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Abstracts from the 20th International Symposium on Signal Transduction at the Blood-Brain Barriers Abstracts

FLUIDS AND BARRIERS OF THE CNS 2017年第SUPPL 2期14卷 27-27页

作者： [Anonymous] The Jerzy Kukuczka Academy of Physical Education Katowice Poland The Institute of Animal Physiology and Food Research Polish Academy of Sciences Olsztyn Poland University of Miami Miami FL USA Institute of Pharmaceutical Science King’s College London London United Kingdom Department of Ophthalmology and Molecular and Integrative Physiology The University of Michigan Ann Arbor MI USA Department of Internal Medicine and Cardiology The University of Michigan Ann Arbor MI USA School of Medicine Department of Cellular and Molecular Medicine Koc University Istanbul Turkey Department of Cellular and Molecular Medicine Medical Faculty Koc University Istanbul Turkey Department of Neuroscience School of Medicine Koc University Istanbul Turkey Department of Neuroscience Medical Faculty Koc University Istanbul Turkey Department of Laboratory Animals Science Aziz Sancar Experimental Medicine Research Institute Istanbul University Istanbul Turkey Department of Neuroscience Aziz Sancar Experimental Medicine Research Institute Istanbul University Istanbul Turkey School of Medicine Koc University Istanbul Turkey Department of Forensic Science Istanbul Faculty of Medicine Istanbul University Istanbul Turkey Department of Histology and Embryology School of Medicine Koc University Istanbul Turkey Department of Histology and Embryology Istanbul Faculty of Medicine Istanbul University Istanbul Turkey Department of Physiology School of Medicine Koc University Istanbul Turkey Theodor Kocher Institute University of Bern Bern Switzerland Institute of Veterinary Physiology Vetsuisse Faculty University of Zurich Zurich Switzerland Zurich Center for Integrative Human Physiology University of Zurich Zurich Switzerland Zurich Center of Integrative Human Physiology University of Zurich Zurich Switzerland Institute for Veterinary Physiology and Zurich Center for Integrative Human Physiology University of Zurich Zurich Switzerland Institute of Veterinary Physiology Univer

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Publisher Correction: Alpha-synuclein facilitates to form short unconventional microtubules that have a unique function in the axonal transport

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Scientific reports 2018年第1期8卷 8019页

作者： Shiori Toba Mingyue Jin Masami Yamada Kanako Kumamoto Sakiko Matsumoto Takuo Yasunaga Yuko Fukunaga Atsuo Miyazawa Sakiko Fujita Kyoko Itoh Shinji Fushiki Hiroaki Kojima Hideki Wanibuchi Yoshiyuki Arai Takeharu Nagai Shinji Hirotsune Department of Genetic Disease Research Osaka City University Graduate School of Medicine Asahi-machi 1-4-3 Abeno Osaka 545-8585 Japan. Department of Bioscience and Bioinformatics Faculty of Computer Science and Systems Engineering Kyushu Institute of Technology Kawazu 680-4 Iizuka Fukuoka 820-850 Japan. JST-SENTAN 4-1-8 Honcho Kawaguchi Saitama 332-0012 Japan. JST-CREST 4-1-8 Honcho Kawaguchi Saitama 332-0012 Japan. Graduate School of Life Science University of Hyogo 3-2-1 Kouto Kamigori-cho Ako-gun Hyogo 678-1297 Japan. RSC-University of Hyogo Leading Program Center RIKEN SPring-8 Center 1-1-1 Kouto Sayo-cho Sayo-gun Hyogo 679-5148 Japan. Graduate School of Materials Science Nara Institute of Science and Technology 8916-5 Takayama Ikoma Nara 630-0101 Japan. Department of Pathology and Applied Neurobiology Kyoto Prefectural University of Medicine Graduate School of Medical Sciences Kajii-cho Kawaramachi-Hirokoji Kamigyo-ku Kyoto 602-8566 Japan. Advanced ICT Research Institute National Institute of Information and Communications Technology 588-2 Iwaoka Nishi-ku Kobe 651-2492 Japan. Department of Pathology Osaka City University Graduate School of Medicine Asahi-machi 1-4-3 Abeno Osaka 545-8586 Japan. Department of Biomolecular Science and Engineering Institute of Scientific and Industrial Research Osaka University Mihoga-oka 8-1 Osaka 567-0047 Japan. Department of Genetic Disease Research Osaka City University Graduate School of Medicine Asahi-machi 1-4-3 Abeno Osaka 545-8585 Japan. shinjih@med.osaka-cu.ac.jp.

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.

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FAST: Fast annotation with synchronized threads

FAST: Fast annotation with synchronized threads

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IEEE Symposium on Computational Intelligence and bioinformatics and Computational Biology (CIBCB)

作者： Dongjae Kim Aria S. Hahn Niels W. Hanson Kishori M. Konwar Steven J. Hallam Department of Computer Science University of British Columbia Vancouver BC Canada Koonkie Inc. Menlo Park CA USA Department of Microbiology & Immunology University of British Columbia Vancouver BC Canada Data & Analytics KPMG LLC Seattle WA USA Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology Cambridge MA USA Graduate Program in Bioinformatics University of British Columbia Vancouver BC Canada

ISBN: (纸本)9781509000128

FAST is a multi-threaded, I/O optimized Seed-and-Extend alignment program. FAST is extensible to nucleotide sequences making it comparable to both BLASTn and BLASTp, and also features several new usage flags reporting only HSPs meeting user defined e-value cut-offs. FASTs threaded database construction allows fast, low memory database construction e.g., RefSeq (9.4GB) can be indexed in under 5 minutes using 20 threads. The threaded database construction gives users the ability to create custom databases on demand which is useful for tasks requiring self-alignment, such as network construction [30]. Finally, FAST supports incremental database construction enabling users to keep their databases up-to-date by adding sequences without suffering the cost of reformatting the entire database. The FAST source is freely available through GitHub https:// ***/hallamlab/FAST and test datasets can be found on Dropbox https://***/sh/xvvavweuzgqybc4/ AAAWCrRnol67ZsXi2qLQWUuOa?

关键词： Instruction sets Synchronization Random access memory Algorithm design and analysis Data structures Indexes

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Publisher Correction: Protein-altering variants associated with body mass index implicate pathways that control energy intake and expenditure in obesity

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Nature genetics 2018年第5期50卷 766-767页

作者： Valérie Turcot Yingchang Lu Heather M Highland Claudia Schurmann Anne E Justice Rebecca S Fine Jonathan P Bradfield Tõnu Esko Ayush Giri Mariaelisa Graff Xiuqing Guo Audrey E Hendricks Tugce Karaderi Adelheid Lempradl Adam E Locke Anubha Mahajan Eirini Marouli Suthesh Sivapalaratnam Kristin L Young Tamuno Alfred Mary F Feitosa Nicholas G D Masca Alisa K Manning Carolina Medina-Gomez Poorva Mudgal Maggie C Y Ng Alex P Reiner Sailaja Vedantam Sara M Willems Thomas W Winkler Gonçalo Abecasis Katja K Aben Dewan S Alam Sameer E Alharthi Matthew Allison Philippe Amouyel Folkert W Asselbergs Paul L Auer Beverley Balkau Lia E Bang Inês Barroso Lisa Bastarache Marianne Benn Sven Bergmann Lawrence F Bielak Matthias Blüher Michael Boehnke Heiner Boeing Eric Boerwinkle Carsten A Böger Jette Bork-Jensen Michiel L Bots Erwin P Bottinger Donald W Bowden Ivan Brandslund Gerome Breen Murray H Brilliant Linda Broer Marco Brumat Amber A Burt Adam S Butterworth Peter T Campbell Stefania Cappellani David J Carey Eulalia Catamo Mark J Caulfield John C Chambers Daniel I Chasman Yii-Der I Chen Rajiv Chowdhury Cramer Christensen Audrey Y Chu Massimiliano Cocca Francis S Collins James P Cook Janie Corley Jordi Corominas Galbany Amanda J Cox David S Crosslin Gabriel Cuellar-Partida Angela D'Eustacchio John Danesh Gail Davies Paul I W Bakker Mark C H Groot Renée Mutsert Ian J Deary George Dedoussis Ellen W Demerath Martin Heijer Anneke I Hollander Hester M Ruijter Joe G Dennis Josh C Denny Emanuele Di Angelantonio Fotios Drenos Mengmeng Du Marie-Pierre Dubé Alison M Dunning Douglas F Easton Todd L Edwards David Ellinghaus Patrick T Ellinor Paul Elliott Evangelos Evangelou Aliki-Eleni Farmaki I Sadaf Farooqi Jessica D Faul Sascha Fauser Shuang Feng Ele Ferrannini Jean Ferrieres Jose C Florez Ian Ford Myriam Fornage Oscar H Franco Andre Franke Paul W Franks Nele Friedrich Ruth Frikke-Schmidt Tessel E Galesloot Wei Gan Ilaria Gandin Paolo Gasparini Jane Gibson Vilmantas Giedraitis Anette P Gjesing Penny Gordon-Larsen Mathias Gorski Hans-Jörgen Montreal Heart Institute Université de Montréal Montreal Quebec Canada. Division of Epidemiology Department of Medicine Vanderbilt-Ingram Cancer Center Vanderbilt Epidemiology Center Vanderbilt University School of Medicine Nashville TN USA. Charles Bronfman Institute for Personalized Medicine Icahn School of Medicine at Mount Sinai New York NY USA. Genetics of Obesity and Related Metabolic Traits Program Icahn School of Medicine at Mount Sinai New York NY USA. Department of Epidemiology University of North Carolina Chapel Hill NC USA. Human Genetics Center University of Texas School of Public Health University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences University of Texas Health Science Center at Houston Houston TX USA. Broad Institute of MIT and Harvard Cambridge MA USA. Department of Genetics Harvard Medical School Boston MA USA. Division of Endocrinology and Center for Basic and Translational Obesity Research Boston Children's Hospital Boston MA USA. Center for Applied Genomics Division of Human Genetics Children's Hospital of Philadelphia Philadelphia PA USA. Quantinuum Research LLC San Diego CA USA. Estonian Genome Center University of Tartu Tartu Estonia. Division of Epidemiology Department of Medicine Institute for Medicine and Public Health Vanderbilt Genetics Institute Vanderbilt University Nashville TN USA. Institute for Translational Genomics and Population Sciences LABioMed at Harbor-UCLA Medical Center Torrance CA USA. Wellcome Trust Sanger Institute Hinxton UK. Department of Mathematical and Statistical Sciences University of Colorado Denver CO USA. Wellcome Trust Centre for Human Genetics University of Oxford Oxford UK. Department of Biological Sciences Faculty of Arts and Sciences Eastern Mediterranean University Famagusta Cyprus. Max Planck Institute of Immunobiology and Epigenetics Freiburg Germany. Department of Biostatistics and Center for Statistical Genetics University of M

In the version of this article originally published, one of the two authors with the name Wei Zhao was omitted from the author list and the affiliations for both authors were assigned to the single Wei Zhao in the author list. In addition, the ORCID for Wei Zhao (department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA) was incorrectly assigned to author Wei Zhou. The errors have been corrected in the HTML and PDF versions of the article.

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Correction to: FLAGS, frequently mutated genes in public exomes

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BMC medical genomics 2017年第1期10卷 69页

作者： Casper Shyr Maja Tarailo-Graovac Michael Gottlieb Jessica Jy Lee Clara van Karnebeek Wyeth W Wasserman Centre for Molecular Medicine and Therapeutics Child and Family Research Institute Vancouver BC Canada. Treatable Intellectual Disability Endeavour in British Columbia Vancouver Canada. Bioinformatics Graduate Program University of British Columbia Vancouver BC Canada. Department of Medical Genetics University of British Columbia Vancouver BC Canada. Genome Science and Technology Graduate Program University of British Columbia Vancouver BC Canada. Division of Biochemical Diseases BC Children's Hospital Vancouver BC Canada. Department of Pediatrics University of British Columbia Vancouver BC Canada. Centre for Molecular Medicine and Therapeutics Child and Family Research Institute Vancouver BC Canada. wyeth@cmmt.ubc.ca. Department of Medical Genetics University of British Columbia Vancouver BC Canada. wyeth@cmmt.ubc.ca. Treatable Intellectual Disability Endeavour in British Columbia Vancouver Canada. wyeth@cmmt.ubc.ca.

Unfortunately, the original article [1] contained an error. The additional files were included incorrectly. The correct additional files 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 and 14 are published in this correction.

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Effects of gamma irradiation dose-rate on sterile male Aedesaegypti

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AIP Conference Proceedings 2017年第1期1854卷

作者： Beni Ernawan Usman Sumo Friend Tambunan Irawan Sugoro Hadian Iman Sasmita 1Center for Isotopes and Radiation Application-National Nuclear Energy Agency. Jl. Lebak Bulus Raya No. 49 Jakarta 12440 Indonesia. Tel. +62-21-7690709 Fax. +62-21-7691607 2Graduate Program Department of Chemistry Faculty of Mathematics and Natural Science University of Indonesia. Kampus UI Depok West Java 16424 Indonesia 3Bioinformatics Research Group Department of Chemistry Faculty of Mathematics and Natural Science University of Indonesia. Kampus UI Depok West Java 16424 Indonesia

Aedesaegypti is the most important vector for dengue, yellow fever and Zika viruses. Considering its medical importance, vector population control program utilizing radiation-based sterile insect technique (SIT) is one of the potential methods for preventing and limiting the dispersal of these viruses. The present study was undertaken to evaluate the dose-rates effects of γ-sterilization on quality parameters of sterile males. Males *** at the pupal stage were sterilized by applying 70 Gyγ-rays in varies dose-rates, i.e. 0 (control), 300, 600, 900, 1200 and 1500Gy/h utilizing panoramic irradiator. Adult males that emerged from the pupal stage were assessed for their quality parameters, which are the percentage of emergence, longevity, sterility and mating competitiveness. The results herein indicate that there was no major effect of dose-rate on the percentage of emergence, the data showedthat there were no differences between irradiated males compared with control. Generally, the longevity of irradiated males was lower compared to control. The data also demonstrated that longevity was significantly increased at the dose-rate from 300 to 900Gy/h, then decreased at the dose-rate 900 to 1500 Gy/h. Sterility of irradiated maleswas significantly different compared to control, while there was no significantly different at dose rate 300 to 1500 Gy/h. Mating competitiveness of irradiated males was increased at the dose rate from 300 to 1200 Gy/h, then the value was decreased significantly at the dose rate 1500 Gy/h. The dose-rate effects of γ-sterilization were discussed in the context genetic vector control, in particular, the SIT. The results give information and contribute to better understanding towards γ-sterilization optimization and quality parameters of sterile male Ae. aegypti on SIT methods.

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FragGeneScan-plus for scalable high-throughput short-read open reading frame prediction

FragGeneScan-plus for scalable high-throughput short-read op...

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IEEE Symposium on Computational Intelligence and bioinformatics and Computational Biology (CIBCB)

作者： Dongjae Kim Aria S. Hahn Shang-Ju Wu Niels W. Hanson Kishori M. Konwar Steven J. Hallam Department of Computer Science University of British Columbia Vancouver Canada Department of Microbiology University of British Columbia Vancouver Canada Graduate Program in Bioinformatics University of British Columbia Vancouver Canada

A fundamental step in the analysis of environmental sequence information is the prediction of potential genes or open reading frames (ORFs) encoding the metabolic potential of individual cells and entire microbial communities. FragGeneScan, a software designed to predict intact and incomplete ORFs on short sequencing reads combines codon usage bias, sequencing error models and start/stop codon patterns in a hidden Markov model to find the most likely path of hidden states from a given input sequence, provides a promising route for gene recovery in environmental datasets with incomplete assemblies. However, the current implementation of FragGeneScan does not scale efficiently with increasing input data size. Thus, FragGeneScan cannot be applied to contemporary environmental datasets that can exceed 100s of Gb. Here, we present FragGeneScan-Plus, an improved implementation of the FragGeneScan gene prediction model that leverages algorithmic thread synchronization and efficient in-memory data management to utilize multiple CPU cores without blocking I/O operations. FragGeneScan-Plus can process data approximately 5-times faster than FragGeneScan using a single core and approximately 50-times faster using eight hyper-threaded cores when benchmarked against simulated and real world environmental datasets.

关键词： Instruction sets Buffer storage Hidden Markov models Synchronization Predictive models Prediction algorithms Soil

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Assembly independent functional annotation of short-read data using SOFA: Short-ORF functional annotation

Assembly independent functional annotation of short-read dat...

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IEEE Symposium on Computational Intelligence and bioinformatics and Computational Biology (CIBCB)

作者： Aria S. Hahn Niels W. Hanson Dongjae Kim Kishori M. Konwar Steven J. Hallam Department of Microbiology University of British Columbia Vancouver Canada Graduate Program in Bioinformatics University of British Columbia Vancouver Canada Department of Computer Science University of British Columbia Vancouver Canada

Accurate description of the microbial communities driving matter and energy transformations in complex ecosystems such as soils cannot yet be effectively accomplished using assembly-based approaches despite the rise of next generation sequencing technologies. Here we present SOFA, an open source pipeline enabling comparative functional annotation of unassembled short-read data. The pipeline attempts to merge mate pairs in fastq files, predicts open reading frames (ORFs) on merged and unmerged reads as small as 70 bps, and completes an additional step, we term `deduplication'. Deduplication prevents the double counting of ORFs predicted from unmerged paired-end reads by checking for homologous annotations that span the same ORF, allowing for quantitatively accurate predictions. The effectiveness of SOFA is validated with both simulated and bone fide soil metagenomes, and empirical results are compared to existing strategies for obtaining accurate ORF counts, and an analytical model of read duplication. SOFA enables downstream processing stages within the existing MetaPathways pipeline, and is available for download as a stand alone application at https://*** under the MIT license.

关键词： bioinformatics Pipelines Genomics Databases Soil Proteins Assembly

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Reply: ATAD1 encephalopathy and stiff baby syndrome: a recognizable clinical presentation

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Brain : a journal of neurology 2018年第6期141卷 e50页

作者： Juliette Piard George K Essien Umanah Frederike L Harms Leire Abalde-Atristain Daniel Amram Melissa Chang Rong Chen Malik Alawi Vincenzo Salpietro Mark I Rees Seo-Kyung Chung Henry Houlden Alain Verloes Ted M Dawson Valina L Dawson Lionel Van Maldergem Kerstin Kutsche Centre de génétique humaine Université de Franche-Comté Besançon France. Integrative and Cognitive Neurosciences Research Unit EA481 University of Franche-Comté Besançon France. Neuroregeneration and Stem Cell Programs Institute for Cell Engineering Johns Hopkins University School of Medicine Baltimore MD 21205 USA. Department of Neurology Johns Hopkins University School of Medicine Baltimore MD 21205 USA. Institute of Human Genetics University Medical Center Hamburg-Eppendorf 20246 Hamburg Germany. Cellular and Molecular Medicine Graduate Program Johns Hopkins University School of Medicine Baltimore MD 21205 USA. Unité fonctionnelle de génétique clinique Centre hospitalier intercommunal Créteil France. University Medical Center Hamburg-Eppendorf Bioinformatics Core Facility 20246 Hamburg Germany. Heinrich-Pette-Institute Leibniz-Institute for Experimental Virology Virus Genomics Hamburg Germany. Department of Molecular Neuroscience UCL Institute of Neurology London UK. Neurology Research Group Institute of Life Science Swansea University Medical School Swansea University Swansea UK. Department of Genetics Robert-Debré Hospital Paris France. Solomon H. Snyder Department of Neuroscience Johns Hopkins University School of Medicine Baltimore MD 21205 USA. Department of Pharmacology and Molecular Sciences Johns Hopkins University School of Medicine Baltimore MD 21205 USA. Department of Physiology Johns Hopkins University School of Medicine Baltimore MD 21205 USA. Clinical Investigation Center 1431 National Institute of Health and Medical Research (INSERM) University of Franche-Comté Besançon France.

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Corrigendum to: Report: NIA Workshop on Measures of Physiologic Resiliencies in Human Aging

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The journals of gerontology. Series A, Biological sciences and medical sciences 2018年第7期73卷 995页

作者： Evan C Hadley George A Kuchel Anne B Newman Heather G Allore Jenna M Bartley Cindy S Bergeman Michael L Blinov Cathleen S Colon-Emeric Firdaus S Dabhar Laura L Dugan Chhanda Dutta Basil A Eldadah Luigi Ferrucci James L Kirkland Stephen B Kritchevsky Lewis A Lipsitz Neelesh K Nadkarni May J Reed Kenneth E Schmader Felipe Sierra Stephanie A Studenski Ravi Varadhan Jeremy D Walston Heather E Whitson Raymond Yung Division of Geriatrics and Clinical Gerontology National Institutes of Health National Institute on Aging Bethesda Maryland. Department of Medicine Center on Aging University of Connecticut Health Center Farmington. Department of Epidemiology University of Pittsburgh Graduate School of Public Health. Department of Medicine Division of Geriatric Medicine University of Pittsburgh School of Medicine Pennsylvania. Department of Internal Medicine Section of Geriatrics Yale University School of Medicine New Haven Connecticut. Department of Immunology Center on Aging University of Connecticut Health Center University of Connecticut Farmington. Department of Psychology University of Notre Dame Indiana. R. D. Berlin Center for Cell Analysis and Modeling University of Connecticut School of Medicine University of Connecticut Farmington. Duke University School of Medicine Duke University Medical Center. Durham VA Geriatric Research Education and Clinical Center North Carolina. Department of Psychiatry and Behavioral Sciences Stanford University School of Medicine Stanford University California. Department of Medicine Division of Geriatric Medicine Vanderbilt University School of Medicine Vanderbilt University Nashville Tennessee. Office of the Scientific Director National Institute on Aging National Institutes of Health Bethesda Maryland. Robert and Arlene Kogod Center on Aging Mayo Clinic College of Medicine Mayo Clinic Rochester Minnesota. Department of Gerontology and Geriatrics Sticht Center on Aging Wake Forest University School of Medicine Winston-Salem North Carolina. Beth Israel Deaconess Medical Center Harvard Medical School Boston. Institute for Aging Research Hebrew Senior Life Boston Massachusetts. Division of Geriatric Medicine Department of Internal Medicine School of Medicine University of Washington Seattle. Division of Geriatric Medicine Department of Medicine School of Medicine Duke University. Department of Veterans Affairs Medical Center Durham No

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