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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 PDFGonadal sex and temperature independently influence germ cell differentiation and meiotic progression in .
Proc Natl Acad Sci U S A
January 2025
Department of Cell Biology, Duke University Medical Center, Durham, NC 27701.
In species with genetic sex determination (GSD), the sex identity of the soma determines germ cell fate. For example, in mice, XY germ cells that enter an ovary differentiate as oogonia, whereas XX germ cells that enter a testis initiate differentiation as spermatogonia. However, numerous species lack a GSD system and instead display temperature-dependent sex determination (TSD).
View Article and Find Full Text PDFHow and why funders support engaged research.
Proc Natl Acad Sci U S A
January 2025
Ewing Marion Kauffman Foundation, Kansas City, MO 64110.
Research that better aligns policy, practice, and research communities is gaining momentum around the world. This includes engaged research strategies that bring partners, and their diverse perspectives and kinds of knowledge, together to shape research agendas with on-the-ground-needs and to create dynamic problem-solving processes. These approaches aim to generate more equitable and effective solutions to societal challenges.
View Article and Find Full Text PDFComplex tissue regeneration in reveals a phylogenetic signal for enhanced regenerative ability in deomyine rodents.
Proc Natl Acad Sci U S A
January 2025
Department of Biology, University of Kentucky, Lexington, KY 40508.
Identifying why complex tissue regeneration is present or absent in specific vertebrate lineages has remained elusive. One also wonders whether the isolated examples where regeneration is observed represent cases of convergent evolution or are instead the product of phylogenetic inertia from a common ancestral program. Testing alternative hypotheses to identify genetic regulation, cell states, and tissue physiology that explain how regenerative healing emerges in some species requires sampling multiple species among which there is variation in regenerative ability across a phylogenetic framework.
View Article and Find Full Text PDFInvestigation of Transformation Pathways of Polyfluoroalkyl Substances during Chlorine Disinfection.
Environ Sci Technol
January 2025
Department of Civil and Environmental Engineering, University of Missouri, Columbia, Missouri 65211, United States.
Recent regulations on perfluorinated compounds in drinking water underscore the need for a deeper understanding of the formation of perfluorinated compounds from polyfluoroalkyl substances during chlorine disinfection. Among the compounds investigated in this study, N-(3-(dimethylaminopropan-1-yl)perfluoro-1-hexanesulfonamide (N-AP-FHxSA) underwent rapid transformation during chlorination. Within an hour, it produced quantitative yields of various poly- and per-fluorinated products, including perfluorohexanoic acid (PFHxA).
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