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A biosensing system employing nanowell microelectrode arrays to record the intracellular potential of a single cardiomyocyte

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Microsystems & Nanoengineering 2022年第3期8卷 185-198页

作者： Yuting Xiang Haitao Liu Wenjian Yang Zhongyuan xu Yue Wu Zhajian Tang Zhjing Zhu Zhiyong Zeng Depeng Wang Tianxing Wang Ning Hu Diming Zhang Department of Obstetrics and Gynecology Affiliated Dongguan People's HospitalSouthern Medical UniversityDongguan 523058China Research Center for Inelligent Sensing Systems Zhejiang LaboratoryHangzhou 311100China Research Center for Humanoid Sensing Zhejiang LaboratoryHangzhou 311100China Key Laboratory of Novel Target and Drug Study for Neural Repair of Zhejiang Province School of MedicineSchool of Computer&Computing ScienceZhejiang University City CollegeHangzhou 310015China School of Brain Science and Brain Medicine Zhejiang UniversityHangzhou 310058China School of Automation Nanjing University of Science and TechnologyNanjing 210094China College of Energy and Power Engineering Nanjing University of Aeronautics and AstronauticsNanjing 210016China E-Link Care Meditech Co. LtdHangzhou 310011China ZJU-Hangzhou Global Scientific and Technological Innovation Center Department of ChemitryZhejiang UniversityHangzhou 310058China

Electrophysiological recording is a widely used method to investigate cardiovascular pathology,pharmacology and developmental *** arrays record the electrical potential of cells in a minimally invasive and highthroughput ***,commonly used microelectrode arays primarily employ planar microelectrodes and cannot work in applications that require a recording of the intracellular action potential of a single *** this study,we proposed a novel measuring method that is able to record the intracellular action potential of a single cardiomyocyte by using a nanowell patterned microelectrode array(NWMEA).The NWMEA consists of five nanoscale wells at the center of each circular planar *** pulse electroporation was applied to the NWMEA to penetrate the cardiomyocyte membrane,and the intracellular action potential was continuously *** intracellular potential recording of cardiomyocytes by the NWMEA measured a potential signal with a higher quality(213.76±25.85%),reduced noise root-mean-square(~33%),and higher signal-to-noise ratio(254.36±12.61%)when compared to those of the extracellular *** to previously reported nanopillar microelectrodes,the NWMEA could ensure single cell electroporation and acquire high-quality action potential of cardiomyocytes with reduced fabrication *** NWMEA-based biosensing system is a promising tool to record the intracellular action potential of a single cell to broaden the usage of microelectrode arrays in electrophysiological investigation.

关键词： arrays potential record

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Internal Feedback in Biological Control: Architectures and Examples

Internal Feedback in Biological Control: Architectures and E...

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2022 American Control Conference, ACC 2022

作者： Sarma, Anish A. Shuang Lisa Li, Jing Stenberg, Josefin Card, Gwyneth Heckscher, Elizabeth S. Kasthuri, Narayanan Sejnowski, Terrence Doyle, John C. Caltech Computation and Neural Systems Caltech Computing and Mathematical Sciences Kth Royal Institute of Technology Engineering Physics Sweden Hhmi Janelia Research Campus United States University of Chicago Molecular Genetics and Cell Biology United States University of Chicago Neurobiology United States The Salk Institute for Biological Studies Computational Neurobiology Laboratory United States University of California San Diego Biological Sciences United States

ISBN: (数字)9781665451963

ISBN: (纸本)9781665451963

Feedback is ubiquitous in both biological and engineered control systems. In biology, in addition to typical feedback between plant and controller, we observe complex feedback pathways within control systems, which we call internal feedback pathways (IFPs). These IFPs are most familiar in neural systems, our primary case study, but they appear everywhere from bacterial signal transduction to the human immune system. In this paper, we describe these very different examples and introduce the concepts necessary to explain their complex IFPs-particularly the severe speed-accuracy tradeoffs that constrain hardware in biology. We also sketch some minimal theory for extremely simplified toy models that highlight the importance of diversity-enabled sweet spots (DESS) in mitigating the impact of hardware tradeoffs. Standard modern and robust control theory can offer some insights into previously cryptic IFPs in more realistic models, and the new System Level Synthesis theory expands on these insights substantially, as explored in detail in companion papers. © 2022 American Automatic Control Council.

关键词： Feedback

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A biosensing system using a multiparameter nonlinear dynamic analysis of cardiomyocyte beating for drug-induced arrhythmia recognition

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Microsystems & Nanoengineering 2022年第3期8卷 277-290页

作者： Hao Wang Yue Wu Quchao Zou Wenjian Yang Zhongyuan Xu Hao Dong Zhjing Zhu Depeng Wang Tanxing Wang Ning Hu Diming Zhang State Key Laboratory of Optoelectronic Materials and Technologies Guangdong Province Key Laboratory of Display Material and TechnologySchool of Electronics and Information TechnologySun Yat-sen UniversityGuangzhou 510006China Research Center for Itelligent Sensing Systems Zhejiang LabHangzhou 311121China ZJU-Hangzhou Global Scientific and Technological Innovation Center Department of ChemistryThe Second Affiliated Hospital Zhejiang University School of MedicineDepartment of Clinical Medical EngineeringZhejiang UniversityHangzhou 310058China Key Laboratory of Novel Target and Drug Study for Neural Repair of Zhejang Province School of MedicineSchool of Computer&Computing ScienceZhejiang University City CollegeHangzhou 310015China School of Brain Science and Brain Medicine Zhejiang UniversityHangzhou 310058China College of Energy and Power Engineering Nanjing University of Aeronautics and AstronauticsNanjing 210016China E-LinkCare Meditech Co LtdHangzhou 310011China State Key Laboratory of Transducer Technology Chinese Academy of SciencesShanghai 200050China

Cardiovascular disease is the number one cause of death in ***,cardiotoxicity is one of the most important adverse effects assessed by arrhythmia recognition in drug ***,cell-based techniques developed for arhythmia recognition primarily employ linear methods such as time-domain analysis that detect and compare individual waveforms and thus fall short in some applications that require automated and efficient arrhythmia recognition from large *** carried out the frst report to develop a biosensing system that integrated impedance measurement and multiparameter nonlinear dynamic algorithm(MNDA)analysis for druginduced arrhythmia recognition and *** biosensing system cultured cardiomyocytes as physiologically relevant models,used interdigitated electrodes to detect the mechanical beating of the cardiomyocytes,and employed MNDA analysis to recognize drug-induced arrhythmia from the cardiomyocyte beating *** best performing MNDA parameter,approximate entropy,enabled the system to recognize the appearance of sertindoleand norepinephrine-induced arrhythmia in the *** MNDA reconstruction in phase space enabled the system to classify the different arrhythmias and quantify the severity of *** new biosensing system utilizing MNDA provides a promising and alternative method for drug-induced arrhythmia recognition and classification in cardiological and pharmaceutical applications.

关键词： arrhythmia cardio analysis

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Collective activity bursting in networks of excitable systems adaptively coupled to a pool of resources

arXiv

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arXiv 2021年

作者： Franović, Igor Eydam, Sebastian Yanchuk, Serhiy Berner, Rico Scientific Computing Laboratory Center for the Study of Complex Systems Institute of Physics Belgrade University of Belgrade Pregrevica 118 Belgrade11080 Serbia Neural Circuits and Computations Unit RIKEN Center for Brain Science 2-1 Hirosawa Wako351-0198 Japan Institut für Mathematik Technische Universität Berlin Strasse des 17. Juni 136 Berlin10623 Germany Potsdam Institute for Climate Impact Research Potsdam14473 Germany Institut für Theoretische Physik Technische Universität Berlin Hardenbergstr. 36 Berlin10623 Germany Institut für Physik Humboldt-Universität zu Berlin Newtonstraße 15 Berlin12489 Germany

We study the collective dynamics in a network of excitable units (neurons) adaptively interacting with a pool of resources. The resource pool is influenced by the average activity of the network, whereas the feedback from the resources to the network is comprised of components acting homogeneously or inhomogeneously on individual units of the network. Moreover, the resource pool dynamics is assumed to be slow and has an oscillatory degree of freedom. We show that the feedback loop between the network and the resources can give rise to collective activity bursting in the network. To explain the mechanisms behind this emergent phenomenon, we combine the Ott-Antonsen reduction for the collective dynamics of the network and singular perturbation theory to obtain a reduced system describing the interaction between the network mean field and the resources. Copyright © 2021, The Authors. All rights reserved.

关键词： Perturbation techniques

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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 2023年第6期20卷 824-835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

BigNeuron is an open community bench-testing platform with the goal of setting open standards for accurate and fast automatic neuron tracing. We gathered a diverse set of image volumes across several species that is representative of the data obtained in many neuroscience laboratories interested in neuron tracing. Here, we report generated gold standard manual annotations for a subset of the available imaging datasets and quantified tracing quality for 35 automatic tracing algorithms. The goal of generating such a hand-curated diverse dataset is to advance the development of tracing algorithms and enable generalizable benchmarking. Together with image quality features, we pooled the data in an interactive web application that enables users and developers to perform principal component analysis, t-distributed stochastic neighbor embedding, correlation and clustering, visualization of imaging and tracing data, and benchmarking of automatic tracing algorithms in user-defined data subsets. The image quality metrics explain most of the variance in the data, followed by neuromorphological features related to neuron size. We observed that diverse algorithms can provide complementary information to obtain accurate results and developed a method to iteratively combine methods and generate consensus reconstructions. The consensus trees obtained provide estimates of the neuron structure ground truth that typically outperform single algorithms in noisy datasets. However, specific algorithms may outperform the consensus tree strategy in specific imaging conditions. Finally, to aid users in predicting the most accurate automatic tracing results without manual annotations for comparison, we used support vector machine regression to predict reconstruction quality given an image volume and a set of automatic tracings.

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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

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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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26th Annual Computational Neuroscience Meeting (CNS*2017): Part 3 Antwerp, Belgium. 15-20 July 2017 Abstracts

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BMC NEUROSCIENCE 2017年第SUPPL 1期18卷 95-176页

作者： [Anonymous] Department of Neuroscience Yale University New Haven CT 06520 USA Department Physiology & Pharmacology SUNY Downstate Brooklyn NY 11203 USA NYU School of Engineering 6 MetroTech Center Brooklyn NY 11201 USA Departament de Matemàtica Aplicada Universitat Politècnica de Catalunya Barcelona 08028 Spain Institut de Neurobiologie de la Méditerrannée (INMED) INSERM UMR901 Aix-Marseille Univ Marseille France Center of Neural Science New York University New York NY USA Aix-Marseille Univ INSERM INS Inst Neurosci Syst Marseille France Laboratoire de Physique Théorique et Modélisation CNRS UMR 8089 Université de Cergy-Pontoise 95300 Cergy-Pontoise Cedex France Department of Mathematics and Computer Science ENSAT Abdelmalek Essaadi’s University Tangier Morocco Laboratory of Natural Computation Department of Information and Electrical Engineering and Applied Mathematics University of Salerno 84084 Fisciano SA Italy Department of Medicine University of Salerno 84083 Lancusi SA Italy Dipartimento di Fisica Università degli Studi Aldo Moro Bari and INFN Sezione Di Bari Italy Data Analysis Department Ghent University Ghent Belgium Coma Science Group University of Liège Liège Belgium Cruces Hospital and Ikerbasque Research Center Bilbao Spain BIOtech Department of Industrial Engineering University of Trento and IRCS-PAT FBK 38010 Trento Italy Department of Data Analysis Ghent University Ghent 9000 Belgium The Wellcome Trust Centre for Neuroimaging University College London London WC1N 3BG UK Department of Electronic Engineering NED University of Engineering and Technology Karachi Pakistan Blue Brain Project École Polytechnique Fédérale de Lausanne Lausanne Switzerland Departement of Mathematics Swansea University Swansea Wales UK Laboratory for Topology and Neuroscience at the Brain Mind Institute École polytechnique fédérale de Lausanne Lausanne Switzerland Institute of Mathematics University of Aberdeen Aberdeen Scotland UK Department of Integrativ

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25th Annual Computational Neuroscience Meeting CNS-2016, Seogwipo City, South Korea, July 2-7, 2016 Abstracts

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BMC NEUROSCIENCE 2016年第1期17卷 1-112页

作者： [Anonymous] Computational Neurobiology Laboratory The Salk Institute for Biological Studies San Diego USA UNIC CNRS Gif sur Yvette France The European Institute for Theoretical Neuroscience (EITN) Paris France ATR Computational Neuroscience Laboratories Kyoto Japan Krembil Research Institute University Health Network Toronto Canada Department of Physiology University of Toronto Toronto Canada Department of Medicine (Neurology) University of Toronto Toronto Canada Department of Physics University of New Hampshire Durham USA Department of Neurophysiology Nencki Institute of Experimental Biology Warsaw Poland Department of Theory Wigner Research Centre for Physics of the Hungarian Academy of Sciences Budapest Hungary Department of Mathematical Sciences KAIST Daejoen Republic of Korea Department of Mathematics University of Houston Houston USA Department of Biochemistry & Cell Biology and Institute of Biosciences and Bioengineering Rice University Houston USA Department of Biology and Biochemistry University of Houston Houston USA Grupo de Neurocomputación Biológica Dpto. de Ingeniería Informática Escuela Politécnica Superior Universidad Autónoma de Madrid Madrid Spain Department of Biological Sciences University of Southern California Los Angeles USA Center for Neuroscience Korea Institute of Science and Technology Seoul South Korea Department of Neurology Albert Einstein College of Medicine Bronx USA Center for Neuroscience KIST Seoul South Korea Department of Neuroscience University of Science and Technology Daejon South Korea Systems Neuroscience Group QIMR Berghofer Medical Research Institute Herston Australia Department of Psychology Yonsei University Seoul South Korea Department of Psychiatry Kyung Hee University Hospital at Gangdong Seoul South Korea Department of Psychiatry Veterans Administration Boston Healthcare System and Harvard Medical School Brockton USA Department of Electrical and Electronic Engineering The University of Melbourne Parkvil

A1 Functional advantages of cell-type heterogeneity in neural circuits Tatyana O. Sharpee A2 Mesoscopic modeling of propagating waves in visual cortex Alain Destexhe A3 Dynamics and biomarkers of mental disorders Mitsuo Kawato F1 Precise recruitment of spiking output at theta frequencies requires dendritic h-channels in multi-compartment models of oriens-lacunosum/moleculare hippocampal interneurons Vladislav Sekulić, Frances K. Skinner F2 Kernel methods in reconstruction of current sources from extracellular potentials for single cells and the whole brains Daniel K. Wójcik, Chaitanya Chintaluri, Dorottya Cserpán, Zoltán Somogyvári F3 The synchronized periods depend on intracellular transcriptional repression mechanisms in circadian clocks. Jae Kyoung Kim, Zachary P. Kilpatrick, Matthew R. Bennett, Kresimir Josić O1 Assessing irregularity and coordination of spiking-bursting rhythms in central pattern generators Irene Elices, David Arroyo, Rafael Levi, Francisco B. Rodriguez, Pablo Varona O2 Regulation of top-down processing by cortically-projecting parvalbumin positive neurons in basal forebrain Eunjin Hwang, Bowon Kim, Hio-Been Han, Tae Kim, James T. McKenna, Ritchie E. Brown, Robert W. McCarley, Jee Hyun Choi O3 Modeling auditory stream segregation, build-up and bistability James Rankin, Pamela Osborn Popp, John Rinzel O4 Strong competition between tonotopic neural ensembles explains pitch-related dynamics of auditory cortex evoked fields Alejandro Tabas, André Rupp, Emili Balaguer-Ballester O5 A simple model of retinal response to multi-electrode stimulation Matias I. Maturana, David B. Grayden, Shaun L. Cloherty, Tatiana Kameneva, Michael R. Ibbotson, Hamish Meffin O6 Noise correlations in V4 area correlate with behavioral performance in visual discrimination task Veronika Koren, Timm Lochmann, Valentin Dragoi, Klaus Obermayer O7 Input-location dependent gain modulation in cerebellar nucleus neurons Maria Psarrou, Maria Schilstra, Neil Davey, Benjamin Torben-Ni

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From laptops to supercomputers: a single highly scalable code base for spiking neuronal network simulations

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BMC Neuroscience 2013年第1期14卷 1-2页

作者： Susanne Kunkel Abigail Morrison Markus Diesmann Maximilian Schmidt Jochen M Eppler Moritz Helias Hans E Plesser Jun Igarashi Tomoki Fukai Gen Masumoto Shin Ishii Simulation Laboratory Neuroscience - Bernstein Facility Simulation and Database Technology Institute for Advanced Simulation Jülich Aachen Research Alliance Jülich Research Centre Germany Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) Jülich Research Centre and JARA Germany Bernstein Center Freiburg Albert-Ludwig University of Freiburg Germany Institute of Cognitive Neuroscience Faculty of Psychology Ruhr-University Bochum Germany Medical Faculty RWTH University Aachen Germany Laboratory for Neural Circuit Theory RIKEN Brain Science Institute Wako Japan Department of Mathematical Sciences and Technology Norwegian University of Life Sciences Aas Norway High-Performance Computing Team RIKEN Computational Science Research Program Kobe Japan Integrated Systems Biology Laboratory Department of Systems Science Graduate School of Informatics Kyoto University Japan

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