connectivity in working memory circuitry, call for reevaluation of memory performance differences that have previously been attributed to differences in capacity, and support a more nuanced view of visual working memory capacity limitations: strategic tradeoff between storage capacity and memory precision through chunking contribute to flexible capacity limitations that include both discrete and continuous aspects.", + "subject": [ + "Visual working memory", + "Data compression", + "Information theory", + "43 Reinforcement learning", + "Computational modeling", + "Recurrent neural networks" + ], + "keywords": [] + }, + { + "title": "TDP-43 gains function due to perturbed autoregulation in a Tardbp knock-in mouse model of ALS-FTD", + "author": "Matthew A. White, Eosu Kim, Amanda Duffy, Robert Adalbert, Benjamin U. Phillips, Owen M. Peters, Jodie Stephenson, Sujeong Yang, Francesca Massenzio, Ziqiang Lin, Simon Andrews, Anne Segonds-Pichon, Jake Metterville, Lisa M. Saksida, Richard Mead, Richard R Ribchester, Youssef Barhomi, Thomas Serre, Michael P. Coleman, Justin R. Fallon, Timothy J. Bussey, Robert H. Brown, Jemeen Sreedharan", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1038/s41593-018-0113-5", + "doi": "10.1038/s41593-018-0113-5", + "year": 2018, + "month": 3, + "abstract": "Amyotrophic lateral sclerosis–frontotemporal dementia (ALS-FTD) constitutes a devastating disease spectrum characterized by 43-kDa TAR DNA-binding protein (TDP-43) pathology. Understanding how TDP-43 contributes to neurodegeneration will help direct therapeutic efforts. Here we have created a TDP-43 knock-in mouse with a human-equivalent mutation in the endogenous mouse Tardbp gene. TDP-43Q331K mice demonstrate cognitive dysfunction and a paucity of parvalbumin interneurons. Critically, TDP-43 autoregulation is perturbed, leading to a gain of TDP-43 function and altered splicing of Mapt, another pivotal dementia-associated gene. Furthermore, a new approach to stratify transcriptomic data by phenotype in differentially affected mutant mice revealed 471 changes linked with improved behavior. These changes included downregulation of two known modifiers of neurodegeneration, Atxn2 and Arid4a, and upregulation of myelination and translation genes. With one base change in murine Tardbp, this study identifies TDP-43 misregulation as a pathogenic mechanism that may underpin ALS-FTD and exploits phenotypic heterogeneity to yield candidate suppressors of neurodegenerative disease.", + "subject": [], + "keywords": [] + }, + { + "title": "On the stability and dynamics of stochastic spiking neuron models: Nonlinear Hawkes process and point process GLMs", + "author": "Felipe Gerhard, Moritz Deger, Wilson Truccolo", + "publisher": "Public Library of Science (PLoS)", + "url": "http://dx.doi.org/10.1371/journal.pcbi.1005390", + "doi": "10.1371/journal.pcbi.1005390", + "year": 2017, + "month": 2, + "abstract": "Point process generalized linear models (PP-GLMs) provide an important statistical framework for modeling spiking activity in single-neurons and neuronal networks. Stochastic stability is essential when sampling from these models, as done in computational neuroscience to analyze statistical properties of neuronal dynamics and in neuro-engineering to implement closed-loop applications. Here we show, however, that despite passing common goodness-of-fit tests, PP-GLMs estimated from data are often unstable, leading to divergent firing rates. The inclusion of absolute refractory periods is not a satisfactory solution since the activity then typically settles into unphysiological rates. To address these issues, we derive a framework for determining the existence and stability of fixed points of the expected conditional intensity function (CIF) for general PP-GLMs. Specifically, in nonlinear Hawkes PP-GLMs, the CIF is expressed as a function of the previous spike history and exogenous inputs. We use a mean-field quasi-renewal (QR) approximation that decomposes spike history effects into the contribution of the last spike and an average of the CIF over all spike histories prior to the last spike. Fixed points for stationary rates are derived as self-consistent solutions of integral equations. Bifurcation analysis and the number of fixed points predict that the original models can show stable, divergent, and metastable (fragile) dynamics. For fragile models, fluctuations of the single-neuron dynamics predict expected divergence times after which rates approach unphysiologically high values. This metric can be used to estimate the probability of rates to remain physiological for given time periods, e.g., for simulation purposes. We demonstrate the use of the stability framework using simulated single-neuron examples and neurophysiological recordings. Finally, we show how to adapt PP-GLM estimation procedures to guarantee model stability. Overall, our results provide a stability framework for data-driven PP-GLMs and shed new light on the stochastic dynamics of state-of-the-art statistical models of neuronal spiking activity.", + "subject": [ + "Action potentials", + "Approximation methods", + "Simulation and modelling", + "Neaurons", + "Single neuron function", + "Nonlinear dynamics", + "Transfer functions", + "Metastasis" + ], + "keywords": [] + }, + { + "title": "Machine learning algorithm for automatic detection of CT-identifiable hyperdense lesions associated with traumatic brain injury", + "author": "Krishna N. Keshavamurthy, Owen P. Leary, Lisa H. Merck, Benjamin Kimia, Scott Collins, David W. Wright, Jason W. Allen, Jeffrey F. Brock, Derek Merck", + "publisher": "SPIE", + "url": "http://dx.doi.org/10.1117/12.2254227", + "doi": "10.1117/12.2254227", + "year": 2017, + "month": 3, + "abstract": "Traumatic brain injury (TBI) is a major cause of death and disability in the United States. Time to treatment is often related to patient outcome. Access to cerebral imaging data in a timely manner is a vital component of patient care. Current methods of detecting and quantifying intracranial pathology can be time-consuming and require careful review of 2D/3D patient images by a radiologist. Additional time is needed for image protocoling, acquisition, and processing. These steps often occur in series, adding more time to the process and potentially delaying time-dependent management decisions for patients with traumatic brain injury.\nOur team adapted machine learning and computer vision methods to develop a technique that rapidly and automatically detects CT-identifiable lesions. Specifically, we use scale invariant feature transform (SIFT)1 and deep convolutional neural networks (CNN)2 to identify important image features that can distinguish TBI lesions from background data. Our learning algorithm is a linear support vector machine (SVM)3. Further, we also employ tools from topological data analysis (TDA) for gleaning insights into the correlation patterns between healthy and pathological data. The technique was validated using 409 CT scans of the brain, acquired via the Progesterone for the Treatment of Traumatic Brain Injury phase III clinical trial (ProTECT_III) which studied patients with moderate to severe TBI4. CT data were annotated by a central radiologist and included patients with positive and negative scans. Additionally, the largest lesion on each positive scan was manually segmented. We reserved 80% of the data for training the SVM and used the remaining 20% for testing. Preliminary results are promising with 92.55% prediction accuracy (sensitivity = 91.15%, specificity = 93.45%), indicating the potential usefulness of this technique in clinical scenarios.", + "subject": ["Traumatic brain injury", "Computed tomography", "Machine learning", "Brain", "Neuroimaging", "Visualization", "Data analysis"], + "keywords": [] + }, + { + "title": "An engineered home environment for untethered data telemetry from nonhuman primates", + "author": "Marc P. Powell, William R. Britz, James S. Harper, David A. Borton", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.jneumeth.2017.06.013", + "doi": "10.1016/j.jneumeth.2017.06.013", + "year": 2017, + "month": 8, + "abstract": "Background\nWireless neural recording technologies now provide untethered access to large populations of neurons in the nonhuman primate brain. Such technologies enable long-term, continuous interrogation of neural circuits and importantly open the door for chronic neurorehabilitation platforms. For example, by providing continuous consistent closed loop feedback from a brain machine interface, the nervous system can leverage plasticity to integrate more effectively into the system than would be possible in short experimental sessions. However, to fully realize this opportunity necessitates the development of experimental environments that do not hinder wireless data transmission. Traditional nonhuman primate metal cage construction, while durable and standardized around the world, prevents data transmission at the frequencies necessary for high-bandwidth data transfer.\n\nNew method\nTo overcome this limitation, we have engineered and constructed a radio-frequency transparent home environment for nonhuman primates using primarily non-conductive materials.\n\nResults\nComputational modeling and empirical testing were performed to demonstrate the behavior of transmitted signals passing through the enclosure. In addition, neural data were successfully recorded from a freely behaving nonhuman primate inside the housing system.\n\nComparison with existing methods\nOur design outperforms standard metallic home cages by allowing radiation to transmit beyond its boundaries, without significant interference, while simultaneously maintaining the mechanical and operational integrity of existing commercial home cages.\n\nConclusions\nContinuous access to neural signals in combination with other bio-potential and kinematic sensors will empower new insights into unrestrained behavior, aid the development of advanced neural prostheses, and enable neurorehabilitation strategies to be employed outside traditional environments.", + "subject": ["Nonhuman primate", "Wireless neural recording", "Husbandry", "Telemetry", "Freely behaving", "Neurorehabilitation"], + "keywords": [] + }, + { + "title": "Inference and Decoding of Motor Cortex Low-Dimensional Dynamics via Latent State-Space Models", + "author": "Mehdi Aghagolzadeh, Wilson Truccolo", + "publisher": "Institute of Electrical and Electronics Engineers (IEEE)", + "url": "http://dx.doi.org/10.1109/tnsre.2015.2470527", + "doi": "10.1109/tnsre.2015.2470527", + "year": 2016, + "month": 2, + "abstract": "Motor cortex neuronal ensemble spiking activity exhibits strong low-dimensional collective dynamics (i.e., coordinated modes of activity) during behavior. Here, we demonstrate that these low-dimensional dynamics, revealed by unsupervised latent state-space models, can provide as accurate or better reconstruction of movement kinematics as direct decoding from the entire recorded ensemble. Ensembles of single neurons were recorded with triple microelectrode arrays (MEAs) implanted in ventral and dorsal premotor (PMv, PMd) and primary motor (M1) cortices while nonhuman primates performed 3-D reach-to-grasp actions. Low-dimensional dynamics were estimated via various types of latent state-space models including, for example, Poisson linear dynamic system (PLDS) models. Decoding from low-dimensional dynamics was implemented via point process and Kalman filters coupled in series. We also examined decoding based on a predictive subsampling of the recorded population. In this case, a supervised greedy procedure selected neuronal subsets that optimized decoding performance. When comparing decoding based on predictive subsampling and latent state-space models, the size of the neuronal subset was set to the same number of latent state dimensions. Overall, our findings suggest that information about naturalistic reach kinematics present in the recorded population is preserved in the inferred low-dimensional motor cortex dynamics. Furthermore, decoding based on unsupervised PLDS models may also outperform previous approaches based on direct decoding from the recorded population or on predictive subsampling.", + "subject": ["Decoding","Sociology","Statistics","State-space methods","Kinematics","Neurons","Three-dimensional displays", "Motor Cortex","Latent Model","State-space Model","Low-dimensional Dynamics","Latent State-space Models","Neuronal Activity","Neuronal Populations","Linear System","Statistical Properties","Kalman Filter","Primary Motor Cortex","Point Process","Subset Of Neurons","Spiking Activity","Latent State","Spiking Neural Networks","Primary Motor","System Dynamics Model","Microelectrode Arrays","Subset Size","Precision Grip","Spike Count","State-space Approach","Random Subsample","Laplace Approximation","Neural Decoding","Expectation Maximization","Decoding Approach","Separate Areas","Cortical Areas", "Brain-machine interfaces (BMI)","collective dynamics","neural encoding","point processes", "Algorithms","Animals","Behavior"," Animal","Biomechanical Phenomena","Brain-Computer Interfaces","Electrodes"," Implanted","Hand Strength","Macaca mulatta","Microelectrodes","Models"," Neurological","Motor Cortex","Movement","Poisson Distribution","Psychomotor Performance"], + "keywords": [] + }, + { + "title": "Predicting seizures from local field potentials recorded via intracortical microelectrode arrays", + "author": "Mehdi Aghagolzadeh, Leigh R. Hochberg, Sydney S. Cash, Wilson Truccolo", + "publisher": "IEEE", + "url": "http://dx.doi.org/10.1109/embc.2016.7592181", + "doi": "10.1109/embc.2016.7592181", + "year": 2016, + "month": 8, + "abstract": "The need for new therapeutic interventions to treat pharmacologically resistant focal epileptic seizures has led recently to the development of closed-loop systems for seizure control. Once a seizure is predicted/detected by the system, electrical stimulation is delivered to prevent seizure initiation or spread. So far, seizure prediction/detection has been limited to tracking non-invasive electroencephalogram (EEG) or intracranial EEG (iEEG) signals. Here, we examine seizure prediction based on local field potentials (LFPs) from a small neocortical patch recorded via a 10×10 microelectrode array implanted in a patient with focal seizures. We formulate the seizure (ictal) prediction problem in terms of discriminating between interictal and preictal neural activity. Using deep Convolutional Neural Networks (CNNs), we show that periods of preictal activity can be successfully discriminated (80% detection; no false positives) from periods of interictal activity several (2-18) minutes prior to seizure onset. CNN input features consisted of the spectral power of LFP channels (1-second time windows) computed in 50 frequency bands (0-100 Hz; 2 Hz steps). Our preliminary results show that intracortical LFPs may be a promising neural signal for seizure prediction in focal epilepsy.", + "subject": ["Microelectrodes","Epilepsy","Training","Convolution","Neuroscience","Electroencephalography","Hospitals", "Single-unit Recordings","Microelectrode Arrays","Local Field Potential Recordings","Convolutional Neural Network","Neural Activity","Electrical Stimulation","Deep Convolutional Neural Network","Spectral Power","Epileptic Seizures","Seizure Onset","Focal Seizures","Electrocorticography","Focal Epilepsy","Interictal Activity","Low-pass","Spectral Features","Power Spectrum","Prediction Score","Feature Matrix","Neural Data","Convolutional Neural Network Training","Interictal Period", "Electrocorticography","Electrophysiological Phenomena","Microelectrodes","Neural Networks","Seizures","Signal Processing"," Computer-Assisted"], + "keywords": [] + }, + { + "title": "Neural signature of hierarchically structured expectations predicts clustering and transfer of rule sets in reinforcement learning", + "author": "Anne Gabrielle Eva Collins, Michael Joshua Frank", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.cognition.2016.04.002", + "doi": "10.1016/j.cognition.2016.04.002", + "year": 2016, + "month": 7, + "abstract": "Often the world is structured such that distinct sensory contexts signify the same abstract rule set. Learning from feedback thus informs us not only about the value of stimulus-action associations but also about which rule set applies. Hierarchical clustering models suggest that learners discover structure in the environment, clustering distinct sensory events into a single latent rule set. Such structure enables a learner to transfer any newly acquired information to other contexts linked to the same rule set, and facilitates re-use of learned knowledge in novel contexts. Here, we show that humans exhibit this transfer, generalization and clustering during learning. Trial-by-trial model-based analysis of EEG signals revealed that subjects’ reward expectations incorporated this hierarchical structure; these structured neural signals were predictive of behavioral transfer and clustering. These results further our understanding of how humans learn and generalize flexibly by building abstract, behaviorally relevant representations of the complex, high-dimensional sensory environment.", + "subject": ["Structure-learning", "EEG", "Transfer", "Clustering", "Prefrontal cortex"], + "keywords": [] + }, + { + "title": "Multiview Differential Geometry of Curves", + "author": "Ricardo Fabbri, Benjamin B. Kimia", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1007/s11263-016-0912-7", + "doi": "10.1007/s11263-016-0912-7", + "year": 2016, + "month": 5, + "abstract": "The field of multiple view geometry has seen tremendous progress in reconstruction and calibration due to methods for extracting reliable point features and key developments in projective geometry. Point features, however, are not available in certain applications and result in unstructured point cloud reconstructions. General image curves provide a complementary feature when keypoints are scarce, and result in 3D curve geometry, but face challenges not addressed by the usual projective geometry of points and algebraic curves. We address these challenges by laying the theoretical foundations of a framework based on the differential geometry of general curves, including stationary curves, occluding contours, and non-rigid curves, aiming at stereo correspondence, camera estimation (including calibration, pose, and multiview epipolar geometry), and 3D reconstruction given measured image curves. By gathering previous results into a cohesive theory, novel results were made possible, yielding three contributions. First, we derive the differential geometry of an image curve (tangent, curvature, curvature derivative) from that of the underlying space curve (tangent, curvature, curvature derivative, torsion). Second, we derive the differential geometry of a space curve from that of two corresponding image curves. Third, the differential motion of an image curve is derived from camera motion and the differential geometry and motion of the space curve. The availability of such a theory enables novel curve-based multiview reconstruction and camera estimation systems to augment existing point-based approaches. This theory has been used to reconstruct a '3D curve sketch', to determine camera pose from local curve geometry, and tracking; other developments are underway.", + "subject": [], + "keywords": [] + }, + { + "title": "A methodology to analyze treatment zone geometry and variability of percutaneous thermal ablation", + "author": "Krishna N. Keshava, Benjamin B. Kimia, Madeleine Cook, Damian E. Dupuy, Scott A. Collins, Derek Merck", + "publisher": "SPIE", + "url": "http://dx.doi.org/10.1117/12.2082834", + "doi": "10.1117/12.2082834", + "year": 2015, + "month": 3, + "abstract": "A major challenge for image guided tumor ablation is the high treatment variability due to heterogeneous tissue characteristics and thermal sinks. In this work, we present a methodology to analyze the geometry of the treatment zones and treatment zone variability. Our first contribution is an applicator centric co-ordinate system which enables us to compare treatment zones and vendor specifications across patients. Our second contribution is the analysis of the shape of the ablation zone using applicator centric longitudinal 2D cross sections. We present initial results of applying this methodology to analyze the geometry and variability in synthetic examples like ellipsoid, sphere and real microwave ablation zones in lung and liver.", + "subject": [], + "keywords": [] + }, + { + "title": "An end-to-end generative framework for video segmentation and recognition", + "author": "Hilde Kuehne, Juergen Gall, Thomas Serre", + "publisher": "IEEE", + "url": "http://dx.doi.org/10.1109/wacv.2016.7477701", + "doi": "10.1109/wacv.2016.7477701", + "year": 2016, + "month": 3, + "abstract": "We describe an end-to-end generative approach for the segmentation and recognition of human activities. In this approach, a visual representation based on reduced Fisher Vectors is combined with a structured temporal model for recognition. We show that the statistical properties of Fisher Vectors make them an especially suitable front-end for generative models such as Gaussian mixtures. The system is evaluated for both the recognition of complex activities as well as their parsing into action units. Using a variety of video datasets ranging from human cooking activities to animal behaviors, our experiments demonstrate that the resulting architecture outperforms state-of-the-art approaches for larger datasets, i.e. when sufficient amount of data is available for training structured generative models.", + "subject": ["Hidden Markov models","Principal component analysis","Grammar","Data models","Speech recognition","Visualization","TrainingIndex TermsHuman Activities","Activity Of Complex","Parsing","Visual Representation","Mixture Model","Action Recognition","Temporal Model","Video Dataset","Human Activity Recognition","Action Units","Sufficient Amount Of Data","Training Data","Null Hypothesis","Normality Test","Small Datasets","Hidden Markov Model","Transition Probabilities","Speech Recognition","Video Clips","Recognition Accuracy","Sequence Of Units","Context-free Grammar","Gaussian Mixture Model","Activation Segment","Sufficient Training Data","Single Activity","Segmentation Results","Olympic Games","Video Data"], + "keywords": [] + }, + { + "title": "Taming the beast: extracting generalizable knowledge from computational models of cognition", + "author": "Matthew R Nassar, Michael J Frank", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.cobeha.2016.04.003", + "doi": "10.1016/j.cobeha.2016.04.003", + "year": 2016, + "month": 10, + "abstract": "Generalizing knowledge from experimental data requires constructing theories capable of explaining observations and extending beyond them. Computational modeling offers formal quantitative methods for generating and testing theories of cognition and neural processing. These techniques can be used to extract general principles from specific experimental measurements, but introduce dangers inherent to theory: model-based analyses are conditioned on a set of fixed assumptions that impact the interpretations of experimental data. When these conditions are not met, model-based results can be misleading or biased. Recent work in computational modeling has highlighted the implications of this problem and developed new methods for minimizing its negative impact. Here we discuss the issues that arise when data is interpreted through models and strategies for avoiding misinterpretation of data through model fitting.", + "subject": [], + "keywords": [] + }, + { + "title": "Neuromarkers of the common angiotensinogen polymorphism in healthy older adults: A comprehensive assessment of white matter integrity and cognition", + "author": "Lauren E. Salminen, Peter R. Schofield, Kerrie D. Pierce, Yi Zhao, Xi Luo, Youdan Wang, David H. Laidlaw, Ryan P. Cabeen, Thomas E. Conturo, David F. Tate, Erbil Akbudak, Elizabeth M. Lane, Jodi M. Heaps, Jacob D. Bolzenius, Laurie M. Baker, Lee M. Cagle, Robert H. Paul", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.bbr.2015.08.028", + "doi": "10.1016/j.bbr.2015.08.028", + "year": 2016, + "month": 1, + "abstract": "The common angiotensinogen (AGT) M268T polymorphism (rs699; historically referred to as M235T) has been identified as a significant risk factor for cerebrovascular pathologies, yet it is unclear if healthy older adults carrying the threonine amino acid variant have a greater risk for white matter damage in specific fiber tracts. Further, the impact of the threonine variant on cognitive function remains unknown. The present study utilized multiple indices of diffusion tensor imaging (DTI) and neuropsychological assessment to examine the integrity of specific white matter tracts and cognition between individuals with homozygous genotypes of M268T (MetMet n = 27, ThrThr n = 27). Differences in subcortical hyperintensity (SH) volume were also examined between groups. Results indicated that the threonine variant was associated with significantly reduced integrity in the superior longitudinal fasciculus (SLF) and the cingulate gyrus segment of the cingulum bundle (cingulum CG) compared to those with the methionine variant, and poorer cognitive performance on tests of attention/processing speed and language. Despite these associations, integrity of these tracts did not significantly mediate relationships between cognition and genetic status, and SH did not differ significantly between groups. Collectively our results suggest that the threonine variant of M268T is a significant risk factor for abnormalities in specific white matter tracts and cognitive domains in healthy older adults, independent of SH burden.", + "subject": ["AGT", "M235T", "M268T", "rs699", "White matter", "Cognition"], + "keywords": [] + }, + { + "title": "From point process observations to collective neural dynamics: Nonlinear Hawkes process GLMs, low-dimensional dynamics and coarse graining", + "author": "Wilson Truccolo", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.jphysparis.2017.02.004", + "doi": "10.1016/j.jphysparis.2017.02.004", + "year": 2016, + "month": 11, + "abstract": "This review presents a perspective on capturing collective dynamics in recorded neuronal ensembles based on multivariate point process models, inference of low-dimensional dynamics and coarse graining of spatiotemporal measurements. A general probabilistic framework for continuous time point processes reviewed, with an emphasis on multivariate nonlinear Hawkes processes with exogenous inputs. A point process generalized linear model (PP-GLM) framework for the estimation of discrete time multivariate nonlinear Hawkes processes is described. The approach is illustrated with the modeling of collective dynamics in neocortical neuronal ensembles recorded in human and non-human primates, and prediction of single-neuron spiking. A complementary approach to capture collective dynamics based on low-dimensional dynamics ('order parameters') inferred via latent state-space models with point process observations is presented. The approach is illustrated by inferring and decoding low-dimensional dynamics in primate motor cortex during naturalistic reach and grasp movements. Finally, we briefly review hypothesis tests based on conditional inference and spatiotemporal coarse graining for assessing collective dynamics in recorded neuronal ensembles.", + "subject": ["Point processes", "Nonlinear Hawkes process", "Generalized Linear Model", "GLM", "Neural decoding", "Order parameters"], + "keywords": [] + }, + { + "title": "A Computational Cognitive Biomarker for Early-Stage Huntington’s Disease", + "author": "Thomas V. Wiecki, Chrystalina A. Antoniades, Alexander Stevenson, Christopher Kennard, Beth Borowsky, Gail Owen, Blair Leavitt, Raymund Roos, Alexandra Durr, Sarah J. Tabrizi, Michael J. Frank", + "publisher": "Public Library of Science (PLoS)", + "url": "http://dx.doi.org/10.1371/journal.pone.0148409", + "doi": "10.1371/journal.pone.0148409", + "year": 2016, + "month": 2, + "abstract": "Huntington’s disease (HD) is genetically determined but with variability in symptom onset, leading to uncertainty as to when pharmacological intervention should be initiated. Here we take a computational approach based on neurocognitive phenotyping, computational modeling, and classification, in an effort to provide quantitative predictors of HD before symptom onset. A large sample of subjects—consisting of both pre-manifest individuals carrying the HD mutation (pre-HD), and early symptomatic—as well as healthy controls performed the antisaccade conflict task, which requires executive control and response inhibition. While symptomatic HD subjects differed substantially from controls in behavioral measures [reaction time (RT) and error rates], there was no such clear behavioral differences in pre-HD. RT distributions and error rates were fit with an accumulator-based model which summarizes the computational processes involved and which are related to identified mechanisms in more detailed neural models of prefrontal cortex and basal ganglia. Classification based on fitted model parameters revealed a key parameter related to executive control differentiated pre-HD from controls, whereas the response inhibition parameter declined only after symptom onset. These findings demonstrate the utility of computational approaches for classification and prediction of brain disorders, and provide clues as to the underlying neural mechanisms.", + "subject": [], + "keywords": [] + }, + { + "title": "Developing an open platform for evidence-based microwave ablation treatment planning and validation", + "author": "Garron Deshazer, Damian E. Dupuy, Edward Walsh, Punit Prakash, Dillon Fairchild, David Glidden, Scott A. Collins, Madeleine L. Cook, Thomas P. Ryan, Derek Merck", + "publisher": "SPIE", + "url": "http://dx.doi.org/10.1117/12.2081216", + "doi": "10.1117/12.2081216", + "year": 2015, + "month": 3, + "abstract": "The clinical utility of current thermal ablation planning tools is severely limited by treatment variability. We discuss the development of an open platform for evidence-based thermal ablation treatment planning and validation. Improved predictive treatment modeling and consistent outcome analysis are crucial components for useful planning and guidance tools.", + "subject": [], + "keywords": [] + }, + { + "title": "The Necessity of Rostrolateral Prefrontal Cortex for Higher-Level Sequential Behavior", + "author": "Theresa M. Desrochers, Christopher H. Chatham, David Badre", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.neuron.2015.08.026", + "doi": "10.1016/j.neuron.2015.08.026", + "year": 2015, + "month": 9, + "abstract": "Frontal neocortex is thought to support our highest intellectual abilities, including our ability to plan and enact a sequence of tasks toward a desired goal. In everyday life, such task sequences are abstract in that they do not require consistent movement sequences and are often assembled 'on the fly.' Yet, remarkably little is known about the necessity of frontal sub-regions for such control. Participants repeatedly completed sequences of simple tasks during fMRI scanning. Rostrolateral prefrontal cortex (RLPFC) activation ramped over sequence position and reset at the initiation of each new sequence. To establish the necessity and function of RLPFC in this task, participants performed the sequential task while undergoing transcranial magnetic stimulation (TMS) of the RLPFC versus two prefrontal control regions. Across two independent experiments, only RLPFC stimulation increasingly disrupted task performance as each sequence progressed. These data establish RLPFC as necessary for uncertainty resolution during sequence-level control.", + "subject": [], + "keywords": [] + }, + { + "title": "The neuroanatomical delineation of agentic and affiliative extraversion", + "author": "Erica N. Grodin, Tara L. White", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.3758/s13415-014-0331-6", + "doi": "10.3758/s13415-014-0331-6", + "year": 2015, + "month": 2, + "abstract": "Extraversion is a fascinating personality dimension that consists of two major components, agentic extraversion and affiliative extraversion. Agentic extraversion involves incentive motivation and is expressed as a tendency toward assertiveness, persistence, and achievement. Affiliative extraversion involves the positive emotion of social warmth and is expressed as a tendency toward amicability, gregariousness, and affection. Here we investigate the neuroanatomical correlates of the personality traits of agentic and affiliative extraversion using the Multidimensional Personality Questionnaire Brief Form, structural magnetic resonance imaging, and voxel-based morphometry in a sample of 83 healthy adult volunteers. We found that trait agentic extraversion and trait affiliative extraversion were each positively associated with the volume of the medial orbitofrontal cortex bilaterally (t’s ≥ 2.03, r’s ≥ .23, p’s < .05). Agentic extraversion was specifically and positively related to the volume of the left parahippocampal gyrus (t = 4.08, r = .21, p < .05), left cingulate gyrus (t = 4.75, r = .28, p < .05), left caudate (t = 4.29, r = .24, p < .05), and left precentral gyrus (t = 4.00, r = .18, p < .05) in males and females, and the volume of the right nucleus accumbens in males (t = 2.92, r = .20, p < .05). Trait affiliative extraversion was not found to be associated with additional regions beyond the medial orbitofrontal cortex. The findings provide the first evidence of a neuroanatomical dissociation between the personality traits of agentic and affiliative extraversion in healthy adults.", + "subject": [], + "keywords": [] + }, + { + "title": "Fast and adaptive sparse precision matrix estimation in high dimensions", + "author": "Weidong Liu, Xi Luo", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.jmva.2014.11.005", + "doi": "10.1016/j.jmva.2014.11.005", + "year": 2015, + "month": 3, + "abstract": "This paper proposes a new method for estimating sparse precision matrices in the high dimensional setting. It has been popular to study fast computation and adaptive procedures for this problem. We propose a novel approach, called Sparse Column-wise Inverse Operator, to address these two issues. We analyze an adaptive procedure based on cross validation, and establish its convergence rate under the Frobenius norm. The convergence rates under other matrix norms are also established. This method also enjoys the advantage of fast computation for large-scale problems, via a coordinate descent algorithm. Numerical merits are illustrated using both simulated and real datasets. In particular, it performs favorably on an HIV brain tissue dataset and an ADHD resting-state fMRI dataset.", + "subject": ["Adaptivity", "Coordinate descent", "Cross validation", "Gaussian graphical models", "Lasso", "Convergence rates"], + "keywords": [] + }, + { + "title": "Contribution of LFP dynamics to single-neuron spiking variability in motor cortex during movement execution", + "author": "Michael E. Rule, Carlos Vargas-Irwin, John P. Donoghue, Wilson Truccolo", + "publisher": "Frontiers Media SA", + "url": "http://dx.doi.org/10.3389/fnsys.2015.00089", + "doi": "10.3389/fnsys.2015.00089", + "year": 2015, + "month": 6, + "abstract": "Understanding the sources of variability in single-neuron spiking responses is an important open problem for the theory of neural coding. This variability is thought to result primarily from spontaneous collective dynamics in neuronal networks. Here, we investigate how well collective dynamics reflected in motor cortex local field potentials (LFPs) can account for spiking variability during motor behavior. Neural activity was recorded via microelectrode arrays implanted in ventral and dorsal premotor and primary motor cortices of non-human primates performing naturalistic 3-D reaching and grasping actions. Point process models were used to quantify how well LFP features accounted for spiking variability not explained by the measured 3-D reach and grasp kinematics. LFP features included the instantaneous magnitude, phase and analytic-signal components of narrow band-pass filtered (δ,θ,α,β) LFPs, and analytic signal and amplitude envelope features in higher-frequency bands. Multiband LFP features predicted single-neuron spiking (1ms resolution) with substantial accuracy as assessed via ROC analysis. Notably, however, models including both LFP and kinematics features displayed marginal improvement over kinematics-only models. Furthermore, the small predictive information added by LFP features to kinematic models was redundant to information available in fast-timescale (<100 ms) spiking history. Overall, information in multiband LFP features, although predictive of single-neuron spiking during movement execution, was redundant to information available in movement parameters and spiking history. Our findings suggest that, during movement execution, collective dynamics reflected in motor cortex LFPs primarily relate to sensorimotor processes directly controlling movement output, adding little explanatory power to variability not accounted by movement parameters.", + "subject": [], + "keywords": [] + }, + { + "title": "Genetic markers of cholesterol transport and gray matter diffusion: a preliminary study of the CETP I405V polymorphism", + "author": "Lauren E. Salminen, Peter R. Schofield, Kerrie D. Pierce, Xi Luo, Yi Zhao, David H. Laidlaw, Ryan P. Cabeen, Thomas E. Conturo, Elizabeth M. Lane, Jodi M. Heaps, Jacob D. Bolzenius, Laurie M. Baker, Sarah A. Cooley, Staci Scott, Lee M. Cagle, Robert H. Paul", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1007/s00702-015-1434-0", + "doi": "10.1007/s00702-015-1434-0", + "year": 2015, + "month": 8, + "abstract": "Variations of the cholesteryl ester transfer protein polymorphism (CETP I405V/rs5882) have been associated with an increased risk for neurodegeneration, particularly when examined in conjunction with the epsilon 4 isoform of apolipoprotein E (ApoE4). Despite these identified relationships, the impact of I405V on gray matter microstructure remains unknown. The present study examined the impact of the CETP I405V polymorphism on gray matter integrity among 52 healthy adults between ages 51 and 85. Gray matter was measured bilaterally using diffusion tensor imaging (DTI) metrics of fractional anisotropy (FA), mean diffusivity (MD), axial diffusivity (AD), and radial diffusivity (RD). Participants were grouped according to a dominant statistical model (II genotype vs. IV/VV genotypes) and secondary analyses were completed to examine the interactive effects of CETP and ApoE4 on DTI metrics. Compared to individuals with the IV/VV genotypes, II homozygotes demonstrated significantly higher MD in bilateral temporal, parietal, and occipital gray matter. Secondary analyses revealed higher FA and AD in the left temporal lobe of IV/VV genotypes with an ApoE4 allele. Our results provide preliminary evidence that CETP II homozygosity is a predisposing risk factor for gray matter abnormalities in posterior brain regions in healthy older adults, independent of an ApoE4 allele.", + "subject": [], + "keywords": [] + }, + { + "title": "Microscale spatiotemporal dynamics during neocortical propagation of human focal seizures", + "author": "Fabien B. Wagner, Emad N. Eskandar, G. Rees Cosgrove, Joseph R. Madsen, Andrew S. Blum, N. Stevenson Potter, Leigh R. Hochberg, Sydney S. Cash, Wilson Truccolo", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.neuroimage.2015.08.019", + "doi": "10.1016/j.neuroimage.2015.08.019", + "year": 2015, + "month": 11, + "abstract": "Some of the most clinically consequential aspects of focal epilepsy, e.g. loss of consciousness, arise from the generalization or propagation of seizures through local and large-scale neocortical networks. Yet, the dynamics of such neocortical propagation remain poorly understood. Here, we studied the microdynamics of focal seizure propagation in neocortical patches (4 × 4 mm) recorded via high-density microelectrode arrays (MEAs) implanted in people with pharmacologically resistant epilepsy. Our main findings are threefold: (1) a newly developed stage segmentation method, applied to local field potentials (LFPs) and multiunit activity (MUA), revealed a succession of discrete seizure stages, each lasting several seconds. These different stages showed characteristic evolutions in overall activity and spatial patterns, which were relatively consistent across seizures within each of the 5 patients studied. Interestingly, segmented seizure stages based on LFPs or MUA showed a dissociation of their spatiotemporal dynamics, likely reflecting different contributions of non-local synaptic inputs and local network activity. (2) As previously reported, some of the seizures showed a peak in MUA that happened several seconds after local seizure onset and slowly propagated across the MEA. However, other seizures had a more complex structure characterized by, for example, several MUA peaks, more consistent with the succession of discrete stages than the slow propagation of a simple wavefront of increased MUA. In both cases, nevertheless, seizures characterized by spike-wave discharges (SWDs, ~ 2–3 Hz) eventually evolved into patterns of phase-locked MUA and LFPs. (3) Individual SWDs or gamma oscillation cycles (25–60 Hz), characteristic of two different types of recorded seizures, tended to propagate with varying degrees of directionality, directions of propagation and speeds, depending on the identified seizure stage. However, no clear relationship was observed between the MUA peak onset time (in seizures where such peak onset occurred) and changes in MUA or LFP propagation patterns. Overall, our findings indicate that the recruitment of neocortical territories into ictal activity undergoes complex spatiotemporal dynamics evolving in slow discrete states, which are consistent across seizures within each patient. Furthermore, ictal states at finer spatiotemporal scales (individual SWDs or gamma oscillations) are organized by slower time scale network dynamics evolving through these discrete stages.", + "subject": ["Epilepsy", "Collective dynamics", "Secondary generalization", "Cortical waves", "Neural state segmentation"], + "keywords": [] + }, + { + "title": "Latent state-space models for neural decoding", + "author": "Mehdi Aghagolzadeh, Wilson Truccolo", + "publisher": "IEEE", + "url": "http://dx.doi.org/10.1109/embc.2014.6944262", + "doi": "10.1109/embc.2014.6944262", + "year": 2014, + "month": 8, + "abstract": "Ensembles of single-neurons in motor cortex can show strong low-dimensional collective dynamics. In this study, we explore an approach where neural decoding is applied to estimated low-dimensional dynamics instead of to the full recorded neuronal population. A latent state-space model (SSM) approach is used to estimate the low-dimensional neural dynamics from the measured spiking activity in population of neurons. A second state-space model representation is then used to decode kinematics, via a Kalman filter, from the estimated low-dimensional dynamics. The latent SSM-based decoding approach is illustrated on neuronal activity recorded from primary motor cortex in a monkey performing naturalistic 3-D reach and grasp movements. Our analysis show that 3-D reach decoding performance based on estimated low-dimensional dynamics is comparable to the decoding performance based on the full recorded neuronal population.", + "subject": ["Sociology","Decoding","Kinematics","Neurons","State-space methods","Covariance matricesIndex TermsLatent Model","State-space Model","Neural Decoding","Latent State Space","Latent State-space Models","Kinematic","Neuronal Activity","Motor Cortex","Population Activity","Kalman Filter","Primary Motor Cortex","Spiking Activity","Decoding Performance","Decoding Approach","Covariance Matrix","Maximum Likelihood Estimation","Gaussian Noise","State Matrix","Latent State","Spiking Neural Networks","Observation Matrix","Linear Dynamical System","Microelectrode Arrays","Decoding Analysis","Neural Recordings","Spike CountMeSH TermsAnimals","Biomechanical Phenomena","Hand Strength","Haplorhini","Models"," Neurological","Models"," Theoretical","Motor Cortex","Movement","Nerve Net","Neurons"], + "keywords": [] + }, + { + "title": "Eye tracking and pupillometry are indicators of dissociable latent decision processes.", + "author": "James F. Cavanagh, Thomas V. Wiecki, Angad Kochar, Michael J. Frank", + "publisher": "American Psychological Association (APA)", + "url": "http://dx.doi.org/10.1037/a0035813", + "doi": "10.1037/a0035813", + "year": 2014, + "month": 2, + "abstract": "Can you predict what people are going to do just by watching them? This is certainly difficult: it would require a clear mapping between observable indicators and unobservable cognitive states. In this report, we demonstrate how this is possible by monitoring eye gaze and pupil dilation, which predict dissociable biases during decision making. We quantified decision making using the drift diffusion model (DDM), which provides an algorithmic account of how evidence accumulation and response caution contribute to decisions through separate latent parameters of drift rate and decision threshold, respectively. We used a hierarchical Bayesian estimation approach to assess the single trial influence of observable physiological signals on these latent DDM parameters. Increased eye gaze dwell time specifically predicted an increased drift rate toward the fixated option, irrespective of the value of the option. In contrast, greater pupil dilation specifically predicted an increase in decision threshold during difficult decisions. These findings suggest that eye tracking and pupillometry reflect the operations of dissociated latent decision processes.", + "subject": [], + "keywords": [] + }, + { + "title": "A Multi-stage Approach to Curve Extraction", + "author": "Yuliang Guo, Naman Kumar, Maruthi Narayanan, Benjamin Kimia", + "publisher": "Springer International Publishing", + "url": "http://dx.doi.org/10.1007/978-3-319-10590-1_43", + "doi": "10.1007/978-3-319-10590-1_43", + "year": 2014, + "month": 1, + "abstract": "We propose a multi-stage approach to curve extraction where the curve fragment search space is iteratively reduced by removing unlikely candidates using geometric constrains, but without affecting recall, to a point where the application of an objective functional becomes appropriate. The motivation in using multiple stages is to avoid the drawback of using a global functional directly on edges, which can result in non-salient but high scoring curve fragments, which arise from non-uniformly distributed edge evidence. The process progresses in stages from local to global: (i) edges, (ii) curvelets, (iii) unambiguous curve fragments, (iv) resolving ambiguities to generate a full set of curve fragment candidates, (v) merging curve fragments based on a learned photometric and geometric cues as well a novel lateral edge sparsity cue, and (vi) the application of a learned objective functional to get a final selection of curve fragments. The resulting curve fragments are typically visually salient and have been evaluated in two ways. First, we measure the stability of curve fragments when images undergo visual transformations such as change in viewpoints, illumination, and noise, a critical factor for curve fragments to be useful to later visual processes but one often ignored in evaluation. Second, we use a more traditional comparison against human annotation, but using the CFGD dataset and CFGD evaluation strategy rather than the standard BSDS counterpart, which is shown to be not appropriate for evaluating curve fragments. Under both evaluation schemes our results are significantly better than those state of the art algorithms whose implementations are publicly available.", + "subject": ["IEEE Computer Society", "Curve Stability", "Zebra Pattern", "Curve Extraction", "Human Annotation"], + "keywords": [] + }, + { + "title": "Early detection of human focal seizures based on cortical multiunit activity", + "author": "Yun S. Park, Leigh R. Hochberg, Emad N. Eskandar, Sydney S. Cash, Wilson Truccolo", + "publisher": "IEEE", + "url": "http://dx.doi.org/10.1109/embc.2014.6944945", + "doi": "10.1109/embc.2014.6944945", + "year": 2014, + "month": 8, + "abstract": "Approximately 50 million people in the world suffer from epileptic seizures. Reliable early seizure detection could bring significantly beneficial therapeutic alternatives. In recent decades, most approaches have relied on scalp EEG and intracranial EEG signals, but practical early detection for closed-loop seizure control remains challenging. In this study, we present preliminary analyses of an early detection approach based on intracortical neuronal multiunit activity (MUA) recorded from a 96-microelectrode array (MEA). The approach consists of (1) MUA detection from broadband field potentials recorded at 30 kHz by the MEA; (2) MUA feature extraction; (3) cost-sensitive support vector machine classification of ictal and interictal samples; and (4) Kalman-filtering postprocessing. MUA was here defined as the number of threshold crossing (spike counts) applied to the 300 Hz-6 kHz bandpass filtered local field potentials in 0.1 sec time windows. MUA features explored in this study included the mean, variance, and Fano-factor, computed across the MEA channels. In addition, we used the leading eigenvalues of MUA spatial and temporal correlation matrices computed in 1-sec moving time windows. We assessed the seizure detection approach on out-of-sample data from one-participant recordings with six seizure events and 4.73-hour interictal data. The proposed MUA-based detection approach yielded a 100% sensitivity (6/6) and no false positives, and a latency of 4.17 ± 2.27 sec (mean ± SD) with respect to ECoG-identified seizure onsets. These preliminary results indicate intracortical MUA may be a useful signal for early detection of human epileptic seizures.", + "subject": ["Epilepsy","Educational institutions","Support vector machines","Feature extraction","Electroencephalography","Band-pass filters","Broadband communicationIndex TermsEarly Detection","Multi-unit Activity","Seizure Detection","Support Vector Machine","Detection Approach","Kalman Filter","Eigenvalues Of Matrix","Reliable Detection","People In The World","Epileptic Seizures","Spatial Matrix","Seizure Onset","Electrocorticography","Spike Count","Seizure Events","Fano Factor","Threshold Crossings","Approach For Early Detection","Electrode","Spearman Correlation","Radial Basis Function Kernel","Radial Basis Function","Rank CorrelationMeSH TermsEarly Diagnosis","Electroencephalography","Female","Humans","Middle Aged","Seizures","Sensitivity and Specificity","Support Vector Machine"], + "keywords": [] + }, + { + "title": "Neuronal Ensemble Synchrony during Human Focal Seizures", + "author": "W. Truccolo, O. J. Ahmed, M. T. Harrison, E. N. Eskandar, G. R. Cosgrove, J. R. Madsen, A. S. Blum, N. S. Potter, L. R. Hochberg, S. S. Cash", + "publisher": "Society for Neuroscience", + "url": "http://dx.doi.org/10.1523/jneurosci.4567-13.2014", + "doi": "10.1523/jneurosci.4567-13.2014", + "year": 2014, + "month": 7, + "abstract": "Seizures are classically characterized as the expression of hypersynchronous neural activity, yet the true degree of synchrony in neuronal spiking (action potentials) during human seizures remains a fundamental question. We quantified the temporal precision of spike synchrony in ensembles of neocortical neurons during seizures in people with pharmacologically intractable epilepsy. Two seizure types were analyzed: those characterized by sustained gamma (∼40–60 Hz) local field potential (LFP) oscillations or by spike-wave complexes (SWCs; ∼3 Hz). Fine (<10 ms) temporal synchrony was rarely present during gamma-band seizures, where neuronal spiking remained highly irregular and asynchronous. In SWC seizures, phase locking of neuronal spiking to the SWC spike phase induced synchrony at a coarse 50–100 ms level. In addition, transient fine synchrony occurred primarily during the initial ∼20 ms period of the SWC spike phase and varied across subjects and seizures. Sporadic coherence events between neuronal population spike counts and LFPs were observed during SWC seizures in high (∼80 Hz) gamma-band and during high-frequency oscillations (∼130 Hz). Maximum entropy models of the joint neuronal spiking probability, constrained only on single neurons' nonstationary coarse spiking rates and local network activation, explained most of the fine synchrony in both seizure types. Our findings indicate that fine neuronal ensemble synchrony occurs mostly during SWC, not gamma-band, seizures, and primarily during the initial phase of SWC spikes. Furthermore, these fine synchrony events result mostly from transient increases in overall neuronal network spiking rates, rather than changes in precise spiking correlations between specific pairs of neurons.", + "subject": ["collective dynamics", "conditional inference", "epilepsy", "maximum entropy"], + "keywords": [] + }, + { + "title": "Phylogenomic Analyses Support Traditional Relationships within Cnidaria", + "author": "Felipe Zapata, Freya E. Goetz, Stephen A. Smith, Mark Howison, Stefan Siebert, Samuel H. Church, Steven M. Sanders, Cheryl Lewis Ames, Catherine S. McFadden, Scott C. France, Marymegan Daly, Allen G. Collins, Steven H. D. Haddock, Casey W. Dunn, Paulyn Cartwright", + "publisher": "Public Library of Science (PLoS)", + "url": "http://dx.doi.org/10.1371/journal.pone.0139068", + "doi": "10.1371/journal.pone.0139068", + "year": 2015, + "month": 10, + "abstract": "Cnidaria, the sister group to Bilateria, is a highly diverse group of animals in terms of morphology, lifecycles, ecology, and development. How this diversity originated and evolved is not well understood because phylogenetic relationships among major cnidarian lineages are unclear, and recent studies present contrasting phylogenetic hypotheses. Here, we use transcriptome data from 15 newly-sequenced species in combination with 26 publicly available genomes and transcriptomes to assess phylogenetic relationships among major cnidarian lineages. Phylogenetic analyses using different partition schemes and models of molecular evolution, as well as topology tests for alternative phylogenetic relationships, support the monophyly of Medusozoa, Anthozoa, Octocorallia, Hydrozoa, and a clade consisting of Staurozoa, Cubozoa, and Scyphozoa. Support for the monophyly of Hexacorallia is weak due to the equivocal position of Ceriantharia. Taken together, these results further resolve deep cnidarian relationships, largely support traditional phylogenetic views on relationships, and provide a historical framework for studying the evolutionary processes involved in one of the most ancient animal radiations.", + "subject": ["Phylogenetics", "Cnidaria", "Phylogenetic analysis", "Animal phylogenetics", "Transcriptome analysis", "Convergent evolution", "Corals", "Paleogenetics"], + "keywords": [] + }, + { + "title": "Data Management Rubric for Video Data in Organismal Biology", + "author": "Elizabeth L. Brainerd, Richard W. Blob, Tyson L. Hedrick, Andrew T. Creamer, Ulrike K. Müller", + "publisher": "Oxford University Press (OUP)", + "url": "http://dx.doi.org/10.1093/icb/icx060", + "doi": "10.1093/icb/icx060", + "year": 2017, + "month": 7, + "abstract": "Standards-based data management facilitates data preservation, discoverability, and access for effective data reuse within research groups and across communities of researchers. Data sharing requires community consensus on standards for data management, such as storage and formats for digital data preservation, metadata (i.e., contextual data about the data) that should be recorded and stored, and data access. Video imaging is a valuable tool for measuring time-varying phenotypes in organismal biology, with particular application for research in functional morphology, comparative biomechanics, and animal behavior. The raw data are the videos, but videos alone are not sufficient for scientific analysis. Nearly endless videos of animals can be found on YouTube and elsewhere on the web, but these videos have little value for scientific analysis because essential metadata such as true frame rate, spatial calibration, genus and species, weight, age, etc. of organisms, are generally unknown. We have embarked on a project to build community consensus on video data management and metadata standards for organismal biology research. We collected input from colleagues at early stages, organized an open workshop, 'Establishing Standards for Video Data Management,' at the Society for Integrative and Comparative Biology meeting in January 2017, and then collected two more rounds of input on revised versions of the standards. The result we present here is a rubric consisting of nine standards for video data management, with three levels within each standard: good, better, and best practices. The nine standards are: (1) data storage; (2) video file formats; (3) metadata linkage; (4) video data and metadata access; (5) contact information and acceptable use; (6) camera settings; (7) organism(s); (8) recording conditions; and (9) subject matter/topic. The first four standards address data preservation and interoperability for sharing, whereas standards 5–9 establish minimum metadata standards for organismal biology video, and suggest additional metadata that may be useful for some studies. This rubric was developed with substantial input from researchers and students, but still should be viewed as a living document that should be further refined and updated as technology and research practices change. The audience for these standards includes researchers, journals, and granting agencies, and also the developers and curators of databases that may contribute to video data sharing efforts. We offer this project as an example of building community consensus for data management, preservation, and sharing standards, which may be useful for future efforts by the organismal biology research community.", + "subject": [], + "keywords": [] + }, + { + "title": "An Absolute Calibration of Sub-1 keV Nuclear Recoils in Liquid Xenon Using D-D Neutron Scattering Kinematics in the LUX Detector", + "author": "James R Verbus", + "publisher": "Brown University", + "url": "https://repository.library.brown.edu/studio/item/bdr:674209/", + "doi": "10.7301/Z01G0JQ7", + "year": 2016, + "month": 5, + "abstract": "We propose a new technique for the calibration of nuclear recoils in large noble element dual-phase time projection chambers (TPCs) used to search for WIMP dark matter in the local galactic halo. This technique provides a measurement of the low-energy nuclear recoil response of the target media using the measured scattering angle between multiple neutron interactions within the detector volume. Several strategies for improving this calibration technique are discussed, including the creation of a new type of quasi-monoenergetic 272 keV neutron source. We report results from a time-of-flight-based measurement of the neutron energy spectrum produced by an Adelphi Technology, Inc. DD108 neutron generator, confirming its suitability for the proposed calibration. The Large Underground Xenon (LUX) experiment is a dual-phase liquid xenon TPC operating at the Sanford Underground Research Facility in Lead, South Dakota. Our proposed calibration technique for nuclear recoils in liquid xenon was performed in situ in the LUX detector using a collimated beam of mono-energetic 2.45 MeV neutrons produced by the DD108 fusion source. The nuclear recoil energy from the first neutron scatter in the TPC was reconstructed using the measured scattering angle defined by two-site neutron events within the active xenon volume. We measured the absolute charge (Qy) and light (Ly) yields at an average electric field of 180 V/cm for nuclear recoil energies spanning 0.7 to 74 keV and 1.1 to 74 keV, respectively. This calibration of the nuclear recoil signal yields will permit the further refinement of liquid xenon nuclear recoil signal models and clearly demonstrates measurable ionization and scintillation signals in this medium at recoil energies down to O(1 keV). The low-energy reach and reduced systematics of this calibration have particular significance for the low-mass WIMP sensitivity of several leading dark matter experiments.", + "keywords": ["LUX", "liquid xenon", "nuclear recoil", "light yield", "charge yield", "neutron generator", "dark matter", "WIMP", "Dark matter", "Astronomy)"] + }, + { + "title": "Prototype, Surface Commissioning and Photomultiplier Tube Characterization for the Large Underground Xenon (LUX) Direct Dark Matter Search Experiment", + "author": "Carlos H Faham", + "publisher": "Brown University", + "url": "https://repository.library.brown.edu/studio/item/bdr:386139/", + "doi": "10.7301/Z0QV3JV5", + "year": 2014, + "month": 5, + "abstract": "The existence of non-baryonic cold dark matter is well established through a wealth of complementary observations such as the Cosmic Microwave Background, Supernova Type Ia and Big Bang Nucleosynthesis. Despite the overwhelming cosmological evidence, the particle nature of dark matter remains unknown. The leading candidate is a Weakly Interacting Massive Particle (WIMP), a thermal relic from the Big Bang that only interacts through the gravitational and weak forces. A terrestrial detector with high target mass, low background levels and a low energy threshold (keV) should be able to record the rare, faint interactions between ordinary matter and galactic WIMP dark matter. The Large Underground Xenon (LUX) experiment is a 370 kg liquid xenon time projection chamber that aims to detect WIMP recoils with xenon nuclei. The experiment is located a mile underground at the Sanford Underground Research Facility (SURF) in Lead, South Dakota. LUX is poised to become the world's most sensitive dark matter detector after only 2 weeks of exposure and will surpass current detection limits by an order of magnitude after 300 days. The LUX experimental program consists of three phases: (1) the LUX0.1 prototype detector during 2007– 2009, (2) the commissioning and operation of the LUX detector at the Sanford surface laboratory during 2009–2012 and (3) the underground deployment and operation of the detector beginning in 2012. This thesis describes the first two phases of the LUX program. LUX utilizes 122 Hamamatsu R8778 photomultiplier tubes (PMTs) to detect photons produced by particle interactions in liquid xenon. The LUX PMT mounting, high voltage distribution, analog signal shaping and gain calibration system are described in detail. The PMTs are shown to have low radioactive background levels, single-photon sensitivity and a 30% photon detection efficiency at the 175 nm liquid xenon scintillation wavelength. Handling protocols and vacuum integrity control based on ion-initiated afterpulses are presented. Xenon purification and energy calibration results are described for LUX0.1. During the LUX surface run, light collection and statistical position resolution measurements were obtained. Additionally, the xenon circulation path was imaged with alpha particles from a Rn222 injection.", + "keywords": [] + }, + { + "title": "Virtual Reality and Oceanography: Overview, Applications, and Perspective", + "author": "Noah L. Walcutt, Benjamin Knörlein, Tom Sgouros, Ivona Cetinić, Melissa M. Omand", + "publisher": "Frontiers Media SA", + "url": "http://dx.doi.org/10.3389/fmars.2019.00644", + "doi": "10.3389/fmars.2019.00644", + "year": 2019, + "month": 10, + "abstract": "With the ongoing, exponential increase in ocean data from autonomous platforms, satellites, models, and in particular, the growing field of quantitative imaging, there arises a need for scalable and cost-efficient visualization tools to interpret these large volumes of data. With the recent proliferation of consumer grade head-mounted displays, the emerging field of virtual reality (VR) has demonstrated its benefit in numerous disciplines, ranging from medicine to archeology. However, these benefits have not received as much attention in the ocean sciences. Here, we summarize some of the ways that virtual reality has been applied to this field. We highlight a few examples in which we (the authors) demonstrate the utility of VR as a tool for ocean scientists. For oceanic datasets that are well-suited for three-dimensional visualization, virtual reality has the potential to enhance the practice of ocean science.", + "subject": [], + "keywords": [] + }, + { + "title": "Ictal autonomic activity recorded via wearable-sensors plus machine learning can discriminate epileptic and psychogenic nonepileptic seizures", + "author": "A. Zsom, W.C. LaFrance, A.S. Blum, P. Li, L.A. Wahed, M.A. Shaikh, G. Sharma, R. Ranieri, L. Zhang, S. Tsekhan, T. Hamid, J. Levin, W. Truccolo", + "publisher": "IEEE", + "url": "http://dx.doi.org/10.1109/embc.2019.8857552", + "doi": "10.1109/embc.2019.8857552", + "year": 2019, + "month": 7, + "abstract": "Differentiating epileptic seizures (ES) and psychogenic nonepileptic seizures (PNES) is commonly based on electroencephalogram and concurrent video recordings (vEEG). Here, we demonstrate that these two types of seizures can be discriminated based on signals related to autonomic nervous system activity recorded via wearable sensors. We used Empatica E4 Wristband sensors worn on both arms in vEEG confirmed seizures, and machine learning methods to train classifiers, specifically, extreme gradient boosting (XGBoost). Classification performance achieved a predictive accuracy of 78 ± 1.5% on previously unseen data for whether a seizure was epileptic or psychogenic, which is 6 standard deviations above the baseline of 68% accuracy. Our dataset contained altogether 35 seizures from 18 patients out of which 8 patients had 13 convulsive seizures. Prediction of seizure type was based on simple features derived from the segments of autonomic activity measurements (electrodermal activity, body temperature, blood volume pulse, and heart rate) and forearm acceleration. Features related to heart rate and electrodermal activity were ranked as the top predictors in XGBoost classifiers. We found that patients with PNES had a higher ictal heart rate and electrodermal activity than patients with ES. In contrast to existing published studies of mainly convulsive seizures, our classifier focuses on autonomic signals to differentiate convulsive or nonconvulsive semiology ES from PNES. Our results show that autonomic activity recorded via wearable sensors provides promising signals for detection and discrimination of psychogenic and epileptic seizures, but more work is necessary to improve the predictive power of the model.", + "subject": [], + "keywords": [] + }, + { + "title": "Automated identification of multinucleated germ cells with U-Net", + "author": "Samuel Bell, Andras Zsom, Justin Conley, Daniel Spade", + "publisher": "Public Library of Science (PLoS)", + "url": "http://dx.doi.org/10.1371/journal.pone.0229967", + "doi": "10.1371/journal.pone.0229967", + "year": 2020, + "month": 7, + "abstract": "Phthalic acid esters (phthalates) are male reproductive toxicants, which exert their most potent toxicity during fetal development. In the fetal rat, exposure to phthalates reduces testosterone biosynthesis, alters the development of seminiferous cords and other male reproductive tissues, and induces the formation of abnormal multinucleated germ cells (MNGs). Identification of MNGs is a time-intensive process, and it requires specialized training to identify MNGs in histological sections. As a result, MNGs are not routinely quantified in phthalate toxicity experiments. In order to speed up and standardize this process, we have developed an improved method for automated detection of MNGs. Using hand-labeled histological section images with human-identified MNGs, we trained a convolutional neural network with a U-Net architecture to identify MNGs on unlabeled images. With unseen hand-labeled images not used in model training, we assessed the performance of the model, using five different configurations of the data. On average, the model reached near human accuracy, and in the best model, it exceeded it. The use of automated image analysis will allow data on this histopathological endpoint to be more readily collected for analysis of phthalate toxicity. Our trained model application code is available for download at github.com/brown-ccv/mngcount.", + "subject": ["Heart rate","Temperature measurement","Standards","Machine learning","Sensors","Histograms","WristIndex TermsMachine Learning","Epileptic Seizures","Autonomic Activity","Psychogenic Non-epileptic Seizures","Non-epileptic Seizures","Body Temperature","Autonomic Nervous System","Increase In Heart Rate","Wearable Sensors","Autonomic Nervous System Activity","Extreme Gradient Boosting","Seizure Types","Electroencephalogram Recordings","Convulsive Seizures","XGBoost Classifier","Training Set","Null Hypothesis","Kolmogorov-Smirnov Test","Confusion Matrix","Heart Rate Variability","Interictal Period","Hold-out Set","Heart Rate Measurements","Heart Rate In Patients","Feature Importance Measures","Autonomic Dysfunction","Predictive Features","Early Stopping","Tree-based Methods","Number Of TreesMeSH TermsAutonomic Nervous System","Electroencephalography","Epilepsy","Humans","Machine Learning","Seizures","Wearable Electronic Devices"], + "keywords": [] + }, + { + "title": "Automated data extraction from historical city directories: The rise and fall of mid-century gas stations in Providence, RI", + "author": "Samuel Bell, Thomas Marlow, Kai Wombacher, Anina Hitt, Neev Parikh, Andras Zsom, Scott Frickel", + "publisher": "Public Library of Science (PLoS)", + "url": "http://dx.doi.org/10.1371/journal.pone.0220219", + "doi": "10.1371/journal.pone.0220219", + "year": 2020, + "month": 8, + "abstract": "The location of defunct environmentally hazardous businesses like gas stations has many implications for modern American cities. To track down these locations, we present the directoreadr code (github.com/brown-ccv/directoreadr). Using scans of Polk city directories from Providence, RI, directoreadr extracts and parses business location data with a high degree of accuracy. The image processing pipeline ran without any human input for 94.4% of the pages we examined. For the remaining 5.6%, we processed them with some human input. Through hand-checking a sample of three years, we estimate that ~94.6% of historical gas stations are correctly identified and located, with historical street changes and non-standard address formats being the main drivers of errors. As an example use, we look at gas stations, finding that gas stations were most common early in the study period in 1936, beginning a sharp and steady decline around 1950. We are making the dataset produced by directoreadr publicly available. We hope it will be used to explore a range of important questions about socioeconomic patterns in Providence and cities like it during the transformations of the mid-1900s.", + "subject": ["Permeters", "Algorithms", "Grayscale", "Graphics pipelines", "Image processing", "Libraries", "Computer software", "Urban ecnomics"], + "keywords": [] + }, + { + "title": "Mining Spatio-temporal Data on Industrialization from Historical Registries", + "author": "D. Berenbaum, undefined undefined, D. Deighan, T. Marlow, A. Lee, S. Frickel, M. Howison, undefined undefined, undefined undefined, undefined undefined, undefined undefined, undefined undefined", + "publisher": "International Society for Environmental Information Science (ISEIS)", + "url": "http://dx.doi.org/10.3808/jei.201700381", + "doi": "10.3808/jei.201700381", + "year": 2019, + "month": 9, + "abstract": "Despite the growing availability of big data in many fields, historical data on socio-evironmental phenomena are often not available due to a lack of automated and scalable approaches for collecting, digitizing, and assembling them. We have developed a datamining method for extracting tabulated, geocoded data from printed directories. While scanning and optical character recognition (OCR) can digitize printed text, these methods alone do not capture the structure of the underlying data. Our pipeline integrates both page layout analysis and OCR to extract tabular, geocoded data from structured text. We demonstrate the utility of this method by applying it to scanned manufacturing registries from Rhode Island that record 41 years of industrial land use. The resulting spatio-temporal data can be used for socio-environmental analyses of industrialization at a resolution that was not previously possible. In particular, we find strong evidence for the dispersion of manufacturing from the urban core of Providence, the state’s capital, along the Interstate 95 corridor to the north and south.", + "subject": ["structured text", "historical data", "geocoding", "page layout analysis", "socio-environmental analysis"], + "keywords": [] + }, + { + "title": "Development and validation of a multi-dimensional measure of intellectual humility", + "author": "Mark Alfano, Kathryn Iurino, Paul Stey, Brian Robinson, Markus Christen, Feng Yu, Daniel Lapsley", + "publisher": "Public Library of Science (PLoS)", + "url": "http://dx.doi.org/10.1371/journal.pone.0182950", + "doi": "10.1371/journal.pone.0182950", + "year": 2017, + "month": 8, + "abstract": "This paper presents five studies on the development and validation of a scale of intellectual humility. This scale captures cognitive, affective, behavioral, and motivational components of the construct that have been identified by various philosophers in their conceptual analyses of intellectual humility. We find that intellectual humility has four core dimensions: Open-mindedness (versus Arrogance), Intellectual Modesty (versus Vanity), Corrigibility (versus Fragility), and Engagement (versus Boredom). These dimensions display adequate self-informant agreement, and adequate convergent, divergent, and discriminant validity. In particular, Open-mindedness adds predictive power beyond the Big Six for an objective behavioral measure of intellectual humility, and Intellectual Modesty is uniquely related to Narcissism. We find that a similar factor structure emerges in Germanophone participants, giving initial evidence for the model’s cross-cultural generalizability.", + "subject": ["Factor analysis", "Personality traits", "Emotions", "Personality", "Hispanic people", "Human learning", "Human intelligence"], + "keywords": [] + }, + { + "title": "Intracortical neural activity distal to seizure-onset-areas predicts human focal seizures", + "author": "Timothée Proix, Mehdi Aghagolzadeh, Joseph R. Madsen, Rees Cosgrove, Emad Eskandar, Leigh R. Hochberg, Sydney S. Cash, Wilson Truccolo", + "publisher": "Public Library of Science (PLoS)", + "url": "http://dx.doi.org/10.1371/journal.pone.0211847", + "doi": "10.1371/journal.pone.0211847", + "year": 2019, + "month": 7, + "abstract": "The apparent unpredictability of epileptic seizures has a major impact in the quality of life of people with pharmacologically resistant seizures. Here, we present initial results and a proof-of-concept of how focal seizures can be predicted early in advance based on intracortical signals recorded from small neocortical patches away from identified seizure onset areas. We show that machine learning algorithms can discriminate between interictal and preictal periods based on multiunit activity (i.e. thresholded action potential counts) and multi-frequency band local field potentials recorded via 4 X 4 mm2 microelectrode arrays. Microelectrode arrays were implanted in 5 patients undergoing neuromonitoring for resective surgery. Post-implant analysis revealed arrays were outside the seizure onset areas. Preictal periods were defined as the 1-hour period leading to a seizure. A 5-minute gap between the preictal period and the putative seizure onset was enforced to account for potential errors in the determination of actual seizure onset times. We used extreme gradient boosting and long short-term memory networks for prediction. Prediction accuracy based on the area under the receiver operating characteristic curves reached 90% for at least one feature type in each patient. Importantly, successful prediction could be achieved based exclusively on multiunit activity. This result indicates that preictal activity in the recorded neocortical patches involved not only subthreshold postsynaptic potentials, perhaps driven by the distal seizure onset areas, but also neuronal spiking in distal recurrent neocortical networks. Beyond the commonly identified seizure onset areas, our findings point to the engagement of large-scale neuronal networks in the neural dynamics building up toward a seizure. Our initial results obtained on currently available human intracortical microelectrode array recordings warrant new studies on larger datasets, and open new perspectives for seizure prediction and control by emphasizing the contribution of multiscale neural signals in large-scale neuronal networks.", + "subject": ["Eigenvectors", "Action potentials", "Microelectrodes", "Surgical resection", "Neural networks", "Centrality", "Signal filtering", "Medical implants"], + "keywords": [] + }, + { + "title": "Proteinarium: Multi-sample protein-protein interaction analysis and visualization tool", + "author": "David Armanious, Jessica Schuster, George A. Tollefson, Anthony Agudelo, Andrew T. DeWan, Sorin Istrail, James Padbury, Alper Uzun", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.ygeno.2020.07.028", + "doi": "10.1016/j.ygeno.2020.07.028", + "year": 2020, + "month": 11, + "abstract": "We posit the likely architecture of complex diseases is that subgroups of patients share variants in genes in specific networks which are sufficient to give rise to a shared phenotype. We developed Proteinarium, a multi-sample protein-protein interaction (PPI) tool, to identify clusters of patients with shared gene networks. Proteinarium converts user defined seed genes to protein symbols and maps them onto the STRING interactome. A PPI network is built for each sample using Dijkstra's algorithm. Pairwise similarity scores are calculated to compare the networks and cluster the samples. A layered graph of PPI networks for the samples in any cluster can be visualized. To test this newly developed analysis pipeline, we reanalyzed publicly available data sets, from which modest outcomes had previously been achieved. We found significant clusters of patients with unique genes which enhanced the findings in the original study.", + "subject": ["Software", "Protein-protein interactions", "Networks", "Multi-sample", "Data visualization"], + "keywords": [] + }, + { + "title": "Developing Virtual Reality Visualizations for Unsteady Flow Analysis of Dinosaur Track Formation using Scientific Sketching", + "author": "Johannes Novotny, Joshua Tveite, Morgan L. Turner, Stephen Gatesy, Fritz Drury, Peter Falkingham, David H. Laidlaw", + "publisher": "Institute of Electrical and Electronics Engineers (IEEE)", + "url": "http://dx.doi.org/10.1109/tvcg.2019.2898796", + "doi": "10.1109/tvcg.2019.2898796", + "year": 2019, + "month": 5, + "abstract": "We present the results of a two-year design study to developing virtual reality (VR) flow visualization tools for the analysis of dinosaur track creation in a malleable substrate. Using Scientific Sketching methodology, we combined input from illustration artists, visualization experts, and domain scientists to create novel visualization methods. By iteratively improving visualization concepts at multiple levels of abstraction we helped domain scientists to gain insights into the relationship between dinosaur foot movements and substrate deformations. We involved over 20 art and computer science students from a VR design course in a rapid visualization sketching cycle, guided by our paleontologist collaborators through multiple critique sessions. This allowed us to explore a wide range of potential visualization methods and select the most promising methods for actual implementation. Our resulting visualization methods provide paleontologists with effective tools to analyze their data through particle, pathline and time surface visualizations. We also introduce a set of visual metaphors to compare foot motion in relation to substrate deformation by using pathsurfaces. This is one of the first large-scale projects using Scientific Sketching as a development methodology. We discuss how the research questions of our collaborators have evolved during the sketching and prototyping phases. Finally, we provide lessons learned and usage considerations for Scientific Sketching based on the experiences gathered during this project.", + "subject": ["Data visualization","Visualization","Dinosaurs","Three-dimensional displays","Tracking","Foot","Substrates", "Virtually","Steady Flow","Formation Tracking","Dinosaur Tracks","Virtual Reality Visualization","Visualization Tool","Visual Methods","Wide Range Of Methods","Flow Visualization","Design Course","Arts Students","Substantial Deformation","Pathlines","Visual Concepts","Visual Metaphors","Multiple Levels Of Abstraction","Computer Science Students","Simulated Data","Design Methodology","Visualization Techniques","Visual Design","3D Flow","Iterative Development Process","Use Of Virtual Reality","Screen Space","Scientific Visualization","Discrete Element Method","Subsequent Time Steps","Virtual Reality Applications", "Virtual Reality","Scientific Visualization","Flow Visualization","Design Study", "Animals","Art","Computer Graphics","Dinosaurs","Humans","Imaging"," Three-Dimensional","Locomotion","Smart Glasses","Virtual Reality"], + "keywords": [] + }, + { + "title": "Polarization of Valence Orbitals by the Intramolecular Electric Field from a Diffuse Dipole-Bound Electron", + "author": "Dao-Fu Yuan, Yuan Liu, Chen-Hui Qian, G. Stephen Kocheril, Yue-Rou Zhang, Brenda M. Rubenstein, Lai-Sheng Wang", + "publisher": "American Chemical Society (ACS)", + "url": "http://dx.doi.org/10.1021/acs.jpclett.0c02514", + "doi": "10.1021/acs.jpclett.0c02514", + "year": 2020, + "month": 9, + "abstract": "The diffuse electron in a dipole-bound state is spatially well separated from the valence electrons and is known to have negligible effects on the dipole-bound state’s molecular structure. Here, we show that a dipole-bound state is observed in deprotonated 4-(2-phenylethynyl)-phenoxide anions, 348 cm–1 below the anion’s detachment threshold. The photodetachment of the dipole-bound electron is observed to accompany a simultaneous shakeup process in valence orbitals in this aromatic molecular anion. This shakeup process is due to configuration mixing as a result of valence orbital polarization by the intramolecular electric field of the dipole-bound electron. This observation suggests that dipole-bound anions can serve as a new platform to probe how oriented electric fields influence the valence electronic structure of polyatomic molecules.", + "subject": [], + "keywords": [] + }, + { + "title": "Reentrant melting of sodium, magnesium, and aluminum: General trend", + "author": "Qi-Jun Hong, Axel van de Walle", + "publisher": "American Physical Society (APS)", + "url": "http://dx.doi.org/10.1103/physrevb.100.140102", + "doi": "10.1103/physrevb.100.140102", + "year": 2019, + "month": 10, + "abstract": "Reentrant melting (in which a substance's melting point starts to decrease beyond a certain pressure) is believed to be an unusual phenomenon. Among the elements, it has so far only been observed in a very limited number of species, e.g., the alkali metals. Our density functional theory calculations reveal that this behavior actually extends beyond alkali metals to include magnesium, which also undergoes reentrant melting, though at the much higher pressure of ∼300 GPa. We find that the origin of reentrant melting is the faster softening of interatomic interactions in the liquid phase than in the solid, as pressure rises. We propose a simple approach to estimate pressure-volume relations and show that this characteristic softening pattern is widely observed in metallic elements. We verify this prediction in the case of aluminum by finding reentrant melting at ∼4000 GPa. These results suggest that reentrant melting may be a more universal feature than previously thought.", + "subject": ["crystal melting", "liquid-solid phase transition", "density functional theory", "molecular dynamics"], + "keywords": [] + }, + { + "title": "Results of a Search for Sub-GeV Dark Matter Using 2013 LUX Data", + "author": "D. S. Akerib, S. Alsum, H. M. Araújo, X. Bai, J. Balajthy, P. Beltrame, E. P. Bernard, A. Bernstein, T. P. Biesiadzinski, E. M. Boulton, B. Boxer, P. Brás, S. Burdin, D. Byram, M. C. Carmona-Benitez, C. Chan, J. E. Cutter, T. J. R. Davison, E. Druszkiewicz, S. R. Fallon, A. Fan, S. Fiorucci, R. J. Gaitskell, J. Genovesi, C. Ghag, M. G. D. Gilchriese, C. Gwilliam, C. R. Hall, S. J. Haselschwardt, S. A. Hertel, D. P. Hogan, M. Horn, D. Q. Huang, C. M. Ignarra, R. G. Jacobsen, O. Jahangir, W. Ji, K. Kamdin, K. Kazkaz, D. Khaitan, R. Knoche, E. V. Korolkova, S. Kravitz, V. A. Kudryavtsev, B. G. Lenardo, K. T. Lesko, J. Liao, J. Lin, A. Lindote, M. I. Lopes, A. Manalaysay, R. L. Mannino, N. Marangou, M. F. Marzioni, D. N. McKinsey, D.-M. Mei, M. Moongweluwan, J. A. Morad, A. St. J. Murphy, A. Naylor, C. Nehrkorn, H. N. Nelson, F. Neves, K. C. Oliver-Mallory, K. J. Palladino, E. K. Pease, Q. Riffard, G. R. C. Rischbieter, C. Rhyne, P. Rossiter, S. Shaw, T. A. Shutt, C. Silva, M. Solmaz, V. N. Solovov, P. Sorensen, T. J. Sumner, M. Szydagis, D. J. Taylor, W. C. Taylor, B. P. Tennyson, P. A. Terman, D. R. Tiedt, W. H. To, M. Tripathi, L. Tvrznikova, U. Utku, S. Uvarov, V. Velan, R. C. Webb, J. T. White, T. J. Whitis, M. S. Witherell, F. L. H. Wolfs, D. Woodward, J. Xu, K. Yazdani, C. Zhang, undefined undefined", + "publisher": "American Physical Society (APS)", + "url": "http://dx.doi.org/10.1103/physrevlett.122.131301", + "doi": "10.1103/physrevlett.122.131301", + "year": 2019, + "month": 4, + "abstract": "The scattering of dark matter (DM) particles with sub-GeV masses off nuclei is difficult to detect using liquid xenon-based DM search instruments because the energy transfer during nuclear recoils is smaller than the typical detector threshold. However, the tree-level DM-nucleus scattering diagram can be accompanied by simultaneous emission of a bremsstrahlung photon or a so-called 'Migdal' electron. These provide an electron recoil component to the experimental signature at higher energies than the corresponding nuclear recoil. The presence of this signature allows liquid xenon detectors to use both the scintillation and the ionization signals in the analysis where the nuclear recoil signal would not be otherwise visible. We report constraints on spin-independent DM-nucleon scattering for DM particles with masses of 0.4–5  GeV/\uD835\uDC502 using 1.4×104  kg day of search exposure from the 2013 data from the Large Underground Xenon (LUX) experiment for four different classes of mediators. This analysis extends the reach of liquid xenon-based DM search instruments to lower DM masses than has been achieved previously.", + "subject": ["particle dark matter", "weakly interacting massive particles", "dark matter detectors"], + "keywords": [] + }, + { + "title": "Evidence from first-principles calculations for orbital ordering in Ba2NaOsO6: A Mott insulator with strong spin-orbit coupling", + "author": "R. Cong, Ravindra Nanguneri, Brenda Rubenstein, V. F. Mitrović", + "publisher": "American Physical Society (APS)", + "url": "http://dx.doi.org/10.1103/physrevb.100.245141", + "doi": "10.1103/physrevb.100.245141", + "year": 2019, + "month": 12, + "abstract": "", + "subject": [], + "keywords": [] + }, + { + "title": "Accurate Prediction of Bond Dissociation Energies and Barrier Heights for High-Energy Caged Nitro and Nitroamino Compounds Using a Coupled Cluster Theory", + "author": "Vitaly G. Kiselev, C. Franklin Goldsmith", + "publisher": "American Chemical Society (ACS)", + "url": "http://dx.doi.org/10.1021/acs.jpca.9b01506", + "doi": "10.1021/acs.jpca.9b01506", + "year": 2019, + "month": 3, + "abstract": "Highly accurate theoretical values of bond energies and activation barriers of primary decomposition reactions are crucial for reliable predictions of thermal decomposition and detonation-related phenomena of energetic materials (EM). However, due to the prohibitive computational cost, high-level ab initio calculations had been impractical for a large number of important EMs, including, e.g., hexanitrohexaazaisowurtzitane (CL-20). In the present work, we obtained accurate bond dissociation energies and the activation barriers for primary decomposition reactions for a series of novel promising caged polynitroamino and polynitro EMs, viz., CL-20, TEX, octanitrocubane (ONC), and hexanitro derivatives of adamantane, using the recently proposed domain-localized pair natural orbitals (DLPNO) modifications of coupled cluster techniques. DLPNO-CCSD(T) allows for routine quadruple-ζ basis set quality coupled cluster calculations for the species comprised of ∼30 non-H atoms. The benchmarks on a number of simpler congeners of CL-20 and ONC revealed that the DLPNO approach does not deteriorate the quality of the quadruple-ζ coupled cluster procedure. With the aid of this technique, the full set of gas-phase primary decomposition reactions for all 9 conformers of CL-20 was considered. For all species studied, C–NO2 or N–NO2 radical decomposition channels dominate over molecular counterparts. The best theoretical results reported in the literature so far, viz., density functional theory energies of nitro group radical elimination in CL-20 and ONC, underestimate the value by ∼10 kcal mol–1. We also present reliable and accurate gas-phase formation enthalpies for CL-20, ONC, and related species. In a more general sense, these results offer a new level of predictive computational kinetics for polynitro-caged energetic materials.", + "subject": [], + "keywords": [] + }, + { + "title": "Suitability of gridded climate datasets for use in environmental epidemiology", + "author": "Keith R. Spangler, Kate R. Weinberger, Gregory A. Wellenius", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1038/s41370-018-0105-2", + "doi": "10.1038/s41370-018-0105-2", + "year": 2018, + "month": 12, + "abstract": "Epidemiologic analyses of the health effects of meteorological exposures typically rely on observations from the nearest weather station to assess exposure for geographically diverse populations. Gridded climate datasets (GCD) provide spatially resolved weather data that may offer improved exposure estimates, but have not been systematically validated for use in epidemiologic evaluations. As a validation, we linearly regressed daily weather estimates from two GCDs, PRISM and Daymet, to observations from a sample of weather stations across the conterminous United States and compared spatially resolved, population-weighted county average temperatures and heat indices from PRISM to single-pixel PRISM values at the weather stations to identify differences. We found that both Daymet and PRISM accurately estimate ambient temperature and mean heat index at sampled weather stations, but PRISM outperforms Daymet for assessments of humidity and maximum daily heat index. Moreover, spatially-resolved exposure estimates differ from point-based assessments, but with substantial inter-county heterogeneity. We conclude that GCDs offer a potentially useful approach to exposure assessment of meteorological variables that may, in some locations, reduce exposure measurement error, as well as permit assessment of populations distributed far from weather stations.", + "subject": [], + "keywords": [] + }, + { + "title": "Predicting the viability of beta-lactamase: How folding and binding free energies correlate with beta-lactamase fitness", + "author": "Jordan Yang, Nandita Naik, Jagdish Suresh Patel, Christopher S. Wylie, Wenze Gu, Jessie Huang, F. Marty Ytreberg, Mandar T. Naik, Daniel M. Weinreich, Brenda M. Rubenstein", + "publisher": "Public Library of Science (PLoS)", + "url": "http://dx.doi.org/10.1371/journal.pone.0233509", + "doi": "10.1371/journal.pone.0233509", + "year": 2020, + "month": 5, + "abstract": "One of the long-standing holy grails of molecular evolution has been the ability to predict an organism’s fitness directly from its genotype. With such predictive abilities in hand, researchers would be able to more accurately forecast how organisms will evolve and how proteins with novel functions could be engineered, leading to revolutionary advances in medicine and biotechnology. In this work, we assemble the largest reported set of experimental TEM-1 β-lactamase folding free energies and use this data in conjunction with previously acquired fitness data and computational free energy predictions to determine how much of the fitness of β-lactamase can be directly predicted by thermodynamic folding and binding free energies. We focus upon β-lactamase because of its long history as a model enzyme and its central role in antibiotic resistance. Based upon a set of 21 β-lactamase single and double mutants expressly designed to influence protein folding, we first demonstrate that modeling software designed to compute folding free energies such as FoldX and PyRosetta can meaningfully, although not perfectly, predict the experimental folding free energies of single mutants. Interestingly, while these techniques also yield sensible double mutant free energies, we show that they do so for the wrong physical reasons. We then go on to assess how well both experimental and computational folding free energies explain single mutant fitness. We find that folding free energies account for, at most, 24% of the variance in β-lactamase fitness values according to linear models and, somewhat surprisingly, complementing folding free energies with computationally-predicted binding free energies of residues near the active site only increases the folding-only figure by a few percent. This strongly suggests that the majority of β-lactamase’s fitness is controlled by factors other than free energies. Overall, our results shed a bright light on to what extent the community is justified in using thermodynamic measures to infer protein fitness as well as how applicable modern computational techniques for predicting free energies will be to the large data sets of multiply-mutated proteins forthcoming.", + "subject": ["free energy", "protein folding", "thermodynamics", "biochemical simulations", "Monte Carlo method", "molecular dynamics", "crystal structure", "tryptophan"], + "keywords": [] + }, + { + "title": "Dynamic and regulated TAF gene expression during mouse embryonic germ cell development", + "author": "Megan A. Gura, Maria M. Mikedis, Kimberly A. Seymour, Dirk G. de Rooij, David C. Page, Richard N. Freiman", + "publisher": "Public Library of Science (PLoS)", + "url": "http://dx.doi.org/10.1371/journal.pgen.1008515", + "doi": "10.1371/journal.pgen.1008515", + "year": 2020, + "month": 1, + "abstract": "Germ cells undergo many developmental transitions before ultimately becoming either eggs or sperm, and during embryonic development these transitions include epigenetic reprogramming, quiescence, and meiosis. To begin understanding the transcriptional regulation underlying these complex processes, we examined the spatial and temporal expression of TAF4b, a variant TFIID subunit required for fertility, during embryonic germ cell development. By analyzing published datasets and using our own experimental system to validate these expression studies, we determined that both Taf4b mRNA and protein are highly germ cell-enriched and that Taf4b mRNA levels dramatically increase from embryonic day 12.5–18.5. Surprisingly, additional mRNAs encoding other TFIID subunits are coordinately upregulated through this time course, including Taf7l and Taf9b. The expression of several of these germ cell-enriched TFIID genes is dependent upon Dazl and/or Stra8, known regulators of germ cell development and meiosis. Together, these data suggest that germ cells employ a highly specialized and dynamic form of TFIID to drive the transcriptional programs that underlie mammalian germ cell development.", + "subject": ["germ cells", "gene expression", "gonads", "melosis", "ovaries", "spermatocytes", "messenger RNA", "testes"], + "keywords": [] + }, + { + "title": "First direct detection constraint on mirror dark matter kinetic mixing using LUX 2013 data", + "author": "D. S. Akerib, S. Alsum, H. M. Araújo, X. Bai, J. Balajthy, A. Baxter, E. P. Bernard, A. Bernstein, T. P. Biesiadzinski, E. M. Boulton, B. Boxer, P. Brás, S. Burdin, D. Byram, M. C. Carmona-Benitez, C. Chan, J. E. Cutter, L. de Viveiros, E. Druszkiewicz, A. Fan, S. Fiorucci, R. J. Gaitskell, C. Ghag, M. G. D. Gilchriese, C. Gwilliam, C. R. Hall, S. J. Haselschwardt, S. A. Hertel, D. P. Hogan, M. Horn, D. Q. Huang, C. M. Ignarra, R. G. Jacobsen, O. Jahangir, W. Ji, K. Kamdin, K. Kazkaz, D. Khaitan, E. V. Korolkova, S. Kravitz, V. A. Kudryavtsev, E. Leason, B. G. Lenardo, K. T. Lesko, J. Liao, J. Lin, A. Lindote, M. I. Lopes, A. Manalaysay, R. L. Mannino, N. Marangou, M. F. Marzioni, D. N. McKinsey, D.-M. Mei, M. Moongweluwan, J. A. Morad, A. St. J. Murphy, A. Naylor, C. Nehrkorn, H. N. Nelson, F. Neves, A. Nilima, K. C. Oliver-Mallory, K. J. Palladino, E. K. Pease, Q. Riffard, G. R. C. Rischbieter, C. Rhyne, P. Rossiter, S. Shaw, T. A. Shutt, C. Silva, M. Solmaz, V. N. Solovov, P. Sorensen, T. J. Sumner, M. Szydagis, D. J. Taylor, R. Taylor, W. C. Taylor, B. P. Tennyson, P. A. Terman, D. R. Tiedt, W. H. To, M. Tripathi, L. Tvrznikova, U. Utku, S. Uvarov, A. Vacheret, V. Velan, R. C. Webb, J. T. White, T. J. Whitis, M. S. Witherell, F. L. H. Wolfs, D. Woodward, J. Xu, C. Zhang, undefined undefined", + "publisher": "American Physical Society (APS)", + "url": "http://dx.doi.org/10.1103/physrevd.101.012003", + "doi": "10.1103/physrevd.101.012003", + "year": 2020, + "month": 1, + "abstract": "We present the results of a direct detection search for mirror dark matter interactions, using data collected from the Large Underground Xenon experiment during 2013, with an exposure of 95 live−days×118  kg. Here, the calculations of the mirror electron scattering rate in liquid xenon take into account the shielding effects from mirror dark matter captured within the Earth. Annual and diurnal modulation of the dark matter flux and atomic shell effects in xenon are also accounted for. Having found no evidence for an electron recoil signal induced by mirror dark matter interactions we place an upper limit on the kinetic mixing parameter over a range of local mirror electron temperatures between 0.1 and 0.9 keV. This limit shows significant improvement over the previous experimental constraint from orthopositronium decays and significantly reduces the allowed parameter space for the model. We exclude mirror electron temperatures above 0.3 keV at a 90% confidence level, for this model, and constrain the kinetic mixing below this temperature.", + "subject": ["particle dark matter", "hypothetical fermions", "dark matter detectors"], + "keywords": [] + }, + { + "title": "A Challenge to the G ∼ 0 Interpretation of Hydrogen Evolution", + "author": "Per Lindgren, Georg Kastlunger, Andrew A. Peterson", + "publisher": "American Chemical Society (ACS)", + "url": "http://dx.doi.org/10.1021/acscatal.9b02799", + "doi": "10.1021/acscatal.9b02799", + "year": 2019, + "month": 12, + "abstract": "Platinum is a nearly perfect catalyst for the hydrogen evolution reaction, and its high activity has conventionally been explained by its close-to-thermoneutral hydrogen binding energy (G ∼ 0). However, many candidate nonprecious metal catalysts bind hydrogen with similar strengths but exhibit orders-of-magnitude lower activity for this reaction. In this study, we employ electronic structure methods that allow fully potential-dependent reaction barriers to be calculated, in order to develop a complete working picture of hydrogen evolution on platinum. Through the resulting ab initio microkinetic models, we assess the mechanistic origins of Pt’s high activity. Surprisingly, we find that the G ∼ 0 hydrogen atoms are inert in the kinetically relevant region and that the active hydrogen atoms have ΔG’s much weaker, similar to that of gold. These on-top hydrogens have particularly low barriers, which we compare to those of gold, explaining the high reaction rates, and the exponential variations in coverage lead directly to Pt’s strong kinetic response to the applied potential. This explains the unique reactivity of Pt that is missed by conventional Sabatier analyses and suggests true design criteria for nonprecious alternatives.", + "subject": ["hydrogen evolution", "constant-potential DFT", "tafel slopes", "current densities"], + "keywords": [] + }, + { + "title": "Energetics of melting of Yb2O3 and Lu2O3 from drop and catch calorimetry and first principles computations", + "author": "Matthew Fyhrie, Qi-Jun Hong, Denys Kapush, Sergey V. Ushakov, Helena Liu, Axel van de Walle, Alexandra Navrotsky", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.jct.2019.01.008", + "doi": "10.1016/j.jct.2019.01.008", + "year": 2019, + "month": 5, + "abstract": "The energetics of melting of Yb2O3 (Tfus 2707 ± 20 K) and Lu2O3 (Tfus 2762 ± 15 K) were studied experimentally by drop-and-catch (DnC) calorimetry and computationally by ab initio molecular dynamic (AI MD) techniques. Fusion enthalpies for Yb2O3 (102 ± 10) kJ∙mol−1 and Lu2O3 (125 ± 10) kJ∙mol−1 were derived from the steps in enthalpy increments from DnC experiments performed on liquid and solid samples laser heated in an argon flow. Fusion enthalpy values for Yb2O3 and Lu2O3 obtained from AI MD computations were 124 ± 2 kJ/mol and 124 ± 3 kJ/mol, respectively. High temperature heat capacity values for solid and liquid phases and volume change on melting were obtained from AI MD. Computed volume change on melting for both oxides is less than 1%, prompting an experimental investigation due to difference with prior experimental results. Experimental results indicate substantial dissolution of oxygen in liquid Lu2O3.", + "subject": [], + "keywords": [] + }, + { + "title": "On the Coupling of Electron Transfer to Proton Transfer at Electrified Interfaces", + "author": "Aimin Ge, Georg Kastlunger, Jinhui Meng, Per Lindgren, Jia Song, Qiliang Liu, Alexander Zaslavsky, Tianquan Lian, Andrew A. Peterson", + "publisher": "American Chemical Society (ACS)", + "url": "http://dx.doi.org/10.1021/jacs.0c03472", + "doi": "10.1021/jacs.0c03472", + "year": 2020, + "month": 6, + "abstract": "Many electrochemical processes are governed by the transfer of protons to the surface, which can be coupled with electron transfer; this electron transfer is in general non-integer and unknown a priori, but is required to hold the potential constant. In this study, we employ a combination of surface spectroscopic techniques and grand-canonical electronic-structure calculations in order to rigorously understand the thermodynamics of this process. Specifically, we explore the protonation/deprotonation of 4-mercaptobenzoic acid as a function of the applied potential. Using grand-canonical electronic-structure calculations, we directly infer the coupled electron transfer, which we find to be on the order of 0.1 electron per proton; experimentally, we also access this quantity via the potential-dependence of the pKa. We show a striking agreement between the potential-dependence of the measured pKa and that calculated with electronic-structure calculations. We further employ a simple electrostatics-based model to show that this slope can equivalently be interpreted to provide information on the degree of coupled electron transfer or the potential change at the point of the charged species.", + "subject": [], + "keywords": [] + }, + { + "title": "Decreasing HIV transmissions to African American women through interventions for men living with HIV post-incarceration: An agent-based modeling study", + "author": "Joëlla W. Adams, Mark N. Lurie, Maximilian R. F. King, Kathleen A. Brady, Sandro Galea, Samuel R. Friedman, Maria R. Khan, Brandon D. L. Marshall", + "publisher": "Public Library of Science (PLoS)", + "url": "http://dx.doi.org/10.1371/journal.pone.0219361", + "doi": "10.1371/journal.pone.0219361", + "year": 2019, + "month": 7, + "abstract": "Background\nIncarceration and HIV disproportionately impact African American communities. The mass incarceration of African American men is hypothesized to increase HIV acquisition risk for African American women. Interventions optimizing HIV care engagement and minimizing sexual risk behaviors for men living with HIV post-incarceration may decrease HIV incidence.\n\nMethods\nUsing an agent-based model, we simulated a sexual and injection drug using network representing the African American population of Philadelphia. We compared intervention strategies for men living with HIV post-incarceration by the number of averted HIV transmissions to women within the community. Three interventions were evaluated: a 90-90-90 scenario scaling up HIV testing, ART provision, and ART adherence; a behavioral intervention decreasing sexual risk behaviors; and a combination intervention involving both.\n\nResults\nThe status quo scenario projected 2,836 HIV transmissions to women over twenty years. HIV transmissions to women decreased by 29% with the 90-90-90 intervention, 23% with the behavioral intervention, and 37% with both. The number of men living with HIV receiving the intervention needed in order to prevent a single HIV transmission ranged between 6 and 10.\n\nConclusion\nInterventions to improve care engagement and decrease sexual risk behaviors post-incarceration for men living with HIV have the potential to decrease HIV incidence within African American heterosexual networks.", + "subject": ["HIV", "African American people", "medical risk factors", "HIV epidemiology", "Highly-active antiretroviral therapy", "human sexual behavior", "HIV diagnosis and management", "virus testing"], + "keywords": [] + }, + { + "title": "Metal-insulator and magnetic phase diagram of \nCa2RuO4\n from auxiliary field quantum Monte Carlo and dynamical mean field theory", + "author": "Hongxia Hao, Antoine Georges, Andrew J. Millis, Brenda Rubenstein, Qiang Han, Hao Shi", + "publisher": "American Physical Society (APS)", + "url": "http://dx.doi.org/10.1103/physrevb.101.235110", + "doi": "10.1103/physrevb.101.235110", + "year": 2020, + "month": 6, + "abstract": "Layered perovskite ruthenium oxides exhibit a striking series of metal-insulator and magnetic-nonmagnetic phase transitions easily tuned by temperature, pressure, epitaxy, and nonlinear drive. In this work, we combine results from two complementary state-of-the-art many-body methods, auxiliary field quantum Monte Carlo and dynamical mean field theory, to determine the low-temperature phase diagram of Ca2\u2062RuO4. Both methods predict a low-temperature, pressure-driven metal-insulator transition accompanied by a ferromagnetic-antiferromagnetic transition. The properties of the ferromagnetic state vary nonmonotonically with pressure and are dominated by the ruthenium \uD835\uDC51\uD835\uDC65\u2062\uD835\uDC66 orbital, while the properties of the antiferromagnetic state are dominated by the \uD835\uDC51\uD835\uDC65\u2062\uD835\uDC67 and \uD835\uDC51\uD835\uDC66\u2062\uD835\uDC67 orbitals. Differences in the details of the predictions of the two methods are analyzed. This work is theoretically important as it presents the first application of the auxiliary field quantum Monte Carlo method to an orbitally degenerate system with both Mott and Hunds physics and provides an important comparison of the dynamical mean field and auxiliary field quantum Monte Carlo methods.", + "subject": ["Antiferromagnetism", "Ferromagnetism", "Magnetic phase transitions", "Metal-insulator transition", "Phase transitions", "Strongly correlated systems", "Transition metal oxides", "Dynamical mean field theory", "Monte Carlo methods"], + "keywords": [] + }, + { + "title": "Computational Assessment of the Efficacy of Oxidation-Resistant Iridium Coatings for Multiple Principal Component Rhenium Substitutes", + "author": "Helena Liu, Mark Asta, Axel van de Walle", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.scriptamat.2020.07.050", + "doi": "10.1016/j.scriptamat.2020.07.050", + "year": 2020, + "month": 12, + "abstract": "Rhenium is an advanced engineering material valued for its performance under rapid thermal cycling to high temperatures. Due to rhenium’s high cost, alternatives are actively being sought, and hexagonal close packed multiple principal component alloys consisting of Mo, W, Ta and Ru have been previously identified as a promising candidate. Here we assess whether the use of iridium coatings, a widely adopted approach to limit the oxidation of Re, can also be used with this candidate alloy. Specifically, we quantify, through atomistic computations based on density functional theory, the relative diffusion rates of the constituent elements through the protective Ir coating, which is known to be a dominant failure mechanism.", + "subject": ["Grain boundary diffusion", "First-principle calculation", "Refractory metals", "Protective coating"], + "keywords": [] + }, + { + "title": "PPINN: Parareal physics-informed neural network for time-dependent PDEs", + "author": "Xuhui Meng, Zhen Li, Dongkun Zhang, George Em Karniadakis", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.cma.2020.113250", + "doi": "10.1016/j.cma.2020.113250", + "year": 2020, + "month": 10, + "abstract": "Physics-informed neural networks (PINNs) encode physical conservation laws and prior physical knowledge into the neural networks, ensuring the correct physics is represented accurately while alleviating the need for supervised learning to a great degree (Raissi et al., 2019). While effective for relatively short-term time integration, when long time integration of the time-dependent PDEs is sought, the time–space domain may become arbitrarily large and hence training of the neural network may become prohibitively expensive. To this end, we develop a parareal physics-informed neural network (PPINN), hence decomposing a long-time problem into many independent short-time problems supervised by an inexpensive/fast coarse-grained (CG) solver. In particular, the serial CG solver is designed to provide approximate predictions of the solution at discrete times, while initiate many fine PINNs simultaneously to correct the solution iteratively. There is a two-fold benefit from training PINNs with small-data sets rather than working on a large-data set directly, i.e., training of individual PINNs with small-data is much faster, while training the fine PINNs can be readily parallelized. Consequently, compared to the original PINN approach, the proposed PPINN approach may achieve a significant speed-up for long-time integration of PDEs, assuming that the CG solver is fast and can provide reasonable predictions of the solution, hence aiding the PPINN solution to converge in just a few iterations. To investigate the PPINN performance on solving time-dependent PDEs, we first apply the PPINN to solve the Burgers equation, and subsequently we apply the PPINN to solve a two-dimensional nonlinear diffusion–reaction equation. Our results demonstrate that PPINNs converge in a few iterations with significant speed-ups proportional to the number of time-subdomains employed.", + "subject": ["Deep neural network", "Machine learning", "Parallel-in-time", "Long-time integration", "Multiscale", "PINN"], + "keywords": [] + }, + { + "title": "First-principles thermal compatibility between Ru-based Re-substitute alloys and Ir coatings", + "author": "Ruoshi Sun, Mark Asta, Axel van de Walle", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.commatsci.2019.109199", + "doi": "10.1016/j.commatsci.2019.109199", + "year": 2019, + "month": 12, + "abstract": "We perform first-principles calculations to assess the thermal compatibility between Ru-based base alloys and Ir coatings. We use special quasirandom structures for atomistic modeling of disordered \n, \n, and \n alloys, where \n, and the quasiharmonic approximation to obtain thermal expansion coefficients up to 2400 K. Most of the proposed Ru-based alloys show better thermal compatibility with Ir than Re. A four-dimensional thermal expansion model of the Ru–Mo–Ta–W quaternary system is presented.", + "subject": ["Thermal expansion", "Ruthenium alloy", "Ab initio calculation"], + "keywords": [] + }, + { + "title": "Vortex Dynamics of Darrieus Turbines with Intracycle Angular Velocity Control", + "author": "Mukul Dave, Benjamin Strom, Jennifer A. Franck", + "publisher": "American Institute of Aeronautics and Astronautics", + "url": "http://dx.doi.org/10.2514/6.2020-0348", + "doi": "10.2514/6.2020-0348", + "year": 2020, + "month": 1, + "abstract": "Straight-bladed cross-flow turbines, also known as H-Darrieus or vertical-axis turbines, are explored for harvesting wind and hydrokinetic energy. This design offers advantages such as independence from flow direction and ease of manufacturing compared with axial flow turbines. One challenge in the design of straight-bladed cross-flow turbines is the transient occurrence of high apparent angles of attack on the blades. When the apparent angle of attack exceeds the stall angle, separation and vortex shedding reduce efficiency and cause high structural load oscillations. Manipulation of the apparent angle of attack through intracycle control of the angular velocity has shown to increase turbine efficiency up to 59% as shown experimentally by Strom et al. This paper explores intracycle angular velocity control computationally via a Reynolds-Averaged Navier-Stokes (RANS) model for a constricted flow with high blockage and for open-field flow with very low blockage. By creating a sinusoidal profile for angular velocity the simulations demonstrate a 54% increase in efficiency for the constricted flow and 27% for the open-field configuration. In addition to the force and power profiles, the simulations show that minimal flow separation occurs for the constricted flow resulting in a single, strong trailing edge vortex at the end of the upstream motion of the blade. In contrast, large flow separation is observed in the open-field computation resulting in multiple vortices shed from the blade on upstream side that interact with the blade on downstream side.", + "subject": [], + "keywords": [] + }, + { + "title": "Improved measurements of the β-decay response of liquid xenon with the LUX detector", + "author": "D. S. Akerib, S. Alsum, H. M. Araújo, X. Bai, J. Balajthy, A. Baxter, P. Beltrame, E. P. Bernard, A. Bernstein, T. P. Biesiadzinski, E. M. Boulton, B. Boxer, P. Brás, S. Burdin, D. Byram, M. C. Carmona-Benitez, C. Chan, J. E. Cutter, L. de Viveiros, E. Druszkiewicz, S. R. Fallon, A. Fan, S. Fiorucci, R. J. Gaitskell, J. Genovesi, C. Ghag, M. G. D. Gilchriese, C. Gwilliam, C. R. Hall, S. J. Haselschwardt, S. A. Hertel, D. P. Hogan, M. Horn, D. Q. Huang, C. M. Ignarra, R. G. Jacobsen, O. Jahangir, W. Ji, K. Kamdin, K. Kazkaz, D. Khaitan, E. V. Korolkova, S. Kravitz, V. A. Kudryavtsev, E. Leason, B. G. Lenardo, K. T. Lesko, J. Liao, J. Lin, A. Lindote, M. I. Lopes, A. Manalaysay, R. L. Mannino, N. Marangou, M. F. Marzioni, D. N. McKinsey, D.-M. Mei, M. Moongweluwan, J. A. Morad, A. St. J. Murphy, A. Naylor, C. Nehrkorn, H. N. Nelson, F. Neves, A. Nilima, K. C. Oliver-Mallory, K. J. Palladino, E. K. Pease, Q. Riffard, G. R. C. Rischbieter, C. Rhyne, P. Rossiter, S. Shaw, T. A. Shutt, C. Silva, M. Solmaz, V. N. Solovov, P. Sorensen, T. J. Sumner, M. Szydagis, D. J. Taylor, R. Taylor, W. C. Taylor, B. P. Tennyson, P. A. Terman, D. R. Tiedt, W. H. To, M. Tripathi, L. Tvrznikova, U. Utku, S. Uvarov, A. Vacheret, V. Velan, R. C. Webb, J. T. White, T. J. Whitis, M. S. Witherell, F. L. H. Wolfs, D. Woodward, J. Xu, C. Zhang, undefined undefined", + "publisher": "American Physical Society (APS)", + "url": "http://dx.doi.org/10.1103/physrevd.100.022002", + "doi": "10.1103/physrevd.100.022002", + "year": 2019, + "month": 7, + "abstract": "", + "subject": [], + "keywords": [] + }, + { + "title": "Accelerating Variational Transition State Theory via Artificial Neural Networks", + "author": "Xi Chen, C. Franklin Goldsmith", + "publisher": "American Chemical Society (ACS)", + "url": "http://dx.doi.org/10.1021/acs.jpca.9b11507", + "doi": "10.1021/acs.jpca.9b11507", + "year": 2020, + "month": 1, + "abstract": "An application of atomistic machine learning for variational transition state theory is presented. The rate constants for various radical–radical reactions are computed using variable reaction coordinate transition state theory. In order to simplify the calculation process, artificial neural networks are trained on a structured grid of potential energy data. The resulting surrogate potential energy surface is used in classical phase space representations to describe the interaction between two radical species in the gas phase. When the artificial neural network is trained to potential energy alone, the number of explicit electronic structure energy calculations required to compute a rate constant decreases by at least a factor of 4. When forces are included in the training data, the reduction is more dramatic—at least an order of magnitude.", + "subject": ["Chemical calculations", "Energy", "Kinetic parameters", "Neural networks", "Potential energy"], + "keywords": [] + }, + { + "title": "Drag reduction by nanobubble clusters as affected by surface wettability and flow velocity: Molecular dynamics simulation", + "author": "Yan Lu", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.triboint.2019.05.010", + "doi": "10.1016/j.triboint.2019.05.010", + "year": 2019, + "month": 9, + "abstract": "The molecular-dynamics simulation of a ternary (solid–liquid–gas) system was performed to investigate the nucleation of nanobubble clusters and the effect of nanobubble flow on nanochannels. Results showed that the existence of gaseous nanobubbles can replace the dense and orderly absorbed liquid layer in nonbubble flow. Nanochannels with various surface wettabilities were compared. For the hydrophilic surface, nanobubbles were attracted by the solid surface with a large contact angle, and density fluctuations near the surface decreased. Conversely, the hydrophilic surface exhibited repulsion toward nanobubbles. Simulation results indicated that surface wettability may be enhanced toward its intrinsic property with increased driving velocity. Moreover, introducing the hydrophobic property coupled with high velocity had a dramatic positive effect on drag reduction.", + "subject": [], + "keywords": [] + }, + { + "title": "Black hole interiors via spin models", + "author": "David A. Lowe, Mengyang Tong", + "publisher": "American Physical Society (APS)", + "url": "http://dx.doi.org/10.1103/physrevd.102.026008", + "doi": "10.1103/physrevd.102.026008", + "year": 2020, + "month": 7, + "abstract": "To model the interior of a black hole, a study is made of a spin system with long-range random four-spin couplings that exhibits quantum chaos. The black hole limit corresponds to a system where the microstates are approximately degenerate and equally likely, corresponding to the high temperature limit of the spin system. At the leading level of approximation, reconstruction of bulk physics implies that local probes of the black hole should exhibit free propagation and unitary local evolution. We test the conjecture that a particular mean field Hamiltonian provides such a local bulk Hamiltonian by numerically solving the exact Schrodinger equation and comparing the time evolution to the approximate mean field time values. We find excellent agreement between the two time evolutions for timescales smaller than the scrambling time. In earlier work, it was shown bulk evolution along comparable time slices is spoiled by the presence of the curvature singularity, thus the matching found in the present work provides evidence of the success of this approach to interior holography. The numerical solutions also provide a useful testing ground for various measures of quantum chaos and global scrambling. A number of different observables, such as entanglement entropy, out-of-time-order correlators, and trace distance are used to study these effects. This leads to a suitable definition of scrambling time, and evidence is presented showing a logarithmic variation with the system size.", + "subject": ["quantun aspects of black holes", "quantum gravity"], + "keywords": [] + }, + { + "title": "Variable thrust and high efficiency propulsion with oscillating foils at high Reynolds numbers", + "author": "Mukul Dave, Arianne Spaulding, Jennifer A. Franck", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.oceaneng.2020.107833", + "doi": "10.1016/j.oceaneng.2020.107833", + "year": 2020, + "month": 10, + "abstract": "Bio-inspired oscillatory foil propulsion has the ability to traverse various propulsive modes by dynamically changing the foil’s heave and pitch kinematics. This research characterizes the propulsion properties and wake dynamics of a symmetric oscillating foil, specifically targeting the high Reynolds number operation of small to medium surface vessels whose propulsive specifications have a broad range of loads and speeds. An unsteady Reynolds-averaged Navier–Stokes (URANS) solver with a k-\n SST turbulence model is used to sweep through pitch amplitude and frequency at two heave amplitudes of \n and \n at \n. At \n, the maximum thrust coefficient is \n due to the large intercepted flow area of the foil, whereas at a decreased Strouhal number the thrust coefficient decreases and the maximum propulsive efficiency reaches 75%. Results illustrate the kinematics required to transition between the high-efficiency and high-thrust regimes at high Reynolds number and the resulting changes to the vortex wake structure. The unsteady vortex dynamics throughout the heave–pitch cycle strongly influence the characterization of thrust and propulsive efficiency, and are classified into flow regimes based on performance and vortex structure.", + "subject": [], + "keywords": [] + }, + { + "title": "Ongoing intracortical neural activity predicts upcoming interictal epileptiform discharges in human epilepsy", + "author": "Dipta Saha, Timothee Proix, Sydney S. Cash, Wilson Truccolo", + "publisher": "IEEE", + "url": "http://dx.doi.org/10.1109/embc.2019.8857513", + "doi": "10.1109/embc.2019.8857513", + "year": 2019, + "month": 7, + "abstract": "Interictal epileptiform discharges (IEDs) are a hallmark of focal epilepsies. Most previous studies have focused on whether IED events increase seizure likelihood or, on the contrary, act as a protective mechanism. Here, we study instead whether IED events themselves can be predicted based on measured ongoing neural activity. We examined local field potentials (LFPs) and multi-unit activity (MUA) recorded via intracortical 10 × 10 (4 × 4 mm) arrays implanted in two patients with pharmacologically resistant seizures. Seizures in one patient (P1) were characterized by low-voltage fast-activity (LVFA), and IEDs occurred as isolated (100 - 200 ms) spike-wave events. In the other patient (P2), seizures were characterized by complex spike-wave discharges (2 - 3 Hz) and IEDs consisted of bursts of ~ 2 - 3 spike-wave discharges each lasting ~ 300 - 500 ms. We used extreme gradient boosting (XGBoost) classifiers for IED prediction. Inputs to the classifiers consisted of LFP power spectra; In addition, counts of MUA (1-ms and 100-ms time bins) and envelope, as well as leading eigenvalues/eigenvectors of MUA correlation matrices were used as features. Features were computed from moving short-time windows (1 second) immediately preceding IED events (0.3 - 0.5 preictal gap). Classifiers allowed successful IED prediction in both patients, with better results in the case of IED occurring in the LVFA case (area under ROC curve: 0.86). In comparison, LFP features performed comparatively for P1 datasets, while MUA appeared not predictive in the case of P2. Our preliminary results suggest that features of ongoing activity, predictive of upcoming IED events, can be identified based on intracortical recordings, and warrant further investigation in larger datasets. We expect this type of prediction analyses to contribute to a better understanding of the mechanisms underlying the generation of IED events and their contribution to seizure onset.", + "subject": ["Correlation","Neural activity","Microsoft Windows","Epilepsy","Spectral analysis","Microelectrodes","Feature extraction", "Neural Activity","Interictal Discharges","Interictal Epileptiform Discharges","Receiver Operating Characteristic Curve","Correlation Matrix","Activity Characteristics","Power Spectrum","Seizure Onset","Extreme Gradient Boosting","Multi-unit Activity","XGBoost Classifier","Normal Conditions","Time Scale","Predictive Performance","Frequency Band","Antiepileptic Drugs","Patient Datasets","ROC Analysis","Microelectrode Arrays","Neuromonitoring","Spike-and-wave","Pairwise Correlation Matrix", "Electroencephalography","Epilepsies"," Partial","Epilepsy","Forecasting","Humans","Longitudinal Studies","Seizures"], + "keywords": [] + }, + { + "title": "Discriminating between sleep and exercise-induced fatigue using computer vision and behavioral genetics", + "author": "Kelsey N. Schuch, Lakshmi Narasimhan Govindarajan, Yuliang Guo, Saba N. Baskoylu, Sarah Kim, Benjamin Kimia, Thomas Serre, Anne C. Hart", + "publisher": "Informa UK Limited", + "url": "http://dx.doi.org/10.1080/01677063.2020.1804565", + "doi": "10.1080/01677063.2020.1804565", + "year": 2020, + "month": 8, + "abstract": "Following prolonged swimming, Caenorhabditis elegans cycle between active swimming bouts and inactive quiescent bouts. Swimming is exercise for C. elegans and here we suggest that inactive bouts are a recovery state akin to fatigue. It is known that cGMP-dependent kinase (PKG) activity plays a conserved role in sleep, rest, and arousal. Using C. elegans EGL-4 PKG, we first validate a novel learning-based computer vision approach to automatically analyze C. elegans locomotory behavior and an edge detection program that is able to distinguish between activity and inactivity during swimming for long periods of time. We find that C. elegans EGL-4 PKG function impacts timing of exercise-induced quiescent (EIQ) bout onset, fractional quiescence, bout number, and bout duration, suggesting that previously described pathways are engaged during EIQ bouts. However, EIQ bouts are likely not sleep as animals are feeding during the majority of EIQ bouts. We find that genetic perturbation of neurons required for other C. elegans sleep states also does not alter EIQ dynamics. Additionally, we find that EIQ onset is sensitive to age and DAF-16 FOXO function. In summary, we have validated behavioral analysis software that enables a quantitative and detailed assessment of swimming behavior, including EIQ. We found novel EIQ defects in aged animals and animals with mutations in a gene involved in stress tolerance. We anticipate that further use of this software will facilitate the analysis of genes and pathways critical for fatigue and other C. elegans behaviors.", + "subject": ["fatigue", "locomotion", "swimming", "computer vision", "quiescence"], + "keywords": [] + }, + { + "title": "Molecular-continuum simulation of elevated temperature drag reduction by nanostructure-induced vapor layer", + "author": "Yan Lu", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.ijheatmasstransfer.2019.119100", + "doi": "10.1016/j.ijheatmasstransfer.2019.119100", + "year": 2020, + "month": 2, + "abstract": "Vapor lubrication resulting from liquid evaporation on a heated decorated surface and the consequent reduced friction drag are explored via computational fluid dynamics. Molecular dynamics simulation is performed to analyze the vapor layer generated by various cuboid nanostructures. Simulation results indicate that the surface with an elevated temperature provides excessive temperature that may lead to the easy formation of a thick vapor layer. For a cuboid nanostructure, the results indicate that the nanostructure arrangement enhances evaporation. Such enhancement can be affected not only by the large contact area between liquid and solid but also by the adjacent space surfaces of the nanostructure. This study is relevant because it can provide a feasible optimal design approach for nanostructures that exhibits broad prospect for high-temperature microchannel lubrication systems.", + "subject": [], + "keywords": [] + }, + { + "title": "Unveiling the Finite Temperature Physics of Hydrogen Chains via Auxiliary Field Quantum Monte Carlo", + "author": "Yuan Liu, Tong Shen, Hang Zhang, Brenda Rubenstein", + "publisher": "American Chemical Society (ACS)", + "url": "http://dx.doi.org/10.1021/acs.jctc.0c00288", + "doi": "10.1021/acs.jctc.0c00288", + "year": 2020, + "month": 5, + "abstract": "The ability to accurately predict the finite temperature properties and phase diagrams of realistic quantum solids is central to uncovering new phases and engineering materials with novel properties ripe for device applications. Nonetheless, there remain comparatively few many-body techniques capable of elucidating the finite temperature physics of solids from first principles. In this work, we take a significant step toward developing such a technique by generalizing our previous, exact fully ab initio finite temperature Auxiliary Field Quantum Monte Carlo (FT-AFQMC) method to model periodic solids and employing it to uncover the finite temperature physics of periodic hydrogen chains. Our chains’ unit cells consist of 10 hydrogen atoms modeled in a minimal basis, and we sample 5 k-points from the first Brillouin zone to arrive at a supercell consisting of 50 orbitals and 50 electrons. Based upon our calculations of these chains’ many-body energies, free energies, entropies, heat capacities, double and natural occupancies, and charge and spin correlation functions, we outline their metal–insulator and magnetic ordering as a function of both H–H bond distance and temperature. At low temperatures approaching the ground state, we observe both metal–insulator and ferromagnetic–antiferromagnetic crossovers at bond lengths between 0.5 and 0.75 Å. We then demonstrate how this low-temperature ordering evolves into a metallic phase with decreasing magnetic order at higher temperatures. In order to contextualize our results, we compare the features we observe to those previously seen in one-dimensional, half-filled Hubbard models at finite temperature and in ground state hydrogen chains. Interestingly, we identify signatures of the Pomeranchuk effect in hydrogen chains for the first time and show that spin and charge excitations that typically arise at distinct temperatures in the Hubbard model are indistinguishably coupled in these systems. Beyond qualitatively revealing the many-body phase behavior of hydrogen chains in a numerically exact manner without invoking the phaseless approximation, our efforts shed light on the further theoretical developments that will be required to construct the phase diagrams of the more complex transition metal, lanthanide, and actinide solids of longstanding interest to physicists.", + "subject": ["Energy", "Hamiltonians", "Hydrogen", "Internal energy", "Quantum mechanics"], + "keywords": [] + }, + { + "title": "Extending light WIMP searches to single scintillation photons in LUX", + "author": "D. S. Akerib, S. Alsum, H. M. Araújo, X. Bai, J. Balajthy, A. Baxter, P. Beltrame, E. P. Bernard, A. Bernstein, T. P. Biesiadzinski, E. M. Boulton, B. Boxer, P. Brás, S. Burdin, D. Byram, M. C. Carmona-Benitez, C. Chan, J. E. Cutter, L. de Viveiros, E. Druszkiewicz, S. R. Fallon, A. Fan, S. Fiorucci, R. J. Gaitskell, J. Genovesi, C. Ghag, M. G. D. Gilchriese, C. Gwilliam, C. R. Hall, S. J. Haselschwardt, S. A. Hertel, D. P. Hogan, M. Horn, D. Q. Huang, C. M. Ignarra, R. G. Jacobsen, O. Jahangir, W. Ji, K. Kamdin, K. Kazkaz, D. Khaitan, E. V. Korolkova, S. Kravitz, V. A. Kudryavtsev, E. Leason, B. G. Lenardo, K. T. Lesko, J. Liao, J. Lin, A. Lindote, M. I. Lopes, B. López Paredes, A. Manalaysay, R. L. Mannino, N. Marangou, M. F. Marzioni, D. N. McKinsey, D. M. Mei, M. Moongweluwan, J. A. Morad, A. St. J. Murphy, A. Naylor, C. Nehrkorn, H. N. Nelson, F. Neves, A. Nilima, K. C. Oliver-Mallory, K. J. Palladino, E. K. Pease, Q. Riffard, G. R. C. Rischbieter, C. Rhyne, P. Rossiter, S. Shaw, T. A. Shutt, C. Silva, M. Solmaz, V. N. Solovov, P. Sorensen, T. J. Sumner, M. Szydagis, D. J. Taylor, R. Taylor, W. C. Taylor, B. P. Tennyson, P. A. Terman, D. R. Tiedt, W. H. To, M. Tripathi, L. Tvrznikova, U. Utku, S. Uvarov, A. Vacheret, V. Velan, R. C. Webb, J. T. White, T. J. Whitis, M. S. Witherell, F. L. H. Wolfs, D. Woodward, J. Xu, C. Zhang, undefined undefined", + "publisher": "American Physical Society (APS)", + "url": "http://dx.doi.org/10.1103/physrevd.101.042001", + "doi": "10.1103/physrevd.101.042001", + "year": 2020, + "month": 2, + "abstract": "We present a novel analysis technique for liquid xenon time projection chambers that allows for a lower threshold by relying on events with a prompt scintillation signal consisting of single detected photons. The energy threshold of the LUX dark matter experiment is primarily determined by the smallest scintillation response detectable, which previously required a twofold coincidence signal in its photomultiplier arrays, enforced in data analysis. The technique presented here exploits the double photoelectron emission effect observed in some photomultiplier models at vacuum ultraviolet wavelengths. We demonstrate this analysis using an electron recoil calibration dataset and place new constraints on the spin-independent scattering cross section of weakly interacting massive particles (WIMPs) down to 2.5  GeV/\uD835\uDC502 WIMP mass using the 2013 LUX dataset. This new technique is promising to enhance light WIMP and astrophysical neutrino searches in next-generation liquid xenon experiments.", + "subject": ["dark matter", "particle dark matter", "weakly interacting massive particles", "dark matter detectors", "particles", "fields", "gravitation", "cosmotology", "astrophysics"], + "keywords": [] + }, + { + "title": "Lipid coating and end functionalization govern the formation and stability of transmembrane carbon nanotube porins", + "author": "Chun Shen, Guijin Zou, Wanlin Guo, Huajian Gao", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.carbon.2020.04.011", + "doi": "10.1016/j.carbon.2020.04.011", + "year": 2020, + "month": 8, + "abstract": "Carbon nanotube (CNT) based transmembrane porins have attracted a lot of recent interest due to their excellent transport properties for water, ions and biomolecules. In experiments, CNTs with a length of about 10 nm can penetrate and form stable transmembrane channels across lipid membranes, while in sharp contrast, similar 10 nm long pristine CNTs were found parallelly clamped inside the hydrophobic core of a lipid bilayer in simulations. This apparent paradox has motivated the present study, where we performed all-atom molecular dynamics simulations to show that lipid molecules initially coated on the CNTs play an essential role in the formation and stabilization of the CNT porins. We demonstrate that, as a lipid coated CNT is inserted into the membrane, lipid molecules arrange themselves into a bicelle on the CNT outside the membrane, providing mechanical support to stabilize the transmembrane configuration of the CNT porin. Further analysis shows that the lipid coating density and end-functionalization strongly influence the CNT insertion into a lipid membrane. These findings shed light on the mechanism of formation and stabilization of CNT porins and provide a theoretical basis to design related transmembrane transport systems.", + "subject": [], + "keywords": [] + }, + { + "title": "Self-Cleaning of Hydrophobic Rough Surfaces by Coalescence-Induced Wetting Transition", + "author": "Kaixuan Zhang, Zhen Li, Martin Maxey, Shuo Chen, George Em Karniadakis", + "publisher": "American Chemical Society (ACS)", + "url": "http://dx.doi.org/10.1021/acs.langmuir.8b03664", + "doi": "10.1021/acs.langmuir.8b03664", + "year": 2019, + "month": 1, + "abstract": "The superhydrophobic leaves of a lotus plant and other natural surfaces with self-cleaning function have been studied intensively for the development of artificial biomimetic surfaces. The surface roughness generated by hierarchical structures is a crucial property required for superhydrophobicity and self-cleaning. Here, we demonstrate a novel self-cleaning mechanism of textured surfaces attributed to a spontaneous coalescence-induced wetting transition. We focus on the wetting transition as it represents a new mechanism, which can explain why droplets on rough surfaces are able to change from the highly adhesive Wenzel state to the low adhesion Cassie–Baxter state and achieve self-cleaning. In particular, we perform many-body dissipative particle dynamics simulations of liquid droplets (with a diameter of 89 μm) sitting on mechanically textured substrates. We quantitatively investigate the wetting behavior of an isolated droplet as well as coalescence of droplets for both Cassie–Baxter and Wenzel states. Our simulation results reveal that droplets in the Cassie–Baxter state have much lower contact angle hysteresis and smaller hydrodynamic resistance than droplets in the Wenzel state. When small neighboring droplets coalesce into bigger ones on textured hydrophobic substrates, we observe a spontaneous wetting transition from the Wenzel state to the Cassie–Baxter state, which is powered by the surface energy released upon coalescence of the droplets. For superhydrophobic surfaces, the released surface energy may be sufficient to cause a jumping motion of droplets off the surface, in which case adding one more droplet to the coalescence may increase the jumping velocity by one order of magnitude. When multiple droplets are involved, we found that the spatial distribution of liquid components in the coalesced droplet can be controlled by properly designing the overall arrangement of droplets and the distance between them. These findings offer new insights for designing effective biomimetic self-cleaning surfaces by enhancing spontaneous Wenzel-to-Cassie wetting transitions, and additionally, for developing new noncontact methods to manipulate liquids inside the small droplets via multiple-droplet coalescence.", + "subject": ["Contact angle", "Hydrophobicity", "Liquids", "Surface energy","Wetting"], + "keywords": [] + }, + { + "title": "Age of Both Parents Influences Reproduction and Egg Dumping Behavior in Drosophila melanogaster", + "author": "Jim A Mossman, Russyan Mark S Mabeza, Emma Blake, Neha Mehta, David M Rand", + "publisher": "Oxford University Press (OUP)", + "url": "http://dx.doi.org/10.1093/jhered/esz009", + "doi": "10.1093/jhered/esz009", + "year": 2019, + "month": 2, + "abstract": "Trans-generational maternal effects have been shown to influence a broad range of offspring phenotypes. However, very little is known about paternal trans-generational effects. Here, we tested the trans-generational effects of maternal and paternal age, and their interaction, on daughter and son reproductive fitness in Drosophila melanogaster. We found significant effects of parent ages on offspring reproductive fitness during a 10 day postfertilization period. In daughters, older (45 days old) mothers conferred lower reproductive fitness compared with younger mothers (3 days old). In sons, father’s age significantly affected reproductive fitness. The effects of 2 old parents were additive in both sexes and reproductive fitness was lowest when the focal individual had 2 old parents. Interestingly, daughter fertility was sensitive to father’s age but son fertility was insensitive to mother’s age, suggesting a sexual asymmetry in trans-generational effects. We found the egg-laying dynamics in daughters dramatically shaped this relationship. Daughters with 2 old parents demonstrated an extreme egg dumping behavior on day 1 and laid >2.35× the number of eggs than the other 3 age class treatments. Our study reveals significant trans-generational maternal and paternal age effects on fertility and an association with a novel egg laying behavioral phenotype in Drosophila.", + "subject": ["age", "carry-over effects", "fertility", "parental", "paternal", "trans-generational"], + "keywords": [] + }, + { + "title": "Anisotropy of Langmuir turbulence and the Langmuir-enhanced mixed layer entrainment", + "author": "Qing Li, Baylor Fox-Kemper", + "publisher": "American Physical Society (APS)", + "url": "http://dx.doi.org/10.1103/physrevfluids.5.013803", + "doi": "10.1103/physrevfluids.5.013803", + "year": 2020, + "month": 1, + "abstract": "The anisotropy and structure of turbulence simulated by large-eddy simulations with and without Stokes-drift forcing are analyzed, with an emphasis on the linkage between the distinctive structure of Langmuir turbulence near the surface where cellular vortices aligned with the wind and wave propagation direction are apparent and the Langmuir-enhanced mixed layer entrainment at the base of the ocean surface boundary layer (OSBL) where turbulent structures differ. The tensor invariants of the Reynolds stresses, the variance of vertical velocity and buoyancy, and the velocity gradient statistics are used to categorize turbulence structures as a function of depth, including an extension of the barycentric map to show the direction as well as the magnitude of turbulence anisotropy and a vector-invariant extension of the Okubo-Weiss parameter. The extended anisotropic barycentric map and the velocity gradient statistics are demonstrated to be useful, providing compact information of the anisotropy, orientation, and structure of turbulent flows. It is found that the distinctive anisotropy and structures of Langmuir turbulence are quickly lost below regions where Stokes drift shear is significant and vortices are apparent, consistent with past observations and model results. As a result, the turbulent structures near the base of the OSBL are not significantly affected by the presence of Stokes drift above but are instead dominated by local Eulerian shear, except in one important manner. Langmuir turbulence does affect the mixed layer entrainment by providing extra available turbulent kinetic energy (TKE) via enhanced near-surface TKE production and higher vertical TKE transport energizing the turbulent structures near the base of the OSBL. The additional TKE is utilized by structures similar to those that exist without Stokes drift forcing in terms of anisotropy of their Reynolds stresses, but they are more energetic because of the Langmuir turbulence. Thus, parametrizing the major aspects of Langmuir turbulence on entrainment at the base of the OSBL can be incorporated through enhancing available energy without other modifications.", + "subject": ["mixing in geophysical flows", "oceanography", "turbulence", "fluid dynamics"], + "keywords": [] + }, + { + "title": "A machine learning approach to fracture mechanics problems", + "author": "Xing Liu, Christos E. Athanasiou, Nitin P. Padture, Brian W. Sheldon, Huajian Gao", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.actamat.2020.03.016", + "doi": "10.1016/j.actamat.2020.03.016", + "year": 2020, + "month": 5, + "abstract": "Analytical and empirical solutions to engineering problems are usually preferred because of their convenience in applications. However, they are not always accessible in complex problems. A new class of solutions, based on machine learning (ML) models such as regression trees and neural networks (NNs), are proposed and their feasibility and value are demonstrated through the analysis of fracture toughness measurements. It is found that both solutions based on regression trees and NNs can provide accurate results for the specific problem, but NN-based solutions outperform regression-tree-based solutions in terms of their simplicity. This example demonstrates that ML solutions are a major improvement over analytical and empirical solutions in terms of both reliable functionality and rapid deployment. When analytical solutions are not available, the use of ML solutions can overcome the limitations of empirical solutions and substantially change the way that engineering problems are solved.", + "subject": ["machine learning", "analytical methods", "mechanical properties testing", "fracture"], + "keywords": [] + }, + { + "title": "Assessing Phase Diagram Accuracy", + "author": "Axel van de Walle, Qijun Hong", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1007/s11669-019-00711-5", + "doi": "10.1007/s11669-019-00711-5", + "year": 2019, + "month": 1, + "abstract": "Assessing the predictive power of any computational model requires the definition of an appropriate metric or figure-of-merit (e.g. mean square error, maximum error, etc). However, quantifying errors in an alloy phase diagram with a single figure-of-merit is a considerably more complex problem. The 'distance' between phase boundaries is not a uniquely defined concept and different phase diagrams may differ in the possible stable phases which they predict, making it unclear which 'distance' to measure. Given the difficulty associated with such metrics, we instead propose to use differences in predicted phase fractions between different phase diagrams as the basis of a suitable metric. We prove that our criterion satisfies all the properties of the mathematical notion of a norm or of a metric, in addition to other properties directly relevant to phase stability problems. We illustrate the use of such criterion to the study of the convergence of assessments performed on the same alloy system by different authors over time.", + "subject": [], + "keywords": [] + }, + { + "title": "Maximizing Thermoelectric Figures of Merit by Uniaxially Straining Indium Selenide", + "author": "Leonard W. Sprague, Cancan Huang, Jeong-Pil Song, Brenda M. Rubenstein", + "publisher": "American Chemical Society (ACS)", + "url": "http://dx.doi.org/10.1021/acs.jpcc.9b05681", + "doi": "10.1021/acs.jpcc.9b05681", + "year": 2019, + "month": 10, + "abstract": "A majority of the electricity currently generated is regrettably lost as heat. Engineering high-efficiency thermoelectric materials which can convert waste heat back into electricity is therefore vital for reducing our energy fingerprint. ZT, a dimensionless figure of merit, acts as a beacon of promising thermoelectric materials. However, engineering materials with large ZT values is practically challenging, since maximizing ZT requires optimizing many interdependent material properties. Motivated by recent studies on bulk indium selenide that suggest it may have favorable thermoelectric properties, here we present the thermoelectric properties of monolayer indium selenide in the presence of uniaxial strain using first-principles calculations conjoined with semiclassical Boltzmann transport theory. Our calculations indicate that conduction band convergence occurs at a compressive strain of −6% along the zigzag direction and results in an enhancement of ZT for p-type indium selenide at room temperature. Further enhancements occur at −7% as the valence bands similarly converge, reaching a maximum ZT value of 0.46, which is one of the largest monolayer InSe figures of merit recorded to date at room temperature. The importance of strain is directly reflected by the enhanced transport coefficients observed at strains nearing those which give rise to the band degeneracies we observe. Our studies demonstrate that strain-induced transitions can play a key role in the engineering of promising thermoelectric materials.", + "subject": [], + "keywords": [] + }, + { + "title": "Feature Design for Protein Interface Hotspots Using KFC2 and Rosetta", + "author": "Franziska Seeger, Anna Little, Yang Chen, Tina Woolf, Haiyan Cheng, Julie C. Mitchell", + "publisher": "Springer International Publishing", + "url": "http://dx.doi.org/10.1007/978-3-030-11566-1_8", + "doi": "10.1007/978-3-030-11566-1_8", + "year": 2019, + "month": 3, + "abstract": "Protein–protein interactions regulate many essential biological processes and play an important role in health and disease. The process of experimentally characterizing protein residues that contribute the most to protein–protein interaction affinity and specificity is laborious. Thus, developing models that accurately characterize hotspots at protein–protein interfaces provides important information about how to inhibit therapeutically relevant protein–protein interactions. During the course of the ICERM WiSDM workshop 2017, we combined the KFC2a protein–protein interaction hotspot prediction features with Rosetta scoring function terms and interface filter metrics. A two-way and three-way forward selection strategy was employed to train support vector machine classifiers, as was a reverse feature elimination strategy. From these results, we identified subsets of KFC2a and Rosetta combined features that show improved performance over KFC2a features alone.", + "subject": [], + "keywords": [] + }, + { + "title": "An Explicit Divergence-Free DG Method for Incompressible Magnetohydrodynamics", + "author": "Guosheng Fu", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1007/s10915-019-00909-2", + "doi": "10.1007/s10915-019-00909-2", + "year": 2019, + "month": 1, + "abstract": "We extend the recently introduced explicit divergence-free DG scheme for incompressible hydrodynamics (Fu in Comput Methods Appl Mech Eng 345:502–517, 2019) to the incompressible magnetohydrodynamics. A globally divergence-free finite element space is used for both the velocity and the magnetic field. Highlights of the scheme include global and local conservation properties, high-order accuracy, energy-stability, and pressure-robustness. When forward Euler time stepping is used, we need two symmetric positive definite hybrid-mixed Poisson solvers (one for velocity and one for magnetic field) to advance the solution to the next time level. Since we treat both viscosity in the momentum equation and resistivity in the magnetic induction equation explicitly, the method shall be best suited for inviscid or high-Reynolds number, low resistivity flows so that the CFL constraint is not too restrictive.", + "subject": [], + "keywords": [] + }, + { + "title": "Auxiliary field quantum Monte Carlo for multiband Hubbard models: Controlling the sign and phase problems to capture Hund's physics", + "author": "Hongxia Hao, Brenda M. Rubenstein, Hao Shi", + "publisher": "American Physical Society (APS)", + "url": "http://dx.doi.org/10.1103/physrevb.99.235142", + "doi": "10.1103/physrevb.99.235142", + "year": 2019, + "month": 6, + "abstract": "In the study of strongly correlated, many-electron systems, the Hubbard-Kanamori (HK) model has emerged as one of the prototypes for transition metal oxide physics. The model is multiband in nature and contains Hund's coupling terms, which have pronounced effects on metal-insulator transitions, high-temperature superconductivity, and other physical properties. In the following, we present a complete theoretical framework for treating the HK model using the ground-state auxiliary field quantum Monte Carlo (AFQMC) method and analyze its performance on few-band models whose parameters approximate those observed in ruthenates, rhodates, and other materials exhibiting Hund's physics. Unlike previous studies, the constrained path and phaseless approximations are used to respectively control the sign and phase problems, which enables high-accuracy modeling of the HK model's ground-state properties within parameter regimes of experimental interest. We demonstrate that, after careful consideration of the Hubbard-Stratonovich transformations and trial wave functions employed, relative errors in the energy of less than 1% can routinely be achieved for moderate to large values of the Hund's coupling constant. Crucially, our methodology also accurately predicts magnetic ordering and phase transitions. The results presented open the door to more predictive modeling of Hund's physics within a wide range of strongly correlated materials using AFQMC.", + "subject": [], + "keywords": [] + }, + { + "title": "Swimming with small and large amplitude waves in a confined liquid crystal", + "author": "Madison S. Krieger, Saverio E. Spagnolie, Thomas R. Powers", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.jnnfm.2019.104185", + "doi": "10.1016/j.jnnfm.2019.104185", + "year": 2019, + "month": 11, + "abstract": "Boundaries can have a significant impact on the physics of microorganism locomotion. Here we examine the effects of confinement by a rigid boundary or symmetric channel on undulatory locomotion in an anisotropic fluid, treated as a nematic liquid crystal. The competition between hydrodynamics, fluid elasticity, and anchoring conditions results in a complex locomotion problem with unique transport properties. We examine this problem analytically using a well-known mathematical model, an infinite swimming sheet with small wave amplitude, and numerically for large amplitude waves using a modification of the immersed boundary method. For a prescribed stroke and strong planar anchoring in the narrow channel, we demonstrate that the swimming speed approaches its Newtonian value, though the power required to maintain the swimmer’s speed depends on the properties of the liquid crystal. We also show that an unusual prograde swimming (in the direction of transverse wave propagation) theorized to exist at small wave amplitude persists at large amplitude, and that the presence of a sufficiently close boundary returns the swimming behavior to the more standard retrograde motion (opposite the direction of the traveling wave).", + "subject": [], + "keywords": [] + }, + { + "title": "Independent nonlinear component analysis", + "author": "Susanne M. Schennach, Florian Gunsilius", + "publisher": "The IFS", + "url": "http://dx.doi.org/10.1920/wp.cem.2019.4619", + "doi": "10.1920/wp.cem.2019.4619", + "year": 2019, + "month": 9, + "abstract": "The idea of summarizing the information contained in a large number of variables by a small number of “factors” or “principal components” has been broadly adopted in economics and statistics. This paper introduces a generalization of the widely used principal component analysis (PCA) to nonlinear settings, thus providing a new tool for dimension reduction and exploratory data analysis or representation. The distinguishing features of the method include (i) the ability to always deliver truly independent factors (as opposed to the merely uncorre-lated factors of PCA); (ii) the reliance on the theory of optimal transport and Brenier maps to obtain a robust and efficient computational algorithm; (iii) the use of a new multivariate additive entropy decomposition to determine the principal nonlinear components that capture most of the information content of the data and (iv) formally nesting PCA as a special case, for linear Gaussian factor models. We illustrate the method’s effectiveness in an application to the prediction of excess bond returns from a large number of macro factors.", + "subject": [], + "keywords": [] + }, + { + "title": "First principles calculations of the electric field gradient tensors of Ba2NaOsO6, a Mott insulator with strong spin orbit coupling", + "author": "Rong Cong, Ravindra Nanguneri, Brenda Rubenstein, V F Mitrović", + "publisher": "IOP Publishing", + "url": "http://dx.doi.org/10.1088/1361-648x/ab9056", + "doi": "10.1088/1361-648x/ab9056", + "year": 2020, + "month": 7, + "abstract": "We present first principles calculations of the electrostatic properties of Ba2NaOsO6 (BNOO), a 5d1 Mott insulator with strong spin orbit coupling (SOC) in its low temperature quantum phases. In light of recent NMR experiments showing that BNOO develops a local octahedral distortion that is accompanied by the emergence of an electric field gradient (EFG) and precedes the formation of long range magnetic order (Lu et al 2017 Nat. Commun. 8 14407, Liu et al 2018 Phys. Rev. B 97 224103; Liu et al 2018 Physica B 536 863), we calculated BNOO's EFG tensor for several different model distortions. The local orthorhombic distortion that we identified as most strongly agreeing with experiment corresponds to a Q2 distortion mode of the Na–O octahedra, in agreement with conclusions given in (Liu et al 2018 Phys. Rev. B 97 224103). Furthermore, we found that the EFG is insensitive to the type of underlying magnetic order. By combining NMR results with first principles modeling, we have thus forged a more complete understanding of BNOO's structural and magnetic properties, which could not be achieved based upon experiment or theory alone.", + "subject": [], + "keywords": [] + }, + { + "title": "Stability of stochastic finite-size spiking-neuron networks: Comparing mean-field, 1-loop correction and quasi-renewal approximations", + "author": "Dmitrii Todorov, Wilson Truccolo", + "publisher": "IEEE", + "url": "http://dx.doi.org/10.1109/embc.2019.8857101", + "doi": "10.1109/embc.2019.8857101", + "year": 2019, + "month": 7, + "abstract": "We examine the stability and qualitative dynamics of stochastic neuronal networks specified as multivariate non-linear Hawkes processes and related point-process generalized linear models that incorporate both auto- and cross-history effects. In particular, we adapt previous theoretical approximations based on mean field and mean field plus 1-loop correction to incorporate absolute refractory periods and other auto-history effects. Furthermore, we extend previous quasi-renewal approximations to the multivariate case, i.e. neuronal networks. The best sensitivity and specificity performance, in terms of predicting stability and divergence to nonphysiologically high firing rates in the examined simulations, was obtained by a variant of the quasi-renewal approximation.", + "subject": ["Neurons","Brain modeling","Predictive models","History","Stability analysis","Adaptation models","Data models", "Mean-field","Stable Network","Finite-size Networks","1-loop Corrections","Divergence","Neural Circuits","Firing Rate","Point Process","Theoretical Estimates","Refractory Period","Simulation Model","Neuronal Activity","Theoretical Approaches","Neuronal Populations","Fixed Point","Multivalent","Linear Response","Functional Dynamics","Neuron Model","Process Theory","Temporal Filtering","Spike Trains","Mean Firing Rate","Input-output Function","Stable Matrix","Finite Value", "Action Potentials","Computer Simulation","Linear Models","Neurons","Stochastic Processes"], + "keywords": [] + }, + { + "title": "Estimation of non-null SNP effect size distributions enables the detection of enriched genes underlying complex traits", + "author": "Wei Cheng, Sohini Ramachandran, Lorin Crawford", + "publisher": "Public Library of Science (PLoS)", + "url": "http://dx.doi.org/10.1371/journal.pgen.1008855", + "doi": "10.1371/journal.pgen.1008855", + "year": 2020, + "month": 6, + "abstract": "Traditional univariate genome-wide association studies generate false positives and negatives due to difficulties distinguishing associated variants from variants with spurious nonzero effects that do not directly influence the trait. Recent efforts have been directed at identifying genes or signaling pathways enriched for mutations in quantitative traits or case-control studies, but these can be computationally costly and hampered by strict model assumptions. Here, we present gene-ε, a new approach for identifying statistical associations between sets of variants and quantitative traits. Our key insight is that enrichment studies on the gene-level are improved when we reformulate the genome-wide SNP-level null hypothesis to identify spurious small-to-intermediate SNP effects and classify them as non-causal. gene-ε efficiently identifies enriched genes under a variety of simulated genetic architectures, achieving greater than a 90% true positive rate at 1% false positive rate for polygenic traits. Lastly, we apply gene-ε to summary statistics derived from six quantitative traits using European-ancestry individuals in the UK Biobank, and identify enriched genes that are in biologically relevant pathways.", + "subject": ["genome-wide association studies", "single nucleotide polymorphisms", "heredity", "magma", "quantitative traits", "simulation and modeling", "genome analysis", "genomics statistics"], + "keywords": [] + }, + { + "title": "Data-driven selection and parameter estimation for DNA methylation mathematical models", + "author": "Karen Larson, Loukas Zagkos, Mark Mc Auley, Jason Roberts, Nikos I. Kavallaris, Anastasios Matzavinos", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.jtbi.2019.01.012", + "doi": "10.1016/j.jtbi.2019.01.012", + "year": 2019, + "month": 4, + "abstract": "Epigenetics is coming to the fore as a key process which underpins health. In particular emerging experimental evidence has associated alterations to DNA methylation status with healthspan and aging. Mammalian DNA methylation status is maintained by an intricate array of biochemical and molecular processes. It can be argued changes to these fundamental cellular processes ultimately drive the formation of aberrant DNA methylation patterns, which are a hallmark of diseases, such as cancer, Alzheimer’s disease and cardiovascular disease. In recent years mathematical models have been used as effective tools to help advance our understanding of the dynamics which underpin DNA methylation. In this paper we present linear and nonlinear models which encapsulate the dynamics of the molecular mechanisms which define DNA methylation. Applying a recently developed Bayesian algorithm for parameter estimation and model selection, we are able to estimate distributions of parameters which include nominal parameter values. Using limited noisy observations, the method also identified which methylation model the observations originated from, signaling that our method has practical applications in identifying what models best match the biological data for DNA methylation.", + "subject": ["DNA methylation", "Model selection", "Parameter estimation", "Gene promoter", "CpG dyads"], + "keywords": [] + }, + { + "title": "Alignment by Composition", + "author": "Berk Sevilmis, Benjamin Kimia", + "publisher": "IEEE", + "url": "http://dx.doi.org/10.1109/wacv.2019.00218", + "doi": "10.1109/wacv.2019.00218", + "year": 2019, + "month": 1, + "abstract": "We propose an unsupervised method to establish dense semantic correspondences between images depicting different instances of the same object category. We posit that alignment is compositional in nature and requires the detection of a similar visual concept between images. We realize this in a top-down fashion using objectness, saliency, and visual similarity cues to co-localize the regions of holistic foreground objects. Jointly maximizing visual similarity and bounding the geometric distortion induced by their configuration, the target foreground object is then composed by the subregions of the source foreground object. The resultant composition is used to form a dense motion field enabling the alignment. Experimental results on several benchmark datasets support the efficacy of the proposed method.", + "subject": ["Proposals","Feature extraction","Semantics","Visualization","Distortion","Search problems","Solid modeling", "Benchmark Datasets","Density Field","Geometric Distortion","Visual Similarity","Foreground Objects","Visual Concepts","Convolutional Neural Network","Fluidic","Bounding Box","Image Pairs","Affine Transformation","Object Parts","Matching Score","Saliency Map","Thin-plate Spline","Delaunay Triangulation","Object Instances","Low Distortion","Background Clutter","Object Bounding Boxes","Dense Correspondence","Beam Search","Candidate Matches","Foreground Regions","Factor Graph","Piecewise Affine","Matching Accuracy","Coordinating Center","Successful Alignment","Search Algorithm"], + "keywords": [] + }, + { + "title": "Transcriptomic Response to Feeding and Starvation in a Herbivorous Dinoflagellate", + "author": "Ewelina T. Rubin, Shu Cheng, Amanda L. Montalbano, Susanne Menden-Deuer, Tatiana A. Rynearson", + "publisher": "Frontiers Media SA", + "url": "http://dx.doi.org/10.3389/fmars.2019.00246", + "doi": "10.3389/fmars.2019.00246", + "year": 2019, + "month": 5, + "abstract": "Grazing by heterotrophic protists influences plankton population dynamics, community composition, and the flux of carbon through marine planktonic food webs. To gain insight into the molecular underpinnings of grazing in dinoflagellates, a group of important heterotrophic protists, we used a RNA-Seq approach to investigate the transcriptomic response of Oxyrrhis marina under fed and starved conditions with three different phytoplankton prey (Isochrysis galbana and two strains of Heterosigma akashiwo). In response to fed and starved conditions, 1,576 transcripts were significantly differentially expressed in O. marina. Fed O. marina cells upregulated transcripts involved in the synthesis of essential fatty acids and storage carbohydrates suggesting that the predator was food satiated and excess glucose was being stored as an energy reserve. Transcripts encoding voltage-gated ion channels were also upregulated during grazing, and they are known to be involved in the detection of mechanical stimuli and the regulation of swimming behavior in several eukaryotic protists. Fed O. marina cells upregulated kinases, which can dictate cell shape changes and may be associated with phagocytosis. During starvation, upregulated O. marina transcripts included those involved in the degradation of energy-storage molecules like glucan 1,4-alpha-glycosidase and those involved in antioxidant activities and autophagy, like acid ceramidase that are associated with the digestion of polar lipids present in cell membranes. Starved O. marina also upregulated transcripts with high similarity to proton pumping proteorhodopsins suggesting that this heterotrophic protist may supplement its energy requirement during starvation with a light harvesting mechanism. Although herbivorous grazing is a pivotal transformation in the C cycle, logistical constraints limit our investigations of environmental and biological drivers. The molecular signals identified here provide new insights into the metabolic regulation of feeding and starvation in marine heterotrophic protists and can fuel hypothesis-driven research into predators’ metabolic response to prey availability.", + "subject": [], + "keywords": [] + }, + { + "title": "Software tools for thermodynamic calculation of mechanically unstable phases from first-principles data", + "author": "Sara Kadkhodaei, Axel van de Walle", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.cpc.2019.01.008", + "doi": "10.1016/j.cpc.2019.01.008", + "year": 2020, + "month": 1, + "abstract": "This paper introduces the P4 software package, a set of software tools that automate the process of vibrational free energy calculation for mechanically unstable phases. The Piecewise Polynomial Potential Partitioning (P4) method is a recently developed method that tackles the issue of phonon instabilities in solid solutions and compounds. The method efficiently explores the system’s ab-initio energy surface by discrete sampling of local minima, which is combined with a continuous sampling of the vicinity of these local minima via a constrained harmonic lattice dynamic approach. The free energy values obtained by this toolkit can be used in thermodynamic assessments and phase diagram calculations. As a unique advantage, it provides the tool to calculate the vibrational free energy in a wide composition range in alloys. This feature is not practically achievable by relying only on brute-force molecular dynamics or random sampling techniques.", + "subject": [], + "keywords": [] + }, + { + "title": "NephromycesEncodes a Urate Metabolism Pathway and Predicted Peroxisomes, Demonstrating That These Are Not Ancient Losses of Apicomplexans", + "author": "Christopher Paight, Claudio H Slamovits, Mary Beth Saffo, Christopher E Lane", + "publisher": "Oxford University Press (OUP)", + "url": "http://dx.doi.org/10.1093/gbe/evy251", + "doi": "10.1093/gbe/evy251", + "year": 2018, + "month": 11, + "abstract": "The phylum Apicomplexa is a quintessentially parasitic lineage, whose members infect a broad range of animals. One exception to this may be the apicomplexan genus Nephromyces, which has been described as having a mutualistic relationship with its host. Here we analyze transcriptome data from Nephromyces and its parasitic sister taxon, Cardiosporidium, revealing an ancestral purine degradation pathway thought to have been lost early in apicomplexan evolution. The predicted localization of many of the purine degradation enzymes to peroxisomes, and the in silico identification of a full set of peroxisome proteins, indicates that loss of both features in other apicomplexans occurred multiple times. The degradation of purines is thought to play a key role in the unusual relationship between Nephromyces and its host. Transcriptome data confirm previous biochemical results of a functional pathway for the utilization of uric acid as a primary nitrogen source for this unusual apicomplexan.", + "subject": ["apicomplexan", "tunicates", "peroxisomes", "purine degradation", "Nephromyces", "Cardiosporidium"], + "keywords": [] + }, + { + "title": "One-dimensional modeling of fractional flow reserve in coronary artery disease: Uncertainty quantification and Bayesian optimization", + "author": "Minglang Yin, Alireza Yazdani, George Em Karniadakis", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.cma.2019.05.005", + "doi": "10.1016/j.cma.2019.05.005", + "year": 2019, + "month": 8, + "abstract": "Non-invasive estimation of fractional flow reserve (FFR) values, the key index in the diagnosis of obstructive coronary artery disease, is a promising alternative to traditional way of performing invasive coronary angiography. With the advances in computational fluid dynamics (CFD), one can estimate FFR based on the solution obtained in a reconstructed coronary geometry from coronary computed tomography (CT) angiography. However, the computational cost to perform three-dimensional (3D) simulations has limited the use of CFD in most clinical settings. This could become more restrictive if one aims to quantify the uncertainty associated with FFR calculations due to the uncertainty in anatomic and physiologic properties as a significant number of 3D simulations is required to sample a relatively large parametric space. We have developed a predictive probabilistic model of FFR, which quantifies the uncertainty of the predicted values with significantly lower computational costs. Based on global sensitivity analysis, we first identify the important physiologic and anatomic parameters that impact the predictions of FFR. Our approach is to employ one-dimensional blood flow simulations of coronary trees that offer fast FFR predictions with uncertainty quantification in computing blood pressure and flow distributions within the coronaries. This is complemented with a multifidelity algorithm that is used to infer their optimal values using available patient-specific clinical measurements.", + "subject": [], + "keywords": [] + }, + { + "title": "Experimental characterization and hyperelastic constitutive modeling of open-cell elastomeric foams", + "author": "Alexander K. Landauer, Xiuqi Li, Christian Franck, David L. Henann", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.jmps.2019.103701", + "doi": "10.1016/j.jmps.2019.103701", + "year": 2019, + "month": 12, + "abstract": "Open-cell elastomeric foams – materials consisting of an elastomeric matrix and a connected pore space – exhibit mechanical behavior marked by high compressibility and strong coupling between the volumetric and distortional responses. In this paper, we present a methodology for the experimental characterization and constitutive modeling of non-localizing, isotropic, open-cell elastomeric foam materials under quasi-static, equilibrium loading. We conduct large-deformation, homogeneous simple compression/tension experiments on three relative densities of a polyurethane-based elastomeric foam to inform a phenomenological, isotropic, hyperelastic constitutive model. The model is based on the invariants of the logarithmic strain and accounts for high compressibility and strong volumetric-distortional coupling. To validate the predictive capability of the model, we consider three types of validation experiments that involve inhomogeneous deformation: spherical and conical indentation, simple-shear-like deformation both without and with a fixed amount of pre-compression, and tension of a specimen with circular holes. We compare load-displacement responses as well as full displacement fields from the validation experiments against corresponding model predictions obtained using finite-element-based numerical simulations and demonstrate that the model is capable of accurately capturing the experimental response.", + "subject": ["B foam material", "B constitutive behaviour", "B elastic material", "B finite strain", "C mechanical testing"], + "keywords": [] + }, + { + "title": "High density colloidal particle flux using modulated nondegenerate counter-propagating optical beams", + "author": "Velat Kilic, Nabil M. Lawandy", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.optcom.2018.10.016", + "doi": "10.1016/j.optcom.2018.10.016", + "year": 2019, + "month": 2, + "abstract": "We analyze, through numerical simulations, a method for generating unidirectional flux in colloidal systems using non-degenerate two-wave mixing. The approach uses a bidirectional PZT modulation and a laser grating amplitude modulation to suppress the reversal of the grating velocity with each cycle of the PZT. The dependence of the particle flux on modulation frequency is determined through numerical solution of the differential equations and the suppression of sedimentation in an extended colloidal system is analyzed.", + "subject": ["laser trapping", "two-wave mixing", "nonlinear wave mixing", "nanoparticles", "sedimentation"], + "keywords": [] + }, + { + "title": "Transsacadic Information and Corollary Discharge in Local Field Potentials of Macaque V1", + "author": "Michael A. Paradiso, Seth Akers-Campbell, Octavio Ruiz, James E. Niemeyer, Stuart Geman, Jackson Loper", + "publisher": "Frontiers Media SA", + "url": "http://dx.doi.org/10.3389/fnint.2018.00063", + "doi": "10.3389/fnint.2018.00063", + "year": 2019, + "month": 1, + "abstract": "Approximately three times per second, human visual perception is interrupted by a saccadic eye movement. In addition to taking the eyes to a new location, several lines of evidence suggest that the saccades play multiple roles in visual perception. Indeed, it may be crucial that visual processing is informed about movements of the eyes in order to analyze visual input distinctly and efficiently on each fixation and preserve stable visual perception of the world across saccades. A variety of studies has demonstrated that activity in multiple brain areas is modulated by saccades. The hypothesis tested here is that these signals carry significant information that could be used in visual processing. To test this hypothesis, local field potentials (LFPs) were simultaneously recorded from multiple electrodes in macaque primary visual cortex (V1); support vector machines (SVMs) were used to classify the peri-saccadic LFPs. We find that LFPs in area V1 carry information that can be used to distinguish neural activity associated with fixations from saccades, precisely estimate the onset time of fixations, and reliably infer the directions of saccades. This information may be used by the brain in processes including visual stability, saccadic suppression, receptive field (RF) remapping, fixation amplification, and trans-saccadic visual perception.", + "subject": [], + "keywords": [] + }, + { + "title": "Digital Scholarship Planning: A Perspective on the CNI-ARL Workshop", + "author": "Anna R. Craft", + "publisher": "Informa UK Limited", + "url": "http://dx.doi.org/10.1080/00987913.2018.1433930", + "doi": "10.1080/00987913.2018.1433930", + "year": 2018, + "month": 1, + "abstract": "The CNI-ARL Digital Scholarship Planning Workshop at Brown University, November 8–10, 2017, was an intensive, focused workshop for institutions at all stages of the digital scholarship planning process. This report, based on one participant's experience, touches on some of the highlights and takeaways from the sessions, which focused on campus needs and partnerships; staffing; governance and funding models; the applications of library and other content collections in teaching, learning, and research; student roles in digital scholarship; space and place; and the institutionalization of digital scholarship. A fundamental concept of the workshop was the acknowledgement of the wide variety of models and services digital scholarship can encompass and the critical need for each institution to pursue digital scholarship services that are in line with its strengths and the needs of its particular constituencies.", + "subject": ["academic libraries", "digital humanities", "digital projects", "digital scholarhip", "library spaces", "research support"], + "keywords": [] + }, + { + "title": "Synthesis of All-Inorganic Cd-Doped CsPbCl3 Perovskite Nanocrystals with Dual-Wavelength Emission", + "author": "Tong Cai, Hanjun Yang, Katie Hills-Kimball, Jeong-Pil Song, Hua Zhu, Elan Hofman, Weiwei Zheng, Brenda M. Rubenstein, Ou Chen", + "publisher": "American Chemical Society (ACS)", + "url": "http://dx.doi.org/10.1021/acs.jpclett.8b03412", + "doi": "10.1021/acs.jpclett.8b03412", + "year": 2018, + "month": 12, + "abstract": "Doped lead halide perovskite nanocrystals (NCs) have garnered significant attention due to their superior optoelectronic properties. Here, we report a synthesis of Cd-doped CsPbCl3 NCs by decoupling Pb- and Cl-precursors in a hot injection method. The resulting Cd-doped perovskite NCs manifest a dual-wavelength emission profile with the first reported example of Cd-dopant emission. By controlling Cd-dopant concentration, the emission profile can be tuned with a dopant emission quantum yield of up to 8%. A new secondary emission (∼610 nm) is induced by an energy transfer process from photoexcited hosts to Cd-dopants and a subsequent electronic transition from the excited state (3Eg) to the ground state (1A1g) of [CdCl6]4– units. This electronic transition matches well with a first-principles density functional theory calculation. Further, the optical behavior of Cd-doped CsPbCl3 NCs can be altered through postsynthetic anion-exchange reactions. Our studies present a new model system for doping chemistry studies in semiconductors for various optoelectronic applications.", + "subject": ["doping", "impurities", "ions", "perovskites", "physical and chemical processes"], + "keywords": [] + }, + { + "title": "A hands-on introduction to revisiting a Geant simulated event with a unique pair of seeds numbers", + "author": "J. Liao, R. Gaitskell", + "publisher": "IOP Publishing", + "url": "http://dx.doi.org/10.1088/1748-0221/13/11/p11008", + "doi": "10.1088/1748-0221/13/11/p11008", + "year": 2018, + "month": 11, + "abstract": "This paper presents a hands-on introduction to revisiting a Geant simulated event by a unique pair of seeds numbers. The revisiting can be achieved in two steps: in the first step, for every event, we assign a pair of numbers as two seeds numbers of a random engine of Geant, \"RanecuEngine\", and save the two seeds numbers into a Ntuple. In the second step, for an interesting event, we revisit it by re-assigning the two seeds numbers of the event to the \"RanecuEngine\" and run the same simulative scripts again. This way, we can re-access all info of the interesting event, including the trajectory of the event if visualization is feasible on the machine. As an example, we show in details how to apply the technique to visualize interesting events on a local PC for a large-scale Geant simulation accomplished on a High Performance Computer (HPC) cluster at Brown University.", + "subject": [], + "keywords": [] + }, + { + "title": "Improving the impact of HIV pre-exposure prophylaxis implementation in small urban centers among men who have sex with men: An agent-based modelling study", + "author": "Jason R. Gantenberg, Maximilian King, Madeline C. Montgomery, Omar Galárraga, Mattia Prosperi, Philip A. Chan, Brandon D. L. Marshall", + "publisher": "Public Library of Science (PLoS)", + "url": "http://dx.doi.org/10.1371/journal.pone.0199915", + "doi": "10.1371/journal.pone.0199915", + "year": 2018, + "month": 7, + "abstract": "Objectives\nIdentifying prescribing strategies that improve the efficiency of PrEP should increase its impact at the population level. This study identifies PrEP allocation criteria that most effectively reduce 10-year HIV incidence by 25%, in accordance with the US National HIV/AIDS Strategy’s goal for the proportionate reduction in new diagnoses.\n\nMethods\nWe used a discrete-time stochastic agent-based model to simulate several PrEP engagement strategies. The model represented MSM aged 15–74 in Rhode Island and was calibrated to statewide prevalence from 2009–2014. We simulated HIV transmission in the absence of PrEP and compared the following PrEP engagement scenarios: 1) allocation to the current patient population; 2) random allocation; 3) allocation to MSM with greater than 5 sexual partners in one year; 4) allocation to MSM with greater than 10 sexual partners in one year.\n\nFor each scenario and coverage level we estimated the number and proportion of infections averted and the person-years on PrEP per averted infection.\n\nResults\nIn 2014, HIV prevalence before PrEP implementation was between 4% and 5%. In the No PrEP scenario 826 new infections (95% simulation limits [SL]: 711, 955) occurred over 10 years, with an incidence rate of 3.51 per 1000 person-years (95% SL: 3.00, 4.08). Prevalence rose to 7.4% (95% SL: 6.7, 8.1). None of the PrEP scenarios reduced new HIV infections by 25% while covering less than 15% of the HIV-uninfected population. At 15% coverage, allocating PrEP to the current patient population, MSM with greater than 5 sexual partners in a year, and MSM with greater than 10 partners reduced new infections by at least 25%, requiring 161 (95% SL: 115, 289), 150 (95% SL: 107, 252), and 128 (95% SL: 100, 184) person-years on PrEP per averted infection, respectively.\n\nConclusions\nEngaging MSM with high numbers of sexual partners would improve the population-level impact and efficiency of PrEP in settings where PrEP coverage remains low. However, the sustained population-level PrEP coverage needed to reduce new infections by 25% is substantially higher than current levels of PrEP uptake.", + "subject": [], + "keywords": [] + }, + { + "title": "A new class of synthetic retinoid antibiotics effective against bacterial persisters", + "author": "Wooseong Kim, Wenpeng Zhu, Gabriel Lambert Hendricks, Daria Van Tyne, Andrew D. Steele, Colleen E. Keohane, Nico Fricke, Annie L. Conery, Steven Shen, Wen Pan, Kiho Lee, Rajmohan Rajamuthiah, Beth Burgwyn Fuchs, Petia M. Vlahovska, William M. Wuest, Michael S. Gilmore, Huajian Gao, Frederick M. Ausubel, Eleftherios Mylonakis", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1038/nature26157", + "doi": "10.1038/nature26157", + "year": 2018, + "month": 3, + "abstract": "A challenge in the treatment of Staphylococcus aureus infections is the high prevalence of methicillin-resistant S. aureus (MRSA) strains and the formation of non-growing, dormant ‘persister’ subpopulations that exhibit high levels of tolerance to antibiotics1,2,3 and have a role in chronic or recurrent infections4,5. As conventional antibiotics are not effective in the treatment of infections caused by such bacteria, novel antibacterial therapeutics are urgently required. Here we used a Caenorhabditis elegans–MRSA infection screen6 to identify two synthetic retinoids, CD437 and CD1530, which kill both growing and persister MRSA cells by disrupting lipid bilayers. CD437 and CD1530 exhibit high killing rates, synergism with gentamicin, and a low probability of resistance selection. All-atom molecular dynamics simulations demonstrated that the ability of retinoids to penetrate and embed in lipid bilayers correlates with their bactericidal ability. An analogue of CD437 was found to retain anti-persister activity and show an improved cytotoxicity profile. Both CD437 and this analogue, alone or in combination with gentamicin, exhibit considerable efficacy in a mouse model of chronic MRSA infection. With further development and optimization, synthetic retinoids have the potential to become a new class of antimicrobials for the treatment of Gram-positive bacterial infections that are currently difficult to cure.", + "subject": [], + "keywords": [] + }, + { + "title": "Plasmon-Enhanced Thin-Film Perovskite Solar Cells", + "author": "Tianyi Shen, Stylianos Siontas, Domenico Pacifici", + "publisher": "American Chemical Society (ACS)", + "url": "http://dx.doi.org/10.1021/acs.jpcc.8b07063", + "doi": "10.1021/acs.jpcc.8b07063", + "year": 2018, + "month": 9, + "abstract": "We report on plasmon-enhanced hybrid organic–inorganic perovskite solar cells with methylammonium lead iodide (MAPbI3) as the active absorbing material. Three-dimensional finite-difference time-domain simulations were performed on perovskite solar cells that consist of perovskite films with varied thicknesses on top of corrugated gold electrodes with different light trapping geometries, such as arrays of nanoholes and nanodisks. The absorption within the perovskite and gold films was estimated by calculating the electric field at every mesh point within the simulation volume, which allowed for the calculation of the solar cell power conversion efficiency (PCE) as a function of relevant design parameters. Optimal nanostructure designs were obtained by systematically varying the geometry dimensions. The results show that 100 nm-thick perovskite films on top of corrugated gold electrodes can exhibit up to 52% increase in PCE compared to their flat counterparts (i.e., from 19.2% for a flat cell to 29.2% for an optimized nanocorrugated cell). Moreover, we show that a 150 nm-thick perovskite film cell with opportunely corrugated back metal contacts can exhibit a PCE value of 31.3%, which is comparable to that of a 400 nm-thick bulk-like cell (31.6%). These findings may pave the way for plasmon-enhanced high-performance perovskite solar cells with ultrathin absorbing layers.", + "subject": [], + "keywords": [] + }, + { + "title": "Search for annual and diurnal rate modulations in the LUX experiment", + "author": "D. S. Akerib, S. Alsum, H. M. Araújo, X. Bai, J. Balajthy, P. Beltrame, E. P. Bernard, A. Bernstein, T. P. Biesiadzinski, E. M. Boulton, B. Boxer, P. Brás, S. Burdin, D. Byram, M. C. Carmona-Benitez, C. Chan, J. E. Cutter, T. J. R. Davison, E. Druszkiewicz, S. R. Fallon, A. Fan, S. Fiorucci, R. J. Gaitskell, J. Genovesi, C. Ghag, M. G. D. Gilchriese, C. Gwilliam, C. R. Hall, S. J. Haselschwardt, S. A. Hertel, D. P. Hogan, M. Horn, D. Q. Huang, C. M. Ignarra, R. G. Jacobsen, W. Ji, K. Kamdin, K. Kazkaz, D. Khaitan, R. Knoche, E. V. Korolkova, S. Kravitz, V. A. Kudryavtsev, B. G. Lenardo, K. T. Lesko, J. Liao, J. Lin, A. Lindote, M. I. Lopes, A. Manalaysay, R. L. Mannino, N. Marangou, M. F. Marzioni, D. N. McKinsey, D.-M. Mei, M. Moongweluwan, J. A. Morad, A. St. J. Murphy, C. Nehrkorn, H. N. Nelson, F. Neves, K. C. Oliver-Mallory, K. J. Palladino, E. K. Pease, G. R. C. Rischbieter, C. Rhyne, P. Rossiter, S. Shaw, T. A. Shutt, C. Silva, M. Solmaz, V. N. Solovov, P. Sorensen, T. J. Sumner, M. Szydagis, D. J. Taylor, W. C. Taylor, B. P. Tennyson, P. A. Terman, D. R. Tiedt, W. H. To, M. Tripathi, L. Tvrznikova, U. Utku, S. Uvarov, V. Velan, J. R. Verbus, R. C. Webb, J. T. White, T. J. Whitis, M. S. Witherell, F. L. H. Wolfs, D. Woodward, J. Xu, K. Yazdani, C. Zhang, undefined undefined", + "publisher": "American Physical Society (APS)", + "url": "http://dx.doi.org/10.1103/physrevd.98.062005", + "doi": "10.1103/physrevd.98.062005", + "year": 2018, + "month": 9, + "abstract": "Various dark matter models predict annual and diurnal modulations of dark matter interaction rates in Earth-based experiments as a result of the Earth’s motion in the halo. Observation of such features can provide generic evidence for detection of dark matter interactions. This paper reports a search for both annual and diurnal rate modulations in the LUX dark matter experiment using over 20 calendar months of data acquired between 2013 and 2016. This search focuses on electron recoil events at low energies, where leptophilic dark matter interactions are expected to occur and where the DAMA experiment has observed a strong rate modulation for over two decades. By using the innermost volume of the LUX detector and developing robust cuts and corrections, we obtained a stable event rate of 2.3±0.2  cpd/keVee/tonne, which is among the lowest in all dark matter experiments. No statistically significant annual modulation was observed in energy windows up to 26  keVee. Between 2 and 6  keVee, this analysis demonstrates the most sensitive annual modulation search up to date, with 9.2\u2062\uD835\uDF0E tension with the DAMA/LIBRA result. We also report no observation of diurnal modulations above 0.2  cpd/keVee/tonne amplitude between 2 and 6  keVee.", + "subject": ["dark matter", "particle dark matter", "weakly interacting massive particles", "calorimeters", "dark matter detectors", "scintillators", "time-projection chambers"], + "keywords": [] + }, + { + "title": "Accurate Predictions of Electron Binding Energies of Dipole-Bound Anions via Quantum Monte Carlo Methods", + "author": "Hongxia Hao, James Shee, Shiv Upadhyay, Can Ataca, Kenneth D. Jordan, Brenda M. Rubenstein", + "publisher": "American Chemical Society (ACS)", + "url": "http://dx.doi.org/10.1021/acs.jpclett.8b02733", + "doi": "10.1021/acs.jpclett.8b02733", + "year": 2018, + "month": 10, + "abstract": "Neutral molecules with sufficiently large dipole moments can bind electrons in diffuse nonvalence orbitals with most of their charge density far from the nuclei, forming so-called dipole-bound anions. Because long-range correlation effects play an important role in the binding of an excess electron and overall binding energies are often only on the order of 10s–100s of wave numbers, predictively modeling dipole-bound anions remains a challenge. Here, we demonstrate that quantum Monte Carlo methods can accurately characterize molecular dipole-bound anions with near-threshold dipole moments. We also show that correlated sampling Auxiliary Field Quantum Monte Carlo is particularly well-suited for resolving the fine energy differences between the neutral and anionic species. These results shed light on the fundamental limitations of quantum Monte Carlo methods and pave the way toward using them for the study of weakly bound species that are too large to model using traditional electron structure methods.", + "subject": [], + "keywords": [] + }, + { + "title": "The Thermodynamic Database Database", + "author": "Axel van de Walle, Chiraag Nataraj, Zi-Kui Liu", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.calphad.2018.04.003", + "doi": "10.1016/j.calphad.2018.04.003", + "year": 2018, + "month": 6, + "abstract": "This paper describes an effort to organize the condensed phases thermodynamic data freely available in electronic form within the scientific literature through the design of a special-purpose search engine indexing data electronically available in the “thermodynamic database” (TDB) format. This focus is motivated by the fact that it is widely used and can be readily read or imported into most thermodynamic modeling software. This form of data also provides a rather complete thermodynamic description of a given system and thus enables researchers to generate any phase diagram cross-section of interest, a capability typically not available in traditional phase diagram handbooks. For convenience, users can quickly preview selected cross sections directly online. In designing this system, special emphasis was devoted to ensuring that the bibliographic references of the original data sources are transparently reported and to providing links to the original data sources, rather than the data itself, in order to enforce access rights. This effort was made possible by combining and building upon a number of key components, such as the CALPHAD journal's supplementary information section, the NIMS database, the NIST materials data repository, the Crossref bibliographic service, and various thermodynamic (OpenCalphad, ATAT) and graphical (gnuplot, XTK) software.", + "subject": [], + "keywords": [] + }, + { + "title": "Ab Initio Finite Temperature Auxiliary Field Quantum Monte Carlo", + "author": "Yuan Liu, Minsik Cho, Brenda Rubenstein", + "publisher": "American Chemical Society (ACS)", + "url": "http://dx.doi.org/10.1021/acs.jctc.8b00569", + "doi": "10.1021/acs.jctc.8b00569", + "year": 2018, + "month": 8, + "abstract": "We present an ab initio auxiliary field quantum Monte Carlo method for studying the electronic structure of molecules, solids, and model Hamiltonians at finite temperature. The algorithm marries the ab initio phaseless auxiliary field quantum Monte Carlo algorithm known to produce high accuracy ground state energies of molecules and solids with its finite temperature variant, long used by condensed matter physicists for studying model Hamiltonian phase diagrams, to yield a phaseless, ab initio finite temperature method. We demonstrate that the method produces internal energies within chemical accuracy of exact diagonalization results across a wide range of temperatures for H2O (STO-3G), C2 (STO-6G), the one-dimensional hydrogen chain (STO-6G), and the multiorbital Hubbard model. Our method effectively controls the phase problem through importance sampling, often even without invoking the phaseless approximation, down to temperatures at which the systems studied approach their ground states and may therefore be viewed as exact over wide temperature ranges. This technique embodies a versatile tool for studying the finite temperature phase diagrams of a plethora of systems whose properties cannot be captured by a Hubbard U term alone. Our results moreover illustrate that the severity of the phase problem for model Hamiltonians far exceeds that for many molecules at all of the temperatures studied.", + "subject": [], + "keywords": [] + }, + { + "title": "Effects of continuous bisphenol A exposure from early gestation on 90 day old rat testes function and sperm molecular profiles: A CLARITY-BPA consortium study", + "author": "Edward Dere, Linnea M. Anderson, Susan M. Huse, Daniel J. Spade, Elizabeth McDonnell-Clark, Samantha J. Madnick, Susan J. Hall, Luísa Camacho, Sherry M. Lewis, Michelle M. Vanlandingham, Kim Boekelheide", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.taap.2018.03.021", + "doi": "10.1016/j.taap.2018.03.021", + "year": 2018, + "month": 5, + "abstract": "Bisphenol A (BPA) is a ubiquitous industrial chemical that has been identified as an endocrine disrupting compound (EDC). There is growing concern that early life exposures to EDCs, such as BPA, can adversely affect the male reproductive tract and function. This study was conducted as part of the Consortium Linking Academic and Regulatory Insights on BPA Toxicity (CLARITY-BPA) to further delineate the toxicities associated with continuous exposure to BPA from early gestation, and to comprehensively examine the elicited effects on testes and sperm. NCTR Sprague Dawley rat dams were gavaged from gestational day (GD) 6 until parturition, and their pups were directly gavaged daily from postnatal day (PND) 1 to 90 with BPA (2.5, 25, 250, 2500, 25,000, 250,000 μg/kg/d) or vehicle control. At PND 90, the testes and sperm were collected for evaluation.\n\nThe testes were histologically evaluated for altered germ cell apoptosis, sperm production, and altered spermiation. RNA and DNA isolated from sperm were assessed for elicited changes in global mRNA transcript abundance and altered DNA methylation. Effects of BPA were observed in changes in body, testis and epididymis weights only at the highest administered dose of BPA of 250,000 μg/kg/d. Genome-wide transcriptomic and epigenomic analyses failed to detect robust alterations in sperm mRNA and DNA methylation levels. These data indicate that prolonged exposure starting in utero to BPA over a wide range of levels has little, if any, impact on the testes and sperm molecular profiles of 90 day old rats as assessed by the histopathologic, morphometric, and molecular endpoints evaluated.", + "subject": [], + "keywords": [] + }, + { + "title": "A q-Factor-Based Digital Image Correlation Algorithm (qDIC) for Resolving Finite Deformations with Degenerate Speckle Patterns", + "author": "A. K. Landauer, M. Patel, D. L. Henann, C. Franck", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1007/s11340-018-0377-4", + "doi": "10.1007/s11340-018-0377-4", + "year": 2018, + "month": 3, + "abstract": "Digital image correlation (DIC) has become a widely utilized non-contact, full-field displacement measurement technique for obtaining accurate material kinematics. Despite the significant advances made to date, high resolution reconstruction of finite deformations for images with intrinsically low quality speckle patterns or poor signal-to-noise content has not been fully addressed. In particular, large image distortions imposed by materials undergoing finite deformations create significant challenges for most classical DIC approaches. To address this issue, this paper describes a new open source DIC algorithm (qDIC) that incorporates cross-correlation quality factors (q-factors), which are specifically designed to assess the quality of the reconstructed displacement estimate during the motion reconstruction process. A q-factor provides a robust assessment of the uniqueness and sharpness of the cross-correlation peak, and thus a quantitative estimate of the subset-based displacement measure per given image subset and level of applied deformation. We show that the incorporation of energy- and entropy-based q-factor metrics leads to substantially improved displacement predictions, lower noise floor, and reduced decorrelation even at significant levels of image distortion or poor speckle quality. Furthermore, we show that q-factors can be utilized as a quantitative metric for constructing a hybrid incremental-cumulative displacement correlation scheme for accurately resolving very large homogeneous and inhomogeneous deformations, even in the presence of significant image data loss.", + "subject": [], + "keywords": [] + }, + { + "title": "Computing Evans functions numerically via boundary-value problems", + "author": "Blake Barker, Rose Nguyen, Björn Sandstede, Nathaniel Ventura, Colin Wahl", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.physd.2017.12.002", + "doi": "10.1016/j.physd.2017.12.002", + "year": 2018, + "month": 3, + "abstract": "The Evans function has been used extensively to study spectral stability of travelling-wave solutions in spatially extended partial differential equations. To compute Evans functions numerically, several shooting methods have been developed. In this paper, an alternative scheme for the numerical computation of Evans functions is presented that relies on an appropriate boundary-value problem formulation. Convergence of the algorithm is proved, and several examples, including the computation of eigenvalues for a multi-dimensional problem, are given. The main advantage of the scheme proposed here compared with earlier methods is that the scheme is linear and scalable to large problems.", + "subject": ["Evans function", "linear boundary value problem", "travelling waves"], + "keywords": [] + }, + { + "title": "The spatial sensitivity of Sp converted waves—scattered-wave kernels and their applications to receiver-function migration and inversion", + "author": "N J Mancinelli, K M Fischer", + "publisher": "Oxford University Press (OUP)", + "url": "http://dx.doi.org/10.1093/gji/ggx506", + "doi": "10.1093/gji/ggx506", + "year": 2017, + "month": 11, + "abstract": "We characterize the spatial sensitivity of Sp converted waves to improve constraints on lateral variations in uppermost-mantle velocity gradients, such as the lithosphere–asthenosphere boundary (LAB) and the mid-lithospheric discontinuities. We use SPECFEM2D to generate 2-D scattering kernels that relate perturbations from an elastic half-space to Sp waveforms. We then show that these kernels can be well approximated using ray theory, and develop an approach to calculating kernels for layered background models. As proof of concept, we show that lateral variations in uppermost-mantle discontinuity structure are retrieved by implementing these scattering kernels in the first iteration of a conjugate-directions inversion algorithm. We evaluate the performance of this technique on synthetic seismograms computed for 2-D models with undulations on the LAB of varying amplitude, wavelength and depth. The technique reliably images the position of discontinuities with dips <35° and horizontal wavelengths >100–200 km. In cases of mild topography on a shallow LAB, the relative brightness of the LAB and Moho converters approximately agrees with the ratio of velocity contrasts across the discontinuities. Amplitude retrieval degrades at deeper depths. For dominant periods of 4 s, the minimum station spacing required to produce unaliased results is 5 km, but the application of a Gaussian filter can improve discontinuity imaging where station spacing is greater.", + "subject": ["Composition and structure of the mantle", "Inverse theory", "Waveform inversion", "Body waves", "Coda waves", "Computational seismology", "Wave scattering and diffraction"], + "keywords": [] + }, + { + "title": "Evolution of populations expanding on curved surfaces(a)", + "author": "Daniel A. Beller, Kim M. J. Alards, Francesca Tesser, Ricardo A. Mosna, Federico Toschi, Wolfram Möbius", + "publisher": "IOP Publishing", + "url": "http://dx.doi.org/10.1209/0295-5075/123/58005", + "doi": "10.1209/0295-5075/123/58005", + "year": 2018, + "month": 10, + "abstract": "The expansion of a population into new habitat is a transient process that leaves its footprints in the genetic composition of the expanding population. How the structure of the environment shapes the population front and the evolutionary dynamics during such a range expansion is little understood. Here, we investigate the evolutionary dynamics of populations consisting of many selectively neutral genotypes expanding on curved surfaces. Using a combination of individual-based off-lattice simulations, geometrical arguments, and lattice-based stepping-stone simulations, we characterise the effect of individual bumps on an otherwise flat surface. Compared to the case of a range expansion on a flat surface, we observe a transient relative increase, followed by a decrease, in neutral genetic diversity at the population front. In addition, we find that individuals at the sides of the bump have a dramatically increased expected number of descendants, while their neighbours closer to the bump's centre are far less lucky. Both observations can be explained using an analytical description of straight paths (geodesics) on the curved surface. Complementing previous studies of heterogeneous flat environments, the findings here build our understanding of how complex environments shape the evolutionary dynamics of expanding populations.", + "subject": [], + "keywords": [] + }, + { + "title": "Analysis and design of dual-phase steel microstructure for enhanced ductile fracture resistance", + "author": "Daniel Gerbig, Ankit Srivastava, Shmuel Osovski, Louis G. Hector, Allan Bower", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1007/s10704-017-0235-x", + "doi": "10.1007/s10704-017-0235-x", + "year": 2017, + "month": 7, + "abstract": "The goal of this paper is to predict how the properties of the constituent phases and microstructure of dual phase steels (consisting of ferrite and martensite) influence their fracture resistance. We focus on two commercial low-carbon dual-phase (DP) steels with different ferrite/martensite phase volume fractions and properties. These steels exhibit similar flow behavior and tensile strength but different ductility. Our experimental observations show that the mechanism of ductile fracture in these two DP steels involves nucleation, growth and coalescence of micron scale voids. We thus employ microstructure-based finite element simulations to analyze the ductile fracture of these dual-phase steels. In the microstructure-based simulations, the individual phases of the DP steels are discretely modeled using elastic-viscoplastic constitutive relations for progressively cavitating solids. The flow behavior of the individual phases in both the steels are determined by homogenizing the microscale calibrated crystal plasticity constitutive relations from a previous study (Chen et al. in Acta Mater 65:133–149, 2014) while the damage parameters are determined by void cell model calculations. We then determine microstructural effects on ductile fracture of these steels by analyzing a series of representative volume elements with varying volume fractions, flow and damage behaviors of the constituent phases. Our simulations predict qualitative features of the ductile fracture process in good agreement with experimental observations for both DP steels. A ‘virtual’ DP microstructure, constructed by varying the microstructural parameters in the commercial steels, is predicted to have strength and ductile fracture resistance that is superior to the two commercial DP steels. Our simulations provide guidelines for improving the ductile fracture resistance of DP steels.", + "subject": [], + "keywords": [] + }, + { + "title": "Chromatographic separation of radioactive noble gases from xenon", + "author": "D.S. Akerib, H.M. Araújo, X. Bai, A.J. Bailey, J. Balajthy, P. Beltrame, E.P. Bernard, A. Bernstein, T.P. Biesiadzinski, E.M. Boulton, R. Bramante, S.B. Cahn, M.C. Carmona-Benitez, C. Chan, A.A. Chiller, C. Chiller, T. Coffey, A. Currie, J.E. Cutter, T.J.R. Davison, A. Dobi, J.E.Y. Dobson, E. Druszkiewicz, B.N. Edwards, C.H. Faham, S. Fiorucci, R.J. Gaitskell, V.M. Gehman, C. Ghag, K.R. Gibson, M.G.D. Gilchriese, C.R. Hall, M. Hanhardt, S.J. Haselschwardt, S.A. Hertel, D.P. Hogan, M. Horn, D.Q. Huang, C.M. Ignarra, M. Ihm, R.G. Jacobsen, W. Ji, K. Kamdin, K. Kazkaz, D. Khaitan, R. Knoche, N.A. Larsen, C. Lee, B.G. Lenardo, K.T. Lesko, A. Lindote, M.I. Lopes, A. Manalaysay, R.L. Mannino, M.F. Marzioni, D.N. McKinsey, D.-M. Mei, J. Mock, M. Moongweluwan, J.A. Morad, A.St.J. Murphy, C. Nehrkorn, H.N. Nelson, F. Neves, K. O’Sullivan, K.C. Oliver-Mallory, K.J. Palladino, E.K. Pease, K. Pech, P. Phelps, L. Reichhart, C. Rhyne, S. Shaw, T.A. Shutt, C. Silva, V.N. Solovov, P. Sorensen, S. Stephenson, T.J. Sumner, M. Szydagis, D.J. Taylor, W. Taylor, B.P. Tennyson, P.A. Terman, D.R. Tiedt, W.H. To, M. Tripathi, L. Tvrznikova, S. Uvarov, J.R. Verbus, R.C. Webb, J.T. White, T.J. Whitis, M.S. Witherell, F.L.H. Wolfs, K. Yazdani, S.K. Young, C. Zhang", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.astropartphys.2017.10.014", + "doi": "10.1016/j.astropartphys.2017.10.014", + "year": 2018, + "month": 1, + "abstract": "The Large Underground Xenon (LUX) experiment operates at the Sanford Underground Research Facility to detect nuclear recoils from the hypothetical Weakly Interacting Massive Particles (WIMPs) on a liquid xenon target. Liquid xenon typically contains trace amounts of the noble radioactive isotopes 85Kr and 39Ar that are not removed by the in situ gas purification system. The decays of these isotopes at concentrations typical of research-grade xenon would be a dominant background for a WIMP search experiment. To remove these impurities from the liquid xenon, a chromatographic separation system based on adsorption on activated charcoal was built. 400 kg of xenon was processed, reducing the average concentration of krypton from 130 ppb to 3.5 ppt as measured by a cold-trap assisted mass spectroscopy system. A 50 kg batch spiked to 0.001 g/g of krypton was processed twice and reduced to an upper limit of 0.2 ppt.", + "subject": ["Xenon", "Krypton", "Adsorption", "Chromatography", "Gas Separation", "Dark Matter"], + "keywords": [] + }, + { + "title": "Modeling Microtubule-Based Transport and Anchoring of mRNA", + "author": "Maria-Veronica Ciocanel, Bjorn Sandstede, Samantha P. Jeschonek, Kimberly L. Mowry", + "publisher": "Society for Industrial & Applied Mathematics (SIAM)", + "url": "http://dx.doi.org/10.1137/18m1186083", + "doi": "10.1137/18m1186083", + "year": 2018, + "month": 1, + "abstract": "Localization of messenger RNA (mRNA) at the vegetal cortex plays an important role in the early development of Xenopus laevis oocytes. While it is known that molecular motors are responsible for the transport of mRNA cargo along microtubules to the cortex, the mechanisms of localization remain unclear. We model cargo transport along microtubules using partial differential equations with spatially dependent rates. A theoretical analysis of reduced versions of our model predicts effective velocity and diffusion rates for the cargo and shows that randomness of microtubule networks enhances effective transport. A more complex model using parameters estimated from fluorescence microscopy data reproduces the time and spatial scales of mRNA localization observed in Xenopus oocytes, corroborates experimental hypotheses that anchoring may be necessary to achieve complete localization, and shows that anchoring of mRNA complexes actively transported to the cortex is most effective in achieving robust accumulation at the cortex.", + "subject": ["intracellular transport", "microtubules", "anchoring", "long-time dynamics", "reaction-diffusion model"], + "keywords": [] + }, + { + "title": "Calibration, event reconstruction, data analysis, and limit calculation for the LUX dark matter experiment", + "author": "D. S. Akerib, S. Alsum, H. M. Araújo, X. Bai, A. J. Bailey, J. Balajthy, P. Beltrame, E. P. Bernard, A. Bernstein, T. P. Biesiadzinski, E. M. Boulton, P. Brás, D. Byram, S. B. Cahn, M. C. Carmona-Benitez, C. Chan, A. Currie, J. E. Cutter, T. J. R. Davison, A. Dobi, J. E. Y. Dobson, E. Druszkiewicz, B. N. Edwards, C. H. Faham, S. R. Fallon, A. Fan, S. Fiorucci, R. J. Gaitskell, V. M. Gehman, J. Genovesi, C. Ghag, M. G. D. Gilchriese, C. R. Hall, M. Hanhardt, S. J. Haselschwardt, S. A. Hertel, D. P. Hogan, M. Horn, D. Q. Huang, C. M. Ignarra, R. G. Jacobsen, W. Ji, K. Kamdin, K. Kazkaz, D. Khaitan, R. Knoche, N. A. Larsen, C. Lee, B. G. Lenardo, K. T. Lesko, A. Lindote, M. I. Lopes, A. Manalaysay, R. L. Mannino, M. F. Marzioni, D. N. McKinsey, D.-M. Mei, J. Mock, M. Moongweluwan, J. A. Morad, A. St. J. Murphy, C. Nehrkorn, H. N. Nelson, F. Neves, K. O’Sullivan, K. C. Oliver-Mallory, K. J. Palladino, E. K. Pease, L. Reichhart, C. Rhyne, S. Shaw, T. A. Shutt, C. Silva, M. Solmaz, V. N. Solovov, P. Sorensen, T. J. Sumner, M. Szydagis, D. J. Taylor, W. C. Taylor, B. P. Tennyson, P. A. Terman, D. R. Tiedt, W. H. To, M. Tripathi, L. Tvrznikova, S. Uvarov, V. Velan, J. R. Verbus, R. C. Webb, J. T. White, T. J. Whitis, M. S. Witherell, F. L. H. Wolfs, J. Xu, K. Yazdani, S. K. Young, C. Zhang, undefined undefined", + "publisher": "American Physical Society (APS)", + "url": "http://dx.doi.org/10.1103/physrevd.97.102008", + "doi": "10.1103/physrevd.97.102008", + "year": 2018, + "month": 5, + "abstract": "The LUX experiment has performed searches for dark-matter particles scattering elastically on xenon nuclei, leading to stringent upper limits on the nuclear scattering cross sections for dark matter. Here, for results derived from 1.4×104  kg days of target exposure in 2013, details of the calibration, event-reconstruction, modeling, and statistical tests that underlie the results are presented. Detector performance is characterized, including measured efficiencies, stability of response, position resolution, and discrimination between electron- and nuclear-recoil populations. Models are developed for the drift field, optical properties, background populations, the electron- and nuclear-recoil responses, and the absolute rate of low-energy background events. Innovations in the analysis include in situ measurement of the photomultipliers’ response to xenon scintillation photons, verification of fiducial mass with a low-energy internal calibration source, and new empirical models for low-energy signal yield based on large-sample, in situ calibrations.", + "subject": ["dark matter detectors"], + "keywords": [] + }, + { + "title": "Packing of flexible nanofibers in vesicles", + "author": "Guijin Zou, Xin Yi, Wenpeng Zhu, Huajian Gao", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.eml.2017.12.003", + "doi": "10.1016/j.eml.2017.12.003", + "year": 2018, + "month": 3, + "abstract": "Cellular packing of flexible nanofibers, including natural cytoskeletal microtubules, actin filaments, synthetic nanotubes and nanowires, is of fundamental interest to the understanding of a wide range of cell activities, including cell shape control, cell movement, cell division, and nano-cytotoxicity. Here, we perform molecular dynamics simulations and theoretical analysis to elucidate how the geometrical and mechanical properties of a flexible nanofiber influence its encapsulation within a lipid vesicle. Our analysis indicates that the packing morphology depends on the length and stiffness of the nanofiber, the initial configuration of the nanofiber–vesicle system and the pressure difference across the vesicle membrane. We establish a packing phase diagram based on three distinct vesicle morphologies in equilibrium, including a non-axisymmetric dumpling-shaped vesicle with a strongly curved nanofiber, a cherry-shaped vesicle with a tubular membrane protrusion enclosing a significant portion of the nanofiber, and an axisymmetric lemon-shaped vesicle with a pair of protruding tips induced by the encapsulated nanofiber.\n\n", + "subject": ["nanofiber packing", "nanofiber-vesicle interaction", "membrane protrusion", "nanofiber buckling", "cell shape", "molecular dynamics simulations"], + "keywords": [] + }, + { + "title": "Active learning of constitutive relation from mesoscopic dynamics for macroscopic modeling of non-Newtonian flows", + "author": "Lifei Zhao, Zhen Li, Bruce Caswell, Jie Ouyang, George Em Karniadakis", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.jcp.2018.02.039", + "doi": "10.1016/j.jcp.2018.02.039", + "year": 2018, + "month": 6, + "abstract": "We simulate complex fluids by means of an on-the-fly coupling of the bulk rheology to the underlying microstructure dynamics. In particular, a continuum model of polymeric fluids is constructed without a pre-specified constitutive relation, but instead it is actively learned from mesoscopic simulations where the dynamics of polymer chains is explicitly computed. To couple the bulk rheology of polymeric fluids and the microscale dynamics of polymer chains, the continuum approach (based on the finite volume method) provides the transient flow field as inputs for the (mesoscopic) dissipative particle dynamics (DPD), and in turn DPD returns an effective constitutive relation to close the continuum equations. In this multiscale modeling procedure, we employ an active learning strategy based on Gaussian process regression (GPR) to minimize the number of expensive DPD simulations, where adaptively selected DPD simulations are performed only as necessary. Numerical experiments are carried out for flow past a circular cylinder of a non-Newtonian fluid, modeled at the mesoscopic level by bead-spring chains. The results show that only five DPD simulations are required to achieve an effective closure of the continuum equations at Reynolds number \n. Furthermore, when Re is increased to 100, only one additional DPD simulation is required for constructing an extended GPR-informed model closure. Compared to traditional message-passing multiscale approaches, applying an active learning scheme to multiscale modeling of non-Newtonian fluids can significantly increase the computational efficiency. Although the method demonstrated here obtains only a local viscosity from the polymer dynamics, it can be extended to other multiscale models of complex fluids whose macro-rheology is unknown.\n\n", + "subject": [], + "keywords": [] + }, + { + "title": "Population Genomics and Biogeography of the Northern Acorn Barnacle (Semibalanus balanoides) Using Pooled Sequencing Approaches", + "author": "Joaquin C. B. Nunez, Rebecca G. Elyanow, David A. Ferranti, David M. Rand", + "publisher": "Springer International Publishing", + "url": "http://dx.doi.org/10.1007/13836_2018_58", + "doi": "10.1007/13836_2018_58", + "year": 2018, + "month": 10, + "abstract": "The northern acorn barnacle (Semibalanus balanoides) is a robust system for the study of evolutionary processes in the intertidal. S. balanoides has a well-characterized ecology, a wide circumboreal distribution, and a life history characterized by tractable environmental stressors at various ecological scales. In this chapter, we discuss a variety of topics concerning the development of S. balanoides as a model in ecological genomics as well as inferences of demography and historical phylogeography. In addition, we introduce two novel genomic tools for S. balanoides: the complete mtDNA sequence and the second draft of the nuclear genome (Sbal2). Using these tools, we conducted a reanalysis of previously described mtDNA haplotypes, a and b, as well as genome-wide levels of variation and population structure across the North Atlantic using pooled sequencing approaches. Analyses of sequence data from older and more recent Illumina platforms revealed the effects of technical bias in the estimates of population genomic metrics. We found concordant levels of nuDNA and mtDNA genetic variation with no evidence of demographic bottlenecks. We observed low genome-wide F ST values across the Atlantic, suggesting a large number of ancestral polymorphisms and shared standing variation across the basin. Comparisons of genome-wide estimates of F ST with those derived from a discriminant analysis of principal components uncovered population-structure-informative SNPs. This suggests the existence of latent population structure across broad scales, despite the capacity for extensive planktonic dispersal. Noticeably, our samples collected in Iceland displayed higher similarity to North American populations than to the rest of Europe. We hypothesize this is consistent with a periglacial refugium in Iceland concomitant with a barrier to gene flow caused by the North Atlantic current. Lastly, we discuss challenges and opportunities for the improvement of genomic tools in barnacles. Our reflections in this area are easily generalizable to most natural populations.", + "subject": [], + "keywords": [] + }, + { + "title": "Bayesian Uncertainty Quantification for Particle-Based Simulation of Lipid Bilayer Membranes", + "author": "Clark Bowman, Karen Larson, Alexander Roitershtein, Derek Stein, Anastasios Matzavinos", + "publisher": "Springer International Publishing", + "url": "http://dx.doi.org/10.1007/978-3-319-96842-1_4", + "doi": "10.1007/978-3-319-96842-1_4", + "year": 2018, + "month": -1, + "abstract": "A number of problems of interest in applied mathematics and biology involve the quantification of uncertainty in computational and real-world models. A recent approach to Bayesian uncertainty quantification using transitional Markov chain Monte Carlo (TMCMC) is extremely parallelizable and has opened the door to a variety of applications which were previously too computationally intensive to be practical. In this chapter, we first explore the machinery required to understand and implement Bayesian uncertainty quantification using TMCMC. We then describe dissipative particle dynamics, a computational particle simulation method which is suitable for modeling biological structures on the subcellular level, and develop an example simulation of a lipid membrane in fluid. Finally, we apply the algorithm to a basic model of uncertainty in our lipid simulation, effectively recovering a target set of parameters (along with distributions corresponding to the uncertainty) and demonstrating the practicality of Bayesian uncertainty quantification for complex particle simulations.", + "subject": [], + "keywords": [] + }, + { + "title": "Quantifying Platelet Margination in Diabetic Blood Flow", + "author": "Hung-Yu Chang, Alireza Yazdani, Xuejin Li, Konstantinos A.A. Douglas, Christos S. Mantzoros, George Em Karniadakis", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.bpj.2018.08.031", + "doi": "10.1016/j.bpj.2018.08.031", + "year": 2018, + "month": 10, + "abstract": "Patients with type 2 diabetes mellitus (T2DM) develop thrombotic abnormalities strongly associated with cardiovascular diseases. In addition to the changes of numerous coagulation factors such as elevated levels of thrombin and fibrinogen, the abnormal rheological effects of red blood cells (RBCs) and platelets flowing in blood are crucial in platelet adhesion and thrombus formation in T2DM. An important process contributing to the latter is the platelet margination. We employ the dissipative particle dynamics method to seamlessly model cells, plasma, and vessel walls. We perform a systematic study on RBC and platelet transport in cylindrical vessels by considering different cell shapes, sizes, and RBC deformabilities in healthy and T2DM blood, as well as variable flowrates and hematocrit. In particular, we use cellular-level RBC and platelet models with parameters derived from patient-specific data and present a sensitivity study. We find T2DM RBCs, which are less deformable compared to normal RBCs, lower the transport of platelets toward the vessel walls, whereas platelets with higher mean volume (often observed in T2DM) lead to enhanced margination. Furthermore, increasing the flowrate or hematocrit enhances platelet margination. We also investigated the effect of platelet shape and observed a nonmonotonic variation with the highest near-wall concentration corresponding to platelets with a moderate aspect ratio of 0.38. We examine the role of white blood cells (WBCs), whose count is increased notably in T2DM patients. We find that WBC rolling or WBC adhesion tends to decrease platelet margination due to hydrodynamic effects. To the best of our knowledge, such simulations of blood including all blood cells have not been performed before, and our quantitative findings can help separate the effects of hydrodynamic interactions from adhesive interactions and potentially shed light on the associated pathological processes in T2DM such as increased inflammatory response, platelet activation and adhesion, and ultimately thrombus formation.", + "subject": [], + "keywords": [] + }, + { + "title": "Simulations of Plasma Flow Control Strategies for Trailing Edge Separation", + "author": "Jennifer A. Franck, John Cooney, Neal Fine", + "publisher": "American Institute of Aeronautics and Astronautics", + "url": "http://dx.doi.org/10.2514/6.2018-3524", + "doi": "10.2514/6.2018-3524", + "year": 2018, + "month": 6, + "abstract": "A combined experimental and numerical investigations were conducted to understand the effect of forcing by Dielectric-barrier-discharge (DBD) plasma actuators on the strength of the tip-leakage vortices formed in the tip-gap of a single NACA 65 airfoil. A proof-of-concept experiment was conducted, where the airfoil was mounted with variable tip gaps in the test-section of a suction-type wind tunnel. The objective was to understand the difference of three-dimensional (3D) forcing over regular two-dimensional (2D) actuation. The continuous 3D forcing was generated by using segmented DBD actuators, where the buried electrodes were designed to generate secondary vortices along the tip gap flow, and across the tip gap flow. The flow field was investigated experimentally by dynamic-pressure measurements, and by stereo-particle-image-velocimetry (SPIV). Numerical study was conducted by using RANS computations for different forcing configurations. With a tip gap of 2 mm and free stream velocity of 2.7 m/s, the strength of the tip leakage vortex was significantly attenuated for a blowing ratio of approximately 1. For the segmented forcing cases, the location of the tip-leakage vortex was altered, however no perceptible change in the strength of the vortex was observed compared to the steady forcing. Overall, the effectiveness of forcing decreased with increasing tip-gaps and free-stream velocity.", + "subject": [], + "keywords": [] + }, + { + "title": "Invited paper: Reconciling SGTE and ab initio enthalpies of the elements", + "author": "Axel van de Walle", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.calphad.2017.10.008", + "doi": "10.1016/j.calphad.2017.10.008", + "year": 2018, + "month": 3, + "abstract": "The CALPHAD framework is built on assumption that all phases have a well-defined free energy over all accessible composition, temperature and pressure conditions. Unfortunately, it is common for phases to exhibit mechanical instabilities in at least some range of conditions, thus precluding direct experimental measurements and hindering computational efforts. A pragmatic solution has often been to extrapolate free energies from stable region into the unstable regions, but extrapolations from different systems that share a common phase may not agree and extrapolated free energies can unintentionally lie below the free energy of stable phases. Computational approaches that aim to directly calculate the free energy of unstable phases offer a promising avenue to address these issues. Among them, the recently proposed “inflection detection” scheme lies on a strong theoretical footing. We provide further support for this approach by demonstrating that it yield free energies that agree very well with the widely used SGTE (Scientific Group Thermodata Europe) data for pure elements. This finding suggest that it may be possible to get the best of both worlds: obtain a theoretically justified definition of the free energy of mechanically unstable phases and preserve much of existing empirical standards for the assignments of such free energies.", + "subject": ["mechanical instability", "inflection point", "first-principles calculations"], + "keywords": [] + }, + { + "title": "Packing of flexible 2D materials in vesicles", + "author": "Guijin Zou, Xin Yi, Wenpeng Zhu, Huajian Gao", + "publisher": "IOP Publishing", + "url": "http://dx.doi.org/10.1088/1361-6463/aabf79", + "doi": "10.1088/1361-6463/aabf79", + "year": 2018, + "month": 5, + "abstract": "To understand the mechanics of cellular packing of two-dimensional (2D) materials, we perform systematic molecular dynamics simulations and theoretical analysis to investigate the packing of a flexible circular sheet in a spherical vesicle and the 2D packing problem of a strip in a cylindrical vesicle. Depending on the system dimensions and the bending rigidity ratio between the confined sheet and the vesicle membrane, a variety of packing morphologies are observed, including a conical shape, a shape of three-fold symmetry, a cylindrically curved shape, an axisymmetrically buckled shape, as well as the initial circular shape. A set of buckling analyses lead to phase diagrams of the packing morphologies of the encapsulated sheets. These results may have important implications on the mechanism of intracellular packing and toxicity of 2D materials.", + "subject": [], + "keywords": [] + }, + { + "title": "High strain-rate soft material characterization via inertial cavitation", + "author": "Jonathan B. Estrada, Carlos Barajas, David L. Henann, Eric Johnsen, Christian Franck", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.jmps.2017.12.006", + "doi": "10.1016/j.jmps.2017.12.006", + "year": 2018, + "month": 3, + "abstract": "Mechanical characterization of soft materials at high strain-rates is challenging due to their high compliance, slow wave speeds, and non-linear viscoelasticity. Yet, knowledge of their material behavior is paramount across a spectrum of biological and engineering applications from minimizing tissue damage in ultrasound and laser surgeries to diagnosing and mitigating impact injuries. To address this significant experimental hurdle and the need to accurately measure the viscoelastic properties of soft materials at high strain-rates (103–108 s\n), we present a minimally invasive, local 3D microrheology technique based on inertial microcavitation. By combining high-speed time-lapse imaging with an appropriate theoretical cavitation framework, we demonstrate that this technique has the capability to accurately determine the general viscoelastic material properties of soft matter as compliant as a few kilopascals. Similar to commercial characterization algorithms, we provide the user with significant flexibility in evaluating several constitutive laws to determine the most appropriate physical model for the material under investigation. Given its straightforward implementation into most current microscopy setups, we anticipate that this technique can be easily adopted by anyone interested in characterizing soft material properties at high loading rates including hydrogels, tissues and various polymeric specimens.", + "subject": [], + "keywords": [] + }, + { + "title": "Oxidation suppression during hydrothermal phase reversion allows synthesis of monolayer semiconducting MoS2 in stable aqueous suspension", + "author": "Zhongying Wang, Yin-Jia Zhang, Muchun Liu, Andrew Peterson, Robert H. Hurt", + "publisher": "Royal Society of Chemistry (RSC)", + "url": "http://dx.doi.org/10.1039/c7nr01193h", + "doi": "10.1039/c7nr01193h", + "year": 2017, + "month": 4, + "abstract": "This letter demonstrates a simple method to achieve high-yields of 1H semiconducting MoS2 monolayers in concentrated, colloidally-stable aqueous suspension. The method is based on oxidation suppression during the hydrothermal processing step used for metal-to-semiconductor phase reversion. Accompanying DFT calculations on elementary steps in the MoS2 wet oxidation reaction suggest that a two-site corrosion mechanism is responsible for the observed high reactivity and low stability of 1T metallic MoS2.", + "subject": [], + "keywords": [] + }, + { + "title": "A Bioinformatic Glimpse of Human-Origin Zika Virus Polyprotein", + "author": "Joel K Weltman", + "publisher": "OMICS Publishing Group", + "url": "http://dx.doi.org/10.4172/2161-0703.1000265", + "doi": "10.4172/2161-0703.1000265", + "year": 2017, + "month": 11, + "abstract": "An amino acid position with maximum Shannon information entropy and maximum cumulative mutual information is identified in Zika virus polyprotein. This amino acid position is used to sort the subset of Zika virus polyprotein mutations found exclusively in viruses isolated from human hosts but not from vector Aedes mosquitos. The identified mutational amino acid position is a component of a 20-mer peptide in the NS1 protein that has been reported with putative epitopic activity by Freire et al. It is suggested that the observed dual maxima bioinformatic parameters reported here for an exclusively human mutational site support the proposed function of that site in immunological activity.", + "subject": [], + "keywords": [] + }, + { + "title": "Pathogenic variants that alter protein code often disrupt splicing", + "author": "Rachel Soemedi, Kamil J Cygan, Christy L Rhine, Jing Wang, Charlston Bulacan, John Yang, Pinar Bayrak-Toydemir, Jamie McDonald, William G Fairbrother", + "publisher": "Springer Science and Business Media LLC", + "url": "http://dx.doi.org/10.1038/ng.3837", + "doi": "10.1038/ng.3837", + "year": 2017, + "month": 4, + "abstract": "The lack of tools to identify causative variants from sequencing data greatly limits the promise of precision medicine. Previous studies suggest that one-third of disease-associated alleles alter splicing. We discovered that the alleles causing splicing defects cluster in disease-associated genes (for example, haploinsufficient genes). We analyzed 4,964 published disease-causing exonic mutations using a massively parallel splicing assay (MaPSy), which showed an 81% concordance rate with splicing in patient tissue. Approximately 10% of exonic mutations altered splicing, mostly by disrupting multiple stages of spliceosome assembly. We present a large-scale characterization of exonic splicing mutations using a new technology that facilitates variant classification and keeps pace with variant discovery.", + "subject": [], + "keywords": [] + }, + { + "title": "Limits on Spin-Dependent WIMP-Nucleon Cross Section Obtained from the Complete LUX Exposure", + "author": "D. S. Akerib, S. Alsum, H. M. Araújo, X. Bai, A. J. Bailey, J. Balajthy, P. Beltrame, E. P. Bernard, A. Bernstein, T. P. Biesiadzinski, E. M. Boulton, P. Brás, D. Byram, S. B. Cahn, M. C. Carmona-Benitez, C. Chan, A. A. Chiller, C. Chiller, A. Currie, J. E. Cutter, T. J. R. Davison, A. Dobi, J. E. Y. Dobson, E. Druszkiewicz, B. N. Edwards, C. H. Faham, S. R. Fallon, S. Fiorucci, R. J. Gaitskell, V. M. Gehman, C. Ghag, M. G. D. Gilchriese, C. R. Hall, M. Hanhardt, S. J. Haselschwardt, S. A. Hertel, D. P. Hogan, M. Horn, D. Q. Huang, C. M. Ignarra, R. G. Jacobsen, W. Ji, K. Kamdin, K. Kazkaz, D. Khaitan, R. Knoche, N. A. Larsen, C. Lee, B. G. Lenardo, K. T. Lesko, A. Lindote, M. I. Lopes, A. Manalaysay, R. L. Mannino, M. F. Marzioni, D. N. McKinsey, D.-M. Mei, J. Mock, M. Moongweluwan, J. A. Morad, A. St. J. Murphy, C. Nehrkorn, H. N. Nelson, F. Neves, K. O’Sullivan, K. C. Oliver-Mallory, K. J. Palladino, E. K. Pease, L. Reichhart, C. Rhyne, S. Shaw, T. A. Shutt, C. Silva, M. Solmaz, V. N. Solovov, P. Sorensen, S. Stephenson, T. J. Sumner, M. Szydagis, D. J. Taylor, W. C. Taylor, B. P. Tennyson, P. A. Terman, D. R. Tiedt, W. H. To, M. Tripathi, L. Tvrznikova, S. Uvarov, V. Velan, J. R. Verbus, R. C. Webb, J. T. White, T. J. Whitis, M. S. Witherell, F. L. H. Wolfs, J. Xu, K. Yazdani, S. K. Young, C. Zhang, undefined undefined", + "publisher": "American Physical Society (APS)", + "url": "http://dx.doi.org/10.1103/physrevlett.118.251302", + "doi": "10.1103/physrevlett.118.251302", + "year": 2017, + "month": 6, + "abstract": "We present experimental constraints on the spin-dependent WIMP-nucleon elastic cross sections from the total 129.5  kg yr exposure acquired by the Large Underground Xenon experiment (LUX), operating at the Sanford Underground Research Facility in Lead, South Dakota (USA). A profile likelihood ratio analysis allows 90% C.L. upper limits to be set on the WIMP-neutron (WIMP-proton) cross section of \uD835\uDF0E\uD835\uDC5B=1.6×10−41  cm2 (\uD835\uDF0E\uD835\uDC5D=5×10−40  cm2) at 35  GeV \uD835\uDC50−2, almost a sixfold improvement over the previous LUX spin-dependent results. The spin-dependent WIMP-neutron limit is the most sensitive constraint to date.", + "subject": ["particle dark matter", "weakly interacting massive particles", "dark matter detectors"], + "keywords": [] + }, + { + "title": "Kr83m\n calibration of the 2013 LUX dark matter search", + "author": "D. S. Akerib, S. Alsum, H. M. Araújo, X. Bai, A. J. Bailey, J. Balajthy, P. Beltrame, E. P. Bernard, A. Bernstein, T. P. Biesiadzinski, E. M. Boulton, P. Brás, D. Byram, S. B. Cahn, M. C. Carmona-Benitez, C. Chan, A. Currie, J. E. Cutter, T. J. R. Davison, A. Dobi, E. Druszkiewicz, B. N. Edwards, S. R. Fallon, A. Fan, S. Fiorucci, R. J. Gaitskell, J. Genovesi, C. Ghag, M. G. D. Gilchriese, C. R. Hall, M. Hanhardt, S. J. Haselschwardt, S. A. Hertel, D. P. Hogan, M. Horn, D. Q. Huang, C. M. Ignarra, R. G. Jacobsen, W. Ji, K. Kamdin, K. Kazkaz, D. Khaitan, R. Knoche, N. A. Larsen, B. G. Lenardo, K. T. Lesko, A. Lindote, M. I. Lopes, A. Manalaysay, R. L. Mannino, M. F. Marzioni, D. N. McKinsey, D.-M. Mei, J. Mock, M. Moongweluwan, J. A. Morad, A. St. J. Murphy, C. Nehrkorn, H. N. Nelson, F. Neves, K. O’Sullivan, K. C. Oliver-Mallory, K. J. Palladino, E. K. Pease, C. Rhyne, S. Shaw, T. A. Shutt, C. Silva, M. Solmaz, V. N. Solovov, P. Sorensen, T. J. Sumner, M. Szydagis, D. J. Taylor, W. C. Taylor, B. P. Tennyson, P. A. Terman, D. R. Tiedt, W. H. To, M. Tripathi, L. Tvrznikova, S. Uvarov, V. Velan, J. R. Verbus, R. C. Webb, J. T. White, T. J. Whitis, M. S. Witherell, F. L. H. Wolfs, J. Xu, K. Yazdani, S. K. Young, C. Zhang, undefined undefined", + "publisher": "American Physical Society (APS)", + "url": "http://dx.doi.org/10.1103/physrevd.96.112009", + "doi": "10.1103/physrevd.96.112009", + "year": 2017, + "month": 12, + "abstract": "LUX was the first dark matter experiment to use a \n83\u2062m\n Kr \n calibration source. In this paper, we describe the source preparation and injection. We also present several \n83\u2062m\n Kr \n calibration applications in the context of the 2013 LUX exposure, including the measurement of temporal and spatial variation in scintillation and charge signal amplitudes, and several methods to understand the electric field within the time projection chamber.", + "subject": [], + "keywords": [] + }, + { + "title": "Observation of Structural Wavepacket Motion: The Umbrella Mode in Rydberg-Excited N-Methyl Morpholine", + "author": "Yao Zhang, Sanghamitra Deb, Hannes Jónsson, Peter M. Weber", + "publisher": "American Chemical Society (ACS)", + "url": "http://dx.doi.org/10.1021/acs.jpclett.7b01274", + "doi": "10.1021/acs.jpclett.7b01274", + "year": 2017, + "month": 7, + "abstract": "We have observed time-resolved, structural dynamics of a coherent vibrational wavepacket in Rydberg-excited N-methyl morpholine, a molecule with 48 internal degrees of freedom. The molecular structure was established by associating the time-dependent Rydberg electron binding energy, obtained from time-resolved photoionization–photoelectron spectroscopy, to the molecular structure using self-interaction corrected density functional calculations. Optical excitation at 226 nm launches an oscillatory wavepacket in the amine umbrella coordinate with a 650 fs period. Even though the Franck–Condon excitation is at an angle of 17°, the wavepacket settles into an oscillation between 4° and −10° within a fraction of a vibrational period and then dephases with a time constant of 750 fs.", + "subject": ["binding energy", "molecular structure", "molecules", "oscillation", "quantum mechanics"], + "keywords": [] + }, + { + "title": "Mechanical properties of graphene grain boundary and hexagonal boron nitride lateral heterostructure with controlled domain size", + "author": "Anran Wei, Yinfeng Li, Dibakar Datta, Hui Guo, Ziang Lv", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.commatsci.2016.06.026", + "doi": "10.1016/j.commatsci.2016.06.026", + "year": 2017, + "month": 1, + "abstract": "", + "subject": [], + "keywords": [] + }, + { + "title": "Stiffening thermal membranes by cutting", + "author": "Emily R. Russell, Rastko Sknepnek, Mark Bowick", + "publisher": "American Physical Society (APS)", + "url": "http://dx.doi.org/10.1103/physreve.96.013002", + "doi": "10.1103/physreve.96.013002", + "year": 2017, + "month": 7, + "abstract": "", + "subject": [], + "keywords": [] + }, + { + "title": "A resilient and efficient CFD framework: Statistical learning tools for multi-fidelity and heterogeneous information fusion", + "author": "Seungjoon Lee, Ioannis G. Kevrekidis, George Em Karniadakis", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.jcp.2017.05.021", + "doi": "10.1016/j.jcp.2017.05.021", + "year": 2017, + "month": 9, + "abstract": "", + "subject": [], + "keywords": [] + }, + { + "title": "Recent progresses of global minimum searches of nanoclusters with a constrained Basin-Hopping algorithm in the TGMin program", + "author": "Xin Chen, Ya-Fan Zhao, Lai-Sheng Wang, Jun Li", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.comptc.2016.12.028", + "doi": "10.1016/j.comptc.2016.12.028", + "year": 2017, + "month": 5, + "abstract": "", + "subject": [], + "keywords": [] + }, + { + "title": "Tetrahedron-tiling method for crystal structure prediction", + "author": "Qi-Jun Hong, Joseph Yasi, Axel van de Walle", + "publisher": "American Physical Society (APS)", + "url": "http://dx.doi.org/10.1103/physrevmaterials.1.020801", + "doi": "10.1103/physrevmaterials.1.020801", + "year": 2017, + "month": 7, + "abstract": "", + "subject": [], + "keywords": [] + }, + { + "title": "Patient-specific modeling of individual sickle cell behavior under transient hypoxia", + "author": "Xuejin Li, E. Du, Ming Dao, Subra Suresh, George Em Karniadakis", + "publisher": "Public Library of Science (PLoS)", + "url": "http://dx.doi.org/10.1371/journal.pcbi.1005426", + "doi": "10.1371/journal.pcbi.1005426", + "year": 2017, + "month": 3, + "abstract": "", + "subject": [], + "keywords": [] + }, + { + "title": "Probing the Structures of Neutral B11 and B12 Using High-Resolution Photoelectron Imaging of B11– and B12–", + "author": "Joseph Czekner, Ling Fung Cheung, Lai-Sheng Wang", + "publisher": "American Chemical Society (ACS)", + "url": "http://dx.doi.org/10.1021/acs.jpcc.6b10958", + "doi": "10.1021/acs.jpcc.6b10958", + "year": 2016, + "month": 12, + "abstract": "", + "subject": [], + "keywords": [] + }, + { + "title": "Lysines in the RNA Polymerase II C-Terminal Domain Contribute to TAF15 Fibril Recruitment", + "author": "Abigail M. Janke, Da Hee Seo, Vahid Rahmanian, Alexander E. Conicella, Kaylee L. Mathews, Kathleen A. Burke, Jeetain Mittal, Nicolas L. Fawzi", + "publisher": "American Chemical Society (ACS)", + "url": "http://dx.doi.org/10.1021/acs.biochem.7b00310", + "doi": "10.1021/acs.biochem.7b00310", + "year": 2017, + "month": 9, + "abstract": "", + "subject": [], + "keywords": [] + }, + { + "title": "Mitonuclear Interactions Mediate Transcriptional Responses to Hypoxia inDrosophila", + "author": "Jim A. Mossman, Jennifer G. Tross, Nick A. Jourjine, Nan Li, Zhijin Wu, David M. Rand", + "publisher": "Oxford University Press (OUP)", + "url": "http://dx.doi.org/10.1093/molbev/msw246", + "doi": "10.1093/molbev/msw246", + "year": 2016, + "month": 11, + "abstract": "", + "subject": [], + "keywords": [] + }, + { + "title": "Sedimentological evidence for a deltaic origin of the western fan deposit in Jezero crater, Mars and implications for future exploration", + "author": "Timothy A. Goudge, Ralph E. Milliken, James W. Head, John F. Mustard, Caleb I. 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Salomaki, Martin Kolísko, Tomáš Scholz, Roman Kuchta", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.cub.2023.08.064", + "doi": "10.1016/j.cub.2023.08.064", + "year": 2023, + "month": 10, + "abstract": "", + "subject": [], + "keywords": [] + }, + { + "title": "Resting state network connectivity is associated with cognitive flexibility performance in youth in the Adolescent Brain Cognitive Development Study", + "author": "Sarah A. Thomas, Sarah K. Ryan, Jodi Gilman", + "publisher": "Elsevier BV", + "url": "http://dx.doi.org/10.1016/j.neuropsychologia.2023.108708", + "doi": "10.1016/j.neuropsychologia.2023.108708", + "year": 2023, + "month": 12, + "abstract": "", + "subject": [], + "keywords": [] + }, + { + "title": "Machine-learning-assisted determination of electronic correlations from magnetic resonance", + "author": "Anantha Rao, Stephen Carr, Charles Snider, D. E. Feldman, Chandrasekhar Ramanathan, V. F. Mitrović", + "publisher": "American Physical Society (APS)", + "url": "http://dx.doi.org/10.1103/physrevresearch.5.043098", + "doi": "10.1103/physrevresearch.5.043098", + "year": 2023, + "month": 10, + "abstract": "", + "subject": [], + "keywords": [] + }, + { + "title": "A Generalized Bootstrap Procedure of the Standard Error and Confidence Interval Estimation for Inverse Probability of Treatment Weighting", + "author": "Tenglong Li, Jordan Lawson", + "publisher": "Informa UK Limited", + "url": "http://dx.doi.org/10.1080/00273171.2023.2254541", + "doi": "10.1080/00273171.2023.2254541", + "year": 2023, + "month": 9, + "abstract": "", + "subject": [], + "keywords": [] + } +] diff --git a/src/utils/utils.ts b/src/utils/utils.ts index 2d3f30f..ba5827a 100644 --- a/src/utils/utils.ts +++ b/src/utils/utils.ts @@ -20,6 +20,7 @@ export const fetchDoi = async (doi: string): Promise => { DOI: fetchedDoi, published, abstract, + subject, } = await res.json(); if (doi.toLowerCase() !== fetchedDoi.toLowerCase()) { @@ -27,14 +28,15 @@ export const fetchDoi = async (doi: string): Promise => { } return { - title: title ?? '', + title: title ? title.replaceAll(/<[^>]+>/g, '').replaceAll('\n', '') : '', // remove HTML tags author: author.map(({ given, family }) => `${given} ${family}`).join(', '), publisher: publisher ?? '', url: url ?? '', doi: doi ?? '', year: published?.['date-parts'][0][0] ?? -1, month: published?.['date-parts'][0][1] ?? -1, - abstract: abstract ? abstract.replace(/<[^>]+>/g, '') : '', // remove HTML tags + abstract: abstract ?? '', + keywords: [...(subject ?? [])], }; }; diff --git a/types/index.d.ts b/types/index.d.ts index 15c8ef4..2765a55 100644 --- a/types/index.d.ts +++ b/types/index.d.ts @@ -7,6 +7,8 @@ export interface Publication { month: number; year: number; abstract: string; + keywords?: Array; + ngrams?: Array; } export interface User {