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arXiv 2021年

作者： Tanaka, Keigo Fujimoto, Ryuichi Okabe, Nobuhiro Mitsuishi, Ikuyuki Akamatsu, Hiroki Ota, Naomi Oguri, Masamune Nishizawa, Atsushi J. Graduate School of Natural Science & Technology Kanazawa University Kakuma-machi Kanazawa Ishikawa920-1192 Japan Faculty of Mathematics and Physics Kanazawa University Kakuma-machi Kanazawa Ishikawa920-1192 Japan Physics Program Graduate School of Advanced Science and Engineering Hiroshima University 1-3-1 Kagamiyama Higashi-Hiroshima Hiroshima739-8526 Japan Hiroshima Astrophysical Science Center Hiroshima University 1-3-1 Kagamiyama Higashi-Hiroshima Hiroshima739-8526 Japan Core Research for Energetic Universe Hiroshima University 1-3-1 Kagamiyama Higashi-Hiroshima Hiroshima739-8526 Japan Department of Physics Nagoya University Furo-cho Chikusa-ku Nagoya Aichi464-8602 Japan SRON Netherlands Institute for Space Research Sorbonnelaan 2 Utrecht3584 CA Netherlands Department of Physics Nara Women's University Kitauoyanishi-machi Nara630-8506 Japan Department of Physics University of Tokyo Tokyo113-0033 Japan Institute of Astronomy University of Tokyo 2-21-1 Osawa Mitaka Tokyo181-0015 Japan University of Tokyo Chiba277-8582 Japan Institute for Advanced Research Nagoya University Furocho Chikusa-ku Nagoya464-8602 Japan

We represent a joint X-ray, weak-lensing, and optical analysis of the optically-selected merging cluster, HSC J085024+001536, from the Subaru HSC-SSP survey. Both the member galaxy density and the weak-lensing mass map show that the cluster is composed of southeast and northwest components. The two-dimensional weak-lensing analysis shows that the southeast component is the main cluster, and the sub- and main-cluster mass ratio is 0.32+0.75-023. The northwest subcluster is offset by ∼ 700 kpc from the main cluster center, and their relative line-of-sight velocity is ∼ 1300kms−1 from spectroscopic redshifts of member galaxies. The X-ray emission is concentrated around the main cluster, while the gas mass fraction within a sphere of 1' radius of the subcluster is only fgas = 4.0+2.3−33%, indicating that the subcluster gas was stripped by ram pressure. X-ray residual image shows three arc-like excess patterns, of which two are symmetrically located at ∼ 550 kpc from the X-ray morphological center, and the other is close to the X-ray core. The excess close to the subcluster has a cold-front feature where dense-cold gas and thin-hot gas contact. The two outer excesses are tangentially elongated about ∼ 450 − 650 kpc, suggesting that the cluster is merged with a non-zero impact parameter. Overall features revealed by the multi-wavelength datasets indicate that the cluster is at the second impact or later. Since the optically-defined merger catalog is unbiased for merger boost of the intracluster medium, X-ray follow-up observations will pave the way to understand merger physics at various phases. Copyright © 2021, The Authors. All rights reserved.

关键词： Merging

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Computationally designed proteins mimic antibody immune evasion in viral evolution

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Immunity 2025年

作者： Youssef, Noor Gurev, Sarah Ghantous, Fadi Brock, Kelly P. Jaimes, Javier A. Thadani, Nicole N. Dauphin, Ann Sherman, Amy C. Yurkovetskiy, Leonid Soto, Daria Estanboulieh, Ralph Kotzen, Ben Notin, Pascal Kollasch, Aaron W. Cohen, Alexander A. Dross, Sandra E. Erasmus, Jesse Fuller, Deborah H. Bjorkman, Pamela J. Lemieux, Jacob E. Luban, Jeremy Seaman, Michael S. Marks, Debora S. Department of Systems Biology Harvard Medical School Boston 02115 MA United States Broad Institute of Harvard and MIT Cambridge 02139 MA United States Department of Electrical Engineering and Computer Science MIT Cambridge 02139 MA United States Center for Virology and Vaccine Research Beth Israel Deaconess Medical Center Boston 02215 MA United States Program in Molecular Medicine University of Massachusetts Chan Medical School Worcester 01655 MA United States Division of Infectious Diseases Department of Medicine Brigham and Women's Hospital Boston 02115 MA United States Massachusetts General Hospital Boston 02114 MA United States Division of Biology and Biological Engineering California Institute of Technology Pasadena 91125 CA United States Department of Microbiology University of Washington Seattle 98195 WA United States National Primate Research Center Seattle 98109 WA United States HDT Bio Seattle 98109 WA United States Massachusetts Consortium on Pathogen Readiness Boston 02115 MA United States Ragon Institute of MGH MIT and Harvard Cambridge 02139 MA United States

Recurrent waves of viral infection necessitate vaccines and therapeutics that remain effective against emerging viruses. Our ability to evaluate interventions is currently limited to assessments against past or circulating variants, which likely differ in their immune escape potential compared with future variants. To address this, we developed EVE-Vax, a computational method for designing antigens that foreshadow immune escape observed in future viral variants. We designed 83 SARS-CoV-2 spike proteins that transduced ACE2-positive cells and displayed neutralization resistance comparable to variants that emerged up to 12 months later in the COVID-19 pandemic. Designed spikes foretold antibody escape from B.1-BA.4/5 bivalent booster sera seen in later variants. The designed constructs also highlighted the increased neutralization breadth elicited by nanoparticle-based, compared with mRNA-based, boosters in non-human primates. Our approach offers targeted panels of synthetic proteins that map the immune landscape for early vaccine and therapeutic evaluation against future viral strains. © 2025 The Authors

关键词： antibody escape generative protein models immune landscape machine learning protein design vaccine evaluation viral evolution

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Macrophage Polarization: Remote Switching of Elastic Movement of Decorated Ligand Nanostructures Controls the Adhesion-Regulated Polarization of Host Macrophages (Adv. Funct. Mater. 21/2021)

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Advanced Functional Materials 2021年第21期31卷

作者： Ramar Thangam Myeong Soo Kim Gunhyu Bae Yuri Kim Nayeon Kang Sungkyu Lee Hee Joon Jung Jinhyeok Jang Hyojun Choi Na Li Minjin Kim Sangwoo Park Seong Yeol Kim Thomas Myeongseok Koo Hong En Fu Yoo Sang Jeon Andreja Ambriović-Ristov Jae-Jun Song Soo Young Kim Steve Park Qiang Wei Changhyun Ko Ki-Bum Lee Ramasamy Paulmurugan Young Keun Kim Heemin Kang Department of Materials Science and Engineering Korea University Seoul 02841 Republic of Korea Institute for High Technology Materials and Devices Korea University Seoul 02841 Republic of Korea Department of Materials Science and Engineering Northwestern University Evanston IL 60208 USA International Institute for Nanotechnology Evanston IL 60208 USA NUANCE Center Northwestern University Evanston IL 60208 USA Department of Otorhinolaryngology-Head and Neck Surgery Korea University College of Medicine Seoul 08308 Republic of Korea Institute of Green Manufacturing Technology Korea University Seoul 02841 Republic of Korea Laboratory for Cell Biology and Signalling Division of Molecular Biology Ruđer Bošković Institute Zagreb 10000 Croatia Department of Materials Science and Engineering Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Republic of Korea College of Polymer Science and Engineering State Key Laboratory of Polymer Materials and Engineering Sichuan University Chengdu 610065 China Department of Applied Physics College of Engineering Sookmyung Women's University Seoul 04310 Republic of Korea Department of Chemistry and Chemical Biology Rutgers University Piscataway NJ 08854 USA Department of Radiology Molecular Imaging Program at Stanford Stanford University School of Medicine Stanford University Palo Alto CA 94304 USA Department of Radiology Canary Center at Stanford for Cancer Early Detection Stanford University School of Medicine Stanford University Palo Alto CA 94304 USA Department of Biomicrosystem Technology Korea University Seoul 02841 Republic of Korea

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ψ(2S) Suppression in Pb-Pb Collisions at the LHC

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Physical Review Letters 2024年第4期132卷 042301-042301页

作者： S. Acharya D. Adamová A. Adler G. Aglieri Rinella M. Agnello N. Agrawal Z. Ahammed S. Ahmad S. U. Ahn I. Ahuja A. Akindinov M. Al-Turany D. Aleksandrov B. Alessandro H. M. Alfanda R. Alfaro Molina B. Ali A. Alici N. Alizadehvandchali A. Alkin J. Alme G. Alocco T. Alt I. Altsybeev M. N. Anaam C. Andrei A. Andronic V. Anguelov F. Antinori P. Antonioli N. Apadula L. Aphecetche H. Appelshäuser C. Arata S. Arcelli M. Aresti R. Arnaldi I. C. Arsene M. Arslandok A. Augustinus R. Averbeck M. D. Azmi A. Badalà J. Bae Y. W. Baek X. Bai R. Bailhache Y. Bailung A. Balbino A. Baldisseri B. Balis D. Banerjee Z. Banoo R. Barbera F. Barile L. Barioglio M. Barlou G. G. Barnaföldi L. S. Barnby V. Barret L. Barreto C. Bartels K. Barth E. Bartsch F. Baruffaldi N. Bastid S. Basu G. Batigne D. Battistini B. Batyunya D. Bauri J. L. Bazo Alba I. G. Bearden C. Beattie P. Becht D. Behera I. Belikov A. D. C. Bell Hechavarria F. Bellini R. Bellwied S. Belokurova V. Belyaev G. Bencedi S. Beole A. Bercuci Y. Berdnikov A. Berdnikova L. Bergmann M. G. Besoiu L. Betev P. P. Bhaduri A. Bhasin M. A. Bhat B. Bhattacharjee L. Bianchi N. Bianchi J. Bielčík J. Bielčíková J. Biernat A. P. Bigot A. Bilandzic G. Biro S. Biswas N. Bize J. T. Blair D. Blau M. B. Blidaru N. Bluhme C. Blume G. Boca F. Bock T. Bodova A. Bogdanov S. Boi J. Bok L. Boldizsár A. Bolozdynya M. Bombara P. M. Bond G. Bonomi H. Borel A. Borissov A. G. Borquez Carcamo H. Bossi E. Botta Y. E. M. Bouziani L. Bratrud P. Braun-Munzinger M. Bregant M. Broz G. E. Bruno D. Budnikov H. Buesching S. Bufalino O. Bugnon P. Buhler Z. Buthelezi S. A. Bysiak M. Cai H. Caines A. Caliva E. Calvo Villar J. M. M. Camacho P. Camerini F. D. M. Canedo M. Carabas A. A. Carballo F. Carnesecchi R. Caron J. Castillo Castellanos F. Catalano C. Ceballos Sanchez I. Chakaberia P. Chakraborty S. Chandra S. Chapeland M. Chartier S. Chattopadhyay T. G. Chavez T. Cheng C. Cheshkov B. Cheynis V. Chibante Barroso D. D. Chinellato E. S. Chizzali J. Cho S. Cho P. Chochula P. Christakoglou C. H. Christensen P. Christianse Université Clermont Auvergne CNRS/IN2P3 LPC Clermont-Ferrand France Nuclear Physics Institute of the Czech Academy of Sciences Husinec-Řež Czech Republic Johann-Wolfgang-Goethe Universität Frankfurt Institut für Informatik Fachbereich Informatik und Mathematik Frankfurt Germany European Organization for Nuclear Research (CERN) Geneva Switzerland Dipartimento DISAT del Politecnico and Sezione INFN Turin Italy INFN Sezione di Bologna Bologna Italy Variable Energy Cyclotron Centre Homi Bhabha National Institute Kolkata India Department of Physics Aligarh Muslim University Aligarh India Korea Institute of Science and Technology Information Daejeon Republic of Korea Faculty of Science P.J. Šafárik University Košice Slovak Republic Affiliated with an institute covered by a cooperation agreement with CERN Research Division and ExtreMe Matter Institute EMMI GSI Helmholtzzentrum für Schwerionenforschung GmbH Darmstadt Germany INFN Sezione di Torino Turin Italy Central China Normal University Wuhan China Instituto de Física Universidad Nacional Autónoma de México Mexico City Mexico Dipartimento di Fisica e Astronomia dell’Università and Sezione INFN Bologna Italy University of Houston Houston Texas USA Department of Physics and Technology University of Bergen Bergen Norway INFN Sezione di Cagliari Cagliari Italy Institut für Kernphysik Johann Wolfgang Goethe-Universität Frankfurt Frankfurt Germany Horia Hulubei National Institute of Physics and Nuclear Engineering Bucharest Romania Westfälische Wilhelms-Universität Münster Institut für Kernphysik Munster Germany Physikalisches Institut Ruprecht-Karls-Universität Heidelberg Heidelberg Germany INFN Sezione di Padova Padova Italy Lawrence Berkeley National Laboratory Berkeley California USA SUBATECH IMT Atlantique Nantes Université CNRS-IN2P3 Nantes France Laboratoire de Physique Subatomique et de Cosmologie Université Grenoble-Alpes CNRS-IN2P3 Grenoble France Department of Physics University of Oslo

The production of the ψ(2S) charmonium state was measured with ALICE in Pb-Pb collisions at sNN=5.02 TeV, in the dimuon decay channel. A significant signal was observed for the first time at LHC energies down to zer... 详细信息

关键词： Color confinement Relativistic heavy-ion collisions Quarkonia

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First Measurement of Antideuteron Number Fluctuations at Energies Available at the Large Hadron Collider

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Physical Review Letters 2023年第4期131卷 041901-041901页

作者： S. Acharya D. Adamová A. Adler G. Aglieri Rinella M. Agnello N. Agrawal Z. Ahammed S. Ahmad S. U. Ahn I. Ahuja A. Akindinov M. Al-Turany D. Aleksandrov B. Alessandro H. M. Alfanda R. Alfaro Molina B. Ali Y. Ali A. Alici N. Alizadehvandchali A. Alkin J. Alme G. Alocco T. Alt I. Altsybeev M. N. Anaam C. Andrei A. Andronic V. Anguelov F. Antinori P. Antonioli C. Anuj N. Apadula L. Aphecetche H. Appelshäuser S. Arcelli R. Arnaldi I. C. Arsene M. Arslandok A. Augustinus R. Averbeck S. Aziz M. D. Azmi A. Badalà Y. W. Baek X. Bai R. Bailhache Y. Bailung R. Bala A. Balbino A. Baldisseri B. Balis D. Banerjee Z. Banoo R. Barbera L. Barioglio M. Barlou G. G. Barnaföldi L. S. Barnby V. Barret L. Barreto C. Bartels K. Barth E. Bartsch F. Baruffaldi N. Bastid S. Basu G. Batigne D. Battistini B. Batyunya D. Bauri J. L. Bazo Alba I. G. Bearden C. Beattie P. Becht D. Behera I. Belikov A. D. C. Bell Hechavarria R. Bellwied S. Belokurova V. Belyaev G. Bencedi S. Beole A. Bercuci Y. Berdnikov A. Berdnikova L. Bergmann M. G. Besoiu L. Betev P. P. Bhaduri A. Bhasin I. R. Bhat M. A. Bhat B. Bhattacharjee L. Bianchi N. Bianchi J. Bielčík J. Bielčíková J. Biernat A. Bilandzic G. Biro S. Biswas J. T. Blair D. Blau M. B. Blidaru N. Bluhme C. Blume G. Boca F. Bock T. Bodova A. Bogdanov S. Boi J. Bok L. Boldizsár A. Bolozdynya M. Bombara P. M. Bond G. Bonomi H. Borel A. Borissov H. Bossi E. Botta L. Bratrud P. Braun-Munzinger M. Bregant M. Broz G. E. Bruno M. D. Buckland D. Budnikov H. Buesching S. Bufalino O. Bugnon P. Buhler Z. Buthelezi J. B. Butt A. Bylinkin S. A. Bysiak M. Cai H. Caines A. Caliva E. Calvo Villar J. M. M. Camacho R. S. Camacho P. Camerini F. D. M. Canedo M. Carabas F. Carnesecchi R. Caron J. Castillo Castellanos F. Catalano C. Ceballos Sanchez I. Chakaberia P. Chakraborty S. Chandra S. Chapeland M. Chartier S. Chattopadhyay T. G. Chavez T. Cheng C. Cheshkov B. Cheynis V. Chibante Barroso D. D. Chinellato E. S. Chizzali S. Cho P. Chochula P. Christakoglou C. H. Christensen P. Christiansen T. Chujo M. Ciacco C. Cicalo L. C Université Clermont Auvergne CNRS/IN2P3 LPC Clermont-Ferrand France Variable Energy Cyclotron Centre Homi Bhabha National Institute Kolkata India Nuclear Physics Institute of the Czech Academy of Sciences Husinec-Řež Czech Republic Johann-Wolfgang-Goethe Universität Frankfurt Institut für Informatik Fachbereich Informatik und Mathematik Frankfurt Germany European Organization for Nuclear Research (CERN) Geneva Switzerland Dipartimento DISAT del Politecnico and Sezione INFN Turin Italy INFN Sezione di Bologna Bologna Italy Department of Physics Aligarh Muslim University Aligarh India Korea Institute of Science and Technology Information Daejeon Republic of Korea Faculty of Science P.J. Šafárik University Košice Slovak Republic Affiliated with an institute covered by a cooperation agreement with CERN Research Division and ExtreMe Matter Institute EMMI GSI Helmholtzzentrum für Schwerionenforschung GmbH Darmstadt Germany INFN Sezione di Torino Turin Italy Central China Normal University Wuhan China Instituto de Física Universidad Nacional Autónoma de México Mexico City Mexico COMSATS University Islamabad Islamabad Pakistan Dipartimento di Fisica e Astronomia dell’Università and Sezione INFN Bologna Italy University of Houston Houston Texas USA Department of Physics and Technology University of Bergen Bergen Norway INFN Sezione di Cagliari Cagliari Italy Institut für Kernphysik Johann Wolfgang Goethe-Universität Frankfurt Frankfurt Germany Horia Hulubei National Institute of Physics and Nuclear Engineering Bucharest Romania Westfälische Wilhelms-Universität Münster Institut für Kernphysik Münster Germany Physikalisches Institut Ruprecht-Karls-Universität Heidelberg Heidelberg Germany INFN Sezione di Padova Padova Italy Lawrence Berkeley National Laboratory Berkeley California USA SUBATECH IMT Atlantique Nantes Université CNRS-IN2P3 Nantes France Department of Physics University of Oslo Oslo Norway Yale University New Haven Connecticut USA L

The first measurement of event-by-event antideuteron number fluctuations in high energy heavy-ion collisions is presented. The measurements are carried out at midrapidity (|η|<0.8) as a function of collision centrality in Pb-Pb collisions at sNN=5.02 TeV using the ALICE detector. A significant negative correlation between the produced antiprotons and antideuterons is observed in all collision centralities. The results are compared with a state-of-the-art coalescence calculation. While it describes the ratio of higher order cumulants of the antideuteron multiplicity distribution, it fails to describe quantitatively the magnitude of the correlation between antiproton and antideuteron production. On the other hand, thermal-statistical model calculations describe all the measured observables within uncertainties only for correlation volumes that are different with respect to those describing proton yields and a similar measurement of net-proton number fluctuations.

关键词： Hadron-hadron interactions

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A Causal Roadmap for Generating High-Quality Real-World Evidence

arXiv

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arXiv 2023年

作者： Dang, Lauren E. Gruber, Susan Lee, Hana Dahabreh, Issa Stuart, Elizabeth A. Williamson, Brian D. Wyss, Richard Díaz, Iván Ghosh, Debashis Kıcıman, Emre Alemayehu, Demissie Hoffman, Katherine L. Vossen, Carla Y. Huml, Raymond A. Ravn, Henrik Kvist, Kajsa Pratley, Richard Shih, Mei-Chiung Pennello, Gene Martin, David Waddy, Salina P. Barr, Charles E. Akacha, Mouna Buse, John B. van der Laan, Mark Petersen, Maya Department of Biostatistics University of California BerkeleyCA United States TL Revolution CambridgeMA United States Office of Biostatistics Office of Translational Sciences Center for Drug Evaluation and Research U.S. Food and Drug Administration Silver SpringMD United States Department of Epidemiology Harvard T.H. Chan School of Public Health BostonMA United States Department of Mental Health Johns Hopkins Bloomberg School of Public Health BaltimoreMD United States Biostatistics Division Kaiser Permanente Washington Health Research Institute SeattleWA United States Division of Pharmacoepidemiology and Pharmacoeconomics Brigham and Women’s Hospital Harvard Medical School BostonMA United States Division of Biostatistics Department of Population Health New York University Grossman School of Medicine New YorkNY United States Department of Biostatistics and Informatics Colorado School of Public Health University of Colorado Anschutz Medical Campus AuroraCO United States Microsoft Research RedmondWA United States Global Biometrics and Data Management Pfizer Inc. New YorkNY United States Department of Epidemiology Mailman School of Public Health Columbia University New YorkNY United States Syneos Health Clinical Solutions Amsterdam Netherlands Syneos Health Clinical Solutions MorrisvilleNC United States Novo Nordisk Søborg Denmark AdventHealth Translational Research Institute OrlandoFL United States Cooperative Studies Program Coordinating Center VA Palo Alto Health Care System Palo AltoCA United States Department of Biomedical Data Science Stanford University StanfordCA United States Division of Imaging Diagnostics and Software Reliability Office of Science and Engineering Laboratories Center for Devices and Radiological Health U.S. Food and Drug Administration Silver SpringMD United States Global Real World Evidence Group Moderna CambridgeMA United States National Center for Advancing Translational Sciences BethesdaMD United States G

Increasing emphasis on the use of real-world evidence (RWE) to support clinical policy and regulatory decision-making has led to a proliferation of guidance, advice, and frameworks from regulatory agencies, academia, professional societies, and industry. A broad spectrum of studies use real-world data (RWD) to produce RWE, ranging from randomized controlled trials with outcomes assessed using RWD to fully observational studies. Yet many RWE study proposals lack sufficient detail to evaluate adequacy, and many analyses of RWD suffer from implausible assumptions, other methodological flaws, or inappropriate interpretations. The Causal Roadmap is an explicit, itemized, iterative process that guides investigators to pre-specify analytic study designs;it addresses a wide range of guidance within a single framework. By requiring transparent evaluation of causal assumptions and facilitating objective comparisons of design and analysis choices based on pre-specified criteria, the Roadmap can help investigators to evaluate the quality of evidence that a given study is likely to produce, specify a study to generate high-quality RWE, and communicate effectively with regulatory agencies and other stakeholders. This paper aims to disseminate and extend the Causal Roadmap framework for use by clinical and translational researchers, with companion papers demonstrating application of the Causal Roadmap for specific use cases. Copyright © 2023, The Authors. All rights reserved.

关键词： Decision making

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CellLENS enables cross-domain information fusion for enhanced cell population delineation in single-cell spatial omics data

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Nature immunology 2025年 2025 May 22页

作者： Bokai Zhu Sheng Gao Shuxiao Chen Yuchen Wang Jason Yeung Yunhao Bai Amy Y Huang Yao Yu Yeo Guanrui Liao Shulin Mao Zhenghui G Jiang Scott J Rodig Ka-Chun Wong Alex K Shalek Garry P Nolan Sizun Jiang Zongming Ma Ragon Institute of MGH MIT and Harvard Cambridge MA USA. Broad Institute of MIT and Harvard Cambridge MA USA. Massachusetts Institute of Technology Cambridge MA USA. Department of Statistics and Data Science The Wharton School University of Pennsylvania Philadelphia PA USA. Center for Virology and Vaccine Research Beth Israel Deaconess Medical Center Harvard Medical School Boston MA USA. Department of Computer Science City University of Hong Kong Hong Kong People's Republic of China. Dana-Farber Cancer Institute Boston MA USA. Center of Hepato-Pancreato-Biliary Surgery The First Affiliated Hospital of Sun Yat-sen University Guangzhou People's Republic of China. Division of Genetics and Genomics Boston Children's Hospital Harvard Medical School Boston MA USA. Program in Biological and Biomedical Sciences Harvard Medical School Boston MA USA. Division of Gastroenterology/Liver Center Beth Israel Deaconess Medical Center Harvard Medical School Boston MA USA. Department of Pathology Brigham and Women's Hospital Harvard Medical School Boston MA USA. Institute for Medical Engineering and Science Massachusetts Institute of Technology Cambridge MA USA. Department of Chemistry Massachusetts Institute of Technology Cambridge MA USA. Koch Institute for Integrative Cancer Research Massachusetts Institute of Technology Cambridge MA USA. Department of Pathology Stanford University Stanford CA USA. gnolan@stanford.edu. Broad Institute of MIT and Harvard Cambridge MA USA. sjiang3@bidmc.harvard.edu. Center for Virology and Vaccine Research Beth Israel Deaconess Medical Center Harvard Medical School Boston MA USA. sjiang3@bidmc.harvard.edu. Dana-Farber Cancer Institute Boston MA USA. sjiang3@bidmc.harvard.edu. Department of Pathology Brigham and Women's Hospital Harvard Medical School Boston MA USA. sjiang3@bidmc.harvard.edu. Department of Statistics and Data Science Yale University New Haven CT USA. zongming.ma@yale.edu.

Delineating cell populations is crucial for understanding immune function in health and disease. Spatial omics technologies offer insights by capturing three complementary domains: single-cell molecular biomarker expression, cellular spatial relationships and tissue architecture. However, current computational methods often fail to fully integrate these multidimensional data, particularly for immune cell populations and intrinsic functional states. We introduce Cell Local Environment and Neighborhood Scan (CellLENS), a self-supervised computational method that learns cellular representations by fusing information across three spatial omics domains (expression, neighborhood and image). CellLENS markedly enhances de novo discovery of biologically relevant immune cell populations at fine granularity by integrating individual cells' molecular profiles with their neighborhood context and tissue localization. By applying CellLENS to diverse spatial proteomic and transcriptomic datasets across multiple tissue types and disease settings, we uncover unique immune cell populations functionally stratified according to their spatial contexts. Our work demonstrates the power of multi-domain data integration in spatial omics to reveal insights into immune cell heterogeneity and tissue-specific functions.

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A consensus protocol for functional connectivity analysis in the rat brain (vol 26, pg 673, 2023)

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NATURE NEUROscience 2023年第6期26卷 1127-1128页

作者： Grandjean, Joanes Desrosiers-Gregoire, Gabriel Anckaerts, Cynthia Angeles-Valdez, Diego Ayad, Fadi Barriere, David A. Blockx, Ines Bortel, Aleksandra Broadwater, Margaret Cardoso, Beatriz M. Celestine, Marina Chavez-Negrete, Jorge E. Choi, Sangcheon Christiaen, Emma Clavijo, Perrin Colon-Perez, Luis Cramer, Samuel Daniele, Tolomeo Dempsey, Elaine Diao, Yujian Doelemeyer, Arno Dopfel, David Dvorakova, Lenka Falfan-Melgoza, Claudia Fernandes, Francisca F. Fowler, Caitlin F. Fuentes-Ibanez, Antonio Garin, Clement M. Gelderman, Eveline Golden, Carla E. M. Guo, Chao C. G. Henckens, Marloes J. A. G. Hennessy, Lauren A. Herman, Peter Hofwijks, Nita Horien, Corey Ionescu, Tudor M. Jones, Jolyon Kaesser, Johannes Kim, Eugene Lambers, Henriette Lazari, Alberto Lee, Sung-Ho Lillywhite, Amanda Liu, Yikang Liu, Yanyan Y. Lopez-Castro, Alejandra Lopez-Gil, Xavier Ma, Zilu MacNicol, Eilidh Madularu, Dan Mandino, Francesca Marciano, Sabina McAuslan, Matthew J. McCunn, Patrick McIntosh, Alison Meng, Xianzong Meyer-Baese, Lisa Missault, Stephan Moro, Federico Naessens, Daphne M. P. Nava-Gomez, Laura J. Nonaka, Hiroi Ortiz, Juan J. Paasonen, Jaakko Peeters, Lore M. Pereira, Mickael Perez, Pablo D. Pompilus, Marjory Prior, Malcolm Rakhmatullin, Rustam Reimann, Henning M. Reinwald, Jonathan Del Rio, Rodrigo Triana Rivera-Olvera, Alejandro Ruiz-Perez, Daniel Russo, Gabriele Rutten, Tobias J. Ryoke, Rie Sack, Markus Salvan, Piergiorgio Sanganahalli, Basavaraju G. Schroeter, Aileen Seewoo, Bhedita J. Selingue, Erwan Seuwen, Aline Shi, Bowen Sirmpilatze, Nikoloz Smith, Joanna A. B. Smith, Corrie Sobczak, Filip Stenroos, Petteri J. Straathof, Milou Strobelt, Sandra Sumiyoshi, Akira Takahashi, Kengo Torres-Garcia, Maria E. Tudela, Raul van den Berg, Monica van der Marel, Kajo van Hout, Aran T. B. Vertullo, Roberta Vidal, Benjamin Vrooman, Roel M. Wang, Victora X. Wank, Isabel Watson, David J. G. Yin, Ting Zhang, Yongzhi Zurbruegg, Stefan Achard, Sophie Alcauter, Sarael Auer, Dorothee P. Barbier, Emmanuel L. Baudewig, Juergen Beckmann, Chri Donders Institute for Brain Behaviour and Cognition Radboud University Nijmegen The Netherlands Department for Medical Imaging Radboud University Medical Center Nijmegen The Netherlands Cerebral Imaging Centre Douglas Mental Health University Institute Verdun QC Canada Integrated Program in Neuroscience McGill University Montreal QC Canada Bio-imaging Lab University of Antwerp Antwerp Belgium µNEURO Research Centre of Excellence University of Antwerp Antwerp Belgium Instituto de Neurobiología Universidad Nacional Autónoma de México Campus Juriquilla Querétaro Mexico Biological and Biomedical Engineering McGill University Montreal QC Canada McConnell Brain Imaging Centre McGill University Montreal QC Canada Montreal Neurological Institute McGill University Montreal QC Canada UMR INRAE/CNRS 7247 Physiologie des Comportements et de la Reproduction Physiologie de la reproduction et des comportements Centre de recherche INRAE de Nouzilly Tours France Department of Neurology and Neurosurgery McGill University Montreal QC Canada Center for Animal MRI University of North Carolina at Chapel Hill Chapel Hill NC USA Department of Neurology University of North Carolina at Chapel Hill Chapel Hill NC USA Biomedical Research Imaging Center University of North Carolina at Chapel Hill Chapel Hill NC USA Preclinical MRI Champalimaud Research Champalimaud Centre for the Unknown Lisbon Portugal Laboratoire des Maladies Neurodégénératives Molecular Imaging Research Center (MIRCen) Université Paris-Saclay Commissariat à l’Énergie Atomique et aux Énergies Alternatives (CEA) CNRS Fontenay-aux-Roses France Departamento de Neurobiología Conductual y Cognitiva Instituto de Neurobiología Universidad Nacional Autónoma de México Campus Juriquilla Querétaro México Translational Neuroimaging and Neural Control Group High-Field Magnetic Resonance Max Planck Institute for Biological Cybernetics Tuebingen Germany Graduate Training Centre of Neuroscience International Max

Task-free functional connectivity in animal models provides an experimental framework to examine connectivity phenomena under controlled conditions and allows for comparisons with data modalities collected under invasive or terminal procedures. Currently, animal acquisitions are performed with varying protocols and analyses that hamper result comparison and integration. Here we introduce StandardRat, a consensus rat functional magnetic resonance imaging acquisition protocol tested across 20 centers. To develop this protocol with optimized acquisition and processing parameters, we initially aggregated 65 functional imaging datasets acquired from rats across 46 centers. We developed a reproducible pipeline for analyzing rat data acquired with diverse protocols and determined experimental and processing parameters associated with the robust detection of functional connectivity across centers. We show that the standardized protocol enhances biologically plausible functional connectivity patterns relative to previous acquisitions. The protocol and processing pipeline described here is openly shared with the neuroimaging community to promote interoperability and cooperation toward tackling the most important challenges in neuroscience.

关键词： Databases Neural circuits

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Exploring the Strong Interaction of Three-Body Systems at the LHC

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Physical Review X 2024年第3期14卷 031051页

作者： S. Acharya D. Adamová G. Aglieri Rinella M. Agnello N. Agrawal Z. Ahammed S. Ahmad S. U. Ahn I. Ahuja A. Akindinov M. Al-Turany D. Aleksandrov B. Alessandro H. M. Alfanda R. Alfaro Molina B. Ali A. Alici N. Alizadehvandchali A. Alkin J. Alme G. Alocco T. Alt A. R. Altamura I. Altsybeev J. R. Alvarado M. N. Anaam C. Andrei N. Andreou A. Andronic V. Anguelov F. Antinori P. Antonioli N. Apadula L. Aphecetche H. Appelshäuser C. Arata S. Arcelli M. Aresti R. Arnaldi J. G. M. C. A. Arneiro I. C. Arsene M. Arslandok A. Augustinus R. Averbeck M. D. Azmi H. Baba A. Badalà J. Bae Y. W. Baek X. Bai R. Bailhache Y. Bailung A. Balbino A. Baldisseri B. Balis D. Banerjee Z. Banoo R. Barbera F. Barile L. Barioglio M. Barlou B. Barman G. G. Barnaföldi L. S. Barnby V. Barret L. Barreto C. Bartels K. Barth E. Bartsch N. Bastid S. Basu G. Batigne D. Battistini B. Batyunya D. Bauri J. L. Bazo Alba I. G. Bearden C. Beattie P. Becht D. Behera I. Belikov A. D. C. Bell Hechavarria F. Bellini R. Bellwied S. Belokurova Y. A. V. Beltran G. Bencedi S. Beole Y. Berdnikov A. Berdnikova L. Bergmann M. G. Besoiu L. Betev P. P. Bhaduri A. Bhasin M. A. Bhat B. Bhattacharjee L. Bianchi N. Bianchi J. Bielčík J. Bielčíková J. Biernat A. P. Bigot A. Bilandzic G. Biro S. Biswas N. Bize J. T. Blair D. Blau M. B. Blidaru N. Bluhme C. Blume G. Boca F. Bock T. Bodova A. Bogdanov S. Boi J. Bok L. Boldizsár M. Bombara P. M. Bond G. Bonomi H. Borel A. Borissov A. G. Borquez Carcamo H. Bossi E. Botta Y. E. M. Bouziani L. Bratrud P. Braun-Munzinger M. Bregant M. Broz G. E. Bruno M. D. Buckland D. Budnikov H. Buesching S. Bufalino P. Buhler N. Burmasov Z. Buthelezi A. Bylinkin S. A. Bysiak M. Cai H. Caines A. Caliva E. Calvo Villar J. M. M. Camacho P. Camerini F. D. M. Canedo S. L. Cantway M. Carabas A. A. Carballo F. Carnesecchi R. Caron L. A. D. Carvalho J. Castillo Castellanos F. Catalano C. Ceballos Sanchez I. Chakaberia P. Chakraborty S. Chandra S. Chapeland M. Chartier S. Chattopadhyay T. Cheng C. Cheshkov B. Cheynis V. Chibante Barroso D. D. Chinellato E. Université Clermont Auvergne CNRS/IN2P3 LPC Clermont-Ferrand France Nuclear Physics Institute of the Czech Academy of Sciences Husinec-Řež Czech Republic Geneva Switzerland Dipartimento DISAT del Politecnico and Sezione INFN Turin Italy INFN Sezione di Bologna Bologna Italy Variable Energy Cyclotron Centre Homi Bhabha National Institute Kolkata India Department of Physics Aligarh Muslim University Aligarh India Korea Institute of Science and Technology Information Daejeon Republic of Korea Faculty of Science P.J. Šafárik University Košice Slovak Republic Affiliated with an institute covered by a cooperation agreement with CERN Research Division and ExtreMe Matter Institute EMMI GSI Helmholtzzentrum für Schwerionenforschung GmbH Darmstadt Germany INFN Sezione di Torino Turin Italy Central China Normal University Wuhan China Instituto de Física Universidad Nacional Autónoma de México Mexico City Mexico Dipartimento di Fisica e Astronomia dell’Università Bologna Italy and Sezione INFN Bologna Italy University of Houston Houston Texas USA Department of Physics and Technology University of Bergen Bergen Norway INFN Sezione di Cagliari Cagliari Italy Institut für Kernphysik Johann Wolfgang Goethe-Universität Frankfurt Frankfurt Germany INFN Sezione di Bari Bari Italy Physik Department Technische Universität München Munich Germany High Energy Physics Group Universidad Autónoma de Puebla Puebla Mexico Horia Hulubei National Institute of Physics and Nuclear Engineering Bucharest Romania University of Derby Derby United Kingdom Universität Münster Institut für Kernphysik Münster Germany Physikalisches Institut Ruprecht-Karls-Universität Heidelberg Heidelberg Germany INFN Sezione di Padova Padova Italy Lawrence Berkeley National Laboratory Berkeley California USA SUBATECH IMT Atlantique Nantes Université CNRS-IN2P3 Nantes France Laboratoire de Physique Subatomique et de Cosmologie Université Grenoble-Alpes CNRS-IN2P3 Grenoble France Dipar

Deuterons are atomic nuclei composed of a neutron and a proton held together by the strong interaction. Unbound ensembles composed of a deuteron and a third nucleon have been investigated in the past using scattering experiments, and they constitute a fundamental reference in nuclear physics to constrain nuclear interactions and the properties of nuclei. In this work, K+−d and p−d femtoscopic correlations measured by the ALICE Collaboration in proton-proton (pp) collisions at s=13 TeV at the Large Hadron Collider (LHC) are presented. It is demonstrated that correlations in momentum space between deuterons and kaons or protons allow us to study three-hadron systems at distances comparable with the proton radius. The analysis of the K+−d correlation shows that the relative distances at which deuterons and protons or kaons are produced are around 2 fm. The analysis of the p−d correlation shows that only a full three-body calculation that accounts for the internal structure of the deuteron can explain the data. In particular, the sensitivity of the observable to the short-range part of the interaction is demonstrated. These results indicate that correlations involving light nuclei in pp collisions at the LHC will also provide access to any three-body system in the strange and charm sectors.

关键词： Hadron-hadron interactions

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Measurements of Chemical Potentials in Pb-Pb Collisions at sNN=5.02 TeV

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Physical Review Letters 2024年第9期133卷 092301页

作者： S. Acharya D. Adamová G. Aglieri Rinella L. Aglietta M. Agnello N. Agrawal Z. Ahammed S. Ahmad S. U. Ahn I. Ahuja A. Akindinov M. Al-Turany D. Aleksandrov B. Alessandro H. M. Alfanda R. Alfaro Molina B. Ali A. Alici N. Alizadehvandchali A. Alkin J. Alme G. Alocco T. Alt A. R. Altamura I. Altsybeev J. R. Alvarado M. N. Anaam C. Andrei N. Andreou A. Andronic E. Andronov V. Anguelov F. Antinori P. Antonioli N. Apadula L. Aphecetche H. Appelshäuser C. Arata S. Arcelli M. Aresti R. Arnaldi J. G. M. C. A. Arneiro I. C. Arsene M. Arslandok A. Augustinus R. Averbeck M. D. Azmi H. Baba A. Badalà J. Bae Y. W. Baek X. Bai R. Bailhache Y. Bailung R. Bala A. Balbino A. Baldisseri B. Balis D. Banerjee Z. Banoo F. Barile L. Barioglio M. Barlou B. Barman G. G. Barnaföldi L. S. Barnby E. Barreau V. Barret L. Barreto C. Bartels K. Barth E. Bartsch N. Bastid S. Basu G. Batigne D. Battistini B. Batyunya D. Bauri J. L. Bazo Alba I. G. Bearden C. Beattie P. Becht D. Behera I. Belikov A. D. C. Bell Hechavarria F. Bellini R. Bellwied S. Belokurova L. G. E. Beltran Y. A. V. Beltran G. Bencedi S. Beole Y. Berdnikov A. Berdnikova L. Bergmann M. G. Besoiu L. Betev P. P. Bhaduri A. Bhasin M. A. Bhat B. Bhattacharjee L. Bianchi N. Bianchi J. Bielčík J. Bielčíková A. P. Bigot A. Bilandzic G. Biro S. Biswas N. Bize J. T. Blair D. Blau M. B. Blidaru N. Bluhme C. Blume G. Boca F. Bock T. Bodova S. Boi J. Bok L. Boldizsár M. Bombara P. M. Bond G. Bonomi H. Borel A. Borissov A. G. Borquez Carcamo H. Bossi E. Botta Y. E. M. Bouziani L. Bratrud P. Braun-Munzinger M. Bregant M. Broz G. E. Bruno M. D. Buckland D. Budnikov H. Buesching S. Bufalino P. Buhler N. Burmasov Z. Buthelezi A. Bylinkin S. A. Bysiak J. C. Cabanillas Noris M. Cai H. Caines A. Caliva E. Calvo Villar J. M. M. Camacho P. Camerini F. D. M. Canedo S. L. Cantway M. Carabas A. A. Carballo F. Carnesecchi R. Caron L. A. D. Carvalho J. Castillo Castellanos F. Catalano S. Cattaruzzi C. Ceballos Sanchez R. Cerri I. Chakaberia P. Chakraborty S. Chandra S. Chapeland M. Chartier S. Chattopadhyay Université Clermont Auvergne CNRS/IN2P3 LPC Clermont-Ferrand France Nuclear Physics Institute of the Czech Academy of Sciences Husinec-Řež Czech Republic European Organization for Nuclear Research (CERN) Geneva Switzerland Dipartimento di Fisica dell’Università and Sezione INFN Turin Italy Dipartimento DISAT del Politecnico and Sezione INFN Turin Italy Dipartimento di Fisica e Astronomia dell’Università and Sezione INFN Bologna Italy Variable Energy Cyclotron Centre Homi Bhabha National Institute Kolkata India Department of Physics Aligarh Muslim University Aligarh India Korea Institute of Science and Technology Information Daejeon Republic of Korea Faculty of Science P.J. Šafárik University Košice Slovak Republic Affiliated with an institute covered by a cooperation agreement with CERN Research Division and ExtreMe Matter Institute EMMI GSI Helmholtzzentrum für Schwerionenforschung GmbH Darmstadt Germany INFN Sezione di Torino Turin Italy Central China Normal University Wuhan China Instituto de Física Universidad Nacional Autónoma de México Mexico City Mexico University of Houston Houston Texas USA Department of Physics and Technology University of Bergen Bergen Norway INFN Sezione di Cagliari Cagliari Italy Institut für Kernphysik Johann Wolfgang Goethe-Universität Frankfurt Frankfurt Germany INFN Sezione di Bari Bari Italy Physik Department Technische Universität München Munich Germany High Energy Physics Group Universidad Autónoma de Puebla Puebla Mexico Horia Hulubei National Institute of Physics and Nuclear Engineering Bucharest Romania University of Derby Derby United Kingdom Universität Münster Institut für Kernphysik Munster Germany Physikalisches Institut Ruprecht-Karls-Universität Heidelberg Heidelberg Germany INFN Sezione di Padova Padova Italy INFN Sezione di Bologna Bologna Italy Lawrence Berkeley National Laboratory Berkeley California USA SUBATECH IMT Atlantique Nantes Université CNRS-IN2P3 Nantes France Laboratoire d

This Letter presents the most precise measurement to date of the matter-antimatter imbalance at midrapidity in Pb-Pb collisions at a center-of-mass energy per nucleon pair sNN=5.02 TeV. Using the Statistical Hadronization framework, it is possible to obtain the value of the electric charge and baryon chemical potentials, μQ=−0.18±0.90 MeV and μB=0.71±0.45 MeV, with unprecedented precision. A centrality-differential study of the antiparticle-to-particle yield ratios of charged pions, protons, Ω baryons, and light (hyper)nuclei is performed. These results indicate that the system created in Pb-Pb collisions at the LHC is on average baryon-free and electrically neutral at midrapidity.

关键词： Particle & resonance production QCD phase transitions Quark-gluon plasma Relativistic heavy-ion collisions

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