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arXiv 2018年

作者： Mocchiutti, E. Bonvicini, V. Danailov, M. Furlanetto, E. Gadedjisso-Tossou, K.S. Guffanti, D. Pizzolotto, C. Rachevski, A. Stoychev, L. Vallazza, E. Zampa, G. Niemela, J. Ishida, K. Adamczak, A. Baccolo, G. Benocci, R. Bertoni, R. Bonesini, M. Chignoli, F. Clemenza, M. Curioni, A. Maggi, V. Mazza, R. Moretti, M. Nastasi, M. Previtali, E. Bakalov, D. Danev, P. Stoilov, M. Baldazzi, G. Campana, R. D'Antone, I. Furini, M. Fuschino, F. Labanti, C. Margotti, A. Meneghini, S. Morgante, G. Rignanese, L.P. Rossi, P.L. Zuffa, M. Cervi, T. de Bari, A. Menegolli, A. de Vecchi, C. Nardò, R. Rossella, M. Tomaselli, A. Colace, L. de Vincenzi, M. Iaciofano, A. Somma, F. Tortora, L. Ramponi, R. Vacchi, A. Sezione di Trieste via A. Valerio 2 Trieste34127 Italy Elettra-Sincrotrone Trieste S.C.p.A. SS14 Km 163.5 BasovizzaTrieste34149 Italy Mathematics and Informatics Department Udine University via delle Scienze 206 Udine Italy Abdus Salam International Centre for Theoretical Physics Strada Costiera 11 Trieste Italy Département de physique Université de Lomé 01 BP 1515 Lomé Togo Gran Sasso Science Institute - INFN-LNGS via F. Crispi 7 L’Aquila Italy RIKEN-RAL RIKEN Nishina Center for Accelerator-Based Science 2-1 Hirosawa Wako Saitama351-0198 Japan Institute of Nuclear Physics Polish Academy of Sciences Radzikowskiego 152 KrakówPL31342 Poland Sezione di Milano Bicocca piazza della Scienza 3 Milano Italy Università di Milano Bicocca Dip. di Fisica "G. Occhialini" piazza della Scienza 3 Milano Italy Università di Milano Bicocca Dip. di Scienze dell’Ambiente e della Terra piazza della Scienza 1 Miano Italy Institute for Nuclear Research and Nuclear Energy Bulgarian Academy of Sciences blvd. Tsarigradsko ch. 72 Sofia1142 Bulgaria Sezione di Bologna viale Berti Pichat 6/2 Bologna Italy Department of Physics and Astronomy University of Bologna viale Berti Pichat 6/2 Bologna Italy INAF-IAFS Bologna Area della Ricerca via P. Gobetti 101 Bologna Italy Department of Physics University of Pavia via Bassi 6 Pavia Italy Sezione di Pavia via Bassi 6 Pavia Italy Department of Electrical Computer and Biomedical Engineering University of Pavia via Ferrata 5 Pavia Italy Sezione di Roma Tre via della Vasca Navale 84 Roma Italy Dipartimento di Ingegneria Università degli Studi Roma Tre via V. Volterra 62 Roma Italy Dipartimento di Matematica e Fisica Università di Roma Tre via della Vasca Navale 84 Roma Italy Dipartimento di Scienze Università di Roma Tre viale G. Marconi 446 Roma Italy Sezione di Milano Politecnico piazza Leonardo da Vinci 32 Milano20133 Italy

The main goal of the FAMU experiment is the measurement of the hyperfine splitting (hfs) in the 1S state of muonic hydrogen ∆Ehfs(µ−p)1S. The physical process behind this experiment is the following: µp are formed in a mixture of hydrogen and a higher-Z gas. When absorbing a photon at resonance-energy ∆Ehfs ≈ 0.182 eV, in subsequent collisions with the surrounding H2 molecules, the µp is quickly de-excited and accelerated by ∼ 2/3 of the excitation energy. The observable is the time distribution of the K-lines X-rays emitted from the µZ formed by muon transfer (µp) + Z → (µZ)∗ + p, a reaction whose rate depends on the µp kinetic energy. The maximal response, to the tuned laser wavelength, of the time distribution of X-ray from K-lines of the (µZ)∗ cascade indicate the resonance. During the preparatory phase of the FAMU experiment, several measurements have been performed both to validate the methodology and to prepare the best configuration of target and detectors for the spectroscopic measurement. We present here the crucial study of the energy dependence of the transfer rate from muonic hydrogen to oxygen (Λµp→µO), precisely measured for the first time. Copyright © 2018, The Authors. All rights reserved.

关键词： Kinetic energy

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Designing ecosystems of intelligence from first principles

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Collective Intelligence 2024年第1期3卷

作者： Karl J Friston Maxwell JD Ramstead Alex B Kiefer Alexander Tschantz Christopher L Buckley Mahault Albarracin Riddhi J Pitliya Conor Heins Brennan Klein Beren Millidge Dalton AR Sakthivadivel Toby St Clere Smithe Magnus Koudahl Safae Essafi Tremblay Capm Petersen Kaiser Fung Jason G Fox Steven Swanson Dan Mapes Gabriel René VERSES Research Lab Los Angeles CA USA (KJF MJDR ABK AT CLB MA RJP CH BK BM DARS TSCS MK SET CP KF JGF SS DM GR) Wellcome Centre for Human Neuroimaging University College London London UK (KJF MJDR) Department of Philosophy Monash University Melbourne VIC Australia (ABK) Department of Informatics University of Sussex Brighton UK (CLB) Department of Computer Science Université du Québec à Montréal Montréal QC Canada (MA) Department of Experimental Psychology University of Oxford Oxford UK (RJP TSCS) Department of Collective Behaviour Max Planck Institute of Animal Behavior Konstanz Germany (CH) Department of Biology University of Konstanz Konstanz Germany (CH) Centre for the Advanced Study of Collective Behaviour University of Konstanz Konstanz Germany (CH) Network Science Institute Northeastern University Boston MA USA (BK) Brain Network Dynamics Unit University of Oxford Oxford UK (BM) Department of Mathematics Stony Brook University New York NY USA (DARS) Department of Physics and Astronomy Stony Brook University New York NY USA (DARS) Department of Biomedical Engineering Stony Brook University New York NY USA (DARS) Topos Institute Berkeley CA USA (TSCS) Department of Electrical Engineering Eindhoven University of Technology Eindhoven Netherlands (MK) Department of Philosophy Université du Québec à Montréal Montréal QC Canada (SET)

This white paper lays out a vision of research and development in the field of artificial intelligence for the next decade (and beyond). Its denouement is a cyber-physical ecosystem of natural and synthetic sense-making, in which humans are integral participants—what we call “shared intelligence.” This vision is premised on active inference, a formulation of adaptive behavior that can be read as a physics of intelligence, and which inherits from the physics of self-organization. In this context, we understand intelligence as the capacity to accumulate evidence for a generative model of one’s sensed world—also known as self-evidencing. Formally, this corresponds to maximizing (Bayesian) model evidence, via belief updating over several scales, that is, inference, learning, and model selection. Operationally, this self-evidencing can be realized via (variational) message passing or belief propagation on a factor graph. Crucially, active inference foregrounds an existential imperative of intelligent systems; namely, curiosity or the resolution of uncertainty. This same imperative underwrites belief sharing in ensembles of agents, in which certain aspects (i.e., factors) of each agent’s generative world model provide a common ground or frame of reference. Active inference plays a foundational role in this ecology of belief sharing—leading to a formal account of collective intelligence that rests on shared narratives and goals. We also consider the kinds of communication protocols that must be developed to enable such an ecosystem of intelligences and motivate the development of a shared hyper-spatial modeling language and transaction protocol, as a first—and key—step towards such an ecology.

关键词： Active inference free energy principle artificial intelligence belief updating belief propagation

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The Brain Tumor Segmentation (BraTS) Challenge 2023: Focus on Pediatrics (CBTN-CONNECT-DIPGR-ASNR-MICCAI BraTS-PEDs)

arXiv

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arXiv 2023年

作者： Kazerooni, Anahita Fathi Khalili, Nastaran Liu, Xinyang Haldar, Debanjan Jiang, Zhifan Anwar, Syed Muhammed Albrecht, Jake Adewole, Maruf Anazodo, Udunna Anderson, Hannah Bagheri, Sina Baid, Ujjwal Bergquist, Timothy Borja, Austin J. Calabrese, Evan Chung, Verena Conte, Gian-Marco Dako, Farouk Eddy, James Ezhov, Ivan Familiar, Ariana Farahani, Keyvan Haldar, Shuvanjan Iglesias, Juan Eugenio Janas, Anastasia Johansen, Elaine Jones, Blaise V. Kofler, Florian LaBella, Dominic Lai, Hollie Anne Van Leemput, Koen Li, Hongwei Bran Maleki, Nazanin McAllister, Aaron S. Meier, Zeke Menze, Bjoern Moawad, Ahmed W. Nandolia, Khanak K. Pavaine, Julija Piraud, Marie Poussaint, Tina Prabhu, Sanjay P. Reitman, Zachary Rodriguez, Andres Rudie, Jeffrey D. Sanchez-Montano, Mariana Shaikh, Ibraheem Salman Shah, Lubdha M. Sheth, Nakul Shinohara, Russel Taki Tu, Wenxin Viswanathan, Karthik Wang, Chunhao Ware, Jeffrey B. Wiestler, Benedikt Wiggins, Walter Zapaishchykova, Anna Aboian, Mariam Bornhorst, Miriam de Blank, Peter Deutsch, Michelle Fouladi, Maryam Hoffman, Lindsey Kann, Benjamin Lazow, Margot Mikael, Leonie Nabavizadeh, Ali Packer, Roger Resnick, Adam Rood, Brian Vossough, Arastoo Bakas, Spyridon Linguraru, Marius George Children’s Hospital of Philadelphia PhiladelphiaPA United States Department of Neurosurgery University of Pennsylvania PhiladelphiaPA United States University of Pennsylvania PhiladelphiaPA United States Sheikh Zayed Institute for Pediatric Surgical Innovation Children’s National Hospital WashingtonDC United States Department of Neurosurgery Thomas Jefferson University Hospital PA United States Sage Bionetworks United States Lab Crestview Radiology Lagos Nigeria McGill University MontrealQC Canada Department of Radiology Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Department of Neurosurgery The University of Southern California CA United States Department of Radiology Duke University Medical Center United States Mayo Clinic MN United States Center for Global Health Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Department of Informatics Technical University Munich Germany TranslaTUM - Central Institute for Translational Cancer Research Technical University of Munich Germany Cancer Imaging Program National Cancer Institute National Institutes of Health BethesdaMD United States Biomedical Engineering Rutgers University New BrunswickNJ United States Athinoula A Martinos Center for Biomedical Imaging Massachusetts General Hospital BostonMA United States Yale University New HavenCT United States PrecisionFDA U.S. Food and Drug Administration Silver SpringMD United States Cincinnati Children’s Hospital Medical Center United States Helmholtz AI Helmholtz Munich Germany Department of Radiation Oncology Duke University Medical Center United States Department of Radiology Children’s Health Orange County CA United States Department of Applied Mathematics and Computer Science Technical University of Denmark Denmark Department of Radiol

Pediatric tumors of the central nervous system are the most common cause of cancer-related death in children. The five-year survival rate for high-grade gliomas in children is less than 20%. Due to their rarity, the diagnosis of these entities is often delayed, their treatment is mainly based on historic treatment concepts, and clinical trials require multi-institutional collaborations. The MICCAI Brain Tumor Segmentation (BraTS) Challenge is a landmark community benchmark event with a successful history of 12 years of resource creation for the segmentation and analysis of adult glioma. Here we present the CBTN-CONNECT-DIPGR-ASNR-MICCAI BraTS-PEDs 2023 challenge, which represents the first BraTS challenge focused on pediatric brain tumors with data acquired across multiple international consortia dedicated to pediatric neuro-oncology and clinical trials. The BraTS-PEDs 2023 challenge focuses on benchmarking the development of volumentric segmentation algorithms for pediatric brain glioma through standardized quantitative performance evaluation metrics utilized across the BraTS 2023 cluster of challenges. Models gaining knowledge from the BraTS-PEDs multi-parametric structural MRI (mpMRI) training data will be evaluated on separate validation and unseen test mpMRI dataof high-grade pediatric glioma. The CBTN-CONNECT-DIPGR-ASNR-MICCAI BraTS-PEDs 2023 challenge brings together clinicians and AI/imaging scientists to lead to faster development of automated segmentation techniques that could benefit clinical trials, and ultimately the care of children with brain tumors. © 2023, CC BY.

关键词： Tumors

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Correction: Variability of temperature measurements recorded by a wearable device by biological sex

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Biology of sex differences 2023年第1期14卷 82页

作者： Lauryn Keeler Bruce Patrick Kasl Severine Soltani Varun K Viswanath Wendy Hartogensis Stephan Dilchert Frederick M Hecht Anoushka Chowdhary Claudine Anglo Leena Pandya Subhasis Dasgupta Ilkay Altintas Amarnath Gupta Ashley E Mason Benjamin L Smarr Department of Biomedical Informatics UC San Diego Health University of California San Diego San Diego CA USA. Gene Lay Department of Bioengineering University of California San Diego 9500 Gilman Dr La Jolla San Diego CA USA. Bioinformatics and Systems Biology University of California San Diego San Diego CA USA. Department of Electrical and Computer Engineering University of California San Diego La Jolla CA USA. Osher Center for Integrative Health University of California San Francisco San Francisco CA USA. Department of Management Zicklin School of Business Baruch College The City University of New York New York NY USA. San Diego Supercomputer Center University of California San Diego San Diego CA USA. Halıcıoğlu Data Science Institute University of California San Diego San Diego CA USA. Gene Lay Department of Bioengineering University of California San Diego 9500 Gilman Dr La Jolla San Diego CA USA. bsmarr@eng.ucsd.edu. Halıcıoğlu Data Science Institute University of California San Diego San Diego CA USA. bsmarr@eng.ucsd.edu.

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Author Correction: Pathway and network analysis of more than 2500 whole cancer genomes

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Nature communications 2022年第1期13卷 7566页

作者： Matthew A Reyna David Haan Marta Paczkowska Lieven P C Verbeke Miguel Vazquez Abdullah Kahraman Sergio Pulido-Tamayo Jonathan Barenboim Lina Wadi Priyanka Dhingra Raunak Shrestha Gad Getz Michael S Lawrence Jakob Skou Pedersen Mark A Rubin David A Wheeler Søren Brunak Jose M G Izarzugaza Ekta Khurana Kathleen Marchal Christian von Mering S Cenk Sahinalp Alfonso Valencia Jüri Reimand Joshua M Stuart Benjamin J Raphael Department of Computer Science Princeton University Princeton NJ 08540 USA. Department of Biomedical Informatics Emory University Atlanta GA 30322 USA. Department of Biomolecular Engineering and UC Santa Cruz Genomics Institute University of California Santa Cruz Santa Cruz CA 95060 USA. Computational Biology Program Ontario Institute for Cancer Research Toronto Ontario Canada. Department of Information Technology IDLab Ghent University IMEC Ghent the Netherlands. Department of Plant Biotechnology and Bioinformatics Ghent University Ghent the Netherlands. Barcelona Supercomputing Center (BSC) Barcelona 08034 Spain. Department of Clinical and Molecular Medicine Faculty of Medicine and Health Sciences Norwegian University of Science and Technology Trondheim Norway. Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics University of Zurich CH-8057 Zurich Switzerland. Department of Pathology and Molecular Pathology University Hospital Zurich CH-8091 Zurich Switzerland. Department of Physiology and Biophysics Weill Cornell Medicine New York NY 10065 USA. Vancouver Prostate Centre 2660 Oak Street Vancouver BC V6H 3Z6 Canada. The Broad Institute of MIT and Harvard Cambridge MA 02124 USA. Massachusetts General Hospital Center for Cancer Research Charlestown MA 02129 USA. Harvard Medical School 250 Longwood Avenue Boston MA 02115 USA. Massachusetts General Hospital Department of Pathology Boston MA 02114 USA. Department of Molecular Medicine (MOMA) Aarhus University Hospital Aarhus Denmark. Bioinformatics Research Centre (BiRC) Aarhus University Aarhus Denmark. Human Genome Sequencing Center Baylor College of Medicine Houston TX 77030 USA. DTU Bioinformatics Department of Bio and Health Informatics Technical University of Denmark Kemitorvet 2800 Kongens Lyngby Denmark. Novo Nordisk Foundation Center for Protein Research Faculty of Health and Medical Sciences University of Copenhagen 2200 Copenhagen Denmark. De

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The Brain Tumor Segmentation (BraTS-METS) Challenge 2023: Brain Metastasis Segmentation on Pre-treatment MRI

arXiv

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arXiv 2023年

作者： Moawad, Ahmed W. Janas, Anastasia Baid, Ujjwal Ramakrishnan, Divya Saluja, Rachit Ashraf, Nader Jekel, Leon Amiruddin, Raisa Adewole, Maruf Albrecht, Jake Anazodo, Udunna Aneja, Sanjay Anwar, Syed Muhammad Bergquist, Timothy Calabrese, Evan Chiang, Veronica Chung, Verena Conte, Gian Marco Marco Dako, Farouk Eddy, James Ezhov, Ivan Familiar, Ariana Farahani, Keyvan Iglesias, Juan Eugenio Jiang, Zhifan Johanson, Elaine Kazerooni, Anahita Fathi Kofler, Florian Krantchev, Kiril LaBella, Dominic Van Leemput, Koen Li, Hongwei Bran Linguraru, Marius George Link, Katherine E. Liu, Xinyang Maleki, Nazanin Meier, Zeke Menze, Bjoern H. Moy, Harrison Osenberg, Klara Piraud, Marie Reitman, Zachary Shinohara, Russel Takeshi Tahon, Nourel hoda Nada, Ayman Velichko, Yuri S. Wang, Chunhao Wiestler, Benedikt Wiggins, Walter Shafique, Umber Willms, Klara Avesta, Arman Bousabarah, Khaled Chakrabarty, Satrajit Gennaro, Nicolo Holler, Wolfgang Kaur, Manpreet LaMontagne, Pamela Lin, MingDe Lost, Jan Marcus, Daniel S. Maresca, Ryan Merkaj, Sarah Nada, Ayaman Pedersen, Gabriel Cassinelli von Reppert, Marc Sotiras, Aristeidis Teytelboym, Oleg Tillmans, Niklas Westerhoff, Malte Youssef, Ayda Godfrey, Devon Floyd, Scott Rauschecker, Andreas Villanueva-Meyer, Javier Pflüger, Irada Cho, Jaeyoung Bendszus, Martin Brugnara, Gianluca Cramer, Justin Perez-Carillo, Gloria Guzman J. Johnson, Derek R. Kam, Anthony Kwan, Benjamin Yin Ming Lai, Lillian Lall, Neil U. Memon, Fatima Patro, Satya Narayana Petrovic, Bojan So, Tiffany Y. Thompson, Gerard Wu, Lei Schrickel, E. Brooke Bansal, Anu Barkhof, Frederik Besada, Cristina Chu, Sammy Druzgal, Jason Dusoi, Alexandru Farage, Luciano Feltrin, Fabricio Fong, Amy Fung, Steve H. Gray, R. Ian Ikuta, Ichiro Iv, Michael Postma, Alida A. Mahajan, Amit Joyner, David Krumpelman, Chase Letourneau-Guillon, Laurent Lincoln, Christie M. Maros, Mate E. Miller, Elka Morón, Fanny Nimchinsky, Esther A. Ozsarlak, Ozkan Patel, Uresh Rohatgi, Saurabh Saha, Atin Sayah, Anousheh Schwartz, Eric D. Shih, Robert Shiroishi, Mark Trinity health Mid Atlantic Hosiptals DarbyPA United States Department of Radiology and Biomedical Imaging Yale School of Medicine New HavenCT United States Division of Computational Pathology Department of Pathology and Laboratory Medicine School of Medicine Indiana University IndianapolisIN United States Department of Electical and Computer Engineering Cornell University Cornell Tech New YorkNY United States Department of Radiology Weill Cornell Medicine New YorkNY United States ImagineQuant Children’s Hospital of Philadelphia PhiladelphiaPA United States College of Medicine Alfaisal University Riyadh Saudi Arabia DKFZ Division of Translational Neurooncology The WTZ German Cancer Consortium DKTK Partner Site University Hospital Essen Essen Germany Medical Artificial Intelligence Lab Crestview Radiology Lagos Nigeria Sage Bionetworks SeattleWA United States Montreal Neurological Institute McGill University Montreal Canada lab Crestview Radiology Lagos Nigeria Department of Therapeutic Radiology Yale School of Medicine New HavenCT United States Sheikh Zayed Institute for Pediatric Surgical Innovation Children’s National Hospital WashingtonDC United States Department of Radiology Mayo Clinic RochesterMN United States Department of Radiology Duke University Medical Center DurhamNC United States Department of Neurosurgery Yale School of Medicine New HavenCT United States Center for Global Health Perelman School of Medicine University of Pennsylvania PA United States Department of Informatics Technical University Munich Germany Children’s Hospital of Philadelphia University of Pennsylvania PhiladelphiaPA United States Cancer Imaging Program National Cancer Institute National Institutes of Health BethesdaMD United States Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital BostonMA United States Children’s National Hospital WashingtonDC United States PrecisionFDA U.S. Food and Drug Administration S

The translation of AI-generated brain metastases (BM) segmentation into clinical practice relies heavily on diverse, high-quality annotated medical imaging datasets. The BraTS-METS 2023 challenge has gained momentum for testing and benchmarking algorithms using rigorously annotated internationally compiled real-world datasets. This study presents the results of the segmentation challenge and characterizes the challenging cases that impacted the performance of the winning algorithms. Untreated brain metastases on standard anatomic MRI sequences (T1, T2, FLAIR, T1PG) from eight contributed international datasets were annotated in stepwise method: published UNET algorithms, student, neuroradiologist, final approver neuroradiologist. Segmentations were ranked based on lesion-wise Dice and Hausdorff distance (HD95) scores. False positives (FP) and false negatives (FN) were rigorously penalized, receiving a score of 0 for Dice and a fixed penalty of 374 for HD95. The mean scores for the teams were calculated. Eight datasets comprising 1303 studies were annotated, with 402 studies (3076 lesions) released on Synapse as publicly available datasets to challenge competitors. Additionally, 31 studies (139 lesions) were held out for validation, and 59 studies (218 lesions) were used for testing. Segmentation accuracy was measured as rank across subjects, with the winning team achieving a LesionWise mean score of 7.9. The Dice score for the winning team was 0.65 ± 0.25. Common errors among the leading teams included false negatives for small lesions and misregistration of masks in space. The Dice scores and lesion detection rates of all algorithms diminished with decreasing tumor size, particularly for tumors smaller than 100 mm3. In conclusion, algorithms for BM segmentation require further refinement to balance high sensitivity in lesion detection with the minimization of false positives and negatives. The BraTS-METS 2023 challenge successfully curated well-annotated, diverse d

关键词： Image segmentation

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The Brain Tumor Segmentation (BraTS) Challenge: Local Synthesis of Healthy Brain Tissue via Inpainting

arXiv

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arXiv 2023年

作者： Kofler, Florian Steinbauer, Felix Meissen, Felix Graf, Robert Ehrlich, Stefan K. Reinke, Annika Oswald, Eva Waldmannstetter, Diana Hoelzl, Florian Horvath, Izabela Turgut, Oezguen Shit, Suprosanna Bukas, Christina Yang, Kaiyuan Paetzold, Johannes C. de da Rosa, Ezequiel Mekki, Isra Vinayahalingam, Shankeeth Kassem, Hasan Zhang, Juexin Chen, Ke Weng, Ying Durrer, Alicia Cattin, Philippe C. Wolleb, Julia Sadique, M.S. Rahman, M.M. Farzana, W. Temtam, A. Iftekharuddin, K.M. Adewole, Maruf Anwar, Syed Muhammad Baid, Ujjwal Janas, Anastasia Kazerooni, Anahita Fathi LaBella, Dominic Bran Li, Hongwei Moawad, Ahmed W. Conte, Gian-Marco Farahani, Keyvan Eddy, James Sheller, Micah Pati, Sarthak Karagyris, Alexandros Aristizabal, Alejandro Bergquist, Timothy Chung, Verena Shinohara, Russell Takeshi Dako, Farouk Wiggins, Walter Reitman, Zachary Wang, Chunhao Liu, Xinyang Jiang, Zhifan Johanson, Elaine Meier, Zeke Familiar, Ariana Davatzikos, Christos Freymann, John Kirby, Justin Bilello, Michel Fathallah-Shaykh, Hassan M. Wiest, Roland Kirschke, Jan Colen, Rivka R. Kotrotsou, Aikaterini Lamontagne, Pamela Marcus, Daniel Milchenko, Mikhail Nazeri, Arash Weber, Marc-André Mahajan, Abhishek Mohan, Suyash Mongan, John Hess, Christopher Cha, Soonmee Villanueva-Meyer, Javier Colak, Errol Crivellaro, Priscila Jakab, Andras Fatade, Abiodun Omidiji, Olubukola Akinola Lagos, Rachel Olatunji, O.O. Khanna, Goldey Kirkpatrick, John Alonso-Basanta, Michelle Rashid, Arif Bornhorst, Miriam Nabavizadeh, Ali Lepore, Natasha Palmer, Joshua Porras, Antonio Albrecht, Jake Anazodo, Udunna Aboian, Mariam Calabrese, Evan Rudie, Jeffrey David Linguraru, Marius George Iglesias, Juan Eugenio Van Leemput, Koen Bakas, Spyridon Wiestler, Benedikt Ezhov, Ivan Piraud, Marie Menze, Bjoern H. Helmholtz AI Germany Technical University of Munich Germany Helmholtz Munich Germany Klinikum Rechts der Isar Munich Germany SETLabs Research GmbH Healthcare Technologies Munich Germany Heidelberg Division of Intelligent Medical Systems Germany Heidelberg HI Helmholtz Imaging Germany Institute of Clinical Neuroimmunology Faculty of Medicine Ludwig Maximilian University Munich Germany University of Zurich Switzerland Helmholtz Research Center Munich Germany Imperial College London United Kingdom Icometrix Leuven Belgium Department of Oral and Maxillofacial Surgery Radboudumc Netherlands Department of Artificial Intelligence Radboud University Netherlands MLCommons University of Nottingham Ningbo China Ningbo315100 China Center for medical Image Analysis and Navigation Department of Biomedical Engineering University of Basel Allschwil Switzerland Old Dominion University NorfolkVA23529 United States Lab Crestview Radiology Lagos Nigeria Children's National Hospital WashingtonDC United States George Washington University WashingtonDC United States University of Pennsylvania PhiladelphiaPA United States Department of Radiology Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Yale University New HavenCT United States Children's Hospital of Philadelphia University of Pennsylvania PhiladelphiaPA United States Duke University Medical Center Department of Radiation Oncology United States Athinoula A Martinos Center for Biomedical Imaging Massachusetts General Hospital BostonMA United States Department of Neuroradiology Technical University of Munich Munich Germany Mercy Catholic Medical Center DarbyPA United States Department of Radiology Mayo Clinic RochesterMN United States Cancer Imaging Program National Cancer Institute National Institutes of Health BethesdaMD20814 U

A myriad of algorithms for the automatic analysis of brain MR images is available to support clinicians in their decision-making. For brain tumor patients, the image acquisition time series typically starts with an already pathological scan. This poses problems, as many algorithms are designed to analyze healthy brains and provide no guarantee for images featuring lesions. Examples include but are not limited to algorithms for brain anatomy parcellation, tissue segmentation, and brain extraction. To solve this dilemma, we introduce the BraTS inpainting challenge. Here, the participants explore inpainting techniques to synthesize healthy brain scans from lesioned ones. The following manuscript contains the task formulation, dataset, and submission procedure. Later, it will be updated to summarize the findings of the challenge. The challenge is organized as part of the ASNR-BraTS MICCAI challenge. Copyright © 2023, The Authors. All rights reserved.

关键词： Magnetic resonance imaging

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HERMES: Gamma Ray Burst and Gravitational Wave counterpart hunter

arXiv

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arXiv 2024年

作者： Ghirlanda, G. Nava, L. Salafia, O. Fiore, F. Campana, R. Salvaterra, R. Sanna, A. Leone, W. Evangelista, Y. Dilillo, G. Puccetti, S. Santangelo, A. Trenti, M. Guzmán, A. Hedderman, P. Amelino-Camelia, G. Barbera, M. Baroni, G. Bechini, M. Bellutti, P. Bertuccio, G. Borghi, G. Brandonisio, A. Burderi, L. Cabras, C. Chen, T. Citossi, M. Colagrossi, A. Crupi, R. De Cecio, F. Dedolli, I. Del Santo, M. Demenev, E. Di Salvo, T. Ficorella, F. Gačnik, D. Gandola, M. Gao, N. Gomboc, A. Grassi, M. Iaria, R. La Rosa, G. Lo Cicero, U. Malcovati, P. Manca, A. Marchesini, E.J. Maselli, A. Mele, F. Nogara, P. Pepponi, G. Perri, M. Picciotto, A. Pirrotta, S. Prinetto, J. Quirino, M. Riggio, A. Řípa, J. Russo, F. Selčan, D. Silvestrini, S. Sottile, G. Thomas, M.L. Tiberia, A. Trevisan, S. Troisi, I. Tsvetkova, A. Vacchi, A. Werner, N. Zanotti, G. Zorzi, N. MerateI-23807 Italy INFN – Sezione di Milano-Bicocca piazza della Scienza 3 MilanoI-20126 Italy INAF – Osservatorio Astronomico di Trieste Via G.B. Tiepolo 11 TriesteI–34143 Italy IFPU Institut for Fundamental Physics of the Universe Via Beirut 2 TriesteI-34014 Italy INAF – OAS Via Piero Gobetti 101 BolognaI-40129 Italy INFN — Sezione di Bologna Viale Berti Pichat 6/2 BolognaI-40127 Italy INAF Istituto di Astrofisica Spaziale e Fisica Cosmica di Milano Via A. Corti 12 Milano20133 Italy Dipartimento di Fisica Università degli Studi di Cagliari SP Monserrato–Sestu km 0.7 Monserrato09042 Italy Povo38122 Italy RomaI-00133 Italy RomaI-00133 Italy Agenzia Spaziale Italiana Via del Politecnico snc Roma00133 Italy Institut für Astronomie und Astrophysik Universität Tübingen Sand 1 TübingenD-72076 Germany School of Physics University of Melbourne ParkvilleVIC3010 Australia Australian Research Council Centre of Excellence for All-Sky Astrophysics in 3-Dimensions Australia Physics Department Federico II University via Cintia 21 NapoliI-80126 Italy Politecnico di Milano Department of Aerospace Science and Technology Milan Italy Fondazione Bruno Kessler Center for Sensors and Devices Trento Italy Politecnico di Milano Department of Electronics Information and Bioengineering Como Italy Dipartimento di Matematica e Informatica Università degli Studi di Cagliari SP Monserrato–Sestu km 0.7 Monserrato09042 Italy Key Laboratory of Particle Astrophysics Institute of High Energy Physics Chinese Academy of Sciences Beijing100049 China INAF - IASF Palermo Via Ugo La Malfa 153 Palermo90146 Italy Dipartimento di Fisica e Chimica Universita‘degli Studi di Palermo via Archirafi 36 PalermoI-90123 Italy SkyLabs d.o.o. Zagrebška c. 104 Maribor2000 Slovenia Center for Astrophysics and Cosmology University of Nova Gorica Vipavska 13 Nova Gorica5000 Slovenia Department of Electrical Computer and Biomedical Engineering University of Pavia I

Gamma Ray Bursts (GRBs) bridge relativistic astrophysics and multi–messenger astronomy. Space–based γ/X–ray wide field detectors have proven essential to detect and localize the highly variable GRB prompt emission, which is also a counterpart of gravitational wave events. We study the capabilities to detect long and short GRBs by the High Energy Rapid Modular Ensemble of Satellites (HERMES) Pathfinder (HP) and SpIRIT, namely a swarm of six 3U CubeSats to be launched in early 2025, and a 6U CubeSat launched on December 1st 2023. We also study the capabilities of two advanced configurations of swarms of >8 satellites with improved detector performances (HERMES Constellations). The HERMES detectors, sensitive down to ∼ 2-3 keV, will be able to detect faint/soft GRBs which comprise X-ray flashes and high redshift bursts. By combining state-of-the-art long and short GRB population models with a description of the single module performance, we estimate that HP will detect ∼ 195+−2221 long GRBs (3.4+−0038 at redshift z > 6) and ∼ 19+−53 short GRBs per year. The larger HERMES Constellations under study can detect between ∼ 1300 and ∼ 3000 long GRBs per year and between ∼ 160 and ∼ 400 short GRBs per year, depending on the chosen configuration, with a rate of long GRBs above z > 6 between 30 and 75 per year. Finally, we explore the capabilities of HERMES to detect short GRBs as electromagnetic counterparts of binary neutron star (BNS) mergers detected as gravitational signals by current and future ground–based interferometers. Under the assumption that the GRB jets are structured, we estimate that HP can provide up to ∼1 (14) yr−1 joint detections during the fifth LIGO-Virgo-KAGRA observing run (Einstein Telescope single triangle 10–km–arm configuration). These numbers become ∼ 4 (100) yr−1, respectively, for the HERMES Constellation configuration. © 2024, CC BY.

关键词： Gravity waves

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11th German Conference on Chemoinformatics (GCC 2015) Abstracts

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JOURNAL OF CHEMinformatics 2016年第SUPPL 1期8卷 1-27页

作者： [Anonymous] GDCh-CIC Division Associated Board Member Beilstein-Institut zur Förderung der Chemischen Wissenschaften Trakehner Str. 7-9 60487 Frankfurt Germany. ufechner@beilstein-institut.de. Division Medicinal Chemistry Amsterdam Institute for Molecules Medicines and Systems (AIMMS) VU University Amsterdam The Netherlands. Centre for Bioinformatics Uni Hamburg Bundesstr. 43 20146 Hamburg Germany. Sanofi-Aventis Deutschland GmbH 65926 Frankfurt am Main Germany. stefan.guessregen@***. Sanofi-Aventis Deutschland GmbH 65926 Frankfurt am Main Germany. GlaxoSmithKline Stevenage SG1 2NY UK. nicola.j.richmond@***. Discngine Paris 75011 France. Organisch-Chemisches Institut Westfälische Wilhelms-Universität Münster Germany. marwin.segler@wwu.de. Organisch-Chemisches Institut Westfälische Wilhelms-Universität Münster Germany. Bundeskriminalamt Wiesbaden Central Analytics II 65173 Wiesbaden Germany. Department of Chemistry and Biochemistry University of California Santa Barbara CA 93111 USA. shea@chem.ucsb.edu. Department of Chemistry and Biochemistry University of California Santa Barbara CA 93111 USA. Chemistry Department Ludwig-Maximilians-Universität München Butenandtstr. 7 81377 Munich Germany. Inorganic Chemistry and Center for Nanointegration University of Duisburg-Essen Essen Germany. CAM-D Technologies Essen Germany. Institute for Bioinformatics and Chemoinformatics Westphalian University of Applied Sciences Recklinghausen Germany. Institute for Bioinformatics and Chemoinformatics Westphalian University of Applied Sciences Recklinghausen Germany. achim.zielesny@w-hs.de. Leiden University Leiden Netherlands. j.fraaije@chem.leidenuniv.nl. Culgi BV Berlin Germany. Physikalische Chemie III TU Dortmund 44227 Dortmund Germany. stefan.kast@tu-dortmund.de. Centre for Molecular Informatics Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW United Kingdom. kcb27@cam.ac.uk. Centre for Molecular Informatics Department of Chemistry

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Highlights from the 11th ISCB Student Council Symposium 2015. Dublin, Ireland. 10 July 2015

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BMC bioinformatics 2016年第3期17 Suppl 3卷 95页

作者： Katie Wilkins Mehedi Hassan Margherita Francescatto Jakob Jespersen R. Gonzalo Parra Bart Cuypers Dan DeBlasio Alexander Junge Anupama Jigisha Farzana Rahman Griet Laenen Sander Willems Lieven Thorrez Yves Moreau Nagarajan Raju Sonia Pankaj Chothani C. Ramakrishnan Masakazu Sekijima M. Michael Gromiha Paddy J Slator Nigel J Burroughs Przemysław Szałaj Zhonghui Tang Paul Michalski Oskar Luo Xingwang Li Yijun Ruan Dariusz Plewczynski Giulia Fiscon Emanuel Weitschek Massimo Ciccozzi Paola Bertolazzi Giovanni Felici Pieter Meysman Manu Vanaerschot Maya Berg Hideo Imamura Jean-Claude Dujardin Kris Laukens Westa Domanova James R. Krycer Rima Chaudhuri Pengyi Yang Fatemeh Vafaee Daniel J. Fazakerley Sean J. Humphrey David E. James Zdenka Kuncic Plant Pathology and Plant-Microbe Biology Section School of Integrative Plant Science Cornell University Ithaca USA Graduate Field of Computational Biology Cornell University Ithaca USA School of Computing & Mathematics University of South Wales Cardiff UK Department of Genome Biology for Neurodegenerative Diseases German Center for Neurodegenerative Diseases (DZNE) within the Helmholtz Association ᅟ Germany Department of Surgery Massachusetts General Hospital The Broad Institute of MIT and Harvard Boston USA Department of Systems Biology Technical University of Denmark Kemitorvet Denmark Protein Physiology Lab Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires Buenos Aires Argentina Molecular Parasitology Unit (MPU) Institute of Tropical Medicine Antwerp Belgium Advanced Database Research and Modeling (ADReM) research group University of Antwerp Antwerpen Belgium Department of Computer Science University of Arizona Tucson USA Department of Veterinary Clinical and Animal Sciences Center for non-coding RNA in Technology and Health University of Copenhagen Copenhagen Denmark University College Dublin Dublin Ireland Department of Electrical Engineering (ESAT) STADIUS Center for Dynamical Systems Signal Processing and Data Analytics KU Leuven Leuven Belgium Minds Medical IT Department Leuven Belgium Scientific Institute of Public Health (WIV-ISP) Platform of Biotechnology and Molecular Biology (PBB) Brussels Belgium Department of Development and Regeneration @ Kulak KU Leuven Kortrijk Belgium Department of Biotechnology Bhupat and Jyoti Metha School of Biosciences Indian Institute of Technology Madras Chennai India Philips Research North America Briarcliff Manor USA Global Scientific Information and Computing Center (GSIC) Tokyo Institute of Technology Tokyo Japan Systems Biology Centre University of Warwick Senate House Coventry UK Systems Biology Doctoral Training Centre University of Warwick Senate House Coventry UK Center for B

A1 Highlights from the eleventh ISCB Student Council Symposium 2015 Katie Wilkins, Mehedi Hassan, Margherita Francescatto, Jakob Jespersen, R. Gonzalo Parra, Bart Cuypers, Dan DeBlasio, Alexander Junge, Anupama Jigisha, Farzana Rahman O1 Prioritizing a drug’s targets using both gene expression and structural similarity Griet Laenen, Sander Willems, Lieven Thorrez, Yves Moreau O2 Organism specific protein-RNA recognition: A computational analysis of protein-RNA complex structures from different organisms Nagarajan Raju, Sonia Pankaj Chothani, C. Ramakrishnan, Masakazu Sekijima; M. Michael Gromiha O3 Detection of Heterogeneity in Single Particle Tracking Trajectories Paddy J Slator, Nigel J Burroughs O4 3D-NOME: 3D NucleOme Multiscale Engine for data-driven modeling of three-dimensional genome architecture Przemysław Szałaj, Zhonghui Tang, Paul Michalski, Oskar Luo, Xingwang Li, Yijun Ruan, Dariusz Plewczynski O5 A novel feature selection method to extract multiple adjacent solutions for viral genomic sequences classification Giulia Fiscon, Emanuel Weitschek, Massimo Ciccozzi, Paola Bertolazzi, Giovanni Felici O6 A Systems Biology Compendium for Leishmania donovani Bart Cuypers, Pieter Meysman, Manu Vanaerschot, Maya Berg, Hideo Imamura, Jean-Claude Dujardin, Kris Laukens O7 Unravelling signal coordination from large scale phosphorylation kinetic data Westa Domanova, James R. Krycer, Rima Chaudhuri, Pengyi Yang, Fatemeh Vafaee, Daniel J. Fazakerley, Sean J. Humphrey, David E. James, Zdenka Kuncic

关键词： Visceral Leishmaniasis Feature Selection Method Frequent Itemset Mining Leishmania Donovani Student Council

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