Results

PaperS7599

Complex Mammalian-like Hematopoietic System Found in a Colonial Chordate

Benyamin Rosental, Mark Kowarsky, Jun Seita, Daniel M. Corey, Katherine J. Ishizuka, Karla J. Palmeri, Shih-Yu Chen, Rahul Sinha, Jennifer Okamoto, Gary Mantalas, Lucia Manni, Tal Raveh, D. Nathaniel Clarke, Jonathan M. Tsai, Aaron M. Newman, Norma F. Neff, Garry P. Nolan, Stephen R. Quake, Irving L. Weissman, Ayelet Voskoboynik. ebi.ac.uk. December 5, 2018.

The authors report candidate blood-forming and immune-cell populations in a colonial tunicate, using expression comparisons, transplantation and functional assays. Mammalian similarities remain qualified by missing lymphoid signatures, cross-reactivity, autofluorescence and incomplete stem-cell benchmarks.

Complete supplied manuscript and tables; apparatus missing
PaperS7589

Defining human cardiac transcription factor hierarchies using integrated single-cell heterogeneity analysis

Jared M. Churko, Priyanka Garg, Barbara Treutlein, Meenakshi Venkatasubramanian, Haodi Wu, Jaecheol Lee, Quinton N. Wessells, Shih-Yu Chen, Wen-Yi Chen, Kashish Chetal, Gary Mantalas, Norma Neff, Eric Jabart, Arun Sharma, Garry P. Nolan, Nathan Salomonis, Joseph C. Wu. ebi.ac.uk. November 21, 2018.

The study analyzes heterogeneity in cultured cardiac differentiation and tests selected regulators. Selected cells and related perturbations provide conditional support, rather than independent donor or clinical replication. A reporting-summary conflict and several negative results remain unresolved.

Supplied main text read; large workbooks partial
PaperS7571

Neurological, Cognitive, and Psychological Findings Among Survivors of Ebola Virus Disease From the 1995 Ebola Outbreak in Kikwit, Democratic Republic of Congo: A Cross-sectional Study

J Daniel Kelly, Nicole A Hoff, D’Andre Spencer, Kamy Musene, Matthew S Bramble, David McIlwain, Daniel Okitundu, Travis C Porco, George W Rutherford, M Maria Glymour, Zach Bjornson, Patrick Mukadi, Emile Okitolonda-Wemakoy, Garry P Nolan, Jean Jacques Muyembe-Tamfum, Anne W Rimoin. ebi.ac.uk. August 10, 2018.

A selected 2017 cross-sectional study compared 20 Ebola survivors with 187 contacts from the Kikwit outbreak community. Cognitive and psychological score associations do not establish persistent causal brain injury, clinical diagnoses or 22 years of longitudinal follow-up. Small samples, instrument limitations and inconsistent source values remain explicit. Nolan is a coauthor; no UAP programme is discussed.

Supplied article and supporting text read; original layouts unavailable
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
PaperS7583

SRC/ABL inhibition disrupts CRLF2-driven signaling to induce cell death in B-cell acute lymphoblastic leukemia

Jolanda Sarno, Angela M Savino, Chiara Buracchi, Chiara Palmi, Stefania Pinto, Cristina Bugarin, Astraea Jager, Silvia Bresolin, Ruth C Barber, Daniela Silvestri, Shai Israeli, Martin JS Dyer, Giovanni Cazzaniga, Garry P Nolan, Andrea Biondi, Kara L Davis, Giuseppe Gaipa. ebi.ac.uk. May 1, 2018.

A preclinical leukemia study reports signaling and cell-viability responses to SRC/ABL inhibition. Results vary across selected samples, cell models and treatment conditions. Negative findings, limited sample availability and statistical inconsistencies qualify the claims. The supplied main text and supplement are read; clinical effectiveness and UAP relevance are not established.

Supplied main text and supplement read; original main layout incomplete
PaperS7587

DRUG-NEM: Optimizing drug combinations using single-cell perturbation response to account for intratumoral heterogeneity

Benedict Anchang, Kara L. Davis, Harris G. Fienberg, Brian D. Williamson, Sean C. Bendall, Loukia G. Karacosta, Robert Tibshirani, Garry P. Nolan, Sylvia K. Plevritis. ebi.ac.uk. April 13, 2018.

DRUG-NEM ranks drug combinations using selected single-cell signaling responses. Its short-term surrogates and fixed-subpopulation assumptions limit interpretation. Repeated analyses are not new patients, and cell-line validation does not establish clinical benefit. The supplied main text is read; supporting information remains missing.

Supplied main text and mathematics read; apparatus partial
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
PaperS7577

An immune clock of human pregnancy

Nima Aghaeepour, Edward A. Ganio, David Mcilwain, Amy S. Tsai, Martha Tingle, Sofie Van Gassen, Dyani K. Gaudilliere, Quentin Baca, Leslie McNeil, Robin Okada, Mohammad S. Ghaemi, David Furman, Ronald J. Wong, Virginia D. Winn, Maurice L. Druzin, Yaser Y. El-Sayed, Cecele Quaintance, Ronald Gibbs, Gary L. Darmstadt, Gary M. Shaw, David K. Stevenson, Robert Tibshirani, Garry P. Nolan, David B. Lewis, Martin S. Angst, Brice Gaudilliere. ebi.ac.uk. September 1, 2017.

An observational immune model tracks term-pregnancy chronology in18 training and10 validation participants. Performance falls in validation; preterm pregnancies were excluded. Correlations do not establish causal immune mechanisms or preterm prediction. Source value, demographic and metadata conflicts accompany missing original article layouts and raw data. Nolan assisted interpretation and writing and disclosed equity interests.

Complete supplied main text and11-page supplement read; original main PDF and raw gaps
PaperS7574

Reversibility of Defective Hematopoiesis Caused by Telomere Shortening in Telomerase Knockout Mice

Aparna Raval, Gregory K. Behbehani, Le Xuan Truong Nguyen, Daniel Thomas, Brenda Kusler, Alina Garbuzov, John Ramunas, Colin Holbrook, Christopher Y. Park, Helen Blau, Garry P. Nolan, Steven E. Artandi, Beverly S. Mitchell. journals.plos.org. July 2, 2015.

Selected mouse experiments report recovery of blood and cell readouts after telomerase reactivation, while finding no measurable telomere-length increase. Proposed explanations and a leukemia model remain separate from observations. Native cell-label, genotype, caption and statistical-bound conflicts persist. Nolan contributed analysis and tools and disclosed an instrument-manufacturer financial interest.

Defined supplied article and static apparatus read; raw and Word-layout gaps
PaperS7558

Mass cytometry as a platform for the discovery of cellular biomarkers to guide effective rheumatic disease therapy

Nitya Nair, Henrik E. Mei, Shih-Yu Chen, Matthew Hale, Garry P. Nolan, Holden T. Maecker, Mark Genovese, C. Garrison Fathman, Chan C. Whiting. ebi.ac.uk. May 18, 2015.

This 2015 review discusses mass cytometry as a possible aid to rheumatic-disease research. Its preliminary illustration compares one patient with one healthy control; concurrent treatment and assay timing limit interpretation. The authors explicitly consider residual drug neutralizing added TNF as an alternative to changed cell signaling. The illustration does not establish a validated biomarker or clinical recommendation. Nolan is a verified coauthor, while detailed individual contribution roles are not supplied.

Complete supplied review text and figures read
PaperS7579

Early reprogramming regulators identified by prospective isolation and mass cytometry

Ernesto Lujan, Eli R. Zunder, Yi Han Ng, Isabel N. Goronzy, Garry P. Nolan, Marius Wernig. ebi.ac.uk. April 1, 2015.

A mouse-cell study associates early reprogramming with a transient marker state, while showing that marker usefulness changes with time and model. Bulk colonies and unique reprogramming events are different outcomes. Limited replication, negative controls and speculative human extension remain explicit. The supplied manuscript text is read; full diagrams, tables and publisher corrections remain incomplete.

Complete supplied manuscript text read; meaningful apparatus partial
PaperS7595

Information-Based Physics, Influence, and Forces

James Lyons Walsh, Kevin H. Knuth. arxiv.org. November 8, 2014.

Walsh and Knuth extend an influence-network model to conditional force relations. Observer coordination, rate assignments and approximations underlie the calculation. They acknowledge incomplete understanding of a required connectivity condition. No empirical UAP mechanism is demonstrated.

Complete supplied ten-page preprint read

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