PNAS nexus最新文献_第2页

Correction to: GraphAge: Unleashing the power of graph neural network to decode epigenetic aging. 修正：graphhage：释放图形神经网络的力量来解码表观遗传老化。

IF 3.8

PNAS nexus Pub Date : 2025-09-17 eCollection Date: 2025-09-01 DOI: 10.1093/pnasnexus/pgaf294

引用次数: 0

Long-term scratching analysis of mice using machine learning. 使用机器学习对小鼠进行长期抓挠分析。

IF 3.8

PNAS nexus Pub Date : 2025-09-17 eCollection Date: 2025-09-01 DOI: 10.1093/pnasnexus/pgaf292

Koji Kobayashi, Yusuke Miyazaki, Naoaki Sakamoto, Masahito Yamamoto, Nanae Nagata, Takahisa Murata

引用次数: 0

Welfare optimization for resource allocation with peer effects. 具有对等效应的资源配置福利优化。

IF 3.8

PNAS nexus Pub Date : 2025-09-16 eCollection Date: 2025-09-01 DOI: 10.1093/pnasnexus/pgaf298

Zirou Qiu, Daniel J Rosenkrantz, Matthew O Jackson, Simon A Levin, S S Ravi, Richard E Stearns, Madhav V Marathe

{"title":"Welfare optimization for resource allocation with peer effects.","authors":"Zirou Qiu, Daniel J Rosenkrantz, Matthew O Jackson, Simon A Levin, S S Ravi, Richard E Stearns, Madhav V Marathe","doi":"10.1093/pnasnexus/pgaf298","DOIUrl":"10.1093/pnasnexus/pgaf298","url":null,"abstract":"Allocating students to schools or universities, people to teams or groups, people to urban housing, and matching users on social platforms are prominent examples of allocating limited goods, spaces, or positions to optimize social welfare. We study a welfare maximization problem that arises when such resource allocation scenarios involve peer effects, where people have preferences over the others who are nearby (e.g. their classmates, teammates, neighbors, or partners). We first develop a unified mathematical framework for this \"position allocation problem,\" which assigns people to positions in a given network, with people caring about both their positions and their neighbors' attributes. We show that welfare maximization for the corresponding position allocation problem is computationally intractable, even when people have preferences that depend only on who is allocated to nearby positions, and those preferences satisfy simple constraints that arise naturally in urban and other real-world systems. In contrast to this computational lower bound, we show that if people can be classified into a fixed number of (demographic) groups and the network satisfies certain realistic spatial conditions, then efficiently computable allocations can be obtained for many natural scenarios. Importantly, the achieved social welfare is either optimal or arbitrarily close to optimal for natural forms of preferences. Our methods provide a foundation for position allocation with peer effects, and guide the design of optimal allocation strategies when people can be classified into a fixed number of groups in which members share similar preferences.","PeriodicalId":74468,"journal":{"name":"PNAS nexus","volume":"4 9","pages":"pgaf298"},"PeriodicalIF":3.8,"publicationDate":"2025-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12461859/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145187498","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Correction to: Critical assessment of the ability of Boolean threshold models to describe gene regulatory network dynamics. 修正：布尔阈值模型描述基因调控网络动态的能力的关键评估。

IF 3.8

PNAS nexus Pub Date : 2025-09-15 eCollection Date: 2025-09-01 DOI: 10.1093/pnasnexus/pgaf290

引用次数: 0

The RNA effector SERRATE is required for the Arabidopsis polycistronic ctr1-10 main open reading frame translation. RNA效应因子SERRATE是拟南芥多顺反子ctr1-10主开放阅读框翻译所必需的。

IF 3.8

PNAS nexus Pub Date : 2025-09-15 eCollection Date: 2025-09-01 DOI: 10.1093/pnasnexus/pgaf296

Ying Zhang, Chi-Kuang Wen

{"title":"The RNA effector SERRATE is required for the Arabidopsis polycistronic ctr1-10 main open reading frame translation.","authors":"Ying Zhang, Chi-Kuang Wen","doi":"10.1093/pnasnexus/pgaf296","DOIUrl":"10.1093/pnasnexus/pgaf296","url":null,"abstract":"The T-DNA insertion at the 5'-untranslated region (5'-UTR) of CONSTITUTIVE TRIPLE-RESPONSE1 (CTR1) results in an extended 5'-UTR of the ctr1-10 mRNA, and the main ORF (mORF) translation requires FRAGILE HISTIDINE TRIAD (FHIT) in the face of upstream open reading frame (uORF) inhibition. The RNA effector SERRATE (SE) was isolated from an enhancer screen for ctr1-10, and CTR1 levels were substantially reduced in se ctr1-10 plants. RNA profiling and genetic analyses revealed changes in CTR1 levels independent of pri-miRNA or ctr1-10 mRNA processing. Ribosome footprinting analyses revealed an impact on ctr1-10 mORF translation efficiency by se. Mutation of the SE-binding cap-binding complex component CAP BINDING PROTEIN20 (CBP20) had effects similar to those of se on CTR1 levels in ctr1-10 plants. Sucrose density gradient fractionation of membrane proteins was used to determine the associations of SE with polysome fractions. In situ editing that disrupted an upstream ATG codon proximal to the ctr1-10 mORF elevated CTR1 levels in an SE-independent manner. Our study revealed the involvement of SE/CBP20 in the translational regulation of polycistronic ctr1-10 mRNAs independent of miRNA biosynthesis and ctr1-10 mRNA processing, advancing the knowledge of the heterogeneity of the translation machinery, which plays roles in fine translation control.","PeriodicalId":74468,"journal":{"name":"PNAS nexus","volume":"4 9","pages":"pgaf296"},"PeriodicalIF":3.8,"publicationDate":"2025-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12461873/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145187458","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Acetylation of lysine 49 on Ctnnb1 drives naïve pluripotency in murine stem cells by modulating Nanog function. Ctnnb1上赖氨酸49的乙酰化通过调节Nanog功能驱动小鼠干细胞naïve多能性。

IF 3.8

PNAS nexus Pub Date : 2025-09-12 eCollection Date: 2025-10-01 DOI: 10.1093/pnasnexus/pgaf297

Toshiyuki Takehara, Mahito Nakanishi, Raku Son, Hirofumi Suemori, Yasuhiro Murakawa, Takeshi Teramura

{"title":"Acetylation of lysine 49 on Ctnnb1 drives naïve pluripotency in murine stem cells by modulating Nanog function.","authors":"Toshiyuki Takehara, Mahito Nakanishi, Raku Son, Hirofumi Suemori, Yasuhiro Murakawa, Takeshi Teramura","doi":"10.1093/pnasnexus/pgaf297","DOIUrl":"https://doi.org/10.1093/pnasnexus/pgaf297","url":null,"abstract":"Naïve pluripotency represents the ground state of mammalian development. A comprehensive understanding of the molecular mechanisms governing its establishment is crucial for elucidating the unique properties of embryonic cells and the regulatory mechanisms controlling cell fate determination. However, the key molecule to robustly achieve naïve pluripotency with minimal manipulation remains unclear. We found that the acetylation status of lysine 49 (K49) of Catenin beta-1 (Ctnnb1) plays a critical role in naïve pluripotency of murine stem cells. Deacetylated Ctnnb1 at K49 binds to transcription factor Nanog, impeding its repressor function and thereby promoting differentiation. Remarkably, treatment with IQ1, an inhibitor of interaction between acetyltransferase Ep300 and Ctnnb1, enhances acetylation at K49 of Ctnnb1, enabling the establishment and long-term maintenance of embryonic stem cells independently of the leukemia inhibitory factor, and also driving complete conversion of epiblast stem cells to the naïve state. This study reveals the critical role of Ctnnb1 in naïve pluripotency and introduces an effective strategy for its induction and maintenance.","PeriodicalId":74468,"journal":{"name":"PNAS nexus","volume":"4 10","pages":"pgaf297"},"PeriodicalIF":3.8,"publicationDate":"2025-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12501846/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145253997","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Unveiling the relationship between aesthetic experiences and attention through a cross-experiment validation of their processing biomarkers. 通过对审美体验和注意力加工生物标志物的交叉实验验证揭示两者之间的关系。

IF 3.8

PNAS nexus Pub Date : 2025-09-09 eCollection Date: 2025-10-01 DOI: 10.1093/pnasnexus/pgaf288

Paolo Barbieri, Martina Berto, Pietro Sarasso, Jacopo Frascaroli, Giacomo Handjaras, Francesca Piovesan, Giorgio Gnecco, Davide Bottari, Irene Ronga

{"title":"Unveiling the relationship between aesthetic experiences and attention through a cross-experiment validation of their processing biomarkers.","authors":"Paolo Barbieri, Martina Berto, Pietro Sarasso, Jacopo Frascaroli, Giacomo Handjaras, Francesca Piovesan, Giorgio Gnecco, Davide Bottari, Irene Ronga","doi":"10.1093/pnasnexus/pgaf288","DOIUrl":"https://doi.org/10.1093/pnasnexus/pgaf288","url":null,"abstract":"A centuries-old tradition encompassing philosophy, psychology, and artistic practice describes aesthetic experiences as characterized by a special state of heightened attention toward external stimuli (i.e. an \"aesthetic attitude\"). In recent years, this view has motivated wide-ranging claims about the nature of our aesthetic encounters and the cognitive benefits of exposure to art. Despite sustained efforts from a growing stream of interdisciplinary research, however, it is still unclear whether aesthetic experiences can be systematically linked to observable attentional enhancements. In this study, we address this long-standing question using electroencephalography (EEG) and advanced machine learning (ML) techniques. We performed a series of EEG experiments measuring brain activity elicited by synthetic and natural images during an aesthetic (beauty judgments) and a pragmatic (symmetry judgments) task. Visual evoked potentials and neural oscillations were used to assess whether the aesthetic task induces attentional enhancements. In line with our hypotheses, the power of alpha and beta prestimulus oscillations significantly decreased in the aesthetic vs. pragmatic task. Furthermore, larger late positive potentials and N170 responses (the latter for natural images only) were found in the aesthetic vs. pragmatic task. ML analyses further showed that prestimulus neural oscillations and N170 responses were systematically able to predict the type of task. Overall, our results highlight the presence of a perceptual processing enhancement and a heightened state of attention in aesthetic contexts. The upshot is a clearer understanding of the dynamics and neural underpinnings of our aesthetic experiences.","PeriodicalId":74468,"journal":{"name":"PNAS nexus","volume":"4 10","pages":"pgaf288"},"PeriodicalIF":3.8,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12501847/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145254076","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Extremophile hotspots linked to containerized industrial waste dumping in a deep-sea basin. 极端微生物热点与在深海盆地倾倒的集装箱工业废物有关。

IF 3.8

PNAS nexus Pub Date : 2025-09-09 eCollection Date: 2025-09-01 DOI: 10.1093/pnasnexus/pgaf260

Johanna Gutleben, Sheila Podell, Kira Mizell, Douglas Sweeney, Carlos Neira, Lisa A Levin, Paul R Jensen

{"title":"Extremophile hotspots linked to containerized industrial waste dumping in a deep-sea basin.","authors":"Johanna Gutleben, Sheila Podell, Kira Mizell, Douglas Sweeney, Carlos Neira, Lisa A Levin, Paul R Jensen","doi":"10.1093/pnasnexus/pgaf260","DOIUrl":"10.1093/pnasnexus/pgaf260","url":null,"abstract":"Decaying barrels on the seafloor linked to DDT contamination have raised concerns about the public health implications of decades old industrial waste dumped off the coast of Los Angeles. To explore their contents, we collected sediment cores perpendicular to five deep-sea barrels. The concentration of DDT and its breakdown products were highly elevated relative to control sites yet did not vary with distance from the barrels, suggesting that they were not associated with the contamination. Sediment cores collected through white halos surrounding three barrels were enriched in calcite and had elevated pH. The associated microbial communities were low diversity and dominated by alkalophilic bacteria with metagenome-assembled genomes adapted to high pH. A solid concretion sampled between a white halo and barrel was composed of brucite, a magnesium hydroxide mineral that forms at high pH. Based on these findings, we postulate that leakage of containerized alkaline waste triggered the formation of mineral concretions that are slowly dissolving and raising the pH of the surrounding sediment pore water. This selects for taxa adapted to extreme alkalinity and drives the precipitation of \"anthropogenic\" carbonates forming white halos, which serve as a visual identifier of barrels that contained alkaline waste. Remarkably, containerized alkaline waste discarded >50 years ago represents a persistent pollutant creating localized mineral formations and microbial communities that resemble those observed at some hydrothermal systems. These formations were observed at one-third of the visually identified barrels in the San Pedro Basin and have unforeseen, long-term consequences for benthic communities in the region.","PeriodicalId":74468,"journal":{"name":"PNAS nexus","volume":"4 9","pages":"pgaf260"},"PeriodicalIF":3.8,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12418377/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145042519","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Microbial living materials promote coral larval settlement. 微生物活性物质促进珊瑚幼虫定居。

IF 3.8

PNAS nexus Pub Date : 2025-09-09 eCollection Date: 2025-09-01 DOI: 10.1093/pnasnexus/pgaf268

Natalie Levy, Samapti Kundu, Marnie Freckelton, Julie Dinasquet, Isabel Flores, Claudia T Galindo-Martínez, Martin Tresguerres, Vanessa De La Garza, Yazhi Sun, Zahra Karimi, Crawford Drury, Christopher P Jury, Joshua R Hancock, Shaochen Chen, Michael G Hadfield, Daniel Wangpraseurt

{"title":"Microbial living materials promote coral larval settlement.","authors":"Natalie Levy, Samapti Kundu, Marnie Freckelton, Julie Dinasquet, Isabel Flores, Claudia T Galindo-Martínez, Martin Tresguerres, Vanessa De La Garza, Yazhi Sun, Zahra Karimi, Crawford Drury, Christopher P Jury, Joshua R Hancock, Shaochen Chen, Michael G Hadfield, Daniel Wangpraseurt","doi":"10.1093/pnasnexus/pgaf268","DOIUrl":"10.1093/pnasnexus/pgaf268","url":null,"abstract":"The global decline of coral reefs calls for new strategies to rapidly restock coral populations and maintain ecosystem functions and services. Low recruitment success on degraded reefs hampers coral sexual propagation and leads to reduced genetic diversity and impaired reef resilience. Here, we introduce a Bacterial Reef Ink (Brink) to assist in coral larval settlement. Brink is a photopolymerized living material that can be rapidly applied to restoration substrates and has been formulated to cultivate two settlement-inducing bacterial strains (Cellulophaga lytica and Thalassotalea euphylliae). Settlement assays performed with broadcast spawning (Montipora capitata) and brooding (Pocillopora acuta) Indo-Pacific corals showed that Brink-coated substrates increased settlement >5-fold compared with uncoated control substrates. Brink can be applied as a flat coating or patterned using light-assisted 3D bioprinting, enabling diverse applications in reef restoration and engineering. This approach demonstrates the potential of functional living materials to enhance coral ecosystem engineering and support coral reef rehabilitation.","PeriodicalId":74468,"journal":{"name":"PNAS nexus","volume":"4 9","pages":"pgaf268"},"PeriodicalIF":3.8,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12418380/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145042551","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

AI-based satellite survey offers independent assessment of migratory wildebeest numbers in the Serengeti. 基于人工智能的卫星调查提供了对塞伦盖蒂迁徙角马数量的独立评估。

IF 3.8

PNAS nexus Pub Date : 2025-09-09 eCollection Date: 2025-09-01 DOI: 10.1093/pnasnexus/pgaf264

Isla Duporge, Zijing Wu, Zeyu Xu, Peng Gong, Daniel Rubenstein, David W Macdonald, Anthony R E Sinclair, Simon Levin, Stephen J Lee, Tiejun Wang

{"title":"AI-based satellite survey offers independent assessment of migratory wildebeest numbers in the Serengeti.","authors":"Isla Duporge, Zijing Wu, Zeyu Xu, Peng Gong, Daniel Rubenstein, David W Macdonald, Anthony R E Sinclair, Simon Levin, Stephen J Lee, Tiejun Wang","doi":"10.1093/pnasnexus/pgaf264","DOIUrl":"10.1093/pnasnexus/pgaf264","url":null,"abstract":"The Great Wildebeest Migrationin the Serengeti-Mara ecosystem is a globally iconic wildlife phenomenon that supports the health and biodiversity of the region by supporting predator populations, regulating herbivore densities, and driving nutrient cycling. This study presents the first AI-powered satellite survey, using two deep learning-based models (U-Net and YOLOv8) to detect and count wildebeest over more than 4,000 km² across two consecutive years in August 2022 and 2023 with F1 scores reaching 0.830 (Precision: 0.832, Recall: 0.838). The satellite-based results show fewer than 600,000 individuals-approximately half the widely cited estimate of 1.3 million wildebeest, which has remained largely unchanged since the 1970s. While some variation may arise from differences in spatial and temporal coverage between survey methods, the satellite approach employs rigorously validated AI models with demonstrated accuracy. Rather than undermining previous methods, this discrepancy underscores the importance of using independent and complementary monitoring tools to refine population estimates and improve our understanding of wildebeest movement dynamics.","PeriodicalId":74468,"journal":{"name":"PNAS nexus","volume":"4 9","pages":"pgaf264"},"PeriodicalIF":3.8,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12418379/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145042572","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0