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Network and systems Medicine 2021年第1期4卷 2-50页

作者： Zanin, Massimiliano Aitya, Nadim A.A. Basilio, José Baumbach, Jan Benis, Arriel Behera, Chandan K. Bucholc, Magda Castiglione, Filippo Chouvarda, Ioanna Comte, Blandine Dao, Tien-Tuan Ding, Xuemei Pujos-Guillot, Estelle Filipovic, Nenad Finn, David P. Glass, David H. Harel, Nissim Iesmantas, Tomas Ivanoska, Ilinka Joshi, Alok Boudjeltia, Karim Zouaoui Kaoui, Badr Kaur, Daman Maguire, Liam P. McClean, Paula L. McCombe, Niamh De Miranda, João Luís Moisescu, Mihnea Alexandru Pappalardo, Francesco Polster, Annikka Prasad, Girijesh Rozman, Damjana Sacala, Ioan Sanchez-Bornot, Jose M. Schmid, Johannes A. Sharp, Trevor Solé-Casals, Jordi Spiwok, Vojtěch Spyrou, George M. Stalidzans, Egils Stres, Blaa Sustersic, Tijana Symeonidis, Ioannis Tieri, Paolo Todd, Stephen Van Steen, Kristel Veneva, Milena Wang, Da-Hui Wang, Haiying Wang, Hui Watterson, Steven Wong-Lin, Kongfatt Yang, Su Zou, Xin Schmidt, Harald H.H.W. Centro de Tecnología Biomédica Universidad Politécnica de Madrid Madrid Spain Intelligent Systems Research Centre School of Computing Engineering and Intelligent Systems Ulster University Ulster United Kingdom Center for Physiology and Pharmacology Institute of Vascular Biology and Thrombosis Research Medical University of Vienna Vienna Austria TUM School of Life Sciences Weihenstephan Technical University of Munich Freising Germany Holon Israel CNR National Research Council IAC Institute for Applied Computing Rome Italy Lab of Computing Medical Informatics and Biomedical Imaging Technologies School of Medicine Aristotle University of Thessaloniki Thessaloniki Greece Université Clermont Auvergne INRAE UNH Plateforme d'Exploration du Métabolisme MetaboHUB Clermont Clermont-Ferrand France Université de Technologie de Compiègne Compiègne France Labex MS2T Control of Technological Systems-of-Systems CNRS and Université de Technologie de Compiègne Compiègne France Faculty of Engineering University of Kragujevac Kragujevac Serbia Kragujevac Serbia Steinbeis Advanced Risk Technologies Institute Doo Kragujevac Kragujevac Serbia Pharmacology and Therapeutics School of Medicine Galway Neuroscience Centre National University of Ireland Galway Ireland School of Computing Ulster University Ulster United Kingdom Holon Israel Department of Mathematics and Natural Sciences Kaunas University of Technology Kaunas Lithuania Faculty of Computer Science and Engineering Ss. Cyril and Methodius University Skopje Macedonia Medicine Faculty Université Libre de Bruxelles CHU de Charleroi Charleroi Belgium Northern Ireland Centre for Stratified Medicine Biomedical Sciences Research Institute Ulster University Ulster United Kingdom Escola Superior de Tecnologia e Gestão Instituto Politécnico de Portalegre Portalegre Portugal Instituto Superior Técnico Universidade de Lisboa Lisboa Portugal Faculty of Automatic Control and Computers University Politehnica of B

Background: systems Medicine is a novel approach to medicine, that is, an interdisciplinary field that considers the human body as a system, composed of multiple parts and of complex relationships at multiple levels, and further integrated into an environment. Exploring systems Medicine implies understanding and combining concepts coming from diametral different fields, including medicine, biology, statistics, modeling and simulation, and data science. Such heterogeneity leads to semantic issues, which may slow down implementation and fruitful interaction between these highly diverse fields. Methods: In this review, we collect and explain more than100 terms related to systems Medicine. These include both modeling and data science terms and basic systems medicine terms, along with some synthetic definitions, examples of applications, and lists of relevant references. Results: This glossary aims at being a first aid kit for the systems Medicine researcher facing an unfamiliar term, where he/she can get a first understanding of them, and, more importantly, examples and references for digging into the topic. © Massimiliano Zanin et al., 2021;Published by Mary Ann Liebert, Inc. 2021.

关键词： Semantics

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Correction: The role of [68Ga]Ga-PSMA PET/CT in primary staging of newly diagnosed prostate cancer: predictive value of PET-derived parameters for risk stratification through machine learning

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Clinical and Translational Imaging 2024年第1期13卷 93-93页

作者： Jafari, Esmail Dadgar, Habibollah Zarei, Amin Samimi, Rezvan Manafi-Farid, Reyhaneh Divband, GhasemAli Nikkholgh, Babak Fallahi, Babak Amini, HamidReza Ahmadzadehfar, Hojjat Keshavarz, Ahmad Assadi, Majid The Persian Gulf Nuclear Medicine Research Center Department of Nuclear Medicine Molecular Imaging and Theranostics School of Medicine Bushehr Medical University Hospital Bushehr University of Medical Sciences Bushehr Iran Cancer Research Center RAZAVI Hospital Imam Reza International University Mashhad Iran Khatam PET/CT Center Tehran Iran Research Center for Nuclear Medicine Shariati Hospital Tehran University of Medical Sciences Tehran Iran Department of Nuclear Medicine Klinikum Westfalen Dortmund Germany Department of Nuclear Medicine Institute of Radiology Neuroradiology and Nuclear Medicine University Hospital Knappschaftskrankenhaus Bochum Germany IoT and Signal Processing Research Group ICT Research Institute Faculty of Intelligent Systems Engineering and Data Science Persian Gulf University Bushehr Iran

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Using artificial intelligence to document the hidden RNA virosphere

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四川生理科学杂志 2024年第10期46卷 2345-2345页

作者： Xin Hou National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases State Key Laboratory for Biocontrol School of Medicine Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University Shenzhen China Apsara Lab Alibaba Cloud Intelligence Alibaba Group Hangzhou China Wuhan Centers for Disease Control and Prevention Wuhan China Polar Research Institute of China Shanghai China Department of Nursing The Fifth Affiliated Hospital Sun Yat-sen University Zhuhai China School of Geospatial Engineering and Science Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Sun Yat-sen University Zhuhai China Key Laboratory of Comprehensive Observation of Polar Environment Ministry of Education Sun Yat-sen University Zhuhai China Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary Institute of Biodiversity Science and Institute of Eco-Chongming School of Life Sciences Fudan University Shanghai Shanghai China Centre for Virus Research Westmead Institute for Medical Research Westmead NSW Australia School of Medical Sciences The University of Sydney Sydney NSW 2006 Australia College of Life Sciences Zhejiang University Hangzhou China School of Life Science Guangzhou University Guangzhou China Key Laboratory of Pathogen Infection Prevention and Control (MOE) State Key Laboratory of Respiratory Health and Multimorbidity National Institute of Pathogen Biology Chinese Academy of Medical Sciences & Peking Union Medical College Beijing China School of Public Health (Shenzhen) Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University Shenzhen China Guangzhou National Laboratory Guangzhou International Bio-Island Guangzhou China Department of Infectious Diseases and Public Health Jockey Club College of Veterinary Medicine and Life Sciences City University of Hong Kong Hong Kong SAR China Laboratory of Data Disco

Current metagenomic tools can fail to identify highly divergent RNA *** developed a deep learning algorithm,termed LucaProt,to discover highly divergent RNA-dependent RNA polymerase(RdRP)sequences in 10,487 metatranscriptomes generated from diverse global *** integrates both sequence and predicted structural information,enabling the accurate detection of RdRP *** this approach,we identified 161,979 potential RNA virus species and 180 RNA virus supergroups,including many previously poorly studied groups,as well as RNA virus genomes of exceptional length(up to 47,250 nucleotides)and genomic complexity.

关键词： artificial exceptional integrate

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Strategic priorities for transformative progress in advancing biology with proteomics and artificial intelligence

arXiv

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arXiv 2025年

作者： Sun, Yingying Jun, A. Liu, Zhiwei Sun, Rui Qian, Liujia Payne, Samuel H. Bittremieux, Wout Ralser, Markus Li, Chen Chen, Yi Dong, Zhen Perez-Riverol, Yasset Khan, Asif Sander, Chris Aebersold, Ruedi Vizcaíno, Juan Antonio Krieger, Jonathan R. Yao, Jianhua Wen, Han Zhang, Linfeng Zhu, Yunping Xuan, Yue Sun, Benjamin Boyang Qiao, Liang Hermjakob, Henning Tang, Haixu Gao, Huanhuan Deng, Yamin Zhong, Qing Chang, Cheng Bandeira, Nuno Li, Ming Weinan, E. Sun, Siqi Yang, Yuedong Omenn, Gilbert S. Zhang, Yue Xu, Ping Fu, Yan Liu, Xiaowen Overall, Christopher M. Wang, Yu Deutsch, Eric W. Chen, Luonan Cox, Jürgen Demichev, Vadim He, Fuchu Huang, Jiaxing Jin, Huilin Liu, Chao Li, Nan Luan, Zhongzhi Song, Jiangning Yu, Kaicheng Wan, Wanggen Wang, Tai Zhang, Kang Zhang, Le Bell, Peter A. Mann, Matthias Zhang, Bing Guo, Tiannan Affiliated Hangzhou First People’s Hospital State Key Laboratory of Medical Proteomics School of Medicine Westlake University Zhejiang Province Hangzhou China Westlake Center for Intelligent Proteomics Westlake Laboratory of Life Sciences and Biomedicine Zhejiang Province Hangzhou China Biology Department Brigham Young University ProvoUT84602 United States Department of Computer Science University of Antwerp Antwerp2020 Belgium Department of Biochemistry CharitéUniversitätsmedizin Berlin Berlin Germany Biomedicine Discovery Institute Department of Biochemistry and Molecular Biology Monash University MelbourneVICVIC 3800 Australia Wellcome Genome Campus Hinxton CambridgeCB10 1SD United Kingdom Harvard Medical School Ludwig Center at Harvard United States Harvard Medical School Broad Institute Ludwig Center at Harvard Dana-Farber Cancer Institute United States Department of Biology Institute of Molecular Systems Biology ETH Zürich Zürich Switzerland Bruker Ltd. MiltonONL9T 6P4 Canada AI for Life Sciences Lab Tencent Shenzhen518057 China State Key Laboratory of Medical Proteomics AI for Science Institute Beijing100080 China Beijing Institute of Lifeomics Beijing102206 China Thermo Fisher Scientific GmbH Hanna-Kunath Str. 11 Bremen28199 Germany Informatics and Predictive Sciences Research Bristol Myers Squibb United States Department of Chemistry Fudan University Songhu Road 2005 Shanghai200438 China Department of Computer Science Luddy School of Informatics Computing and Engineering Indiana University IN47408 United States ProCan® Children’s Medical Research Institute Faculty of Medicine and Health The University of Sydney WestmeadNSW Australia La Jolla CA United States Central China Institute of Artificial Intelligence University of Waterloo Canada AI for Science Institute Center for Machine Learning Research School of Mathematical Sciences Peking University China Research Institute of Intelligent Complex Systems Fudan U

Artificial intelligence (AI) is transforming scientific research, including proteomics. Advances in mass spectrometry (MS)-based proteomics data quality, diversity, and scale, combined with groundbreaking AI techniques, are unlocking new challenges and opportunities in biological discovery. Here, we highlight key areas where AI is driving innovation, from data analysis to new biological insights. These include developing an AI-friendly ecosystem for proteomics data generation, sharing, and analysis;improving peptide and protein identification and quantification;characterizing protein-protein interactions and protein complexes;advancing spatial and perturbation proteomics;integrating multi-omics data;and ultimately enabling AI-empowered virtual cells. © 2025, CC BY.

关键词： Biotic

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The 2024 Motile Active Matter Roadmap

arXiv

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arXiv 2024年

作者： Gompper, Gerhard Stone, Howard A. Kurzthaler, Christina Saintillan, David Peruani, Fernado Fedosov, Dmitry A. Auth, Thorsten Cottin-Bizonne, Cecile Ybert, Christophe Clément, Eric Darnige, Thierry Lindner, Anke Goldstein, Raymond E. Liebchen, Benno Binysh, Jack Souslov, Anton Isa, Lucio di Leonardo, Roberto Frangipane, Giacomo Gu, Hongri Nelson, Bradley J. Brauns, Fridtjof Marchetti, M. Cristina Cichos, Frank Heuthe, Veit-Lorenz Bechinger, Clemens Korman, Amos Feinerman, Ofer Cavagna, Andrea Giardina, Irene Jeckel, Hannah Drescher, Knut Theoretical Physics of Living Matter Institute for Advanced Simulation Forschungszentrum Jülich Jülich Germany Princeton University Department of Mechanical and Aerospace Engineering PrincetonNJ United States Max Planck Institute for the Physics of Complex Systems Center for Systems Biology Dresden Cluster of Excellence Physics of Life TU Dresden Dresden Germany University of California San Diego United States CY Cergy Paris University France Université de Lyon Université Claude Bernard Lyon 1 CNRS Institut Lumière Matière Villeurbanne France Laboratoire PMMH-ESPCI UMR 7636 CNRS-PSL-Research University Sorbonne Université Université Paris Cité Paris France Institut Universitaire de France Paris France Department of Applied Mathematics and Theoretical Physics University of Cambridge Cambridge United Kingdom Technische Universität Darmstadt Darmstadt64289 Germany Institute of Physics Universiteit van Amsterdam Science Park 904 Amsterdam1098 XH Netherlands T.C.M. Group Cavendish Laboratory University of Cambridge CambridgeCB3 0HE United Kingdom Laboratory for Soft Materials and Interfaces Department of Materials ETH Zurich Zurich8093 Switzerland Dipartimento di Fisica Sapienza Università di Roma Italy Department of Physics University of Konstanz Konstanz Germany Institute of Robotics and Intelligent Systems ETH Zürich Zurich Switzerland Kavli Institute for Theoretical Physics University of California Santa BarbaraCA93106 United States Department of Physics University of California Santa BarbaraCA93106 United States Molecular Nanophotonics Leipzig University Leipzig04013 Germany UMI FILOFOCS Israel Department of Physics of Complex Systems Weizmann Institute of Science Israel Rome Italy Dipartimento di Fisica Sapienza Università di Roma INFN Unità di Roma 1 Rome Italy Department of Biology and Biological Engineering California Institute of Technology Pasadena91125 United States Biozentrum University of Basel Basel4056 Switzerl

Activity and autonomous motion are fundamental aspects of many living and engineering systems. Here, the scale of biological agents covers a wide range, from nanomotors, cytoskeleton, and cells, to insects, fish, birds, and people. Inspired by biological active systems, various types of autonomous synthetic nano- and micromachines have been designed, which provide the basis for multifunctional, highly responsive, intelligent active materials. A major challenge for understanding and designing active matter is their inherent non-equilibrium nature due to persistent energy consumption, which invalidates equilibrium concepts such as free energy, detailed balance, and time-reversal symmetry. Furthermore, interactions in ensembles of active agents are often non-additive and non-reciprocal. An important aspect of biological agents is their ability to sense the environment, process this information, and adjust their motion accordingly. It is an important goal for the engineering of microrobotic systems to achieve similar functionality. With many fundamental properties of motile active matter now reasonably well understood and under control, the ground is prepared for the study of physical aspects and mechanisms of motion in complex environments, of the behavior of systems with new physical features like chirality, of the development of novel micromachines and microbots, of the emergent collective behavior and swarming of intelligent self-propelled particles, and of particular features of microbial systems. The vast complexity of phenomena and mechanisms involved in the self-organization and dynamics of motile active matter poses major challenges, which can only be addressed by a truly interdisciplinary effort involving scientists from biology, chemistry, ecology, engineering, mathematics, and physics. The 2024 motile active matter roadmap of Journal of Physics: Condensed Matter reviews the current state of the art of the field and provides guidance for further progress in t

关键词： Microrobots

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Regulating the electrode-electrolyte interface in Li-S batteries with 2,5-dimercapto-1,3,4-thiadiazole additives

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Journal of colloid and interface science 2025年 697卷 137953页

作者： Xiaohui Song Rui Huang Xin Liang Yang Wang Qian Hou Binghui Ge Qiaobao Zhang Febri Baskoro Afriyanti Sumboja Rong Xiang Hongfa Xiang Zhimei Huang School of Materials Science and Engineering Hefei University of Technology Hefei 230009 PR China. Electronic address: Xiaohuisong@***. School of Materials Science and Engineering Hefei University of Technology Hefei 230009 PR China. School of Energy Materials and Chemical Engineering Hefei University Hefei 230601 PR China. Information Materials and Intelligent Sensing Laboratory of Anhui Province Institutes of Physical Science and Information Technology Anhui University Hefei 230601 PR China. State Key Laboratory of Physical Chemistry of Solid Surfaces College of Materials Xiamen University Xiamen Fujian 361005 PR China. Material Science and Engineering Research Group Faculty of Mechanical and Aerospace Engineering Institut Teknologi Bandung Jl. Ganesha 10 Bandung 40132 Indonesia. State Key Laboratory of Fluid Power and Mechatronic Systems Zhejiang Provincial Key Laboratory for Atomic-level Manufacturing School of Mechanical Engineering Zhejiang University Hangzhou 310027 PR China. School of Materials Science and Engineering Hefei University of Technology Hefei 230009 PR China. Electronic address: huangzm@***.

The commercialization of Li-S batteries is constrained by the unstable interface, severe shuttle of polysulfides, and sluggish kinetic conversion reactions. Electrolyte regulation is a straightforward and efficient way to tackle those mentioned issues. Herein, a multifunctional electrolyte additive of 2,5-Dimercapto-1,3,4-thiadiazole (DMTD) is introduced in the ether-based electrolyte, which can be lithiated into Li-DMTD when contacted with the Li or LiS during the discharge process. The generated Li-DMTD can operate as a highly ionic-conducting protective coating on the Li surface, inhibiting the formation of Li dendrites, and increasing interface stability. Then, it is reversibly oligomerized with LiS, forming two organosulfur oligomers during the ensuing electrochemical process. Such a modified reaction routine can reduce the shuttle effect and speed up the reaction kinetics of LiS at the cathode, preventing cathode passivation and boosting active material utilization. As a result, The Li||Li symmetric cells with DMTD exhibit about 5-fold cycle life than the reference cell under 5 mA cm current density. Meanwhile, the initial charge voltage of Li||LiS battery is greatly decreased from 3.7 V to 3.0 V with DMTD, and the assembled Li-S cell shows an improved capacity retention from 45.7 % to 81.2 % after 320 cycles. Therefore, this work successfully tackled the critical issues by designing functional organosulfur electrolyte additives in LSBs, which provides theoretical guidance for the electrolyte design in LSBs.

关键词： Electrolyte additive Lithium dendrites Lithium-sulfur batteries Multi-functional electrolyte Shuttle effect

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Deep learning methods for automatic evaluation of delayed enhancement-MRI. The results of the EMIDEC challenge

arXiv

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arXiv 2021年

作者： Lalande, Alain Chen, Zhihao Pommier, Thibaut Decourselle, Thomas Qayyum, Abdul Salomon, Michel Ginhac, Dominique Skandarani, Youssef Boucher, Arnaud Brahim, Khawla de Bruijne, Marleen Camarasa, Robin Correia, Teresa M. Feng, Xue Girum, Kibrom B. Hennemuth, Anja Huellebrand, Markus Hussain, Raabid Ivantsits, Matthias Ma, Jun Meyer, Craig Sharma, Rishabh Shi, Jixi Tsekos, Nikolaos V. Varela, Marta Wang, Xiyue Yang, Sen Zhang, Hannu Zhang, Yichi Zhou, Yuncheng Zhuang, Xiahai Couturier, Raphael Meriaudeau, Fabrice ImViA laboratory University of Burgundy Dijon France MRI department University Hospital of Dijon Dijon France Femto-ST laboratory University of Franche-Comté Belfort France Cardiology department University Hospital of Dijon Dijon France CASIS Company Quetigny France National Engineering School of Sousse University of Sousse Sousse Tunisia LASEE laboratory National Engineering School of Monastir University of Monastir Monastir Tunisia Biomedical Imaging Group Rotterdam Erasmus MC Rotterdam Netherlands Department of Radiology and Nuclear Medicine Erasmus MC Rotterdam Netherlands Department of Computer Science University of Copenhagen Copenhagen Denmark Centre of Marine Sciences University of Algarve Faro Portugal School of Biomedical Engineering and Imaging Sciences King’s College London London United Kingdom Department of Biomedical Engineering University of Virginia Charlottesville United States Charité – Universitätsmedizin Berlin Berlin Germany Fraunhofer MEVIS Bremen Germany German Centre for Cardiovascular Research Berlin Germany Department of Mathematics Nanjing University of Science and Technology Nanjing China Data Analysis and Intelligent Systems Lab Department of Computer Science University of Houston Houston United States Medical Robotics and Imaging Lab Department of Computer Science University of Houston Houston United States National Heart and Lung Institute Imperial College London London United Kingdom College of Computer Science Sichuan University Chengdu China College of Biomedical Engineering Sichuan University Chengdu China School of Biological Science and Medical Engineering Beihang University Beijing China School of Data Science Fudan University Shanghai China

A key factor for assessing the state of the heart after myocardial infarction (MI) is to measure whether the myocardium segment is viable after reperfusion or revascularization therapy. Delayed enhancement-MRI or DE-MRI, which is performed several minutes after injection of the contrast agent, provides high contrast between viable and nonviable myocardium and is therefore a method of choice to evaluate the extent of MI. To automatically assess myocardial status, the results of the EMIDEC challenge that focused on this task are presented in this paper. The challenge’s main objectives were twofold. First, to evaluate if deep learning methods can distinguish between normal and pathological cases. Second, to automatically calculate the extent of myocardial infarction. The publicly available database consists of 150 exams divided into 50 cases with normal MRI after injection of a contrast agent and 100 cases with myocardial infarction (and then with a hyperenhanced area on DE-MRI), whatever their inclusion in the cardiac emergency department. Along with MRI, clinical characteristics are also provided. The obtained results issued from several works show that the automatic classification of an exam is a reachable task (the best method providing an accuracy of 0.92), and the automatic segmentation of the myocardium is possible. However, the segmentation of the diseased area needs to be improved, mainly due to the small size of these areas and the lack of contrast with the surrounding structures. © 2021, CC BY-NC-SA.

关键词： Cardiology

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INTRODUCTION

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Bulletin of the American Meteorological Society 2024年第8期105卷 S1-S11页

作者： Boyer, T. Blunden, J. Dunn, R.J.H. NOAA/NESDIS National Centers for Environmental Information Silver Spring Maryland NOAA/NESDIS National Centers for Environmental Information Asheville North Carolina Met Office Hadley Centre Exeter United Kingdom European Centre for Medium-Range Weather Forecasts Reading United Kingdom University of Maryland College Park Maryland Scripps Institution of Oceanography University of California San Diego La Jolla California NOAA/NWS National Centers for Environmental Prediction Climate Prediction Center College Park Maryland Brandenburg University of Technology (BTU) Cottbus-Senftenberg Germany Servicio Meteorológico Nacional Buenos Aires Argentina NOAA/OAR Physical Sciences Laboratory Boulder Colorado European Centre for Medium-Range Weather Forecasts Bonn Germany Center for Geophysical Research and School of Physics University of Costa Rica San José Costa Rica Department of Meteorology and National Centre for Earth Observation University of Reading Reading United Kingdom Centro Nacional de Monitoramento e Alertas de Desastres Naturais CEMADEN São Paulo Brazil Université Grenoble Alpes Institut des Géosciences de l’Environnement IRD CNRS Grenoble INP Grenoble France Hampton University Hampton Virginia Seychelles Meteorological Authority Mahe Seychelles Section for Glaciers Ice and Snow Norwegian Water Resources and Energy Directorate Oslo Norway National Research Institute for Agriculture Food and Environment (INRAE) CARRTEL Université Savoie Mont Blanc Thonon les Bains France Graduate School of Agriculture Osaka Metropolitan University Sakai Japan Science Faculty Universidad Nacional de Colombia Bogotá Colombia University of Bremen Bremen Germany NOAA Global Monitoring Laboratory Boulder Colorado Servicio Nacional de Meteorología e Hidrología del Perú Lima Perú Centro de Investigaciones sobre Desertificación – Spanish National Research Council (CSIC-UV-GVA) Valencia Spain Hydro-Climate Extremes Lab (H-CEL) Ghent University Ghent Belgium Department o

In 2023, La Niña conditions that generally prevailed in the eastern Pacific Ocean from mid-2020 into early 2023 gave way to a strong El Niño by October. Atmospheric concentrations of Earth’s major greenhouse gases—carbon dioxide, methane, and nitrous oxide—all increased to record-high levels. The annual global average carbon dioxide concentration in the atmosphere rose to 419.3±0.1 ppm, which is 50% greater than the pre-industrial level. The growth from 2022 to 2023 was 2.8 ppm, the fourth highest in the record since the 1960s. The combined short-term effects of El Niño and the long-term effects of increasing levels of heat-trapping gases in the atmosphere contributed to new records for many essential climate variables reported here. The annual global temperature across land and oceans was the highest in records dating as far back as 1850, with the last seven months (June–December) having each been record warm. Over land, the globally averaged temperature was also record high. Dozens of countries reported record or near-record warmth for the year, including China and continental Europe as a whole (warmest on record), India and Russia (second warmest), and Canada (third warmest). Intense and widespread heatwaves were reported around the world. In Vietnam, an all-time national maximum temperature record of 44.2°C was observed at Tuong Duong on 7 May, surpassing the previous record of 43.4°C at Huong Khe on 20 April 2019. In Brazil, the air temperature reached 44.8°C in Araçuaí in Minas Gerais on 20 November, potentially a new national record and 12.8°C above normal. The effect of rising temperatures was apparent in the cryosphere, where snow cover extent by June 2023 was the smallest in the 56-year record for North America and seventh smallest for the Northern Hemisphere overall. Heatwaves contributed to the greatest average mass balance loss for Alpine glaciers around the world since the start of the record in 1970. Due to rapid volume loss beginning in 2021, St. A

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Why is the Winner the Best?

Why is the Winner the Best?

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Conference on Computer Vision and Pattern Recognition (CVPR)

作者： M. Eisenmann A. Reinke V. Weru M. D. Tizabi F. Isensee T. J. Adler S. Ali V. Andrearczyk M. Aubreville U. Baid S. Bakas N. Balu S. Bano J. Bernal S. Bodenstedt A. Casella V. Cheplygina M. Daum M. De Bruijne A. Depeursinge R. Dorent J. Egger D. G. Ellis S. Engelhardt M. Ganz N. Ghatwary G. Girard P. Godau A. Gupta L. Hansen K. Harada M. Heinrich N. Heller A. Hering A. Huaulmé P. Jannin A. E. Kavur O. Kodym M. Kozubek J. Li H. Li J. Ma C. Martín-Isla B. Menze A. Noble V. Oreiller N. Padoy S. Pati K. Payette T. Rädsch J. Rafael-Patiño V. Singh Bawa S. Speidel C. H. Sudre K. Van Wijnen M. Wagner D. Wei A. Yamlahi M. H. Yap C. Yuan M. Zenk A. Zia D. Zimmerer D. Aydogan B. Bhattarai L. Bloch R. Brüngel J. Cho C. Choi Q. Dou I. Ezhov C. M. Friedrich C. Fuller R. R. Gaire A. Galdran Á. García Faura M. Grammatikopoulou S. Hong M. Jahanifar I. Jang A. Kadkhodamohammadi I. Kang F. Kofler S. Kondo H. Kuijf M. Li M. Luu T. Martinčič P. Morais M. A. Naser B. Oliveira D. Owen S. Pang J. Park S. Park S. Płotka E. Puybareau N. Rajpoot K. Ryu N. Saeed A. Shephard P. Shi D. Štepec R. Subedi G. Tochon H. R. Torres H. Urien J. L. Vilaça K. A. Wahid H. Wang J. Wang L. Wang X. Wang B. Wiestler M. Wodzinski F. Xia J. Xie Z. Xiong S. Yang Y. Yang Z. Zhao K. Maier-Hein P. F. Jäger A. Kopp-Schneider L. Maier-Hein Division of Intelligent Medical Systems German Cancer Research Center (DKFZ) Heidelberg Germany Helmholtz Imaging German Cancer Research Center (DKFZ) Heidelberg Germany Faculty of Mathematics and Computer Science Heidelberg University Heidelberg Germany Division of Biostatistics German Cancer Research Center (DKFZ) Heidelberg Germany Division of Medical Image Computing German Cancer Research Center (DKFZ) Heidelberg Germany Faculty of Engineering and Physical Sciences School of Computing University of Leeds Leeds UK Institute of Informatics School of Management HES-SO Valais-Wallis University of Applied Sciences and Arts Western Switzerland Sierre Switzerland Department of Nuclear Medicine and Molecular Imaging Lausanne University Hospital Lausanne Switzerland Technische Hochschule Ingolstadt Ingolstadt Germany Center for Artificial Intelligence and Data Science for Integrated Diagnostics (AI2D) and Center for Biomedical Image Computing and Analytics (CBICA) University of Pennsylvania Philadelphia PA USA Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania Philadelphia PA USA Department of Radiology Perelman School of Medicine University of Pennsylvania Philadelphia PA USA Department of Radiology University of Washington Seattle WA USA Department of Computer Science Wellcome/EPSRC Centre for Interventional and Surgical Sciences (WEISS) University College London London UK Universitat Autònoma de Barcelona & Computer Vision Center Barcelona Spain Division of Translational Surgical Oncology National Center for Tumor Diseases (NCT/UCC) Dresden Dresden Germany Department of Advanced Robotics Istituto Italiano di Tecnologia Italy Department of Electronics Information and Bioengineering Politecnico di Milano Milan Italy IT University of Copenhagen Copenhagen Denmark Department of General Visceral and Transplantation Surgery Heidelberg University Hospital Heidelberg Germany Department of Radiology and Nuc

International benchmarking competitions have become fundamental for the comparative performance assessment of image analysis methods. However, little attention has been given to investigating what can be learnt from these competitions. Do they really generate scientific progress? What are common and successful participation strategies? What makes a solution superior to a competing method? To address this gap in the literature, we performed a multicenter study with all 80 competitions that were conducted in the scope of IEEE ISBI 2021 and MICCAI 2021. Statistical analyses performed based on comprehensive descriptions of the submitted algorithms linked to their rank as well as the underlying participation strategies revealed common characteristics of winning solutions. These typically include the use of multi-task learning (63%) and/or multi-stage pipelines (61%), and a focus on augmentation (100%), image preprocessing (97%), data curation (79%), and post-processing (66%). The “typical” lead of a winning team is a computer scientist with a doctoral degree, five years of experience in biomedical image analysis, and four years of experience in deep learning. Two core general development strategies stood out for highly-ranked teams: the reflection of the metrics in the method design and the focus on analyzing and handling failure cases. According to the organizers, 43% of the winning algorithms exceeded the state of the art but only 11% completely solved the respective domain problem. The insights of our study could help researchers (1) improve algorithm development strategies when approaching new problems, and (2) focus on open research questions revealed by this work.

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From FAIR to CURE: Guidelines for Computational Models of Biological systems

arXiv

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arXiv 2025年

作者： Sauro, Herbert M. Agmon, Eran Blinov, Michael L. Gennari, John H. Hellerstein, Joe Heydarabadipour, Adel Hunter, Peter Jardine, Bartholomew E. May, Elebeoba Nickerson, David P. Smith, Lucian P. Bader, Gary D. Bergmann, Frank Boyle, Patrick M. Dräger, Andreas Faeder, James R. Feng, Song Freire, Juliana Fröhlich, Fabian Glazier, James A. Gorochowski, Thomas E. Helikar, Tomas Hoops, Stefan Imoukhuede, Princess Keating, Sarah M. Konig, Matthias Laubenbacher, Reinhard Loew, Leslie M. Lopez, Carlos F. Lytton, William W. McCulloch, Andrew Mendes, Pedro Myers, Chris J. Myers, Jerry G. Mulugeta, Lealem Niarakis, Anna van Niekerk, David D. Olivier, Brett G. Patrie, Alexander A. Quardokus, Ellen M. Radde, Nicole Rohwer, Johann M. Sahle, Sven Schaff, James C. Sego, T.J. Shin, Janis Snoep, Jacky L. Vadigepalli, Rajanikanth Wiley, H. Steve Waltemath, Dagmar Moraru, Ion Department of Bioengineering University of Washington SeattleWA98195-5061 United States Intelligent Systems Engineering and Biocomplexity Institute Indiana University Street BloomingtonIN47408 United States Center for Cardiovascular Biology University of Washington SeattleWA98195-5061 United States eScience Institute University of Washington SeattleWA98195-5061 United States Institute for Stem Cell and Regenerative Medicine University of Washington SeattleWA98195-5061 United States School of Biological Sciences University of Bristol 24 Tyndall Avenue BristolBS8 1TQ United Kingdom Departments of Physiology & Pharmacology Neurology Downstate Health Science University BrooklynNY11203 United States Department of Neurology Kings County Hospital BrooklynNY11203 United States NASA-John H. Glenn Research Center MS 110-3 21000 Brookpark Road ClevelandOH44135 United States Center for Cell Analysis and Modeling UConn Health 263 Farmington Avenue FarmingtonCT06030-6406 United States Amsterdam Institute for Life and Environment Vrije Universiteit Amsterdam De Boelelaan 1108 Amsterdam1081 HZ Netherlands Department of Pathology and Genomic Medicine Thomas Jefferson University 1020 Locust St PhiladelphiaPA19107 United States Biological Sciences Division Pacific Northwest National Laboratory 902 Battelle Blvd RichlandWA99354 United States Auckland Bioengineering Institute University of Auckland Auckland1010 New Zealand Center of Integrative Biology University of Toulouse III-Paul Sabatier 165 Rue Marianne Grunberg-Manago Toulouse31400 France Lifeware Group Inria Building Alan Turing 1 Rue Honoré d’Estienne d’Orves Palaiseau91120 France Multiscale Modeling Group Altos Labs Redwood CityCA94065 United States partner site Tübingen Tübingen Germany Ottfried-Müller-Str. 37 Tübingen72076 Germany 06120 Germany Department of Computer Science Center for Data Science New York University New YorkNY11201 United States Department of Bi

Guidelines for managing scientific data have been established under the FAIR principles requiring that data be Findable, Accessible, Interoperable, and Reusable. In many scientific disciplines, especially computational biology, both data and models are key to progress. For this reason, and recognizing that such models are a very special type of "data", we argue that computational models, especially mechanistic models prevalent in medicine, physiology and systems biology, deserve a complementary set of guidelines. We propose the CURE principles, emphasizing that models should be Credible, Understandable, Reproducible, and Extensible. We delve into each principle, discussing verification, validation, and uncertainty quantification for model credibility;the clarity of model descriptions and annotations for understandability;adherence to standards and open science practices for reproducibility;and the use of open standards and modular code for extensibility and reuse. We outline recommended and baseline requirements for each aspect of CURE, aiming to enhance the impact and trustworthiness of computational models, particularly in biomedical applications where credibility is paramount. Our perspective underscores the need for a more disciplined approach to modeling, aligning with emerging trends such as Digital Twins and emphasizing the importance of data and modeling standards for interoperability and reuse. Finally, we emphasize that given the non-trivial effort required to implement the guidelines, the community moves to automate as many of the guidelines as possible. © 2025, CC BY.

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