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1,637 results for “Colitis”
Labeled Images for Ulcerative Colitis (LIMUC) Dataset
<h1><strong>Dataset Details</strong></h1> <p>The LIMUC dataset compromises 11276 images from 564 patients and 1043 colonoscopy procedures, who underwent colonoscopy for ulcerative colitis between December 2011 and July 2019 at the Department of Gastroenterology in Marmara University School of Medicine. Two experienced gastroenterologists blindly reviewed and classified all images according to the Mayo endoscopic score (MES). Images that were differently labeled by two reviewers were also labeled by a third experienced reviewer independently without seeing their previous labels. The final MES for differently labeled images was determined using majority voting.</p> <p><br><strong>Mayo 0:</strong> 6105 (54.14%)<br><strong>Mayo 1:</strong> 3052 (27.70%)<br><strong>Mayo 2:</strong> 1254 (11.12%)<br><strong>Mayo 3:</strong> 865 (7.67%)</p> <p><strong>patient_based_classified_images:</strong> Images of each patient are separated according to Mayo classes. If a train-val-test splitting is to be made according to the ratios desired by the user, this folder should be used.</p> <p><strong>train_and_validation_sets:</strong> Train and validation sets used in the <a href="https://academic.oup.com/ibdjournal/advance-article-abstract/doi/10.1093/ibd/izac226/6830946">research paper</a>. Using the scripts in dataset's GitHub repository, same 10-fold can be generated for replicating the results.</p> <p><strong>test_set:</strong> Test set used for performance measurement in the research paper. For a fair performance comparisons, this should be used to report performances.</p> <h1><strong>Suggested Metrics</strong></h1> <p>Since there are imbalances and ordinality among classes (Mayo-0, Mayo-1, Mayo-2, Mayo-3), quadratic weighted kappa (QWK) can be used as the main performance metric. The QWK is one of the commonly used statistics for the assessment of agreement on an ordinal scale and it is one of the best singular performance metrics for this problem regarding class imbalances. Mean absolute error (MAE), macro F1 score, or macro accuracy can be used as alternative performance metrics.</p> <h1><strong>LIMUC Code Repository</strong></h1> <p>Many scripts for preprocessing, splitting, training, and validating the dataset are provided in <a href="https://github.com/GorkemP/labeled-images-for-ulcerative-colitis">this</a> GitHub repository.</p> <h1><strong>Terms and Conditions</strong></h1> <p>The LIMUC dataset is licensed under the <strong>Creative Commons Attribution 4.0 International (CC BY 4.0)</strong> license. This license permits unrestricted use, distribution, and reproduction in any medium, provided that proper attribution is given to the original creators. This ensures that the dataset can be used for both <strong>research and commercial applications</strong> while maintaining transparency and acknowledgment of the contributors.</p> <p>For more details about the license, please refer to: <a>Creative Commons Attribution 4.0 International License</a>.</p> <p>Regarding the questions, please contact <em><strong>polatgorkem@gmail.com.</strong></em></p>
Postmarketing Vedolizumab Milk-Only Lactation Study in Lactating Women With Active Ulcerative Colitis or Crohn's Disease
ClinicalTrials.gov study NCT02559713. IPD Sharing: YES. Countries: 1. Publications: 1.
Special Drug-Use Surveillance Study on Vedolizumab for IV Infusion 300 mg [Ulcerative Colitis]
ClinicalTrials.gov study NCT03824561. IPD Sharing: YES. Countries: 1. Publications: 1.
Efficacy and Safety of Vedolizumab Subcutaneously (SC) as Maintenance Therapy in Ulcerative Colitis
ClinicalTrials.gov study NCT02611830. IPD Sharing: YES. Countries: 31. Publications: 3.
A Study to Evaluate the Safety and Efficacy of Upadacitinib (ABT-494) for Induction and Maintenance Therapy in Participants With Moderately to Severely Active Ulcerative Colitis (UC)
ClinicalTrials.gov study NCT02819635. IPD Sharing: YES. Countries: 46. Publications: 13.
A Study of Long-term Effects of Vedolizumab Subcutaneous in Adults With Ulcerative Colitis and Crohn's Disease
ClinicalTrials.gov study NCT02620046. IPD Sharing: YES. Countries: 33. Publications: 1.
An Open-label Study of Vedolizumab (MLN0002) in Participants With Ulcerative Colitis and Crohn's Disease
ClinicalTrials.gov study NCT00790933. IPD Sharing: YES. Countries: 10. Publications: 6.
Extended Access Program of Vedolizumab IV in Ulcerative Colitis and Crohn's Disease
ClinicalTrials.gov study NCT02743806. IPD Sharing: YES. Countries: 18. Publications: 1.
A Study of the Efficacy and Safety of Upadacitinib (ABT-494) in Participants With Moderately to Severely Active Ulcerative Colitis
ClinicalTrials.gov study NCT03653026. IPD Sharing: YES. Countries: 44. Publications: 9.
Safety and Efficacy of MMX Mesalamine/Mesalazine in Pediatric Subjects With Mild to Moderate Ulcerative Colitis
ClinicalTrials.gov study NCT02093663. IPD Sharing: YES. Countries: 7. Publications: 1.
Ability to Maintain or Achieve Clinical and Endoscopic Remission With MMX Mesalamine Once Daily in Adults With Ulcerative Colitis
ClinicalTrials.gov study NCT01124149. IPD Sharing: YES. Countries: 15. Publications: 3.
Effect of Probiotic Supplementation on the Immune System in Patients With Ulcerative Colitis in Amman, Jordan
ClinicalTrials.gov study NCT04223479. IPD Sharing: NO. Countries: 1. Publications: 14.
Vedolizumab Intravenous (IV) Dose Optimization in Ulcerative Colitis
ClinicalTrials.gov study NCT03029143. IPD Sharing: YES. Countries: 2. Publications: 1.
A Study to Observe Vedolizumab and Anti-tumour Necrosis Factors (Anti-TNFs) Outcomes in Real-world Biologic Ulcerative Colitis (UC) and Crohn's Disease (CD) Participants
ClinicalTrials.gov study NCT03710486. IPD Sharing: YES. Countries: 2. Publications: 1.
Computational IHC-H&E mapping in mouse models of colitis (IHC WSIs from paired H&E-IHC WSIs, Part 1/2)
Open the record for dataset details and reuse information.
Computational IHC-H&E mapping in mouse models of colitis (H&E WSIs from paired H&E-IHC WSIs)
Open the record for dataset details and reuse information.
Computational IHC-H&E mapping in mouse models of colitis (IHC WSIs from paired H&E-IHC WSIs, Part 2/2)
Open the record for dataset details and reuse information.
Dataset related to article "Neutrophils mediate protection in colitis and carcinogenesis by controlling bacterial invasion and IL-22 production by gdT cells"
<p>This record contains raw data related to article "<strong>Neutrophils mediate protection in colitis and carcinogenesis by controlling bacterial invasion and IL-22 production by gd T cells"</strong></p><p>Abstract</p><p>Neutrophils are the most abundant leukocytes in human blood and play a primary role in resistance against invading microorganisms and in the acute inflammatory response. However, their role in colitis and colitis-associated colorectal cancer is still under debate. Therefore, this study aims to dissect the role of neutrophils in these pathological contexts by using a rigorous genetic approach. Neutrophil-deficient mice (Csf3r-/- mice) were challenged with classic models of colitis and colitis-associated colorectal cancer and the role of neutrophils was assessed by histological, cellular and molecular analyses coupled with adoptive cell transfer and correlative analyses using human datasets. Csf3r-/- mice showed increased susceptibility to colitis and colitis-associated colorectal cancer compared to control Csf3r+/+ mice and adoptive transfer of neutrophils in Csf3r-/- mice reverted the phenotype. In colitis, Csf3r-/- mice showed increased bacterial invasion and reduced number of healing ulcers in the colon, indicating compromised regenerative capacity of epithelial cells. Neutrophils were essential for T cell polarization and IL-22 production. In patients with ulcerative colitis, the expression of CSF3R was positively correlated with IL-22 and IL-23 expression. Moreover, gene signatures associated with epithelial cell development, proliferation and antimicrobial response were enriched in CSF3Rhigh patients. Our data support a model where neutrophils mediate protection against intestinal inflammation and colitis-associated colorectal cancer by controlling the intestinal microbiota and driving the activation of an IL-22-dependent tissue repair pathway.</p><p> </p>
Charting the cellular biogeography in colitis reveals fibroblast trajectories and coordinated spatial remodeling
<p>Scripts associated with the analysis and plotting of data for the Cell paper: Charting the cellular biogeography in colitis reveals fibroblast trajectories and coordinated spatial remodeling</p>
A Spatial Multi-Modal Dissection of Host-Microbiome Interactions within the Colitis Tissue Microenvironment
<p>All processed data used in the manuscript 'A Spatial Multi-Modal Dissection of Host-Microbiome Interactions within the Colitis Tissue Microenvironment'. For more detail please refer to the manuscript. If there is any question please contact Bokai Zhu via email: BZHU0@MGH.HARVARD.EDU.</p> <p>Data folder structure:</p> <p>Main data (eg. presented in main figures etc): Please see .zip file 'data_submission.zip'.</p> <p>Additional data (eg. during revision, or other misc files): Please see .zip file 'data_submission_part2.zip'.</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
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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
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