14 sources for “Scientific background”

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PaperS7524

Single-cell spatial pharmacobiology identifies conserved stromal barriers to therapeutic antibody delivery in human solid tumors

Guolan Lu, John W Hickey, Maximilian Haist, Xulei Qin, Emily Zhao, Abdullah Naveed, Erna Forgo, Marc-A Baertsch, Lucas Mani, Xavier Rovira-Clavé, Andrey Finegersh, Yury Goltsev, Chiara Caraccio, Nynke S van den Berg, Marisa Hom, Deana R Colburg, Brock A Martin, Christina S Kong, Natalie S Lui, George A Fisher, A Dimitrios Colevas, Robert B West, Greg M Thurber, George A Poultsides, Garry P Nolan, Eben L Rosenthal. ebi.ac.uk. June 3, 2026.

An exploratory oncology study examines antibody distribution and tissue organization in small, nested patient cohorts. Several nominal associations weaken after statistical correction or patient sensitivity checks. Alternate measurement on the same tissues adds a different method, without independent patient replication or proven clinical benefit.

Supplied manuscript, figures and supplement read

PaperS7568

SPACEc: a streamlined, interactive Python workflow for multiplexed image processing and analysis

Yuqi Tan, Tim N Kempchen, Martin Becker, Maximilian Haist, Dorien Feyaerts, Jiaqi Liu, Marieta Toma, Yang Xiao, Graham Su, Andrew J Rech, Michael Hölzel, Rong Fan, John W Hickey, Garry P Nolan. ebi.ac.uk. November 27, 2025.

SPACEc combines spatial proteomics processing, cell annotation and neighbourhood analysis. Nolan is credited with supervision. The supplied article, static supplement and reporting form were reviewed; peer-review correspondence is partly read. Reused tissues, expert labels and nested cell counts limit independent replication. Computational comparisons depend on dataset, platform, normalization and metric definitions; funding does not establish a UAP programme.

Complete supplied main and static supplement text read; peer review partial

PaperS7526

Graph Fourier transform for spatial omics representation and analyses of complex organs

Yuzhou Chang, Jixin Liu, Yi Jiang, Anjun Ma, Yao Yu Yeo, Qi Guo, Megan McNutt, Jordan E Krull, Scott J Rodig, Dan H Barouch, Garry P Nolan, Dong Xu, Sizun Jiang, Zihai Li, Bingqiang Liu, Qin Ma. ebi.ac.uk. August 29, 2024.

SpaGFT represents spatial data using graph topology and low-frequency assumptions. Benchmarks vary by dataset, and some methods perform better in particular examples. Selected marker references, repeated tissue regions and alternate analysis methods do not independently establish biological causation or patient replication.

Main text and selected supporting materials read

PaperS7520

Highly multiplexed spatial profiling with CODEX: bioinformatic analysis and application in human disease

Wilson Kuswanto, Garry Nolan, Guolan Lu. ebi.ac.uk. November 21, 2022.

This narrative review explains CODEX tissue imaging, processing limitations and spatial analysis. Its disease examples summarize cited studies; they do not supply a new patient cohort or independent replication. The review calls for stronger causal and prospective validation.

Supplied review text and qualified figures 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

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

PaperS7564

Functional comparison of PBMCs isolated by Cell Preparation Tubes (CPT) vs. Lymphoprep Tubes

Han Chen, Christian M Schürch, Kevin Noble, Kenneth Kim, Peter O Krutzik, Erika O’Donnell, Jason Vander Tuig, Garry P Nolan, David R McIlwain. ebi.ac.uk. March 30, 2020.

A paired laboratory comparison uses three donors, three operators and eighteen processing aliquots to compare CPT and Lymphoprep methods. Differences in collection and centrifugation form part of the method packages. Nonsignificant results do not establish equivalence. Tables contain endpoint exceptions to broad conclusions, and figure captions and antibody lists conflict. Nolan contributed design, analysis and writing; commercial affiliations and funding are specifically attributed.

Complete supplied main and static supplement fields read

PaperS7562

MIBI-TOF: A multiplexed imaging platform relates cellular phenotypes and tissue structure

Leeat Keren, Marc Bosse, Steve Thompson, Tyler Risom, Kausalia Vijayaragavan, Erin McCaffrey, Diana Marquez, Roshan Angoshtari, Noah F. Greenwald, Harris Fienberg, Jennifer Wang, Neeraja Kambham, David Kirkwood, Garry Nolan, Thomas J. Montine, Stephen J. Galli, Robert West, Sean C. Bendall, Michael Angelo. ebi.ac.uk. October 9, 2019.

The authors describe a multiplexed tissue-imaging instrument and its performance under specific settings. The main tumor demonstration uses one patient, eight regions and 11,120 nested cells; a 41-patient comparison reuses earlier work. Static spatial patterns do not establish causal immune recruitment or clinical prediction. Nolan supported the work and held patent and shareholder interests. Sensitivity, depth counts, figure settings and panel recipes contain unresolved inconsistencies.

Complete supplied text and defined static apparatus read

PaperS7565

Role for polo-like kinase 4 in mediation of cytokinesis

Michael F Press, Bin Xie, Simon Davenport, Yu Zhou, Roberta Guzman, Garry P Nolan, Neil O’Brien, Michael Palazzolo, Tak W Mak, Joan S Brugge, Dennis J Slamon. ebi.ac.uk. May 16, 2019.

A cell-line study examines PLK4 localization and cytokinesis through antibody, genetic and inhibitor assays. The cleavage mechanism and cellular inhibitor specificity remain uncertain. Figure captions, sample panels and starting-cell counts conflict, while some replicate and animal-method details are missing. Nolan contributed reagents and analytic tools. Funding, intellectual property and commercial disclosures are specifically attributed.

Complete supplied main and static appendix read; movies unviewed

PodcastS7521

#1203 - Eric Weinstein

Joe Rogan, Eric Weinstein. podscripts.co. November 15, 2018.

Weinstein discusses geometry, institutional experiences and biological analogies. Portal language is mathematical or fictional; Rogan explicitly describes geometric entities as hallucinations during intoxication. These passages do not establish a new UAP observation or government approach.

Supplied transcript text read

PaperS7546

Scalable multi-sample single-cell data analysis by Partition-Assisted Clustering and Multiple Alignments of Networks

Ye Henry Li, Dangna Li, Nikolay Samusik, Xiaowei Wang, Leying Guan, Garry P. Nolan, Wing Hung Wong. ebi.ac.uk. December 27, 2017.

PAC-MAN combines adaptive partitioning and population-network matching to address shifts between cytometry samples. Tests use simulations and prior reference datasets. Validated panels, coherent samples and downstream validation are required. Benchmark ties and losses qualify broad superiority wording; internal clade labels and a thymus percentage conflict between prose and tables. Scientific funding and author credentials do not validate unrelated UAP claims.

Supplied article text and selected apparatus read

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

14 sources for “Scientific background”

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