Mohammed G Alhashim, Kaylie Hausknecht, Michael P Brenner
{"title":"Control of flow behavior in complex fluids using automatic differentiation.","authors":"Mohammed G Alhashim, Kaylie Hausknecht, Michael P Brenner","doi":"10.1073/pnas.2403644122","DOIUrl":"10.1073/pnas.2403644122","url":null,"abstract":"<p><p>Inverse design of complex flows is notoriously challenging because of the high cost of high dimensional optimization. Usually, optimization problems are either restricted to few control parameters, or adjoint-based approaches are used to convert the optimization problem into a boundary value problem. Here, we show that the recent advances in automatic differentiation (AD) provide a generic platform for solving inverse problems in complex fluids. To demonstrate the versatility of the approach, we solve an array of optimization problems related to active matter motion in Newtonian fluids, dispersion in structured porous media, and mixing in journal bearing. Each of these problems highlights the advantages of AD in ease of implementation and computational efficiency to solve high-dimensional optimization problems involving particle-laden flows.</p>","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"122 8","pages":"e2403644122"},"PeriodicalIF":9.4,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143441700","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}
Cheng-Li Chiu, Taige Wang, Ruihua Fan, Kenji Watanabe, Takashi Taniguchi, Xiaomeng Liu, Michael P Zaletel, Ali Yazdani
{"title":"High spatial resolution charge sensing of quantum Hall states.","authors":"Cheng-Li Chiu, Taige Wang, Ruihua Fan, Kenji Watanabe, Takashi Taniguchi, Xiaomeng Liu, Michael P Zaletel, Ali Yazdani","doi":"10.1073/pnas.2424781122","DOIUrl":"10.1073/pnas.2424781122","url":null,"abstract":"<p><p>Charge distribution offers a unique fingerprint of important properties of electronic systems, including dielectric response, charge ordering, and charge fractionalization. We develop an architecture for charge sensing in two-dimensional electronic systems in a strong magnetic field. We probe local change of the chemical potential in a proximitized detector layer using scanning tunneling microscopy, allowing us to infer the chemical potential and the charge profile in the sample. Our technique has both high energy (<0.3 meV) and spatial (<10 nm) resolution exceeding that of previous studies by an order of magnitude. We apply our technique to study the chemical potential of quantum Hall liquids in monolayer graphene under high magnetic fields and their responses to charge impurities. The chemical potential measurement provides a local probe of the thermodynamic gap of quantum Hall ferromagnets and fractional quantum Hall states. The screening charge profile reveals spatially oscillatory response of the quantum Hall liquids to charge impurities and is consistent with the composite Fermi liquid picture close to the half-filling. Our technique also paves the way to map moiré potentials, probe Wigner crystals, and investigate fractional charges in quantum Hall and Chern insulators.</p>","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"122 8","pages":"e2424781122"},"PeriodicalIF":9.4,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143441707","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":"Profile of Mark Kirkpatrick.","authors":"Sandeep Ravindran","doi":"10.1073/pnas.2422883122","DOIUrl":"https://doi.org/10.1073/pnas.2422883122","url":null,"abstract":"","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"122 8","pages":"e2422883122"},"PeriodicalIF":9.4,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143459175","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}
Jie Chen, Peiwen Zhu, Sihui Jin, Zhaokun Zhang, Simei Jiang, Sheng Li, Suning Liu, Qionglin Peng, Yufeng Pan
{"title":"A hormone-to-neuropeptide pathway inhibits sexual receptivity in immature <i>Drosophila</i> females.","authors":"Jie Chen, Peiwen Zhu, Sihui Jin, Zhaokun Zhang, Simei Jiang, Sheng Li, Suning Liu, Qionglin Peng, Yufeng Pan","doi":"10.1073/pnas.2418481122","DOIUrl":"https://doi.org/10.1073/pnas.2418481122","url":null,"abstract":"<p><p>Newborns, typically asexual, undergo a process of sexual transition to reach sexual maturity, but the regulatory mechanism underlying this transition is not clear. Here, we studied how female sexual behavior is modulated during sexual transition by hormones and neuromodulators in <i>Drosophila</i>. We found that neuropeptide Leucokinin (LK) inhibits female receptivity specifically during a sexual transition period in immature females, but not in younger or mature females. Moreover, the steroid hormone ecdysone, which is mainly synthesized in the female ovary during sexual maturation, acts on LK neurons via the ecdysone receptor to suppress sexual receptivity. We further found that LK suppresses female receptivity through its receptor LKR in central pC1 neurons, a decision center for female sexual behavior. These findings reveal a hormone-to-neuropeptide pathway that specifically inhibits sexual behavior during sexual maturation in female <i>Drosophila</i>, shedding light on how hormones and neuromodulators coordinate sexual development and behaviors.</p>","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"122 8","pages":"e2418481122"},"PeriodicalIF":9.4,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143468865","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":"Viral circular RNA-encoded protein, ceVP28, divulges an antiviral response in invertebrates.","authors":"Sirawich Limkul, Tannatorn Phiwthong, Supitcha Wanvimonsuk, Tuangrak Seabkongseng, Phirom Aunkam, Phattarunda Jaree, Waruntorn Luangtrakul, Kanjana Mahanil, Kamonluck Teamtisong, Panlada Tittabutr, Neung Teaumroong, Peter Sarnow, Han-Ching Wang, Kunlaya Somboonwiwat, Pakpoom Boonchuen","doi":"10.1073/pnas.2321707122","DOIUrl":"10.1073/pnas.2321707122","url":null,"abstract":"<p><p>Invertebrates mostly use innate immunity to counteract pathogenic infections. In this study, shrimp was used as a model organism to explore the functions of circular RNAs (circRNAs) derived from white spot syndrome virus (WSSV). We identified four viral circRNAs, termed circWSSV147, circWSSV326, circWSSV458, and circVP28, from transcriptomic data of WSSV-infected shrimp. CircVP28, which contains an internal ribosome entry site, was further characterized to determine its potential as a template for protein translation. We observed the presence of a truncated, circRNA-encoded VP28 (ceVP28) in infected shrimp. Both ceVP28 and its parental counterpart, VP28, share the same host cell binding partner Rab7, which is a host receptor for WSSV. Coadministration of recombinant ceVP28 protein and WSSV to penaeid shrimps reduced both viral copy numbers and mortality upon WSSV challenges. These findings uncovered a host defense mechanism by which a protein encoded by a viral circRNA modulates virus-receptor interactions, resulting in blocking of viral entry.</p>","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"122 8","pages":"e2321707122"},"PeriodicalIF":9.4,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143441779","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":"Correction for Borniego et al., Diverse plant RNAs coat <i>Arabidopsis</i> leaves and are distinct from apoplastic RNAs.","authors":"","doi":"10.1073/pnas.2501042122","DOIUrl":"https://doi.org/10.1073/pnas.2501042122","url":null,"abstract":"","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"122 8","pages":"e2501042122"},"PeriodicalIF":9.4,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143371078","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}
Joleah B Lamb, Nur Abu, Steven R Limbong, Jamaluddin Jompa, William E Feeney, C Drew Harvell
{"title":"Reply to Jones et al.: Opportunities and considerations for valuing seagrass ecosystem services.","authors":"Joleah B Lamb, Nur Abu, Steven R Limbong, Jamaluddin Jompa, William E Feeney, C Drew Harvell","doi":"10.1073/pnas.2500092122","DOIUrl":"https://doi.org/10.1073/pnas.2500092122","url":null,"abstract":"","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"122 8","pages":"e2500092122"},"PeriodicalIF":9.4,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143441771","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}
Benjamin L H Jones, Johan S Eklöf, Richard K F Unsworth, Lucy Coals, Marjolijn J A Christianen, Julian Clifton, Leanne C Cullen-Unsworth, Maricela de la Torre-Castro, Nicole Esteban, Mark Huxham, Narriman S Jiddawi, Len J McKenzie, Masahiro Nakaoka, Lina M Nordlund, Jillian L S Ooi, Anchana Prathep
{"title":"Risks of habitat loss from seaweed cultivation within seagrass.","authors":"Benjamin L H Jones, Johan S Eklöf, Richard K F Unsworth, Lucy Coals, Marjolijn J A Christianen, Julian Clifton, Leanne C Cullen-Unsworth, Maricela de la Torre-Castro, Nicole Esteban, Mark Huxham, Narriman S Jiddawi, Len J McKenzie, Masahiro Nakaoka, Lina M Nordlund, Jillian L S Ooi, Anchana Prathep","doi":"10.1073/pnas.2426971122","DOIUrl":"https://doi.org/10.1073/pnas.2426971122","url":null,"abstract":"","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"122 8","pages":"e2426971122"},"PeriodicalIF":9.4,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143441773","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":"A bacterial effector manipulates host lysosomal protease activity-dependent plasticity in cell death modalities to facilitate infection.","authors":"Zhe Lu, Yong Zhang, Yanzhao Zhong, Lihua Qiang, Pupu Ge, Zehui Lei, Mengyuan Zhao, Yingxu Fang, Bingxi Li, Jing Wang, Qiyao Chai, Cui Hua Liu","doi":"10.1073/pnas.2406715122","DOIUrl":"10.1073/pnas.2406715122","url":null,"abstract":"<p><p>Crosstalk between cell death programs confers appropriate host anti-infection immune responses, but how pathogens co-opt host molecular switches of cell death pathways to reprogram cell death modalities for facilitating infection remains largely unexplored. Here, we identify mammalian cell entry 3C (Mce3C) as a pathogenic cell death regulator secreted by <i>Mycobacterium tuberculosis</i> (Mtb), which causes tuberculosis featured with lung inflammation and necrosis. Mce3C binds host cathepsin B (CTSB), a noncaspase protease acting as a lysosome-derived molecular determinant of cell death modalities, to inhibit its protease activity toward BH3-interacting domain death agonist (BID) and receptor-interacting protein kinase 1 (RIPK1), thereby preventing the production of proapoptotic truncated BID (tBID) while maintaining the abundance of pronecroptotic RIPK1. Disrupting the Mce3C-CTSB interaction promotes host apoptosis while suppressing necroptosis with attenuated Mtb survival and mitigated lung immunopathology in mice. Thus, pathogens manipulate host lysosomal protease activity-dependent plasticity in cell death modalities to promote infection and pathogenicity.</p>","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"122 8","pages":"e2406715122"},"PeriodicalIF":9.4,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143441689","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}
David H Barker, Mary A Carskadon, Caroline Gredvig-Ardito, Chantelle N Hart, Hollie A Raynor, Frank A J L Scheer
{"title":"Independent effects of the human circadian system and sleep/eating cycles on caloric intake in adolescents vary by weight status.","authors":"David H Barker, Mary A Carskadon, Caroline Gredvig-Ardito, Chantelle N Hart, Hollie A Raynor, Frank A J L Scheer","doi":"10.1073/pnas.2407907122","DOIUrl":"10.1073/pnas.2407907122","url":null,"abstract":"<p><p>Late-day eating is linked to increased obesity risk; however, whether the endogenous circadian system independently influences caloric intake and if this control differs among individuals based on weight status is unknown. Here, we investigated in adolescents the independent roles of the endogenous circadian system and of the behavioral sleep/wake cycle (sleep/wake, fasting/eating, rest/activity, dark/dim light, social interaction, posture, etc.) on self-selected caloric intake using a Forced Desynchrony protocol. Fifty-one male and female adolescents across three weight status categories (24 with healthy weight, 13 with overweight, and 14 with obesity) completed the protocol where participants lived on seven 28-h sleep/wake cycles in dim light during wake and complete darkness during sleep. Results suggest that the circadian system and the behavioral cycle each affected caloric intake, with a decrease across the wake episode and an increase from circadian morning to circadian evening in caloric intake. The endogenous circadian rhythm in caloric intake showed a circadian peak-to-trough difference of 196 [CI 95% 164, 226] kcal per meal with peak timing of 296° [288°, 304°; equivalent to ~17:30 in these participants]. In those with overweight/obesity, more calories were consumed later in the waking episode and later in the circadian cycle, and with blunted amplitudes compared to those with healthy weight. Results implicate both the endogenous circadian system and the behavioral cycle in shaping the daily rhythm of food intake. Furthermore, these results help explain the increased drive for caloric intake toward the evening, especially in those at risk for obesity.</p>","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"122 8","pages":"e2407907122"},"PeriodicalIF":9.4,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143441721","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}