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Rapid simulation of glycoprotein structures by grafting and steric exclusion of glycan conformer libraries

Cell 2024年第5期187卷 1296-1311.e26页

作者： Yu-Xi Tsai Ning-En Chang Klaus Reuter Hao-Ting Chang Tzu-Jing Yang Sören von Bülow Vidhi Sehrawat Noémie Zerrouki Matthieu Tuffery Michael Gecht Isabell Louise Grothaus Lucio Colombi Ciacchi Yong-Sheng Wang Min-Feng Hsu Kay-Hooi Khoo Gerhard Hummer Shang-Te Danny Hsu Cyril Hanus Mateusz Sikora Institute of Biological Chemistry Academia Sinica Taipei 11529 Taiwan Institute of Biochemical Sciences National Taiwan University Taipei 10617 Taiwan. Max Planck Computing and Data Facility 85748 Garching Germany. Department of Theoretical Biophysics Max Planck Institute for Biophysics 60438 Frankfurt Germany. Department of Theoretical Biophysics Max Planck Institute for Biophysics 60438 Frankfurt Germany Malopolska Centre of Biotechnology Jagiellonian University 31-007 Kraków Poland. Institute of Psychiatry and Neurosciences of Paris Inserm UMR1266 Université Paris-Cité 75014 Paris France. Hybrid Materials Interfaces Group Faculty of Production Engineering Bremen Center for Computational Materials Science and MAPEX Center for Materials and Processes University of Bremen 28359 Bremen Germany. Institute of Biological Chemistry Academia Sinica Taipei 11529 Taiwan. Institute of Biophysics Goethe University 60438 Frankfurt Germany. Institute of Biochemical Sciences National Taiwan University Taipei 10617 Taiwan International Institute for Sustainability with Knotted Chiral Meta Matter (WPI-SKCM(2)) Hiroshima University Hiroshima 739-8526 Japan. Electronic address: sthsu@gate.sinica.edu.tw. Institute of Psychiatry and Neurosciences of Paris Inserm UMR1266 Université Paris-Cité 75014 Paris France GHU Psychiatrie et Neurosciences de Paris 75014 Paris France. Electronic address: cyril.hanus@inserm.fr. Malopolska Centre of Biotechnology Jagiellonian University 31-007 Kraków Poland. Electronic address: mateusz.sikora@uj.edu.pl.

Most membrane proteins are modified by covalent addition of complex sugars through N- and O-glycosylation. Unlike proteins, glycans do not typically adopt specific secondary structures and remain very mobile, shielding potentially large fractions of protein surface. High glycan conformational freedom hinders complete structural elucidation of glycoproteins. Computer simulations may be used to model glycosylated proteins but require hundreds of thousands of computing hours on supercomputers, thus limiting routine use. Here, we describe GlycoSHIELD, a reductionist method that can be implemented on personal computers to graft realistic ensembles of glycan conformers onto static protein structures in minutes. Using molecular dynamics simulation, small-angle X-ray scattering, cryoelectron microscopy, and mass spectrometry, we show that this open-access toolkit provides enhanced models of glycoprotein structures. Focusing on N-cadherin, human coronavirus spike proteins, and gamma-aminobutyric acid receptors, we show that GlycoSHIELD can shed light on the impact of glycans on the conformation and activity of complex glycoproteins.

关键词： GABAA receptor N-cadherin SAXS coronavirus S protein cryo-EM glycans glycoproteins mass spectrometry molecular dynamics

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Polarimetric geometric modeling for mm-VLBI observations of black holes

arXiv

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arXiv 2023年

作者： Roelofs, Freek Johnson, Michael D. Chael, Andrew Janssen, Michael Wielgus, Maciek Broderick, Avery E. Akiyama, Kazunori Alberdi, Antxon Alef, Walter Algaba, Juan Carlos Anantua, Richard Asada, Keiichi Azulay, Rebecca Bach, Uwe Baczko, Anne-Kathrin Ball, David Baloković, Mislav Barrett, John Bauböck, Michi Benson, Bradford A. Bintley, Dan Blackburn, Lindy Blundell, Raymond Bouman, Katherine L. Bower, Geoffrey C. Boyce, Hope Bremer, Michael Brinkerink, Christiaan D. Brissenden, Roger Britzen, Silke Broguiere, Dominique Bronzwaer, Thomas Bustamante, Sandra Byun, Do-Young Carlstrom, John E. Ceccobello, Chiara Chan, Chi-Kwan Chang, Dominic O. Chatterjee, Koushik Chatterjee, Shami Chen, Ming-Tang Chen, Yongjun Cheng, Xiaopeng Cho, Ilje Christian, Pierre Conroy, Nicholas S. Conway, John E. Cordes, James M. Crawford, Thomas M. Crew, Geoffrey B. Cruz-Osorio, Alejandro Cui, Yuzhu Dahale, Rohan Davelaar, Jordy De Laurentis, Mariafelicia Deane, Roger Dempsey, Jessica Desvignes, Gregory Dexter, Jason Dhruv, Vedant Doeleman, Sheperd S. Dougal, Sean Dzib, Sergio A. Eatough, Ralph P. Emami, Razieh Falcke, Heino Farah, Joseph Fish, Vincent L. Fomalont, Ed Ford, H. Alyson Foschi, Marianna Fraga-Encinas, Raquel Freeman, William T. Friberg, Per Fromm, Christian M. Fuentes, Antonio Galison, Peter Gammie, Charles F. García, Roberto Gentaz, Olivier Georgiev, Boris Goddi, Ciriaco Gold, Roman Gómez-Ruiz, Arturo I. Gómez, José L. Gu, Minfeng Gurwell, Mark Hada, Kazuhiro Haggard, Daryl Haworth, Kari Hecht, Michael H. Hesper, Ronald Heumann, Dirk Ho, Luis C. Ho, Paul Honma, Mareki Huang, Chih-Wei L. Huang, Lei Hughes, David H. Ikeda, Shiro Impellizzeri, C.M. Violette Inoue, Makoto Issaoun, Sara James, David J. Jannuzi, Buell T. Jeter, Britton Jiang, Wu Jiménez-Rosales, Alejandra Jorstad, Svetlana Joshi, Abhishek V. Jung, Taehyun Karami, Mansour Karuppusamy, Ramesh Kawashima, Tomohisa Keating, Garrett K. Kettenis, Mark Kim, Dong-Jin Kim, Jae-Young Kim, Jongsoo Kim, Junhan Kino, Motoki Koay, Jun Yi Kocherlakota, Prashant Kofuji, Yutaro Koch, Center for Astrophysics Harvard & Smithsonian 60 Garden Street CambridgeMA02138 United States Black Hole Initiative Harvard University 20 Garden Street CambridgeMA02138 United States Radboud University P.O. Box 9010 Nijmegen6500 GL Netherlands Black Hole Initiative Harvard University 20 Garden Street CambridgeMA02138 United States Princeton Gravity Initiative Princeton University Jadwin Hall PrincetonNJ08544 United States Max-Planck-Institut für Radioastronomie Auf dem Hügel 69 BonnD-53121 Germany Perimeter Institute for Theoretical Physics 31 Caroline Street North WaterlooONN2L 2Y5 Canada Department of Physics and Astronomy University of Waterloo 200 University Avenue West WaterlooONN2L 3G1 Canada Waterloo Centre for Astrophysics University of Waterloo WaterlooONN2L 3G1 Canada Massachusetts Institute of Technology Haystack Observatory 99 Millstone Road WestfordMA01886 United States National Astronomical Observatory of Japan 2-21-1 Osawa Mitaka Tokyo181-8588 Japan Instituto de Astrofísica de Andalucía-CSIC Glorieta de la Astronomía s/n GranadaE-18008 Spain Department of Physics Faculty of Science Universiti Malaya Kuala Lumpur50603 Malaysia Department of Physics & Astronomy The University of Texas at San Antonio One UTSA Circle San AntonioTX78249 United States Institute of Astronomy and Astrophysics Academia Sinica 11F of Astronomy-Mathematics Building AS/NTU No. 1 Sec. 4 Roosevelt Rd. Taipei10617 Taiwan Departament d’Astronomia i Astrofísica Universitat de València C. Dr. Moliner 50 València BurjassotE-46100 Spain Observatori Astronòmic Universitat de València C. Catedrático José Beltrán 2 València PaternaE-46980 Spain Department of Space Earth and Environment Chalmers University of Technology Onsala Space Observatory OnsalaSE-43992 Sweden Steward Observatory Department of Astronomy University of Arizona 933 N. Cherry Ave. TucsonAZ85721 United States Yale Center for Astronomy & Astrophysics Yale Universit

The Event Horizon Telescope (EHT) is a millimeter very-long-baseline interferometry (VLBI) array which has imaged the apparent shadows of the supermassive black holes M87∗ and Sagittarius A∗. Polarimetric data from these observations contain a wealth of information on the black hole and accretion flow properties. In this work, we develop polarimetric geometric modeling methods for mm-VLBI data, focusing on approaches that fit data products with differing degrees of invariance to broad classes of calibration errors. We establish a fitting procedure using a polarimetric "m-ring" model to approximate the image structure near a black hole. By fitting this model to synthetic EHT data from general relativistic magnetohydrodynamic (GRMHD) models, we show that the linear and circular polarization structure can be successfully approximated with relatively few model parameters. We then fit this model to EHT observations of M87∗ taken in 2017. In total intensity and linear polarization, the m-ring fits are consistent with previous results from imaging methods. In circular polarization, the m-ring fits indicate the presence of event-horizon-scale circular polarization structure, with a persistent dipolar asymmetry and orientation across several days. The same structure was recovered independently of observing band, used data products, and model assumptions. Despite this broad agreement, imaging methods do not produce similarly consistent results. Our circular polarization results, which imposed additional assumptions on the source structure, should thus be interpreted with some caution. Polarimetric geometric modeling provides a useful and powerful method to constrain the properties of horizon-scale polarized emission, particularly for sparse arrays like the EHT. © 2023, CC BY.

关键词： Polarimeters

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AGlobal benchmark of algorithms for segmentinglate gadolinium-enhanced cardiac magnetic resonance imaging

arXiv

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arXiv 2020年

作者： Xiong, Zhaohan Xia, Qing Hu, Zhiqiang Huang, Ning Bian, Cheng Zheng, Yefeng Vesal, Sulaiman Ravikumar, Nishant Maier, Andreas Yang, Xin Heng, Pheng-Ann Ni, Dong Li, Caizi Tong, Qianqian Si, Weixin Puybareau, Elodie Khoudli, Younes Géraud, Thierry Chen, Chen Bai, Wenjia Rueckert, Daniel Xu, Lingchao Zhuang, Xiahai Luo, Xinzhe Jia, Shuman Sermesant, Maxime Liu, Yashu Wang, Kuanquan Borra, Davide Masci, Alessandro Corsi, Cristiana De Vente, Coen Veta, Mitko Karim, Rashed Preetha, Chandrakanth Jayachandran Engelhardt, Sandy Qiao, Menyun Wang, Yuanyuan Tao, Qian Nuñez-Garcia, Marta Camara, Oscar Savioli, Nicolo Lamata, Pablo Zhao, Jichao Auckland Bioengineering Institute University of Auckland Auckland New Zealand State Key Lab of Virtual Reality Technology and Systems Beihang University Beijing China School of Electronics Engineering and Computer Science Peking University Beijing China SenseTime Inc Shenzhen China Tencent Jarvis Laboratory Shenzhen China Pattern Recognition Lab Friedrich-Alexander-Universität Erlangen-Nürnberg Erlangen Germany Department of Computer Science and Engineering Chinese University of Hong Kong Hong Kong National-Regional Key Technology Engineering Laboratory for Medical Ultrasound School of Biomedical Engineering Shenzhen University Shenzhen China School of Computer Science Wuhan University Wuhan China Shenzhen Key Laboratory of Virtual Reality and Human Interaction Technology Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen China Epita Research and Development Laboratory Paris France Department of Computing Imperial College London London United Kingdom School of Naval Architecture Shanghai Jiao Tong University Ocean & Civil Engineering Shanghai China School of Data Science Fudan University Shanghai China Epione Research Group Universite Cote d'Azur Inria Sophia Antipolis France Harbin Institute of Technology School of Computer Science and Technology Harbin China Department of Electric University of Bologna Electronic and Information Engineering Cesena Italy Department of Biomedical Engineering Eindhoven University of Technology Eindhoven Netherlands School of Biomedical Engineering and Imaging Sciences Kings College London London United Kingdom Faculty of Electrical Engineering and Information Technology University of Magdeburg Magdeburg Germany Heidelberg University Hospital Germany Biomedical Engineering Center Fudan University Shanghai China Department of Radiology Leiden University Medical Center Leiden Netherlands Department of Information and Communication Technologies Universitat Pompeu Fabra Barcelona Spain D

Segmentation of cardiac images, particularly late gadolinium-enhanced magnetic resonance imaging (LGE-MRI)widely used for visualizing diseased cardiacstructures, is a crucial first step for clinical diagnosis and treatment. However, direct segmentation ofLGE-MRIsischallenging due to *** most clinical studies have relied on manual and labor-intensive approaches, automatic methods are of high interest, particularly optimized machine learning *** address this, we organized the "2018 Left Atrium Segmentation Challenge" using 154 3D LGE-MRIs, currently the world's largest cardiac LGE-MRI dataset, and associated labels of the left atriumsegmented by three medical experts,ultimately attractingthe participation of27 international teams. In this paper, extensive analysis of the submitted algorithms using technical and biological metrics was performed by undergoing subgroup analysis and conducting hyper-parameter analysis,offeringan overall picture ofthe major design choices of convolutional neural networks(CNNs) and practical considerations for achieving state-of-the-art left atrium segmentation. Results show the top methodachieved a dice score of 93.2%and a mean surface to a surface distance of 0.7mm, significantly outperforming prior state-of-the-art. Particularly, our analysisdemonstrated that double, sequentially usedCNNs, in which a first CNN is used for automatic region-of-interestlocalization and a subsequent CNN is used for refinedregional segmentation, achieved far superiorresults than traditional methods and pipelinescontaining *** findings from this study can potentially be extended to other imaging datasets and modalities, having an impact on the wider medical imaging *** large-scale benchmarking study makes a significant step towards much-improved segmentation methods for cardiac LGE-MRIs, and will serveas animportant benchmark for evaluating and comparing the future works in the field. Copyright © 2020, Th

关键词： Magnetic resonance imaging

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Searching for GRBs at VHE with MAGIC: The status before CTA

arXiv

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arXiv 2019年

作者： Berti, Alessio Antonelli, Lucio Angelo Bošnjak, Zeljka Cortina, Juan Covino, Stefano D’Elia, Valerio do Souto Espiñeira, Elia Fukami, Satoshi Inoue, Susumu Longo, Francesco Miceli, Davide Moretti, Elena Nava, Lara Noda, Koji Nozaki, Seya Peresano, Michele Suda, Yusuke Will, Martin University of Torino INFN Torino Torino Italy INAF National Institute for Astrophysics Rome Italy Faculty of Electrical Engineering and Computing University of Zagreb Zagreb Croatia CIEMAT Madrid Spain INAF Osservatorio Astronomico di Brera Merate Italy Space Science Data Center - Agenzia Spaziale Italiana Rome Italy Spain ICRR University of Tokyo Kashiwa Chiba Japan RIKEN Wako Saitama Japan University of Trieste INFN Trieste Trieste Italy University of Udine INFN Trieste Udine Italy Department of Physics Kyoto University Kyoto Japan Max-Planck-Institut für Physik Munich Germany

Gamma-Ray Bursts (GRBs) are one of the main targets for current and next generation Imaging Atmospheric Cherenkov Telescopes (IACTs). Given their transient behavior, especially in the case of their prompt emission phase, performing fast follow-up observations is challenging for IACTs, which have a narrow field of view and limited duty cycle. Despite this, MAGIC plays a major role in the search for Very High Energy (VHE, E>100 GeV) gamma-ray emission from GRBs: this is possible thanks to its fast repositioning speed, low energy threshold and high sensitivity at the lowest energies. In 2013 the MAGIC GRB automatic procedure was upgraded, increasing the number of GRBs followed in the prompt and early afterglow phases and decreasing dramatically hardware failures during fast repositioning. Currently, only GRB 190114C was firmly detected in the VHE band, while for other GRBs no significant detection was achieved. In such a case, upper limits (ULs) can give insight into the physics driving such eluding sources, especially on their emission mechanisms. In this contribution we report on the status of the GRB follow-up with MAGIC and focus on the ULs and results obtained from a sample of GRBs observed between 2013 and 2018. This GRB catalog is the result of the MAGIC well-designed and tested follow-up procedure, and it serves as a precursor of GRBs observation with the next generation IACT system, the Cherenkov Telescope Array (CTA). Copyright © 2019, The Authors. All rights reserved.

关键词： Gamma rays

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Childhood adversities and their associations with mental disorders in the World Mental Health International College Student surveys initiative

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Psychiatry research 2025年 351卷

作者： Mathilde M Husky Sue Lee Nancy A Sampson Shelby Borowski Yesica Albor Ahmad N Alhadi Jordi Alonso Nouf K Al-Saud Yasmin A Altwaijri Claes Andersson Lukoye Atwoli Caroline Ayuya Muaka Patricia M Báez-Mansur Laura Ballester Jason Bantjes Harald Baumeister Marcus Bendtsen Corina Benjet Anne H Berman Ronny Bruffaerts Paula Carrasco Silver C N Chan Irina F Cohut María Anabell Covarrubias Díaz Couder Paula Cristóbal-Narváez Marcelo A Crockett Pim Cuijpers Oana A David Dong Dong David D Ebert Carlos G Forero Jorge Gaete Margalida Gili Raúl Gutiérrez-García Josep Maria Haro Penelope Hasking Xanthe Hunt Florence Jaguga Leontien Jansen Álvaro I Langer Irene Léniz Yan Liu Christine Lochner Scarlett Mac-Ginty Vania Martínez Andre Mason Muthoni Mathai Margaret McLafferty Elaine K Murray Catherine M Musyoka Cătălin Nedelcea Daniel Núñez Siobhan M O'Neill José A Piqueras Codruta A Popescu Charlene Rapsey Kealagh Robinson Tiscar Rodriguez-Jimenez Wylene Saal Damian Scarf Oi-Ling Siu Dan J Stein Sascha Y Struijs Cristina T Tomoiaga Karla Patricia Valdés-García Eunice Vargas-Contreras Shelby Vereecke Daniel V Vigo Angel Y Wang Samuel Y S Wong Ronald C Kessler Active Team Bordeaux Population Health Research Center INSERM U1219 University of Bordeaux France. Department of Health Care Policy Harvard Medical School Boston MA USA. Center for Global Mental Health Research Instituto Nacional de Psiquiatría Ramón de la Fuente Muñiz Mexico City Mexico. Department of Psychiatry College of Medicine King Saud University Riyadh Saudi Arabia SABIC Psychological Health Research & Applications Chair (SPHRAC) Department of Psychiatry College of Medicine King Saud University Riyadh Saudi Arabia. Health Services Research Group Hospital del Mar Research Institute Barcelona Spain Department of Medicine and Life Sciences Pompeu Fabra University (UPF) Barcelona Spain Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública Instituto de Salud Carlos III (CIBERESP ISCIII) Madrid Spain. Biostatistics Epidemiology and Scientific Computing Department King Faisal Specialist Hospital and Research Centre Riyadh Saudi Arabia. Department of Criminology Malmö University Malmö Sweden. Department of Medicine Medical College East Africa the Aga Khan University Nairobi Kenya Brain and Mind Institute the Aga Khan University Nairobi Kenya Department of Mental Health and Behavioural Sciences Moi University School of Medicine Eldoret Kenya. Department of Psychology & Counselling Daystar University Nairobi Kenya. Coordinación de Desarrollo Académico y Servicios Educativos Universidad la Salle Ciudad Victoria Ciudad Victoria Mexico. Mental Health Alcohol Substance Use and Tobacco Research Unit South African Medical Research Council Cape Town South Africa Department of Psychiatry and Mental Health University of Cape Town Cape Town South Africa. Department of Clinical Psychology and Psychotherapy Ulm University Ulm Germany. Department of Health Medicine and Caring Sciences Linköping University Linkoping Sweden. Department of Psychology Uppsala University Uppsala Sweden. Center for Public Health Psychiatry Department of Neuros

PURPOSE:This study investigates associations of childhood adversities (CAs) with lifetime prevalence, 12-month prevalence, and 12-month persistence of mental disorders in a large cross-national sample of university students. METHODS:data came from epidemiologic surveys carried out by the World Mental Health International College Student (WMH-ICS)Initiative across 18 countries (n=60,719). The web-based surveys screened for lifetime and 12-month prevalence and age-of-onset of common DSM-5 disorders (Major Depressive Disorder, Bipolar I/II Disorder, Generalized Anxiety Disorder, Panic Disorder, Posttraumatic Stress Disorder, Alcohol and Drug Use disorders, Attention-Deficit/Hyperactivity Disorder) and five types of CAs (family dysfunction, emotional abuse, physical abuse, sexual abuse, neglect). Multivariable Poisson regression models estimated associations of CA type, number, and frequency with disorders. RESULTS:The majority of incoming students reported exposure to at least one CA (64.9%), including 50.0 % family dysfunction, 42.2 % emotional abuse, 21.2 % physical abuse, 18.8 % neglect, and 5.0 % sexual abuse. Lifetime and 12-month disorders were significantly associated with CAs in multivariable models, although associations with disorder persistence were weaker. Population attributable risk proportions of 12-month disorders associated with CAs were in the range of 40.7-61.0 % for anxiety and mood disorders and 13.5-55.2 % for substance use disorders. CONCLUSION:Six out of ten university students arrive at university having been exposed to CAs. These students have substantially higher risk of mental disorders than other students, primarily due to associations with lifetime risk rather than persistence. Given the considerable distress and impairment caused by mental disorders, these results underscore the need for primary and secondary prevention efforts.

关键词： ADHD Anxiety Childhood adversities Depression Mental disorders Persistence Substance use disorder university students

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Comparative validation of machine learning algorithms for surgical workflow and skill analysis with the heichole benchmark

arXiv

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arXiv 2021年

作者： Wagner, Martin Müller-Stich, Beat-Peter Kisilenko, Anna Tran, Duc Heger, Patrick Mündermann, Lars Lubotsky, David M. Müller, Benjamin Davitashvili, Tornike Capek, Manuela Reinke, Annika Yu, Tong Vardazaryan, Armine Innocent Nwoye, Chinedu Padoy, Nicolas Liu, Xinyang Lee, Eung-Joo Disch, Constantin Meine, Hans Xia, Tong Jia, Fucang Kondo, Satoshi Reiter, Wolfgang Jin, Yueming Long, Yonghao Jiang, Meirui Dou, Qi Heng, Pheng Ann Twick, Isabell Kirtac, Kadir Hosgor, Enes Bolmgren, Jon Lindström Stenzel, Michael von Siemens, Björn Kenngott, Hannes G. Nickel, Felix von Frankenberg, Moritz Mathis-Ullrich, Franziska Maier-Hein, Lena Speidel, Stefanie Bodenstedt, Sebastian Department for General Visceral and Transplantation Surgery Heidelberg University Hospital Im Neuenheimer Feld 420 Heidelberg69120 Germany Heidelberg Im Neuenheimer Feld 460 Heidelberg69120 Germany Data Assisted Solutions Corporate Research & Technology KARL STORZ SE & Co. KG Dr. Karl-Storz-Str. 34 Tuttlingen78332 Germany Im Neuenheimer Feld 223 Heidelberg69120 Germany Im Neuenheimer Feld 223 Heidelberg69120 Germany Faculty of Mathematics and Computer Science Heidelberg University Im Neuenheimer Feld 205 Heidelberg69120 Germany ICube University of Strasbourg CNRS France 300 bd Sébastien Brant - CS 10413 Illkirch CedexF-67412 France IHU Strasbourg France 1 Place de l'hôpital Strasbourg67000 France Sheikh Zayed Institute for Pediatric Surgical Innovation Children's National Hospital 111 Michigan Ave NW WashingtonDC20010 United States University of Maryland College Park 2405 A V Williams Building College ParkMD20742 United States Fraunhofer Institute for Digital Medicine MEVIS Max-von-Laue-Str. 2 Bremen28359 Germany University of Bremen FB3 Medical Image Computing Group ℅ Fraunhofer MEVIS Am Fallturm 1 Bremen28359 Germany Lab for Medical Imaging and Digital Surgery Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen518055 China Konika Minolta Inc. JP TOWER 2-7-2 Marunouchi Chiyoda-ku Tokyo100-7015 Japan Wintegral GmbH Ehrenbreitsteiner Str. 36 München80993 Germany Department of Computer Science and Engineering Ho Sin-Hang Engineering Building The Chinese University of Hong Kong Sha Tin NT Hong Kong Caresyntax GmbH Komturstr. 18A Berlin12099 Germany Department of Surgery Salem Hospital of the Evangelische Stadtmission Heidelberg Zeppelinstrasse 11-33 Heidelberg69121 Germany Health Robotics and Automation Laboratory Institute for Anthropomatics and Robotics Karlsruhe Institute of Technology Geb. 40.28 KIT Campus Süd Engler-Bunte-Ring 8 Karlsruhe76131 Germany Medical Faculty Heidelberg Uni

PURPOSE: Surgical workflow and skill analysis are key technologies for the next generation of cognitive surgical assistance systems. These systems could increase the safety of the operation through context-sensitive warnings and semi-autonomous robotic assistance or improve training of surgeons via data-driven feedback. In surgical workflow analysis up to 91% average precision has been reported for phase recognition on an open data single-center video dataset. In this work we investigated the generalizability of phase recognition algorithms in a multi-center setting including more difficult recognition tasks such as surgical action and surgical skill. METHODS: To achieve this goal, a dataset with 33 laparoscopic cholecystectomy videos from three surgical centers with a total operation time of 22 hours was created. Labels included framewise annotation of seven surgical phases with 250 phase transitions, 5514 occurences of four surgical actions, 6980 occurences of 21 surgical instruments from seven instrument categories and 495 skill classifications in five skill dimensions. The dataset was used in the 2019 international Endoscopic Vision challenge, sub-challenge for surgical workflow and skill analysis. Here, 12 research teams trained and submitted their machine learning algorithms for recognition of phase, action, instrument and/or skill assessment. RESULTS: F1-scores were achieved for phase recognition between 23.9% and 67.7% (n=9 teams), for instrument presence detection between 38.5% and 63.8% (n=8 teams), but for action recognition only between 21.8% and 23.3% (n=5 teams). The average absolute error for skill assessment was 0.78 (n=1 team). CONCLUSION: Surgical workflow and skill analysis are promising technologies to support the surgical team, but are not solved yet, as shown by our comparison of machine learning algorithms. This novel HeiChole benchmark can be used for comparable evaluation and validation of future work. In future studies, it is of utmost impo

关键词： Learning algorithms

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Utility, Costs and Cost-Utility of Amyloid-PET in the Diagnostic Process of Memory Clinic Patients: A Trial-Based Economic Evaluation From AMYPAD-DPMS

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European journal of neurology 2025年第6期32卷

作者： Ingrid S van Maurik Daniele Altomare Lyduine E Collij Camilia Caprioglio Christian Moro Valentina Garibotto Jean-François Demonet Philip Scheltens Gill Farrer Rosella Gismondi Andrew W Stephens Jean Domingo Gispert José Luis Molinuevo Oriol Grau-Rivera Paul Edison Zuzana Walker Frank Jessen Alexander Dzrezga Philip Zeyen Pierre Payoux Laure Saint-Aubert Julien Delrieu Agneta Nordberg Frederik Barkhof Giovanni B Frisoni Johannes Berkhof Alzheimer Center Amsterdam Neurology Amsterdam UMC Location VUmc Vrije Universiteit Amsterdam the Netherlands. Amsterdam Neuroscience Neurodegeneration Amsterdam the Netherlands. Amsterdam UMC Vrije Universiteit Amsterdam Department of Epidemiology and Data Science Amsterdam Public Health Institute Amsterdam the Netherlands. Northwest Academy Northwest Clinics Alkmaar Alkmaar the Netherlands. Competence Centre on Ageing (CCA) Department of Business Economics Health and Social Care (DEASS) University of Applied Sciences and Arts of Southern Switzerland (SUPSI) Manno Switzerland. Laboratory of Neuroimaging of Aging (LANVIE) University of Geneva Geneva Switzerland. Geneva Memory Center Geneva University Hospitals Geneva Switzerland. Department of Radiology and Nuclear Medicine Amsterdam University Medical Center Amsterdam Neuroscience Amsterdam the Netherlands. Amsterdam Neuroscience Brain Imaging Amsterdam the Netherlands. Division of Nuclear Medicine and Molecular Imaging Department of Medical Imaging University Hospitals of Geneva Geneva Switzerland. NIMTlab Faculty of Medicine Geneva University Geneva Switzerland. CIBM Center for Biomedical Imaging Geneva Switzerland. Leenaards Memory Center Lausanne University Hospital (CHUV) Lausanne Switzerland. EQT Life Sciences Amsterdam the Netherlands. GE Healthcare Amersham UK. Life Molecular Imaging GmbH Berlin Germany. Barcelonaβeta Brain Research Center (BBRC) Pasqual Maragall Foundation Barcelona Spain. Hospital del Mar Medical Research Institute (IMIM) Barcelona Spain. Centro de Investigación Biomédica en Red Bioingeniería Biomateriales y Nanomedicina (CIBER-BBN) Barcelona Spain. H. Lundbeck A/S Copenhagen Denmark. Centro de Investigación Biomédica en Red de Fragilidad y Envejecimiento Saludable (CIBERFES) Madrid Spain. Division of Neurology Department of Brain Sciences Imperial College London UK. Division of Psychiatry University College London London UK. St. Margaret's Hospital Essex Partnership Uni

BACKGROUND:Amyloid positron emission tomography (PET) is instrumental in achieving an accurate diagnosis and may help to limit health-seeking behavior. Currently, amyloid-PET is not routinely used in clinical practice due to lack of evidence on cost-utility. We assessed the cost-utility of early versus no amyloid-PET in the diagnostic work-up of memory clinic patients after 6 months. METHODS:We assessed cost-utility of patients enrolled in AMYPAD-DPMS (EudraCT Number: 2017-002527-21) from six European memory clinics and randomized in ARM1; early amyloid-PET, ARM2; no amyloid-PET or ARM3; (amyloid-PET at request of the managing physician). ARM3 was not part of the cost-utility analysis. The EuroQol classification system (EQ-5D-5L), visual analogue scale (VAS), and ICEpop Capability measure for older people (ICECAP-O) were collected at baseline and 6 months. Costs were calculated from cost diaries at baseline, 3 and 6 months. The incremental cost-effectiveness ratio (ICER) was calculated using EQ-5D-5L and a societal perspective. RESULTS:From April 2018, to October 2020, 844 participants were screened and 840 were randomized (290 ARM1; 270 ARM2 and 280 ARM3). N = 514 (250 ARM1; 264 ARM2) were included in the economic evaluation. Amyloid-PET resulted in higher costs at 6 months (ARM1 vs. ARM2 ∆€1384, bootstrapped 95% CI [7, 2761]). No significant difference in EQ-5D-5L, VAS or ICECAP-O was found. The incremental cost-effectiveness ratio (ICER) was €461,333 per QALY. CONCLUSION:Although patients receive an early etiological diagnosis, the cost-utility after 6 months is not favorable for amyloid-PET. The cost-utility will need to be reassessed when considering amyloid-PET to select patients for anti-amyloid biologics.

关键词： Alzheimer's disease amyloid‐PET cost‐utility early diagnosis

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A Direct Proof of Improved Biased Random Walk with Gastric Cancer dataset

A Direct Proof of Improved Biased Random Walk with Gastric C...

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International Conference on Applied Mathematics & Computer science

作者： Choon Sen Seah Shahreen Kasim Mohd Farhan Md Fudzee Mohd Saberi Mohamad Rd Rohmat Saedudin Deden Witarsyah Rohayanti Hassan Mohd Arfian Ismail Rodziah Atan Soft Computing and Data Mining Centre Faculty of Computer Sciences and Information Technology Universiti Tun Hussein Onn Malaysia Faculty of Creative Technology and Heritage Universiti Malaysia Kelantan School of Industrial Engineering Telkom University Laboratory of Biodiversity and Bioinformatics Universiti Teknologi Malaysia Faculty of Computer Systems and Software Engineering Universiti Malaysia Pahang Department of Software Engineering & Information System Faculty of Computer Science and Information Technology University Putra Malaysia (UPM)

ISBN: (数字)9781728132587

ISBN: (纸本)9781728132594

The relationship between the weight of a single genes and the connection between the genes had been studied. Chemistry and physical sciences have proved the attraction between molecules. Molecules are attracted to each other by bond. This paper is presented to disclose the relationship between weight and connectivity of nodes with biased random walk. An equation of biased random walk which named as significant directed random walk is formed to enhance the connectivity of nodes in directed graph via weigh. To be completely biased to the random walk, references data is implement as directed graph. Weight of genes will be used as one of the parameter in the formula. While the adjacency matrix is further enhanced by Warshall's algorithm to increases the accessibility of nodes via vector. The evolution of random walk is disclosed in this paper as well. Significant directed random walk will be used to prove the importance of weight in this paper. Comparison of the result between biased random walk is presented to prove the enhancement of random walk.

关键词： Biased random walk Cancer classification Gene expression dataset Random walk cancer classification Biased Ganglia one-parameter Mentoring Physical science

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The dynamical state of eROSITA clusters and its impact on the brightest cluster galaxy luminosity

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天文学与天体物理 2025年第1期698卷

作者： A. Zenteno M. Kluge R. Kharkrang D. Hernandez-Lang G. Damke A. Saro R. Monteiro-Oliveira E. R. Carrasco M. Salvato J. Comparat M. Fabricius J. Snigula P. Arevalo H. Cuevas J. L. Nilo Castellon A. Ramirez S. Véliz Astudillo M. Landriau A. D. Myers E. Schlafly F. Valdes B. A. Weaver J. J. Mohr S. Grandis M. Klein A. Liu E. Bulbul X. Zhang J. S. Sanders Y. E. Bahar V. Ghirardini M. E. Ramos F. Balzer Cerro Tololo Inter-American Observatory NSF’s National Optical-Infrared Astronomy Research Laboratory Casilla 603 La Serena Chile Max Planck Institute for Extraterrestrial Physics Giessenbachstrasse 1 85748 Garching Germany Université Paris-Saclay CNRS Institut d’Astrophysique Spatiale 91405 Orsay France Faculty of Physics Ludwig-Maximilians-Universität München Scheinerstr. 1 81679 Munich Germany ICSC – Italian Research Center on High Performance Computing Big Data and Quantum Computing Bologna Italy INAF – Osservatorio Astronomico di Trieste via G. B. Tiepolo 11 34143 Trieste Italy IFPU – Institute for Fundamental Physics of the Universe Via Beirut 2 34014 Trieste Italy Astronomy Unit Department of Physics University of Trieste via Tiepolo 11 34131 Trieste Italy INFN – National Institute for Nuclear Physics Via Valerio 2 I-34127 Trieste Italy Institute of Astronomy and Astrophysics Academia Sinica Taipei 10617 Taiwan International Gemini Observatory/NSF NOIRLab Casilla 603 La Serena Chile Instituto de Física y Astronomía Universidad de Valparaíso Gran Bretaña 1111 Valparaíso Chile Millennium Nucleus on Transversal Research and Technology to Explore Supermassive Black Holes (TITANS) Valparaíso Chile Departamento de Astronomía Universidad de La Serena Av. Raúl Bitrán 1305 La Serena Chile Lawrence Berkeley National Laboratory 1 Cyclotron Road Berkeley CA 94720 USA Department of Physics and Astronomy University of Wyoming 1000 E. University Dept. 3905 Laramie WY 82071 USA Space Telescope Science Institute 3700 San Martin Drive Baltimore MD 21218 USA NSF’s National Optical/Infrared Research Laboratory (NOIRLab) 950 N. Cherry Ave Tucson AZ 85732 USA Universität Innsbruck Institut für Astro-und Teilchenphysik Technikerstr. 25/8 6020 Innsbruck Austria

Context. The first Spectrum-Roentgen-Gamma (SRG) eROSITA public release contains 12 247 clusters and groups from its first 6 months of operation. We used the offset between the brightest cluster galaxy (BCG) and the X-ray peak (DBCG − X) to classify the cluster dynamical state of 3946 galaxy clusters and ***. We aim to investigate the evolution of the merger and relaxed cluster distributions with redshift and mass, and the distributions’ impact on the ***. We used the X-ray peak from the eROSITA survey and the BCG position from the LS DR10 optical data, which includes the DECam eROSITA Survey optical data, to measure the DBCG − X offset. We modelled the distribution of DBCG − X, in units of R500, as the sum of two Rayleigh distributions representing the cluster’s relaxed and disturbed populations, and explored their evolution with redshift and mass. To explore the impact of the cluster’s dynamical state on the BCG luminosity, we separated the main sample according to the dynamical state. We defined clusters as relaxed if DBCG − X R500, disturbed if DBCG − X > 0.5R500, and ‘diverse’ if 0.25R500 DBCG − X ***. We find no evolution of the merging fraction with redshift or mass. The width of the relaxed distribution increases with redshift, while the width of the two Rayleigh distributions decreases with mass. The analysis reveals that BCGs in relaxed clusters are brighter than BCGs in both the disturbed and diverse cluster populations. The most significant differences are found for high-mass clusters at higher ***. The results suggest that BCGs in low-mass clusters are less centrally bound than those in high-mass systems, irrespective of the dynamical state. Over time, BCGs in relaxed clusters progressively align with the potential centre. This alignment correlates with their luminosity growth relative to BCGs in dynamically disturbed clusters, underscoring the critical role of the cluster’s dynamical state in regulating BCG ev

关键词： galaxies: clusters: general

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Euclid preparation. Simulations and nonlinearities beyond ΛCDM. 2. Results from non-standard simulations

arXiv

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arXiv 2024年

作者： Rácz, G. Breton, M.-A. Fiorini, B. Le Brun, A.M.C. Winther, H.-A. Sakr, Z. Pizzuti, L. Ragagnin, A. Gayoux, T. Altamura, E. Carella, E. Pardede, K. Verza, G. Koyama, K. Baldi, M. Pourtsidou, A. Vernizzi, F. Adame, A.G. Adamek, J. Avila, S. Carbone, C. Despali, G. Giocoli, C. Hernández-Aguayo, C. Hassani, F. Kunz, M. Li, B. Rasera, Y. Yepes, G. Gonzalez-Perez, V. Corasaniti, P.-S. García-Bellido, J. Hamaus, N. Kiessling, A. Marinucci, M. Moretti, C. Mota, D.F. Piga, L. Pisani, A. Szapudi, I. Tallada-Crespí, P. Aghanim, N. Andreon, S. Baccigalupi, C. Bardelli, S. Bonino, D. Branchini, E. Brescia, M. Brinchmann, J. Camera, S. Capobianco, V. Cardone, V.F. Carretero, J. Casas, S. Castellano, M. Castignani, G. Cavuoti, S. Cimatti, A. Colodro-Conde, C. Congedo, G. Conselice, C.J. Conversi, L. Copin, Y. Courbin, F. Courtois, H.M. Da Silva, A. Degaudenzi, H. De Lucia, G. Douspis, M. Dubath, F. Duncan, C.A.J. Dupac, X. Dusini, S. Ealet, A. Farina, M. Farrens, S. Ferriol, S. Fosalba, P. Frailis, M. Franceschi, E. Fumana, M. Galeotta, S. Gillis, B. Gómez-Alvarez, P. Grazian, A. Grupp, F. Haugan, S.V.H. Holmes, W. Hormuth, F. Hornstrup, A. Ilić, S. Jahnke, K. Jhabvala, M. Joachimi, B. Keihänen, E. Kermiche, S. Kilbinger, M. Kitching, T. Kubik, B. Kurki-Suonio, H. Lilje, P.B. Lindholm, V. Lloro, I. Mainetti, G. Maiorano, E. Mansutti, O. Marggraf, O. Markovic, K. Martinelli, M. Martinet, N. Marulli, F. Massey, R. Medinaceli, E. Mei, S. Mellier, Y. Meneghetti, M. Meylan, G. Moresco, M. Moscardini, L. Niemi, S.-M. Padilla, C. Paltani, S. Pasian, F. Pedersen, K. Percival, W.J. Pettorino, V. Pires, S. Polenta, G. Poncet, M. Popa, L.A. Raison, F. Rebolo, R. Renzi, A. Rhodes, J. Riccio, G. Romelli, E. Roncarelli, M. Saglia, R. Salvignol, J.-C. Sánchez, A.G. Sapone, D. Sartoris, B. Schirmer, M. Schrabback, T. Secroun, A. Seidel, G. Serrano, S. Sirignano, C. Sirri, G. Stanco, L. Jet Propulsion Laboratory California Institute of Technology 4800 Oak Grove Drive PasadenaCA91109 United States Department of Physics University of Helsinki P.O. Box 64 00014 Finland Campus UAB Carrer de Can Magrans s/n Barcelona08193 Spain Campus UAB Carrer de Can Magrans s/n Cerdanyola del Vallés Barcelona08193 Spain Laboratoire Univers et Théorie Observatoire de Paris Université PSL Université Paris Cité CNRS Meudon92190 France Institute of Cosmology and Gravitation University of Portsmouth PortsmouthPO1 3FX United Kingdom School of Physics and Astronomy Queen Mary University of London Mile End Road LondonE1 4NS United Kingdom Institut d’Astrophysique de Paris UMR 7095 CNRS Sorbonne Université 98 bis boulevard Arago Paris75014 France Institute of Theoretical Astrophysics University of Oslo P.O. Box 1029 Blindern Oslo0315 Norway Institut für Theoretische Physik University of Heidelberg Philosophenweg 16 Heidelberg69120 Germany Université de Toulouse CNRS UPS CNES 14 Av. Edouard Belin Toulouse31400 France Université St Joseph Faculty of Sciences Beirut Lebanon Dipartimento di Fisica "G. Occhialini" Università degli Studi di Milano Bicocca Piazza della Scienza 3 Milano20126 Italy INAF-Osservatorio di Astrofisica e Scienza dello Spazio di Bologna Via Piero Gobetti 93/3 Bologna40129 Italy IFPU Institute for Fundamental Physics of the Universe via Beirut 2 Trieste34151 Italy Dipartimento di Fisica e Astronomia "Augusto Righi" Alma Mater Studiorum Università di Bologna via Piero Gobetti 93/2 Bologna40129 Italy ICSC - Centro Nazionale di Ricerca in High Performance Computing Big Data e Quantum Computing Via Magnanelli 2 Bologna Italy Jodrell Bank Centre for Astrophysics Department of Physics and Astronomy University of Manchester Oxford Road ManchesterM13 9PL United Kingdom INAF-IASF Milano Via Alfonso Corti 12 Milano20133 Italy Dipartimento di Fisica "Aldo Pontremoli" Università degli Studi di Milano Via Celoria 16

The Euclid mission will measure cosmological parameters with unprecedented precision. To distinguish between cosmological models, it is essential to generate realistic mock observables from cosmological simulations that were run in both the standard Λ-cold-dark-matter (ΛCDM) paradigm and in many non-standard models beyond ΛCDM. We present the scientific results from a suite of cosmological N-body simulations using non-standard models including dynamical dark energy, k-essence, interacting dark energy, modified gravity, massive neutrinos, and primordial non-Gaussianities. We investigate how these models affect the large-scale-structure formation and evolution in addition to providing synthetic observables that can be used to test and constrain these models with Euclid data. We developed a custom pipeline based on the Rockstar halo finder and the nbodykit large-scale structure toolkit to analyse the particle output of non-standard simulations and generate mock observables such as halo and void catalogues, mass density fields, and power spectra in a consistent way. We compare these observables with those from the standard ΛCDM model and quantify the deviations. We find that non-standard cosmological models can leave significant imprints on the synthetic observables that we have generated. Our results demonstrate that non-standard cosmological N-body simulations provide valuable insights into the physics of dark energy and dark matter, which is essential to maximising the scientific return of Euclid. © 2024, CC BY.

关键词： Dark energy

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