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This study is part of the Pharmaceutical Research and Manufacturers of America (PhRMA) initiative on predictive models of efficacy, safety, and compound properties. The overall goal of this part was to assess the predictability of human pharmacokinetics (PK) from preclinical data and to provide comparisons of available prediction methods from the literature, as appropriate, using a representative blinded dataset of drug candidates. The key objectives were to (i) appropriately assemble and blind a diverse dataset of in vitro, preclinical in vivo, and clinical data for multiple drug candidates, (ii) evaluate the dataset with empirical and physiological methodologies from the literature used to predict human PK properties and plasma concentration-time profiles, (iii) compare the predicted properties with the observed clinical data to assess the prediction accuracy using routine statistical techniques and to evaluate prediction method(s) based on the degree of accuracy of each prediction method, and (iv) compile and summarize results for publication. Another objective was to provide a mechanistic understanding as to why one methodology provided better predictions than another, after analyzing the poor predictions. A total of 108 clinical lead compounds were collected from 12 PhRMA member companies. This dataset contains intravenous (n = 19) and oral pharmacokinetic data (n = 107) in humans as well as the corresponding preclinical in vitro, in vivo, and physicochemical data. All data were blinded to protect the anonymity of both the data and the company submitting the data. This manuscript, which is the first of a series of manuscripts, summarizes the PhRMA initiative and the 108 compound dataset. More details on the predictability of each method are reported in companion manuscripts.
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http://dx.doi.org/10.1002/jps.22554 | DOI Listing |
Mol Syst Biol
September 2025
Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA, USA.
Vascular sites have distinct susceptibility to atherosclerosis and aneurysm, yet the epigenomic and transcriptomic underpinning of vascular site-specific disease risk is largely unknown. Here, we performed single-cell chromatin accessibility (scATACseq) and gene expression profiling (scRNAseq) of mouse vascular tissue from three vascular sites. Through interrogation of epigenomic enhancers and gene regulatory networks, we discovered key regulatory enhancers to not only be cell type, but vascular site-specific.
View Article and Find Full Text PDFJ Neurotrauma
September 2025
Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA.
Mean apparent propagator MRI (MAP-MRI) quantifies subtle alterations in tissue microstructure noninvasively and provides a more nuanced and comprehensive assessment of tissue architectural and structural integrity compared with other diffusion MRI techniques. We investigate the sensitivity of MAP-MRI-derived quantitative imaging biomarkers to detect previously unseen microstructural damage in patients with mild traumatic brain injuries (mTBI), whose clinical scans otherwise appeared normal. We developed and validated an MAP-MRI data processing pipeline for analyzing diffusion-weighted images for use in healthy controls and mTBI patients whose longitudinal scans were obtained from the GE/NFL/mTBI MRI database.
View Article and Find Full Text PDFCell Genom
September 2025
Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA; Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA; Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; In
Missense variants can have pleiotropic effects on protein function, and predicting these effects can be difficult. We performed near-saturation deep mutational scanning of P2RY8, a G protein-coupled receptor that promotes germinal center B cell confinement. We assayed the effect of each variant on surface expression, migration, and proliferation.
View Article and Find Full Text PDFJ Clin Oncol
September 2025
Sidney Kimmel Comprehensive Cancer Center Johns Hopkins University School of Medicine, Baltimore, MD.
Purpose: To assess modified folinic acid/leucovorin, fluorouracil, irinotecan, oxaliplatin (FOLFIRINOX; mFFX) versus gemcitabine/nab-paclitaxel (GnP) in de novo metastatic pancreatic ductal adenocarcinoma (PDAC) and explore predictive biomarkers.
Patients And Methods: Patients were randomly assigned 1:1 to mFFX or GnP with exclusion of germline pathogenic variants in or . The primary end point was progression-free survival (PFS) between arms with 0.
IEEE J Biomed Health Inform
September 2025
Vision Transformer (ViT) applied to structural magnetic resonance images has demonstrated success in the diagnosis of Alzheimer's disease (AD) and mild cognitive impairment (MCI). However, three key challenges have yet to be well addressed: 1) ViT requires a large labeled dataset to mitigate overfitting while most of the current AD-related sMRI data fall short in the sample sizes. 2) ViT neglects the within-patch feature learning, e.
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