Results

PaperS7482

The extra-islet pancreas supports autoimmunity in human type 1 diabetes

Graham L Barlow, Christian M Schürch, Salil S Bhate, Darci J Phillips, Arabella Young, Shen Dong, Hunter A Martinez, Gernot Kaber, Nadine Nagy, Sasvath Ramachandran, Janet Meng, Eva Korpos, Jeffrey A Bluestone, Garry P Nolan, Paul L Bollyky. ebi.ac.uk. April 15, 2025.

Barlow, Nolan and colleagues examine spatial immune patterns in a small diabetes donor study. The paper and its public reviews retain limits on selection, marker interpretation and causal inference; this is background biomedical research with no UAP-exposure cohort.

Paper text, figures and reviews read
PaperS7694

Multimodal and spatially resolved profiling identifies distinct patterns of T cell infiltration in nodal B cell lymphoma entities

Tobias Roider, Marc A Baertsch, Donnacha Fitzgerald, Harald Vöhringer, Berit J Brinkmann, Felix Czernilofsky, Mareike Knoll, Laura Llaó-Cid, Anna Mathioudaki, Bianca Faßbender, Maxime Herbon, Tobias Lautwein, Peter-Martin Bruch, Nora Liebers, Christian M Schürch, Verena Passerini, Marc Seifert, Alexander Brobeil, Gunhild Mechtersheimer, Carsten Müller-Tidow, Oliver Weigert, Martina Seiffert, Garry P Nolan, Wolfgang Huber, Sascha Dietrich. pmc.ncbi.nlm.nih.gov. February 20, 2024.

This lymphoma study maps T-cell composition across 101 lymph-node samples and imaging specimens from 19 patients. Cells, cores and repeated assays remain dependent. External cohorts associate signatures with survival, but thresholds are data-derived and endpoint wording conflicts remain. Spatial proximity and inferred trajectories do not establish mechanism or clinical accuracy. Nolan contributes resources, supervision and funding acquisition; commercial roles and research support do not establish a classified UAP approach.

Complete specialist supplied XML text; native apparatus unreviewed
PaperS7692

Organization of the human intestine at single-cell resolution

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. pmc.ncbi.nlm.nih.gov. July 19, 2023.

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.

Complete specialist supplied XML text; native apparatus unreviewed
PaperS7683

Expanded vacuum-stable gels for multiplexed high-resolution spatial histopathology

Yunhao Bai, Bokai Zhu, John-Paul Oliveria, Bryan J. Cannon, Dorien Feyaerts, Marc Bosse, Kausalia Vijayaragavan, Noah F. Greenwald, Darci Phillips, Christian M. Schürch, Samuel M. Naik, Edward A. Ganio, Brice Gaudilliere, Scott J. Rodig, Michael B. Miller, Michael Angelo, Sean C. Bendall, Xavier Rovira-Clavé, Garry P. Nolan, Sizun Jiang. pmc.ncbi.nlm.nih.gov. July 7, 2023.

This proof-of-concept study introduces ExPRESSO for higher-resolution imaging of archived tissue on existing mass-spectrometry platforms. The reported lateral enlargement is about 3.7-fold, with axial compression, edge distortion and marker-specific signal limits. Alzheimer’s examples use six individuals, not hundreds of patients; vessel counts and image fields are nested observations. Nolan’s disclosed FDA funding and instrument-company interests are explicit. The study does not report UAP patients, a secret government approach or a clinical diagnostic trial.

Complete supplied XML text; original figures and supplements unreviewed
PaperS7693

A tissue atlas of ulcerative colitis revealing evidence of sex-dependent differences in disease-driving inflammatory cell types and resistance to TNF inhibitor therapy

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. pmc.ncbi.nlm.nih.gov. January 20, 2023.

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.

Complete root supplied XML text; native apparatus unreviewed
PaperS7555

CellSeg: a robust, pre-trained nucleus segmentation and pixel quantification software for highly multiplexed fluorescence images

Michael Y. Lee, Jacob S. Bedia, Salil S. Bhate, Graham L. Barlow, Darci Phillips, Wendy J. Fantl, Garry P. Nolan, Christian M. Schürch. ebi.ac.uk. January 18, 2022.

CellSeg combines a pretrained nucleus-segmentation model with image scaling, stitching, mask expansion and pixel statistics. Historical benchmark scores and representative tissue examples have different provenance and settings; densely packed tissue remains difficult. A colorectal comparison reuses 140 samples from 35 people and provides author-described gating and correlation. Correlation does not establish exhaustive cell truth or universal clinical accuracy. Source-native metric definitions, count conflicts and caption errors are preserved.

Supplied text and six figures read
PaperS7688

Immune cell topography predicts response to PD-1 blockade in cutaneous T cell lymphoma

Darci Phillips, Magdalena Matusiak, Belén Rivero Gutierrez, Salil S Bhate, Graham L Barlow, Sizun Jiang, Janos Demeter, Kimberly S Smythe, Robert H Pierce, Steven P Fling, Nirasha Ramchurren, Martin A Cheever, Yury Goltsev, Robert B West, Michael S Khodadoust, Youn H Kim, Christian M Schürch, Garry P Nolan. ebi.ac.uk. November 18, 2021.

This observational tissue analysis links immune-cell topography to pembrolizumab response in14selected lymphoma patients from an earlier24-patient trial. Seventy regions and large cell counts remain nested within those patients. Assay validation and resampling reuse the same cohort, without an independent clinical test. Several abundance and signature measures were null; the proposed chemokine mechanism is not causally demonstrated. Nolan is a corresponding coauthor/joint supervisor. Published government grants and commercial/patent disclosures remain attributed, without establishing a classified approach or UAP programme.

Complete specialist supplied XML text; native graphics unreviewed
PaperS7677

Virtual and augmented reality for biomedical applications

Mythreye Venkatesan, Harini Mohan, Justin R Ryan, Christian M Schürch, Garry P Nolan, David H Frakes, Ahmet F Coskun. ebi.ac.uk. July 2021.

This Nolan-coauthored review surveys biomedical virtual and augmented reality and presents illustrative case studies. It retains practical limitations: some training performs worse than hands-on instruction, a surgical comparison found no significant improvement in several broader outcomes, and image quality, tracking, cost, privacy and discomfort constrain use. Demonstrations and reported funding are distinct from proven clinical benefit or classified UAP access.

Complete supplied XML text; original figures and supplements unreviewed
PaperS7561

Highly Multiplexed Phenotyping of Immunoregulatory Proteins in the Tumor Microenvironment by CODEX Tissue Imaging

Darci Phillips, Christian M Schürch, Michael S Khodadoust, Youn H Kim, Garry P Nolan, Sizun Jiang. ebi.ac.uk. May 19, 2021.

The authors develop a multiplexed imaging panel using eight previously treated tumor specimens. The 25,456 analyzed cells are nested within eight sampled cores, rather than independent patients. Cell types combine clustering with manual refinement; spatial marker patterns do not establish functional causation or clinical treatment prediction. Nolan supervised and revised the study, while Jiang is corresponding author. Channel labels, figure pointers and plotted units remain inconsistent in the supplied source.

Complete supplied text and received apparatus read
PaperS7560

Highly multiplexed tissue imaging using repeated oligonucleotide exchange reaction

Julia Kennedy‐Darling, Salil S Bhate, John W Hickey, Sarah Black, Graham L Barlow, Gustavo Vazquez, Vishal G Venkataraaman, Nikolay Samusik, Yury Goltsev, Christian M Schürch, Garry P Nolan. ebi.ac.uk. March 10, 2021.

The authors demonstrate repeated three-color imaging of DNA-tagged antibodies on five human tissue sections from five donors. Millions of segmented cells do not become independent human subjects. Barcode and repeated-cycle validation experiments each have one experimental replicate. Cell-type assignment and spatial associations depend on segmentation, markers and manual annotation. Barcode counts, omitted sequences, reagent labels, geometry and timing remain inconsistent in the supplied material. Nolan is a cosenior and corresponding coauthor.

Complete supplied text and received apparatus read
PaperS7620

Nanoscopic subcellular imaging enabled by ion beam tomography

Ahmet F Coskun, Guojun Han, Shambavi Ganesh, Shih-Yu Chen, Xavier Rovira Clavé, Stefan Harmsen, Sizun Jiang, Christian M Schürch, Yunhao Bai, Chuck Hitzman, Garry P Nolan. ebi.ac.uk. February 4, 2021.

The authors demonstrate destructive ion-beam imaging and computational reconstruction in fixed cells and selected tissue. Calibration resolution, localization precision and theoretical capability remain distinct. Nested depth slices and reconstruction-derived ground truth limit independence. The method is a research demonstration, with no clinical efficacy or UAP finding established.

Complete supplied main, mathematics and figures; supplements unreceived
PaperS7624

Coordinated Cellular Neighborhoods Orchestrate Antitumoral Immunity at the Colorectal Cancer Invasive Front

Christian M Schürch, Salil S Bhate, Graham L Barlow, Darci J Phillips, Luca Noti, Inti Zlobec, Pauline Chu, Sarah Black, Janos Demeter, David R McIlwain, Shigemi Kinoshita, Nikolay Samusik, Yury Goltsev, Garry P Nolan. ebi.ac.uk. September 3, 2020.

The authors analyze spatial immune patterns in selected colorectal-cancer tissue. Thirty-five patients supply140 dependent tissue cores; repeated cells, regions and holdouts do not create new cohorts. Survival findings and correlation-based “communication” are exploratory. A linked correction adds Shigemi Kinoshita to the author list. No clinical efficacy or UAP finding is established.

Complete supplied main, figures and correction; bounded supplementary review

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