综合性期刊最新文献

{"title":"Shapes of ideal stalagmites.","authors":"Piotr Szymczak, Anthony J C Ladd, Matej Lipar, Dean Pekarovič","doi":"10.1073/pnas.2513263122","DOIUrl":"https://doi.org/10.1073/pnas.2513263122","url":null,"abstract":"<p><p>Stalagmites are isolated columns of calcium carbonate growing on a cave floor; their growth is driven by the constant dripping of supersaturated solutions from the roof of the cave. In this paper, we derive a closed-form expression for the shape of a steadily growing stalagmite. Our analysis gives rise to three distinct shapes, all of them observable in nature, with the shape characterized by a single dimensionless parameter. Transitions between different shapes occur at a specific value of this parameter, with additional selection rules determining the shape and size of stalagmites evolving under specific cave conditions. Our theory shows that the stalagmite shape influences the [Formula: see text] isotope shifts, which are an important source of paleoclimatic information.</p>","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"122 42","pages":"e2513263122"},"PeriodicalIF":9.1,"publicationDate":"2025-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145308893","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"T cell receptor specificity landscape revealed through de novo peptide design.","authors":"Gian Marco Visani, Michael N Pun, Anastasia A Minervina, Philip Bradley, Paul G Thomas, Armita Nourmohammad","doi":"10.1073/pnas.2504783122","DOIUrl":"https://doi.org/10.1073/pnas.2504783122","url":null,"abstract":"<p><p>T cells play a key role in adaptive immunity by mounting specific responses against diverse pathogens. Effective bindings between T cell receptors (TCRs) and pathogen derived peptides presented on major histocompatibility complexes (MHCs) mediate immune responses. However, predicting these interactions remains challenging due to limited functional data on T cell reactivities. Here, we introduce a computational approach to predict TCR interactions with peptides presented on MHC-I alleles, and to design immunogenic peptides for specified TCR-MHC complexes. Our method leverages HERMES, a structure-based machine learning model trained on the protein universe to predict amino acid preferences based on local structural environments. Despite no direct training on TCR-pMHC data, HERMES's implicit physical reasoning enables us to make accurate predictions of both TCR-pMHC binding affinities and T cell activities across diverse viral and cancer epitopes, achieving up to 0.72 correlation with experimental data. Leveraging our TCR recognition model, we develop a computational protocol for de novo design of immunogenic peptides. Through experimental validation in three TCR-MHC systems, we demonstrate that our designs-with up to five substitutions from the native sequence-activate T cells at success rates of up to 50%. Last, we use our generative framework to quantify the diversity of the peptide recognition landscape for various TCR-MHC's, offering key insights into T cell specificity. Our approach provides a platform for immunogenic peptide and neoantigen design, as well as for evaluating TCR specificity, offering a computational framework to inform design of engineered T cell therapies and vaccines.</p>","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"122 42","pages":"e2504783122"},"PeriodicalIF":9.1,"publicationDate":"2025-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145308894","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrative mapping reveals molecular features underlying the mechanism of nucleocytoplasmic transport.","authors":"Barak Raveh, Roi Eliasian, Shaked Rashkovits, Daniel Russel, Ryo Hayama, Samuel Sparks, Digvijay Singh, Roderick Y H Lim, Elizabeth Villa, Michael P Rout, David Cowburn, Andrej Sali","doi":"10.1073/pnas.2507559122","DOIUrl":"https://doi.org/10.1073/pnas.2507559122","url":null,"abstract":"<p><p>Nuclear pore complexes (NPCs) enable rapid, selective, and robust nucleocytoplasmic transport. To explain how transport emerges from the system components and their interactions, we used experimental data and theoretical information to construct an integrative Brownian dynamics model of transport through an NPC, coupled to a kinetic model of transport in the cell. The model recapitulates key aspects of transport for a wide range of molecular cargoes, including preribosomes and viral capsids. Our model quantifies how flexible phenylalanine-glycine (FG) repeat proteins create an entropic barrier to passive diffusion and how this barrier is selectively lowered in facilitated diffusion by the many transient interactions of nuclear transport receptors with the FG repeats. Selective transport is enhanced by \"fuzzy\" multivalent interactions, redundant FG repeat mass, coupling to the energy-dependent RanGTP concentration gradient, and exponential dependence of transport kinetics on the transport barrier. Our model will facilitate rational modulation of the NPC and its artificial mimics.</p>","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"122 42","pages":"e2507559122"},"PeriodicalIF":9.1,"publicationDate":"2025-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145308892","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Corrigendum to “E3 ubiquitin ligase RNF128 attenuates colitis and colorectal tumorigenesis by triggering the degradation of IL-6 receptors” [J. Adv. Res. 72 (2025) 107–120]","authors":"Tian Sheng He, Kuntai Cai, Weiling Lai, Jingge Yu, Furong Qing, Ao Shen, Lina Sui, Wenji He, Weihua Wang, Qiuxiang Xiao, Xiong Lei, Tianfu Guo, Zhiping Liu","doi":"10.1016/j.jare.2025.10.013","DOIUrl":"https://doi.org/10.1016/j.jare.2025.10.013","url":null,"abstract":"The authors regret the oversight in Fig. 5J and Fig. S6A. While organizing the experimental data for this article, they unexpectedly found that some images in these figures were presented incorrectly.","PeriodicalId":14952,"journal":{"name":"Journal of Advanced Research","volume":"116 1","pages":""},"PeriodicalIF":10.7,"publicationDate":"2025-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145314697","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Local microwave sensing of excitons and their electrical environment.","authors":"Zhurun Ji,Mark E Barber,Ziyan Zhu,Carlos R Kometter,Jiachen Yu,Kenji Watanabe,Takashi Taniguchi,Mengkun Liu,Thomas P Devereaux,Benjamin E Feldman,Zhixun Shen","doi":"10.1038/s41467-025-64280-7","DOIUrl":"https://doi.org/10.1038/s41467-025-64280-7","url":null,"abstract":"Excitons in atomically thin transition metal dichalcogenides (TMDs) possess intriguing optical properties, drawing interest for both technology and fundamental research. However, as the demands for nanodevice applications and the exploration of fundamental physics push toward smaller, subwavelength scales, studying them locally is challenging. In this work, we introduce a cryogenic scanning probe photoelectrical sensing technique, termed exciton-resonant microwave impedance microscopy (ER-MIM), to measure the excitonic responses in a monolayer MoSe2 device at 1.5K. From the microwave signal changes, we identify exciton polarons and their Rydberg states. Building on these observations, we systemically reveal the local and nonlocal effects of carrier density, inhomogeneous electric fields, as well as dielectric screening on excitons, beyond the reach of conventional probes. By further integrating deep learning techniques, we precisely extracted the electrical parameters surrounding excitons, demonstrating a quantified, exciton-assisted nanoscale electrometry. Our results provide new insight into exciton-environment interactions, establish ER-MIM as a powerful optoelectronic sensing platform, and open avenues for exciton-based quantum control and device technologies.","PeriodicalId":19066,"journal":{"name":"Nature Communications","volume":"54 1","pages":"9236"},"PeriodicalIF":16.6,"publicationDate":"2025-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145311202","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Prevalence and drug resistance profiles of nontuberculous mycobacteria isolated from Iranian fish pond waters.","authors":"Xiaqian Cui, Yu Zhang, Yancui Cai, Sale Zhang, Ying Li, Haifang Wang, Fatemeh Sakhaee, Seyed Davar Siadat, Abolfazl Fateh","doi":"10.1038/s41598-025-20286-1","DOIUrl":"https://doi.org/10.1038/s41598-025-20286-1","url":null,"abstract":"","PeriodicalId":21811,"journal":{"name":"Scientific Reports","volume":"15 1","pages":"36363"},"PeriodicalIF":3.9,"publicationDate":"2025-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145313851","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dietary variability and micronutrient status of individuals with Yaws infection in Ghana: A case-control study.","authors":"Abigail Agbanyo, Michael Ntiamoah Oppong, Ruth Dede Tuwor, Pius Takyi, Felix Wireko, Philemon Boasiako Antwi, Dzifa Kofi Ahiatrogah, Aloysius Dzigbordi Loglo, Bernadette Agbavor, Alex Owusu-Ofori, Richard Odame Phillips, Yaw Ampem Amoako","doi":"10.1371/journal.pone.0334628","DOIUrl":"https://doi.org/10.1371/journal.pone.0334628","url":null,"abstract":"<p><strong>Background: </strong>Yaws is a neglected tropical skin disease mainly affecting children under 15 years. It is targeted for eradication by 2030 through Mass Drug Administration (MDA) of a single oral dose of azithromycin (30 mg/kg), which has achieved about a 95% cure rate. Despite this, the disease persists in endemic countries. Eradication requires addressing contributing factors, including the role of nutrition in yaws; yet this remains underexplored. This study assessed the nutritional status of individuals in yaws-endemic areas using a case-control design.</p><p><strong>Methods: </strong>A case-control study was conducted from May to November 2024 in 33 communities across two districts in Ghana. Cases were Dual Path Platform (DPP) positive individuals, matched by age and sex with healthy controls. Data collection included demographic and anthropometric measurements and a Ghana-specific multi-pass 24-hour dietary recall.</p><p><strong>Results: </strong>A total of 64 cases and 64 matched controls [median age 11.5 years, Interquartile range (IQR) 9-13.8] were enrolled. Moderate stunting was found in 27% of cases and 22% of controls; severe stunting in 6% and 5%, respectively. Roots and tubers were consumed by all participants, while fruit intake was low (5% overall; 3% in cases, 8% in controls). Controls generally had slightly higher micronutrient intake than cases, except for energy (1754 ± 657 kcal vs. 1726 ± 707.3 kcal), fat (55.15 ± 28.04 g vs. 51.83 ± 27.04 g), and vitamin C (108.7 ± 42.24 mg vs. 107.7 ± 53.18 mg). No statistically significant differences in nutrient adequacy were found between healed and non-healed yaws cases (p > 0.05), though participants with non-healed lesions more often had inadequate intakes of energy (88% vs. 80%), fibre (100% vs. 96%), iron (63% vs. 54%), zinc (75% vs. 71%), and vitamin B12 (63% vs. 55%).</p><p><strong>Conclusion: </strong>In these yaws-endemic districts, we observed high levels of undernutrition and micronutrient deficiencies among both cases and controls. Although nutritional status was not independently linked to poorer treatment outcomes, the burden of malnutrition underscores the need for integrated health interventions. Further research is warranted to clarify the relationship between chronic nutritional deficiencies and yaws outcomes.</p>","PeriodicalId":20189,"journal":{"name":"PLoS ONE","volume":"20 10","pages":"e0334628"},"PeriodicalIF":2.6,"publicationDate":"2025-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145313294","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of different physical therapy training protocols on patients with idiopathic scoliosis: Short-term results.","authors":"Haohan Lu, Min Li, Naizhen Wang, Guobiao Ye, Feilong Zhu, Mingling Guo, Cheng Zeng","doi":"10.1371/journal.pone.0334713","DOIUrl":"https://doi.org/10.1371/journal.pone.0334713","url":null,"abstract":"<p><strong>Background: </strong>Idiopathic scoliosis (IS), a three-dimensional spinal deformity common in adolescents, can be treated with numerous approaches, including Schroth, Spiral stabilization (SPS), and core exercises, to improve spinal alignment and health. However, few studies have shown the superiority of one treatment over another.</p><p><strong>Objective: </strong>This retrospective cohort study was designed to evaluate the efficacy of three distinct physical therapy protocols in managing IS among adolescents aged 6-18 years with Cobb angles ≤40°.</p><p><strong>Methods: </strong>A total of 61 patients were allocated to one of three therapeutic groups. Each group received interventions twice weekly for 10 sessions. Primary outcomes were assessed by measuring changes in the Cobb angle, whereas secondary outcomes included evaluations of pain (visual analog scale, VAS), the angle of trunk rotation (ATR), trunk aesthetic clinical evaluation (TRACE), radiographic parameters (Alignment of the C7 plumbline (C7PL), clavicle angle, and pelvic obliquity), and quality of life (the Scoliosis Research Society-22 questionnaire,SRS-22).</p><p><strong>Results: </strong>The findings revealed significant within-group improvements in the Cobb angle, pain, and trunk rotation for all interventions (p < 0.05). Notably, between-group comparisons indicated that both the Schroth and SPS modalities resulted in greater reductions in the Cobb angle and trunk rotation than core stabilization exercises did (p < 0.05). Moreover, SPS resulted in superior enhancements in the clavicle angle and dynamic postural control, whereas Schroth yielded significant improvements in C7PL alignment.</p><p><strong>Conclusion: </strong>This short-term study underscores the relative effectiveness of the Schroth and SPS interventions in managing three-dimensional spinal deformities and enhancing dynamic postural control while recognizing the limitations of core stabilization exercises for scoliosis.</p><p><strong>Clinical trial registration: </strong>This retrospective analysis of a clinical trial has been registered in the Chinese Clinical Trial Registry (ChiCTR2500096077) https://www.google.com/search?client=firefox-b-d&q=ChiCTR2500096077.</p>","PeriodicalId":20189,"journal":{"name":"PLoS ONE","volume":"20 10","pages":"e0334713"},"PeriodicalIF":2.6,"publicationDate":"2025-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145313295","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"AQuaRef: machine learning accelerated quantum refinement of protein structures.","authors":"Roman Zubatyuk, Malgorzata Biczysko, Kavindri Ranasinghe, Nigel W Moriarty, Hatice Gokcan, Holger Kruse, Billy K Poon, Paul D Adams, Mark P Waller, Adrian E Roitberg, Olexandr Isayev, Pavel V Afonine","doi":"10.1038/s41467-025-64313-1","DOIUrl":"https://doi.org/10.1038/s41467-025-64313-1","url":null,"abstract":"<p><p>Cryo-EM and X-ray crystallography provide crucial experimental data for obtaining atomic-detail models of biomacromolecules. Refining these models relies on library-based stereochemical data, which, in addition to being limited to known chemical entities, do not include meaningful noncovalent interactions. Quantum mechanical (QM) calculations could alleviate these issues but are too expensive for large molecules. Here we present a novel AI-enabled Quantum Refinement (AQuaRef) based on AIMNet2 machine learned interatomic potential (MLIP) mimicking QM at substantially lower computational costs. By refining 41 cryo-EM and 30 X-ray structures, we show that this approach yields atomic models with superior geometric quality compared to standard techniques, while maintaining an equal or better fit to experimental data. Notably, AQuaRef aids in determining proton positions, as illustrated in the challenging case of short hydrogen bonds in the parkinsonism-associated human protein DJ-1 and its bacterial homolog YajL.</p>","PeriodicalId":19066,"journal":{"name":"Nature Communications","volume":"16 1","pages":"9224"},"PeriodicalIF":15.7,"publicationDate":"2025-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145313325","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Assessment of drug-related problems among breast cancer patients in a cancer specialty center in Nepal.","authors":"Aman Kumar Sah, Roshan Prajapati, Nabin Pathak, Sushil Panta, Shila Gurung","doi":"10.1371/journal.pone.0334703","DOIUrl":"https://doi.org/10.1371/journal.pone.0334703","url":null,"abstract":"<p><strong>Introduction: </strong>Breast cancer is the leading cancer among women globally, and its management typically involves surgery, radiotherapy, and chemotherapy. This combination of complex treatment increases the risk of drug-related problems (DRPs), which can negatively impact the quality of life as it prolongs the hospital stays, increases healthcare costs, and leads to morbidity and mortality. Research on DRPs in the context of breast cancer patients in Nepal is limited; therefore, this study aimed to identify DRPs, assess their prevalence, and examine their associated factors, while emphasizing the importance of pharmaceutical care.</p><p><strong>Methods: </strong>A cross-sectional study was conducted at Bhaktapur Cancer Hospital, Nepal, from February to May 2024. The medical records of 92 patients were reviewed to identify DRPs using the Pharmaceutical Care Network Europe V9.1 tool, along with related scientific literatures and evidence-based guidelines, and verified by two independent medical oncologists. Descriptive statistics were used to summarize the patient characteristics, while the chi-square test was used to evaluate the associations between socio-demographic and clinical characteristics with the presence of DRPs, with a p-value <0.05 considered statistically significant.</p><p><strong>Results: </strong>DRPs were identified in 91 of 92 patients (98.9%), totaling 104 events. Most DRPs (87.5%) concerned treatment safety, while 12.5% involved treatment effectiveness. Patient-related factors (43.4%) and drug selection (33.3%) were primary causes. Common adverse effects included alopecia (88.0%) and anorexia (84.8%). A significant association was observed between adverse drug reactions (ADRs) and DRPs (Fisher's exact p-value = 0.011).</p><p><strong>Conclusion: </strong>DRPs were highly prevalent among breast cancer patients, mainly due to safety issues, with ADRs significantly contributing to it. Findings highlight the need for larger multicentric and cohort studies, and integration of oncology pharmacy services to optimize pharmaceutical care and minimize DRPs.</p>","PeriodicalId":20189,"journal":{"name":"PLoS ONE","volume":"20 10","pages":"e0334703"},"PeriodicalIF":2.6,"publicationDate":"2025-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145313326","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}