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Learning the language of antibody hypervariability.
Proc Natl Acad Sci U S A
January 2025
Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139.
Protein language models (PLMs) have demonstrated impressive success in modeling proteins. However, general-purpose "foundational" PLMs have limited performance in modeling antibodies due to the latter's hypervariable regions, which do not conform to the evolutionary conservation principles that such models rely on. In this study, we propose a transfer learning framework called Antibody Mutagenesis-Augmented Processing (AbMAP), which fine-tunes foundational models for antibody-sequence inputs by supervising on antibody structure and binding specificity examples.
View Article and Find Full Text PDFA detailed spatiotemporal atlas of the white matter tracts for the fetal brain.
Proc Natl Acad Sci U S A
January 2025
Computational Radiology Laboratory, Boston Children's Hospital, Boston, MA 02115.
This study presents the construction of a comprehensive spatiotemporal atlas of white matter tracts in the fetal brain for every gestational week between 23 and 36 wk using diffusion MRI (dMRI). Our research leverages data collected from fetal MRI scans, capturing the dynamic changes in the brain's architecture and microstructure during this critical period. The atlas includes 60 distinct white matter tracts, including commissural, projection, and association fibers.
View Article and Find Full Text PDFAdvancing the Mechanosensitivity of Atropisomeric Diarylethene Mechanophores through a Lever-Arm Effect.
J Am Chem Soc
January 2025
Department of Chemistry, BioInspired Institute, Syracuse University, Syracuse, New York 13244, United States.
Understanding structure-mechanical activity relationships (SMARs) in polymer mechanochemistry is essential for the rational design of mechanophores with desired properties, yet SMARs in noncovalent mechanical transformations remain relatively underexplored. In this study, we designed a subset of diarylethene mechanophores based on a lever-arm hypothesis and systematically investigated their mechanical activity toward a noncovalent-yet-chemical conversion of atropisomer stereochemistry. Results from Density functional theory (DFT) calculations, single-molecule force spectroscopy (SMFS) measurements, and ultrasonication experiments collectively support the lever-arm hypothesis and confirm the exceptional sensitivity of chemo-mechanical coupling in these atropisomers.
View Article and Find Full Text PDFADELLE: A global testing method for trans-eQTL mapping.
PLoS Genet
January 2025
Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America.
Understanding the genetic regulatory mechanisms of gene expression is an ongoing challenge. Genetic variants that are associated with expression levels are readily identified when they are proximal to the gene (i.e.
View Article and Find Full Text PDFEnhancing air quality predictions in Chile: Integrating ARIMA and Artificial Neural Network models for Quintero and Coyhaique cities.
PLoS One
January 2025
Escuela de Ingeniería Química, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile.
In this comprehensive analysis of Chile's air quality dynamics spanning 2016 to 2021, the utilization of data from the National Air Quality Information System (SINCA) and its network of monitoring stations was undertaken. Quintero, Puchuncaví, and Coyhaique were the focal points of this study, with the primary objective being the construction of predictive models for sulfur dioxide (SO2), fine particulate matter (PM2.5), and coarse particulate matter (PM10).
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