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More than 90% of drugs with preclinical activity fail in human trials, largely due to insufficient efficacy. We hypothesized that adequately powered trials of patient-derived xenografts (PDX) in mice could efficiently define therapeutic activity across heterogeneous tumors. To address this hypothesis, we established a large, publicly available repository of well-characterized leukemia and lymphoma PDXs that undergo orthotopic engraftment, called the Public Repository of Xenografts (PRoXe). PRoXe includes all de-identified information relevant to the primary specimens and the PDXs derived from them. Using this repository, we demonstrate that large studies of acute leukemia PDXs that mimic human randomized clinical trials can characterize drug efficacy and generate transcriptional, functional, and proteomic biomarkers in both treatment-naive and relapsed/refractory disease.
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http://dx.doi.org/10.1016/j.ccell.2016.03.008 | DOI Listing |
Genome Biol
September 2025
Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang, Hangzhou, 310029, China.
Metagenomic analyses of microbial communities have unveiled a substantial level of interspecies and intraspecies genetic diversity by reconstructing metagenome-assembled genomes (MAGs). The MAG database (MAGdb) boasts an impressive collection of 74 representative research papers, spanning clinical, environmental, and animal categories and comprising 13,702 paired-end run accessions of metagenomic sequencing and 99,672 high quality MAGs with manually curated metadata. MAGdb provides a user-friendly interface that users can browse, search, and download MAGs and their corresponding metadata information.
View Article and Find Full Text PDFCancer Immunol Immunother
September 2025
Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
Whole blood (WB) transcriptomics offers a minimal-invasive method to assess patients' immune system. This study aimed to identify transcriptional patterns in WB associated with clinical outcomes in patients treated with immune checkpoint inhibitors (ICIs). We performed RNA-sequencing on pre-treatment WB samples from 145 patients with advanced cancer.
View Article and Find Full Text PDFPLoS One
September 2025
Department of Political Science, Syracuse University, New York, United States of America.
Background: The rapid global spread of the COVID-19 pandemic affected different regions, communities, and individuals in vastly different ways that interdisciplinary social scientists are well-positioned to document and investigate. This paper describes an innovative mixed-methods dataset generated by a research study that was designed to chronicle and preserve evidence of the pandemic's divergent effects: the Pandemic Journaling Project (PJP). The dataset was generated by leveraging digital technology to invite ordinary people around the world to document the impact of the COVID-19 pandemic on their everyday lives over a two-year period (May 2020-May 2022) using text, images, and audio.
View Article and Find Full Text PDFGenome Biol
September 2025
Department of Clinical Pharmacy, Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
Background: Recent advances in high-throughput sequencing technologies have enabled the collection and sharing of a massive amount of omics data, along with its associated metadata-descriptive information that contextualizes the data, including phenotypic traits and experimental design. Enhancing metadata availability is critical to ensure data reusability and reproducibility and to facilitate novel biomedical discoveries through effective data reuse. Yet, incomplete metadata accompanying public omics data may hinder reproducibility and reusability and limit secondary analyses.
View Article and Find Full Text PDFJ Behav Health Serv Res
September 2025
Department of Health Policy and Management, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, 4301 W. Markham St., Little Rock, AR, USA.
Telehealth is increasingly a standard and routine clinical option, indicating a changing outlook for SUD treatment from in-person to the more convenient option of telehealth. As populations across geographies increasingly prefer telehealth, more research is warranted that focuses on how where a person lives is associated with telehealth availability. The authors used the Mental Health and Addiction Treatment Tracking Repository (MATTR 2024) to identify telehealth availability among all known licensed SUD treatment facilities in the USA (N = 10,492 facilities).
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