BioParity.UFO / UAP research

17 sources for “Tissue imaging”

Results

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
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
PaperS7697

Reprogramming of stroma-derived chemokine networks drives the loss of tissue organization in nodal B cell lymphoma

Felix Czernilofsky, Anna Mathioudaki, Lea Jopp-Saile, Raphael Lutz, Dominik Vonficht, Xi Wang, Christina Schniederjohann, Harald Voehringer, Tobias Roider, Marc-Andrea Baertsch, Claus Rodemer, Henry Löffler-Wirth, Michael Grau, Donnacha Fitzgerald, Johannes Mammen, Jan Kosla, Nora Liebers, Peter-Martin Bruch, Diana Ordoñez-Rueda, Alexander Brobeil, Gunhild Mechtersheimer, Caroline Pabst, Carsten Müller-Tidow, Andreas Trumpp, Marc Seifert, Frank Neumann, Mathias Heikenwälder, Vladimir Benes, Wolfgang Huber, Jörg Distler, Georg Lenz, Hans Binder, Reiner Siebert, Garry P. Nolan, Moritz Gerstung, Judith B. Zaugg, Daniel Hübschmann, Simon Haas, Sascha Dietrich. pmc.ncbi.nlm.nih.gov. March 25, 2026.

This lymphoma study combines new tissue profiling, reused datasets, limited cell cultures and retrospective survival associations to propose a model of altered tissue organization. Its assays overlap an earlier Nolan-linked atlas, and cells or repeated measurements are not independent patients. Data-derived survival thresholds and unresolved denominator/method wording qualify clinical interpretation. Nolan provided access to existing imaging and immune datasets; this article does not assign him a funding award or report a classified UAP approach.

Complete specialist supplied XML text; native apparatus unreviewed
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
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
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
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
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
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
PaperS7686

Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer

Magdalena Matusiak, John W. Hickey, David G.P. van IJzendoorn, Guolan Lu, Lukasz Kidziński, Shirley Zhu, Deana R.C. Colburg, Bogdan Luca, Darci J. Phillips, Sky W. Brubaker, Gregory W. Charville, Jeanne Shen, Kyle M. Loh, Derick K. Okwan-Duodu, Garry P. Nolan, Aaron M. Newman, Robert B. West, Matt van de Rijn. ebi.ac.uk. March 27, 2024.

This observational human-tissue study associates distinct macrophage populations with different colon-cancer outcomes: IL4I1 with favorable survival in two reported cohorts and SPP1 with unfavorable survival in one. Nested cells and tissue regions are not independent patients; no adjusted or prospectively validated clinical predictor is established. A reused breast-cancer treatment-response measure is T-cell receptor expansion, a surrogate. Nolan is a Resources coauthor. Public cancer-research grants name other recipients and establish no classified approach or UAP programme. Figures and supplements remain unreviewed.

Complete specialist supplied XML text; native graphics 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

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