{"apiVersion":"1","version":"sha256:faade27e0b75b2aca6311142ff65347b4dacc153e8d28cbdf0e8a237319331f9","data":{"id":"S7693","title":"A tissue atlas of ulcerative colitis revealing evidence of sex-dependent differences in disease-driving inflammatory cell types and resistance to TNF inhibitor therapy","authors":["Aaron T Mayer","Derek R Holman","Anav Sood","Utkarsh Tandon","Salil S Bhate","Sunil Bodapati","Graham L Barlow","Jeff Chang","Sarah Black","Erica C Crenshaw","Alexander N Koron","Sarah E Streett","Sanjiv S Gambhir","William J Sandborn","Brigid S Boland","Trevor Hastie","Robert Tibshirani","John T Chang","Garry P Nolan","Christian M Schürch","Stephan Rogalla"],"publishedDate":"2023-01-20","format":"Paper","url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC9858501/","summary":"This observational ulcerative-colitis atlas describes tissue organization in29patients and five controls. Cells and regions remain nested within individuals. Cross-sectional treatment and sex associations do not establish a resistance mechanism, and19-patient response prediction was unstable and nonsignificant. Nolan is a coauthor with published funding and commercial interests, not a corresponding author. These ordinary scientific attributions supply no classified approach or UAP programme evidence.","subjects":["Imaging","Research methods","Government research funding"],"people":["Garry Nolan"],"review":{"label":"Complete root supplied XML text; native apparatus unreviewed","scope":"Root read all83,735 supplied normalized XML characters in ten contiguous untruncated returns, including all four figure captions, declarations/methods and51reference entries. Whole final analytical REPORT/EVIDENCE also reviewed. Native graphic pixels/PDF layout, one supplementary PDF, individual-level metadata/charts, dataset/code/external protocols and cited originals unreviewed in this lane; earlier independent scopes retained.","gaps":["Four native figure pixels and original journal PDF/layout unviewed; complete caption reading is separate.","One distinct supplementary PDF is listed twice in supplied XML; supplementary methods, FiguresS1–S10,TablesS1–S4 and references were not retrieved/read. No individual-level supplementary metadata or private charts acquired.","Explorer dataset/platform, code, external protocols, cited original bodies and source assay raw data not acquired or audited here; older independently accepted article scopes preserved.","Current correction/version history not independently checked; January20 publication, January30 platform timestamp, receipt and 2022 received/accepted dates remain separate.","34individuals=29UC+five controls;42regions and1,710,973cells are dependent observations.15UC onTNFi/14not at biopsy; response modelling uses19patients(9responders/10nonresponders), not all29UC or all34individuals.","No longitudinal before/after biopsies in this study. Treated/untreated Mayo2 comparison and selection do not establish causal drug response or persistent within-patient niches; mechanistic claims are hypotheses.","Sex-related T-cell association uses one-sided tests and age/Mayo adjustment; treatment response difference missed significance(P<0.055). Residual confounding/behaviour and small cohort remain; no general sex-based clinical recommendation.","Nested patient leave-one-out, internal threshold selection and patient-level permutations address dependence; architecture/patch changes nevertheless yield unstable TNFi prediction. Highest AUROC significanceP0.13; figure4EpatientP0.26/patchP0.19. Internal benchmark performance is not independent clinical validation.","B-cell changes, innate-cell/contact changes and neutrophil-associated predictive signal include nulls. Lack of significance does not establish equivalence or absence of a biological effect.","Body14untreated patients versus figure2A11patients/15tissues remains a subset-description gap. Figure1 seven-color/five-marker wording, figure2G***P<0.01, figure3arrow panel references and severity misclassification wording retained, not silently repaired.","52measured biomarkers versus34clustering markers are distinct scopes;13manually curated cell types/10algorithmic neighbourhoods depend on segmentation, annotation and selected sections. Blinded functional gating is not proof all study stages were blinded.","Front contribution metadata gives Nolan broader roles than the final acknowledgement list; preserve both. He is coauthor, editing/funding recipient in the final list, not a named corresponding author.22NIH-grouped identifiers include IDIQ17X149 as printed; original awards/custody not verified.","Nolan Akoya equity/scientific-board and other EnableMedicine/commercial disclosures are article-time declarations. No current registry audit, proven bias, classified approach, secret programme or UAP patient finding follows."]},"familyId":"NOLAN-UC-TISSUE-ATLAS-2023-ADD1166","citationUrl":"https://bioparity.io/sources/S7693","citation":"Aaron T Mayer, Derek R Holman, Anav Sood, Utkarsh Tandon, Salil S Bhate, Sunil Bodapati, Graham L Barlow, Jeff Chang, Sarah Black, Erica C Crenshaw, Alexander N Koron, Sarah E Streett, Sanjiv S Gambhir, William J Sandborn, Brigid S Boland, Trevor Hastie, Robert Tibshirani, John T Chang, Garry P Nolan, Christian M Schürch, Stephan Rogalla. A tissue atlas of ulcerative colitis revealing evidence of sex-dependent differences in disease-driving inflammatory cell types and resistance to TNF inhibitor therapy. January 20, 2023. BioParity S7693. https://bioparity.io/sources/S7693"}}