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In This Issue Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-12-05
Proceedings of the National Academy of Sciences, Volume 120, Issue 49, December 2023.
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Correction for Zaccone et al., Explaining the low-frequency shear elasticity of confined liquids Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-12-01
Proceedings of the National Academy of Sciences, Volume 120, Issue 49, December 2023.
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Hybrid quantum algorithms for flow problems Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-12-01 Sachin S. BharadwajKatepalli R. SreenivasanaDepartment of Mechanical and Aerospace Engineering, New York University, New York, NY 11201bCourant Institute of Mathematical Sciences, New York University, New York, NY 10012cDepartment of Physics, New York University, New York, NY 10012dCenter for Space Science, New York University, Abu Dhabi 129188, United Arab Emirates
Proceedings of the National Academy of Sciences, Volume 120, Issue 49, December 2023.
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MEnTaT: A machine-learning approach for the identification of mutations to increase protein stability Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-12-01 Samantha N. MuellersKaren N. AllenAdrian WhittyaDepartment of Chemistry, Boston University, Boston, MA 02215
Proceedings of the National Academy of Sciences, Volume 120, Issue 49, December 2023.
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Bimodular architecture of bacterial effector SAP05 that drives ubiquitin-independent targeted protein degradation Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-12-01 Qun LiuAbbas MaqboolFederico G. MirkinYeshveer SinghClare E. M. StevensonDavid M. LawsonSophien KamounWeijie HuangSaskia A. HogenhoutaDepartment of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United KingdombDepartment of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United KingdomcThe Sainsbury Laboratory, University of East Anglia
Proceedings of the National Academy of Sciences, Volume 120, Issue 49, December 2023.
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Fluid dynamics alters liquid–liquid phase separation in confined aqueous two-phase systems Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-12-01 Eric W. HesterSean CarneyVishwesh ShahAlyssa ArnheimBena PatelDino Di CarloAndrea L. BertozziaDepartment of Mathematics, University of California, Los Angeles 90095, CAbCalifornia NanoSystems Institute, University of California, Los Angeles 90095, CAcDepartment of Bioengineering, University of California, Los Angeles 90095, CAdDepartment of Mechanical and Aerospace Engineering, University of California
Proceedings of the National Academy of Sciences, Volume 120, Issue 49, December 2023.
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Coupling during collective cell migration is controlled by a vinculin mechanochemical switch Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-12-06 T. Curtis Shoyer, Evan M. Gates, Jolene I. Cabe, Aarti N. Urs, Daniel E. Conway, Brenton D. Hoffman
The ability of cells to move in a mechanically coupled, coordinated manner, referred to as collective cell migration, is central to many developmental, physiological, and pathophysiological processes. Limited understanding of how mechanical forces and biochemical regulation interact to affect coupling has been a major obstacle to unravelling the underlying mechanisms. Focusing on the linker protein
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pH-dependent structural transitions in cationic ionizable lipid mesophases are critical for lipid nanoparticle function Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-12-06 Julian Philipp, Aleksandra Dabkowska, Anita Reiser, Kilian Frank, Rafał Krzysztoń, Christiane Brummer, Bert Nickel, Clement E. Blanchet, Akhil Sudarsan, Mohd Ibrahim, Svante Johansson, Pia Skantze, Urban Skantze, Sofia Östman, Marie Johansson, Neil Henderson, Kjetil Elvevold, Bård Smedsrød, Nadine Schwierz, Lennart Lindfors, Joachim O. Rädler
Lipid nanoparticles (LNPs) are advanced core-shell particles for messenger RNA (mRNA) based therapies that are made of polyethylene glycol (PEG) lipid, distearoylphosphatidylcholine (DSPC), cationic ionizable lipid (CIL), cholesterol (chol), and mRNA. Yet the mechanism of pH-dependent response that is believed to cause endosomal release of LNPs is not well understood. Here, we show that eGFP (enhanced
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Essential role of MFSD1-GLMP-GIMAP5 in lymphocyte survival and liver homeostasis Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-12-06 Xue Zhong, James J. Moresco, Jolene K. Diedrich, Antonio M. Pinto, Jeffrey A. SoRelle, Jianhui Wang, Katie Keller, Sara Ludwig, Eva Marie Y. Moresco, Bruce Beutler, Jin Huk Choi
We detected ENU-induced alleles of Mfsd1 (encoding the major facilitator superfamily domain containing 1 protein) that caused lymphopenia, splenomegaly, progressive liver pathology, and extramedullary hematopoiesis (EMH). MFSD1 is a lysosomal membrane-bound solute carrier protein with no previously described function in immunity. By proteomic analysis, we identified association between MFSD1 and both
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A suppressor screen in C. elegans identifies a multiprotein interaction that stabilizes the synaptonemal complex Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-12-06 Lisa E. Kursel, Jesus E. Aguayo Martinez, Ofer Rog
Successful chromosome segregation into gametes depends on tightly regulated interactions between the parental chromosomes. During meiosis, chromosomes are aligned end-to-end by an interface called the synaptonemal complex, which also regulates exchanges between them. However, despite the functional and ultrastructural conservation of this essential interface, how protein–protein interactions within
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USP16 is an ISG15 cross-reactive deubiquitinase that targets pro-ISG15 and ISGylated proteins involved in metabolism Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-12-06 Jin Gan, Adán Pinto-Fernández, Dennis Flierman, Jimmy J. L. L. Akkermans, Darragh P. O’Brien, Helene Greenwood, Hannah Claire Scott, Günter Fritz, Klaus-Peter Knobeloch, Jacques Neefjes, Hans van Dam, Huib Ovaa, Hidde L. Ploegh, Benedikt M. Kessler, Paul P. Geurink, Aysegul Sapmaz
Interferon-induced ubiquitin (Ub)-like modifier ISG15 covalently modifies host and viral proteins to restrict viral infections. Its function is counteracted by the canonical deISGylase USP18 or Ub-specific protease 18. Notwithstanding indications for the existence of other ISG15 cross-reactive proteases, these remain to be identified. Here, we identify deubiquitinase USP16 as an ISG15 cross-reactive
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Pathologic vs. protective roles of hypoxia-inducible factor 1 in RPE and photoreceptors in wet vs. dry age-related macular degeneration Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-12-06 Savalan Babapoor-Farrokhran, Yu Qin, Miguel Flores-Bellver, Yueqi Niu, Imran A. Bhutto, Silvia Aparicio-Domingo, Chuanyu Guo, Murilo Rodrigues, Timothy Domashevich, Monika Deshpande, Haley Megarity, Rakesh Chopde, Charles G. Eberhart, Valeria Canto-Soler, Silvia Montaner, Akrit Sodhi
It has previously been reported that antioxidant vitamins can help reduce the risk of vision loss associated with progression to advanced age-related macular degeneration (AMD), a leading cause of visual impairment among the elderly. Nonetheless, how oxidative stress contributes to the development of choroidal neovascularization (CNV) in some AMD patients and geographic atrophy (GA) in others is poorly
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Hippocampal contributions to novel spatial learning are both age-related and age-invariant Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-12-06 Li Zheng, Zhiyao Gao, Stephanie Doner, Alexis Oyao, Martha Forloines, Matthew D. Grilli, Carol A. Barnes, Arne D. Ekstrom
Older adults show declines in spatial memory, although the extent of these alterations is not uniform across the healthy older population. Here, we investigate the stability of neural representations for the same and different spatial environments in a sample of younger and older adults using high-resolution functional MRI of the medial temporal lobes. Older adults showed, on average, lower neural
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Adaptations to infer fitness interdependence promote the evolution of cooperation Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-12-06 Marco Colnaghi, Fernando P. Santos, Paul A. M. Van Lange, Daniel Balliet
The evolution of cooperation is a major question in the biological and behavioral sciences. While most theoretical studies model cooperation in the context of an isolated interaction (e.g., a Prisoner’s Dilemma), humans live in heterogeneous social environments, characterized by large variations in fitness interdependence—the extent to which one’s fitness is affected by others. Theoretical and experimental
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CD5L is a canonical component of circulatory IgM Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-12-06 Nienke Oskam, Maurits A. den Boer, Marie V. Lukassen, Pleuni Ooijevaar-de Heer, Tim S. Veth, Gerard van Mierlo, Szu-Hsueh Lai, Ninotska I. L. Derksen, Victor Yin, Marij Streutker, Vojtech Franc, Marta Šiborová, Mirjam J. A. Damen, Dorien Kos, Arjan Barendregt, Albert Bondt, Johannes B. van Goudoever, Carla J. C. de Haas, Piet C. Aerts, Remy M. Muts, Suzan H. M. Rooijakkers, Gestur Vidarsson, Theo Rispens
Immunoglobulin M (IgM) is an evolutionary conserved key component of humoral immunity, and the first antibody isotype to emerge during an immune response. IgM is a large (1 MDa), multimeric protein, for which both hexameric and pentameric structures have been described, the latter additionally containing a joining (J) chain. Using a combination of single-particle mass spectrometry and mass photometry
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Auditing YouTube’s recommendation system for ideologically congenial, extreme, and problematic recommendations Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-12-05 Muhammad Haroon, Magdalena Wojcieszak, Anshuman Chhabra, Xin Liu, Prasant Mohapatra, Zubair Shafiq
Algorithms of social media platforms are often criticized for recommending ideologically congenial and radical content to their users. Despite these concerns, evidence on such filter bubbles and rabbit holes of radicalization is inconclusive. We conduct an audit of the platform using 100,000 sock puppets that allow us to systematically and at scale isolate the influence of the algorithm in recommendations
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Alternative splicing events as peripheral biomarkers for motor learning deficit caused by adverse prenatal environments Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-12-05 Dipankar J. Dutta, Junko Sasaki, Ankush Bansal, Keiji Sugai, Satoshi Yamashita, Guojiao Li, Christopher Lazarski, Li Wang, Toru Sasaki, Chiho Yamashita, Heather Carryl, Ryo Suzuki, Masato Odawara, Yuka Imamura Kawasawa, Pasko Rakic, Masaaki Torii, Kazue Hashimoto-Torii
Severity of neurobehavioral deficits in children born from adverse pregnancies, such as maternal alcohol consumption and diabetes, does not always correlate with the adversity’s duration and intensity. Therefore, biological signatures for accurate prediction of the severity of neurobehavioral deficits, and robust tools for reliable identification of such biomarkers, have an urgent clinical need. Here
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Excess risk in infant mortality among populations living in flood-prone areas in Bangladesh: A cluster-matched cohort study over three decades, 1988 to 2017 Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-12-05 Francois Rerolle, Benjamin F. Arnold, Tarik Benmarhnia
The Ganges–Brahmaputra–Meghna river basin, running through Tibet, Nepal, Bhutan, Bangladesh, and northern India, is home to more than 618 million people. Annual monsoons bring extensive flooding to the basin, with floods predicted to be more frequent and extreme due to climate change. Yet, evidence regarding the long-term impacts of floods on children’s health is lacking. In this analysis, we used
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Structures of the P. aeruginosa FleQ-FleN master regulators reveal large-scale conformational switching in motility and biofilm control Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-12-05 Lucía Torres-Sánchez, Thibault Géry Sana, Marion Decossas, Yaser Hashem, Petya Violinova Krasteva
Pseudomonas aeruginosa can cause a wide array of chronic and acute infections associated with its ability to rapidly switch between planktonic, biofilm, and dispersed lifestyles, each with a specific arsenal for bacterial survival and virulence. At the cellular level, many of the physiological transitions are orchestrated by the intracellular second messenger c-di-GMP and its receptor-effector FleQ
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The TLR2/TLR6 ligand FSL-1 mitigates radiation-induced hematopoietic injury in mice and nonhuman primates Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-12-05 W. June Brickey, David L. Caudell, Andrew N. Macintyre, John D. Olson, Yanwan Dai, Sirui Li, Gregory O. Dugan, J. Daniel Bourland, Lisa M. O’Donnell, Janet A. Tooze, Guannan Huang, Shuangshuang Yang, Hao Guo, Matthew N. French, Allison N. Schorzman, William C. Zamboni, Gregory D. Sempowski, Zhiguo Li, Kouros Owzar, Nelson J. Chao, J. Mark Cline, Jenny P. Y. Ting
Thrombocytopenia, hemorrhage, anemia, and infection are life-threatening issues following accidental or intentional radiation exposure. Since few therapeutics are available, safe and efficacious small molecules to mitigate radiation-induced injury need to be developed. Our previous study showed the synthetic TLR2/TLR6 ligand fibroblast stimulating lipopeptide (FSL-1) prolonged survival and provided
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Triggered lattice-oxygen oxidation with active-site generation and self-termination of surface reconstruction during water oxidation Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-12-05 Yicheng Wei, Yang Hu, Pengfei Da, Zheng Weng, Pinxian Xi, Chun-Hua Yan
To master the activation law and mechanism of surface lattice oxygen for the oxygen evolution reaction (OER) is critical for the development of efficient water electrolysis. Herein, we propose a strategy for triggering lattice-oxygen oxidation and enabling non-concerted proton–electron transfers during OER conditions by substituting Al in La 0.3 Sr 0.7 CoO 3− δ . According to our experimental data
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Maximum temperatures determine the habitat affiliations of North American mammals Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-12-04 Mahdieh Tourani, Rahel Sollmann, Roland Kays, Jorge Ahumada, Eric Fegraus, Daniel S. Karp
Addressing the ongoing biodiversity crisis requires identifying the winners and losers of global change. Species are often categorized based on how they respond to habitat loss; for example, species restricted to natural environments, those that most often occur in anthropogenic habitats, and generalists that do well in both. However, species might switch habitat affiliations across time and space:
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Assessing residential PM 2.5 concentrations and infiltration factors with high spatiotemporal resolution using crowdsourced sensors Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-12-04 David M. Lunderberg, Yutong Liang, Brett C. Singer, Joshua S. Apte, William W. Nazaroff, Allen H. Goldstein
Building conditions, outdoor climate, and human behavior influence residential concentrations of fine particulate matter (PM 2.5 ). To study PM 2.5 spatiotemporal variability in residences, we acquired paired indoor and outdoor PM 2.5 measurements at 3,977 residences across the United States totaling >10,000 monitor-years of time-resolved data (10-min resolution) from the PurpleAir network. Time-series
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Proximal ejecta of the Bolaven extraterrestrial impact, southern Laos Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-12-04 Kerry Sieh, Dayana Schonwalder Angel, Jason Herrin, Brian Jicha, Brad Singer, Vanpheng Sihavong, Weerachat Wiwegwin, Nathanael Wong, Jia Yong Quah
Sediments in southern Laos and eastern Thailand confirm that the Australasian tektite strewn field came from an extraterrestrial impact crater on the Bolaven Plateau of southern Laos. The principal evidence is the Bolaven diamicton, a pebbly to bouldery breccia that is thickest and coarsest on the plateau. Tektites, the melted target material strewn widely by the forces of the impact 789.0 ± 1.8 ka
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Widespread evidence for elephant exploitation by Last Interglacial Neanderthals on the North European plain Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-12-04 Sabine Gaudzinski-Windheuser, Lutz Kindler, Wil Roebroeks
Neanderthals hunted and butchered straight-tusked elephants, the largest terrestrial mammals of the Pleistocene, in a lake landscape on the North European plain, 125,000 years ago, as recently shown by a study of the Last Interglacial elephant assemblage from Neumark-Nord (Germany). With evidence for a remarkable focus on adult males and on their extended utilization, the data from this location are
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Male androphilia, fraternal birth order, and female fecundity in Samoa: A 10-y retrospective Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-12-04 Scott W. Semenyna, Francisco R. Gómez Jiménez, Doug P. VanderLaan, Paul L. Vasey
Two separate but related literatures have examined familial correlates of male androphilia (i.e., sexual attraction and arousal to masculine adult males). The fraternal birth order effect (FBOE) is a widely established finding that each biological older brother a male has increased the probability of androphilia 20–35% above baseline rates. Other family demographic variables, such as reproduction by
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Biosymbiotic platform for chronic long-range monitoring of biosignals in limited resource settings Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-12-04 Tucker Stuart, Max Farley, Julia Amato, Ryan Thien, Jessica Hanna, Aman Bhatia, David Marshall Clausen, Philipp Gutruf
Remote patient monitoring is a critical component of digital medicine, and the COVID-19 pandemic has further highlighted its importance. Wearable sensors aimed at noninvasive extraction and transmission of high-fidelity physiological data provide an avenue toward at-home diagnostics and therapeutics; however, the infrastructure requirements for such devices limit their use to areas with well-established
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Melting climates shrink North American small mammals Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-12-04 Katherina B. Searing, Mark V. Lomolino, Roberto Rozzi
Mammals play important ecological roles in terrestrial ecosystems, with their particular niches and their impacts on energy flow and nutrient cycling being strongly influenced by one of their most fundamental traits—their body size. Body size influences nearly all of the physiological, behavioral, and ecological traits of mammals, and thus, shifts in body size often serve as key mechanisms of adaptation
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Rex1BD and the 14-3-3 protein control heterochromatin organization at tandem repeats by linking RNAi and HDAC Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-12-04 Jinxin Gao, Wenqi Sun, Jie Li, Hyoju Ban, Tuokai Zhang, Junwei Liao, Namho Kim, Soon Hoo Lee, Qianhua Dong, Robert Madramootoo, Yong Chen, Fei Li
Tandem DNA repeats are often organized into heterochromatin that is crucial for genome organization and stability. Recent studies revealed that individual repeats within tandem DNA repeats can behave very differently. How DNA repeats are assembled into distinct heterochromatin structures remains poorly understood. Here, we developed a genome-wide genetic screen using a reporter gene at different units
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Human anti-C1q autoantibodies bind specifically to solid-phase C1q and enhance phagocytosis but not complement activation Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-12-04 Douwe J. Dijkstra, Fleur S. van de Bovenkamp, Leoni Abendstein, Rob Zuijderduijn, Jos Pool, Cynthia S. M. Kramer, Linda M. Slot, Jan W. Drijfhout, Lisanne de Vor, Kyra A. Gelderman, Suzan H. M. Rooijakkers, Arnaud Zaldumbide, Gestur Vidarsson, Thomas H. Sharp, Paul W. H. I. Parren, Leendert A. Trouw
Autoantibodies directed against complement component C1q are commonly associated with autoimmune diseases, especially systemic lupus erythematosus. Importantly, these anti-C1q autoantibodies are specific for ligand-bound, solid-phase C1q and do not bind to fluid-phase C1q. In patients with anti-C1q, C1q levels are in the normal range, and the autoantibodies are thus not depleting. To study these human
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Potassium jarosite seeding of soils decreases lead and arsenic bioaccessibility: A path toward concomitant remediation Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-12-04 Tyler D. Sowers, Matthew D. Blackmon, Aaron R. Betts, Marissa L. Jerden, Kirk G. Scheckel, Karen D. Bradham
Soils are common sources of metal(loid) contaminant exposure globally. Lead (Pb) and arsenic (As) are of paramount concern due to detrimental neurological and carcinogenic health effects, respectively. Pb and/or As contaminated soils require remediation, typically leading to excavation, a costly and environmentally damaging practice of removing soil to a central location (e.g., hazardous landfill)
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In vivo three-dimensional brain imaging with chemiluminescence probes in Alzheimer’s disease models Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-12-04 Jing Zhang, Carly Wickizer, Weihua Ding, Richard Van, Liuyue Yang, Biyue Zhu, Jun Yang, Yanli Wang, Yongle Wang, Yulong Xu, Can Zhang, Shiqian Shen, Changning Wang, Yihan Shao, Chongzhao Ran
Optical three-dimensional (3D) molecular imaging is highly desirable for providing precise distribution of the target-of-interest in disease models. However, such 3D imaging is still far from wide applications in biomedical research; 3D brain optical molecular imaging, in particular, has rarely been reported. In this report, we designed chemiluminescence probes with high quantum yields, relatively
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Triggering interfacial instabilities during forced imbibition by adjusting the aspect ratio in depth-variable microfluidic porous media Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-12-04 Wenhai Lei, Xukang Lu, Wenbo Gong, Moran Wang
We present a comprehensive description of the aspect ratio impact on interfacial instability in porous media where a wetting liquid displaces a nonwetting fluid. Building on microfluidic experiments, we evidence imbibition scenarios yielding interfacial instabilities and macroscopic morphologies under different depth confinements, which were controlled by aspect ratio and capillary number. We report
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Deformation twin traces on gold surfaces: A pathway to tailored epitaxial growth of 1D semiconductors Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-12-04 Lotan Portal, Iryna Polishchuk, Rotem Zilberberg, Mor Levi, Maria Koifman-Khristosov, Alexander Katsman, Boaz Pokroy
The field of one-dimensional semiconducting materials holds a wide variety of captivating applications, such as photovoltaic cells, electronic devices, catalysis cells, lasers, and more. The tunability of electrical, mechanical, or optical attributes of a semiconductor crystal relies on the ability to control and pattern the crystal’s growth direction, orientation, and dimensions. In this study, we
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Universal Poisson statistics of a passive tracer diffusing in dilute active suspensions Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-12-04 Adrian Baule
The statistics of a passive tracer immersed in a suspension of active particles (swimmers) is derived from first principles by considering a perturbative expansion of the tracer interaction with the microscopic swimmer field. To first order in the swimmer density, the tracer statistics is shown to be exactly represented by a spatial Poisson process combined with independent tracer—swimmer scattering
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Multimodal interactions drive chromatin phase separation and compaction Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-12-04 Tina Ukmar-Godec, Maria-Sol Cima-Omori, Zhadyra Yerkesh, Karthik Eswara, Taekyung Yu, Reshma Ramesh, Gwladys Riviere, Alain Ibanez de Opakua, Wolfgang Fischle, Markus Zweckstetter
Gene silencing is intimately connected to DNA condensation and the formation of transcriptionally inactive heterochromatin by Heterochromatin Protein 1α (HP1α). Because heterochromatin foci are dynamic and HP1α can promote liquid–liquid phase separation, HP1α-mediated phase separation has been proposed as a mechanism of chromatin compaction. The molecular basis of HP1α-driven phase separation and chromatin
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Detection of intact amino acids with a hypervelocity ice grain impact mass spectrometer Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-12-04 Sally E. Burke, Zachary A. Auvil, Karl A. Hanold, Robert E. Continetti
Astrobiology studies are a top priority in answering one of the most fundamental questions in planetary science: Is there life beyond Earth? Saturn’s icy moon Enceladus is a prime target in the search for life in our solar system, identified by NASA as the second-highest priority site for a flagship mission in the next decade. The orbital sampling technique of impact ionization mass spectrometry indicated
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Gut dysbiosis: Ecological causes and causative effects on human disease Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-12-04 Sebastian E. Winter, Andreas J. Bäumler
The gut microbiota plays a role in many human diseases, but high-throughput sequence analysis does not provide a straightforward path for defining healthy microbial communities. Therefore, understanding mechanisms that drive compositional changes during disease (gut dysbiosis) continues to be a central goal in microbiome research. Insights from the microbial pathogenesis field show that an ecological
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Artists are seeking ways to boost firefly conservation. They aren’t the only insects that could benefit Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-11-29 Saima Sidik
Proceedings of the National Academy of Sciences, Volume 120, Issue 49, December 2023.
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Reply to Tannenbaum et al.: Constructive dialogue advancing research on civic honesty Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-11-27 Weiwei ZhangYacheng SunShiyong LiuXinyue ZhouQian YangQi ZhangaResearch Institute of Economics and Management, Southwestern University of Finance and Economics, Chengdu 610074, ChinabDepartment of Marketing School of Economics and Management, Tsinghua University, Beijing 100084, ChinacInstitute of Advanced Studies in Humanities and Social Sciences, Beijing Normal University at Zhuhai, Zhuhai 519087
Proceedings of the National Academy of Sciences, Volume 120, Issue 49, December 2023.
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Reply to Blanco-Pastor: Introgression and heterozygosity complicated grapevine domestication Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-11-27 Hua XiaoZhongjie LiuNan WangBrandon S. GautYongfeng ZhouaNational Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, ChinabDepartment of Ecology and Evolutionary
Proceedings of the National Academy of Sciences, Volume 120, Issue 49, December 2023.
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Correction for Quiroz et al., Cooperative redox and spin activity from three redox congeners of sulfur-bridged iron nitrosyl and nickel dithiolene complexes Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-11-27
Proceedings of the National Academy of Sciences, Volume 120, Issue 49, December 2023.
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Correction for Graetz et al., A comprehensive demographic profile of the US evicted population Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-11-27
Proceedings of the National Academy of Sciences, Volume 120, Issue 49, December 2023.
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A closer look at civic honesty in collectivist cultures Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-11-27 David TannenbaumMichel André MaréchalAlain CohnaEccles School of Business, University of Utah, Salt Lake City, UT 84112bDepartment of Economics, University of Zurich, Zurich CH-8006, SwitzerlandcRady School of Management, University of California, San Diego, CA 92093dSchool of Information, University of Michigan, Ann Arbor, MI 48109
Proceedings of the National Academy of Sciences, Volume 120, Issue 49, December 2023.
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Inclusion of highly admixed genotypes in grapevine genomic analyses leads to an equivocal reconstruction of its domestication history Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-11-27 José Luis Blanco-PastoraDepartamento de Biología, Instituto de Investigación Vitivinícola y Agroalimentaria, Campus de Excelencia Internacional Agroalimentario, Universidad de Cádiz, Puerto Real, Cádiz E-11510, Spain
Proceedings of the National Academy of Sciences, Volume 120, Issue 49, December 2023.
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Genomes of an endangered rattlesnake show that neutral genetic variation predicts adaptive genetic variation and genetic load Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-11-27 Marty KardosaConservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA 98112
Proceedings of the National Academy of Sciences, Volume 120, Issue 49, December 2023.
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Self-organized disordered vegetation patterns with hidden order in arid ecosystems Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-11-27 Salvatore TorquatoaDepartment of Chemistry, Princeton University, Princeton, NJ 08544bDepartment of Physics, Princeton University, Princeton, NJ 08544cPrinceton Materials Institute, Princeton University, Princeton, NJ 08544dProgram in Applied and Computational Mathematics, Princeton University, Princeton, NJ 08544
Proceedings of the National Academy of Sciences, Volume 120, Issue 49, December 2023.
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Slaying the methane minotaur Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-11-27 Euan G. NisbetaDepartment of Earth Sciences, Royal Holloway, University of London, Egham TW20 0EX, United Kingdom
Proceedings of the National Academy of Sciences, Volume 120, Issue 49, December 2023.
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The neurobiology of stress: Vulnerability, resilience, and major depression Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-11-27 Huda AkilEric J. NestleraMichigan Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109bDepartment of Psychiatry, University of Michigan, Ann Arbor, MI 48109cDepartment of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029dFriedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
Proceedings of the National Academy of Sciences, Volume 120, Issue 49, December 2023.
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Neural tracking measures of speech intelligibility: Manipulating intelligibility while keeping acoustics unchanged Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-11-30 I. M. Dushyanthi Karunathilake, Joshua P. Kulasingham, Jonathan Z. Simon
Neural speech tracking has advanced our understanding of how our brains rapidly map an acoustic speech signal onto linguistic representations and ultimately meaning. It remains unclear, however, how speech intelligibility is related to the corresponding neural responses. Many studies addressing this question vary the level of intelligibility by manipulating the acoustic waveform, but this makes it
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Uncovering the semantics of concepts using GPT-4 Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-11-30 Gaël Le Mens, Balázs Kovács, Michael T. Hannan, Guillem Pros
The ability of recent Large Language Models (LLMs) such as GPT-3.5 and GPT-4 to generate human-like texts suggests that social scientists could use these LLMs to construct measures of semantic similarity that match human judgment. In this article, we provide an empirical test of this intuition. We use GPT-4 to construct a measure of typicality—the similarity of a text document to a concept. We evaluate
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Instantons and the quantum bound to chaos Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-11-30 Vijay Ganesh Sadhasivam, Lars Meuser, David R. Reichman, Stuart C. Althorpe
The rate at which information scrambles in a quantum system can be quantified using out-of-time-ordered correlators. A remarkable prediction is that the associated Lyapunov exponent λ that quantifies the scrambling rate in chaotic systems obeys a universal bound λ < 2 π k B T / ħ . Previous numerical and analytical studies have indicated that this bound has a quantum-statistical origin. Here, we use
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Doping-induced assembly interface for noninvasive in vivo local and systemic immunomodulation Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-11-30 Baoning Sha, Shengzhuo Zhao, Minling Gu, Dion Khodagholy, Liping Wang, Guo-Qiang Bi, Zhanhong Du
Peripheral neural interfaces, potent in modulating local and systemic immune responses for disease treatment, face significant challenges due to the peripheral nerves’ broad distribution in tissues like the fascia, periosteum, and skin. The incongruity between static electronic components and the dynamic, complex organization of the peripheral nervous system often leads to interface failure, stalling
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In silico evolution of autoinhibitory domains for a PD-L1 antagonist using deep learning models Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-11-30 Odessa J. Goudy, Amrita Nallathambi, Tomoaki Kinjo, Nicholas Z. Randolph, Brian Kuhlman
There has been considerable progress in the development of computational methods for designing protein–protein interactions, but engineering high-affinity binders without extensive screening and maturation remains challenging. Here, we test a protein design pipeline that uses iterative rounds of deep learning (DL)-based structure prediction (AlphaFold2) and sequence optimization (ProteinMPNN) to design
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Propulsive cell entry diverts pathogens from immune degradation by remodeling the phagocytic synapse Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-11-30 Zihan Zhang, Thomas K. Gaetjens, Jin Ou, Qiong Zhou, Yanqi Yu, D. Paul Mallory, Steven M. Abel, Yan Yu
Phagocytosis is a critical immune function for infection control and tissue homeostasis. During phagocytosis, pathogens are internalized and degraded in phagolysosomes. For pathogens that evade immune degradation, the prevailing view is that virulence factors are required to disrupt the biogenesis of phagolysosomes. In contrast, we present here that physical forces from motile pathogens during cell
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A gain-of-function HCN4 mutant in the HCN domain is responsible for inappropriate sinus tachycardia in a Spanish family Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-11-30 Anabel Cámara-Checa, Francesca Perin, Marcos Rubio-Alarcón, María Dago, Teresa Crespo-García, Josu Rapún, María Marín, Jorge Cebrián, Ricardo Gómez, Francisco Bermúdez-Jiménez, Lorenzo Monserrat, Juan Tamargo, Ricardo Caballero, Juan Jiménez-Jáimez, Eva Delpón
In a family with inappropriate sinus tachycardia (IST), we identified a mutation (p.V240M) of the hyperpolarization-activated cyclic nucleotide–gated type 4 (HCN4) channel, which contributes to the pacemaker current (I f ) in human sinoatrial node cells. Here, we clinically study fifteen family members and functionally analyze the p.V240M variant. Macroscopic (I HCN4 ) and single-channel currents were
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RNA-binding motif protein 10 inactivates c-Myc by partnering with ribosomal proteins uL18 and uL5 Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-11-30 Hyemin Lee, Ji Hoon Jung, Hyun Min Ko, Heewon Park, Allyson M. Segall, Roger L. Sheffmaker, Jieqiong Wang, Wesley D. Frey, Nathan Pham, Yongbo Wang, Yiwei Zhang, James G. Jackson, Shelya X. Zeng, Hua Lu
RNA-binding motif protein 10 (RBM10) is a frequently mutated tumor suppressor in lung adenocarcinoma (LUAD). Yet, it remains unknown whether cancer-derived mutant RBM10 compromises its tumor suppression function and, if so, the molecular insight of the underlying mechanisms. Here, we show that wild-type RBM10 suppresses lung cancer cell growth and proliferation by inactivating c-Myc that is essential
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Massive intein content in Anaeramoeba reveals aspects of intein mobility in eukaryotes Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-11-29 Lucie Gallot-Lavallée, Jon Jerlström-Hultqvist, Paula Zegarra-Vidarte, Dayana E. Salas-Leiva, Courtney W. Stairs, Ivan Čepička, Andrew J. Roger, John M. Archibald
Inteins are self-splicing protein elements found in viruses and all three domains of life. How the DNA encoding these selfish elements spreads within and between genomes is poorly understood, particularly in eukaryotes where inteins are scarce. Here, we show that the nuclear genomes of three strains of Anaeramoeba encode between 45 and 103 inteins, in stark contrast to four found in the most intein-rich
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Beyond spiking networks: The computational advantages of dendritic amplification and input segregation Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-11-29 Cristiano Capone, Cosimo Lupo, Paolo Muratore, Pier Stanislao Paolucci
The brain can efficiently learn a wide range of tasks, motivating the search for biologically inspired learning rules for improving current artificial intelligence technology. Most biological models are composed of point neurons and cannot achieve state-of-the-art performance in machine learning. Recent works have proposed that input segregation (neurons receive sensory information and higher-order
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Low- and high-frequency vibrations synergistically enhance singlet exciton fission through robust vibronic resonances Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2023-11-29 Atandrita Bhattacharyya, Amitav Sahu, Sanjoy Patra, Vivek Tiwari
Singlet exciton fission (SEF) is initiated by ultrafast internal conversion of a singlet exciton into a correlated triplet pair ( T T ) 1 . The “reaction coordinates” for ultrafast SEF even in archetypal systems such as pentacene thin film remain unclear. Couplings between fast electrons and slow nuclei are ubiquitous across a range of phenomena in chemistry. Accordingly, spectroscopic detection of