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arXiv 2025年

作者： Ettorre, Greta Mazzi, Alessandro Girardi, Léo Marigo, Paola Pastorelli, Giada Goudfrooij, Paul Williams, Benjamin F. Bellini, Andrea Bressan, Alessandro Chen, Yang Correnti, Matteo Costa, Guglielmo Dalcanton, Julianne J. Facchini, Pietro Fouesneau, Morgan Nguyen, Chi Thanh Volpato, Guglielmo Dipartimento di Fisica e Astronomia "Galileo Galilei" Università di Padova Vicolo dell’Osservatorio 3 PadovaI-35122 Italy Dipartimento di Fisica e Astronomia "Augusto Righi" Alma Mater Studiorum Università di Bologna Via Gobetti 93/2 BolognaI-40129 Italy INAF - Osservatorio di Astrofisica e Scienza dello Spazio di Bologna Via Gobetti 93/3 Bologna40129 Italy INAF - Osservatorio Astronomico di Padova Vicolo dell’Osservatorio 5 PadovaI-35122 Italy Space Telescope Science Institute 3700 San Martin drive BaltimoreMD21218 United States Department of Astronomy University of Washington Box 351580 SeattleWA98195 United States SISSA International School for Advanced Studies Trieste Italy School of Physics and optoelectronic engineering Anhui University Hefei230601 China National Astronomical Observatories Chinese Academy of Sciences Beijing100101 China INAF - Osservatorio Astronomico di Roma Via Frascati 33 Monteporzio Catone Rome00078 Italy ASI - Space Science Data Center Via del Politecnico RomeI-00133 Italy Université de Lyon Univ Lyon1 ENS de Lyon CNRS Centre de Recherche Astrophysique de Lyon UMR5574 Saint-Genis-LavalF-69230 France Center for Computational Astrophysics Flatiron Institute 162 Fifth Avenue New YorkNY10010 United States Astronomisches Rechen-Institut Zentrum für Astronomie der Universität Heidelberg Mönchhofstr. 12-14 HeidelbergD-69120 Germany Königstuhl 17 Heidelberg69117 Germany INAF - Osservatorio Astronomico di Trieste via Tiepolo 11 Trieste34143 Italy

There has been growing evidence that the rich star clusters in the Magellanic Clouds contain significant fractions of rapidly rotating stars. In this work, we aim to constrain these fractions by studying the colour-magnitude diagrams of four star clusters, selected among those with the most striking signatures of fast rotators. Using isochrones derived from parsec v2.0 stellar tracks, we generate distinct stellar populations, each covering a limited interval of initial rotation rates ωi, referred to as ‘Partial Models’ (PMs). Using optimization algorithms and Monte Carlo Markov Chains, PMs are combined to create the final best-fitting model. In our analysis, we adopt two key assumptions: a uniform age and an isotropic distribution of stellar spin axes within each cluster. The solutions are allowed to explore the entire range of ωi, and different values of age, metallicity, distance and foreground extinction. We find that the rotational velocity distributions in all four clusters reveal a high fraction of stars with ωi close to the break-up value, in all cases. Specifically, the fraction of stars with ωi > 0.7 exceeds 80% in the clusters NGC 419 of the Small Magellanic Cloud (SMC) and NGC 1831 and NGC 1866 of the Large Magellanic Cloud (LMC). For NGC 2203 of the LMC, this fraction is smaller, although it still exceeds 50%, confirming that also this cluster is mainly populated by fast-rotating stars. Copyright © 2025, The Authors. All rights reserved.

关键词： Monte Carlo methods

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Automatic Extraction of Medication Mentions from Tweets-Overview of the BioCreative VII Shared Task 3 Competition

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database : the journal of biological databases and curation 2023年第2023期2023卷 baac108页

作者： Davy Weissenbacher Karen O'Connor Siddharth Rawal Yu Zhang Richard Tzong-Han Tsai Timothy Miller Dongfang Xu Carol Anderson Bo Liu Qing Han Jinfeng Zhang Igor Kulev Berkay Köprü Raul Rodriguez-Esteban Elif Ozkirimli Ammer Ayach Roland Roller Stephen Piccolo Peijin Han V G Vinod Vydiswaran Ramya Tekumalla Juan M Banda Parsa Bagherzadeh Sabine Bergler João F Silva Tiago Almeida Paloma Martinez Renzo Rivera-Zavala Chen-Kai Wang Hong-Jie Dai Luis Alberto Robles Hernandez Graciela Gonzalez-Hernandez Department of Computational Biomedicine Cedars-Sinai Medical Center Los Angeles CA USA. DBEI The Perelman School of Medicine University of Pennsylvania Philadelphia PA USA. Department of Computer Science and Information Engineering National Central University No. 300 Zhongda Rd Zhongli District Taoyuan 320 Taiwan. IoX Center National Taiwan University Da'an District Section 4 Roosevelt Rd No. 1 Barry Lam Hall Taipei 106 Taiwan. Research Center for Humanities and Social Sciences Academia Sinica No. 128 Section 2 Academia Rd Nangang District Taipei 115 Taiwan. Computational Health Informatics Program Boston Children's Hospital Boston MA USA. Department of Pediatrics Harvard Medical School Boston MA USA. NVIDIA Santa Clara CA USA. Department of Statistics Florida State University Tallahassee FL USA. Data and Analytics Chapter F. Hoffmann-La Roche Ltd Switzerland. Pharmaceutical Research and Early Development Roche Innovation Center Basel Switzerland. Speech and Language Technology Lab DFKI Berlin Germany. Department of Biology Brigham Young University Provo UT USA. Department of Computational Medicine and Bioinformatics Medical School University of Michigan Ann Arbor MI USA. Department of Learning Health Sciences Medical School University of Michigan Ann Arbor MI USA. School of Information University of Michigan Ann Arbor MI USA. Department of Computer Science Georgia State University Atlanta GA USA. CLaC Labs Concordia University Montreal Canada. DETI Institute of Electronics and Informatics Engineering of Aveiro University of Aveiro Portugal. Department of Computation University of A Coruña Spain. Computer Science and Engineering Department Universidad Carlos III de Madrid Madrid Spain. Big Data Laboratory Chunghwa Telecom Laboratories Taoyuan Taiwan. Department of Computer Science National Yang Ming Chiao Tung University Hsinchu Taiwan. Department of Electrical Engineering College of Electrical Engineering and Computer Sci

This study presents the outcomes of the shared task competition BioCreative VII (Task 3) focusing on the extraction of medication names from a Twitter user's publicly available tweets (the user's 'timeline'). In general, detecting health-related tweets is notoriously challenging for natural language processing tools. The main challenge, aside from the informality of the language used, is that people tweet about any and all topics, and most of their tweets are not related to health. Thus, finding those tweets in a user's timeline that mention specific health-related concepts such as medications requires addressing extreme imbalance. Task 3 called for detecting tweets in a user's timeline that mentions a medication name and, for each detected mention, extracting its span. The organizers made available a corpus consisting of 182 049 tweets publicly posted by 212 Twitter users with all medication mentions manually annotated. The corpus exhibits the natural distribution of positive tweets, with only 442 tweets (0.2%) mentioning a medication. This task was an opportunity for participants to evaluate methods that are robust to class imbalance beyond the simple lexical match. A total of 65 teams registered, and 16 teams submitted a system run. This study summarizes the corpus created by the organizers and the approaches taken by the participating teams for this challenge. The corpus is freely available at https://***/tasks/biocreative-vii/track-3/. The methods and the results of the competing systems are analyzed with a focus on the approaches taken for learning from class-imbalanced data.

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Author Correction: Medical history predicts phenome-wide disease onset and enables the rapid response to emerging health threats

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Nature communications 2025年第1期16卷 1507页

作者： Jakob Steinfeldt Benjamin Wild Thore Buergel Maik Pietzner Julius Upmeier Zu Belzen Andre Vauvelle Stefan Hegselmann Spiros Denaxas Harry Hemingway Claudia Langenberg Ulf Landmesser John Deanfield Roland Eils Department of Cardiology Angiology and Intensive Care Medicine Deutsches Herzzentrum der Charité (DHZC) Berlin Germany. Charité - Universitätsmedizin Berlin corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin Klinik/Centrum Berlin Germany. Computational Medicine Berlin Institute of Health (BIH) Charite - University Medicine Berlin Berlin Germany. Friede Springer Cardiovascular Prevention Center@Charite Charite - University Medicine Berlin Berlin Germany. Institute of Cardiovascular Sciences University College London London UK. Center for Digital Health Berlin Institute of Health (BIH) Charite - University Medicine Berlin Berlin Germany. MRC Epidemiology Unit Institute of Metabolic Science University of Cambridge Cambridge UK. Precision Health University Research Institute Queen Mary University of London and Barts NHS Trust London UK. Institute of Health Informatics University College London London UK. Institute for Medical Engineering and Science Massachusetts Institute of Technology Massachusetts USA. Pattern Recognition and Image Analysis Lab University of Münster Münster Germany. British Heart Foundation Data Science Centre London UK. Health Data Research UK London UK. National Institute for Health Research Biomedical Research Centre at University College London Hospitals London UK. Berlin Institute of Health (BIH) Charite - University Medicine Berlin Berlin Germany. DZHK (German Centre for Cardiovascular Research) Partner Site Berlin Berlin Berlin Germany. Center for Digital Health Berlin Institute of Health (BIH) Charite - University Medicine Berlin Berlin Germany. roland.eils@bih-charite.de. Health Data Science Unit Heidelberg University Hospital and BioQuant Heidelberg Germany. roland.eils@bih-charite.de.

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Correction: The Effect of Co-Culture of Two Coral Species on Their Bacterial Composition Under Captive Environments

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Marine biotechnology (New York, N.Y.) 2022年第6期24卷 1176页

作者： Keigo Ide Yoshikatsu Nakano Michihiro Ito Yohei Nishikawa Hiroyuki Fujimura Haruko Takeyama Department of Life Science and Medical Bioscience Waseda University Tokyo Japan. Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL) National Institute of Advanced Industrial Science and Technology Tokyo Japan. Tropical Biosphere Research Center University of the Ryukyus Tokyo Japan. Marine Science Section Research Support Division Okinawa Institute of Science and Technology Graduate University Okinawa Japan. Research Organization for Nano and Life Innovation Waseda University Tokyo Japan. Department of Chemistry Biology and Marine Science University of the Ryukyus Okinawa Japan. Department of Life Science and Medical Bioscience Waseda University Tokyo Japan. haruko-takeyama@waseda.jp. Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL) National Institute of Advanced Industrial Science and Technology Tokyo Japan. haruko-takeyama@waseda.jp. Research Organization for Nano and Life Innovation Waseda University Tokyo Japan. haruko-takeyama@waseda.jp. Institute for Advanced Research of Biosystem Dynamics Waseda Research Institute for Science and Engineering Tokyo Japan. haruko-takeyama@waseda.jp.

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Petri Net Control Method for Pipe-line Systems and Its Implementation via CIF3 ⁎

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IFAC-PapersOnLine 2019年第24期52卷 261-266页

作者： YuHao Fu JiLiang Luo Huifeng Wu Jianhong Ye Yi-sheng Huang College Information Science and Engineering Huaqiao University Xiamen 361021 China College Information Science and Engineering Huaqiao University Xiamen 361021 China and also with Fujian Engineering Research Center of Motor Control and System Optimal Schedule Xiamen 361021 China Institute of Intelligent and Software Technology Hangzhou Dianzi University Hangzhou 310018 China Computer Science and Technology Huaqiao University Xiamen 361021 China and also with Fujian Provincial Key Laboratory of Data Intensive Computing Quanzhou 362000 China Department of Electrical Engineering National Ilan University Taiwan

As for a pipe-line system subjected to complex operations, an approach is proposed to synthesize the controller via Petri nets (PNs) such that the plant is run as concurrently as possible and the loads of equipments are balanced. A P-timed and labeled PN is designed to model the whole process of a pipe-line system, where tasks, including transporting material from one tank to another and cleaning tank, are represented by operational places, and level sensors amounted in tanks are represented by labels assigned to transitions. Further, monitor places are designed to resolve the conflict relations among tasks due to the shared valves and pipes. An method is presented to translate an PN controller into a CIF3 (Compositional Interchange Format) model, which can be converted into a PLC program in the CIF3 tool. A beer filtration plant is taken as an example to illustrate the approach, and its simulation experiments are carried out to verify the theoretic results.

关键词： Chemical plant Valve control Petri net CIF3

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WaveNano:a signal-level nanopore base-caller via simultaneous prediction of nucleotide labels and move labels through bi-directional WaveNets

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Frontiers of Electrical and Electronic engineering in China 2018年第4期6卷 359-368页

作者： Sheng Wang Zhen Li Yizhou YU Xin Gao Computational Bioscience Research Center (CBRC) King Abdullah University of Science and Technology (KAUST)Thuwa23955-6900Kingdom of Saudi Arabia Department of Computer Science University of Hong KongHong Kong SAR 999077China School of Science and Engineering Shenzhen Research Institute of Big DataThe Chinese University of Hong Kong Shenzhen 518172China

Background The Oxford MinION nanopore sequencer is the recently appealing third-generation genome sequencing device that is portable and no larger than a cellphone. Despite the benefits of MinION to sequence ultra-long reads in real-time, the high error rate of the existing base-calling methods, especially indels (insertions and deletions), prevents its use in a variety of *** In this paper, we show that such indel errors are largely due to the segmentation process on the input electrical current signal from MinION. All existing methods conduct segmentation and nucleotide label prediction in a sequential manner, in which the errors accumulated in the first step will irreversibly influence the final base-calling. We further show that the indel issue can be significantly reduced via accurate labeling of nucleotide and move labels directly from the raw signal, which can then be efficiently learned by a bi-directionalWaveNet model simultaneously through feature sharing. Our bi-directional WaveNet model with residual blocks and skip connections is able to capture the extremely long dependency in the raw signal. Taking the predicted move as the segmentation guidance, we employ the Viterbi decoding to obtain the final base-calling results from the smoothed nucleotide probability *** Our proposed base-caller, WaveNano, achieves good performance on real MinION sequencing data from Lambda *** The signal-level nanopore base-callerWaveNano can obtain higher base-calling accuracy, and generate fewer insertions/deletions in the base-called sequences.

关键词： nanopore sequencing bi-directional WaveNets base-calling third generation sequencing deep learning

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Flexible x-ray source with tunable polarization and orbital angular momentum from Hermite-Gaussian laser modes driven plasma channel wakefield

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Physical Review Accelerators and Beams 2019年第7期22卷 071302-071302页

作者： B. Lei T. Teter J. W. Wang V. Yu. Kharin C. B. Schroeder M. Zepf S. G. Rykovanov Helmholtz Institute Jena Fröbelstieg 3 07743 Jena Germany Faculty of Physics and Astronomy Friedrich-Schiller-Universität Jena 07743 Jena Germany Shanghai Institute of Optics and Fine Mechanics Chinese Academy of Sciences 201800 Shanghai China Lawrence Berkeley National Laboratory Berkeley California 94720 USA Center for Computational and Data-Intensive Science and Engineering Skolkovo Institute of Science and Technology Moscow 121205 Russia

A plasma channel undulator/wiggler may be created through the plasma wakefield excited by the beating of several Hermite-Gaussian laser modes propagating in a parabolic plasma channel. Control over both the betatron and undulator forces is conveniently achieved by tuning the amplitude ratios, colors, and order numbers of the modes. A special structure of the undulator/wiggler field without the focusing force near the propagation axis is generated inside the plasma wakefield by matching the strengths of the fundamental and first-order Hermite-Gaussian modes. The electron beam only experiences forced undulator oscillations in such a field, which significantly improves the quality of the emitted radiation. Since the value of the undulator strength parameter could be in a wide range, less or larger than unity, it is capable of generating narrow bandwidth x-ray, as well as the synchrotronlike high-energy x/γ-ray, radiation by harmonics. Additionally, controlling the relative phases between the laser modes allows for polarization control of the plasma undulator. High-order harmonics produced from a circularly polarized plasma undulator clearly show the vortex nature and carry well-defined orbital angular momentum.

关键词： Laser wakefield acceleration Laser-plasma interactions Plasma acceleration & new acceleration techniques Plasma waves X-ray generation in plasmas

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A network monitoring game with heterogeneous component criticality levels

arXiv

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arXiv 2019年

作者： Milošević, Jezdimir Dahan, Mathieu Amin, Saurabh Sandberg, Henrik Division of Decision and Control Systems School of Electrical Engineering and Computer Science KTH Royal Institute of Technology Stockholm Sweden Center for Computational Engineering Massachusetts Institute of Technology CambridgeMA United States Department of Civil and Environmental Engineering Institute for Data Systems and Society Massachusetts Institute of Technology Cambridge United States

We consider an attacker-operator game for monitoring a large-scale network that is comprised on components that differ in their criticality levels. In this zero-sum game, the operator seeks to position a limited number of sensors to monitor the network against an attacker who strategically targets a network component. The operator (resp. attacker) seeks to minimize (resp. maximize) the network loss. To study the properties of mixed-strategy Nash Equilibria of this game, we first study two simple instances: (i) When component sets monitored by individual sensor locations are mutually disjoint;(ii) When only a single sensor is positioned, but with possibly overlapping monitoring component sets. Our analysis reveals new insights on how criticality levels impact the players equilibrium strategies. Next, we extend a previously known approach to obtain an approximate Nash equilibrium for the general case of the game. This approach uses solutions to minimum set cover and maximum set packing problems to construct an approximate Nash equilibrium. Finally, we implement a column generation procedure to improve this solution and numerically evaluate the performance of our approach. Copyright © 2019, The Authors. All rights reserved.

关键词： Criticality (nuclear fission)

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Ab initio evaluation of complexation energies for cyclodextrin drug inclusion complexes

arXiv

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arXiv 2020年

作者： Oqmhula, Kenji Hongo, Kenta Maezono, Ryo Ichibha, Tom School of Materials Science JAIST 1-1 Asahidai NomiIshikawa923-1292 Japan Research Center for Advanced Computing Infrastructure JAIST 1-1 Asahidai NomiIshikawa923-1292 Japan Center for Materials Research by Information Integration Research and Services Division of Materials Data and Integrated System National Institute for Materials Science 1-2-1 Sengen Tsukuba305-0047 Japan PRESTO Japan Science and Technology Agency 4-1-8 Honcho Kawaguchi-shi Saitama322-0012 Japan Computational Engineering Applications Unit RIKEN 2-1 Hirosawa Wako Saitama351-0198 Japan School of Information Science JAIST 1-1 Asahidai NomiIshikawa923-1292 Japan

We examined the reliability of exchange-correlation functionals for molecular encapsulations combined by van der Waals forces, comparing their predictions with those of diffusion Monte Carlo method. We established that functionals with D3 dispersion force correction and including sufficient proportion of exact-exchange in long-ranged interaction can comparatively reliably estimate the binding strength. Our finding agrees with a previous ab initio study on argon dimer. However we found that even such functionals may not be able to distinguish the energy differences among different conformations. Copyright © 2020, The Authors. All rights reserved.

关键词： Van der Waals forces

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Atlas of Proteomic signatures of brain structure and its links to brain disorders

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Nature communications 2025年第1期16卷 5092页

作者： Peng Ren Xiao-He Hou Zeyu Li Jia You Yuzhu Li Wei Zhang Weikang Gong Bei Zhang Bangsheng Wu Linbo Wang Chun Shen Yujie Zhao Qing Ma Jujiao Kang Yuchao Jiang Neil Roberts Fan Xu Yong He Jin-Tai Yu Meiyun Wang Wei Cheng Institute of Science and Technology for Brain-Inspired Intelligence State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science Fudan University Shanghai China. Department of Neurology Huashan Hospital Fudan University Shanghai China. Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University) Ministry of Education Shanghai PR China. Department of Neurology Qingdao Hospital University of Health and Rehabilitation Sciences (Qingdao Municipal Hospital) Qingdao China. School of Data Science Fudan University Shanghai China. Centre for Reproductive Health (CRH) Institute for Regeneration and Repair (IRR) University of Edinburgh 4-5 Little France Drive Edinburgh EH15 4UU UK. Institute of Mechanics and Computational Engineering Department of Aeronautics and Astronautics Fudan University Shanghai China. State Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing China. Beijing Key Laboratory of Brain Imaging and Connectomics Beijing Normal University Beijing China. Institute of Science and Technology for Brain-Inspired Intelligence State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science Fudan University Shanghai China. jintai_yu@***. Department of Neurology Huashan Hospital Fudan University Shanghai China. jintai_yu@***. Department of Medical Imaging Henan Provincial People's Hospital & Zhengzhou University People's Hospital Zhengzhou China. mywang@***. Institute of Science and Technology for Brain-Inspired Intelligence State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science Fudan University Shanghai China. wcheng@***. Department of Neurology Huashan Hospital Fudan University Shanghai China. wcheng@***. Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University) Ministry of Education Shanghai PR China. wcheng@fudan.edu.cn. Fudan ISTBI-ZJNU Algorithm Centre for Brain-inspi

Individual variation in brain structure influences deterioration due to disease and comprehensive profiling of the associated proteomic signature advances mechanistic understanding. Here, using data from 4997 UK Biobank participants, we analyzed the associations between 2920 plasma proteins and 272 neuroimaging-derived brain structure measures. We identified 5358 associations between 1143 proteins and 256 brain structure measures, with NCAN and LEP proteins showing the most associations. Functional enrichment implicated these proteins in neurogenesis, immune/apoptotic processes and neurons. Furthermore, bidirectional Mendelian randomization revealed 33 associations between 32 proteins and 23 brain structure measures, and 21 associations between nine brain structure associated proteins and ten brain disorders. Moreover, the significant associations between the identified proteins and mental health were mediated by brain volume and surface area. In summary, this study generates a comprehensive atlas mapping the patterns of association between proteome and brain structure, highlighting their potential value for studying brain disorders.

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