Results

PaperS7508

Estimating time since influenza virus exposure using single-cell proteomic data

Klodiana Rizzo Nervo, Neda Hajiakhoond Bidoki, Han Chen, Zainab Rahil, Zach Bjornson, Kenneth Kim, Bonnie Bock, Melton Affrime, Logan Bauerle, Pham Bao Tran Huynh, David Liebowitz, Sean Tucker, Pier Federico Gherardini, Garry P. Nolan, Nima Aghaeepour, David R. McIlwain. frontiersin.org. March 19, 2026.

Rizzo Nervo, Nolan and colleagues model influenza shedding and time since exposure in two controlled challenge datasets. Preinfection baselines and selected healthy cohorts constrain generalization. Several count, legend, validation-method and error-metric descriptions disagree; this is not a UAP-exposure study.

Article, figures and narrative supplements read
PaperS7701

A multi-omics spatial framework for host-microbiome dissection within the intestinal tissue microenvironment

Bokai Zhu, Yunhao Bai, Yao Yu Yeo, Xiaowei Lu, Xavier Rovira-Clavé, Han Chen, Jason Yeung, Dingani Nkosi, Jonathan Glickman, Antonio Delgado-Gonzalez, Georg K. Gerber, Mike Angelo, Alex K. Shalek, Garry P. Nolan, Sizun Jiang. pmc.ncbi.nlm.nih.gov. January 31, 2025.

This mouse-intestine study combines spatial imaging, gene-expression and glycan measurements to examine inflammation-associated patterns. Its many cells and regions come from eight main-cohort mice, and correlations do not establish microbial causation or clinical performance. Nolan is a corresponding author and joint supervisor. The reviewed scope is partial, with biological-validation sections and Methods excluded; public support and commercial disclosures do not establish a UAP programme or private approach.

Partial specialist XML; validation and Methods excluded
PaperS7570

MAPS: pathologist-level cell type annotation from tissue images through machine learning

Muhammad Shaban, Yunhao Bai, Huaying Qiu, Shulin Mao, Jason Yeung, Yao Yu Yeo, Vignesh Shanmugam, Han Chen, Bokai Zhu, Jason L Weirather, Garry P Nolan, Margaret A Shipp, Scott J Rodig, Sizun Jiang, Faisal Mahmood. ebi.ac.uk. January 2, 2024.

MAPS uses expert-labelled protein-expression data to classify cells. The authors report strong results within datasets, while acknowledging leakage risk from splitting one patient’s CODEX image by cells. Performance falls across cohorts and competing methods sometimes do better. Nolan is a coauthor and supervisor; disclosed commercial interests, reporting differences and missing original materials accompany the findings.

Complete supplied article and supplement text read; original and tiny-label gaps
PaperS7679

Integration of spatial and single-cell data across modalities with weakly linked features

Shuxiao Chen, Bokai Zhu, Sijia Huang, John W Hickey, Kevin Z Lin, Michael Snyder, William J Greenleaf, Garry P Nolan, Nancy R Zhang, Zongming Ma. ebi.ac.uk. September 7, 2023.

This Nolan-coauthored study introduces MaxFuse, a computational method for aligning cell measurements across weakly linked data types. Benchmarks report gains on selected datasets; inferred spatial gene activity is distinguished from measurements actually made in each cell. Reused cell batches and tuned comparisons limit broader conclusions. The article explicitly attributes FDA Medical Countermeasures Initiative contracts and NIH support to Nolan, without reporting a secret approach or classified UAP programme.

Complete supplied XML text; original figures and supplements 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
PaperS7696

Variation of Immune Cell Responses in Humans Reveals Sex-Specific Coordinated Signaling Across Cell Types

Gabriela K. Fragiadakis, Zachary B. Bjornson-Hooper, Deepthi Madhireddy, Karen Sachs, Han Chen, David R. McIlwain, Matthew H. Spitzer, Sean C. Bendall, Garry P. Nolan. pmc.ncbi.nlm.nih.gov. March 28, 2022.

This healthy-donor study describes correlated immune responses and sex-associated differences within one cohort. Its reported prediction tests use donors from that same cohort; clinical or causal conclusions are not established. Root reviewed results, discussion, captions and declarations, with the entire Methods section excluded. FDA contracts are acknowledged at work level without identifying Nolan as their individual recipient. Nolan advised and edited the study; these public acknowledgements do not establish a classified UAP approach.

Partial root supplied XML text; Methods excluded
PaperS7703

A Comprehensive Atlas of Immunological Differences Between Humans, Mice, and Non-Human Primates

Zachary B Bjornson-Hooper, Gabriela K Fragiadakis, Matthew H Spitzer, Han Chen, Deepthi Madhireddy, Kevin Hu, Kelly Lundsten, David R McIlwain, Garry P Nolan. pmc.ncbi.nlm.nih.gov. March 11, 2022.

This comparative immune atlas describes differences among sampled humans, mice and non-human primates. Mouse blood was pooled into six tubes, and the human dataset overlaps a companion study. Selected differences face antibody-affinity and unexplained denominator limits. Nolan advised the study and edited the manuscript. FDA/NIH support is acknowledged without identifying all individual award recipients; it does not establish a UAP programme or private approach. Review excludes operational biological sections, Discussion and Methods.

Partial specialist XML; operational sections and Methods excluded
PaperS7685

Subcellular localization of biomolecules and drug distribution by high-definition ion beam imaging

Xavier Rovira-Clavé, Sizun Jiang, Yunhao Bai, Bokai Zhu, Graham Barlow, Salil Bhate, Ahmet F Coskun, Guojun Han, Chin-Min Kimmy Ho, Chuck Hitzman, Shih-Yu Chen, Felice-Alessio Bava, Garry P Nolan. ebi.ac.uk. July 30, 2021.

This cultured-cell imaging study maps biomolecules and drug distribution at fine spatial scales, with limited skin-tissue validation. Small cell samples and nested voxels limit generalization; 33 fields/cells across treatment groups came from one experiment. The proposed nuclear-pore pumping mechanism is an interpretation, without a demonstrated causal intervention or clinical outcome. Acknowledged NIH, Army and foundation support does not establish a secret approach or UAP programme. Nolan is a corresponding author and joint supervisor. The paper declares no competing interests; native graphics, supplements and underlying data remain unreviewed.

Complete specialist supplied XML text; native graphics unreviewed
PaperS7550

Adjacent Cell Marker Lateral Spillover Compensation and Reinforcement for Multiplexed Images

Yunhao Bai, Bokai Zhu, Xavier Rovira-Clave, Han Chen, Maxim Markovic, Chi Ngai Chan, Tung-Hung Su, David R. McIlwain, Jacob D. Estes, Leeat Keren, Garry P. Nolan, Sizun Jiang. ebi.ac.uk. July 5, 2021.

REDSEA compensates signal leakage between adjacent segmented cells. Published tests compare correction choices against a fallible manual reference and reused imaging data. Retaining signal and removing ambiguous classifications involve tradeoffs; poor segmentation and several other contamination mechanisms remain unresolved. Source counts, caption panels, equation notation and channel lists conflict. Nolan’s declared instrument-company financial interest and funding disclaimer remain part of the evidence.

Supplied article and published supplements read
PaperS7627

Performance of BioFire array or QuickVue influenza A + B test versus a validation qPCR assay for detection of influenza A during a volunteer A/California/2009/H1N1 challenge study

David R McIlwain, Han Chen, Maria Apkarian, Melton Affrime, Bonnie Bock, Kenneth Kim, Nilanjan Mukherjee, Garry P Nolan, Monica M McNeal. ebi.ac.uk. February 25, 2021.

The authors compare BioFire and QuickVue tests with a study-specific qPCR comparator in selected influenza-challenge samples. Repeated matched swabs come from143 volunteers, and the two comparisons use different specimen sets. A linked correction changes the rapid-test table denominator from351 to299. These results do not establish performance in community infections, current product versions or UAP research.

Complete supplied main, correction, native tables and offered static figures
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
PaperS7610

Activation of JUN in fibroblasts promotes pro-fibrotic programme and modulates protective immunity

Lu Cui, Shih-Yu Chen, Tristan Lerbs, Jin-Wook Lee, Pablo Domizi, Sydney Gordon, Yong-hun Kim, Garry Nolan, Paola Betancur, Gerlinde Wernig. ebi.ac.uk. June 3, 2020.

The authors report JUN-associated changes in lung fibroblasts and test mechanisms and interventions in engineered cultures and mouse models. Eleven end-stage cases and three cancer-resection controls define the human comparison. Preclinical findings, sampling biases and explicit toxicity cautions prevent claims of proven treatment benefit or safety in patients.

Complete supplied main text; bounded supplemental visuals

A curated public selection. Source review describes what was read; it does not establish that a claim is true. Our research approach