{"apiVersion":"1","version":"sha256:faade27e0b75b2aca6311142ff65347b4dacc153e8d28cbdf0e8a237319331f9","data":{"id":"S7692","title":"Organization of the human intestine at single-cell resolution","authors":["John W. Hickey","Winston R. Becker","Stephanie A. Nevins","Aaron Horning","Almudena Espin Perez","Chenchen Zhu","Bokai Zhu","Bei Wei","Roxanne Chiu","Derek C. Chen","Daniel L. Cotter","Edward D. Esplin","Annika K. Weimer","Chiara Caraccio","Vishal Venkataraaman","Christian M. Schürch","Sarah Black","Maria Brbić","Kaidi Cao","Shuxiao Chen","Weiruo Zhang","Emma Monte","Nancy R. Zhang","Zongming Ma","Jure Leskovec","Zhengyan Zhang","Shin Lin","Teri Longacre","Sylvia K. Plevritis","Yiing Lin","Garry P. Nolan","William J. Greenleaf","Michael Snyder"],"publishedDate":"2023-07-19","format":"Paper","url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10356619/","summary":"This healthy-adult intestine atlas describes regional tissue composition and spatial organization in nine donors. Millions of cells and regional sections remain nested within donors. Predicted signalling and regulatory associations are hypotheses; subset validation overlaps one donor and does not establish a clinical or causal mechanism. Nolan is a corresponding coauthor and supervisor. Published funding and commercial disclosures provide ordinary research context, without establishing a classified approach or UAP programme.","subjects":["Imaging","Research methods","Government research funding"],"people":["Garry Nolan"],"review":{"label":"Complete specialist supplied XML text; native apparatus unreviewed","scope":"Specialist read all158,493 supplied XML characters in18 contiguous untruncated returns, including six main/ten extended figure captions and94references. Root reviewed entire final analytical packet, not full primary text or pixels. Native graphics/PDF, supplements, source data, code, datasets, reviewer files, cited bodies and current publisher correction history unreviewed in this lane.","gaps":["16 graphic hrefs supplied without pixels; native journal layout/PDF unreceived and unread","SupplementaryDiscussion,ReportingSummary,12SupplementaryFigures,Tables1–10 and PeerReviewFile described or linked, not file bodies reviewed","Donor-specific supplementary metadata not acquired; no private charts/records","SourceDataFigs4–6 linked, not received numeric source tables","HuBMAP HBM692.JRZB.356,10.35079/HBM692.JRZB.356,Dryad and dbGaP phs002272.v1.p1 availability statements read; datasets not downloaded or audited","GitHub links indexed only; code not acquired/run","94 bibliographic entries read; cited originals not retrieved/read by this lane; embedded SARS-related citation not opened","No complete publisher correction/version-history audit; suppliedPMC.1 and ingestiontimestamps not proof of final unchangedpublishedversion","No fullNolancorpus/image/AV or wholeprogrammecompletion claim","Nine adult donors, six male/three female and two reported ancestry groups, limit generalization; children absent and sex differences underpowered. Main imaging eight donors/64sections/2.7million cells; usually one sample per donor region. Cells and sections do not increase donor n.","BMI and hypertension comparisons use small observational donor groups. Regional proportions, normalized density and repeated regions do not establish cause, prognosis or disease-outcome validation.","18/20/22 neighbourhood count scopes and four-donor array sentence versus expanded eight-donor imaging remain explicit. Do not silently harmonize assay-specific counts or compartment denominators.","Cartography B004/B008/B009 overlaps one donor with the initial four-donor prediction cohort. Only58of152predictions are matchable; nine successes are labelled15.3% in body and15.5% in methods.94unmatchable are not94demonstrated failures; no claim all48pairs validated.","MaxFuse92.1% is assigned-cell-type concordance, not exact same-cell measurement or diagnostic accuracy. STELLAR and segmentation checks are within-study annotation apparatus, not a prospective external clinical test.","61regulatory candidates/48repeat criteria and pseudotime/GWAS enrichments are associations, not perturbation, longitudinal lineage, patient diagnosis or gene causation. MUC5B one-sample contamination/rare-cell ambiguity retained; significance correction varies by test.","Nolan is corresponding coauthor/study supervisor, not specifically a named manuscript/figure writer. Work-level NIH/CRUK/Parker/Hope support is not every grant assigned to Nolan. Nevins training identifier remains verbatim5 T32 000044; original award agreements unreviewed.","Nolan declares Pfizer/Vaxart/Celgene/Juno research grants and Akoya equity/advisory role; other authors declare EnableMedicine,10X,Protillion and other interests. These are article-time disclosures, not current registries, proven bias or clandestine work."]},"familyId":"NOLAN-HUMAN-INTESTINE-ATLAS-2023-05915-X","citationUrl":"https://bioparity.io/sources/S7692","citation":"John W. Hickey, Winston R. Becker, Stephanie A. Nevins, Aaron Horning, Almudena Espin Perez, Chenchen Zhu, Bokai Zhu, Bei Wei, Roxanne Chiu, Derek C. Chen, Daniel L. Cotter, Edward D. Esplin, Annika K. Weimer, Chiara Caraccio, Vishal Venkataraaman, Christian M. Schürch, Sarah Black, Maria Brbić, Kaidi Cao, Shuxiao Chen, Weiruo Zhang, Emma Monte, Nancy R. Zhang, Zongming Ma, Jure Leskovec, Zhengyan Zhang, Shin Lin, Teri Longacre, Sylvia K. Plevritis, Yiing Lin, Garry P. Nolan, William J. Greenleaf, Michael Snyder. Organization of the human intestine at single-cell resolution. July 19, 2023. BioParity S7692. https://bioparity.io/sources/S7692"}}