Proceedings of the National Academy of Sciences of the United States of America

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• Asymptotic theory of in-context learning by linear attention AI翻译
  作者：Lu, Yue M.; Letey, Mary; Zavatone-Veth, Jacob A.; Maiti, Anindita; Pehlevan, Cengiz
  作者单位：Harvard University; Harvard University; Harvard University; Harvard University; Perimeter Institute for Theoretical Physics
  摘要：Transformers have a remarkable ability to learn and execute tasks based on examples provided within the input itself, without explicit prior training. It has been argued that this capability, known as in-context learning (ICL), is a cornerstone of Transformers' success, yet questions about the necessary sample complexity, pretraining task diversity, and context length for successful ICL remain unresolved. Here, we provide a precise answer to these questions in an exactly solvable model of ICL ...
• Competition for Hfq drives kinetic selection of mRNA targets by Escherichia coli small noncoding RNAs AI翻译
  作者：Roca, Jorjethe; Chen, Yi- Lan; Woodson, Sarah A.
  作者单位：Johns Hopkins University; Roche Holding; Roche Holding USA
  摘要：Small noncoding RNAs (sRNAs) regulate gene expression in Escherichia coli bacteria in response to diverse stimuli in the environment and the host. Most sRNAs regulate mRNA expression by directly base pairing with complementary sites in the target mRNA with the help of the chaperone protein Hfq. sRNAs and Hfq must rapidly search hundreds of candidate mRNAs for matched (cognate) targets while discriminating against noncognate targets. Here, we use single-molecule fluorescence microscopy to direc...
• Oxidative stress is a shared characteristic of ME/CFS and Long COVID AI翻译
  作者：Shankar, Vishnu; Wilhelmy, Julie; Curtis, Ellis J.; Michael, Basil; Cervantes, Layla; Mallajosyula, Vamsee; Davis, Ronald W.; Snyder, Michael; Younis, Shady; Robinson, William H.; Shankar, Sadasivan; Mischel, Paul S.; Bonilla, Hector; Davis, Mark M.
  作者单位：Stanford University; Stanford University; Stanford University; University of California System; University of California San Diego; Stanford University; Stanford University; Stanford University; Geriatric Research Education & Clinical Center; Stanford University; United States Department of Energy (DOE); SLAC National Accelerator Laboratory; Stanford University; Stanford University; Stanford University; Howard Hughes Medical Institute; Stanford University
  摘要：Over 65 million individuals worldwide are estimated to have Long COVID (LC), a complex multisystemic condition marked by fatigue, post-exertional malaise, and other symptoms resembling myalgic encephalomyelitis/chronic fatigue syndrome (ME/ CFS). With no clinically approved treatments or reliable diagnostic markers, there is an urgent need to define the molecular underpinnings of these conditions. By studying bioenergetic characteristics of peripheral blood lymphocytes in 25 healthy controls, ...
• SpbR controls lipoteichoic acid length by directly inhibiting signal peptidase SpsB in Staphylococcus aureus AI翻译
  作者：Park, Youngseon; Sisley, Tyler A.; Stone, Madeleine C.; Corrigan, Rebecca M.; Vickery, Christopher R.; Gruendling, Angelika; Walker, Suzanne
  作者单位：University College Dublin; Harvard University; Harvard Medical School; Imperial College London; Imperial College London
  摘要：Staphylococcus aureus is a Gram-positive pathogen that causes life-threatening infections. Its cell envelope contains anionic polymers called teichoic acids that are required for cell viability.Teichoic acids come in two forms and are made by different biosynthetic pathways. One form, lipoteichoic acid (LTA), is anchored in the cell membrane; the other form, wall teichoic acid (WTA), is covalently linked to the peptidoglycan cell wall. Although the LTA and WTA biosynthetic pathways have been c...
• Metabolic engineering of Bacillus subtilis for the production of active hemoglobins and myoglobins by improving heme supply AI翻译
  作者：Wang, Song; Zhou, Jingwen; Li, Jianghua; Chen, Jian; Du, Guocheng; Li, Zhengqiang; Lee, Sang Yup; Zhao, Xinrui
  作者单位：Jiangnan University; Jiangnan University; Jiangnan University; Jiangnan University; Jilin University; Korea Advanced Institute of Science & Technology (KAIST); Korea Advanced Institute of Science & Technology (KAIST)
  摘要：Hemoglobins (Hb) and myoglobins (Mb) are important hemoproteins with broad applications in food and medicine. Microbial cell factory is a promising approach for the green and sustainable production of hemoproteins. However, current microbial hosts face the challenges of safety and insufficient heme supply. Here, we report a global regulation strategy, push-restrain-pull-block, to enhance heme supply for producing various active Hb and Mb in food-grade Bacillus subtilis. Initially, the insuffic...
• Reply to Pang et al.: Generalizable ability to track beliefs could be the most parsimonious explanation AI翻译
  作者：Kosinski, Michal
  作者单位：Stanford University
• A circular RNA overcomes acquired resistance to BET inhibitors by antagonizing IGF2BP2-mediated c-MYC translation in TNBC AI翻译
  作者：Guo, Jiawei; Li, Ke; Ming, Yue; Pan, Yitong; Tan, Shuangyan; Ma, Hulin; Chen, Shuang; Duan, Yingying; Peng, Yong
  作者单位：Sichuan University; Sichuan University; Tianfu Jincheng Laboratory
  摘要：Bromodomain-and-extraterminal-domain (BET) proteins are promising therapeutic targets for refractory solid tumors, including triple-negative breast cancer (TNBC). However, acquired resistance to BET inhibitors (BETi) remains a significant clinical challenge. Elucidation of the underlying mechanisms of BETi resistance is therefore of critical importance. In this study, we identified the RNA-binding protein IGF2BP2 as a key driver of acquired BETi resistance in TNBC, primarily through its role i...
• Methane-powered sea spiders: Diverse, epibiotic methanotrophs serve as a source of nutrition for deep-sea methane Sericosura AI翻译
  作者：Guo, Yongzhao; Mayr, Magdalena J.; Pereira, Olivia S.; Levin, Lisa A.; Orphan, Victoria J.; Goffredi, Shana K.
  作者单位：Occidental College; California Institute of Technology; University of California System; University of California San Diego; Scripps Institution of Oceanography
  摘要：Methane seeps harbor uncharacterized animal-microbe symbioses with unique nutritional strategies. Three undescribed sea spider species (family Ammotheidae; genus Sericosura) endemic to methane seeps were found along the eastern Pacific margin, from California to Alaska, hosting diverse methane-and methanol-oxidizing bacteria on their exoskeleton. S13C tissue isotope values of in situ specimens corroborated methane assimilation (-45 parts per thousand, on average). Live animal incubations with ...
• EIAV encodes an accessory protein that antagonizes the host restriction factor equine tetherin AI翻译
  作者：Bai, Bowen; Zhang, Xiangmin; Zhang, Mengmeng; Ma, Weiwei; Li, Jiwei; Zhang, Haili; Na, Lei; Guo, Xing; Lin, Yuezhi; Wang, Xue - Feng; Wang, Xiaojun
  作者单位：Chinese Academy of Agricultural Sciences; Harbin Veterinary Research Institute, CAAS; Chinese Academy of Agricultural Sciences
  摘要：Equine infectious anemia virus (EIAV) is an important model for the study of pathogenesis in lentiviruses. Studies of viral genome organization and replication mechanisms are fundamental to the understanding of virus pathogenicity. In this study, we identified an unique transcript from EIAV in vivo and in vitro by Sanger sequencing and Northern blotting. The transcript contains a complete open reading frame and has length 369 nt. We named the protein encoded by this transcript S4 and demonstra...
• Evolution of gene order in prokaryotes is driven primarily by gene gain and loss AI翻译
  作者：Brezner, Shelly; Garushyants, Sofya K.; Wolf, Yuri I.; Koonin, Eugene V.; Snir, Sagi
  作者单位：University of Haifa; National Institutes of Health (NIH) - USA; NIH National Library of Medicine (NLM); Division of Intramural Research (DIR)
  摘要：Evolution of bacterial and archaeal genomes is highly dynamic, including extensive gene gain via horizontal gene transfer (HGT) and gene loss as well as different types of genome rearrangements, such as inversions and translocations, so that gene order is not highly conserved even among closely related organisms. We sought to quantify the contributions of different genome dynamics processes to the evolution of the gene order in prokaryote genomes, relying on the recently developed, simple, sto...