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arXiv 2023年

作者： Nozaki, Seiya Asano, Katsuaki Escudero, Juan Emery, Gabriel Priyadarshi, Chaitanya Abe, K. Abe, S. Aguasca-Cabot, A. Agudo, I. Crespo, N. Alvarez Antonelli, L.A. Aramo, C. Arbet-Engels, A. Arcaro, C. Artero, M. Asano, K. Aubert, P. Baktash, A. Bamba, A. Larriva, A. Baquero Baroncelli, L. de Almeida, U. Barres Barrio, J.A. Batkovic, I. Baxter, J. González, J. Becerra Bernardini, E. Bernardos, M.I. Medrano, J. Bernete Berti, A. Bhattacharjee, P. Biederbeck, N. Bigongiari, C. Bissaldi, E. Blanch, O. Bonnoli, G. Bordas, P. Bulgarelli, A. Burelli, I. Burmistrov, L. Buscemi, M. Cardillo, M. Caroff, S. Carosi, A. Carrasco, M.S. Cassol, F. Cauz, D. Cerasole, D. Ceribella, G. Chai, Y. Cheng, K. Chiavassa, A. Chikawa, M. Chytka, L. Cifuentes, A. Contreras, J.L. Cortina, J. Costantini, H. Dalchenko, M. Dazzi, F. De Angelis, A. de Lavergne, M. de Bony De Lotto, B. De Lucia, M. de Menezes, R. Del Peral, L. Deleglise, G. Delgado, C. Mengual, J. Delgado della Volpe, D. Dellaiera, M. Di Piano, A. Di Pierro, F. Di Pilato, A. Di Tria, R. Di Venere, L. Díaz, C. Dominik, R.M. Prester, D. Dominis Donini, A. Dorner, D. Doro, M. Eisenberger, L. Elsässer, D. Emery, G. Escudero, J. Ramazani, V. Fallah Ferrara, G. Ferrarotto, F. Fiasson, A. Foffano, L. Coromina, L. Freixas Fröse, S. Fukami, S. Fukazawa, Y. Garcia, E. López, R. Garcia Gasbarra, C. Gasparrini, D. Geyer, D. Paiva, J. Giesbrecht Giglietto, N. Giordano, F. Gliwny, P. Godinovic, N. Grau, R. Green, J. Green, D. Gunji, S. Günther, P. Hackfeld, J. Hadasch, D. Hahn, A. Hashiyama, K. Hassan, T. Hayashi, K. Heckmann, L. Heller, M. Llorente, J. Herrera Hirotani, K. Hoffmann, D. Horns, D. Houles, J. Hrabovsky, M. Hrupec, D. Hui, D. Hütten, M. Iarlori, M. Imazawa, R. Inada, T. Inome, Y. Ioka, K. Iori, M. Ishio, K. Martinez, I. Jimenez Jurysek, J. Kagaya, M. Karas, V. Katagiri, H. Kataoka, J. Kerszberg, D. Kobayashi, Y. Kohri, K. Kong, A. Kubo, H. Kushida, J. Lainez, M. Lamanna, G. Lamastra, A. Le Flour, T. Linhoff, M. Longo, F. López-Coto, R. Max-Planck-Institut für Physik Föhringer Ring 6 München80805 Germany Institute for Cosmic Ray Research University of Tokyo 5-1-5 Kashiwa-no-ha Chiba Kashiwa277-8582 Japan Instituto de Astrofísica de Andalucía-CSIC Glorieta de la Astronomía s/n Granada18008 Spain Aix Marseille Univ CNRS IN2P3 CPPM Marseille France The Barcelona Institute of Science and Technology Campus UAB Bellaterra Barcelona08193 Spain Department of Physics Tokai University Japan Institute for Cosmic Ray Research University of Tokyo Japan Departament de Física Quàntica i Astrofísica Institut de Ciències del Cosmos Universitat de Barcelona IEEC-UB Spain Instituto de Astrofísica de Andalucía-CSIC Spain EMFTEL department IPARCOS Universidad Complutense de Madrid Spain INAF - Osservatorio Astronomico di Roma Italy INFN Sezione di Napoli Italy Max-Planck-Institut für Physik Germany INFN Sezione di Padova Università degli Studi di Padova Italy The Barcelona Institute of Science and Technology Spain LAPP Univ. Grenoble Alpes Univ. Savoie Mont Blanc CNRS-IN2P3 Annecy France Universität Hamburg Institut für Experimentalphysik Germany Graduate School of Science University of Tokyo Japan Universidad del Azuay Ecuador INAF - Osservatorio di Astrofisica e Scienza dello spazio di Bologna Italy Centro Brasileiro de Pesquisas Físicas Brazil Instituto de Astrofísica de Canarias Departamento de Astrofísica Universidad de La Laguna Spain CIEMAT Spain Department of Physics TU Dortmund University Germany INFN Sezione di Bari Politecnico di Bari Italy INAF - Osservatorio Astronomico di Brera Italy INFN Sezione di Trieste Università degli Studi di Udine Italy University of Geneva Département de physique nucléaire et corpusculaire Switzerland INFN Sezione di Catania Italy Italy Aix Marseille Univ CNRS IN2P3 CPPM France INFN Sezione di Bari Università di Bari Italy INFN Sezione di Torino Italy Palacky University Olomouc Faculty of Science Czech Republic University of Alcalá UAH Spain P

The first prototype of LST (LST-1) for the Cherenkov Telescope Array has been in commissioning phase since 2018 and already started scientific observations with the low energy threshold around a few tens of GeV. In 2021, LST-1 observed BL Lac following the alerts based on multi-wavelength observations and detected prominent gamma-ray flares. In addition to the daily flux variability, LST-1 also detected sub-hour-scale intra-night variability reaching 3–4 times higher than the gamma-ray flux from the Crab Nebula above 100 GeV. In this proceeding, we will report the analysis results of LST-1 observations of BL Lac in 2021, especially focusing on flux variability. © 2023, CC BY.

关键词： Gamma rays

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Detection of the 2021 Outburst of RS Ophiuchi with the LST-1

arXiv

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arXiv 2023年

作者： Kobayashi, Yukiho Aguasca-Cabot, Arnau Martín, María Isabel Bernardos Green, David López-Coto, Rubén Abe, K. Abe, S. Aguasca-Cabot, A. Agudo, I. Alvarez Crespo, N. Antonelli, L.A. Aramo, C. Arbet-Engels, A. Arcaro, C. Artero, M. Asano, K. Aubert, P. Baktash, A. Bamba, A. Baquero Larriva, A. Baroncelli, L. Barres de Almeida, U. Barrio, J.A. Batkovic, I. Baxter, J. Becerra González, J. Bernardini, E. Bernardos, M.I. Bernete Medrano, J. Berti, A. Bhattacharjee, P. Biederbeck, N. Bigongiari, C. Bissaldi, E. Blanch, O. Bonnoli, G. Bordas, P. Bulgarelli, A. Burelli, I. Burmistrov, L. Buscemi, M. Cardillo, M. Caroff, S. Carosi, A. Carrasco, M.S. Cassol, F. Cauz, D. Cerasole, D. Ceribella, G. Chai, Y. Cheng, K. Chiavassa, A. Chikawa, M. Chytka, L. Cifuentes, A. Contreras, J.L. Cortina, J. Costantini, H. Dalchenko, M. Dazzi, F. De Angelis, A. de Bony de Lavergne, M. De Lotto, B. De Lucia, M. de Menezes, R. Del Peral, L. Deleglise, G. Delgado, C. Delgado Mengual, J. della Volpe, D. Dellaiera, M. Di Piano, A. Di Pierro, F. Di Pilato, A. Di Tria, R. Di Venere, L. Díaz, C. Dominik, R.M. Dominis Prester, D. Donini, A. Dorner, D. Doro, M. Eisenberger, L. Elsässer, D. Emery, G. Escudero, J. Fallah Ramazani, V. Ferrara, G. Ferrarotto, F. Fiasson, A. Foffano, L. Freixas Coromina, L. Fröse, S. Fukami, S. Fukazawa, Y. Garcia, E. Garcia López, R. Gasbarra, C. Gasparrini, D. Geyer, D. Giesbrecht Paiva, J. Giglietto, N. Giordano, F. Gliwny, P. Godinovic, N. Grau, R. Green, J. Green, D. Gunji, S. Günther, P. Hackfeld, J. Hadasch, D. Hahn, A. Hashiyama, K. Hassan, T. Hayashi, K. Heckmann, L. Heller, M. Herrera Llorente, J. Hirotani, K. Hoffmann, D. Horns, D. Houles, J. Hrabovsky, M. Hrupec, D. Hui, D. Hütten, M. Iarlori, M. Imazawa, R. Inada, T. Inome, Y. Ioka, K. Iori, M. Ishio, K. Jimenez Martinez, I. Jurysek, J. Kagaya, M. Karas, V. Katagiri, H. Kataoka, J. Kerszberg, D. Kobayashi, Y. Kohri, K. Kong, A. Kubo, H. Kushida, J. Lainez, M. Lamanna, G. Lamastra, A. Le Flour, T. Linhoff, M. Institute for Cosmic Ray Research The University of Tokyo 5-1-5 Kashiwa-no-ha Chiba Kashiwa277-8582 Japan Departament de Física Quàntica i Astrofísica Institut de Ciències del Cosmos Universitat de Barcelona IEEC-UB Martí i Franquès 1 Barcelona08028 Spain Instituto de Astrofísica de Andalucía-CSIC Glorieta de la Astronomía s/n Granada18008 Spain Max-Planck-Institut für Physik Föhringer Ring 6 München80805 Germany Department of Physics Tokai University Japan Institute for Cosmic Ray Research University of Tokyo Japan Departament de Física Quàntica i Astrofísica Institut de Ciències del Cosmos Universitat de Barcelona IEEC-UB Spain Instituto de Astrofísica de Andalucía-CSIC Spain EMFTEL department IPARCOS Universidad Complutense de Madrid Spain INAF - Osservatorio Astronomico di Roma Italy INFN Sezione di Napoli Italy Max-Planck-Institut für Physik Germany INFN Sezione di Padova Università degli Studi di Padova Italy The Barcelona Institute of Science and Technology Spain LAPP Univ. Grenoble Alpes Univ. Savoie Mont Blanc CNRS-IN2P3 Annecy France Universität Hamburg Institut für Experimentalphysik Germany Graduate School of Science University of Tokyo Japan Universidad del Azuay Ecuador INAF - Osservatorio di Astrofisica e Scienza dello Spazio di Bologna Italy Centro Brasileiro de Pesquisas Físicas Brazil Instituto de Astrofísica de Canarias Departamento de Astrofísica Universidad de La Laguna Spain CIEMAT Spain Department of Physics TU Dortmund University Germany INFN Sezione di Bari Politecnico di Bari Italy INAF - Osservatorio Astronomico di Brera Italy INFN Sezione di Trieste Università degli Studi di Udine Italy University of Geneva Département de Physique Nucléaire et Corpusculaire Switzerland INFN Sezione di Catania Italy Italy Aix Marseille Univ CNRS IN2P3 CPPM France INFN Sezione di Bari Università di Bari Italy INFN Sezione di Torino Italy Palacky University Olomouc Faculty of Science United States University of Alcalá UAH Spa

Novae are luminous explosions in close binaries which host a white dwarf and a companion donor star. They are triggered by a thermonuclear runaway when the white dwarf accretes a critical amount of matter from the secondary. Though novae are established as high-energy gamma-ray emitters through observations by the Fermi Large Area Telescope (LAT), the origin of the gamma-ray emission, whether it is hadronic or leptonic, had been under intense debate until very recently. RS Ophiuchi (RS Oph) is a well-known recurrent symbiotic nova with a recurrence time scale of 15 years. The most recent outburst of RS Oph in 2021 brought the first detection of very-high-energy (VHE) gamma rays from a nova ever. The first Large-Sized Telescope prototype (LST-1) of the Cherenkov Telescope Array observed this historic event along with H.E.S.S. and MAGIC. The LST-1 observations in the first days after the burst onset show a clear VHE gamma-ray signal from RS Oph. The low energy threshold of LST-1 allows us to reconstruct the RS Oph gamma-ray spectrum down to ∼30 GeV, providing the best connection of the VHE gamma-ray data to the Fermi LAT energy range. The results from the analysis of the LST-1 observations are consistent with those obtained with H.E.S.S. and MAGIC, and also support a hadronic origin for the observed gamma-ray fluxes. In this contribution, we will present the analysis results of the LST-1 observations of the 2021 outburst of RS Oph. © 2023, CC BY.

关键词： Telescopes

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The mutational constraint spectrum quantified from variation in 141,456 humans (vol 581, pg 434, 2020)

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NATURE 2021年第7846期590卷 E53-E53页

作者： Karczewski, Konrad J. Francioli, Laurent C. Tiao, Grace Cummings, Beryl B. Alfoldi, Jessica Wang, Qingbo Collins, Ryan L. Laricchia, Kristen M. Ganna, Andrea Birnbaum, Daniel P. Gauthier, Laura D. Brand, Harrison Solomonson, Matthew Watts, Nicholas A. Rhodes, Daniel Singer-Berk, Moriel England, Eleina M. Seaby, Eleanor G. Kosmicki, Jack A. Walters, Raymond K. Tashman, Katherine Farjoun, Yossi Banks, Eric Poterba, Timothy Wang, Arcturus Seed, Cotton Whiffin, Nicola Chong, Jessica X. Samocha, Kaitlin E. Pierce-Hoffman, Emma Zappala, Zachary O'Donnell-Luria, Anne H. Minikel, Eric Vallabh Weisburd, Ben Lek, Monkol Ware, James S. Vittal, Christopher Armean, Irina M. Bergelson, Louis Cibulskis, Kristian Connolly, Kristen M. Covarrubias, Miguel Donnelly, Stacey Ferriera, Steven Gabriel, Stacey Gentry, Jeff Gupta, Namrata Jeandet, Thibault Kaplan, Diane Llanwarne, Christopher Munshi, Ruchi Novod, Sam Petrillo, Nikelle Roazen, David Ruano-Rubio, Valentin Saltzman, Andrea Schleicher, Molly Soto, Jose Tibbetts, Kathleen Tolonen, Charlotte Wade, Gordon Talkowski, Michael E. Aggregation, Genome Neale, Benjamin M. Daly, Mark J. MacArthur, Daniel G. Program in Medical and Population Genetics Broad Institute of MIT and Harvard Cambridge MA USA Analytic and Translational Genetics Unit Massachusetts General Hospital Boston MA USA Program in Biological and Biomedical Sciences Harvard Medical School Boston MA USA Program in Bioinformatics and Integrative Genomics Harvard Medical School Boston MA USA Center for Genomic Medicine Massachusetts General Hospital Boston MA USA Institute for Molecular Medicine Finland Helsinki Finland Stanley Center for Psychiatric Research Broad Institute of MIT and Harvard Cambridge MA USA National Heart & Lung Institute and MRC London Institute of Medical Sciences Imperial College London London UK Cardiovascular Research Centre Royal Brompton & Harefield Hospitals NHS Trust London UK Vertex Pharmaceuticals Inc Boston MA USA Division of Genetics and Genomics Boston Children’s Hospital Boston MA USA Department of Pediatrics Harvard Medical School Boston MA USA Broad Genomics Broad Institute of MIT and Harvard Cambridge MA USA Department of Neurology Harvard Medical School Boston MA USA Cardiac Arrhythmia Service and Cardiovascular Research Center Massachusetts General Hospital Boston MA USA Estonian Genome Center Institute of Genomics University of Tartu Tartu Estonia Data Sciences Platform Broad Institute of MIT and Harvard Cambridge MA USA Diabetes Unit Massachusetts General Hospital Boston MA USA Program in Metabolism Broad Institute of MIT and Harvard Cambridge MA USA Department of Medicine Harvard Medical School Boston MA USA Division of General Internal Medicine Massachusetts General Hospital Boston MA USA Department of Public Health Faculty of Medicine University of Helsinki Helsinki Finland Cardiovascular Disease Initiative and Program in Medical and Population Genetics Broad Institute of MIT and Harvard Cambridge MA USA Genomics Diabetes and Endocrinology Lund University Lund Sweden Folkhälsan Institute of Genetics Folkhälsan Research C

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The mutational constraint spectrum quantified from variation in 141,456 humans (vol 581, pg 434, 2020)

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NATURE 2021年第7874期597卷 E3-E4页

作者： Gudmundsson, Sanna Karczewski, Konrad J. Francioli, Laurent C. Tiao, Grace Cummings, Beryl B. Alfoldi, Jessica Wang, Qingbo Collins, Ryan L. Laricchia, Kristen M. Ganna, Andrea Birnbaum, Daniel P. Gauthier, Laura D. Brand, Harrison Solomonson, Matthew Watts, Nicholas A. Rhodes, Daniel Singer-Berk, Moriel England, Eleina M. Seaby, Eleanor G. Kosmicki, Jack A. Walters, Raymond K. Tashman, Katherine Farjoun, Yossi Banks, Eric Poterba, Timothy Wang, Arcturus Seed, Cotton Whiffin, Nicola Chong, Jessica X. Samocha, Kaitlin E. Pierce-Hoffman, Emma Zappala, Zachary O'Donnell-Luria, Anne H. Minikel, Eric Vallabh Weisburd, Ben Lek, Monkol Ware, James S. Vittal, Christopher Armean, Irina M. Bergelson, Louis Cibulskis, Kristian Connolly, Kristen M. Covarrubias, Miguel Donnelly, Stacey Ferriera, Steven Gabriel, Stacey Gentry, Jeff Gupta, Namrata Jeandet, Thibault Kaplan, Diane Llanwarne, Christopher Munshi, Ruchi Novod, Sam Petrillo, Nikelle Roazen, David Ruano-Rubio, Valentin Saltzman, Andrea Schleicher, Molly Soto, Jose Tibbetts, Kathleen Tolonen, Charlotte Wade, Gordon Talkowski, Michael E. Neale, Benjamin M. Daly, Mark J. MacArthur, Daniel G. Program in Medical and Population Genetics Broad Institute of MIT and Harvard Cambridge MA USA Analytic and Translational Genetics Unit Massachusetts General Hospital Boston MA USA Division of Genetics and Genomics Boston Children’s Hospital Boston MA USA Program in Biological and Biomedical Sciences Harvard Medical School Boston MA USA Program in Bioinformatics and Integrative Genomics Harvard Medical School Boston MA USA Center for Genomic Medicine Massachusetts General Hospital Boston MA USA Institute for Molecular Medicine Finland Helsinki Finland Stanley Center for Psychiatric Research Broad Institute of MIT and Harvard Cambridge MA USA National Heart & Lung Institute and MRC London Institute of Medical Sciences Imperial College London London UK Cardiovascular Research Centre Royal Brompton & Harefield Hospitals NHS Trust London UK Vertex Pharmaceuticals Inc Boston MA USA Department of Pediatrics Harvard Medical School Boston MA USA Broad Genomics Broad Institute of MIT and Harvard Cambridge MA USA Department of Neurology Harvard Medical School Boston MA USA Cardiac Arrhythmia Service and Cardiovascular Research Center Massachusetts General Hospital Boston MA USA Estonian Genome Center Institute of Genomics University of Tartu Tartu Estonia Data Sciences Platform Broad Institute of MIT and Harvard Cambridge MA USA Diabetes Unit Massachusetts General Hospital Boston MA USA Program in Metabolism Broad Institute of MIT and Harvard Cambridge MA USA Department of Medicine Harvard Medical School Boston MA USA Division of General Internal Medicine Massachusetts General Hospital Boston MA USA Department of Public Health Faculty of Medicine University of Helsinki Helsinki Finland Cardiovascular Disease Initiative and Program in Medical and Population Genetics Broad Institute of MIT and Harvard Cambridge MA USA Genomics Diabetes and Endocrinology Lund University Lund Sweden Folkhälsan Institute of Genetics Folkhälsan Research C

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Evaluating drug targets through human loss-of-function genetic variation (vol 581, pg 459, 2020)

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NATURE 2021年第7846期590卷 E56-E56页

作者： Minikel, Eric Vallabh Karczewski, Konrad J. Martin, Hilary C. Cummings, Beryl B. Whiffin, Nicola Rhodes, Daniel Alfoldi, Jessica Trembath, Richard C. van Heel, David A. Daly, Mark J. Schreiber, Stuart L. MacArthur, Daniel G. Program in Medical and Population Genetics Broad Institute of MIT and Harvard Cambridge MA USA Stanley Center for Psychiatric Research Broad Institute of MIT and Harvard Cambridge MA USA Chemical Biology and Therapeutics Science Program Broad Institute of MIT and Harvard Cambridge MA USA Analytical and Translational Genetics Unit Massachusetts General Hospital Boston MA USA Program in Biological and Biomedical Sciences Harvard Medical School Boston MA USA Henry and Allison McCance Center for Brain Health Massachusetts General Hospital Boston MA USA Department of Neurology Massachusetts General Hospital Boston MA USA Prion Alliance Cambridge MA USA National Heart and Lung Institute and MRC London Institute of Medical Sciences Imperial College London London UK National Heart & Lung Institute and MRC London Institute of Medical Sciences Imperial College London London UK Cardiovascular Research Centre Royal Brompton & Harefield Hospitals NHS Trust London UK European Molecular Biology Laboratory European Bioinformatics Institute Wellcome Genome Campus Hinxton Cambridge UK Center for Genomic Medicine Massachusetts General Hospital Boston MA USA Program in Bioinformatics and Integrative Genomics Harvard Medical School Boston MA USA Broad Genomics Broad Institute of MIT and Harvard Cambridge MA USA Division of Genetics and Genomics Boston Children’s Hospital Boston MA USA Department of Pediatrics Harvard Medical School Boston MA USA Cardiac Arrhythmia Service and Cardiovascular Research Center Massachusetts General Hospital Boston MA USA Estonian Genome Center Institute of Genomics University of Tartu Tartu Estonia Department of Medicine Harvard Medical School Boston MA USA Cardiac Arrhythmia Service Massachusetts General Hospital Boston MA USA Centre for Population Genomics Garvan Institute of Medical Research and UNSW Sydney Sydney Australia Centre for Population Genomics Murdoch Children’s Research Institute Melbourne Australia Divi

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BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets

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Nature methods 2023年第6期20卷 824-835页

作者： Linus Manubens-Gil Zhi Zhou Hanbo Chen Arvind Ramanathan Xiaoxiao Liu Yufeng Liu Alessandro Bria Todd Gillette Zongcai Ruan Jian Yang Miroslav Radojević Ting Zhao Li Cheng Lei Qu Siqi Liu Kristofer E Bouchard Lin Gu Weidong Cai Shuiwang Ji Badrinath Roysam Ching-Wei Wang Hongchuan Yu Amos Sironi Daniel Maxim Iascone Jie Zhou Erhan Bas Eduardo Conde-Sousa Paulo Aguiar Xiang Li Yujie Li Sumit Nanda Yuan Wang Leila Muresan Pascal Fua Bing Ye Hai-Yan He Jochen F Staiger Manuel Peter Daniel N Cox Michel Simonneau Marcel Oberlaender Gregory Jefferis Kei Ito Paloma Gonzalez-Bellido Jinhyun Kim Edwin Rubel Hollis T Cline Hongkui Zeng Aljoscha Nern Ann-Shyn Chiang Jianhua Yao Jane Roskams Rick Livesey Janine Stevens Tianming Liu Chinh Dang Yike Guo Ning Zhong Georgia Tourassi Sean Hill Michael Hawrylycz Christof Koch Erik Meijering Giorgio A Ascoli Hanchuan Peng Institute for Brain and Intelligence Southeast University Nanjing China. Microsoft Corporation Redmond WA USA. Tencent AI Lab Bellevue WA USA. Computing Environment and Life Sciences Directorate Argonne National Laboratory Lemont IL USA. Kaya Medical Seattle WA USA. University of Cassino and Southern Lazio Cassino Italy. Center for Neural Informatics Structures and Plasticity Krasnow Institute for Advanced Study George Mason University Fairfax VA USA. Faculty of Information Technology Beijing University of Technology Beijing China. Beijing International Collaboration Base on Brain Informatics and Wisdom Services Beijing China. Nuctech Netherlands Rotterdam the Netherlands. Janelia Research Campus Howard Hughes Medical Institute Ashburn VA USA. Department of Electrical and Computer Engineering University of Alberta Edmonton Alberta Canada. Ministry of Education Key Laboratory of Intelligent Computation and Signal Processing Anhui University Hefei China. Paige AI New York NY USA. Scientific Data Division and Biological Systems and Engineering Division Lawrence Berkeley National Lab Berkeley CA USA. Helen Wills Neuroscience Institute and Redwood Center for Theoretical Neuroscience UC Berkeley Berkeley CA USA. RIKEN AIP Tokyo Japan. Research Center for Advanced Science and Technology (RCAST) The University of Tokyo Tokyo Japan. School of Computer Science University of Sydney Sydney New South Wales Australia. Texas A&M University College Station TX USA. Cullen College of Engineering University of Houston Houston TX USA. Graduate Institute of Biomedical Engineering National Taiwan University of Science and Technology Taipei Taiwan. National Centre for Computer Animation Bournemouth University Poole UK. PROPHESEE Paris France. Department of Neuroscience Columbia University New York NY USA. Mortimer B. Zuckerman Mind Brain Behavior Institute Columbia University New York NY USA. Department of Computer Science Northern Illinois Universit

BigNeuron is an open community bench-testing platform with the goal of setting open standards for accurate and fast automatic neuron tracing. We gathered a diverse set of image volumes across several species that is representative of the data obtained in many neuroscience laboratories interested in neuron tracing. Here, we report generated gold standard manual annotations for a subset of the available imaging datasets and quantified tracing quality for 35 automatic tracing algorithms. The goal of generating such a hand-curated diverse dataset is to advance the development of tracing algorithms and enable generalizable benchmarking. Together with image quality features, we pooled the data in an interactive web application that enables users and developers to perform principal component analysis, t-distributed stochastic neighbor embedding, correlation and clustering, visualization of imaging and tracing data, and benchmarking of automatic tracing algorithms in user-defined data subsets. The image quality metrics explain most of the variance in the data, followed by neuromorphological features related to neuron size. We observed that diverse algorithms can provide complementary information to obtain accurate results and developed a method to iteratively combine methods and generate consensus reconstructions. The consensus trees obtained provide estimates of the neuron structure ground truth that typically outperform single algorithms in noisy datasets. However, specific algorithms may outperform the consensus tree strategy in specific imaging conditions. Finally, to aid users in predicting the most accurate automatic tracing results without manual annotations for comparison, we used support vector machine regression to predict reconstruction quality given an image volume and a set of automatic tracings.

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Kidney multiome-based genetic scorecard reveals convergent coding and regulatory variants

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Science (New York, N.Y.) 2025年第6734期387卷 eadp4753页

作者： Liu, Hongbo Abedini, Amin Ha, Eunji Ma, Ziyuan Sheng, Xin Dumoulin, Bernhard Qiu, Chengxiang Aranyi, Tamas Li, Shen Dittrich, Nicole Chen, Hua-Chang Tao, Ran Tarng, Der-Cherng Hsieh, Feng-Jen Chen, Shih-Ann Yang, Shun-Fa Lee, Mei-Yueh Kwok, Pui-Yan Wu, Jer-Yuarn Chen, Chien-Hsiun Khan, Atlas Limdi, Nita A. Wei, Wei-Qi Walunas, Theresa L. Karlson, Elizabeth W. Kenny, Eimear E. Luo, Yuan Kottyan, Leah Connolly, John J. Jarvik, Gail P. Weng, Chunhua Shang, Ning Cole, Joanne B. Mercader, Josep M. Mandla, Ravi Majarian, Timothy D. Florez, Jose C. Haas, Mary E. Lotta, Luca A. Drivas, Theodore G. Vy, Ha My T Nadkarni, Girish N. Wiley, Laura K. Wilson, Melissa P. Gignoux, Christopher R. Rasheed, Humaira Thomas, Laurent F. Åsvold, Bjørn Olav Brumpton, Ben M. Hallan, Stein I. Hveem, Kristian Zheng, Jie Hellwege, Jacklyn N. Zawistowski, Matthew Zöllner, Sebastian Franceschini, Nora Hu, Hailong Zhou, Jianfu Kiryluk, Krzysztof Ritchie, Marylyn D. Palmer, Matthew Edwards, Todd L. Voight, Benjamin F. Hung, Adriana M. Susztak, Katalin Department of Medicine Renal Electrolyte and Hypertension Division University of Pennsylvania Philadelphia PA United States Institute of Diabetes Obesity and Metabolism University of Pennsylvania Philadelphia PA United States Department of Genetics University of Pennsylvania Philadelphia PA United States Penn-CHOP Kidney Innovation Center University of Pennsylvania Philadelphia PA United States Liangzhu Laboratory Zhejiang University 1369 West Wenyi Road Hangzhou Zhejiang China Department of Nephrology Children' Hospital Zhejiang University School of Medicine National Clinical Research Center for Child Health Hangzhou Zhejiang China Institute of Molecular Life Sciences HUN-REN Research Center for Natural Sciences Budapest Hungary Department of Molecular Biology Semmelweis University Budapest Hungary Department of Medicine Federal University of São Paulo São Paulo Brazil Department of Biostatistics Vanderbilt University Medical Center Nashville TN United States Vanderbilt Genetics Institute Vanderbilt University Medical Center Nashville TN United States Institute of Clinical Medicine School of Medicine National Yang Ming Chiao Tung University ROC Taipei Taiwan Division of Nephrology Department of Medicine Taipei Veterans General Hospital ROC Taipei Taiwan Institute of Biomedical Sciences Academia Sinica ROC Taipei Taiwan Cardiovascular Center Taichung Veterans General Hospital Taichung Taiwan ROC National Chung Hsing University Taichung Taiwan ROC Heart Rhythm Center Division of Cardiology Department of Medicine Taipei Veterans General Hospital ROC Taipei Taiwan Department of Internal Medicine College of Medicine National Yang Ming Chiao Tung University ROC Taipei Taiwan Institute of Medicine Chung Shan Medical University Taichung Taiwan ROC Department of Medical Research Chung Shan Medical University Hospital Taichung Taiwan ROC Division of Endocrinology and Metabolism Department of Internal Medicine Kaohsiung Medical Universit

Kidney dysfunction is a major cause of mortality, but its genetic architecture remains elusive. In this study, we conducted a multiancestry genome-wide association study in 2.2 million individuals and identified 1026 (97 previously unknown) independent loci. Ancestry-specific analysis indicated an attenuation of newly identified signals on common variants in European ancestry populations and the power of population diversity for further discoveries. We defined genotype effects on allele-specific gene expression and regulatory circuitries in more than 700 human kidneys and 237,000 cells. We found 1363 coding variants disrupting 782 genes, with 601 genes also targeted by regulatory variants and convergence in 161 genes. Integrating 32 types of genetic information, we present the "Kidney Disease Genetic Scorecard" for prioritizing potentially causal genes, cell types, and druggable targets for kidney disease.

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Surveillance of avian influenza through bird guano in remote regions of the global south to uncover transmission dynamics

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Nature communications 2025年第1期16卷 4900页

作者： Dhammika Leshan Wannigama Mohan Amarasiri Phatthranit Phattharapornjaroen Cameron Hurst Charin Modchang John Jefferson V Besa Kazuhiko Miyanaga Longzhu Cui Stefan Fernandez Angkana T Huang Puey Ounjai W K C P Werawatte Ali Hosseini Rad S M Porames Vatanaprasan Dylan John Jay Thammakorn Saethang Sirirat Luk-In Phitsanuruk Kanthawee Wanwara Thuptimdang Ratana Tacharoenmuang Bernadina Cynthia S P H Spencer Vitharana Natharin Ngamwongsatit Hitoshi Ishikawa Takashi Furukawa Yangzhong Wang Andrew C Singer Naveen Kumar Devanga Ragupathi Tanittha Chatsuwan Kazunari Sei Asuka Nanbo Asada Leelahavanichkul Talerngsak Kanjanabuch Hiroshi Hamamoto Paul G Higgins Daisuke Sano Anthony Kicic José O Valdebenito Jonas Bonnedahl Sam Trowsdale Parichart Hongsing Aisha Khatib Kenji Shibuya Shuichi Abe Department of Infectious Diseases Faculty of Medicine Yamagata University Yamagata Japan. leshanwannigama@med.id.yamagata-u.ac.jp. Department of Infectious Diseases and Infection Control Yamagata Prefectural Central Hospital Yamagata Japan. leshanwannigama@med.id.yamagata-u.ac.jp. Pathogen Hunter's Research Collaborative Team Department of Infectious Diseases and Infection Control Yamagata Prefectural Central Hospital Yamagata Japan. leshanwannigama@med.id.yamagata-u.ac.jp. Yamagata Prefectural University of Health Sciences Kamiyanagi Yamagata Japan. leshanwannigama@med.id.yamagata-u.ac.jp. The Lygodium Ceylon Health and Environmental Policy Research Center Colombo Sri Lanka. leshanwannigama@med.id.yamagata-u.ac.jp. Biofilms and Antimicrobial Resistance Consortium of ODA receiving countries The University of Sheffield Sheffield UK. leshanwannigama@med.id.yamagata-u.ac.jp. Pathogen Hunter's Research Collaborative Team Department of Infectious Diseases and Infection Control Yamagata Prefectural Central Hospital Yamagata Japan. Department of Civil and Environmental Engineering Graduate School of Engineering Tohoku University Sendai Miyagi Japan. Faculty of Health Science Technology Chulabhorn Royal Academy Bangkok Thailand. HRH Princess Chulabhorn Disaster and Emergency Medicine Center Chulabhorn Royal Academy Bangkok Thailand. Department of Clinical Epidemiology Faculty of Medicine Thammasat University Rangsit Thailand. Center of Excellence in Applied Epidemiology Thammasat University Rangsit Thailand. Mater Research Institute University of Queensland Brisbane QLD Australia. Biophysics Group Department of Physics Faculty of Science Mahidol University Bangkok Thailand. Centre of Excellence in Mathematics MHESI Bangkok Thailand. Thailand Center of Excellence in Physics Ministry of Higher Education Science Research and Innovation Bangkok Thailand. Department of Infectious Diseases and Infection Control Yamagata Prefectural Central Hospital Yamagata Japan. Co

Avian influenza viruses (AIVs) pose a growing global health threat, particularly in low- and middle-income countries (LMICs), where limited surveillance capacity and under-resourced healthcare systems hinder timely detection and response. Migratory birds play a significant role in the transboundary spread of AIVs, yet data from key regions along migratory flyways remain sparse. To address these surveillance gaps, we conducted a study between December 2021 and February 2023 using fresh bird guano collected across 10 countries in the Global South. Here, we show that remote, uninhabited regions in previously unsampled areas harbor a high diversity of AIV strains, with H5N1 emerging as the most prevalent. Some of these H5N1 samples also carry mutations that may make them less responsive to the antiviral drug oseltamivir. Our findings documented the presence of AIVs in several underrepresented regions and highlighted critical transmission hotspots where viral evolution may be accelerating. These results underscore the urgent need for geographically targeted surveillance to detect emerging variants, inform public health interventions, and reduce the risk of zoonotic spillover.

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Evaluating Large Language Models for Enhancing Radiology Specialty Examination: A Comparative Study with Human Performance

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Academic radiology 2025年

作者： Hao-Yun Liu Shyh-Jye Chen Weichung Wang Chung-Hsi Lee Hsian-He Hsu Shu-Huei Shen Hong-Jen Chiou Wen-Jeng Lee Department of Medical Imaging National Taiwan University Hospital Hsin-Chu Branch Br. No.25 Lane 442 Sec.1 Jingguo Rd. Hsinchu City 300 Taiwan ROC (H.Y.L.) National Taiwan University College of Medicine No.1 Jen Ai Road Section 1 Taipei 100 Taiwan ROC (H.Y.L.). Department of Medical Imaging National Taiwan University Hospital No. 7 Zhongshan S. Rd. Zhongzheng Dist. Taipei City 100229 Taiwan (S.J.C. W.J.L.). Institute of Applied Mathematical Sciences Department of Mathematics and Data Science Degree Program National Taiwan University No. 1 Sec. 4 Roosevelt Rd. Taipei 106319 Taiwan (W.W.). Graduate Institute of Health and Biotechnology Law Taipei Medical University 250 Wuxing Street Taipei City Taiwan (C.H.L.). Department of Radiology Tri-Service General Hospital National Defense Medical Center No.325 Sec.2 Chenggong Rd. Neihu District Taipei City Taiwan (H.H.H.). Department of Radiology Taipei Veterans General Hospital No.201 Sec. 2 Shipai Rd. Beitou District Taipei City Taiwan (S.H.S. H.J.C.) National Yang Ming Chiao Tung University School of Medicine No. 118 Sec. 1 Zhongxiao West Road Taipei City 100 Taiwan (S.H.S. H.J.C.). Department of Medical Imaging National Taiwan University Hospital No. 7 Zhongshan S. Rd. Zhongzheng Dist. Taipei City 100229 Taiwan (S.J.C. W.J.L.). Electronic address: wenjeng@***.

RATIONALE AND OBJECTIVES:The radiology specialty examination assesses clinical decision-making, image interpretation, and diagnostic reasoning. With the expansion of medical knowledge, traditional test design faces challenges in maintaining accuracy and relevance. Large language models (LLMs) demonstrate potential in medical education. This study evaluates LLM performance in radiology specialty exams, explores their role in assessing question difficulty, and investigates their reasoning processes, aiming to develop a more objective and efficient framework for exam design. MATERIALS AND METHODS:This study compared the performance of LLMs and human examinees in a radiology specialty examination. Three LLMs (GPT-4o, o1-preview, and GPT-3.5-turbo-1106) were evaluated under zero-shot conditions. Exam accuracy, examinee accuracy, discrimination index, and point-biserial correlation were used to assess LLMs' ability to predict question difficulty and reasoning processes. The data provided by the Taiwan Radiological Society ensures comparability between AI and human performance. RESULTS:As for accuracy, GPT-4o (88.0%) and o1-preview (90.9%) outperformed human examinees (76.3%), whereas GPT-3.5-turbo-1106 showed significantly lower accuracy (50.2%). Question difficulty analysis revealed that newer LLMs excel in solving complex questions, while GPT-3.5-turbo-1106 exhibited greater performance variability. Discrimination index and point-biserial Correlation analyses demonstrated that GPT-4o and o1-preview accurately identified key differentiating questions, closely mirroring human reasoning patterns. These findings suggest that advanced LLMs can assess medical examination difficulty, offering potential applications in exam standardization and question evaluation. CONCLUSION:This study evaluated the problem-solving capabilities of GPT-3.5-turbo-1106, GPT-4o, and o1-preview in a radiology specialty examination. LLMs should be utilized as tools for assessing exam question difficu

关键词： Accuracy Evaluation GPT LLMs Radiology specialty examination

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Community-developed checklists for publishing images and image analyses

arXiv

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arXiv 2023年

作者： Schmied, Christopher Nelson, Michael S. Avilov, Sergiy Bakker, Gert-Jan Bertocchi, Cristina Bischof, Johanna Boehm, Ulrike Brocher, Jan Carvalho, Mariana Chiritescu, Catalin Christopher, Jana Cimini, Beth A. Conde-Sousa, Eduardo Ebner, Michael Ecker, Rupert Eliceiri, Kevin Fernandez-Rodriguez, Julia Gaudreault, Nathalie Gelman, Laurent Grunwald, David Gu, Tingting Halidi, Nadia Hammer, Mathias Hartley, Matthew Held, Marie Jug, Florian Kapoor, Varun Koksoy, Ayse Aslihan Lacoste, Judith Le Dévédec, Sylvia Le Guyader, Sylvie Liu, Penghuan Martins, Gabriel G. Mathur, Aastha Miura, Kota Llopis, Paula Montero Nitschke, Roland North, Alison Parslow, Adam C. Payne-Dwyer, Alex Plantard, Laure Ali, Rizwan Schroth-Diez, Britta Schütz, Lucas Scott, Ryan T. Seitz, Arne Selchow, Olaf Sharma, Ved P. Spitaler, Martin Srinivasan, Sathya Strambio-De-Castillia, Caterina Taatjes, Douglas Tischer, Christian Jambor, HelenaKlara Fondazione Human Technopole Viale Rita Levi-Montalcini 1 Milano20157 Italy Department of Biomedical Engineering University of Wisconsin-Madison MadisonWI53706 United States Max Planck Institute of Immunobiology and Epigenetics Freiburg79108 Germany Medical BioSciences department Radboud University Medical Centre Nijmegen Netherlands Laboratory for Molecular mechanics of cell adhesions Pontificia Universidad Católica de Chile Santiago Chile Osaka University Graduate School of Engineering Science Japan Euro-BioImaging ERIC Bio-Hub Meyerhofstr. 1 Heidelberg69117 Germany Carl Zeiss AG Carl-Zeiss-Straße 22 Oberkochen73447 Germany BioVoxxel Scientific Image Processing and Analysis Eugen-Roth-Strasse 8 Ludwigshafen67071 Germany Nanophotonics and BioImaging Facility at INL International Iberian Nanotechnology Laboratory 4715-330 Portugal Phi Optics Inc. 1800 S. Oak St Ste 106 ChampaignIL61820 United States Biochemistry Center Heidelberg Heidelberg University Germany Imaging Platform Broad Institute CambridgeMA02142 United States i3S Instituto de Investigação e Inovação Em Saúde and INEB Instituto de Engenharia Biomédica Universidade do Porto Porto Portugal Translational Research Institute Queensland University of Technology 37 Kent Street WoolloongabbaQLD4102 Australia School of Biomedical Sciences Faculty of Health Queensland University of Technology BrisbaneQLD4059 Australia TissueGnostics GmbH Vienna1020 Austria Department of Medical Physics and Biomedical Engineering University of Wisconsin-Madison MadisonWI53706 United States Centre for Cellular Imaging Core Facility Sahlgrenska Academy University of Gothenburg Sweden Allen Institute for Cell Science SeattleWA United States Friedrich Miescher Institute for Biomedical Research Basel Switzerland RNA Therapeutics Institute University of Massachusetts Chan Medical School WorcesterMA01605 United States University of Oklahoma NormanOK United States Advanced Light Microscopy Unit Ce

Images document scientific discoveries and are prevalent in modern biomedical research. Microscopy imaging in particular is currently undergoing rapid technological advancements. However for scientists wishing to publish the obtained images and image analyses results, there are to date no unified guidelines. Consequently, microscopy images and image data in publications may be unclear or difficult to interpret. Here we present community-developed checklists for preparing light microscopy images and image analysis for publications. These checklists offer authors, readers, and publishers key recommendations for image formatting and annotation, color selection, data availability, and for reporting image analysis workflows. The goal of our guidelines is to increase the clarity and reproducibility of image figures and thereby heighten the quality and explanatory power of microscopy data is in publications. © 2023, CC BY-SA.

关键词： Image analysis

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