7 papers for “Validation limits”

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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

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

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

PaperS7563

Joint Modeling and Registration of Cell Populations in Cohorts of High-Dimensional Flow Cytometric Data

Saumyadipta Pyne, Sharon X. Lee, Kui Wang, Jonathan Irish, Pablo Tamayo, Marc-Danie Nazaire, Tarn Duong, Shu-Kay Ng, David Hafler, Ronald Levy, Garry P. Nolan, Jill Mesirov, Geoffrey J. McLachlan. ebi.ac.uk. July 1, 2014.

JCM models and registers cell populations across preprocessed flow-cytometry samples. Its demonstrations reuse three prior datasets, with manual gates, selected panels and selected benchmark samples. The implemented model restricts the general formulation. Exploratory results and nested cells do not establish prospective clinical prediction or independent replication. Nolan contributed materials, tools and writing. Source inconsistencies in timing, marker counts, tables, references and equations remain unresolved.

Complete supplied main and static supplements read

PaperS7576

Entropy-Based Search Algorithm for Experimental Design

N. K. Malakar, K. H. Knuth. arxiv.org. August 29, 2010.

Nested Entropy Sampling searches for informative experiments in synthetic two-dimensional landscapes. Small sample counts can become trapped at local peaks, while higher counts reduce compression. The robot example is a simulation, and reported computation savings count entropy evaluations. Finite successes do not establish global convergence or physical measurement validation.

Complete supplied8-page preprint read; final proceedings and implementation gaps

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