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Translation dysregulation in cancer as a source for targetable antigens

Cancer Cell 2025年第5期43卷 823-840.e18,20页

作者： Weller, Chen Bartok, Osnat McGinnis, Christopher S. Palashati, Heyilimu Chang, Tian-Gen Malko, Dmitry Shmueli, Merav D. Nagao, Asuteka Hayoun, Deborah Murayama, Ayaka Sakaguchi, Yuriko Poulis, Panagiotis Khatib, Aseel Erlanger Avigdor, Bracha Gordon, Sagi Cohen Shvefel, Sapir Zemanek, Marie J. Nielsen, Morten M. Boura-Halfon, Sigalit Sagie, Shira Gumpert, Nofar Yang, Weiwen Alexeev, Dmitry Kyriakidou, Pelgia Yao, Winnie Zerbib, Mirie Greenberg, Polina Benedek, Gil Litchfield, Kevin Petrovich-Kopitman, Ekaterina Nagler, Adi Oren, Roni Ben-Dor, Shifra Levin, Yishai Pilpel, Yitzhak Rodnina, Marina Cox, Jürgen Merbl, Yifat Satpathy, Ansuman T. Carmi, Yaron Erhard, Florian Suzuki, Tsutomu Buskirk, Allen R. Olweus, Johanna Ruppin, Eytan Schlosser, Andreas Samuels, Yardena Department of Molecular Cell Biology Weizmann Institute of Science Rehovot 7610001 Israel Department of Pathology Stanford University Stanford 94305 CA United States Parker Institute for Cancer Immunotherapy San Francisco 94129 CA United States Department of Cancer Immunology Institute for Cancer Research Oslo University Hospital Oslo 0379 Norway Precision Immunotherapy Alliance University of Oslo Oslo Norway Cancer Data Science Laboratory Center for Cancer Research National Cancer Institute National Institutes of Health Bethesda 20892 MD United States Department of Systems Immunology Weizmann Institute of Science Rehovot 7610001 Israel Department of Chemistry and Biotechnology of Engineering The University of Tokyo Tokyo 113-8656 Japan Department of Physical Biochemistry Max Planck Institute for Multidisciplinary Sciences Göttingen 37077 Germany Department of Pathology Sackler School of Medicine Tel Aviv University Tel Aviv 69978 Israel Department of Immunology and Regenerative Biology Weizmann Institute of Science Rehovot 7610001 Israel Computational Systems Biochemistry Research Group Max-Planck Institute of Biochemistry Martinsried 82152 Germany Department of Veterinary Resources Weizmann Institute of Science Rehovot 7610001 Israel Tissue Typing and Immunogenetics Unit Hadassah Hebrew University Hospital Jerusalem 9112102 Israel CRUK Lung Cancer Centre of Excellence University College London Cancer Institute London WC1E 6DD United Kingdom Tumour Immunogenomics and Immunosurveillance Laboratory University College London Cancer Institute London WC1E 6DD United Kingdom Department of Life Science Core Facilities Weizmann Institute of Science Rehovot 7610001 Israel Bioinformatics Unit Department of Life Sciences Core Facilities Weizmann Institute of Science Rehovot 7610001 Israel de Botton Institute for Protein Profiling the Nancy and Stephen Grand Israel National Center for Personalized Medicine Weizmann Institute of Science Rehovot

Aberrant peptides presented by major histocompatibility complex (MHC) molecules are targets for tumor eradication, as these peptides can be recognized as foreign by T cells. Protein synthesis in malignant cells is dysregulated, which may result in the generation and presentation of aberrant peptides that can be exploited for T cell-based therapies. To investigate the role of translational dysregulation in immunological tumor control, we disrupt translation fidelity by deleting tRNA wybutosine (yW)-synthesizing protein 2 (TYW2) in tumor cells and characterize the downstream impact on translation fidelity and immunogenicity using immunopeptidomics, genomics, and functional assays. These analyses reveal that TYW2 knockout (KO) cells generate immunogenic out-of-frame peptides. Furthermore, Tyw2 loss increases tumor immunogenicity and leads to anti-programmed cell death 1 (PD-1) checkpoint blockade sensitivity in vivo. Importantly, reduced TYW2 expression is associated with increased response to checkpoint blockade in patients. Together, we demonstrate that defects in translation fidelity drive tumor immunogenicity and may be leveraged for cancer immunotherapy. © 2025 The Author(s)

关键词： cancer immunopeptidome immune checkpoint blockade neoantigens non-canonical peptides translation fidelity

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WALLABY Pilot Survey & ASymba: Comparing H i Detection Asymmetries to the SIMBA Simulation

arXiv

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arXiv 2025年

作者： Perron-Cormier, Mathieu Deg, Nathan Spekkens, Kristine Richardson, Mark L.A. Glowacki, Marcin Oman, Kyle A. Verheijen, Marc A.W. Hank, Nadine A.N. Blyth, Sarah Dénes, Helga Rhee, Jonghwan Elagali, Ahmed Shen, Austin Xiaofan Raja, Wasim Lee-Waddell, Karen Cortese, Luca Catinella, Barbara Westmeier, Tobias Department of Physics Engineering Physics and Astronomy Queen’s University KingstonONK7L 3N6 Canada Arthur B. McDonald Canadian Astroparticle Physics Research Institute 64 Bader Lane KingstonONK7L 3N6 Canada Institute for Astronomy University of Edinburgh Royal Observatory EdinburghEH9 3HJ United Kingdom International Centre for Radio Astronomy Research Curtin University BentleyWA6102 Australia Inter-University Institute for Data Intensive Astronomy Department of Astronomy University of Cape Town Cape Town South Africa Institute for Computational Cosmology Physics Department Durham University South Road DurhamDH1 3LE United Kingdom Centre for Extragalactic Astronomy Physics Department Durham University South Road DurhamDH1 3LE United Kingdom Kapteyn Astronomical Institute University of Groningen Landleven 12 Groningen9747 AD Netherlands Department of Astronomy University of Cape Town Private Bag X3 Rondebosch7701 South Africa School of Physical Sciences and Nanotechnology Yachay Tech University Hacienda San José S/N Urcuquí100119 Ecuador University of Western Australia 35 Stirling Hwy CrawleyWA6009 Australia School of Biological Sciences The University of Western Australia CrawleyWA Australia CSIRO Space and Astronomy PO Box 1130 BentleyWA6102 Australia The University of Western Australia 35 Stirling Highway CrawleyWA6009 Australia Australia

An avenue for understanding cosmological galaxy formation is to compare morphometric parameters in observations and simulations of galaxy assembly. In this second paper of the ASymba: Asymmetries of H i in Simba Galaxies series, we measure atomic gas (H i) asymmetries in spatially-resolved detections from the untargetted WALLABY survey, and compare them to realizations of WALLABY-like mock samples from the SIMBA cosmological simulations. We develop a Scanline Tracing method to create mock galaxy H i datacubes which minimizes shot noise along the spectral dimension compared to particle-based methods, and therefore spurious asymmetry contributions. We compute 1D and 3D asymmetries for spatially-resolved WALLABY Pilot Survey detections, and find that the highest 3D asymmetries (A3D 0.5) stem from interacting systems or detections with strong bridges or tails. We then construct a series of WALLABY-like mock realizations drawn from the SIMBA 50 Mpc simulation volume, and compare their asymmetry distributions. We find that the incidence of high A3D detections is higher in WALLABY than in the SIMBA mocks, but that difference is not statistically significant (p-value = 0.05). The statistical power of quantitative comparisons of asymmetries such as the one presented here will improve as the WALLABY survey progresses, and as simulation volumes and resolutions increase. © 2025, CC BY.

关键词： Shot noise

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Explainable AI: Definition and attributes of a good explanation for health AI

arXiv

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arXiv 2024年

作者： Kyrimi, Evangelia McLachlan, Scott Wohlgemut, Jared M. Perkins, Zane B. Lagnado, David A. Marsh, William Gimson, Alexander Shafti, Ali Ercole, Ari Banerjee, Amitava Glocker, Ben Schafer, Burkhard Gatsonis, Constantine Grosan, Crina Sent, Danielle Berman, David S. Glass, David O'Regan, Declan P. Letsios, Dimitrios Morrissey, Dylan Pisirir, Erhan Leofante, Francesco Soyel, Hamit Williamson, Jon Grieman, Keri Dube, Kudakwashe Mardsen, Max Nagendran, Myura Tai, Nigel Kostopoulou, Olga Jones, Owain Curzon, Paul Stoner, Rebecca S. Tandle, Sankalp Joshi, Shalmali Mossadegh, Somayyeh Buijsman, Stefan Miller, Tim Madai, Vince Istvan School of Electronic Engineering and Computer Science Queen Mary University of London London United Kingdom School of Nursing Midwifery and Palliative Care King's College London London United Kingdom Centre for Trauma Sciences Blizard Institute Queen Mary University of London London United Kingdom Royal London Hospital Barts Health NHS Trust London United Kingdom Department of Experiment Psychology University College London London United Kingdom Cambridge Liver Unit Addenbrooke's Hospital Cambridge University Hospitals Hills Road Box 210 Cambridge United Kingdom University of Cambridge United Kingdom Cambridge Consultants Ltd. United Kingdom Division of Anaesthesia Cambridge Centre for AI in Medicine University of Cambridge Cambridge United Kingdom Magdelene College University of Cambridge United Kingdom Institute of Health Informatics University College London London United Kingdom Department of Computing Imperial College London London United Kingdom SCRIPT Centre for IT and IP Law School of Law University of Edinburgh United Kingdom Center for Statistical Sciences School of Public Health Brown University Providence United States Research Group Artificial Intelligence HU University of Applied Sciences Utrecht Netherlands Jheronimus Academy of Data Science Tilburg University Eindhoven University of Technology s-Hertogenbosch Netherlands Centre for Theoretical Physics Queen Mary University of London London United Kingdom School of Computing Ulster University Belfast United Kingdom MRC Laboratory of Medical Sciences Imperial College London London United Kingdom Department of Informatics King's College London United Kingdom Physiotherapy Department Barts Health NHS Trust London United Kingdom Sport and Exercise Medicine Queen Mary University of London London United Kingdom School of Electronic Engineering and Computer Science Queen Mary University of London United Kingdom Department of Computing Imperial College London United Kingdom Departmen

Proposals of artificial intelligence (AI) solutions based on increasingly complex and accurate predictive models are becoming ubiquitous across many disciplines. As the complexity of these models grows, transparency and users' understanding often diminish. This suggests that accurate prediction alone is insufficient for making an AI-based solution truly useful. In the development of healthcare systems, this introduces new issues related to accountability and safety. Understanding how and why an AI system makes a recommendation may require complex explanations of its inner workings and reasoning processes. Although research on explainable AI (XAI) has significantly increased in recent years and there is high demand for XAI in medicine, defining what constitutes a good explanation remains ad hoc, and providing adequate explanations continues to be challenging. To fully realize the potential of AI, it is critical to address two fundamental questions about explanations for safety-critical AI applications, such as health-AI: (1) What is an explanation in health-AI? and (2) What are the attributes of a good explanation in health-AI? In this study, we examined published literature and gathered expert opinions through a two-round Delphi study. The research outputs include (1) a definition of what constitutes an explanation in health-AI and (2) a comprehensive list of attributes that characterize a good explanation in health-AI. © 2024, CC BY.

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Vaccinations or Non-Pharmaceutical Interventions: Safe Reopening of Schools in England

Research Square

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Research Square 2021年

作者： Cuesta-Lazaro, Carolina Quera-Bofarull, Arnau Aylett-Bullock, Joseph Lawrence, Bryan N. Fong, Kevin Icaza-Lizaola, Miguel Sedgewick, Aidan Truong, Henry Vernon, Ian Williams, Julian Pagel, Christina Krauss, Frank Institute for Data Science Durham University Durham United Kingdom Institute for Computational Cosmology Durham University Durham United Kingdom Institute for Particle Physics Phenomenology Durham University Durham United Kingdom National Centre for Atmospheric Science University of Reading Reading United Kingdom Departments of Meteorology and Computer Science University of Reading Reading United Kingdom Department of Science Technology Engineering and Public Policy University College London London United Kingdom Department of Anaesthesia University College London Hospital London United Kingdom Centre for Extragalactic Astronomy Durham University Durham United Kingdom Department of Mathematical Sciences Durham University DurhamDH1 3LE United Kingdom Institute for Hazard Risk & Resilience Durham University DurhamDH1 3LE United Kingdom Clinical Operational Research Unit University College London United Kingdom

With high levels of the Delta variant of COVID-19 circulating in England during September 2021, schools are set to reopen with few school-based non-pharmaceutical interventions (NPIs). In this paper, we present simulation results obtained from the individual-based model, JUNE, for English school opening after a prior vaccination campaign using an optimistic set of assumptions about vaccine efficacy and the likelihood of prior-reinfection. We take a scenario-based approach to modelling potential interventions to assess relative changes rather than real-world forecasts. Specifically, we assess the effects of vaccinating those aged 16-17, those aged 12-17, and not vaccinating children at all relative to only vaccinating the adult population, addressing what might have happened had the UK began teenage vaccinations earlier. Vaccinating children in the 12-15 age group would have had a significant impact on the course of the epidemic, saving thousands of lives overall in these simulations. In the absence of such a vaccination campaign our simulations show there could still be a significant positive impact on the epidemic (fewer cases, fewer deaths) by continuing NPI strategies in schools. Our analysis suggests that the best results in terms of lives saved are likely derived from a combination of the now planned vaccination campaign and NPIs in schools. © 2021, CC BY.

关键词： COVID-19

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Geometric Optimisation of Unmanned Aerial Vehicle Trajectories in Uncertain Environments

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Vehicular Communications 2025年 54卷

作者： Akshya, J. Sundarrajan, M. Amutha, S. Dhanaraj, Rajesh Kumar Khadidos, Adil O. Khadidos, Alaa O. Selvarajan, Shitharth Department of Computational Intelligence SRM Institute of Science and Technology Tamil Nadu Kattankulathur 603203 India Department of Networking and Communications SRM Institute of Science and Technology Tamil Nadu Kattankulathur 603203 India Department of Computer Science and Engineering School of Computing Vel Tech Rangarajan Dr.Sagunthala R&D Institute of Science and Technology Chennai India Symbiosis Institute of Computer Studies and Research (SICSR) Symbiosis International (Deemed University) Pune India Department of Information Technology Faculty of Computing and Information Technology King Abdulaziz University Jeddah Saudi Arabia Department of Information Systems Faculty of Computing and Information Technology King Abdulaziz University Jeddah 21589 Saudi Arabia Center of Research Excellence in Artificial Intelligence and Data Science King Abdulaziz University Jeddah Saudi Arabia School of Built Environment Engineering and Computing Leeds Beckett University LS6 3HF Leeds United Kingdom Department of Computer Science and Engineering Chennai Institute of Technology Chennai India Centre for Research Impact & Outcome Chitkara University Institute of Engineering and Technology Chitkara University Punjab Rajpura 140401 India

The problem of efficient trajectory optimisation for Unmanned Aerial Vehicles (UAVS) in dynamic and constrained environments is one where energy efficiency, spatial coverage, and path smoothness need to be balanced. The existing methods, namely RRT*, A*, and Dijkstra, are popular but generally heuristic and do not provide globally optimal solutions. They face significant limitations while dealing with complex geometries, dynamic obstacles, and multi-objective requirements. These challenges call for a mathematically sound framework that seamlessly integrates convex analysis and computational geometry to provide an optimal trajectory planning framework. This research work introduces a convex optimisation framework for UAV trajectory planning which unifies multiple objectives, like minimising energy consumption, maximising spatial coverage, and ensuring the smoothness of the path, into a single convex objective function. More importantly, it indicates that obstacle dynamics and uncertain environmental conditions are handled better by it, so it is relatively easier for safe and efficient navigation. Proven to converge faster and with higher precision than RRT*, A*, and Dijkstra, the approach proposed here enjoys intrinsic convex properties, which ensure global optimality. Qualitative measurements show the efficiency of the proposed framework. The result is energy efficiency of 90%, with 92% coverage, 98% constraint satisfaction, and 95% path smoothness, which is 15-25% better on all metrics than traditional approaches can offer. By bridging between theory in convex optimisation and practice for solving multi-objective problems in a dynamic setting, this study provides a more robust solution for UAV trajectory planning. © 2025 The Author(s)

关键词： computational Geometry Convex Optimisation Delaunay Triangulations Spatial Coverage UAV Trajectory Voronoi Diagrams

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Democratising Knowledge Representation with BioCypher

arXiv

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arXiv 2022年

作者： Lobentanzer, Sebastian Aloy, Patrick Baumbach, Jan Bohar, Balazs Charoentong, Pornpimol Danhauser, Katharina Doğan, Tunca Dreo, Johann Dunham, Ian Fernandez-Torras, Adrià Gyori, Benjamin M. Hartung, Michael Hoyt, Charles Tapley Klein, Christoph Korcsmaros, Tamas Maier, Andreas Mann, Matthias Ochoa, David Pareja-Lorente, Elena Popp, Ferdinand Preusse, Martin Probul, Niklas Schwikowski, Benno Sen, Bünyamin Strauss, Maximilian T. Turei, Denes Ulusoy, Erva Heidrun Wodke, Judith Andrea Saez-Rodriguez, Julio Heidelberg University Faculty of Medicine Heidelberg University Hospital Institute for Computational Biomedicine Bioquant Heidelberg Germany The Barcelona Institute of Science and Technology Catalonia Barcelona Spain Catalonia Barcelona Spain Institute for Computational Systems Biology University of Hamburg Germany Earlham Institute Norwich United Kingdom Biological Research Centre Szeged Hungary Heidelberg University Im Neuenheimer Feld 267 Heidelberg69120 Germany Im Neuenheimer Feld 460 Heidelberg69120 Germany Department of Pediatrics Dr. von Hauner Children’s Hospital University Hospital LMU Munich Germany Biological Data Science Lab Department of Computer Engineering Hacettepe University Ankara Turkey Department of Bioinformatics Graduate School of Health Sciences Hacettepe University Ankara Turkey Computational Systems Biomedicine Lab Department of Computational Biology Institut Pasteur Université Paris Cité Paris France Bioinformatics and Biostatistics Hub Institut Pasteur Université Paris Cité Paris France Wellcome Genome Campus Cambridgeshire HinxtonCB10 1SD United Kingdom Open Targets Wellcome Genome Campus Cambridgeshire HinxtonCB10 1SD United Kingdom Laboratory of Systems Pharmacology Harvard Medical School Boston United States Imperial College London London United Kingdom Quadram Institute Bioscience Norwich United Kingdom Proteomics Program Novo Nordisk Foundation Centre for Protein Research University of Copenhagen Copenhagen Denmark Department of Proteomics and Signal Transduction Max Planck Institute of Biochemistry Martinsried Germany Im Neuenheimer Feld 460 Heidelberg69120 Germany Neuherberg Germany Medical Informatics Laboratory University Medicine Greifswald Germany

Standardising the representation of biomedical knowledge among all researchers is an insurmountable task, hindering the effectiveness of many computational methods. To facilitate harmonisation and interoperability despite this fundamental challenge, we propose to standardise the framework of knowledge graph creation instead. We implement this standardisation in BioCypher, a FAIR (findable, accessible, interoperable, reusable) framework to transparently build biomedical knowledge graphs while preserving provenances of the source data. Mapping the knowledge onto biomedical ontologies helps to balance the needs for harmonisation, human and machine readability, and ease of use and accessibility to nonspecialist researchers. We demonstrate the usefulness of this framework on a variety of use cases, from maintenance of task-specific knowledge stores, to interoperability between biomedical domains, to on-demand building of task-specific knowledge graphs for federated learning. BioCypher (https://***) frees up valuable developer time;we encourage further development and usage by the community. © 2022, CC BY-NC-ND.

关键词： Ontology

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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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Correction to: Clinical and organizational factors associated with mortality during the peak of first COVID-19 wave: the global UNITE-COVID study

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intensive care medicine 2022年第8期48卷 1130-1131页

作者： Massimiliano Greco Thomas De Corte Ari Ercole Massimo Antonelli Elie Azoulay Giuseppe Citerio Andy Conway Morris Gennaro De Pascale Frantisek Duska Paul Elbers Sharon Einav Lui Forni Laura Galarza Armand R J Girbes Giacomo Grasselli Vitaly Gusarov Alasdair Jubb Jozef Kesecioglu Andrea Lavinio Maria Cruz Martin Delgado Johannes Mellinghoff Sheila Nainan Myatra Marlies Ostermann Mariangela Pellegrini Pedro Povoa Stefan J Schaller Jean-Louis Teboul Adrian Wong Jan J De Waele Maurizio Cecconi Department of Biomedical Sciences Humanitas University Via Rita Levi Montalcini 4 Pieve Emanuele 20072 Milan Italy. IRCCS Humanitas Research Hospital Via Manzoni 56 Rozzano 20089 Milan Italy. Department of Internal Medicine and Pediatrics Faculty of Medicine and Health Sciences Ghent University Ghent Belgium. Department of Intensive Care Medicine Ghent University Hospital Ghent Belgium. Cambridge Centre for Artificial Intelligence in Medicine University of Cambridge Cambridge UK. University of Cambridge Division of Anaesthesia Addenbrooke's Hospital Hills Road Cambridge UK. Dipartimento di Scienze dell'Emergenza Anestesiologiche e della Rianimazione Fondazione Policlinico Universitario A. Gemelli IRCCS-Università Cattolica del Sacro Cuore Rome Italy. Istituto di Anestesiologia e Rianimazione Università Cattolica del Sacro Cuore Rome Italy. Médecine Intensive et Réanimation APHP Saint-Louis Hospital Paris University Paris France. Université de Paris Paris France. School of Medicine and Surgery University of Milano-Bicocca Milan Italy. Department Neuroscience Neurointensive Care ASST-Monza Monza Italy. Division of Anaesthesia Department of Medicine University of Cambridge Cambridge UK. Division of Immunology Department of Pathology University of Cambridge Cambridge UK. JVF Intensive Care Unit Addenbrookes Hospital Cambridge UK. Department of Anaesthesia and Intensive Care Third Faculty of Medicine Charles University Prague Czech Republic. FNKV University Hospital in Prague Prague Czech Republic. Department of Intensive Care Medicine Laboratory of Critical Care Computational Intelligence Amsterdam UMC Vrije Universiteit Amsterdam The Netherlands. General Intensive Care Unit of the Shaare Zedek Medical Center Jerusalem Israel. Faculty of Medicine Hebrew University Jerusalem Israel. Department of Critical Care Royal Surrey Hospital and Faculty of Experimental Medicine University of Surrey Guildford UK. Intensive Care Unit Hospital General Un

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PLUMED Tutorials: a collaborative, community-driven learning ecosystem

arXiv

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arXiv 2024年

作者： Tribello, Gareth A. Bonomi, Massimiliano Bussi, Giovanni Camilloni, Carlo Armstrong, Blake I. Arsiccio, Andrea Aureli, Simone Ballabio, Federico Bernetti, Mattia Bonati, Luigi Brookes, Samuel G.H. Faidon Brotzakis, Z. Capelli, Riccardo Ceriotti, Michele Chan, Kam-Tung Cossio, Pilar Dasetty, Siva Donadio, Davide Ensing, Bernd Ferguson, Andrew L. Fraux, Guillaume Gale, Julian D. Gervasio, Francesco Luigi Giorgino, Toni Herringer, Nicholas S.M. Hocky, Glen M. Hoff, Samuel E. Invernizzi, Michele Languin-Cattoën, Olivier Leone, Vanessa Limongelli, Vittorio Lopez-Acevedo, Olga Marinelli, Fabrizio Martinez, Pedro Febrer Masetti, Matteo Mehdi, Shams Michaelides, Angelos Murtada, Mhd Hussein Parrinello, Michele Piaggi, Pablo M. Pietropaolo, Adriana Pietrucci, Fabio Pipolo, Silvio Pritchard, Claire Raiteri, Paolo Raniolo, Stefano Rapetti, Daniele Rizzi, Valerio Rydzewski, Jakub Salvalaglio, Matteo Schran, Christoph Seal, Aniruddha Zadeh, Armin Shayesteh Silva, Tomás F.D. Spiwok, Vojtěch Stirnemann, Guillaume Sucerquia, Daniel Tiwary, Pratyush Valsson, Omar Vendruscolo, Michele Voth, Gregory A. White, Andrew D. Wu, Jiangbo Centre for Quantum Materials and Technology School of Mathematics and Physics Queen’s University Belfast United Kingdom Institut Pasteur Université Paris Cité CNRS UMR 3528 Computational Structural Biology Unit Paris France Via Bonomea 265 Trieste34136 Italy Department of Biosciences University of Milano Milano Italy School of Molecular and Life Sciences Curtin University GPO Box U1987 PerthWA6845 Australia Coriolis Pharma Fraunhoferstrasse 18b Martinsried82152 Germany School of Pharmaceutical Sciences University of Geneva Rue Michel-Servet 1 GenevaCH-1206 Switzerland Institute of Pharmaceutical Sciences of Western Switzerland University of Geneva GenevaCH-1206 Switzerland Swiss Bioinformatics Institute University of Geneva GenevaCH-1206 Switzerland Via Celoria 26 Milan20133 Italy Department of Biomolecular Sciences University of Urbino "Carlo Bo" Piazza Rinascimento 6 Urbino61029 Italy Department of Pharmacy and Biotechnology Alma Mater Studiorum University of Bologna Via Belmeloro 6 Bologna40126 Italy Atomistic Simulations Italian Institute of Technology Genova Italy Yusuf Hamied Department of Chemistry University of Cambridge CambridgeCB2 1EW United Kingdom Institute for Bioinnovation Biomedical Sciences Research Center "Alexander Fleming" Vari16672 Greece Laboratory of Computational Science and Modeling Institut des Matériaux École Polytechnique Fédérale de Lausanne Lausanne1015 Switzerland Department of Chemistry University of California Davis DavisCA95616 United States Center for Computational Mathematics Flatiron Institute New YorkNY10010 United States Center for Computational Biology Flatiron Institute New YorkNY10010 United States Pritzker School of Molecular Engineering University of Chicago ChicagoIL60637 United States AI4Science Lab Informatics Institute University of Amsterdam Science Park 904 Amsterdam1098 XH Netherlands Computational Chemistry Group Van’t Hoff Institute for Molecular Sciences Unive

In computational physics, chemistry, and biology, the implementation of new techniques in a shared and open source software lowers barriers to entry and promotes rapid scientific progress. However, effectively training new software users presents several challenges. Common methods like direct knowledge transfer and in-person workshops are limited in reach and comprehensiveness. Furthermore, while the COVID-19 pandemic highlighted the benefits of online training, traditional online tutorials can quickly become outdated and may not cover all the software’s functionalities. To address these issues, here we introduce "PLUMED Tutorials", a collaborative model for developing, sharing, and updating online tutorials. This initiative utilizes repository management and continuous integration to ensure compatibility with software updates. Moreover, the tutorials are interconnected to form a structured learning path and are enriched with automatic annotations to provide broader context. This paper illustrates the development, features, and advantages of PLUMED Tutorials, aiming to foster an open community for creating and sharing educational resources. © 2024, CC BY.

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Is fixed-node diffusion quantum Monte Carlo reproducible?

arXiv

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arXiv 2025年

作者： Pia, Flaviano Della Shi, Benjamin X. Al-Hamdani, Yasmine S. Alfè, Dario Anderson, Tyler A. Barborini, Matteo Benali, Anouar Casula, Michele Drummond, Neil Dubecký, Matúš Filippi, Claudia Kent, Paul R.C. Krogel, Jaron T. Ríos, Pablo López Lüchow, Arne Luo, Ye Michaelides, Angelos Mitas, Lubos Nakano, Kousuke Needs, Richard Per, Manolo C. Scemama, Anthony Schultze, Jil Shinde, Ravindra Slootman, Emiel Sorella, Sandro Tkatchenko, Alexandre Towler, Mike Umrigar, C.J. Wagner, Lucas K. Wheeler, William A. Zhou, Haihan Zen, Andrea Yusuf Hamied Department of Chemistry University of Cambridge CambridgeCB2 1EW United Kingdom Department of Earth Sciences University College London LondonWC1E 6BT United Kingdom Dipartimento di Fisica Ettore Pancini Università di Napoli Federico II Monte S. Angelo NapoliI-80126 Italy Laboratory of Atomic and Solid State Physics Cornell University IthacaNY14853 United States HPC Platform University of Luxembourg Esch-sur-AlzetteL-4365 Luxembourg Computational Science Division Argonne National Laboratory LemontIL United States Sorbonne Université CNRS UMR 7590 MNHN 4 Place Jussieu Paris75252 France Department of Physics Lancaster University LancasterLA1 4YB United Kingdom Department of Physics Faculty of Science University of Ostrava 30. Dubna 22 Ostrava701 03 Czech Republic MESA+ Institute for Nanotechnology University of Twente Enschede7500 AE Netherlands Computational Sciences and Engineering Division Oak Ridge National Laboratory Oak RidgeTN37831 United States Materials Science and Technology Division Oak Ridge National Laboratory Oak RidgeTN37831 United States Max Planck Institute for Solid State Research Heisenbergstr. 1 Stuttgart70569 Germany Institute of Physical Chemistry RWTH Aachen University Landoltweg 2 Aachen52074 Germany Department of Physics North Carolina State University RaleighNC27695-8202 United States 1-2-1 Sengen Tsukuba Ibaraki305-0047 Japan Theory of Condensed Matter Group Cavendish Laboratory J. J. Thomson Avenue CambridgeCB3 0HE United Kingdom CSIRO Data61 ClaytonVIC3168 Australia Université de Toulouse CNRS UPS Toulouse31062 France International School for Advanced Studies SISSA Trieste34136 Italy Department of Physics and Materials Science University of Luxembourg Luxembourg CityL-1511 Luxembourg The Apuan Alps Centre for Physics Vallico Sotto Italy Department of Physics University of Illinois at Urbana-Champaign UrbanaIL61801 United States Department of Materials Science and Engi

Fixed-node diffusion quantum Monte Carlo (FN-DMC) is a widely-trusted manybody method for solving the Schrödinger equation, known for its reliable predictions of material and molecular properties. Furthermore, its excellent scalabilitywith system complexity and near-perfect utilization of computational power makes FN-DMC ideally positioned to leverage new advances in computing to address increasingly complex scientific problems. Even though the method is widely used as a computational gold standard, reproducibility across the numerous FN-DMC code implementations has yet to be demonstrated. This difficulty stems from the diverse array of DMC algorithms and trial wave functions, compounded by the method's inherent stochastic nature. This study represents a community-wide effort to address the titular question, affirming that: Yes, FN-DMC is reproducible (when handled with care). Using the water-methane dimer as the canonical test case, we compare results from eleven different FN-DMC codes and show that the approximations to treat the non-locality of pseudopotentials are the primary source of the discrepancies between them. In particular, we demonstrate that, for the same choice of determinantal component in the trial wave function, reliable and reproducible predictions can be achieved by employing the T-move (TM), the determinant locality approximation (DLA), or the determinant T-move (DTM) schemes, while the older locality approximation (LA) leads to considerable variability in results. This work lays the foundation to establish accurate and reproducible FN-DMC estimates for all future studies across applications in materials science, physics, chemistry, and biology. © 2025, CC BY.

关键词： Wave functions

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