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Sequence data and association statistics from 12,940 type 2 diabetes cases and controls

Scientific data 2017年第1期4卷 170179页

作者： Jason Flannick Christian Fuchsberger Anubha Mahajan Tanya M Teslovich Vineeta Agarwala Kyle J Gaulton Lizz Caulkins Ryan Koesterer Clement Ma Loukas Moutsianas Davis J McCarthy Manuel A Rivas John R B Perry Xueling Sim Thomas W Blackwell Neil R Robertson N William Rayner Pablo Cingolani Adam E Locke Juan Fernandez Tajes Heather M Highland Josee Dupuis Peter S Chines Cecilia M Lindgren Christopher Hartl Anne U Jackson Han Chen Jeroen R Huyghe Martijn van de Bunt Richard D Pearson Ashish Kumar Martina Müller-Nurasyid Niels Grarup Heather M Stringham Eric R Gamazon Jaehoon Lee Yuhui Chen Robert A Scott Jennifer E Below Peng Chen Jinyan Huang Min Jin Go Michael L Stitzel Dorota Pasko Stephen C J Parker Tibor V Varga Todd Green Nicola L Beer Aaron G Day-Williams Teresa Ferreira Tasha Fingerlin Momoko Horikoshi Cheng Hu Iksoo Huh Mohammad Kamran Ikram Bong-Jo Kim Yongkang Kim Young Jin Kim Min-Seok Kwon Juyoung Lee Selyeong Lee Keng-Han Lin Taylor J Maxwell Yoshihiko Nagai Xu Wang Ryan P Welch Joon Yoon Weihua Zhang Nir Barzilai Benjamin F Voight Bok-Ghee Han Christopher P Jenkinson Teemu Kuulasmaa Johanna Kuusisto Alisa Manning Maggie C Y Ng Nicholette D Palmer Beverley Balkau Alena Stančáková Hanna E Abboud Heiner Boeing Vilmantas Giedraitis Dorairaj Prabhakaran Omri Gottesman James Scott Jason Carey Phoenix Kwan George Grant Joshua D Smith Benjamin M Neale Shaun Purcell Adam S Butterworth Joanna M M Howson Heung Man Lee Yingchang Lu Soo-Heon Kwak Wei Zhao John Danesh Vincent K L Lam Kyong Soo Park Danish Saleheen Wing Yee So Claudia H T Tam Uzma Afzal David Aguilar Rector Arya Tin Aung Edmund Chan Carmen Navarro Ching-Yu Cheng Domenico Palli Adolfo Correa Joanne E Curran Dennis Rybin Vidya S Farook Sharon P Fowler Barry I Freedman Michael Griswold Daniel Esten Hale Pamela J Hicks Chiea-Chuen Khor Satish Kumar Benjamin Lehne Dorothée Thuillier Wei Yen Lim Jianjun Liu Marie Loh Solomon K Musani Sobha Puppala William R Scott Loïc Yengo Sian-Tsung Tan Herman A Taylor Farook Thameem Gregory Wilson Tien Yin Wong Pål Rasmu Department of Molecular Biology Massachusetts General Hospital Boston Massachusetts USA. Program in Medical and Population Genetics Broad Institute Cambridge Massachusetts USA. Department of Biostatistics and Center for Statistical Genetics University of Michigan Ann Arbor Michigan USA. Wellcome Trust Centre for Human Genetics Nuffield Department of Medicine University of Oxford Oxford UK. Harvard-MIT Division of Health Sciences and Technology Massachusetts Institute of Technology Cambridge Massachusetts USA. Department of Statistics University of Oxford Oxford UK. Genetics of Complex Traits University of Exeter Medical School University of Exeter Exeter UK. MRC Epidemiology Unit Institute of Metabolic Science University of Cambridge Cambridge UK. Department of Twin Research and Genetic Epidemiology King's College London London UK. Oxford Centre for Diabetes Endocrinology and Metabolism Radcliffe Department of Medicine University of Oxford Oxford UK. Department of Human Genetics Wellcome Trust Sanger Institute Hinxton Cambridgeshire UK. School of Computer Science McGill University Montreal Quebec Canada. McGill University and Génome Québec Innovation Centre Montreal Quebec Canada. Human Genetics Center The University of Texas Graduate School of Biomedical Sciences at Houston The University of Texas Health Science Center at Houston Houston Texas USA. Department of Biostatistics Boston University School of Public Health Boston Massachusetts USA. National Heart Lung and Blood Institute's Framingham Heart Study Framingham Massachusetts USA. Medical Genomics and Metabolic Genetics Branch National Human Genome Research Institute National Institutes of Health Bethesda Maryland USA. Department of Biostatistics Harvard School of Public Health Boston Massachusetts USA. Chronic Disease Epidemiology Swiss Tropical and Public Health Institute University of Basel Basel Switzerland. Institute of Genetic Epidemiology Helmholtz Zentrum München German R

To investigate the genetic basis of type 2 diabetes (T2D) to high resolution, the GoT2D and T2D-GENES consortia catalogued variation from whole-genome sequencing of 2,657 European individuals and exome sequencing of 12,940 individuals of multiple ancestries. Over 27M SNPs, indels, and structural variants were identified, including 99% of low-frequency (minor allele frequency [MAF] 0.1-5%) non-coding variants in the whole-genome sequenced individuals and 99.7% of low-frequency coding variants in the whole-exome sequenced individuals. Each variant was tested for association with T2D in the sequenced individuals, and, to increase power, most were tested in larger numbers of individuals (>80% of low-frequency coding variants in ~82 K Europeans via the exome chip, and ~90% of low-frequency non-coding variants in ~44 K Europeans via genotype imputation). The variants, genotypes, and association statistics from these analyses provide the largest reference to date of human genetic information relevant to T2D, for use in activities such as T2D-focused genotype imputation, functional characterization of variants or genes, and other novel analyses to detect associations between sequence variation and T2D.

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Detecting anomalous behaviors using structural properties of social networks

Detecting anomalous behaviors using structural properties of...

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6th International Conference on Social Computing, Behavioral-Cultural Modeling and Prediction, SBP 2013

作者： Altshuler, Yaniv Fire, Michael Shmueli, Erez Elovici, Yuval Bruckstein, Alfred Pentland, Alex Lazer, David MIT Media Lab. United States Deutsche Telekom Lab. Department of Information Systems Engineering Ben-Gurion University Israel Computer Science Department Technion - Israeli Institute of Technology Israel College of Computer and Information Science Department of Political Science Northeastern University United States

ISBN: (纸本)9783642372094

In this paper we discuss the analysis of mobile networks communication patterns in the presence of some anomalous "real world event". We argue that given limited analysis resources (namely, limited number of network edges we can analyze), it is best to select edges that are located around 'hubs' in the network, resulting in an improved ability to detect such events. We demonstrate this method using a dataset containing the call log data of 3 years from a major mobile carrier in a developed European nation. © 2013 Springer-Verlag.

关键词： Wireless networks

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Image spectrum decomposition and narrow-band noise removal based on 2D separable nonuniform filter banks

Image spectrum decomposition and narrow-band noise removal b...

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2013 IEEE International Conference on Signal Processing, Communications and Computing, ICSPCC 2013

作者： Zhong, Wei Zhang, Qin Ye, Long Liang, Lili Dong, Lihong Key Lab of Media Audio and Video of Ministry of Education Communication University of China Beijing 100024 China Faculty of Automation and Information Engineering Xi'an University of Technology Xi'an 710048 China Department of Computer and Information Engineering Jiangxi Agricultural University Nanchang 330045 China

ISBN: (纸本)9781479910274

In this paper, a simple but effective method is proposed for image spectrum decomposition and denoising, due to the fact that the image cannot be decomposed flexibly in a transform domain. According to its spectrum distribution, the image decomposition is carried out by merging the corresponding filters of a uniform cosine-modulated filter bank, resulting 2D separable nonuniform filter banks. This method performs efficiently when the power spectrum of the image is distributed concentratedly. Moreover, if the image is corrupted by a narrow-band noise in the region where its power spectrum is low, the noise can be easily detected and removed by using the proposed idea of spectrum decomposition. A simulation of image Barbara is given to demonstrate that the proposed method is capable of achieving good performance in decomposing the power spectrum and removing the narrow-band noise involved. © 2013 IEEE.

关键词： Power spectrum

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Connecting stakeholders through context logging 13

Connecting stakeholders through context logging

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15th International Conference on Human-computer Interaction with Mobile Devices and Services, MobileHCI 2013

作者： Vihavainen, Sami Karhu, Kimmo Botero, Andrea Helsinki Institute for Information Technology HIIT Aalto University Espoo Finland Department of Computer Science and Engineering School of Science Aalto University Espoo Finland Department of Media School of Arts Design and Architecture Aalto University Espoo Finland

ISBN: (纸本)9781450322737

Logging users' physical context through the sensors of mobile devices and the abilities to track users' online behavior has increasingly evolved. In this poster abstract we will present a work in progress in understanding how various stakeholders can be connected through context logging technologies, and the underlying motivations. We will (1) describe the general components and information flow of context logging systems, (2) frame the primary stakeholders from the context logging point of view, (3) discuss the application areas through the different stakeholders and their goals for applying context logging. Moreover, we will present ContextLogger3, a context-logging tool that combines automatically acquired sensor and mobile activity data and manually user created textual notes. We conclude by suggesting that designers should systematically consider implementing affordances for fostering design conversation between the users that log/are logged and the other stakeholders. We also suggest considering affordances that enable users to have manual control on context logging to narrow the gap between the realities represented by the automatic context logging and those perceived by the user. © 2013 Authors.

关键词： stakeholders context logging automation manual mobile

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Abstracts from the 3rd International Genomic Medicine Conference (3rd IGMC 2015) : Jeddah, Kingdom of Saudi Arabia. 30 November - 3 December 2015

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BMC genomics 2016年第6期17 Suppl 6卷 487页

作者： Jerry W. Shay Noriko Homma Ruyun Zhou Muhammad Imran Naseer Adeel G. Chaudhary Mohammed Al-Qahtani Nobutaka Hirokawa Maryam Goudarzi Albert J. Fornace Saleh Baeesa Deema Hussain Mohammed Bangash Fahad Alghamdi Hans-Juergen Schulten Angel Carracedo Ishaq Khan Hanadi Qashqari Nawal Madkhali Mohamad Saka Kulvinder S. Saini Awatif Jamal Jaudah Al-Maghrabi Adel Abuzenadah Adeel Chaudhary Mohammed Al Qahtani Ghazi Damanhouri Heba Alkhatabi Anne Goodeve Laura Crookes Nikolas Niksic Nicholas Beauchamp Adel M. Abuzenadah Jim Vaught Bruce Budowle Mourad Assidi Abdelbaset Buhmeida Leena Merdad Sudhir Kumar Sayaka Miura Karen Gomez Mahmood Rasool Ahmed Rebai Sajjad Karim Hend F. Nour Eldin Heba Abusamra Elham M. Alhathli Nada Salem Mohammed H. Al-Qahtani Hossam Faheem Ashok Agarwa Eberhard Nieschlag Joachim Wistuba Oliver S. Damm Mohd A. Beg Taha A. Abdel-Meguid Hisham A. Mosli Osama S. Bajouh Serdar Coskun Muhammad Abu-Elmagd Ashraf Dallol Sahar Hakamy Wejdan Al-Qahtani Asia Al-Harbi Shireen Hussain Burak Ozkosem Rick DuBois Safia S. Messaoudi Maryam T. Dandana Touhami Mahjoub Wassim Y. Almawi S. Abdalla M. Nabil Al-Aama Asmaa Elzawahry Tsuyoshi Takahashi Sachiyo Mimaki Eisaku Furukawa Rie Nakatsuka Isao Kurosaka Takahiko Nishigaki Hiromi Nakamura Satoshi Serada Tetsuji Naka Seiichi Hirota Tatsuhiro Shibata Katsuya Tsuchihara Toshirou Nishida Mamoru Kato Sajid Mehmood Naeem Mahmood Ashraf Awais Asif Muhammad Bilal Malik Siddique Mehmood Aadil Hussain Qazi Mohammad Sajid Jamal Mughees Uddin Siddiqui Mohammad A. Alzohairy Mohammad A. Al Karaawi Taoufik Nedjadi Heba Al-Khattabi Adel Al-Ammari Ahmed Al-Sayyad Hédia Zitouni Nozha Raguema Marwa Ben Ali Wided Malah Raja Lfalah Wassim Almawi Mohammed Elanbari Andrey Ptitsyn Sana Mahjoub Rabeb El Ghali Bechir Achour Nidhal Ben Amor Brahim N’siri Hamid Morjani Esam Azhar Vera Chayeb Maryam Dendena Hedia Zitouni Khedija Zouari-Limayem Bassem Refaat Ahmed M. Ashshi Sarah A. Batwa Hazem Ramadan Amal Awad Ahmed Ateya Adel Galal Ahmed El-Shemi Ahmad Ashshi Mohammed Basalamah Youjin Na Cha University of Texas Southwestern Medical Center Dallas USA Department of Cell Biology and Anatomy Graduate School of Medicine the University of Tokyo Tokyo Japan Center of Excellence in Genomic Medicine Research King Abdulaziz University Jeddah Saudi Arabia Department of Biochemistry and Molecular & Cellular Biology Lombardi Comprehensive Cancer Center Georgetown University Washington USA Department of Oncology Lombardi Comprehensive Cancer Center Georgetown University Washington USA Department of Radiation Medicine Lombardi Comprehensive Cancer Center Georgetown University Washington USA Center of Excellence in Genomic Medicine Research (CEGMR) King Abdulaziz University Jeddah Kingdom of Saudi Arabia King Fahd Medical Research Centre King Abdulaziz University Jeddah Saudi Arabia Centre of Excellence in Genomic Medicine Research King Abdulaziz University Jeddah Saudi Arabia Sheffield Diagnostic Genetic Service Sheffield Children’s NHS Foundation Trust Western Bank Sheffield UK Center of Innovations in Personalized Medicine King Abdulaziz University Jeddah Saudi Arabia President ISBER Editor-in-Chief Biopreservation & Biobanking ᅟ USA Institute of Applied Genetics Department of Molecular and Medical Genetics University of North Texas Health Science Center Fort Worth USA Department of Dental Public Health Faculty of Dentistry King Abdulaziz University Jeddah Saudi Arabia Institute for Genomics and Evolutionary Medicine Temple University Philadelphia USA Center of Excellence in Genomic Medicine King Abdulaziz University Jeddah Kingdom of Saudi Arabia Laboratory of Molecular and Cellular Screening Processes (Bioinformatics Group) Centre of Biotechnology of Sfax Sfax Tunisia Fujitsu Technology Solutions International ᅟ ᅟ Case Western Reserve University School of Medicine and Lerner College of Medicine Cleveland Clinic Foundation Cleveland USA American Center for Reproductive Medicine Andrology Center Cleveland USA Center for Reproductive Medicine and

O1 Regulation of genes by telomere length over long distances Jerry W. Shay O2 The microtubule destabilizer KIF2A regulates the postnatal establishment of neuronal circuits in addition to prenatal cell survival, cell migration, and axon elongation, and its loss leading to malformation of cortical development and severe epilepsy Noriko Homma, Ruyun Zhou, Muhammad Imran Naseer, Adeel G. Chaudhary, Mohammed Al-Qahtani, Nobutaka Hirokawa O3 Integration of metagenomics and metabolomics in gut microbiome research Maryam Goudarzi, Albert J. Fornace Jr. O4 A unique integrated system to discern pathogenesis of central nervous system tumors Saleh Baeesa, Deema Hussain, Mohammed Bangash, Fahad Alghamdi, Hans-Juergen Schulten, Angel Carracedo, Ishaq Khan, Hanadi Qashqari, Nawal Madkhali, Mohamad Saka, Kulvinder S. Saini, Awatif Jamal, Jaudah Al-Maghrabi, Adel Abuzenadah, Adeel Chaudhary, Mohammed Al Qahtani, Ghazi Damanhouri O5 RPL27A is a target of miR-595 and deficiency contributes to ribosomal dysgenesis Heba Alkhatabi O6 Next generation DNA sequencing panels for haemostatic and platelet disorders and for Fanconi anaemia in routine diagnostic service Anne Goodeve, Laura Crookes, Nikolas Niksic, Nicholas Beauchamp O7 Targeted sequencing panels and their utilization in personalized medicine Adel M. Abuzenadah O8 International biobanking in the era of precision medicine Jim Vaught O9 Biobank and biodata for clinical and forensic applications Bruce Budowle, Mourad Assidi, Abdelbaset Buhmeida O10 Tissue microarray technique: a powerful adjunct tool for molecular profiling of solid tumors Jaudah Al-Maghrabi O11 The CEGMR biobanking unit: achievements, challenges and future plans Abdelbaset Buhmeida, Mourad Assidi, Leena Merdad O12 Phylomedicine of tumors Sudhir Kumar, Sayaka Miura, Karen Gomez O13 Clinical implementation of pharmacogenomics for colorectal cancer treatment Angel Carracedo, Mahmood Rasool O14 From association to causality: translation of GWAS findings for genomic me

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Multi-feature canonical correlation analysis for face photo-sketch image retrieval 13

Multi-feature canonical correlation analysis for face photo-...

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21st ACM International Conference on Multimedia, MM 2013

作者： Gong, Dihong Li, Zhifeng Liu, Jianzhuang Qiao, Yu Shenzhen Key Lab of Computer Vision and Pattern Recognition Chinese Academy of Sciences Shenzhen Institutes of Advanced Technology China Media Lab Huawei Technologies Co. Ltd. China Department of Information Engineering Chinese University of Hong Kong Hong Kong

ISBN: (纸本)9781450324045

Automatic face photo-sketch image retrieval has attracted great attention in recent years due to its important applications in real life. The major difficulty in automatic face photo-sketch image retrieval lies in the fact that there exists great discrepancy between the different image modalities (photo and sketch). In order to reduce such discrepancy and improve the performance of automatic face photo-sketch image retrieval, we propose a new framework called multi-feature canonical correlation analysis (MCCA) to effectively address this problem. The MCCA is an extension and improvement of the canonical correlation analysis (CCA) algorithm using multiple features combined with two different random sampling methods in feature space and sample space. In this framework, we first represent each photo or sketch using a patch-based local feature representation scheme, in which histograms of oriented gradients (HOG) and multi-scale local binary pattern (MLBP) serve as the local descriptors. Canonical correlation analysis (CCA) is then performed on a collection of random subspaces to construct an ensemble of classifiers for photo-sketch image retrieval. Extensive experiments on two public-domain face photo-sketch datasets (CUFS and CUFSF) clearly show that the proposed approach obtains a substantial improvement over the state-of-the-art. Copyright © 2013 ACM.

关键词： Image retrieval

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Facial landmark localization based on hierarchical pose regression with cascaded random ferns 13

Facial landmark localization based on hierarchical pose regr...

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21st ACM International Conference on Multimedia, MM 2013

作者： Zhang, Zhanpeng Zhang, Wei Liu, Jianzhuang Tang, Xiaoou Shenzhen Key Lab of Computer Vision and Pattern Recognition Chinese Academy of Sciences Shenzhen Institutes of Advanced Technology China Department of Information Engineering Chinese University of Hong Kong Hong Kong Media Lab Huawei Technologies Co. Ltd. China

ISBN: (纸本)9781450324045

The main challenge of facial landmark localization in realworld application is that the large changes of head pose and facial expressions cause substantial image appearance variations. To avoid high dimensional regression in the 3D and 2D facial pose spaces simultaneously, we propose a hierarchical pose regression approach, estimating the head rotation, facial components and landmarks hierarchically. The regression process works in a unified cascaded fern framework. We present generalized gradient boosted ferns (GBFs) for the regression framework, which give better performance than traditional ferns. The framework also achieves real time performance. We verify our method on the latest benchmark datasets. The results show that it outperforms state-of-theart methods in both accuracy and speed. Copyright © 2013 ACM.

关键词： Regression analysis

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Result prediction system for Multi-Tenant database of University

Result prediction system for Multi-Tenant database of Univer...

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IEEE International Advance Computing Conference, IACC

作者： Amit Kumar Tiwari Divya Rohatgi Akhilesh Pandey Anil Kumar Singh Department of Computer Science & Engineering Devprayag Institute of Technical Studies Allahabad India Department of Computer Engineering Pillai Institute of Information Technology Engineering Media Studies and Research Mumbai India Department of Computer Science & Engineering Motilal Nehru National Institute of Technology Allahabad India

ISBN: (纸本)9781467345279

The main problem of higher educational institutions is to increase the performance of their students. For this purpose, they always scan students' performance in the class test and quiz of different subjects and take appropriate decision like arrangement of extra lectures on conceptual topics so that they can improve student performance in the examination. They also face the problem to predict the student performance in the examination. If the number of students is less, say 20 to 30 then these analysis can be done manually because teachers can give attention to an individual, but if the student strength is large then it will become a tough task. Our objective is to prepare a Multi-Tenant database for University and propose a result prediction system that can be used to predict the result of any student in coming examinations.

关键词： Databases Educational institutions Predictive models Internet Training Linear regression HTML

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Impact of neighbor awareness at the MAC layer in a Vehicular Ad-Hoc Network (VANET)

Impact of neighbor awareness at the MAC layer in a Vehicular...

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IEEE International Symposium on Wireless Vehicular Communications (WiVeC)

作者： Marthinus J. Booysen Sherali Zeadally Gert-Jan van Rooyen Department of Electrical and Electronic Engineering and the MIH Media Lab Stellenbosch University Stellenbosch South Africa Department of Computer Science and Information Technology University of the District of Columbia Washington DC USA

Despite various proposed Medium Access Control (MAC) approaches, efficient medium access in VANET remains a significant challenge, especially for the broadcast of safety messages. A key contributing factor to packet loss is the hidden terminal problem, which is exacerbated by the high node mobility apparent in VANET. Since the hidden terminal problem is fundamentally a problem of lack of awareness, this work evaluates the effects of increased neighbor awareness at the MAC layer. An increased awareness of neighboring nodes' slot allocation in a TDMA-based MAC, directly impacts on the number of available slots. Therefore, the effects of TDMA frame size is also evaluated for different awareness ranges. To support the analysis, a TDMA-based MAC with configurable neighbor awareness and configurable TDMA frame size is used. The impact is assessed using the packet delivery ratio, receiver throughput, and end-to-end latency. The results show packet delivery ratio and receiver throughput to increase for increased awareness ranges, up to an optimal of 3 hops, after which performance worsens. An increase in TDMA frame size leads to an increase in packet delivery ratio for small awareness ranges, and an oscillating increase for large awareness ranges. The receiver throughput also initially increases for an increased TDMA frame size, but reaches an optimum, also at 3 hops.

关键词： Time division multiple access Receivers Throughput Vehicular ad hoc networks Resource management media Access Protocol Measurement

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Contemplations on results from investigating the Personal Epistemology of computing students

Contemplations on results from investigating the Personal Ep...

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Frontiers in Education (FIE) Conference

作者： Roger McDermott Iain Pirie Cary Laxer Åsa Cajander Mats Daniels School of Computing Science and Digital Media Robert Gordon University Aberdeen UK Department of Information Technology Uppsala University Uppsala Sweden Department of Computer Science and Software Engineering Rose-Hulman Institute of Technology Terre-Haute IN USA

“Personal Epistemology” is the analysis of the ways in which an individual perceives what constitutes knowledge, its boundaries, how it is justified, and how it is related to learning. While investigation of metacognitive strategies used by students is now an established research topic within computer Science and information technology education, the study of personal epistemology is relatively undeveloped. This is so despite there being significant epistemological issues associated with learning the subject itself, such as those concerned with the way in which programming exercises change from convergent to divergent problems, or the process by which software project management problems very quickly become ill-defined. In this paper, we describe a preliminary investigation into the personal epistemology of two cohorts of computing students. We review some models of personal epistemological development and describe an empirical study in which we investigated the dimensions of epistemological beliefs of two cohorts of computing students. The results show that there appears to be a wide range of epistemological belief amongst computing students. Finally, we make some observations about the importance of personal epistemology for learning in computer Science and outline further work in this area.

关键词： Educational institutions Loading computer science Psychology Knowledge acquisition Context

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