From d1a89225d01993ad8c385d0b18b978dd4a6dd1df Mon Sep 17 00:00:00 2001 From: Santosh Bhosale Date: Wed, 1 May 2024 11:38:35 -0700 Subject: [PATCH] deleted --- .../{FD89808F-output.json => 4836CB44-output.json} | 5 +---- .Rproj.user/224B9E6C/sources/prop/11366684 | 2 +- .../224B9E6C/sources/session-b8d86596/A21CD174 | 8 ++++---- .../sources/session-b8d86596/A21CD174-contents | 2 +- .../Serum-Proteomics-Pre-diabetic/index.qmd.json | 2 +- .quarto/preview/lock | 2 +- .quarto/xref/03c744e1 | 2 +- .quarto/xref/06dba913 | 2 +- .quarto/xref/0ecb96e6 | 2 +- .quarto/xref/375be950 | 2 +- .quarto/xref/52dc296d | 2 +- .quarto/xref/62a219a9 | 2 +- .quarto/xref/b45646c3 | 2 +- .quarto/xref/e7b8555f | 2 +- .quarto/xref/edff53e8 | 2 +- blog/Serum-Proteomics-Pre-diabetic/index.qmd | 2 +- docs/blog/Serum-Proteomics-Pre-diabetic/index.html | 14 ++++---------- docs/blog/index.html | 2 +- docs/search.json | 2 +- 19 files changed, 25 insertions(+), 34 deletions(-) rename .Rproj.user/224B9E6C/jobs/{FD89808F-output.json => 4836CB44-output.json} (78%) diff --git a/.Rproj.user/224B9E6C/jobs/FD89808F-output.json b/.Rproj.user/224B9E6C/jobs/4836CB44-output.json similarity index 78% rename from .Rproj.user/224B9E6C/jobs/FD89808F-output.json rename to .Rproj.user/224B9E6C/jobs/4836CB44-output.json index 2364083..c9f5cf4 100644 --- a/.Rproj.user/224B9E6C/jobs/FD89808F-output.json +++ b/.Rproj.user/224B9E6C/jobs/4836CB44-output.json @@ -10,11 +10,8 @@ [1,"\r[ 8/11] blog\\Serum-Proteomics-of-mother-infant-dyads-T1D-risk\\index.qmd\n"] [1,"\r[ 9/11] blog\\Serum-Proteomics-Pre-diabetic\\index.qmd\n"] [1,"\r[10/11] cv\\index.qmd\n"] -[1,"failed to create process.\r\n"] -[1,"WARNING: Unable to perform code-link (code-link requires R packages rmarkdown, downlit, and xml2)\n\r[11/11] index.qmd\n"] +[1,"failed to create process.\r\nWARNING: Unable to perform code-link (code-link requires R packages rmarkdown, downlit, and xml2)\n\r[11/11] index.qmd\n"] [1,"\n"] [1,"Watching files for changes\nBrowse at http://localhost:22222/\n"] [1,"GET: /\n"] [1," /img/logo.png (404: Not Found)\n"] -[1,"GET: /blog/\n"] -[1," /img/logo.png (404: Not Found)\n"] diff --git a/.Rproj.user/224B9E6C/sources/prop/11366684 b/.Rproj.user/224B9E6C/sources/prop/11366684 index f637558..b9fa434 100644 --- a/.Rproj.user/224B9E6C/sources/prop/11366684 +++ b/.Rproj.user/224B9E6C/sources/prop/11366684 @@ -7,5 +7,5 @@ "rmdVisualWrapConfigured": "true", "docOutlineVisible": "1", "rmdVisualCollapsedChunks": "", - "rmdVisualModeLocation": "2526:1606.6666259765625" + "rmdVisualModeLocation": "2499:1039.3333740234375" } \ No newline at end of file diff --git a/.Rproj.user/224B9E6C/sources/session-b8d86596/A21CD174 b/.Rproj.user/224B9E6C/sources/session-b8d86596/A21CD174 index 9866787..797d1dc 100644 --- a/.Rproj.user/224B9E6C/sources/session-b8d86596/A21CD174 +++ b/.Rproj.user/224B9E6C/sources/session-b8d86596/A21CD174 @@ -3,7 +3,7 @@ "path": "~/GitHub/santoshdbhosale.github.io/blog/Serum-Proteomics-Pre-diabetic/index.qmd", "project_path": "blog/Serum-Proteomics-Pre-diabetic/index.qmd", "type": "quarto_markdown", - "hash": "1497668379", + "hash": "0", "contents": "", "dirty": false, "created": 1714540255280.0, @@ -18,14 +18,14 @@ "rmdVisualWrapConfigured": "true", "docOutlineVisible": "1", "rmdVisualCollapsedChunks": "", - "rmdVisualModeLocation": "2526:1606.6666259765625" + "rmdVisualModeLocation": "2499:1039.3333740234375" }, "folds": "", - "lastKnownWriteTime": 1714540730, + "lastKnownWriteTime": 1714588690, "encoding": "UTF-8", "collab_server": "", "source_window": "", - "last_content_update": 1714540730177, + "last_content_update": 1714588690856, "read_only": false, "read_only_alternatives": [] } \ No newline at end of file diff --git a/.Rproj.user/224B9E6C/sources/session-b8d86596/A21CD174-contents b/.Rproj.user/224B9E6C/sources/session-b8d86596/A21CD174-contents index 1ca329e..228562f 100644 --- a/.Rproj.user/224B9E6C/sources/session-b8d86596/A21CD174-contents +++ b/.Rproj.user/224B9E6C/sources/session-b8d86596/A21CD174-contents @@ -13,4 +13,4 @@ We utilized such unique samples from the DIPP cohort to identify early serum pro Previous serum proteomics biomarker studies of T1D have typically compared disease end points with control groups, i.e. the differences between patients with T1D and healthy controls. In contrast to the published reports, to our knowledge we have shown for the [**first time serum proteomics profile of pre-diabetic children**](https://diabetes.diabetesjournals.org/content/64/6/2265), mapping the changes from early infancy, seroconversion and diagnosis. The main finding included lower and higher levels of APOC4 and AFAM in cases compared to controls respectively and, the combination of this two proteins classified T1D developing children from controls with 91% success rate with an area under the curve value of 0.85. Notably the levels of APOC4 were found to be lower even before seroconversion. -![Top scoring pair analysis](fig/tsp.png) +![](fig/tsp.png) diff --git a/.quarto/idx/blog/Serum-Proteomics-Pre-diabetic/index.qmd.json b/.quarto/idx/blog/Serum-Proteomics-Pre-diabetic/index.qmd.json index 5100e76..54b5a22 100644 --- a/.quarto/idx/blog/Serum-Proteomics-Pre-diabetic/index.qmd.json +++ b/.quarto/idx/blog/Serum-Proteomics-Pre-diabetic/index.qmd.json @@ -1 +1 @@ -{"title":"Serum Proteomics Pre diabetic","markdown":{"yaml":{"title":"Serum Proteomics Pre diabetic","date":"2020-10-27","categories":["publications","serum"],"image":"fig/tsp.png"},"containsRefs":false,"markdown":"\n\nType-1 diabetes (T1D) is an autoimmune disease that is characterized by the destruction of the insulin producing β cells in the Islets of Langerhans of the pancreas. 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The DIPP cohort has collected blood serum samples at 3 to 6 months intervals from children with a genetically conferred T1D risk and tested for T1D associated autoantibodies. **These longitudinal series of samples cover all the stages of disease progression from birth to clinical T1D and matching samples from carefully matched healthy children.**\n\nWe utilized such unique samples from the DIPP cohort to identify early serum protein biomarkers associated with T1D using quantitative mass spectrometry based approach. The study involved LC-MS/MS analysis with both iTRAQ and label-free quantification strategy on the immunodepleted serum.\n\nPrevious serum proteomics biomarker studies of T1D have typically compared disease end points with control groups, i.e. the differences between patients with T1D and healthy controls. In contrast to the published reports, to our knowledge we have shown for the [**first time serum proteomics profile of pre-diabetic children**](https://diabetes.diabetesjournals.org/content/64/6/2265), mapping the changes from early infancy, seroconversion and diagnosis. The main finding included lower and higher levels of APOC4 and AFAM in cases compared to controls respectively and, the combination of this two proteins classified T1D developing children from controls with 91% success rate with an area under the curve value of 0.85. Notably the levels of APOC4 were found to be lower even before seroconversion.\n\n![Top scoring pair analysis](fig/tsp.png)\n","srcMarkdownNoYaml":"\n\nType-1 diabetes (T1D) is an autoimmune disease that is characterized by the destruction of the insulin producing β cells in the Islets of Langerhans of the pancreas. Currently the measurement of autoantibodies (Aabs) like islet-cell autoantibodies, protein tyrosine phosphatase, glutamic acid decarboxylase, insulin and zinc transporter Slc30A8 protein indicates the manifestation of β cells autoimmunity and increased disease risk. However, the destruction of β cells usually starts early in life and symptoms appears when 90% of the cells are destroyed. The time period of appearance of first Aabs to the onset of the clinical disease can vary from 1 month to over 10 years, moreover, not all Aab positive subjects develop T1D. Thus additional indicators of early disease process and progression are needed. To identify disease associated changes, a careful selection of study group is essential such as **The Finnish Type-1 Diabetes Prediction and Prevention project [DIPP](https://dipp.fi/?page_id=5239&lang=en)** has initiated in 1994. The DIPP cohort has collected blood serum samples at 3 to 6 months intervals from children with a genetically conferred T1D risk and tested for T1D associated autoantibodies. **These longitudinal series of samples cover all the stages of disease progression from birth to clinical T1D and matching samples from carefully matched healthy children.**\n\nWe utilized such unique samples from the DIPP cohort to identify early serum protein biomarkers associated with T1D using quantitative mass spectrometry based approach. The study involved LC-MS/MS analysis with both iTRAQ and label-free quantification strategy on the immunodepleted serum.\n\nPrevious serum proteomics biomarker studies of T1D have typically compared disease end points with control groups, i.e. the differences between patients with T1D and healthy controls. In contrast to the published reports, to our knowledge we have shown for the [**first time serum proteomics profile of pre-diabetic children**](https://diabetes.diabetesjournals.org/content/64/6/2265), mapping the changes from early infancy, seroconversion and diagnosis. The main finding included lower and higher levels of APOC4 and AFAM in cases compared to controls respectively and, the combination of this two proteins classified T1D developing children from controls with 91% success rate with an area under the curve value of 0.85. 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The DIPP cohort has collected blood serum samples at 3 to 6 months intervals from children with a genetically conferred T1D risk and tested for T1D associated autoantibodies. **These longitudinal series of samples cover all the stages of disease progression from birth to clinical T1D and matching samples from carefully matched healthy children.**\n\nWe utilized such unique samples from the DIPP cohort to identify early serum protein biomarkers associated with T1D using quantitative mass spectrometry based approach. The study involved LC-MS/MS analysis with both iTRAQ and label-free quantification strategy on the immunodepleted serum.\n\nPrevious serum proteomics biomarker studies of T1D have typically compared disease end points with control groups, i.e. the differences between patients with T1D and healthy controls. In contrast to the published reports, to our knowledge we have shown for the [**first time serum proteomics profile of pre-diabetic children**](https://diabetes.diabetesjournals.org/content/64/6/2265), mapping the changes from early infancy, seroconversion and diagnosis. The main finding included lower and higher levels of APOC4 and AFAM in cases compared to controls respectively and, the combination of this two proteins classified T1D developing children from controls with 91% success rate with an area under the curve value of 0.85. Notably the levels of APOC4 were found to be lower even before seroconversion.\n\n![](fig/tsp.png)\n","srcMarkdownNoYaml":"\n\nType-1 diabetes (T1D) is an autoimmune disease that is characterized by the destruction of the insulin producing β cells in the Islets of Langerhans of the pancreas. 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The DIPP cohort has collected blood serum samples at 3 to 6 months intervals from children with a genetically conferred T1D risk and tested for T1D associated autoantibodies. **These longitudinal series of samples cover all the stages of disease progression from birth to clinical T1D and matching samples from carefully matched healthy children.**\n\nWe utilized such unique samples from the DIPP cohort to identify early serum protein biomarkers associated with T1D using quantitative mass spectrometry based approach. The study involved LC-MS/MS analysis with both iTRAQ and label-free quantification strategy on the immunodepleted serum.\n\nPrevious serum proteomics biomarker studies of T1D have typically compared disease end points with control groups, i.e. the differences between patients with T1D and healthy controls. In contrast to the published reports, to our knowledge we have shown for the [**first time serum proteomics profile of pre-diabetic children**](https://diabetes.diabetesjournals.org/content/64/6/2265), mapping the changes from early infancy, seroconversion and diagnosis. The main finding included lower and higher levels of APOC4 and AFAM in cases compared to controls respectively and, the combination of this two proteins classified T1D developing children from controls with 91% success rate with an area under the curve value of 0.85. 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cohort to identify early serum pro Previous serum proteomics biomarker studies of T1D have typically compared disease end points with control groups, i.e. the differences between patients with T1D and healthy controls. In contrast to the published reports, to our knowledge we have shown for the [**first time serum proteomics profile of pre-diabetic children**](https://diabetes.diabetesjournals.org/content/64/6/2265), mapping the changes from early infancy, seroconversion and diagnosis. The main finding included lower and higher levels of APOC4 and AFAM in cases compared to controls respectively and, the combination of this two proteins classified T1D developing children from controls with 91% success rate with an area under the curve value of 0.85. Notably the levels of APOC4 were found to be lower even before seroconversion. -![Top scoring pair analysis](fig/tsp.png) +![](fig/tsp.png) diff --git a/docs/blog/Serum-Proteomics-Pre-diabetic/index.html b/docs/blog/Serum-Proteomics-Pre-diabetic/index.html index ab4cce6..5f467f7 100644 --- a/docs/blog/Serum-Proteomics-Pre-diabetic/index.html +++ b/docs/blog/Serum-Proteomics-Pre-diabetic/index.html @@ -70,7 +70,7 @@ - +
@@ -134,10 +134,9 @@
- + -
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@@ -171,12 +170,7 @@

Serum Proteomics Pre diabetic

Type-1 diabetes (T1D) is an autoimmune disease that is characterized by the destruction of the insulin producing β cells in the Islets of Langerhans of the pancreas. Currently the measurement of autoantibodies (Aabs) like islet-cell autoantibodies, protein tyrosine phosphatase, glutamic acid decarboxylase, insulin and zinc transporter Slc30A8 protein indicates the manifestation of β cells autoimmunity and increased disease risk. However, the destruction of β cells usually starts early in life and symptoms appears when 90% of the cells are destroyed. The time period of appearance of first Aabs to the onset of the clinical disease can vary from 1 month to over 10 years, moreover, not all Aab positive subjects develop T1D. Thus additional indicators of early disease process and progression are needed. To identify disease associated changes, a careful selection of study group is essential such as The Finnish Type-1 Diabetes Prediction and Prevention project DIPP has initiated in 1994. The DIPP cohort has collected blood serum samples at 3 to 6 months intervals from children with a genetically conferred T1D risk and tested for T1D associated autoantibodies. These longitudinal series of samples cover all the stages of disease progression from birth to clinical T1D and matching samples from carefully matched healthy children.

We utilized such unique samples from the DIPP cohort to identify early serum protein biomarkers associated with T1D using quantitative mass spectrometry based approach. The study involved LC-MS/MS analysis with both iTRAQ and label-free quantification strategy on the immunodepleted serum.

Previous serum proteomics biomarker studies of T1D have typically compared disease end points with control groups, i.e. the differences between patients with T1D and healthy controls. In contrast to the published reports, to our knowledge we have shown for the first time serum proteomics profile of pre-diabetic children, mapping the changes from early infancy, seroconversion and diagnosis. The main finding included lower and higher levels of APOC4 and AFAM in cases compared to controls respectively and, the combination of this two proteins classified T1D developing children from controls with 91% success rate with an area under the curve value of 0.85. Notably the levels of APOC4 were found to be lower even before seroconversion.

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-
-

-
Top scoring pair analysis
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+

diff --git a/docs/blog/index.html b/docs/blog/index.html index 3ac3bf1..61d2dd7 100644 --- a/docs/blog/index.html +++ b/docs/blog/index.html @@ -311,7 +311,7 @@

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diff --git a/docs/search.json b/docs/search.json index 1b4e074..d15788c 100644 --- a/docs/search.json +++ b/docs/search.json @@ -11,7 +11,7 @@ "href": "blog/Serum-Proteomics-Pre-diabetic/index.html", "title": "Serum Proteomics Pre diabetic", "section": "", - "text": "Type-1 diabetes (T1D) is an autoimmune disease that is characterized by the destruction of the insulin producing β cells in the Islets of Langerhans of the pancreas. Currently the measurement of autoantibodies (Aabs) like islet-cell autoantibodies, protein tyrosine phosphatase, glutamic acid decarboxylase, insulin and zinc transporter Slc30A8 protein indicates the manifestation of β cells autoimmunity and increased disease risk. However, the destruction of β cells usually starts early in life and symptoms appears when 90% of the cells are destroyed. The time period of appearance of first Aabs to the onset of the clinical disease can vary from 1 month to over 10 years, moreover, not all Aab positive subjects develop T1D. Thus additional indicators of early disease process and progression are needed. To identify disease associated changes, a careful selection of study group is essential such as The Finnish Type-1 Diabetes Prediction and Prevention project DIPP has initiated in 1994. The DIPP cohort has collected blood serum samples at 3 to 6 months intervals from children with a genetically conferred T1D risk and tested for T1D associated autoantibodies. These longitudinal series of samples cover all the stages of disease progression from birth to clinical T1D and matching samples from carefully matched healthy children.\nWe utilized such unique samples from the DIPP cohort to identify early serum protein biomarkers associated with T1D using quantitative mass spectrometry based approach. The study involved LC-MS/MS analysis with both iTRAQ and label-free quantification strategy on the immunodepleted serum.\nPrevious serum proteomics biomarker studies of T1D have typically compared disease end points with control groups, i.e. the differences between patients with T1D and healthy controls. In contrast to the published reports, to our knowledge we have shown for the first time serum proteomics profile of pre-diabetic children, mapping the changes from early infancy, seroconversion and diagnosis. The main finding included lower and higher levels of APOC4 and AFAM in cases compared to controls respectively and, the combination of this two proteins classified T1D developing children from controls with 91% success rate with an area under the curve value of 0.85. Notably the levels of APOC4 were found to be lower even before seroconversion.\n\n\n\nTop scoring pair analysis" + "text": "Type-1 diabetes (T1D) is an autoimmune disease that is characterized by the destruction of the insulin producing β cells in the Islets of Langerhans of the pancreas. Currently the measurement of autoantibodies (Aabs) like islet-cell autoantibodies, protein tyrosine phosphatase, glutamic acid decarboxylase, insulin and zinc transporter Slc30A8 protein indicates the manifestation of β cells autoimmunity and increased disease risk. However, the destruction of β cells usually starts early in life and symptoms appears when 90% of the cells are destroyed. The time period of appearance of first Aabs to the onset of the clinical disease can vary from 1 month to over 10 years, moreover, not all Aab positive subjects develop T1D. Thus additional indicators of early disease process and progression are needed. To identify disease associated changes, a careful selection of study group is essential such as The Finnish Type-1 Diabetes Prediction and Prevention project DIPP has initiated in 1994. The DIPP cohort has collected blood serum samples at 3 to 6 months intervals from children with a genetically conferred T1D risk and tested for T1D associated autoantibodies. These longitudinal series of samples cover all the stages of disease progression from birth to clinical T1D and matching samples from carefully matched healthy children.\nWe utilized such unique samples from the DIPP cohort to identify early serum protein biomarkers associated with T1D using quantitative mass spectrometry based approach. The study involved LC-MS/MS analysis with both iTRAQ and label-free quantification strategy on the immunodepleted serum.\nPrevious serum proteomics biomarker studies of T1D have typically compared disease end points with control groups, i.e. the differences between patients with T1D and healthy controls. In contrast to the published reports, to our knowledge we have shown for the first time serum proteomics profile of pre-diabetic children, mapping the changes from early infancy, seroconversion and diagnosis. The main finding included lower and higher levels of APOC4 and AFAM in cases compared to controls respectively and, the combination of this two proteins classified T1D developing children from controls with 91% success rate with an area under the curve value of 0.85. Notably the levels of APOC4 were found to be lower even before seroconversion." }, { "objectID": "blog/Serum-Proteomics-Atherosclerosis/index.html",