BioParity.UFO / UAP research

7 papers for “Nikolay Samusik”

Results

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
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
PaperS7608

Ultra-high throughput single-cell analysis of proteins and RNAs by split-pool synthesis

Maeve O’Huallachain, Felice-Alessio Bava, Mary Shen, Carolina Dallett, Sri Paladugu, Nikolay Samusik, Simon Yu, Razika Hussein, Grantland R. Hillman, Samuel Higgins, Melanie Lou, Angelica Trejo, Laura Qin, Yu Chuan Tai, Shigemi M. Kinoshita, Astraea Jager, Deval Lashkari, Yury Goltsev, Sedide Ozturk, Garry P. Nolan. ebi.ac.uk. May 7, 2020.

The authors demonstrate split-pool barcoding for protein and targeted RNA measurements in cell lines, human blood-cell material and mouse cells. Large theoretical barcode capacity is distinct from measured event recovery. Uneven RNA detection, cell losses, exclusions, doublets and source discrepancies limit interpretation; no clinical or UAP validation follows.

Complete supplied main and correction text; partial supplemental visuals
PaperS7614

Deep Profiling of Mouse Splenic Architecture with CODEX Multiplexed Imaging

Yury Goltsev, Nikolay Samusik, Julia Kennedy-Darling, Salil Bhate, Matthew Hale, Gustavo Vazquez, Sarah Black, Garry P. Nolan. ebi.ac.uk. August 9, 2018.

CODEX imaging maps cells and neighborhoods in nine mouse spleens. Most changing contacts track cell abundance rather than stronger inferred interactions. Neighborhood associations leave causal direction open. Image classification used test-set patches for tuning, and reported precision is not clinical accuracy. Financial interests and processing limits are retained.

Complete supplied main, figures, S1/S2 cells and S4 PDF
PaperS7500

Single-cell mass cytometry reveals distinct populations of brain myeloid cells in mouse neuroinflammation and neurodegeneration models

Bahareh Ajami, Nikolay Samusik, Peter Wieghofer, Peggy P. Ho, Andrea Crotti, Zach Bjornson, Marco Prinz, Wendy J. Fantl, Garry P. Nolan, Lawrence Steinman. med.stanford.edu. March 5, 2018.

Ajami, Nolan and colleagues analyse brain myeloid populations in mouse disease models. Mouse treatment findings do not establish human therapy or UAP-related illness. Pooling, statistical assumptions and inconsistencies constrain interpretation.

Paper, methods, figures and checklist read
PaperS7593

Commonly Occurring Cell Subsets in High-Grade Serous Ovarian Tumors Identified by Single-Cell Mass Cytometry

Veronica D. Gonzalez, Nikolay Samusik, Tiffany J. Chen, Erica S. Savig, Nima Aghaeepour, David A. Quigley, Ying-Wen Huang, Valeria Giangarrà, Alexander D. Borowsky, Neil E. Hubbard, Shih-Yu Chen, Guojun Han, Alan Ashworth, Thomas J. Kipps, Jonathan S. Berek, Garry P. Nolan, Wendy J. Fantl. ebi.ac.uk. February 13, 2018.

Mass cytometry identifies tumor-cell subsets and outcome associations in a small ovarian-cancer cohort. Dominant and hybrid clusters did not individually correlate with relapse. Same-cohort marker selection and missing independent validation limit interpretation; cell-line response is not demonstrated patient benefit.

Supplied author manuscript read; figures and supplement missing
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