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20th Annual Conference on Research in Computational Molecular Biology, RECOMB 2016

作者： Sahlin, Kristoffer Frånberg, Mattias Arvestad, Lars KTH Royal Institute of Technology Science for Life Laboratory School of Computer Science and Communication Stockholm Sweden Atherosclerosis Research Unit Department of Medicine Solna Sweden Karolinska Institutet Stockholm Sweden Department of Numerical Analysis and Computer Science Stockholm University Stockholm Sweden Stockholm Sweden

ISBN: (纸本)9783319319568

Reads from paired-end and mate-pair libraries are often utilized to find structural variation in genomes, and one common approach is to use their fragment length for detection. After aligning readpairs to the reference, read-pair distances are analyzed for statistically significant deviations. However, previously proposed methods are based on a simplified model of observed fragment lengths that does not agree with data. We show how this model limits statistical analysis of identifying variants and propose a new model, by adapting a model we have previously introduced for contig scaffolding, which agrees with data. From this model we derive an improved null hypothesis that, when applied in the variant caller CLEVER, reduces the number of false positives and corrects a bias that contributes to more deletion calls than insertion calls. A reference implementation is freely available at https://***/ksahlin/GetDistr. © Springer International Publishing Switzerland 2016.

关键词： Scaffolds

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The Liver Tumor Segmentation Benchmark (LiTS)

arXiv

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arXiv 2019年

作者： Bilic, Patrick Christ, Patrick Li, Hongwei Bran Vorontsov, Eugene Ben-Cohen, Avi Kaissis, Georgios Szeskin, Adi Jacobs, Colin Mamani, Gabriel Efrain Humpire Chartrand, Gabriel Lohöfer, Fabian Holch, Julian Walter Sommer, Wieland Hofmann, Felix Hostettler, Alexandre Lev-Cohain, Naama Drozdzal, Michal Amitai, Michal Marianne Vivanti, Refael Sosna, Jacob Ezhov, Ivan Sekuboyina, Anjany Navarro, Fernando Kofler, Florian Paetzold, Johannes C. Shit, Suprosanna Hu, Xiaobin Lipková, Jana Rempfler, Markus Piraud, Marie Kirschke, Jan Wiestler, Benedikt Zhang, Zhiheng Hülsemeyer, Christian Beetz, Marcel Ettlinger, Florian Antonelli, Michela Bae, Woong Bellver, Míriam Bi, Lei Chen, Hao Chlebus, Grzegorz Dam, Erik B. Dou, Qi Fu, Chi-Wing Georgescu, Bogdan Giró-I-Nieto, Xavier Gruen, Felix Han, Xu Heng, Pheng-Ann Hesser, Jürgen Moltz, Jan Hendrik Igel, Christian Isensee, Fabian Jäger, Paul Jia, Fucang Kaluva, Krishna Chaitanya Khened, Mahendra Kim, Ildoo Kim, Jae-Hun Kim, Sungwoong Kohl, Simon Konopczynski, Tomasz Kori, Avinash Krishnamurthi, Ganapathy Li, Fan Li, Hongchao Li, Junbo Li, Xiaomeng Lowengrub, John Ma, Jun Maier-Hein, Klaus Maninis, Kevis-Kokitsi Meine, Hans Merhof, Dorit Pai, Akshay Perslev, Mathias Petersen, Jens Pont-Tuset, Jordi Qi, Jin Qi, Xiaojuan Rippel, Oliver Roth, Karsten Sarasua, Ignacio Schenk, Andrea Shen, Zengming Torres, Jordi Wachinger, Christian Wang, Chunliang Weninger, Leon Wu, Jianrong Xu, Daguang Yang, Xiaoping Yu, Simon Chun-Ho Yuan, Yading Yue, Miao Zhang, Liping Cardoso, Jorge Bakas, Spyridon Braren, Rickmer Heinemann, Volker Pal, Christopher Tang, An Kadoury, Samuel Soler, Luc van Ginneken, Bram Greenspan, Hayit Joskowicz, Leo Menze, Bjoern Department of Informatics Technical University of Munich Germany Department of Quantitative Biomedicine University of Zurich Switzerland Ecole Polytechnique de Montréal Canada Department of Medical Imaging Radboud University Medical Center Nijmegen Netherlands Department of Biomedical Engineering Tel-Aviv University Israel Germany Pattern Analysis and Learning Group Department of Radiation Oncology Heidelberg University Hospital Heidelberg Germany Philips Research China Philips China Innovation Campus Shanghai China School of Biomedical Engineering & Imaging Sciences King0s College London London United Kingdom Institute for AI in Medicine Technical University of Munich Germany Department of Computer Science Guangdong University of Foreign Studies China Institute for diagnostic and interventional radiology Klinikum rechts der Isar Technical University of Munich Germany Institute for Diagnostic and Interventional Neuroradiology Klinikum Rechts der Isar Technical University of Munich Germany Department of Hepatobiliary Surgery The Affiliated Drum Tower Hospital Nanjing University Medical School China Department of Computing Imperial College London London United Kingdom Institute for Tissue Engineering and Regenerative Medicine Helmholtz Zentrum München Neuherberg Germany Brigham and Women's Hospital Harvard Medical School United States School of Computer Science and Engineering The Hebrew University of Jerusalem Israel University of Pennsylvania PA United States Pte. Ltd. Singapore Medical Imaging and Reconstruction Lab Department of Engineering Design Indian Institute of Technology Madras India Sensetime Shanghai China Department of Radiology Perelman School of Medicine University of Pennsylvania United States Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania PA United States Co. Ltd China MontréalQC Canada Department of Radiology Radiation Oncology and Nuclear Medicine University of Montréal

In this work, we report the set-up and results of the Liver Tumor Segmentation Benchmark (LiTS), which was organized in conjunction with the IEEE International Symposium on Biomedical Imaging (ISBI) 2017 and the International Conferences on Medical Image computing and Computer-Assisted Intervention (MICCAI) 2017 and 2018. The image dataset is diverse and contains primary and secondary tumors with varied sizes and appearances with various lesion-to-background levels (hyper-/hypo-dense), created in collaboration with seven hospitals and research institutions. Seventy-five submitted liver and liver tumor segmentation algorithms were trained on a set of 131 computed tomography (CT) volumes and were tested on 70 unseen test images acquired from different patients. We found that not a single algorithm performed best for both liver and liver tumors in the three events. The best liver segmentation algorithm achieved a Dice score of 0.963, whereas, for tumor segmentation, the best algorithms achieved Dices scores of 0.674 (ISBI 2017), 0.702 (MICCAI 2017), and 0.739 (MICCAI 2018). Retrospectively, we performed additional analysis on liver tumor detection and revealed that not all top-performing segmentation algorithms worked well for tumor detection. The best liver tumor detection method achieved a lesion-wise recall of 0.458 (ISBI 2017), 0.515 (MICCAI 2017), and 0.554 (MICCAI 2018), indicating the need for further research. LiTS remains an active benchmark and resource for research, e.g., contributing the liver-related segmentation tasks in http://***/. In addition, both data and online evaluation are accessible via ***. © 2019, CC BY-NC-ND.

关键词： Deep learning

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The global spectrum of tree crown architecture

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Nature communications 2025年第1期16卷 4876页

作者： Tommaso Jucker Fabian Jörg Fischer Jérôme Chave David A Coomes John Caspersen Arshad Ali Grace Jopaul Loubota Panzou Ted R Feldpausch Daniel Falster Vladimir A Usoltsev Toby D Jackson Stephen Adu-Bredu Luciana F Alves Mohammad Aminpour Bhely Angoboy Ilondea Niels P R Anten Cécile Antin Yousef Askari Narayanan Ayyappan Lindsay F Banin Nicolas Barbier John J Battles Hans Beeckman Yannick E Bocko Ben Bond-Lamberty Frans Bongers Samuel Bowers Michiel van Breugel Arthur Chantrain Rajeev Chaudhary Jingyu Dai Michele Dalponte Kangbéni Dimobe Jean-Christophe Domec Jean-Louis Doucet Juan Manuel Dupuy Rada Remko A Duursma Moisés Enríquez Karin Y van Ewijk William Farfán-Rios Adeline Fayolle Marco Ferretti Eric Forni David I Forrester Hammad Gilani John L Godlee Matthias Haeni Jefferson S Hall Jie-Kun He Andreas Hemp José L Hernández-Stefanoni Steven I Higgins Robert J Holdaway Kiramat Hussain Lindsay B Hutley Tomoaki Ichie Yoshiko Iida Hai-Sheng Jiang Puspa Raj Joshi Hasan Kaboli Maryam Kazempour Larsary Tanaka Kenzo Brian D Kloeppel Takashi S Kohyama Suwash Kunwar Shem Kuyah Jakub Kvasnica Siliang Lin Emily R Lines Hongyan Liu Craig Lorimer Jean-Joël Loumeto Yadvinder Malhi Peter L Marshall Eskil Mattsson Radim Matula Jorge A Meave Sylvanus Mensah Xiangcheng Mi Stéphane T Momo Glenn R Moncrieff Francisco Mora Rodrigo Muñoz Sarath P Nissanka Zamah Shari Nur Hajar Kevin L O'Hara Steven Pearce Raphaël Pelissier Pablo L Peri Pierre Ploton Lourens Poorter Mohsen Javanmiri Pour Hassan Pourbabaei Sabina C Ribeiro Casey Ryan Anvar Sanaei Jennifer Sanger Michael Schlund Giacomo Sellan Alexander Shenkin Bonaventure Sonké Frank J Sterck Martin Svátek Kentaro Takagi Anna T Trugman Matthew A Vadeboncoeur Ahmad Valipour Mark C Vanderwel Alejandra G Vovides Peter Waldner Weiwei Wang Li-Qiu Wang Christian Wirth Murray Woods Wenhua Xiang Fabiano de Aquino Ximenes Yaozhan Xu Toshihiro Yamada Miguel A Zavala Niklaus E Zimmermann School of Biological Sciences University of Bristol Bristol BS8 1TQ UK. t.jucker@bristol.ac.uk. School of Biological Sciences University of Bristol Bristol BS8 1TQ UK. UMR5300 Centre de Recherche sur la Biodiversité et l'Environnement CNRS INPT IRD Université de Toulouse Bât 4R1 118 route de Narbonne 31062 Toulouse France. Conservation Research Institute University of Cambridge Cambridge CB2 3EA UK. Institute of Forestry and Conservation University of Toronto 33 Willcocks Street Toronto ON M5S 3B3 Canada. Forest Ecology Research Group College of Life Sciences Hebei University Baoding 071002 Hebei China. Institut Supérieur des Sciences Géographiques Environnementales et de l'Aménagement (ISSGEA) Université DENIS SASSOU-N'GUESSO Kintélé République du Congo. Laboratoire de Biodiversité de Gestion des Ecosystèmes et de l'Environnement (LBGE) Faculté des Sciences et Techniques Université Marien NGOUABI BP 69 Brazzaville Brazzaville République du Congo. Faculty of Environment Science and Economy University of Exeter Exeter EX4 4QE UK. Evolution & Ecology Research Centre University of New South Wales Sydney NSW Sydney Australia. Department of Forest Mensuration and Management Ural State Forest Engineering and Economic University Yekaterinburg Russia. Forestry Research Institute of Ghana Council for Scientific and Industrial Research University Kumasi Ghana. Center for Tropical Research Institute of the Environment and Sustainability University of California Los Angeles Los Angeles CA USA. Natural Recourses and Watershed Management Office West Azerbaijan Province Urmia Iran. Institut National pour l'Etude et la Recherche Agronomiques BP 2037 Kinshasa Democratic Republic of the Congo. Université Pédagogique Nationale BP 8815 Kinshasa-Ngaliema Democratic Republic of the Congo. Center for Crop Systems Analysis Wageningen University & Research Wageningen Netherlands. AMAP lab Montpellier University IRD CIRAD CNRS INRAE Montpellier France. Rese

Trees can differ enormously in their crown architectural traits, such as the scaling relationships between tree height, crown width and stem diameter. Yet despite the importance of crown architecture in shaping the structure and function of terrestrial ecosystems, we lack a complete picture of what drives this incredible diversity in crown shapes. Using data from 374,888 globally distributed trees, we explore how climate, disturbance, competition, functional traits, and evolutionary history constrain the height and crown width scaling relationships of 1914 tree species. We find that variation in height-diameter scaling relationships is primarily controlled by water availability and light competition. Conversely, crown width is predominantly shaped by exposure to wind and fire, while also covarying with functional traits related to mechanical stability and photosynthesis. Additionally, we identify several plant lineages with highly distinctive stem and crown forms, such as the exceedingly slender dipterocarps of Southeast Asia, or the extremely wide crowns of legume trees in African savannas. Our study charts the global spectrum of tree crown architecture and pinpoints the processes that shape the 3D structure of woody ecosystems.

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Characterising acute and chronic care needs: insights from the Global Burden of Disease Study 2019

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Nature communications 2025年第1期16卷 4235-4235页

作者： Cecilia Anza-Ramirez J. Jaime Miranda Benedetta Armocida Jorge César Correia Harriette Gillian Christine Van Spall David Beran Amirali Aali Kalkidan Hassen Abate Semagn Mekonnen Abate Cristiana Abbafati Mohsen Abbasi-Kangevari Zeinab Abbasi-Kangevari Zahra Aryan Sina Azadnajafabad Mohammadreza Azangou-Khyavy Seyyed-Hadi Ghamari Mohammad Keykhaei Javad Khanali Sara Momtazmanesh Fateme Montazeri Shayan Rahmani Mohammad-Mahdi Rashidi Nazila Rezaei Negar Rezaei Sahar Saeedi Moghaddam Hossein Hassanian-Moghaddam Ali-Asghar Kolahi Ali Nikoobar Hedayat Abbastabar Ahmed M. Abdel-Azeem Michael Abdelmasseh Juan Sanabria Sherief Abd-Elsalam Ahmed Abdelwahab Gholamreza Abdoli Mohammad Abdollahi Meriem Abdoun Deldar Morad Abdulah Abu Yousuf Md Abdullah Ame Mehadi Abdurehman Getachew Abebe Aidin Abedi Chirag P. Doshi Vida Abedi Hassan Abidi Richard Gyan Aboagye Hassan Abolhassani Nima Rezaei Lucas Guimarães Abreu Michael R. M. Abrigo Yonas Derso Abtew Hiwa Abubaker Ali Eman Abu-Gharbieh Hiba Jawdat Barqawi Rabih Halwani Maha Mohamed Saber-Ayad Iman M. Talaat Ahmed Abu-Zaid Manfred Mario Kokou Accrombessi Juan Manuel Acuna Denberu Eshetie Adane Tigist Demssew Adane Isaac Yeboah Addo Giovanni Addolorato Oluwafemi Atanda Adeagbo Victor Adekanmbi Miracle Ayomikun Adesina Isaac Iyinoluwa Olufadewa Olatunji O. Adetokunboh Daniel Adedayo Adeyinka Qorinah Estiningtyas Sakilah Adnani Aanuoluwapo Adeyimika Afolabi Olayinka Stephen Ilesanmi Muhammad Sohail Afzal Saira Afzal Gina Agarwal Prerna Agarwal Pradyumna Agasthi Anurag Agrawal Marcela Agudelo-Botero Adolfo Martinez-Valle Bright Opoku Ahinkorah Aqeel Ahmad Sajjad Ahmad Sohail Ahmad Tauseef Ahmad Ali Ahmadi Siamak Sabour Keivan Ahmadi Sanjay Basu Sepideh Ahmadi Ali Ahmed Shaun Wen Huey Lee Ayman Ahmed Haroon Ahmed Jivan Qasim Ahmed Gahin Abdulraheem Tayib Yahya Yahya Luai A. Ahmed Iffat Elbarazi Syed Mahboob Shah Janardhana P. Aithala Marjan Ajami Budi Aji Hossein Akbarialiabad Yibeltal Akelew Meisam Akhlaghdoust Elham Jamshidi Addis Aklilu Azene Tesfaye Melat Woldemariam Maxwell Ak CRONICAS Center of Excellence in Chronic Diseases Universidad Peruana Cayetano Heredia Lima Peru School of Medicine Universidad Peruana Cayetano Heredia Lima Peru Sydney School of Public Health Faculty of Medicine and Health University of Sydney Sydney NSW Australia Faculty of Epidemiology and Population Health London School of Hygiene & Tropical Medicine London UK Division of Tropical and Humanitarian Medicine University of Geneva Geneva Switzerland Department of Cardiovascular Endocrine-metabolic Diseases and Aging Istituto Superiore di Sanità Rome Italy Division of Endocrinology Diabetology Nutrition and Therapeutic Patient Education Department of Medicine Geneva University Hospitals Geneva Switzerland Department of Medicine and Department of Health Research Evidence and Impact McMaster University Hamilton ON Canada Research Institute of St. Joe’s Hamilton ON Canada Population Health Research Institute Hamilton Canada Geneva University Hospitals Geneva Switzerland Faculty of Medicine Mashhad University of Medical Sciences Mashhad Iran Department of Nutrition and Dietetics Jimma University Jimma Ethiopia Anesthesiology Department Dilla University Addis Ababa Ethiopia Department of Juridical and Economic Studies La Sapienza University Rome Italy Non-Communicable Diseases Research Center Tehran University of Medical Sciences Tehran Iran Social Determinants of Health Research Center Shahid Beheshti University of Medical Sciences Tehran Iran Brigham and Women’s Hospital Harvard University Boston MA USA Students’ Scientific Research Center (SSRC) Tehran University of Medical Sciences Tehran Iran School of Medicine Tehran University of Medical Sciences Tehran Iran School of Medicine Shahid Beheshti University of Medical Sciences Tehran Iran Endocrinology and Metabolism Research Institute Tehran University of Medical Sciences Tehran Iran Chapter of Addiction Medicine University of Sydney Sydney NSW Australia Advanced Diagnostic and Intervent

Chronic care manages long-term, progressive conditions, while acute care addresses short-term conditions. Chronic conditions increasingly strain health systems, which are often unprepared for these demands. This study examines the burden of conditions requiring acute versus chronic care, including sequelae. Conditions and sequelae from the Global Burden of Diseases Study 2019 were classified into acute or chronic care categories. Data were analysed by age, sex, and socio-demographic index, presenting total numbers and contributions to burden metrics such as Disability-Adjusted Life Years (DALYs), Years Lived with Disability (YLD), and Years of Life Lost (YLL). Approximately 68% of DALYs were attributed to chronic care, while 27% were due to acute care. Chronic care needs increased with age, representing 86% of YLDs and 71% of YLLs, and accounting for 93% of YLDs from sequelae. These findings highlight that chronic care needs far exceed acute care needs globally, necessitating health systems to adapt accordingly. © 2025. The Author(s).

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Genetic analysis of over 1 million people identifies 535 new loci associated with blood pressure traits (vol 50, pg 1412, 2018)

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NATURE GENETICS 2018年第12期50卷 1755-1755页

作者： Evangelou, Evangelos Warren, Helen R. Mosen-Ansorena, David Mifsud, Borbala Pazoki, Raha Gao, He Ntritsos, Georgios Dimou, Niki Cabrera, Claudia P. Karaman, Ibrahim Fu Liang Ng Evangelou, Marina Witkowska, Katarzyna Tzanis, Evan Hellwege, Jacklyn N. Giri, Ayush Edwards, Digna R. Velez Sun, Yan V. Cho, Kelly Gaziano, J. Michael Wilson, Peter W. F. Tsao, Philip S. Kovesdy, Csaba P. Esko, Tonu Magi, Reedik Milani, Lili Almgren, Peter Boutin, Thibaud Debette, Stephanie Ding, Jun Giulianini, Franco Holliday, Elizabeth G. Jackson, Anne U. Li-Gao, Ruifang Lin, Wei-Yu Luan, Jian'an Mangino, Massimo Oldmeadow, Christopher Prins, Bram Peter Qian, Yong Sargurupremraj, Muralidharan Shah, Nabi Surendran, Praveen Theriault, Sebastien Verweij, Niek Willems, Sara M. Zhao, Jing-Hua Amouyel, Philippe Connell, John de Mutsert, Renee Doney, Alex S. F. Farrall, Martin Menni, Cristina Morris, Andrew D. Noordam, Raymond Pare, Guillaume Poulter, Neil R. Shields, Denis C. Stanton, Alice Thom, Simon Abecasis, Goncalo Amin, Najaf Arking, Dan E. Ayers, Kristin L. Barbieri, Caterina M. Batini, Chiara Bis, Joshua C. Blake, Tineka Bochud, Murielle Boehnke, Michael Boerwinkle, Eric Boomsma, Dorret I. Bottinger, Erwin P. Braund, Peter S. Brumat, Marco Campbell, Archie Campbell, Harry Chakravarti, Aravinda Chambers, John C. Chauhan, Ganesh Ciullo, Marina Cocca, Massimiliano Collins, Francis Cordell, Heather J. Davies, Gail de Borst, Martin H. de Geus, Eco J. Deary, Ian J. Deelen, Joris Del Greco, Fabiola M. Demirkale, Cumhur Yusuf Dorr, Marcus Ehret, Georg B. Elosua, Roberto Enroth, Stefan Erzurumluoglu, A. Mesut Ferreira, Teresa Franberg, Mattias Franco, Oscar H. Gandin, Ilaria Gasparini, Paolo Giedraitis, Vilmantas Gieger, Christian Girotto, Giorgia Goel, Anuj Gow, Alan J. Gudnason, Vilmundur Guo, Xiuqing Gyllensten, Ulf Hamsten, Anders Harris, Tamara B. Harris, Sarah E. Hartman, Catharina A. Havulinna, Aki S. Hicks, Andrew A. Hofer, Edith Hofman, Albert Hottenga, Jouke-Jan Huffman, Jennifer E. Hwang, Shih-Jen Ingelsson, Erik James, Alan Jansen Department of Epidemiology and Biostatistics Imperial College London London UK Department of Hygiene and Epidemiology University of Ioannina Medical School Ioannina Greece William Harvey Research Institute Barts and The London School of Medicine and Dentistry Queen Mary University of London London UK National Institute for Health Research Barts Cardiovascular Biomedical Research Center Queen Mary University of London London UK MRC-PHE Centre for Environment and Health Imperial College London London UK Department of Mathematics Imperial College London London UK Division of Epidemiology Department of Medicine Institute for Medicine and Public Health Vanderbilt Genetics Institute Vanderbilt University Medical Center Tennessee Valley Healthcare System (626)/Vanderbilt University Nashville TN USA Vanderbilt Genetics Institute Vanderbilt Epidemiology Center Department of Obstetrics and Gynecology Vanderbilt University Medical Center Tennessee Valley Health Systems VA Nashville TN USA Department of Epidemiology Emory University Rollins School of Public Health Atlanta GA USA Department of Biomedical Informatics Emory University School of Medicine Atlanta GA USA Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC) VA Boston Healthcare System Boston MA USA Division of Aging Department of Medicine Brigham and Women’s Hospital Department of Medicine Harvard Medical School Boston MA USA Atlanta VAMC and Emory Clinical Cardiovascular Research Institute Atlanta GA USA VA Palo Alto Health Care System Division of Cardiovascular Medicine Stanford University School of Medicine Stanford CA USA Nephrology Section Memphis VA Medical Center and University of Tennessee Health Science Center Memphis TN USA Estonian Genome Center University of Tartu Tartu Estonia Program in Medical and Population Genetics Broad Institute of Harvard and MIT Cambridge MA USA Department Clinical Sciences Malmö Lund University Malmö Sweden MRC Human Genetics Un

High blood pressure is a highly heritable and modifiable risk factor for cardiovascular disease. We report the largest genetic association study of blood pressure traits (systolic, diastolic and pulse pressure) to date in over 1 million people of European ancestry. We identify 535 novel blood pressure loci that not only offer new biological insights into blood pressure regulation but also highlight shared genetic architecture between blood pressure and lifestyle exposures. Our findings identify new biological pathways for blood pressure regulation with potential for improved cardiovascular disease prevention in the future.

关键词： Cardiovascular diseases Genome informatics Genome-wide association studies

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26th Annual Computational Neuroscience Meeting (CNS*2017) of the Organization for Computational Neuroscience Antwerp, Belgium, July 15-20, 2017

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BMC NEUROscience 2017年第SUPPL 1期18卷 59-59页

作者： [Anonymous] Indiana University Purdue University Indianapolis Indianapolis IN 46032 USA Stark Neurosciences Research Institute Indiana University School of Medicine Indianapolis IN 46032 USA Department of Mathematics East Carolina University Greenville NC 27858 USA Jülich Supercomputing Centre Forschungszentrum Jülich 52425 Jülich Germany Future Systems Swiss National Supercomputing Centre 8092 Zurich Switzerland User Engagement and Support Swiss National Supercomputing Centre 6900 Lugano Switzerland Institut de Neurosciences des Systèmes Aix Marseille Univ 13005 Marseille France Simulation Lab Neuroscience Forschungszentrum Jülich Jülich Germany Department of Experimental Psychology Ghent University 9000 Ghent Belgium Donders Center for Cognitive Neuroimaging Radboud University 6525HR Nijmegen The Netherlands Department of Electrical Computer and Energy Engineering University of Colorado Boulder CO 80309 USA Department of Neurosurgery Johns Hopkins School of Medicine Baltimore MD 21287 USA Department of Neurology Johns Hopkins School of Medicine Baltimore MD 21287 USA Department of Otolaryngology Johns Hopkins School of Medicine Baltimore MD 21287 USA INSERM U968 Paris France Sorbonne Universités UPMC University Paris 06 UMR_S 968 Institut de la Vision Paris France CNRS UMR_7210 Paris France Department of Computer Architecture and Technology University of Granada (CITIC) Granada Spain Sorbonne Universités UPMC Univ Paris 06 INSERM CNRS Institut de la Vision Paris France Department of Adaptive Machine Systems Osaka University Osaka Japan Department of Computer Science University of Cergy-Pontoise Cergy-Pontoise France Department of Physics and Astronomy College of Charleston Charleston SC 29424 USA School of Physics Faculty of Science University of Sydney Sydney NSW 2006 Australia Center of Excellence for Integrative Brain Function Australian Research Council Sydney Australia Max Planck Institute for Human Cognitive and Brain Sciences Saxony Lei

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Consolidation of concentrated suspensions – numerical simulations using a two-phase fluid model

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computing and Visualization in science 2014年第1期3卷 39-45页

作者： Gustavsson, Katarina Oppelstrup, Jesper Department of Numerical Analysis and Computing Science Royal Institute of Technology S-100 44 Stockholm Sweden SE

We investigate numerically a mathematical model of a consolidation process of a dense, flocculated suspension. The suspension is treated as a two-constituent mixture of a fluid and solid particles by an Eulerian two-phase fluid model. We characterize the suspension by constitutive relations concerning the stresses, interaction forces and inter-particle forces. A numerical solver for a two dimensional test case is developed using finite difference methods both in time and space. In the numerical experiments, the suspension is confined to a closed box and consolidates due to a constant gravity field directed toward the bottom. To study the effect of shear, 2D simulations are performed where the bottom wall of the box is moving with a constant speed.

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A finite element based level-set method for multiphase flow applications

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computing and Visualization in science 2014年第1期3卷 93-101页

作者： Anna-Karin Tornberg Björn Engquist Department of Numerical Analysis and Computing Science Royal Institute of Technology S-100 44 Stockholm Sweden (e-mail: annak@nada.kth.se/engquist@nada.kth.se) SE

A numerical method for simulating incompressible two-dimensional multiphase flow is presented. The method is based on a level-set formulation discretized by a finite-element technique. The treatment of the specific features of this problem, such as surface tension forces acting at the interfaces separating two immiscible fluids, as well as the density and viscosity jumps that in general occur across such interfaces, have been integrated into the finite-element framework. Using a method based on the weak formulation of the Navier-Stokes equations has its advantages. In this formulation, the singular surface tension forces are included through line integrals along the interfaces, which are easily approximated quantities. In addition, differentiation of the discontinuous viscosity is avoided. The discontinuous density and viscosity are included in the finite element integrals. A strategy for the evaluation of integrals with discontinuous integrands has been developed based on a rigorous analysis of the errors associated with the evaluation of such integrals. numerical tests have been performed. For the case of a rising buoyant bubble the results are in good agreement with results from a front-tracking method. The run presented here is a run including topology changes, where initially separated areas of one fluid merge in different stages due to buoyancy effects.

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Signature of an anticipatory response in area VI as modeled by a probabilistic model and a spiking neural network

Signature of an anticipatory response in area VI as modeled ...

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2014 International Joint Conference on Neural Networks, IJCNN 2014

作者： Kaplan, Bernhard A. Khoei, Mina A. Lansner, Anders Perrinet, Laurent U. Department of Computational Biology Royal Institute of Technology Stockholm Sweden Institut de Neurosciences de la Timone UMR 7289 CNRS - Aix-Marseille Université Marseille France Stockholm Brain Institute Karolinska Institute Stockholm Sweden Department of Numerical Analysis and Computer Science Stockholm University Stockholm Sweden

ISBN: (纸本)9781479914845

As it is confronted to inherent neural delays, how does the visual system create a coherent representation of a rapidly changing environment? In this paper, we investigate the role of motion-based prediction in estimating motion trajectories compensating for delayed information sampling. In particular, we investigate how anisotropic diffusion of information may explain the development of anticipatory response as recorded in a neural populations to an approaching stimulus. We validate this using an abstract probabilistic framework and a spiking neural network (SNN) model. Inspired by a mechanism proposed by Nijhawan [1], we first use a Bayesian particle filter framework and introduce a diagonal motion-based prediction model which extrapolates the estimated response to a delayed stimulus in the direction of the trajectory. In the SNN implementation, we have used this pattern of anisotropic, recurrent connections between excitatory cells as mechanism for motion-extrapolation. Consistent with recent experimental data collected in extracellular recordings of macaque primary visual cortex [2], we have simulated different trajectory lengths and have explored how anticipatory responses may be dependent on the information accumulated along the trajectory. We show that both our probabilistic framework and the SNN model can replicate the experimental data qualitatively. Most importantly, we highlight requirements for the development of a trajectory-dependent anticipatory response, and in particular the anisotropic nature of the connectivity pattern which leads to the motion extrapolation mechanism. © 2014 IEEE.

关键词： Extrapolation

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On Diffuse Interface Modeling and Simulation of Surfactants in Two-Phase Fluid Flow

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Communications in Computational Physics 2013年第9期14卷 879-915页

作者： Stefan Engblom Minh Do-Quang Gustav Amberg Anna-Karin Tornberg Division of Scientific Computing Department of Information TechnologyUppsala UniversitySE-75105 UppsalaSweden Linne Flow Centre Department of MechanicsSchool of Engineering ScienceRoyal Institute of TechnologyS-10044 StockholmSweden Linne Flow Centre Department of Numerical AnalysisSchool of Computer Science and CommunicationRoyal Institute of TechnologyS-10044 StockholmSweden

An existing phase-fieldmodel of two immiscible fluids with a single soluble surfactant present is discussed in *** analyze the well-posedness of the model and provide strong evidence that it is mathematically ill-posed for a large set of physically relevant *** a consequence,critical modifications to the model are suggested that substantially increase the domain of *** designed numerical simulations offer informative demonstrations as to the sharpness of our theoretical results and the qualities of the physical model.A fully coupled hydrodynamic test-case demonstrates the potential to capture also non-trivial effects on the overall flow.

关键词： Phase-field model Cahn-Hilliard equation surface active agent Ginzburg-Landau free energy well-posedness

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