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arXiv 2023年

作者： Moawad, Ahmed W. Janas, Anastasia Baid, Ujjwal Ramakrishnan, Divya Saluja, Rachit Ashraf, Nader Jekel, Leon Amiruddin, Raisa Adewole, Maruf Albrecht, Jake Anazodo, Udunna Aneja, Sanjay Anwar, Syed Muhammad Bergquist, Timothy Calabrese, Evan Chiang, Veronica Chung, Verena Conte, Gian Marco Marco Dako, Farouk Eddy, James Ezhov, Ivan Familiar, Ariana Farahani, Keyvan Iglesias, Juan Eugenio Jiang, Zhifan Johanson, Elaine Kazerooni, Anahita Fathi Kofler, Florian Krantchev, Kiril LaBella, Dominic Van Leemput, Koen Li, Hongwei Bran Linguraru, Marius George Link, Katherine E. Liu, Xinyang Maleki, Nazanin Meier, Zeke Menze, Bjoern H. Moy, Harrison Osenberg, Klara Piraud, Marie Reitman, Zachary Shinohara, Russel Takeshi Tahon, Nourel hoda Nada, Ayman Velichko, Yuri S. Wang, Chunhao Wiestler, Benedikt Wiggins, Walter Shafique, Umber Willms, Klara Avesta, Arman Bousabarah, Khaled Chakrabarty, Satrajit Gennaro, Nicolo Holler, Wolfgang Kaur, Manpreet LaMontagne, Pamela Lin, MingDe Lost, Jan Marcus, Daniel S. Maresca, Ryan Merkaj, Sarah Nada, Ayaman Pedersen, Gabriel Cassinelli von Reppert, Marc Sotiras, Aristeidis Teytelboym, Oleg Tillmans, Niklas Westerhoff, Malte Youssef, Ayda Godfrey, Devon Floyd, Scott Rauschecker, Andreas Villanueva-Meyer, Javier Pflüger, Irada Cho, Jaeyoung Bendszus, Martin Brugnara, Gianluca Cramer, Justin Perez-Carillo, Gloria Guzman J. Johnson, Derek R. Kam, Anthony Kwan, Benjamin Yin Ming Lai, Lillian Lall, Neil U. Memon, Fatima Patro, Satya Narayana Petrovic, Bojan So, Tiffany Y. Thompson, Gerard Wu, Lei Schrickel, E. Brooke Bansal, Anu Barkhof, Frederik Besada, Cristina Chu, Sammy Druzgal, Jason Dusoi, Alexandru Farage, Luciano Feltrin, Fabricio Fong, Amy Fung, Steve H. Gray, R. Ian Ikuta, Ichiro Iv, Michael Postma, Alida A. Mahajan, Amit Joyner, David Krumpelman, Chase Letourneau-Guillon, Laurent Lincoln, Christie M. Maros, Mate E. Miller, Elka Morón, Fanny Nimchinsky, Esther A. Ozsarlak, Ozkan Patel, Uresh Rohatgi, Saurabh Saha, Atin Sayah, Anousheh Schwartz, Eric D. Shih, Robert Shiroishi, Mark Trinity health Mid Atlantic Hosiptals DarbyPA United States Department of Radiology and Biomedical Imaging Yale School of Medicine New HavenCT United States Division of Computational Pathology Department of Pathology and Laboratory Medicine School of Medicine Indiana University IndianapolisIN United States Department of Electical and Computer Engineering Cornell University Cornell Tech New YorkNY United States Department of Radiology Weill Cornell Medicine New YorkNY United States ImagineQuant Children’s Hospital of Philadelphia PhiladelphiaPA United States College of Medicine Alfaisal University Riyadh Saudi Arabia DKFZ Division of Translational Neurooncology The WTZ German Cancer Consortium DKTK Partner Site University Hospital Essen Essen Germany Medical Artificial Intelligence Lab Crestview Radiology Lagos Nigeria Sage Bionetworks SeattleWA United States Montreal Neurological Institute McGill University Montreal Canada lab Crestview Radiology Lagos Nigeria Department of Therapeutic Radiology Yale School of Medicine New HavenCT United States Sheikh Zayed Institute for Pediatric Surgical Innovation Children’s National Hospital WashingtonDC United States Department of Radiology Mayo Clinic RochesterMN United States Department of Radiology Duke University Medical Center DurhamNC United States Department of Neurosurgery Yale School of Medicine New HavenCT United States Center for Global Health Perelman School of Medicine University of Pennsylvania PA United States Department of Informatics Technical University Munich Germany Children’s Hospital of Philadelphia University of Pennsylvania PhiladelphiaPA United States Cancer Imaging Program National Cancer Institute National Institutes of Health BethesdaMD United States Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital BostonMA United States Children’s National Hospital WashingtonDC United States PrecisionFDA U.S. Food and Drug Administration S

The translation of AI-generated brain metastases (BM) segmentation into clinical practice relies heavily on diverse, high-quality annotated medical imaging datasets. The BraTS-METS 2023 challenge has gained momentum for testing and benchmarking algorithms using rigorously annotated internationally compiled real-world datasets. This study presents the results of the segmentation challenge and characterizes the challenging cases that impacted the performance of the winning algorithms. Untreated brain metastases on standard anatomic MRI sequences (T1, T2, FLAIR, T1PG) from eight contributed international datasets were annotated in stepwise method: published UNET algorithms, student, neuroradiologist, final approver neuroradiologist. Segmentations were ranked based on lesion-wise Dice and Hausdorff distance (HD95) scores. False positives (FP) and false negatives (FN) were rigorously penalized, receiving a score of 0 for Dice and a fixed penalty of 374 for HD95. The mean scores for the teams were calculated. Eight datasets comprising 1303 studies were annotated, with 402 studies (3076 lesions) released on Synapse as publicly available datasets to challenge competitors. Additionally, 31 studies (139 lesions) were held out for validation, and 59 studies (218 lesions) were used for testing. Segmentation accuracy was measured as rank across subjects, with the winning team achieving a LesionWise mean score of 7.9. The Dice score for the winning team was 0.65 ± 0.25. Common errors among the leading teams included false negatives for small lesions and misregistration of masks in space. The Dice scores and lesion detection rates of all algorithms diminished with decreasing tumor size, particularly for tumors smaller than 100 mm3. In conclusion, algorithms for BM segmentation require further refinement to balance high sensitivity in lesion detection with the minimization of false positives and negatives. The BraTS-METS 2023 challenge successfully curated well-annotated, diverse d

关键词： Image segmentation

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Spatial-Temporal pattern analysis and prediction of air quality in Taiwan

Spatial-Temporal pattern analysis and prediction of air qual...

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IEEE International Conference on Ubi-Media Computing

作者： Ping-Wei Soh Kai-Hsiang Chen Jen-Wei Huang Hone-Jay Chu Institute of Computer and Communication Engineering National Cheng Kung University Tainan Taiwan PhD Program for Multimedia Systems and Intelligent Computing National Cheng Kung University and Academia Sinica Tainan Taiwan Department of Electrical Engineering National Cheng Kung University Tainan Taiwan Department of Geomatics National Cheng Kung University Tainan Taiwan

This study explores the spatial-temporal patterns of particulate matter (PM) in Taiwan. Probability map of PM and daily patterns are discussed in this study. Data mining provides more detailed spatial-temporal information for PM variations and trends. The proposed model will show that data mining provides a relatively high goodness of fit and sufficient space-time explanatory power, particularly air pollution frequency and affect areas. In the proposed model, a method using Dynamic Time Warping is proposed to analyse temporal similarity between stations. The proposed model can eliminate global effect on a single station through the performance of multiple stations. The proposed model will further be used for prediction of PM2.5. The prediction results will discuss the spatial-temporal relations between stations. This study will investigate the distribution of PM and its cyclicality.

关键词： Predictive models Time series analysis Atmospheric modeling Air pollution Conferences Data mining

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SOPHIA: Soft Orthotic Physiotherapy Hand Interactive Aid

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Frontiers in Mechanical engineering 2017年 3卷

作者： McConnell, Alistair C. Vallejo, Marta Moioli, Renan Cipriano Brasil, Fabricio L. Secciani, Nicola Nemitz, Markus P. Riquart, Cecile P. Corne, David W. Vargas, Patricia A. Stokes, Adam A. Robotics Lab School of Mathematical and Computer Sciences Heriot-Watt University Edinburgh United Kingdom Stokes Research Group School of Engineering Institute for Integrated Micro and Nano Systems The University of Edinburgh Edinburgh United Kingdom Graduate Program in Neuroengineering Edmond and Lily Safra International Institute of Neuroscience Santos Dumont Institute Macaiba Brazil

This work describes the design, fabrication, and initial testing of a Soft Orthotic Physiotherapy Hand Interactive Aid (SOPHIA) for stroke rehabilitation. SOPHIA consists of (1) a soft robotic exoskeleton, (2) a microcontroller-based control system driven by a brain–machine interface (BMI), and (3) a sensorized glove for passive rehabilitation. In contrast to other rehabilitation devices, SOPHIA is the first modular prototype of a rehabilitation system that is capable of three tasks: aiding extension based assistive rehabilitation, monitoring patient exercises, and guiding passive rehabilitation. Our results show that this prototype of the device is capable of helping healthy subjects to open their hand. Finger extension is triggered by a command from the BMI, while using a variety of sensors to ensure a safe motion. All data gathered from the device will be used to guide further improvements to the prototype, aiming at developing specifications for the next generation device, which could be used in future clinical trials. © Copyright © 2017 McConnell, Vallejo, Moioli, Brasil, Secciani, Nemitz, Riquart, Corne, Vargas and Stokes.

关键词： Orthotics

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Heuristic regression method for descriptive data analysis 16

Heuristic regression method for descriptive data analysis

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16th International Conference on Environment and Electrical engineering, EEEIC 2016

作者： Gomes, Flavio A. Gomes, Viviane M. Assis, Alfredo De O. Reis, Marcio R. Da C. Da Cruz, Gelson Calixto, Wesley P. Electrical Mechanical and Computer Engineering School University of Goias Brazil Experimental and Technological Research and Study Group Federal Institute of Goias Brazil Program in Electronic Systems and Automation University of Brasilia Brazil

ISBN: (纸本)9781509023196

The purpose of this paper is to use the hybridized optimization method in order to find mathematical structures for analysis of experimental data. The heuristic optimization method will be hybridized with deterministic optimization method in order to that structures found require not knowledge about data generated experimentally. Three case studies are proposed and discussed to validate the results. The proposed method has viable solution for the analysis of experimental data and extrapolation, with mathematical expression reduced. © 2016 IEEE.

关键词： Heuristic methods

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Ten simple rules for reproducible research in jupyter notebooks

arXiv

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arXiv 2018年

作者： Rule, Adam Birmingham, Amanda Zuniga, Cristal Altintas, Ilkay Huang, Shih-Cheng Knight, Rob Moshiri, Niema Nguyen, Mai H. Rosenthal, Sara Brin Pérez, Fernando Rose, Peter W. Design Lab UC San Diego San DiegoCA United States Center for Computational Biology and Bioinformatics UC San Diego San DiegoCA United States Department of Pediatrics UC San Diego San DiegoCA United States Data Science Hub San Diego Supercomputer Center UC San Diego San DiegoCA United States Departments of Bioengineering and Computer Science and Engineering Center for Microbiome Innovation UC San Diego San DiegoCA United States Bioinformatics and Systems Biology Graduate Program UC San Diego San DiegoCA United States Department of Statistics Berkeley Institute for Data Science UC Berkeley Lawrence Berkeley National Laboratory BerkeleyCA United States Biomedical Informatics Graduate Program Stanford University StanfordCA United States

Reproducibility of computational studies is a hallmark of scientific methodology. It enables researchers to build with confidence on the methods and findings of others, reuse and extend computational pipelines, and thereby drive scientific progress. Since many experimental studies rely on computational analyses, biologists need guidance on how to set up and document reproducible data analyses or simulations. In this paper, we address several questions about reproducibility. For example, what are the technical and non-technical barriers to reproducible computational studies? What opportunities and challenges do computational notebooks offer to overcome some of these barriers? What tools are available and how can they be used effectively? We have developed a set of rules to serve as a guide to scientists with a specific focus on computational notebook systems, such as Jupyter Notebooks, which have become a tool of choice for many applications. Notebooks combine detailed workflows with narrative text and visualization of results. Combined with software repositories and open source licensing, notebooks are powerful tools for transparent, collaborative, reproducible, and reusable data analyses. Copyright © 2018, The Authors. All rights reserved.

关键词： Digital storage

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Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing

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Nature biotechnology 2020年第4期38卷 504页

作者： Christian Lieven Moritz E Beber Brett G Olivier Frank T Bergmann Meric Ataman Parizad Babaei Jennifer A Bartell Lars M Blank Siddharth Chauhan Kevin Correia Christian Diener Andreas Dräger Birgitta E Ebert Janaka N Edirisinghe José P Faria Adam M Feist Georgios Fengos Ronan M T Fleming Beatriz García-Jiménez Vassily Hatzimanikatis Wout van Helvoirt Christopher S Henry Henning Hermjakob Markus J Herrgård Ali Kaafarani Hyun Uk Kim Zachary King Steffen Klamt Edda Klipp Jasper J Koehorst Matthias König Meiyappan Lakshmanan Dong-Yup Lee Sang Yup Lee Sunjae Lee Nathan E Lewis Filipe Liu Hongwu Ma Daniel Machado Radhakrishnan Mahadevan Paulo Maia Adil Mardinoglu Gregory L Medlock Jonathan M Monk Jens Nielsen Lars Keld Nielsen Juan Nogales Intawat Nookaew Bernhard O Palsson Jason A Papin Kiran R Patil Mark Poolman Nathan D Price Osbaldo Resendis-Antonio Anne Richelle Isabel Rocha Benjamín J Sánchez Peter J Schaap Rahuman S Malik Sheriff Saeed Shoaie Nikolaus Sonnenschein Bas Teusink Paulo Vilaça Jon Olav Vik Judith A H Wodke Joana C Xavier Qianqian Yuan Maksim Zakhartsev Cheng Zhang Novo Nordisk Foundation Center for Biosustainability Technical University of Denmark Lyngby Denmark. Systems Biology Lab Amsterdam Institute of Molecular and Life Sciences (AIMMS) Vrije Universiteit Amsterdam Amsterdam the Netherlands. BioQUANT/COS Heidelberg University Heidelberg Germany. Ecole Polytechnique Fédérale de Lausanne Laboratory of Computational Systems Biotechnology Lausanne Switzerland. iAMB-Institute of Applied Microbiology ABBt-Aachen Biology and Biotechnology RWTH Aachen University Aachen Germany. Department of Bioengineering University of California La Jolla CA USA. Department of Chemical Engineering and Applied Chemistry University of Toronto Toronto Ontario Canada. Human Systems Biology Laboratory Instituto Nacional de Medicina Genomica & Coordinación de la Investigación Científica-Red de Apoyo a la Investigación UNAM Mexico City Mexico. Institute for Systems Biology Seattle WA USA. Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens Institute for Biomedical Informatics (IBMI) Tübingen Germany. Department of Computer Science University of Tübingen Tübingen Germany. German Center for Infection Research (DZIF) partner site Tübingen Tübingen Germany. Australian Institute for Bioengineering and Nanotechnology The University of Queensland Brisbane Queensland Australia. Argonne National Laboratory Lemont IL USA. Analytical Biosciences Division of Systems Biomedicine and Pharmacology Leiden Academic Centre for Drug Research Leiden University Leiden the Netherlands. Department of Systems Biology Centro Nacional de Biotecnología Consejo Superior de Investigaciones Científicas (CNB-CSIC) Madrid Spain. Centro de Biotecnología y Genómica de Plantas (CBGP UPM-INIA) Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) Madrid Spain. Department of Animal and Aquacultural Sciences Faculty of Biosciences Norwegian University of Life Sciences Oslo Norway

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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Applying the MVC EA-IRPM to reporting-guidelines in medicine: A strategy that is a web system

Applying the MVC EA-IRPM to reporting-guidelines in medicine...

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IEEE EMBS International Conference on Information Technology Applications in Biomedicine (ITAB)

作者： Patrick Letouze J. I. M. de Souza Valéria Martins Silva Glaubos Climaco F. B. Chagas Joao Y. Ishihara Faculty of Computer Science Universidade Federal do Tocantins Palmas Brazil Universidade Federal do Tocantins Palmas TO BR Graduate Program of Systems' Engineering and Computation Universidade Federal do Rio de Janeiro Rio de Janeiro Brazil Department of Informatics Universidade Federal do Maranh/ ao - UFMA Faculty of Computer Science Faculdade Pitagoras Imperatriz Imperatriz Brazil Faculty of Electrical Engineering Universidade de Brasília Brasília Brazil

ISBN: (纸本)9781509041800

Reporting-Guidelines in Medicine play an important role in promoting the quality of reports in health-related research. For instance, a poorly reported research may induce misinterpretation and inappropriate clinical settings. Basically, three major issues regarding Reporting-Guidelines in Medicine has to be addressed: (1) the existence of lots of reporting guidelines covering a broad spectrum of medical research increases the difficulties when reporting a medical research because it may not be clear which guidelines are applicable, or if all related guidelines are considered; (2) most guideline developers have not described how their guidance was developed, consequently tracking guidelines and features for evaluation, or even for correcting, may be not possible; (3) few guideline developers have evaluated the effectiveness of their guidance, then the real value that the guideline brings to reporting the research is not assured. Hence, we propose a solution to these three issues based on the Model-View-Controller Evolutionary Acquisition Interdisciplinary Research Project Management (MVC EA-IRPM) that is simultaneously a strategy and a web system for the development and management of reporting guidelines.

关键词： Guidelines Project management Planning Adaptation models Phase measurement systems architecture Systematics

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Self-Powered Triboelectric Inertial Sensor Ball for IoT and Wearable Applications

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Journal of Physics: Conference Series 2018年第1期1052卷

作者： Qiongfeng Shi Hao Wang Tianyiyi He Chengkuo Lee Department of Electrical and Computer Engineering National University of Singapore 4 Engineering Drive 3 Singapore 117576 Center for Intelligent Sensors and MEMS National University of Singapore E6 #05-11F 5 Engineering Drive 1 Singapore 117608 Hybrid-Integrated Flexible (Stretchable) Electronic Systems Program National University of Singapore E6 #05-4 5 Engineering Drive 1 Singapore 117608

Motion monitoring can provide useful information for rehabilitation or diagnostics purpose. Recently, triboelectric nanogenerator (TENG) has developed rapidly as a promising technology for energy harvesting and self-powered sensing. However, research effort of using TENG for multi-axis acceleration sensing is very limited. What is more, rotation sensing has not been achieved by TENG to date. Here we propose a 3-dimensional (3D) symmetric triboelectric nanogenerator based inertial sensor ball (TENG-Ball) for self-powered multi-axis acceleration and rotation sensing. The TENG-Ball has great potential in motion monitoring, internet-of-things (IoT) and wearable applications.

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Distributed multi-robot coordination for dynamic perimeter surveillance in uncertain environments

Distributed multi-robot coordination for dynamic perimeter s...

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IEEE International Conference on Robotics and Automation (ICRA)

作者： Alexander Jahn Reza Javanmard Alitappeh David Saldaña Luciano C. A. Pimenta Andre G. Santos Mario F. M. Campos Graduate Program in Electrical Engineering (PPGEE) National Institute of Science and Technology for Cooperative Autonomous Systems Applied to Security and Environment Departamento de Informatica Universidade Federal de Vicosa Computer Science Department Universidade Federal de Minas Gerais Universidade Federal de Minas Gerais Belo Horizonte MG BR

In this work, multiple robots circulate around the boundary of a desired region in order to create a virtual fence. The aim of the this fence is to avoid internal or external agents crossing through the delimited area. In this paper, we propose a distributed technique that allows a team of robots to plan the deformation of the boundary shape in order to escort the safe region from one place to a goal. Our proposal is composed of two parts. First, we present a distributed planning method for the dynamic boundary. We model the resulting plan as a twice differentiable function. Second, we use the obtained function to guide the robot team, where every member uses only local information for the controller. The robots distribute themselves along the time-varying perimeter and patrol around it. We show in simulation how the robots behave in partially/totally unknown environments with static obstacles.

关键词： Shape Robot kinematics Trajectory Planning Robot sensing systems Dynamics

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Guest editorial: The 2016 capstone design conference

Guest editorial: The 2016 capstone design conference

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作者： Brackin, Patsy Howe, Susannah Rogers, Peter Stanfill, R. Keith Beyerlein, Steven Kanai, Junichi Vallino, Jim Palo, Scott Department of Mechanical Engineering Rose-Hulman Institute of Technology 5500 Wabash Avenue CM 165 Terre HauteIN47803 United States Picker Engineering Program Smith College 151 Ford Hall NorthamptonMA01063 United States Department of Engineering Education Ohio State University 3070 Smith Laboratory 174 W. 18th Avenue ColumbusOH43210 United States Engineering Innovation Institute University of Florida P.O. Box 116000 GainesvilleFL32611-6000 United States Department of Mechanical Engineering University of Idaho 875 Perimeter Drive MoscowID83844-0902 United States Department of Electrical Computer and Systems Engineering Rensselaer Polytechnic Institute TroyNY United States Department of Software Engineering Rochester Institute of Technology 134 Lomb Memorial Drive RochesterNY14623-5608 United States Department of Aerospace Engineering Sciences University of Colorado 429 UCB BoulderCO80309 United States

The goal of the 2016 Capstone Design Conference held in Columbus, OH was to build upon the success of previous conferences (2007 and 2010 in Boulder, CO, 2012 in Champaign, IL, and 2014 in Columbus, OH) and expand the community of educators, students, and industry members engaged in discussing, analyzing, and improving capstone design education. Sessions at the 2016 Capstone Design Conference were designed for vibrant sharing of ideas and experiences across the capstone community via interactive panel sessions, poster session socials, hands-on workshops, and other formal and informal networking activities. This editorial discusses conference planning, structure, and feedback. Technical papers that follow in this issue document scholarship surrounding noteworthy capstone course innovations. Most of these began as four page peer-reviewed papers included in the conference proceedings. © 2017 TEMPUS Publications.

关键词： Teaching

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