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Highlights from the 11th ISCB Student Council Symposium 2015. Dublin, Ireland. 10 July 2015

BMC bioinformatics 2016年第3期17 Suppl 3卷 95页

作者： Katie Wilkins Mehedi Hassan Margherita Francescatto Jakob Jespersen R. Gonzalo Parra Bart Cuypers Dan DeBlasio Alexander Junge Anupama Jigisha Farzana Rahman Griet Laenen Sander Willems Lieven Thorrez Yves Moreau Nagarajan Raju Sonia Pankaj Chothani C. Ramakrishnan Masakazu Sekijima M. Michael Gromiha Paddy J Slator Nigel J Burroughs Przemysław Szałaj Zhonghui Tang Paul Michalski Oskar Luo Xingwang Li Yijun Ruan Dariusz Plewczynski Giulia Fiscon Emanuel Weitschek Massimo Ciccozzi Paola Bertolazzi Giovanni Felici Pieter Meysman Manu Vanaerschot Maya Berg Hideo Imamura Jean-Claude Dujardin Kris Laukens Westa Domanova James R. Krycer Rima Chaudhuri Pengyi Yang Fatemeh Vafaee Daniel J. Fazakerley Sean J. Humphrey David E. James Zdenka Kuncic Plant Pathology and Plant-Microbe Biology Section School of Integrative Plant Science Cornell University Ithaca USA Graduate Field of Computational Biology Cornell University Ithaca USA School of Computing & Mathematics University of South Wales Cardiff UK Department of Genome Biology for Neurodegenerative Diseases German Center for Neurodegenerative Diseases (DZNE) within the Helmholtz Association ᅟ Germany Department of Surgery Massachusetts General Hospital The Broad Institute of MIT and Harvard Boston USA Department of Systems Biology Technical University of Denmark Kemitorvet Denmark Protein Physiology Lab Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires Buenos Aires Argentina Molecular Parasitology Unit (MPU) Institute of Tropical Medicine Antwerp Belgium Advanced Database Research and Modeling (ADReM) research group University of Antwerp Antwerpen Belgium Department of Computer Science University of Arizona Tucson USA Department of Veterinary Clinical and Animal Sciences Center for non-coding RNA in Technology and Health University of Copenhagen Copenhagen Denmark University College Dublin Dublin Ireland Department of Electrical Engineering (ESAT) STADIUS Center for Dynamical Systems Signal Processing and Data Analytics KU Leuven Leuven Belgium Minds Medical IT Department Leuven Belgium Scientific Institute of Public Health (WIV-ISP) Platform of Biotechnology and Molecular Biology (PBB) Brussels Belgium Department of Development and Regeneration @ Kulak KU Leuven Kortrijk Belgium Department of Biotechnology Bhupat and Jyoti Metha School of Biosciences Indian Institute of Technology Madras Chennai India Philips Research North America Briarcliff Manor USA Global Scientific Information and Computing Center (GSIC) Tokyo Institute of Technology Tokyo Japan Systems Biology Centre University of Warwick Senate House Coventry UK Systems Biology Doctoral Training Centre University of Warwick Senate House Coventry UK Center for B

A1 Highlights from the eleventh ISCB Student Council Symposium 2015 Katie Wilkins, Mehedi Hassan, Margherita Francescatto, Jakob Jespersen, R. Gonzalo Parra, Bart Cuypers, Dan DeBlasio, Alexander Junge, Anupama Jigisha, Farzana Rahman O1 Prioritizing a drug’s targets using both gene expression and structural similarity Griet Laenen, Sander Willems, Lieven Thorrez, Yves Moreau O2 Organism specific protein-RNA recognition: A computational analysis of protein-RNA complex structures from different organisms Nagarajan Raju, Sonia Pankaj Chothani, C. Ramakrishnan, Masakazu Sekijima; M. Michael Gromiha O3 Detection of Heterogeneity in Single Particle Tracking Trajectories Paddy J Slator, Nigel J Burroughs O4 3D-NOME: 3D NucleOme Multiscale Engine for data-driven modeling of three-dimensional genome architecture Przemysław Szałaj, Zhonghui Tang, Paul Michalski, Oskar Luo, Xingwang Li, Yijun Ruan, Dariusz Plewczynski O5 A novel feature selection method to extract multiple adjacent solutions for viral genomic sequences classification Giulia Fiscon, Emanuel Weitschek, Massimo Ciccozzi, Paola Bertolazzi, Giovanni Felici O6 A systems Biology Compendium for Leishmania donovani Bart Cuypers, Pieter Meysman, Manu Vanaerschot, Maya Berg, Hideo Imamura, Jean-Claude Dujardin, Kris Laukens O7 Unravelling signal coordination from large scale phosphorylation kinetic data Westa Domanova, James R. Krycer, Rima Chaudhuri, Pengyi Yang, Fatemeh Vafaee, Daniel J. Fazakerley, Sean J. Humphrey, David E. James, Zdenka Kuncic

关键词： Visceral Leishmaniasis Feature Selection Method Frequent Itemset Mining Leishmania Donovani Student Council

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Erratum to: Methods for evaluating medical tests and biomarkers

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Diagnostic and prognostic research 2017年第1期1卷 11页

作者： Gowri Gopalakrishna Miranda Langendam Rob Scholten Patrick Bossuyt Mariska Leeflang Anna Noel-Storr James Thomas Iain Marshall Byron Wallace Penny Whiting Clare Davenport Gowri GopalaKrishna Isabel de Salis Sue Mallett Robert Wolff Richard Riley Marie Westwood Jos Kleinen Gary Collins Hans Reitsma Karel Moons Antonia Zapf Annika Hoyer Katharina Kramer Oliver Kuss J Ensor J J Deeks E C Martin R D Riley Gerta Rücker Susanne Steinhauser Martin Schumacher Joie Ensor Kym Snell Brian Willis Thomas Debray Jon Deeks Lavinia Ferrante di Ruffano Sian Taylor-Phillips Chris Hyde Stuart A Taylor Gauraang Batnagar Lavinia Ferrante Di Ruffano Farah Seedat Aileen Clarke Sarah Byron Frances Nixon Rebecca Albrow Thomas Walker Carla Deakin Zhivko Zhelev Harriet Hunt Yaling Yang Lucy Abel James Buchanan Thomas Fanshawe Bethany Shinkins Laure Wynants Jan Verbakel Sabine Van Huffel Dirk Timmerman Ben Van Calster Aeliko Zwinderman Jason Oke Jack O'Sullivan Rafael Perera Brian Nicholson Hannah L Bromley Tracy E Roberts Adele Francis Denniis Petrie G Bruce Mann Kinga Malottki Holly Smith Lucinda Billingham Alice Sitch Oke Gerke Mie Holm-Vilstrup Eivind Antonsen Segtnan Ulrich Halekoh Poul Flemming Høilund-Carlsen Bernard G Francq Jac Dinnes Julie Parkes Walter Gregory Jenny Hewison Doug Altman William Rosenberg Peter Selby Julien Asselineau Paul Perez Aïssatou Paye Emilie Bessede Cécile Proust-Lima Christiana Naaktgeboren Joris de Groot Anne Rutjes Johannes Reitsma Emmanuel Ogundimu Jonathan Cook Yannick Le Manach Yvonne Vergouwe Romin Pajouheshnia Rolf Groenwold Karen Moons Linda Peelen Daan Nieboer Bavo De Cock Micael J Pencina Ewout W Steyerberg Jennifer Cooper Nick Parsons Chris Stinton Steve Smith Andy Dickens Rachel Jordan Alexandra Enocson David Fitzmaurice Peymane Adab Charles Boachie Gaj Vidmar Karoline Freeman Martin Connock Rachel Court Carl Moons Jessica Harris Andrew Mumford Zoe Plummer Kurtis Lee Barnaby Reeves Chris Rogers Veerle Verheyden Gianni D Angelini Gavin J Murphy Jeremy Huddy Melody Ni Katherine Good Graham Cooke 1Department of Clinical Epidemiology Biostatistics & Bioinformatics Academic Medical Center University of Amsterdam Amsterdam The Netherlands. 2Cochrane Netherlands Julius Center for Health Sciences and Primary Care University Medical Center Utrecht Utrecht Netherlands. 234Department of Clinical Epidemiology Biostatistics & Bioinformatics Academic Medical Center University of Amsterdam Amsterdam The Netherlands. 49Department of Clinical Epidemiology Biostatistics & Bioinformatics Academic Medical Center University of Amsterdam Amsterdam The Netherlands. 3Cochrane Dementia and Cognitive Improvement Group University of Oxford Oxford UK. 4EPPI-Centre Department of Social Science University College London London UK. 5Division of Health and Social Care Research King's College London London UK. 6College of Computer and Information Science Northeastern University Boston USA. 13University Hospitals Bristol NHS Foundation Trust School of Social and Community Medicine Bristol UK. 275Institute of Applied Health Research University of Birmingham Birmingham UK. 9Department of Clinical Epidemiology Biostatistics & Bioinformatics Academic Medical Center University of Amsterdam Amsterdam The Netherlands. 10School of Social and Community Medicine University of Bristol Bristol UK. 179Institute of Applied Health Research University of Birmingham Birmingham UK. 12Kleijnen Systematic Reviews Ltd York UK. 25Research Institute for Primary Care and Health Sciences Keele University Keele UK. 188Centre for Statistics in Medicine Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences University of Oxford Oxford UK. 191Julius Center for Health Sciences and Primary Care University Medical Center Utrecht 3584 CG Utrecht Netherlands. 237Julius Center for Health Sciences and Primary Care University Medical Center Utrecht 3584 CG Utrecht Netherlands. 18Department of Medical Statistics University Medical Center Göttingen Göttingen Germany. 19Institute for B

[This corrects the article DOI: 10.1186/s41512-016-0001-y.].

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Signaling enabler in high-speed system design by using hybrid stackup printed circuit board

Signaling enabler in high-speed system design by using hybri...

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International Microsystems, Packaging, Assembly and Circuits Technology (IMPACT)

作者： Thonas Su Jimmy Hsu Chunfei Ye Xiaoning Ye Adrian Grigoras Data Center Platform Application Engineer Intel Asia-Pacific Research & Development Ltd. Taipei Taiwan Republic of China Datacenter and Connected Systems Group Intel Corporation DuPont WA USA

FR4 is a commonly used material in industry to build printed circuit boards. However signals propagating in this media have significant attenuation when the frequency is going higher and higher. In this paper, hybrid PCB stack-up is studied for signal integrity design, where only specific layers of the board use low loss dielectric while the others are fabricated with traditional FR4 in order to have optimized cost-performance. The investigation focuses on full channel signal integrity analysis based on the proposed hybrid stackup. Simulations for Intel ® Quick Path Interconnect (Intel ® QPI) show noticeable improvement. Such a hybrid stackup is normally less costly than all low loss PCB stackup, thus achieving a good compromising between cost and performance for system design and production.

关键词： Routing Materials Indexes Crosstalk Printed circuits Loss measurement Decision feedback equalizers

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11th German Conference on Chemoinformatics (GCC 2015) Abstracts

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JOURNAL OF CHEMINFORMATICS 2016年第SUPPL 1期8卷 1-27页

作者： [Anonymous] GDCh-CIC Division Associated Board Member Beilstein-Institut zur Förderung der Chemischen Wissenschaften Trakehner Str. 7-9 60487 Frankfurt Germany. ufechner@beilstein-institut.de. Division Medicinal Chemistry Amsterdam Institute for Molecules Medicines and Systems (AIMMS) VU University Amsterdam The Netherlands. Centre for Bioinformatics Uni Hamburg Bundesstr. 43 20146 Hamburg Germany. Sanofi-Aventis Deutschland GmbH 65926 Frankfurt am Main Germany. stefan.guessregen@***. Sanofi-Aventis Deutschland GmbH 65926 Frankfurt am Main Germany. GlaxoSmithKline Stevenage SG1 2NY UK. nicola.j.richmond@***. Discngine Paris 75011 France. Organisch-Chemisches Institut Westfälische Wilhelms-Universität Münster Germany. marwin.segler@wwu.de. Organisch-Chemisches Institut Westfälische Wilhelms-Universität Münster Germany. Bundeskriminalamt Wiesbaden Central Analytics II 65173 Wiesbaden Germany. Department of Chemistry and Biochemistry University of California Santa Barbara CA 93111 USA. shea@chem.ucsb.edu. Department of Chemistry and Biochemistry University of California Santa Barbara CA 93111 USA. Chemistry Department Ludwig-Maximilians-Universität München Butenandtstr. 7 81377 Munich Germany. Inorganic Chemistry and Center for Nanointegration University of Duisburg-Essen Essen Germany. CAM-D Technologies Essen Germany. Institute for Bioinformatics and Chemoinformatics Westphalian University of Applied Sciences Recklinghausen Germany. Institute for Bioinformatics and Chemoinformatics Westphalian University of Applied Sciences Recklinghausen Germany. achim.zielesny@w-hs.de. Leiden University Leiden Netherlands. j.fraaije@chem.leidenuniv.nl. Culgi BV Berlin Germany. Physikalische Chemie III TU Dortmund 44227 Dortmund Germany. stefan.kast@tu-dortmund.de. Centre for Molecular Informatics Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW United Kingdom. kcb27@cam.ac.uk. Centre for Molecular Informatics Department of Chemistry

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Unobservable settling vibration on head-positioning control in hard disk drives

Unobservable settling vibration on head-positioning control ...

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作者： Atsumi, Takenori Messner, William C. Hitachi Research Laboratory Research and Development Group Hitachi Ltd. Fujisawa Kanagawa 252-0888 Japan Data Storage Systems Center Carnegie Mellon University Pittsburgh PA 15213 United States

ISBN: (纸本)9783902661937

In this paper, we study the unobserved vibrations of the head in hard disk drives which may lead to destruction of user data. We show that the acceleration input excites the mechanical resonance near the sampling frequency of the hold in the settling characteristics after the track-seeking control. We also show that the degree to which these oscillations are unobservable depends on the sampling frequency of the sampler. Then we define the index of unobservable position based on its RMS amplitude to estimate effect of the unobservable oscillations of mechanical resonances in the positioning control system. These phenomena are confirmed through the experiments using the actual head-positioning system of the hard disk drive. Consequently the vibrations caused by the mechanical resonances around sampling frequency are not only difficult to observe but readily excited by the control input. Therefore, the head-positioning control system must be designed such that the sampling frequency is away from mechanical resonances. © 2011 IFAC.

关键词： Transient analysis

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Finding Robust Itemsets under Subsampling

Finding Robust Itemsets under Subsampling

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IEEE International Conference on data Mining (ICDM)

作者： Nikolaj Tatti Fabian Moerchen University of Antwerp Antwerp Belgium Integrated Data Systems Siemens AG Corporate Research and Development Princeton NJ USA

ISBN: (纸本)9781457720758

Mining frequent patterns is plagued by the problem of pattern explosion making pattern reduction techniques a key challenge in pattern mining. In this paper we propose a novel theoretical framework for pattern reduction. We do this by measuring the robustness of a property of an item set such as closed ness or non-derivability. The robustness of a property is the probability that this property holds on random subsets of the original data. We study four properties: closed, free, non-derivable and totally shattered item sets, demonstrating how we can compute the robustness analytically without actually sampling the data. Our concept of robustness has many advantages: Unlike statistical approaches for reducing patterns, we do not assume a null hypothesis or any noise model and the patterns reported are simply a subset of all patterns with this property as opposed to approximate patterns for which the property does not really hold. If the underlying property is monotonic, then the measure is also monotonic, allowing us to efficiently mine robust item sets. We further derive a parameter-free technique for ranking item sets that can be used for top-k approaches. Our experiments demonstrate that we can successfully use the robustness measure to reduce the number of patterns and that ranking yields interesting itemsets.

关键词： Itemsets Robustness Vectors data mining TV Random variables Polynomials

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Unobservable Settling Vibration on Head-Positioning Control in Hard Disk Drives

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IFAC Proceedings Volumes 2011年第1期44卷 4052-4060页

作者： Takenori Atsumi William C. Messner Hitachi Research Laboratory Research and Development Group Hitachi Ltd. Fujisawa Kanagawa 252-0888 Japan Data Storage Systems Center Carnegie Mellon University Pittsburgh PA 15213 USA

Abstract In this paper, we study the unobserved vibrations of the head in hard disk drives which may lead to destruction of user data. We show that the acceleration input excites the mechanical resonance near the sampling frequency of the hold in the settling characteristics after the track-seeking control. We also show that the degree to which these oscillations are unobservable depends on the sampling frequency of the sampler. Then we define the index of unobservable position based on its RMS amplitude to estimate effect of the unobservable oscillations of mechanical resonances in the positioning control system. These phenomena are confirmed through the experiments using the actual head-positioning system of the hard disk drive. Consequently the vibrations caused by the mechanical resonances around sampling frequency are not only difficult to observe but readily excited by the control input. Therefore, the head-positioning control system must be designed such that the sampling frequency is away from mechanical resonances.

关键词： Unobservable Transient responses Mechatronic systems Sampled-data systems Vibration and modal analysis

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Confusion matrix-based feature selection

Confusion matrix-based feature selection

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22nd Midwest Artificial Intelligence and Cognitive Science Conference, MAICS 2011

作者： Visa, Sofia Ramsay, Brian Ralescu, Anca Van Der Knaap, Esther Computer Science Department College of Wooster Wooster OH United States Sentry Data Systems Inc. Fort Lauderdale FL United States Computer Science Department University of Cincinnati Cincinnati OH United States Ohio Agricultural Research and Development Center Ohio State University Wooster OH United States

This paper introduces a new technique for feature selection and illustrates it on a real data set. Namely, the proposed approach creates subsets of attributes based on two criteria: (1) individual attributes have high discrimination (classification) power;and (2) the attributes in the subset are complementary - that is, they misclassify different classes. The method uses information from a confusion matrix and evaluates one attribute at a time. Keywords: classification, attribute selection, confusion matrix, k-nearest neighbors;.

关键词： Image resolution

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Fault parameter estimation with data assimilation on infrasound variations due to big earthquakes

Fault parameter estimation with data assimilation on infraso...

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作者： Nagao, Hiromichi Kobayashi, Naoki Nakano, Shin'ya Higuchi, Tomoyuki Research and Development Center for Data Assimilation Institute of Statistical Mathematics Research Organization for Information and Systems 10-3 Midori-cho Tachikawa Tokyo 190-8562 Japan Department of Solid Planetary Sciences Institute of Space and Astronautical Science Japan Aerospace Exploration Agency 3-1-3 Yoshinodai Chuo-ku Sagamihara 252-5210 Japan Department of Statistical Modeling Institute of Statistical Mathematics Research Organization for Information and Systems 10-3 Midori-cho Tachikawa Tokyo 190-8562 Japan Institute of Statistical Mathematics Research Organization for Information and Systems 10-3 Midori-cho Tachikawa Tokyo 190-8562 Japan

ISBN: (纸本)9781457702679

A procedure to estimate, in the framework of data assimilation, fault parameters from excited infrasound phenomena due to big earthquakes is proposed. Seismoacousic waves generated by several point sources are simulated by the convolution of the relevant seismic source mechanism and the Green's function constructed from normal modes of an assumed Earth's model. Unknown parameters in a rupturing fault model are estimated in order to explain real observed infrasound variations in detail. As an example, the proposed procedure is applied to infrasound variations associated with the Iwate-Miyagi Nairiku Earthquake that occurred in northeast Japan in June 2008. Coseismic infrasound variations are numerically simulated using an appropriate fault model and a one-dimensional coupled structure model consisting of the solid Earth and the atmosphere. Fault parameters, such as rupture velocity and scalar seismic moment, are determined using the particle filter algorithm to fit the long-period components of the observed infrasound variations. The posterior distribution obtained for each fault parameter indicates that infrasound data contain sufficient information as well as seismic data. © 2011 IEEE.

关键词： Earthquakes

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Fault parameter estimation with data assimilation on infrasound variations due to big earthquakes

Fault parameter estimation with data assimilation on infraso...

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International Conference on Information Fusion

作者： Hiromichi Nagao Shin'ya Nakano Naoki Kobayashi Tomoyuki Higuchi Research and Development Center of Data Assimilation The Institute of Statistical Mathematics Research Organization for Information and Systems Tachikawa Tokyo Japan Department of Solid Planetary Sciences Institute of Space and Astronautical Science Japan AeroSpace Exploration Agency Sagamihara Japan

关键词： Atmospheric modeling Earth Terrestrial atmosphere Earthquakes Mathematical model Atmospheric waves Numerical models

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