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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 PDFGeometrically modulated contact forces enable hula hoop levitation.
Proc Natl Acad Sci U S A
January 2025
Applied Mathematics Laboratory, Courant Institute of Mathematical Sciences, Department of Mathematics, New York University, New York, NY 10012.
Mechanical systems with moving points of contact-including rolling, sliding, and impacts-are common in engineering applications and everyday experiences. The challenges in analyzing such systems are compounded when an object dynamically explores the complex surface shape of a moving structure, as arises in familiar but poorly understood contexts such as hula hooping. We study this activity as a unique form of mechanical levitation against gravity and identify the conditions required for the stable suspension of an object rolling around a gyrating body.
View Article and Find Full Text PDFUnveiling hidden reaction kinetics of carbon dioxide in supercritical aqueous solutions.
Proc Natl Acad Sci U S A
January 2025
Department of Physics, The Hong Kong University of Science and Technology, Hong Kong, China.
Dissolution of CO in water followed by the subsequent hydrolysis reactions is of great importance to the global carbon cycle, and carbon capture and storage. Despite numerous previous studies, the reactions are still not fully understood at the atomistic scale. Here, we combined ab initio molecular dynamics (AIMD) simulations with Markov state models to elucidate the reaction mechanisms and kinetics of CO in supercritical water both in the bulk and nanoconfined states.
View Article and Find Full Text PDFClimate change could amplify weak synchrony in large marine ecosystems.
Proc Natl Acad Sci U S A
January 2025
Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045.
Climate change is increasing the frequency of large-scale, extreme environmental events and flattening environmental gradients. Whether such changes will cause spatially synchronous, large-scale population declines depends on mechanisms that limit metapopulation synchrony, thereby promoting rescue effects and stability. Using long-term data and empirical dynamic models, we quantified spatial heterogeneity in density dependence, spatial heterogeneity in environmental responses, and environmental gradients to assess their role in inhibiting synchrony across 36 marine fish and invertebrate species.
View Article and Find Full Text PDFExploring associations between the FTO rs9939609 genotype and plasma concentrations of appetite-related hormones in adults with obesity.
PLoS One
January 2025
Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway.
Associations between variants in the FTO locus and plasma concentrations of appetite related hormones are inconsistent, and might not work in a dose dependent fashion in people with obesity. Moreover, it is relevant to report meal related plasma concentrations of these hormones in persons with obesity given the growing interest in their pharmacological potential in obesity therapy. We find it clinically relevant to examine associations between the SNP rs9939609 genotypes and homeostatic appetite regulation in individuals with BMI ≥35 kg/m2.
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