BioParity.UFO / UAP research

64 papers for “Garry P. Nolan”

Results

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
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
PaperS7553

Strategies for Accurate Cell Type Identification in CODEX Multiplexed Imaging Data

John W. Hickey, Yuqi Tan, Garry P. Nolan, Yury Goltsev. ebi.ac.uk. August 13, 2021.

The study compares 20 cell-annotation pipelines using four healthy-colon tissue blocks from one donor. Agreement improves with broader labels, but both reference sets use the same images and one explicitly favors a pipeline being evaluated. The authors recommend checking expression patterns and image locations when assigning cell types. Marker counts, a worked F-score example and several caption or settings inconsistencies remain documented. These results do not establish universal clinical accuracy or a UAP connection.

Supplied text and scoped apparatus read
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
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
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
PaperS7617

ACE2 localizes to the respiratory cilia and is not increased by ACE inhibitors or ARBs

Ivan T. Lee et al.. ebi.ac.uk. October 28, 2020.

The authors localize ACE2 staining to respiratory cilia and compare receptor expression across medication groups. Small subgroups, treatment indication, age imbalance and retrospective confounding qualify the comparisons. Negative or nonsignificant results do not establish equivalence, infection protection or clinical benefit. The study reports localization and expression rather than a treatment trial.

Complete supplied main, figures and two supplements; peer review unreviewed
PaperS7625

Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma

Andrew L Ji, Adam J Rubin, Kim Thrane, Sizun Jiang, David L Reynolds, Robin M Meyers, Margaret G Guo, Benson M George, Annelie Mollbrink, Joseph Bergenstråhle, Ludvig Larsson, Yunhao Bai, Bokai Zhu, Aparna Bhaduri, Jordan M Meyers, Xavier Rovira-Clavé, S Tyler Hollmig, Sumaira Z Aasi, Garry P Nolan, Joakim Lundeberg, Paul A Khavari. ebi.ac.uk. July 23, 2020.

The authors combine sequencing and imaging to describe selected squamous-cancer tissue, including a tumour-specific keratinocyte population. Cells, spots and fields depend on small patient subsets. Predicted interactions and proximity do not establish causal immune suppression. A linked correction repairs duplicated and mislabeled figure material; its unchanged-conclusions statement is attributed to the authors.

Complete supplied main, correction, S5 cells and S3 signature cells; remaining gaps

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