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Considerations and recommendations from the ISMRM Diffusion Study Group for preclinical diffusion MRI: Part 2 — Ex vivo imaging: added value and acquisition

arXiv

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arXiv 2022年

作者： Schilling, Kurt G. Grussu, Francesco Ianus, Andrada Hansen, Brian Howard, Amy F.D. Barrett, Rachel L.C. Aggarwal, Manisha Michielse, Stijn Nasrallah, Fatima Syeda, Warda Wang, Nian Veraart, Jelle Roebroeck, Alard Bagdasarian, Andrew F. Eichner, Cornelius Sepehrband, Farshid Zimmermann, Jan Soustelle, Lucas Bowman, Christien Tendler, Benjamin C. Hertanu, Andreea Jeurissen, Ben Verhoye, Marleen Frydman, Lucio de Looij, Yohan van Hike, David Dunn, Jeff F. Miller, Karla Landman, Bennett A. Shemesh, Noam Anderson, Adam McKinnon, Emilie Farquharson, Shawna Acqua, Flavio Dell Pierpaoli, Carlo Drobnjak, Ivana Leemans, Alexander Harkins, Kevin D. Descoteaux, Maxime Xu, Duan Huang, Hao Santin, Mathieu D. Grant, Samuel C. Obenaus, Andre Kim, Gene S. Wu, Dan Le Bihan, Denis Blackband, Stephen J. Ciobanu, Luisa Fieremans, Els Bai, Ruiliang Leergaard, Trygve B. Zhang, Jiangyang Dyrby, Tim B. Allan Johnson, G. Cohen-Adad, Julien Budde, Matthew D. Jelescu, Ileana O. Radiology and Radiological Sciences Vanderbilt University Medical Center NashvilleTN United States Vanderbilt University Institute of Imaging Science Vanderbilt University NashvilleTN United States Radiomics Group Vall d’Hebron Institute of Oncology Vall d’Hebron Barcelona Hospital Campus Barcelona Spain Queen Square MS Centre Queen Square Institute of Neurology Faculty of Brain Sciences University College London London United Kingdom Champalimaud Research Champalimaud Foundation Lisbon Portugal Center of Functionally Integrative Neuroscience Aarhus University Aarhus Denmark Department of Bioengineering Imperial College London London United Kingdom FMRIB Centre Wellcome Centre for Integrative Neuroimaging Nuffield Department of Clinical Neurosciences University of Oxford Oxford United Kingdom Department of Neuroimaging Institute of Psychiatry Psychology and Neuroscience King's College London London United Kingdom NatBrainLab Department of Forensics and Neurodevelopmental Sciences Institute of Psychiatry Psychology and Neuroscience King's College London London United Kingdom Russell H. Morgan Department of Radiology and Radiological Science Johns Hopkins University School of Medicine BaltimoreMD United States Maastricht University Medical Center Maastricht Netherlands The Queensland Brain Institute The University of Queensland Queensland Australia Melbourne Neuropsychiatry Centre The University of Melbourne ParkvilleVIC Australia Department of Radiology and Imaging Sciences Indiana University IN United States Stark Neurosciences Research Institute Indiana University School of Medicine IN United States Center for Biomedical Imaging NYU Grossman School of Medicine New YorkNY United States Faculty of psychology and Neuroscience Maastricht University Maastricht Netherlands Department of Chemical & Biomedical Engineering FAMU-FSU College of Engineering Florida State University TallahasseeFL United States Center for Interdisciplinary Magnetic Re

The value of preclinical diffusion MRI (dMRI) is substantial. While dMRI enables in vivo non-invasive characterization of tissue, ex vivo dMRI is increasingly being used to probe tissue microstructure and brain connectivity. Ex vivo dMRI has several experimental advantages including higher signal-to-noise ratio (SNR) and spatial resolution compared to in vivo studies, and enabling more advanced diffusion contrasts for improved microstructure and connectivity characterization. Another major advantage of ex vivo dMRI is the direct comparison with histological data, as a crucial methodological validation. However, there are a number of considerations that must be made when performing ex vivo experiments. The steps from tissue preparation, image acquisition and processing, and interpretation of results are complex, with many decisions that not only differ dramatically from in vivo imaging of small animals, but ultimately affect what questions can be answered using the data. This work represents "Part 2" of a 3-part series of recommendations and considerations for preclinical dMRI. We describe best practices for dMRI of ex vivo tissue, with a focus on the value that ex vivo imaging adds to the field of dMRI and considerations in ex vivo image acquisition. We first give general considerations and foundational knowledge that must be considered when designing experiments. We briefly describe differences in specimens and models and discuss why some may be more or less appropriate for different studies. We then give guidelines for ex vivo protocols, including tissue fixation, sample preparation, and MR scanning. In each section, we attempt to provide guidelines and recommendations, but also highlight areas for which no guidelines exist (and why), and where future work should lie. An overarching goal herein is to enhance the rigor and reproducibility of ex vivo dMRI acquisitions and analyses, and thereby advance biomedical knowledge. © 2022, CC BY.

关键词： Image acquisition

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Beyond Low Earth Orbit: Biological Research, Artificial Intelligence, and Self-Driving Labs

arXiv

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arXiv 2021年

作者： Sanders, Lauren M. Yang, Jason H. Scott, Ryan T. Qutub, Amina Ann Martin, Hector Garcia Berrios, Daniel C. Hastings, Jaden J.A. Rask, Jon Mackintosh, Graham Hoarfrost, Adrienne L. Chalk, Stuart Kalantari, John Khezeli, Kia Antonsen, Erik L. Babdor, Joel Barker, Richard Baranzini, Sergio E. Beheshti, Afshin Delgado-Aparicio, Guillermo M. Glicksberg, Benjamin S. Greene, Casey S. Haendel, Melissa Hamid, Arif A. Heller, Philip Jamieson, Daniel Jarvis, Katelyn J. Komarova, Svetlana V. Komorowski, Matthieu Kothiyal, Prachi Mahabal, Ashish Manor, Uri Mason, Christopher E. Matar, Mona Mias, George I. Miller, Jack Myers, Jerry G. Nelson, Charlotte Oribello, Jonathan Park, Seung-Min Parsons-Wingerter, Patricia Prabhu, R.K. Reynolds, Robert J. Saravia-Butler, Amanda Saria, Suchi Sawyer, Aenor Singh, Nitin Kumar Soboczenski, Frank Snyder, Michael Soman, Karthik Theriot, Corey A. van Valen, David Venkateswaran, Kasthuri Warren, Liz Worthey, Liz Zitnik, Marinka Costes, Sylvain V. Blue Marble Space Institute of Science Space Biosciences Division NASA Ames Research Center Moffett Field CA94035 United States Center for Emerging and Re-Emerging Pathogens Department of Microbiology Biochemistry and Molecular Genetics Rutgers New Jersey Medical School NewarkNJ07103 United States KBR Space Biosciences Division NASA Ames Research Center Moffett Field CA94035 United States AI MATRIX Consortium Department of Biomedical Engineering University of Texas San Antonio and UT Health Sciences San AntonioTX78249 United States Biological Systems and Engineering Division Lawrence Berkeley National Lab. BerkeleyCA94608 United States DOE Agile BioFoundry EmeryvilleCA94608 United States Joint BioEnergy Institute EmeryvilleCA94608 United States Department of Physiology and Biophysics Weill Cornell Medicine New YorkNY10065 United States Office of the Center Director NASA Ames Research Center Moffett Field CA94035 United States Bay Area Environmental Research Institute NASA Ames Research Center Moffett Field CA94035 United States Space Biosciences Division NASA Ames Research Center Moffett Field CA94035 United States Department of Chemistry University of North Florida JacksonvilleFL32224 United States Center for Individualized Medicine Department of Surgery Department of Quantitative Health Sciences Mayo Clinic RochesterMN55905 United States Department of Emergency Medicine Center for Space Medicine Baylor College of Medicine HoustonTX77030 United States Department of Microbiology and Immunology Department of Otolaryngology Head and Neck Surgery University of California San Francisco San FranciscoCA94143 United States The Gilroy AstroBiology Research Group The University of Wisconsin - Madison MadisonWI53706 United States Weill Institute for Neurosciences Department of Neurology University of California San Francisco San FranciscoCA94158 United States Data Science Analytics Georgia Institute of Technology Lima15024

Space biology research aims to understand fundamental effects of spaceflight on organisms, develop foundational knowledge to support deep space exploration, and ultimately bioengineer spacecraft and habitats to stabilize the ecosystem of plants, crops, microbes, animals, and humans for sustained multi-planetary life. To advance these aims, the field leverages experiments, platforms, data, and model organisms from both spaceborne and ground-analog studies. As research is extended beyond low Earth orbit, experiments and platforms must be maximally autonomous, light, agile, and intelligent to expedite knowledge discovery. Here we present a summary of recommendations from a workshop organized by the National Aeronautics and Space Administration on artificial intelligence, machine learning, and modeling applications which offer key solutions toward these space biology challenges. In the next decade, the synthesis of artificial intelligence into the field of space biology will deepen the biological understanding of spaceflight effects, facilitate predictive modeling and analytics, support maximally autonomous and reproducible experiments, and efficiently manage spaceborne data and metadata, all with the goal to enable life to thrive in deep space. © 2021, CC BY.

关键词： Predictive analytics

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Synthetic learning set for object pose estimation: Initial experiments

Synthetic learning set for object pose estimation: Initial e...

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International Conference on Ubiquitous Robots and Ambient Intelligence (URAI)

作者： Joo-Haeng Lee Woo-Han Yun Jaeyeon Lee Jaehong Kim Computer Software Dept. University of Science and Technology Daejeon Korea Human-Machine Interaction Group ETRI Daejeon Korea

We summarize a method to generate a synthetic learning set for object pose estimation in robotic manipulation tasks. Exploiting modern computer graphics techniques, our synthetic learning set satisfies the requirements both in quantitative diversity and qualitative precision. We report the partial results of initial experiments and discuss some future research directions.

关键词： Pose estimation Cameras Robots Feature extraction Lighting Rendering (computer graphics)

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Identifying harm events in clinical care through medical narratives

arXiv

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arXiv 2017年

作者： Cohan, Arman Ratwani, Raj Fong, Allan Goharian, Nazli Information Retrieval Lab Dept. of Computer Science Georgetown University National Center for Human Factors in Healthcare MedStar Health

Preventable medical errors are estimated to be among the leading causes of injury and death in the United States. To prevent such errors, healthcare systems have implemented patient safety and incident reporting systems. These systems enable clinicians to report unsafe conditions and cases where patients have been harmed due to errors in medical care. These reports are narratives in natural language and while they provide detailed information about the situation, it is non-trivial to perform large scale analysis for identifying common causes of errors and harm to the patients. In this work, we present a method based on attentive convolutional and recurrent networks for identifying harm events in patient care and categorize the harm based on its severity level. We demonstrate that our methods can significantly improve the performance over existing methods in identifying harm in clinical care. Copyright © 2017, The Authors. All rights reserved.

关键词： Errors

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Usability of programming languages: Special interest group (SIG) meeting at CHI 2016

Usability of programming languages: Special interest group (...

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34th Annual CHI Conference on human Factors in Computing Systems, CHI EA 2016

作者： Myers, Brad A. Stefik, Andreas Hanenberg, Stefan Kaijanaho, Antti-Juhani Burnett, Margaret Turbak, Franklyn Wadler, Philip Human-Comp. Interaction Inst. Carnegie Mellon University United States Computer Science University of Nevada Las Vegas United States Dept. of CS and Business IS Univ. of Duisburg-Essen Germany Department of Math. Inf. Tech. University of Jyvaskyla Finland School of EECS Oregon State University United States Computer Science Department Wellesley College United States School of Informatics University of Edinburgh United Kingdom

ISBN: (纸本)9781450340823

Programming languages form the interface between programmers (the users) and the computation that they desire the computer to execute. Although studies exist for some aspects of programming language design (such as conditionals), other aspects have received little or no human factors evaluations. Designers thus have little they can rely on if they want to make new languages highly usable, and users cannot easily chose a language based on usability criteria. This SIG will bring together researchers and practitioners interested in increasing the dept. and breadth of studies on the usability of programming languages, and ultimately in improving the usability of future languages. © 2016 Authors.

关键词： human computer interaction

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Leveraging and integrating Eastern and Western insights for human engagement studies in HCI 33

Leveraging and integrating Eastern and Western insights for ...

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33rd Annual CHI Conference on human Factors in Computing Systems, CHI EA 2015

作者： Law, Effie Lai-Chong Silpasuwanchai, Chaklam Ren, Xiangshi Bardzell, Jeffrey Clemmensen, Torkil Liu, Yan Department of Computer Science University of Leicester LeicesterLEI 7RH United Kingdom School of Information Kochi University of Technology Kami-Kochi Japan Centre for Human Computer Interaction Kochi University of Technology Kami-Kochi Japan School of Informatics and Computing Indiana University United States Dept. of IT Management Copenhagen Business School Denmark Department of Computing Hong Kong Polytechnic University Hong Kong

ISBN: (纸本)9781450331463

human engagement is at the heart of every interactive technology. However, a concrete framework for synergizing the capabilities of humans and technologies to allow fully engaging interactions to happen is yet to be developed. We posit that such a framework should be grounded in a deeper understanding of human nature (e.g., mind-body relations), which in the field of HCI has primarily been built upon the Western philosophies. There are scattered, underexplored Eastern philosophies (e.g., Yijing, Zen) that may provide new lens and tools to analyze how humans interact with resources in their environments, including technological artefacts. Discussions of leveraging and possibly integrating Eastern and Western insights for human engagement studies will be an exciting and a radical forum for the HCI community.

关键词： Philosophical aspects

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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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More mobile & not so well-connected yet: Users' mobility inference model and 6 month field study

More mobile & not so well-connected yet: Users' mobility inf...

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International Conference on Ultra Modern Telecommunications and Workshops (ICUMT)

作者： Katarzyna Wac Gerardo Pinar Mattia Gustarini Jerome Marchanoff Dept. of Computer Science Human-Centric Computing University of Copenhagen Copenhagen Denmark Center for Informatics Quality of Life technologies University of Geneva Geneva Switzerland

Smartphones assist their users throughout daily life activities. There is much emphasis on the user's mobility support in the research at large. However, we have a weak understanding about users mobility (are they really moving?) and how well connected are they across their typical day. First, to infer mobility state of users, we derived and evaluated the accuracy of a machine learning-based model, i.e., MobilitySensor, which is based solely on smartphone built-in sensors. It is a tree-based model, defined for each network operator and its average accuracy reaches 91%. Next, we leverage our algorithm to explore the mobility of 34 users served by 3 different Swiss operators (OP) during a period of six months, correlating it with their connectivity. The user study results showed that users are statistically significantly more mobile than we observed in the past (21±7% of the time, i.e., up to 4.3h vs. 13±12%, i.e., 2.7h in 2011) and when they are mobile, 4G network is available to them 38±12% of the time. Furthermore, when mobile, depending on their operator, they may be provided with up to around 10% of the time with 2.5G connectivity (for OP1 and OP2 vs. only 4% OP3), or provided mainly with 3G (49% for OP1 vs. 34% for OP3). Based on the results we provide a set of design implications for application providers, users and operators alike, all striving to improve the mobile users' quality of experience (QoE).

关键词： Mobile communication Current measurement Mobile computing Quality of service Global Positioning System Context Radiation detectors

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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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Exploring health topics in Chinese social media: An analysis of Sina Weibo 28

Exploring health topics in Chinese social media: An analysis...

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28th AAAI Conference on Artificial Intelligence, AAAI 2014

作者： Wang, Shiliang Paul, Michael J. Dredze, Mark Dept. of Computer Science Human Language Technology Center of Excellence Johns Hopkins University BaltimoreMD21218 United States

ISBN: (纸本)9781577356752

This paper seeks to identify and characterize health-related topics discussed on the Chinese microblogging website, Sina Weibo. We identified nearly 1 million messages containing health-related keywords, filtered from a dataset of 93 million messages spanning five years. We applied probabilistic topic models to this dataset and identified the prominent health topics. We show that a variety of health topics are discussed in Sina Weibo, and that four flu-related topics are correlated with monthly influenza case rates in China. © Copyright 2014, Association for the Advancement of Artificial Intelligence (***). All rights reserved.

关键词： Health

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