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arXiv 2019年

作者： Luo, Yong Wen, Yonggang Tao, Dacheng Gui, Jie Xu, Chao School of Electronics Engineering and Computer Science Peking University Beijing China Division of Networks and Distributed Systems School of Computer Engineering Nanyang Technological University Singapore Centre for Quantum Computation & Intelligent Systems Faculty of Engineering & Information Technology University of Technology Sydney Sydney Australia Centre for Quantum Computation & Intelligent Systems Faculty of Engineering and Information Technology University of Technology Sydney 81 Broadway Street UltimoNSW2007 Australia Hefei Institute of Intelligent Machines Chinese Academy of Sciences Hefei230031 China Center for Research on Intelligent Perception and Computing National Laboratory of Pattern Recognition Institute of Automation Chinese Academy of Sciences Beijing100190 China

The features used in many image analysis-based applications are frequently of very high dimension. Feature extraction offers several advantages in high-dimensional cases, and many recent studies have used multi-task feature extraction approaches, which often outperform single-task feature extraction approaches. However, most of these methods are limited in that they only consider data represented by a single type of feature, even though features usually represent images from multiple modalities. We therefore propose a novel large margin multi-modal multi-task feature extraction (LM3FE) framework for handling multi-modal features for image classification. In particular, LM3FE simultaneously learns the feature extraction matrix for each modality and the modality combination coefficients. In this way, LM3FE not only handles correlated and noisy features, but also utilizes the complementarity of different modalities to further help reduce feature redundancy in each modality. The large margin principle employed also helps to extract strongly predictive features so that they are more suitable for prediction (e.g., classification). An alternating algorithm is developed for problem optimization and each sub-problem can be efficiently solved. Experiments on two challenging real-world image datasets demonstrate the effectiveness and superiority of the proposed method. Copyright © 2019, The Authors. All rights reserved.

关键词： Feature extraction

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The Brain Tumor Sequence Registration (BraTS-Reg) Challenge: Establishing Correspondence Between Pre-Operative and Follow-up MRI Scans of Diffuse Glioma Patients

arXiv

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arXiv 2021年

作者： Baheti, Bhakti Chakrabarty, Satrajit Akbari, Hamed Bilello, Michel Wiestler, Benedikt Schwarting, Julian Calabrese, Evan Rudie, Jeffrey Abidi, Syed Mousa, Mina Villanueva-Meyer, Javier Fields, Brandon K.K. Kofler, Florian Shinohara, Russell Takeshi Iglesias, Juan Eugenio Mok, Tony C.W. Chung, Albert C.S. Wodzinski, Marek Jurgas, Artur Marini, Niccolò Atzori, Manfredo Müller, Henning Grosbröhmer, Christoph Siebert, Hanna Hansen, Lasse Heinrich, Mattias P. Canalini, Luca Klein, Jan Gerken, Annika Heldmann, Stefan Hering, Alessa Hahn, Horst K. Meng, Mingyuan Bi, Lei Feng, Dagan Kim, Jinman Zeineldinal, Ramy A. Karar, Mohamed E. Mathis-Ullrich, Franziska Burgert, Oliver Abderezaei, Javid Pionteck, Aymeric Chopra, Agamdeep Kurt, Mehmet Yan, Kewei Yan, Yonghong Tang, Zhe Ma, Jianqiang Nasser, Sahar Almahfouz Kurian, Nikhil Cherian Meena, Mohit Shamsi, Saqib Sethi, Amit Tustison, Nicholas J. Avants, Brian B. Cook, Philip Gee, James C. Tian, Lin Greer, Hastings Niethammer, Marc Hoopesar, Andrew Hoffmannas, Malte Dalcaar, Adrian V. Christodoulidis, Stergios Estiene, Théo Vakalopoulou, Maria Paragios, Nikos Marcus, Daniel S. Davatzikos, Christos Sotiras, Aristeidis Menze, Bjoern Bakas, Spyridon Waldmannstetter, Diana Division of Computational Pathology Department of Pathology and Laboratory Medicine Indiana University School of Medicine IndianapolisIN United States Department of Electrical and Systems Engineering Washington University in St. Louis St. LouisMO United States GE HealthCare San RamonCA United States University of Pennsylvania PhiladelphiaPA United States Department of Radiology Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Mallinckrodt Institute of Radiology Washington University School of Medicine St. LouisMO United States Institute for Informatics Data Science & Biostatistics Washington University School of Medicine St. LouisMO United States Department of Bioengineering Santa Clara University Santa ClaraCA United States Department of Quantitative Biomedicine University of Zurich Zurich Switzerland Department of Computer Science TUM School of Computation Information and Technology Technical University of Munich Munich Germany Department of Diagnostic and Interventional Neuroradiology School of Medicine Klinikum rechts der Isar Technical University of Munich Munich Germany Department of Nuclear Medicine University Hospital Regensburg Regensburg Germany University Hospital Regensburg Regensburg Germany Department of Radiology & Biomedical Imaging University of California San FranciscoCA United States Department of Radiology Duke University Medical Center DurhamNC United States Department of Radiology University of California San DiegoCA United States Helmholtz AI Helmholtz Munich Neuherberg Germany Penn Statistics in Imaging and Visualization Center Department of Biostatistics Epidemiology and Informatics University of Pennsylvania Philadelphia United States Massachusetts General Hospital Harvard Medical School United States Centre for Medical Imaging Computing University College London United Kingdom The Hong Kong University of Science and Technology Hong Kong University of Applied Sciences West

Registration of longitudinal brain Magnetic Resonance Imaging (MRI) scans containing pathologies is challenging due to dramatic changes in tissue appearance. Although there has been considerable progress in developing general-purpose medical image registration techniques, they have not yet attained the requisite precision and reliability for this task, highlighting its inherent complexity. Here we describe the Brain Tumor Sequence Registration (BraTS-Reg) challenge, as the first public benchmark environment for deformable registration algorithms focusing on estimating correspondences between pre-operative and follow-up scans of the same patient diagnosed with a diffuse brain glioma. The challenge was conducted in conjunction with both the IEEE International Symposium on Biomedical Imaging (ISBI) 2022 and the International Conference on Medical Image Computing and computer-Assisted Intervention (MICCAI) 2022. The BraTS-Reg data comprise de-identified multi-institutional multi-parametric MRI (mpMRI) scans, curated for size and resolution according to a canonical anatomical template, and divided into training, validation, and testing sets. Clinical experts annotated ground truth (GT) landmark points of anatomical locations distinct across the temporal domain. The training data with their GT annotations, were publicly released to enable the development of registration algorithms. The validation data, without their GT annotations, were also released to allow for algorithmic evaluation prior to the testing phase, which only allowed submission of containerized algorithms for evaluation on hidden hold-out testing data. Quantitative evaluation and ranking was based on the Median Euclidean Error (MEE), Robustness, and the determinant of the Jacobian of the displacement field. The top-ranked methodologies yielded similar performance across all evaluation metrics and shared several methodological commonalities, including pre-alignment, deep neural networks, inverse consistency

关键词： Magnetic resonance imaging

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Establishment of a low-tumorigenic MDCK cell line and study of differential molecular networks

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Biologicals : journal of the International Association of Biological Standardization 2020年 68卷 112-121页

作者： Gui-Lan Ma Zi-Lin Qiao Dan He Jiao Wang Yan-Yan Kong Xiao-Yong Xin Feng-Qin Wen Shi-Jun Bao Zhong-Ren Ma Fu-Shuai Wang Jiang Xie Yong-Hao Hu College of Veterinary Medicine Gansu Agricultural University Lanzhou 730030 PR China Gansu Tech Innovation Center of Animal Cell Biomedical Research Center Northwest Minzu University Lanzhou 730030 PR China. Electronic address: cnsff_20@***. Gansu Tech Innovation Center of Animal Cell Biomedical Research Center Northwest Minzu University Lanzhou 730030 PR China. Electronic address: qiaozilin@***. Gansu Tech Innovation Center of Animal Cell Biomedical Research Center Northwest Minzu University Lanzhou 730030 PR China. Electronic address: hedan1018@***. Laboratory of Molecular Neural Biology School of Life Sciences Shanghai University Shanghai China. Electronic address: jo717@***. Huashan Hospital Affiliated to Fudan University Shanghai China. Electronic address: kongyanyan@***. College of Veterinary Medicine Gansu Agricultural University Lanzhou 730030 PR China. Electronic address: xingxy@***. College of Veterinary Medicine Gansu Agricultural University Lanzhou 730030 PR China. Electronic address: 46292083@***. College of Veterinary Medicine Gansu Agricultural University Lanzhou 730030 PR China. Electronic address: bsjgn@***. Gansu Tech Innovation Center of Animal Cell Biomedical Research Center Northwest Minzu University Lanzhou 730030 PR China. Electronic address: mazhr@***. Laboratory of Molecular Neural Biology School of Life Sciences Shanghai University Shanghai China. Electronic address: 768537285@***. School of Computer Engineering and Science Shanghai University Shanghai China. Electronic address: jiangx@***. College of Veterinary Medicine Gansu Agricultural University Lanzhou 730030 PR China. Electronic address: yhh0817@***.

Influenza is an acute respiratory infection caused by the influenza virus, and vaccination against influenza is considered the best way to prevent the onset and spread. MDCK (Madin-Darby canine kidney) cells are typically used to isolate the influenza virus, however, their high tumorigenicity is the main controversy in the production of influenza vaccines. Here, MDCK-C09 and MDCK-C35 monoclonal cell lines were established, which were proven to be low in tumorigenicity. RNA-seq of MDCK-C09, MDCK-C35, and MDCK-W73 cells was performed to investigate the putative tumorigenicity mechanisms. Tumor-related molecular interaction analysis of the differentially expressed genes indicates that hub genes, such as CUL3 and EGFR, may play essential roles in tumorigenicity differences between MDCK-C (MDCK-C09 and MDCK-C35) and MDCK-W (MDCK-W73) cells. Moreover, the analysis of cell proliferation regulation-associated molecular interaction shows that downregulated JUN and MYC, for instance, mediate increased proliferation of these cells. The present study provides a new low-tumorigenic MDCK cell line and describes the potential molecular mechanism for the low tumorigenicity and high proliferation rate.

关键词： MDCK cells Molecular interactions Monoclonal technique Tumorigenicity

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Roadmap on quantum nanotechnologies

arXiv

引用

arXiv 2021年

作者： Laucht, Arne Hohls, Frank Ubbelohde, Niels Fernando Gonzalez-Zalba, M. Reilly, David J. Stobbe, Søren Schröder, Tim Scarlino, Pasquale Koski, Jonne V. Dzurak, Andrew Yang, Chih-Hwan Yoneda, Jun Kuemmeth, Ferdinand Bluhm, Hendrik Pla, Jarryd Hill, Charles Salfi, Joe Oiwa, Akira Muhonen, Juha T. Verhagen, Ewold LaHaye, M.D. Kim, Hyun Ho Tsen, Adam W. Culcer, Dimitrie Geresdi, Attila Mol, Jan A. Mohan, Varun Jain, Prashant K. Baugh, Jonathan Centre for Quantum Computation and Communication Technology School of Electrical Engineering and Telecommunications UNSW SydneyNSW2052 Australia Physikalisch-Technische Bundesanstalt Braunschweig38116 Germany Quantum Motion Technologies Nexus Discovery Way LeedsLS2 3AA United Kingdom School of Physics University of Sydney SydneyNSW2006 Australia Microsoft Corporation Station Q Sydney University of Sydney SydneyNSW2006 Australia Department of Photonics Engineering DTU Fotonik Technical University of Denmark Building 343 Kgs. LyngbyDK-2800 Denmark Department of Physics Humboldt-Universität zu Berlin Berlin12489 Germany Department of Physics ETH Zürich ZürichCH-8093 Switzerland Niels Bohr Institute University of Copenhagen Copenhagen2100 Denmark JARA-FIT Institute for Quantum Information RWTH Aachen University and Forschungszentrum Jülich Aachen52074 Germany School of Physics University of Melbourne Melbourne Australia Department of Electrical and Computer Engineering The University of British Columbia VancouverBCV6T 1Z4 Canada The Institute of Scientific and Industrial Research Osaka University Ibaraki Osaka567-0047 Japan Center for Quantum Information and Quantum Biology Institute for open and Transdisciplinary Research Initiative Osaka University Osaka560-8531 Japan Center for Nanophotonics AMOLF Amsterdam1098 XG Netherlands School of Physics The University of New South Wales Sydney2052 Australia Australian Research Council Centre of Excellence in Future Low-Energy Electronics Technologies UNSW Node The University of New South Wales Sydney2052 Australia QuTech and Kavli Institute of Nanoscience Delft University of Technology Delft2600 GA Netherlands School of Physics and Astronomy Queen Mary University of London E1 4NS United Kingdom Department of Materials Science and Engineering University of Illinois at Urbana-Champaign UrbanaIL61801 United States Department of Chemistry University of Illinois at Urbana-Champaign Urbana

Quantum phenomena are typically observable at length and time scales smaller than those of our everyday experience, often involving individual particles or excitations. The past few decades have seen a revolution in the ability to structure matter at the nanoscale, and experiments at the single particle level have become commonplace. This has opened wide new avenues for exploring and harnessing quantum mechanical effects in condensed matter. These quantum phenomena, in turn, have the potential to revolutionize the way we communicate, compute and probe the nanoscale world. Here, we review developments in key areas of quantum research in light of the nanotechnologies that enable them, with a view to what the future holds. Materials and devices with nanoscale features are used for quantum metrology and sensing, as building blocks for quantum computing, and as sources and detectors for quantum communication. They enable explorations of quantum behaviour and unconventional states in nano- and opto-mechanical systems, low-dimensional systems, molecular devices, nano-plasmonics, quantum electrodynamics, scanning tunnelling microscopy, and more. This rapidly expanding intersection of nanotechnology and quantum science/technology is mutually beneficial to both fields, laying claim to some of the most exciting scientific leaps of the last decade, with more on the horizon. © 2021, CC BY.

关键词： Quantum computers

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Author Correction: BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets

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Nature methods 2024年第10期21卷 1959页

作者： Linus Manubens-Gil Zhi Zhou Hanbo Chen Arvind Ramanathan Xiaoxiao Liu Yufeng Liu Alessandro Bria Todd Gillette Zongcai Ruan Jian Yang Miroslav Radojević Ting Zhao Li Cheng Lei Qu Siqi Liu Kristofer E Bouchard Lin Gu Weidong Cai Shuiwang Ji Badrinath Roysam Ching-Wei Wang Hongchuan Yu Amos Sironi Daniel Maxim Iascone Jie Zhou Erhan Bas Eduardo Conde-Sousa Paulo Aguiar Xiang Li Yujie Li Sumit Nanda Yuan Wang Leila Muresan Pascal Fua Bing Ye Hai-Yan He Jochen F Staiger Manuel Peter Daniel N Cox Michel Simonneau Marcel Oberlaender Gregory Jefferis Kei Ito Paloma Gonzalez-Bellido Jinhyun Kim Edwin Rubel Hollis T Cline Hongkui Zeng Aljoscha Nern Ann-Shyn Chiang Jianhua Yao Jane Roskams Rick Livesey Janine Stevens Tianming Liu Chinh Dang Yike Guo Ning Zhong Georgia Tourassi Sean Hill Michael Hawrylycz Christof Koch Erik Meijering Giorgio A Ascoli Hanchuan Peng Institute for Brain and Intelligence Southeast University Nanjing China. Microsoft Corporation Redmond WA USA. Tencent AI Lab Bellevue WA USA. Computing Environment and Life Sciences Directorate Argonne National Laboratory Lemont IL USA. Kaya Medical Seattle WA USA. University of Cassino and Southern Lazio Cassino Italy. Center for Neural Informatics Structures and Plasticity Krasnow Institute for Advanced Study George Mason University Fairfax VA USA. Faculty of Information Technology Beijing University of Technology Beijing China. Beijing International Collaboration Base on Brain Informatics and Wisdom Services Beijing China. Nuctech Netherlands Rotterdam the Netherlands. Janelia Research Campus Howard Hughes Medical Institute Ashburn VA USA. Department of Electrical and Computer Engineering University of Alberta Edmonton Alberta Canada. Ministry of Education Key Laboratory of Intelligent Computation and Signal Processing Anhui University Hefei China. Paige AI New York NY USA. Scientific Data Division and Biological Systems and Engineering Division Lawrence Berkeley National Lab Berkeley CA USA. Helen Wills Neuroscience Institute and Redwood Center for Theoretical Neuroscience UC Berkeley Berkeley CA USA. RIKEN AIP Tokyo Japan. Research Center for Advanced Science and Technology (RCAST) The University of Tokyo Tokyo Japan. School of Computer Science University of Sydney Sydney New South Wales Australia. Texas A&M University College Station TX USA. Cullen College of Engineering University of Houston Houston TX USA. Graduate Institute of Biomedical Engineering National Taiwan University of Science and Technology Taipei Taiwan. National Centre for Computer Animation Bournemouth University Poole UK. PROPHESEE Paris France. Department of Neuroscience Columbia University New York NY USA. Mortimer B. Zuckerman Mind Brain Behavior Institute Columbia University New York NY USA. Department of Computer Science Northern Illinois Universit

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National identity predicts public health support during a global pandemic (vol 13, 517, 2022)

引用

NATURE COMMUNICATIONS 2022年第1期13卷 517-517页

作者： Van Bavel, Jay J. Cichocka, Aleksandra Capraro, Valerio Sjastad, Hallgeir Nezlek, John B. Pavlovic, Tomislav Alfano, Mark Gelfand, Michele J. Azevedo, Flavio Birtel, Michele D. Cislak, Aleksandra Lockwood, Patricia L. Ross, Robert Malcolm Abts, Koen Agadullina, Elena Aruta, John Jamir Benzon Besharati, Sahba Nomvula Bor, Alexander Choma, Becky L. Crabtree, Charles David Cunningham, William A. De, Koustav Ejaz, Waqas Elbaek, Christian T. Findor, Andrej Flichtentrei, Daniel Franc, Renata Gjoneska, Biljana Gruber, June Gualda, Estrella Horiuchi, Yusaku Huynh, Toan Luu Duc Ibanez, Agustin Imran, Mostak Ahamed Israelashvili, Jacob Jasko, Katarzyna Kantorowicz, Jaroslaw Kantorowicz-Reznichenko, Elena Krouwel, Andre Laakasuo, Michael Lamm, Claus Leygue, Caroline Lin, Ming-Jen Mansoor, Mohammad Sabbir Marie, Antoine Mayiwar, Lewend Mazepus, Honorata McHugh, Cillian Minda, John Paul Mitkidis, Panagiotis Olsson, Andreas Otterbring, Tobias Packer, Dominic J. Perry, Anat Petersen, Michael Bang Puthillam, Arathy Riano-Moreno, Julian C. Rothmund, Tobias Santamaria-Garcia, Hernando Schmid, Petra C. Stoyanov, Drozdstoy Tewari, Shruti Todosijevic, Bojan Tsakiris, Manos Tung, Hans H. Umbres, Radu G. Vanags, Edmunds Vlasceanu, Madalina Vonasch, Andrew Yucel, Meltem Zhang, Yucheng Abad, Mohcine Adler, Eli Akrawi, Narin Mdarhri, Hamza Alaoui Amara, Hanane Amodio, David M. Antazo, Benedict G. Apps, Matthew Ay, F. Ceren Ba, Mouhamadou Hady Barbosa, Sergio Bastian, Brock Berg, Anton Bernal-Zarate, Maria P. Bernstein, Michael Bialek, Michal Bilancini, Ennio Bogatyreva, Natalia Boncinelli, Leonardo Booth, Jonathan E. Borau, Sylvie Buchel, Ondrej Cameron, C. Daryl Carvalho, Chrissie F. Celadin, Tatiana Cerami, Chiara Chalise, Hom Nath Cheng, Xiaojun Cian, Luca Cockcroft, Kate Conway, Jane Cordoba-Delgado, Mateo Andres Crespi, Chiara Crouzevialle, Marie Cutler, Jo Cypryanska, Marzena Dabrowska, Justyna Daniels, Michael A. Davis, Victoria H. Dayley, Pamala N. Delouvee, Sylvain Denkovski, Ognjan Dezecache, Guillaume Dhaliwal, Nathan A. Diato, Department of Psychology and Neural Science New York University New York NY USA School of Psychology University of Kent Canterbury England Department of Economics Middlesex University London London England Department of Strategy and Management Norwegian School of Economics Bergen Norway SWPS University of Social Sciences and Humanities Poznań Poland Department of Psychological Sciences College of William and Mary Williamsburg VA USA Institute of Social Sciences Ivo Pilar Zagreb Croatia Department of Philosophy Macquarie University Sydney NSW Australia Stanford Graduate School of Business Stanford University Stanford CA USA Institute of Communication Science Friedrich-Schiller University Jena Jena Germany School of Human Sciences Institute for Lifecourse Development University of Greenwich London England Department of Experimental Psychology University of Oxford Oxford England Center for Human Brain Health School of Psychology University of Birmingham Birmingham England Department of Psychology Macquarie University Sydney NSW Australia KU Leuven Leuven Belgium National Research University Higher School of Economics (HSE) Moscow Russia De La Salle University Manila Philippines Department of Psychology University of the Witwatersrand Johannesburg South Africa Department of Political Science Aarhus University Aarhus Denmark X University Toronto Canada Department of Government Dartmouth College Hanover NH USA Department of Psychology University of Toronto Toronto ON Canada Gatton College of Business and Economics University of Kentucky Lexington KY USA Department of Mass Communication National University of Science and Technology (NUST) Islamabad Pakistan Department of Management Aarhus University Aarhus Denmark Faculty of Social and Economic Sciences Comenius University Bratislava Slovakia IntraMed Buenos Aires Argentina Macedonian Academy of Sciences and Arts North Macedonia Republic of North Macedonia University of Colorado Boulder Bould

Changing collective behaviour and supporting non-pharmaceutical interventions is an important component in mitigating virus transmission during a pandemic. In a large international collaboration (Study 1, N = 49,968 across 67 countries), we investigated self-reported factors associated with public health behaviours (e.g., spatial distancing and stricter hygiene) and endorsed public policy interventions (e.g., closing bars and restaurants) during the early stage of the COVID-19 pandemic (April-May 2020). Respondents who reported identifying more strongly with their nation consistently reported greater engagement in public health behaviours and support for public health policies. Results were similar for representative and non-representative national samples. Study 2 (N = 42 countries) conceptually replicated the central finding using aggregate indices of national identity (obtained using the World Values Survey) and a measure of actual behaviour change during the pandemic (obtained from Google mobility reports). Higher levels of national identification prior to the pandemic predicted lower mobility during the early stage of the pandemic (r = −0.40). We discuss the potential implications of links between national identity, leadership, and public health for managing COVID-19 and future pandemics. Understanding collective behaviour is an important aspect of managing the pandemic response. Here the authors show in a large global study that participants that reported identifying more strongly with their nation reported greater engagement in public health behaviours and support for public health policies in the context of the pandemic.

关键词： Viral infection Human behaviour

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Design of microresonators to minimize thermal noise below the standard quantum limit

arXiv

引用

arXiv 2019年

作者： Sharifi, S. Banadaki, Y.M. Cullen, T. Veronis, G. Dowling, J.P. Corbitt, T. Department of Physics and Astronomy Louisiana State University Baton RougeLA70803 United States School of Electrical Engineering & Computer Science Louisiana State University Baton RougeLA70803 United States Center for Computation and Technology Louisiana State University Baton RougeLA70808 United States Hearne Institute for Theoretical Physics Louisiana State University Baton RougeLA70803 United States Department of Computer Science Southern University Baton RougeLA70813 United States

We present a design for a new microresonator whose geometry is optimized to maximize subStandard Quantum Limit (SQL) performance. The new design is predicted to have thermal noise well below the SQL across a broad range of frequencies when operated at 10K. The performance of this designed microresonator will allow it to serve as a test-bed for quantum non-demolition measurements, and to open new regimes of precision measurement that are relevant for many practical sensing applications, including advanced gravitational wave detectors. Copyright © 2019, The Authors. All rights reserved.

关键词： Resonators

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An Algorithm for Describing the Convex and Concave Shape of Protein Surface

An Algorithm for Describing the Convex and Concave Shape of ...

引用

2018国际计算机前沿大会（原国际青年计算机大会）

作者： Wei Wang Keliang Li Hehe Lv Lin Sun Hongjun Zhang Jinling Shi Shiguang Zhang Yun Zhou Yuan Zhao Jingjing Xv Department of Computer Science and Technology College of Computer and Information Engineering Henan Normal University Laboratory of Computation Intelligence and Information Processing Engineering Technology Research Center for Computing Intelligence and Data Mining School of Aviation Engineering Anyang University School of International Education Xuchang University

Protein surface plays a key role in many biological *** proteins participate in the life activities of cells via binding to other proteins or ligand molecules. It is an important work to study protein structure and function by analyzing the protein surface shape. Based on the CX algorithm and the 2 D fngerprint-base method, we proposed a FCX method to identify the morphology of bulges and depressions on the protein surface. The experimental results show that the FCX algorithm has a more desirable outcome than CX algorithm. The FCX algorithm has a higher correlation with the convex and concave features than CX values with solvent accessibility, solvent accessibility, and Bfactor's Pearson correlation coefficient. This result shows that the FCX algorithm can describe the shape of the protein surface residues more accurately than the CX algorithm.

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Correction to: Reaction of human walking to transient block of vision: analysis in the context of indirect, referent control of motor actions

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Experimental brain research 2023年第7期241卷 1973页

作者： Otella Shoja Farzad Towhidkhah Hamidollah Hassanlouei Mindy F Levin Alireza Bahramian Sylvie Nadeau Lei Zhang Anatol G Feldman Department of Neuroscience University of Montreal Montreal QC Canada. Department of Biomedical Engineering Amirkabir University of Technology Tehran Iran. Department of Motor Behaviour Faculty of Sport Science and Health Shahid Beheshti University Tehran Iran. School of Physical and Occupational Therapy McGill University Montreal QC Canada. Center for Interdisciplinary Research in Rehabilitation of Greater Montreal (CRIR) Montreal QC Canada. Faculté de Médecine-École de Réadaptation Montreal QC Canada. Institute for Neural Computation Ruhr University Bochum Bochum Germany. Department of Neuroscience University of Montreal Montreal QC Canada. anatol.g.feldman@umontreal.ca. Center for Interdisciplinary Research in Rehabilitation of Greater Montreal (CRIR) Montreal QC Canada. anatol.g.feldman@umontreal.ca. Institut de réadaptation Gingras-Lindsay-de-Montréal (IRGLM) 6300 Darlington Montreal QC H3S 2J4 Canada. anatol.g.feldman@umontreal.ca.

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ParSECH: Parallel sequencing error correction with hadoop for large-scale genome sequences 9

ParSECH: Parallel sequencing error correction with hadoop fo...

引用

9th International Conference on Bioinformatics and computational Biology, BICOB 2017

作者： Das, Arghya Kusum Shams, Shayan Goswami, Sayan Platania, Richard Lee, Kisung Park, Seung-Jong School of Electrical Engineering and Computer Science Center for Computation and Technology Louisiana State University Baton RougeLA70808 United States

ISBN: (纸本)9781943436071

A scalable and accurate error correction tool is essential for all next-generation sequencing (NGS) projects as high-throughput sequencing machines have started producing terabytes of data with significantly higher error-rates compared to conventional Sanger sequencing. In this paper, we develop ParSECH, a scalable and fully distributed error correction software based on kappa;-mer spectrum analysis, without the need of a reference genome. To achieve high scalability over terabytes of data and hundreds of cores, ParSECH utilizes two opensource big data frameworks: Hadoop and Hazelcast. To achieve high accuracy, unlike existing error correction tools that use a single kappa;-mer coverage cutoff to detect errors, ParSECH determines the skewness involved in the kappa;-mer coverage of each individual read, followed by correcting the errors in each read separately for low and high coverage regions of the genome. We demonstrate the scalability of ParSECH by correcting the errors of both simulated and real whole human genome data with coverage ranging from 2x to 40x. ParSECH can correct the largest dataset (452GB human genome), which could not be handled by the existing error correction tools, in about 39 hours. For a small *** genome dataset, ParSECH demonstrates 94% accuracy, higher than 90% accuracy of Quake.

关键词： Error correction

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