-
作者：Gujral, Onkar; Bafna, Mihir; Alm, Eric; Berger, Bonnie
作者单位：Massachusetts Institute of Technology (MIT); Massachusetts Institute of Technology (MIT); Massachusetts Institute of Technology (MIT); Massachusetts Institute of Technology (MIT)
摘要：Foundation models in biology-particularly protein language models (PLMs)-have enabled ground-breaking predictions in protein structure, function, and beyond. However, the black-box nature of these representations limits transparency and explainability, posing challenges for human-AI collaboration and leaving open questions about their human-interpretable features. Here, we leverage sparse autoencoders (SAEs) and a variant, transcoders, from natural language processing to extract, in a complete...
-
作者：Park, Jong - Duk; Lee, Seoung Rak; Dhennezel, Catherine; Taylor, Noel; Dame, Andrea; Kadoki, Motohiko; Pishchany, Gleb; Graham, Daniel B.; Xavier, Ramnik J.; Seyedsayamdost, Mohammad R.
作者单位：Princeton University; Pusan National University; Pusan National University; Harvard University; Massachusetts Institute of Technology (MIT); Broad Institute; Harvard University; Harvard University Medical Affiliates; Massachusetts General Hospital; Harvard University; Harvard Medical School; Harvard University; Harvard University Medical Affiliates; Massachusetts General Hospital; Princeton University
摘要：The gut microbiota plays a pivotal role in maintaining human health with dysbiosis linked to a variety of diseases. Metagenome sequencing and robust statistical analysis have linked specific strains, including the gut bacterium Campylobacter concisus, to Crohn's disease and ulcerative colitis, together known as inflammatory bowel disease (IBD). However, the roles of this and other strains in disease progression remain to be investigated. Herein, we assess the contribution of C. concisus second...
-
作者：Brumfield, Kyle D.; Usmani, Moiz; Long, Daniel M.; Lupari, Henry A.; Pope, Robert K.; Jutla, Antarpreet S.; Huq, Anwar; Colwell, Rita R.
作者单位：University System of Maryland; University of Maryland College Park; University System of Maryland; University of Maryland College Park; University of Alabama System; University of Alabama Birmingham; National Biodefense Analysis & Countermeasures Center; State University System of Florida; University of Florida; University System of Maryland; University of Maryland College Park
摘要：Climate change significantly impacts the incidence and abundance of microorganisms, including those essential for environmental cycles and those pathogenic to humans and animals. Shifts in conditions favorable for microbial growth have expanded the geographic range of many pathogens, contributing to the emergence and reemergence of infectious diseases. Waterborne diseases pose severe risks in regions where adverse climate conditions intersect with population vulnerabilities, especially inadequ...
-
作者：Gavrilets, Sergey; Seabright, Paul
作者单位：University of Tennessee System; University of Tennessee Knoxville; University of Tennessee System; University of Tennessee Knoxville; Universite de Toulouse; Universite Toulouse 1 Capitole; Toulouse School of Economics; Universite de Toulouse; Universite Toulouse 1 Capitole; Toulouse School of Economics
摘要：People and cultures differ in the extent to which they view the world as a zero-sum environment (where one person's gain is another's loss) or a positive-sum environment (where certain actions can benefit everyone). These beliefs shape individuals' willingness to work, invest, collaborate, or show hostility toward out-groups, and accept or reject various social policies. We model dyadic interactions in a heterogeneous population where individuals biased toward a zero-sum worldview are more lik...
-
作者：Ogawa, Yuki; Nguyen, Duc V. M.; Ogawa, Ayano; Rasband, Matthew N.
作者单位：Baylor College of Medicine
摘要：The visualization and manipulation of proteins in neurons is widely used to deduce their functions. While every experimental approach has limitations, the concurrent knock-in and knockout of two different proteins can be especially challenging. To this end, we developed Hide-and-Seek genome editing, which allows the simultaneous visualization and knockout of proteins in neurons using Adeno-associated viral vectors and the CRISPR/Cas9 system. We demonstrate the efficacy and flexibility of this ...
-
作者：Vanni, Stefano
作者单位：University of Fribourg; University of Fribourg
-
作者：Chen, Xuemin; Yao, Liangrui; Li, Wenwen; Ma, Shanshan; Yuan, Xingyun; Yang, Yang; Yuan, Yuan; Liu, Yumei; Liu, Lan; Wang, Huaibin; Gellert, Martin; Yang, Wei
作者单位：Anhui University; National Institutes of Health (NIH) - USA; NIH National Institute of Diabetes & Digestive & Kidney Diseases (NIDDK)
摘要：The recombination activating genes 1 and 2 (RAG1/2) recombinase, which initiates V(D)J recombination in jawed vertebrates, evolved from RNaseH-like transposases such as Transib and ProtoRAG. However, its postcleavage transposase activity is strictly suppressed. Previous structural studies have focused only on the conserved core domains of RAG1/2, leaving the regulatory mechanisms of the noncore regions unclear. To investigate how RAG1/2 suppresses transposition and regulates DNA cleavage, we d...
-
作者：Yang, Siyan; Ji, Bingqiang; Feng, Yawei; Jin, Yuankai; Xu, Wanghuai; Lu, Jingyi; Qin, Xuezhi; Zhang, Huanhuan; Li, Mingyu; Xu, Zhenyu; Liu, Xiaonan; Xu, Luqing; Wang, Dehui; Wen, Rongfu; Wang, Zhenying; Wang, Steven; Ma, Xuehu; Wang, Zuankai
-
作者：Carey, John
-
作者：Salazar-Miranda, Arianna; Fan, Zhuangyuan; Baick, Michael; Hampton, Keith N.; Duarte, Fabio; Loo, Becky P. Y.; Glaeser, Edward; Ratti, Carlo
作者单位：Yale University; University of Hong Kong; Michigan State University; Massachusetts Institute of Technology (MIT); Harvard University; Polytechnic University of Milan
摘要：We analyze changes in pedestrian behavior over a 30-y period in four urban public spaces located in New York, Boston, and Philadelphia. Building on William Whyte's observational work, which involved manual video analysis of pedestrian behaviors, we employ computer vision and deep learning techniques to examine video footage from 1979-80 and 2008-10. Our analysis measures changes in walking speed, lingering behavior, group sizes, and group formation. We find that the average walking speed has i...
