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Author Correction: A systems biology approach uncovers cell-specific gene regulatory effects of genetic associations in multiple sclerosis

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Nature communications 2019年第1期10卷 2956页

作者： Lohith Madireddy Kicheol Kim Xiaoming Jia Adam Santaniello Stacy J. Caillier Bruce A. C. Cree Roland Henry Stephen L. Hauser Jorge R. Oksenberg Sergio E. Baranzini Nikolaos A. Patsopoulos Philip De Jager Chris Cotsapas Matthew R. Lincoln David A. Hafler Steffan D. Bos Hanne F. Harbo Tone Berge Elisabeth G. Celius Ashley Beecham Jacob McCauley Margaret A. Pericak-Vance Till F. M. Andlauer Christiane Gasperi Bernhard Hemmer Lisa F. Barcellos Luisa Bernardinelli Filippo Martinelli-Boneschi David R. Booth Graeme J. Stewart Farren Briggs Jonathan Haines Manuel Comabella Giancarlo Comi Federica Esposito Sandra D’Alfonso Katrina Dedham Pierre Duquette Efthimios Dardiotis Bertrand Fontaine An Goris Bénédicte Dubois Pierre-Antoine Gourraud Georgios Hadjigeorgiou Clive Hawkins Seema Kalra Rogier Hintzen Dana Horakova Noriko Isobe Jun-ichi Kira Michael Khalil Ingrid Kockum Tomas Olsson Christina M. Lill Felix Luessi Frauke Zipp Roland Martin Annette Oturai Aarno Palotie Janna Saarela Adrian Ivinson Bruce V. Taylor Alastair Compston Stephen Sawcer Weill Institute for Neurosciences Department of Neurology University of California San Francisco San Francisco CA 94158 USA Bakar Institute for Computational Health Science. University of California San Francisco San Francisco CA 94158 USA Systems Biology and Computer Science Program Ann Romney Center for Neurological Diseases Department of Neurology and Division of Genetics Department of Medicine Brigham & Women’s Hospital Harvard Medical School Boston MA 02115 USA Broad Institute of Harvard University and Massachusetts Institute of Technology Cambridge MA 02142 USA Department of Neurology Center for Translational and Computational Neuroimmunology and Multiple Sclerosis Center Columbia University Medical Center New York NY 10032 USA Departments of Neurology Yale School of Medicine 300 George St New Haven CT 06511 USA Department of Genetics Yale School of Medicine 300 George St New Haven CT 06511 USA Institute of Clinical Medicine University of Oslo Oslo 0318 Norway Department of Neurology Oslo University Hospital Oslo 0424 Norway Department of Mechanical Electronics and Chemical Engineering Oslo Metropolitan University Oslo 0167 Norway Institute of Health and Society University of Oslo Oslo 0318 Norway John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL 33136 USA Dr. John T. Macdonald Foundation Department of Human Genetics University of Miami Miller School of Medicine Miami FL 33136 USA Department of Neurology Klinikum rechts der Isar School of Medicine Technical University of Munich 81675 Munich Germany Munich Cluster for Systems Neurology (SyNergy) 81377 Munich Germany Division of Epidemiology School of Public HealthUniversity of California 324 Stanley Hall MC#3220 Berkeley CA 94720 USA Section of Biostatistics Neurophyisiology and Psychiatry Unit of medical and genomic statistics Universita of Pavia Pavia 27100 Italy Department of Biomedical Sciences for Health Univers

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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Calibrationless parallel imaging reconstruction based on structured low-rank matrix completion

Calibrationless parallel imaging reconstruction based on str...

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作者： Shin, Peter J. Larson, Peder E. Z. Ohliger, Michael A. Elad, Michael Pauly, John M. Vigneron, Daniel B. Lustig, Michael Department of Radiology and Biomedical Imaging University of California at San Francisco San FranciscoCA United States UC Berkeley-UCSF Graduate Program in Bioengineering CA United States Department of Electrical Engineering and Computer Science University of California at Berkeley BerkeleyCA United States Department of Computer Science Technion'Israel Institute of Technology Haifa Israel Magnetic Resonance Systems Research Laboratory Department of Electrical Engineering Stanford University StanfordCA United States

Purpose: A calibrationless parallel imaging reconstruction method, termed simultaneous autocalibrating and k-space estimation (SAKE), is presented. It is a data-driven, coil-by-coil reconstruction method that does not require a separate calibration step for estimating coil sensitivity information. Methods: In SAKE, an undersampled, multichannel dataset is structured into a single data matrix. The reconstruction is then formulated as a structured low-rank matrix completion problem. An iterative solution that implements a projection-ontosets algorithm with singular value thresholding is described. Results: Reconstruction results are demonstrated for retrospectively and prospectively undersampled, multichannel Cartesian data having no calibration signals. Additionally, non-Cartesian data reconstruction is presented. Finally, improved image quality is demonstrated by combining SAKE with wavelet-based compressed sensing. Conclusion: Because estimation of coil sensitivity information is not needed, the proposed method could potentially benefit MR applications where acquiring accurate calibration data is limiting or not possible at all. © 2013 Wiley Periodicals, Inc.

关键词： Compressed sensing

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Erratum to: The real cost of sequencing: scaling computation to keep pace with data generation

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Genome biology 2016年第1期17卷 78页

作者： Paul Muir Shantao Li Shaoke Lou Daifeng Wang Daniel J Spakowicz Leonidas Salichos Jing Zhang George M Weinstock Farren Isaacs Joel Rozowsky Mark Gerstein Department of Molecular Cellular and Developmental Biology Yale University New Haven CT 06520 USA. Systems Biology Institute Yale University West Haven CT 06516 USA. Integrated Graduate Program in Physical and Engineering Biology Yale University New Haven CT 06520 USA. Program in Computational Biology and Bioinformatics Yale University New Haven CT 06520 USA. Department of Molecular Biophysics and Biochemistry Yale University New Haven CT 06520 USA. The Jackson Laboratory for Genomic Medicine Farmington CT 06032 USA. Program in Computational Biology and Bioinformatics Yale University New Haven CT 06520 USA. mark@***. Department of Molecular Biophysics and Biochemistry Yale University New Haven CT 06520 USA. mark@***. Department of Computer Science Yale University New Haven CT 06520 USA. mark@***.

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Unobtrusive Monitoring of ECG-derived Features During Daily Smartphone Use

Unobtrusive Monitoring of ECG-derived Features During Daily ...

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Annual International Conference of the IEEE engineering in Medicine and Biology Society

作者： Sungjun Kwon Seungwoo Kang Youngki Lee Chungkuk Yoo Kwangsuk Park Interdisciplinary Program of Bioengineering Seoul National University Department of Computer Science Korea Advanced Institute of Science and Technology (KAIST) Department of Information Systems at Singapore Management University Department of Biomedical Engineering College of Medicine Seoul National University

ISBN: (纸本)9781424479276

Heart rate variability (HRV) is known to be one of the representative ECG-derived features that are useful for diverse pervasive healthcare applications. The advancement in daily physiological monitoring technology is enabling monitoring of HRV in people's everyday lives. In this study, we evaluate the feasibility of measuring ECG-derived features such as HRV, only using the smartphone-integrated ECG sensors system named Sinabro. We conducted the evaluation with 13 subjects in five predetermined smartphone use cases. The result shows the potential that the smartphone-based sensing system can support daily monitoring of ECG-derived features;The average errors of HRV over all participants ranged from 1.65% to 5.83% (SD: 2.54～10.87) for five use cases. Also, all of individual HRV parameters showed less than 5% of average errors for the three reliable cases.

关键词： Power system stability Circuit stability Stability criteria Transient analysis Steady-state

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A web-based, hospital-wide health care-associated bloodstream infection surveillance and classification system: Development and evaluation

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JMIR Medical Informatics 2015年第3期3卷 e31页

作者： Tseng, Yi-Ju Wu, Jung-Hsuan Lin, Hui-Chi Chen, Ming-Yuan Ping, Xiao-Ou Sun, Chun-Chuan Shang, Rung-Ji Sheng, Wang-Huei Chen, Yee-Chun Lai, Feipei Chang, Shan-Chwen Graduate Institute of Biomedical Electronics and Bioinformatics National Taiwan University Taipei Taiwan Computational Health Informatics Program Boston Children's Hospital Boston MA United States Department of Electrical Engineering National Taiwan University Taipei Taiwan Center for Infection Control National Taiwan University Hospital Taipei Taiwan National Taiwan University Hospital Information Systems Office Taipei Taiwan Department of Computer Science and Information Engineering National Taiwan University Taipei Taiwan Department of Internal Medicine National Taiwan University Hospital and College of Medicine Taipei Taiwan National Health Research Institutes National Institute of Infectious Diseases and Vaccinology Miaoli Taiwan

Background: Surveillance of health care-associated infections is an essential component of infection prevention programs, but conventional systems are labor intensive and performance dependent. Objective: To develop an automatic surveillance and classification system for health care-associated bloodstream infection (HABSI), and to evaluate its performance by comparing it with a conventional infection control personnel (ICP)-based surveillance system. Methods: We developed a Web-based system that was integrated into the medical information system of a 2200-bed teaching hospital in Taiwan. The system automatically detects and classifies HABSIs. Results: In this study, the number of computer-detected HABSIs correlated closely with the number of HABSIs detected by ICP by department (n=20;r=.999 P<.001) and by time (n=14;r=.941;P<.001). Compared with reference standards, this system performed excellently with regard to sensitivity (98.16%), specificity (99.96%), positive predictive value (95.81%), and negative predictive value (99.98%). The system enabled decreasing the delay in confirmation of HABSI cases, on average, by 29 days. Conclusions: This system provides reliable and objective HABSI data for quality indicators, improving the delay caused by a conventional surveillance system. © 2020 JMIR Publications Inc. All rights reserved.

关键词： Health care-associated infection Infection control Information systems Surveillance Web-based services

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Extracting Semantic Information from Patent Claims Using Phrasal Structure Annotations

Extracting Semantic Information from Patent Claims Using Phr...

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Brazilian Conference on Intelligent systems (BRACIS)

作者： Danilo Silva de Carvalho Felipe Maia Galvão França Priscila Machado Vieira Lima Systems Engineering and Computer Science Program-COPPE Universidade Federal do Rio de Janeiro Rio de Janeiro Brazil Instituto Tércio Pacitti (NCE) Universidade Federal do Rio de Janeiro Rio de Janeiro Brazil

The rapid change of trading values from tangible assets to Intelectual Property has put both businesses and academia in a race to acquire and protect the rights to exploit such property. This is mainly accomplished in the form of patent issuing by the governments, being time consuming and complicated due to the vast amount of documents that need to be analyzed in order to assert the novelty or validity of a patent application. Patent information retrieval research is thus growing quickly to support document analysis across multiple domains and information systems. One of the big challenges in patent analysis is the identification of the elements of innovation (concepts, processes, materials) and the relations between them, in the patent text. This paper presents a method for extracting semantic information from patent claims by using semantic annotations on phrasal structures, abstracting domain ontology information and outputting ontology-friendly structures to achieve generalization. An extraction system built upon the method is briefly evaluated on a document sample from INPI, the Brazilian patent office, a challenging information source.

关键词： Semantics Patents Syntactics Data mining Training Ontologies Testing

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A reconfigurable ray-tracing Multi-Processor SoC with hardware replication-aware instruction set extension

A reconfigurable ray-tracing Multi-Processor SoC with hardwa...

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13th International Conference on Algorithms and Architectures for Parallel Processing, ICA3PP 2013

作者： Nery, Alexandre S. Nedjah, Nadia França, Felipe M.G. Jozwiak, Lech Corporaal, Henk LAM - Computer Architecture and Microeletronics Laboratory Systems Engineering and Computer Science Program COPPE Federal University of Rio de Janeiro Brazil Department of Electronics Engineering and Telecommunications Faculty of Engineering State University of Rio de Janeiro Brazil Department of Electrical Engineering - Electronic Systems Eindhoven University of Technology Netherlands

ISBN: (纸本)9783319038582

Application code and processor parallelization, together with instruction set customization, are the most common and effective ways to enhance the performance and efficiency of application-specific processors (ASIPs). Both the effective code parallelization and data/task parallelism exploitation, as well as effective instruction set customization, enable an ASIP to achieve a significant performance improvement using limited extra hardware resources. However, a naive parallelization or instruction set customization may not result in the required performance improvement, leading to a waste of computing and energy resources. Therefore, when performing parallelization or custom instruction selection, complex tradeoffs between processing speed, circuit area and power consumption must be closely observed. In this paper, we propose and discuss an efficient ASIP-based Multi-Processor System-on-a-Chip (MPSoC) design for ray-tracing, exploiting application parallelism and hardware replication-aware instruction set customization. Without hardware sharing among the custom instructions units, the proposed parallel ray-tracer MPSoC design with custom instructions achieves 77% speed up in comparison to a single microprocessor design with the default instruction set. However, with the replication-aware instruction set customization, the speed up increases to 81%. © Springer International Publishing Switzerland 2013.

关键词： Integrated circuit design

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Development and evaluation of a hospital-wide healthcare-associated surgical site infection detection algorithm

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Journal of Microbiology, Immunology and Infection 2015年第2期48卷 S43-S43页

作者： Yi-Ju Tseng Bo-Chiang Huang Hui-Chi Lin Ming-Yuan Chen Rung-Ji Shang Wang-Huei Sheng Yee-Chun Chen Feipei Lai Shan-Chwen Chang Children's Hospital Informatics Program Boston Children's Hospital Boston MA USA Graduate Institute of Biomedical Electronics and Bioinformatics National Taiwan University Taiwan Center for Infection Control National Taiwan University Hospital (NTUH) Taiwan Information Systems Office NTUH Taipei Taiwan Department of Internal Medicine NTUH and College of Medicine Taiwan National Institute of Infectious Diseases and Vaccinology National Health Research Institutes Taiwan Department of Computer Science and Information Engineering National Taiwan University Taiwan

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Provenance traces of the swift parallel scripting system 13

Provenance traces of the swift parallel scripting system

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Joint EDBT/ICDT 2013 Workshops

作者： Gadelha Jr., Luiz M. R. Wilde, Michael Mattoso, Marta Foster, Ian National Laboratory for Scientific Computing Brazil Mathematics and Computer Science Division Argonne National Laboratory United States Computation Institute Argonne National Laboratory University of Chicago United States Computer and Systems Engineering Program Federal University of Rio de Janeiro Brazil Department of Computer Science University of Chicago United States

ISBN: (纸本)9781450315999

In this abstract, we describe provenance traces generated from executions of scientific workflows managed by the Swift parallel scripting system. They follow a provenance data model, used by MTCProv, the provenance management component of Swift. It is similar to PROV, representing most of its core concepts and including additional information about the scientific domain, computational resource consumption, and prospective provenance. We describe provenance queries that follow patterns commonly found in high performance computing and that are straightforward to support with MTCProv's built-in procedures. These queries often involve costly relational join operations and recursion, providing a relevant case for benchmarking. © 2013 Authors.

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Hardware-based parallel firefly algorithm for embedded applications

Hardware-based parallel firefly algorithm for embedded appli...

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2013 NASA/ESA Conference on Adaptive Hardware and systems, AHS 2013

作者： Muñoz, Daniel M. Llanos, Carlos H. Dos Santos Coelho, Leandro Ayala-Rincón, Mauricio Electronics Engineering Graduate Program Faculty of Gama University of Brasilia Brasilia DF Brazil Department of Mechanical Engineering Automation and Control Group/GRACO University of Brasilia Brasilia DF Brazil Industrial and Systems Engineering Graduate Program LAS/PPGEPS Pontifical Catholic University of Parana Curitiba Parana Brazil Departments of Computer Science and Mathematics University of Brasilia Brasilia DF Brazil

ISBN: (纸本)9781467363839

The firefly algorithm (FA) is a new population-based metaheuristic bioinspired on the behavior of the flashing characteristics of fireflies. As a population-based algorithm, the FA suffers from large execution times specifically for embedded optimization problems with computational limitations. For reducing execution times we propose a hardware parallel architecture of the FA algorithm that facilitates the implementation in Field programmable Gate Arrays (FPGAs). In addition, this work proposes the application of the opposition-based learning (OBL) approach to the FA algorithm. The respective hardware implementation (HPOFA) was mapped into a Virtex5 FPGA device and numerical experiments using four well-known benchmark problems demonstrate that the opposition-based approach allows the FA algorithm to improve its functionality, preserving the swarm diversity and avoiding the premature convergence problem. Synthesis results point out that the HPOFA architecture is effectively mapped in hardware and is suitable for embedded applications. © 2013 IEEE.

关键词： Parallel architectures

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