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6,650 results for “pancreatitis”
An Intravenous Pancreatic Cancer Therapeutic: Characterization of CRISPR/Cas9n-modified Clostridium novyi-Non Toxic Supplementary Information Histology Slides Part 5
<p>H&E and Gram stained whole slide scans for blinded cohorts from publication titled ‘An Intravenous Pancreatic Cancer Therapeutic: Characterization of CRISPR/Cas9n-modified <em>Clostridium novyi-</em>Non Toxic’ published in PLOS One 2023.</p> <p>Excerpt from methods section of publication detailing acquisition of this data: "Formalin-fixed tissue samples were processed for paraffin embedding by the means of dehydration, clearing and paraffin infiltration (Lynx II Tissue Processor). The paraffin embedded tissue samples were sectioned using a Leica Rotatory Microtome RM2125 RTS at 5um thickness. Designated tissue sections were subsequently de-paraffined and stained with H&E and gram staining as per standard histology protocols (Leica Autostainer XL). Whole slide scanning (WSI) was performed by a Panoramic 250 whole slide scanner at 20x magnification (3D Histech) using a Carl-Zeiss Plan-Apochromat 20x / NA 0.8 objective."</p> <p>Please note when downloading the image files that the folder containing all of the .data files <strong>cannot</strong> contain the corresponding .mxrs file. The .mxrs and the folder containing the .data files <strong>must</strong> have identical names and be at the same file level (as uploaded). Files of this type can be opened by the open source software FIJI or QuPath, among others.</p> <p>Cohorts have been uploaded with viewers blinded to treatment groups to allow for unbiased review should it be desired, with a cohort key uploaded separately (doi: ##). Files are grouped so that all major organs from a single mouse are in the same compressed folder.</p>
An Intravenous Pancreatic Cancer Therapeutic: Characterization of CRISPR/Cas9n-modified Clostridium novyi-Non Toxic Supplementary Information Histology Slides Part 4
<p>H&E and Gram stained whole slide scans for blinded cohorts from publication titled ‘An Intravenous Pancreatic Cancer Therapeutic: Characterization of CRISPR/Cas9n-modified <em>Clostridium novyi-</em>Non Toxic’ published in PLOS One 2023.</p> <p>Excerpt from methods section of publication detailing acquisition of this data: "Formalin-fixed tissue samples were processed for paraffin embedding by the means of dehydration, clearing and paraffin infiltration (Lynx II Tissue Processor). The paraffin embedded tissue samples were sectioned using a Leica Rotatory Microtome RM2125 RTS at 5um thickness. Designated tissue sections were subsequently de-paraffined and stained with H&E and gram staining as per standard histology protocols (Leica Autostainer XL). Whole slide scanning (WSI) was performed by a Panoramic 250 whole slide scanner at 20x magnification (3D Histech) using a Carl-Zeiss Plan-Apochromat 20x / NA 0.8 objective."</p> <p>Please note when downloading the image files that the folder containing all of the .data files <strong>cannot</strong> contain the corresponding .mxrs file. The .mxrs and the folder containing the .data files <strong>must</strong> have identical names and be at the same file level (as uploaded). Files of this type can be opened by the open source software FIJI or QuPath, among others.</p> <p>Cohorts have been uploaded with viewers blinded to treatment groups to allow for unbiased review should it be desired, with a cohort key uploaded separately (doi: ##). Files are grouped so that all major organs from a single mouse are in the same compressed folder.</p>
Endoscopic Ultrasound-guided Ethanol Injection of Pancreatic Cystic Neoplasms
ClinicalTrials.gov study NCT02158039. IPD Sharing: UNDECIDED. Countries: 1. Publications: 1.
Study of Lanreotide Autogel 120 mg in Patients With Non-functioning Entero- Pancreatic Endocrine Tumour
ClinicalTrials.gov study NCT00842348. IPD Sharing: YES. Countries: 9. Publications: 2.
Study of Lanreotide Autogel in Non-functioning Entero-pancreatic Endocrine Tumours
ClinicalTrials.gov study NCT00353496. IPD Sharing: YES. Countries: 15. Publications: 3.
Study of Efficacy and Safety of NIS793 (With and Without Spartalizumab) in Combination With SOC Chemotherapy in First-line Metastatic Pancreatic Ductal Adenocarcinoma (mPDAC)
ClinicalTrials.gov study NCT04390763. IPD Sharing: YES. Countries: 14. Publications: 0.
A Study to Assess the Effectiveness and Safety of Irinotecan Liposome Injection, 5-fluorouracil/Leucovorin Plus Oxaliplatin in Patients Not Previously Treated for Metastatic Pancreatic Cancer, Compare
ClinicalTrials.gov study NCT04083235. IPD Sharing: YES. Countries: 18. Publications: 1.
The kinase ERK plays a conserved dominant role in the heterogeneity of epithelial-mesenchymal transition in pancreatic cancer cells
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Survival-associated cellular response maintained in pancreatic ductal adenocarcinoma (PDAC) switched between soft and stiff 3D microgel culture
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Baron2016 GSE84133 Pancreatic Islets Dataset for Besca
<p>The gene expression matrix was downloaded from GEO (<a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE84133">https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE84133</a>), originally published by Baron M, Veres A, Wolock SL, et al. A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure. <em>Cell Syst</em>. 2016;3(4):346-360.e4. doi:10.1016/j.cels.2016.08.011. We reprocessed the dataset using the Besca package (https://github.com/bedapub/besca).</p> <p> </p> <p> </p>
CTRC gene polymorphism (p.G60G, c.180) in acute pancreatitis
<p>The aim of the study was to determine the relationship between the presence of G60G polymorphism (c.180C>T; rs497078) <em>CTRC</em> and the incidence as well as the clinical course of acute pancreatitis (AP). The study included 299 patients with acute pancreatitis, inhabitants of the Kielce Region in Poland, who gave their informed consent for collecting genetic material. The control group consisted of 417 healthy inhabitants. </p>
Cadherin-11 deficiency-induced changes in pancreatic ductal adenocarcinoma
<p class="MsoNormal"><span>Pancreatic ductal adenocarcinoma (PDAC) is one of the top five deadliest forms of cancer with very few treatment options. The 5-year survival rate for PDAC is 10% following diagnosis. Cadherin 11 (Cdh11), a cell-to-cell adhesion molecule, has been suggested to promote tumor growth and immunosuppression in PDAC, and Cdh11 inhibition significantly extended survival in mice with PDAC. However, the mechanisms by which Cdh11 deficiency influences PDAC progression and anti-tumor immune responses have yet to be fully elucidated. To investigate <em>Cdh11</em>-deficiency induced changes in PDAC tumor microenvironment (TME), we crossed <em>p48-Cre; LSL-Kras<sup>G12D/+</sup>; LSL-Trp53<sup>R172H/+</sup></em> (KPC) mice with <em>Cdh11<sup>+/-</sup></em> mice and performed single-cell RNA sequencing (scRNA-seq) of the non-immune (CD45<sup>-</sup>) and immune (CD45<sup>+</sup>) compartment of KPC tumor-bearing <em>Cdh11</em> proficient (<em>KPC-Cdh11<sup>+/+</sup></em>) and <em>Cdh11</em> deficient (<em>KPC-Cdh11<sup>+/-</sup></em>) mice. Our analysis showed that <em>Cdh11</em> is expressed primarily in cancer-associated fibroblasts (CAFs) and at low levels in epithelial cells undergoing epithelial-to-mesenchymal transition (EMT). <em>Cdh11</em> deficiency altered the molecular profile of CAFs, leading to a decrease in the expression of myofibroblast markers such as <em>Acta2</em> and <em>Tagln</em> and cytokines such as <em>Il6</em>, <em>Il33</em> and Midkine<em> (Mdk)</em>. We also observed a significant decrease in the presence of monocytes/macrophages and neutrophils in <em>KPC-Cdh11<sup>+/-</sup></em> tumors while the proportion of T cells was increased. Additionally, myeloid lineage cells from <em>Cdh11</em>-deficient tumors had reduced expression of inflammatory cytokines that have previously been shown to play a role in immune suppression. In summary, our data suggests that <em>Cdh11</em> deficiency significantly alters</span> the fibroblast and immune microenvironments and contributes to the downregulation of inflammatory cytokines, leading to an increase in anti-tumor immunity and enhanced survival.</p>
Multiplexed imaging analysis of human pancreatic islets from donors with and without type 2 diabetes
<p>This record contains tabular data from traditional and multiplexed immunohistochemistry experiments presented in the manuscript <i>Genetic risk converges on regulatory networks mediating early type 2 diabetes</i> (<a href="https://doi.org/10.1038/s41586-023-06693-2">Walker, Saunders & Rai et al., <i>Nature</i> 2023</a>), a body of work that includes tissue imaging, <a href="https://theparkerlab.shinyapps.io/Islet-RNAseq-WGCNA/">sorted islet cell transcriptomics</a>, and islet functional analysis of donors with early-stage type 2 diabetes (T2D) and control donors. Images can be viewed interactively on Pancreatlas (RRID:SCR_018567): <a href="https://pancreatlas.org/datasets/904/explore">https://pancreatlas.org/datasets/904/explore</a>.</p><p>All immunohistochemistry was performed on lightly PFA-fixed human pancreatic tissue (sample characteristics available in Supplementary Table 1). For traditional immunohistochemistry, islets were imaged at 20× with 2× digital zoom using a FV3000 confocal laser scanning microscope (Olympus) or full cross-sections were scanned on a ScanScope FL (Leica/Aperio). Quantitative analysis was carried out using HALO™ (Indica Labs) or Metamorph (Molecular Devices) software. For multiplexed immunohistochemistry, images were acquired using the PhenoCycler (CODEX) Open system (Akoya Biosciences) integrated with a BZ-X810 epifluorescence microscope (Keyence) with a CFI plan Apo I 20x/0.75 objective (Nikon). Image alignment, stitching, background subtraction, and deconvolution were performed using the CODEX Processor v1.7.0.6 (Akoya Biosciences). Cell segmentation and cell type annotations were generated using the HALO HighPlex FL v3.2.1 module (Indica Labs). For cell neighborhood (CN) analysis, two methods were applied in parallel to CODEX data from annotated islets: a community detection method, termed <i>Dynamic CF-IDF</i>, and a <i>k</i>-means approach. Packages used for cell neighborhood analyses are published in <a href="http://github.com/liu-bioinfo-lab/Cellular-Neighborhood-Analysis">Github</a>.</p>
Multiplexed imaging mass cytometry analysis characterizes the vascular niche in pancreatic cancer
<p>All data supporting the publication: "Multiplexed imaging mass cytometry analysis characterizes the vascular niche in pancreatic cancer."</p><p>1. Fully_Processed_OME.TIFF: This folder contains the OME.TIFF files with all markers after compensation and hot pixel removal for visualization of the data. These can be opened with QuPath and other software. </p><p>2. PDAC_IMC_Seurat_FINAL.rds: Seurat object of all cells included in the analysis with cell type and neighborhood annotations, and unintegrated and rPCA-integrated UMAP reductions. </p><p>3. Raw_Data_TIFF_Files: All raw individual TIFF files from the image acquisition</p><p>4. ROI_Selection: Brightfield and IHC images of individual samples showing where the ROIs for each sample are collected </p><p>5. Segmentation_Files: All relevant segmentation files from Mesmer for nuclear and whole cell segmentation. </p><p>6. H&E Images for each case scanned at 40x </p>
Profiling of pancreatic adenocarcinoma using artificial intelligence-based integration of multi-omic and computational pathology features - Validation Data Sets
<p>Two public validation cohorts were utilized in the MT-Pilot study, the Cancer Genome Atlas (TCGA) and cohort-1 Johns Hopkins University (JHU). These datasets included DNA, RNA, clinical data, and tissue protein analytes analyzed for survival outcome prediction using AI/Machine Learning modeling. </p>
Generation of KRAS knockout pancreatic cancer cell line PANC1
<p>We used CRISPR to inactivate mutant KRAS and STAT3 in PANC1 (KRASG12D) pancreatic cancer cell line. Gene expression analysis of KRAS intact vs. knockout cells identified sets of genes involved in protein synthesis, cell differentiation, and metabolic processes, while the expression of MAPK/ERK target genes remained unperturbed.</p>
Transcriptomic profiles of resected 50 pancreatic adenocarcinoma samples
<p><span><span>An aggregated retrospective database with standardized clinicopathological variables was created for patients resected </span><span>in Erasme and Pitié Salpêtrière hospitals. </span>RNA was extracted from the scrapped sections with the ALLPrep FFPE tissue kit<sup>©</sup> following the manufacturer’s instructions for semi-automated RNA extraction via Qiacube instrument (Qiagen, Venlo, The Netherlands). RNA samples were run on an Agilent 2100 bioanalyzer using the RNA 6000 Pico LabChip kit (Agilent, Diegem, Belgium). The bioanalyzer electropherograms were analyzed by Agilent 2100 Expert Software to determine the RNA quantity and quality. RNA samples with DV200 >30% were selected and 100 ng of RNA was used for the library preparation. NGS libraries were prepared using the QuantSeq Library Prep Kit for Illumina (Lexogen) as per manufacturer recommendations’. The libraries were sequenced on NovaSeq using NovaSeq 6000 S2 Reagent Kit with 100 bp single reads.</span></p>
Promoter methylation leads to Hepatocyte Nuclear Factor 4A loss and pancreatic cancer aggressiveness.
<p><i>Efforts to decode pancreatic ductal adenocarcinoma (PDAC) heterogeneity and the consequent therapeutic selection remains a challenge. We aimed to characterize epigenetically regulated pathways involved in PDAC progression.</i></p><p><i>Global DNA methylation analysis in pancreatic cancer patient tissues and cell lines was performed to identify differentially methylated genes. Targeted bisulfite sequencing and in vitro methylation reporter assays were employed to investigate the direct link between sitespecific methylation and transcriptional regulation. A series of in vitro loss- and gain-of function studies, and in vivo xenograft and the KPC (LSL-KrasG12D/+; LSL-Trp53R172H/+; Pdx1-Cre) mouse models were used to assess pancreatic cancer cell properties. Gene and protein expression analyses were performed in three different cohorts of pancreatic cancer patients and correlated to clinicopathological parameters.</i></p><p><i>We identify Hepatocyte Nuclear Factor 4A (HNF4A) as a novel target of hypermethylation in pancreatic cancer and demonstrate that site-specific proximal promoter methylation drives HNF4A transcriptional repression. Expression analyses in patients, indicate the methylation-associated suppression of HNF4A expression in pancreatic cancer tissues. In vitro and in vivo studies reveal that HNF4A is a novel tumor suppressor in pancreatic cancer, regulating cancer growth and aggressiveness. As evidenced in both the KPC mouse model and human pancreatic cancer tissues, HNF4A expression declines significantly in the early stages of the disease. Most importantly, HNF4 loss correlates with poor overall patient survival.</i></p>
Raw data to: Biochemical Analyses of Cystatin-C Dimers and Cathepsin-B reveals a Trypsin-Driven Feedback Mechanism in Acute Pancreatitis
<p>This repository contains the initial structures, full conformational ensembles sampled using the TIGER2hPE replica-exchange MD simulation technique, and clusters resulting from subsequent ccPCA analysis, to extract major complex structures between proteins. Also attached are the initial structures of mCTSB and mCST3 predicted by AlphaFold2.</p> <table> <tbody> <tr> <td> <p><strong>Simulation Nr.</strong></p> </td> <td> <p><strong>Components simulated<br></strong></p> </td> </tr> <tr> <td> <p><strong>1</strong></p> </td> <td> <p>CTSB</p> </td> </tr> <tr> <td> <p><strong>2</strong></p> </td> <td> <p>CTSB</p> </td> </tr> <tr> <td> <p><strong>3</strong></p> </td> <td> <p>CTSB + mCST3</p> </td> </tr> <tr> <td> <p><strong>4</strong></p> </td> <td> <p>CTSL + mCST3</p> </td> </tr> <tr> <td> <p><strong>5</strong></p> </td> <td> <p>CTSB + mCST3-R71</p> </td> </tr> <tr> <td> <p><strong>6</strong></p> </td> <td> <p>CTSB + mCST3-R45</p> </td> </tr> <tr> <td> <p><strong>7</strong></p> </td> <td> <p>CTSB + dCST3-R45</p> </td> </tr> <tr> <td> <p><strong>8</strong></p> </td> <td> <p>CTSB + dCST3-R28</p> </td> </tr> </tbody> </table>
Metagenome-assembled genomes obtained from fecal and salivary microbiomes of pancreatic cancer patients and controls
<p>7,546 MAGs obtained from fecal and salivary metagenomes of pancreatic cancer patients and controls</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.