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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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Subcutaneous Preadipocytes Are Ideal Candidate To Produce A Large Number Of Functional Platelets In a Culture System

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BLOOD 2013年第21期122卷 3271-3271页

作者： Ono-Uruga, Yukako Tanaka, Tatsuya Igari, Atsuko Moriki, Takanori Yokoyama, Kenji Zama, Takeru Horiuchi, Tadashi Murata, Mitsuru Ikeda, Yasuo Suda, Toshio Matsubara, Yumiko Strategic Feasibility Study Program Kanagawa Academy of Science and Technology Kanagawa Japan Faculty of Science and Engineering Life Science and Medical Bioscience Waseda University Tokyo Japan Department of Laboratory Medicine Keio University School of Medicine Tokyo Japan Division of Hematology Department of Internal Medicine Keio University School of Medicine Tokyo Japan Department of Otorhinolaryngology Keio University School of Medicine Tokyo Japan Department of Biochemistry Keio University School of Medicine Tokyo Japan Department of Cell Differentiation The Sakaguchi Laboratory of Developmental Biology Keio University School of Medicine Tokyo Japan

Platelet transfusions are widely used for patients with severe thrombocytopenia. There are, however, practical problems in the current donor-dependent platelet transfusions, such as the limited supply and risk of serious immune reactions. Thus, the development of new strategies for generating platelets for transfusion is crucial. Platelets have been differentiated from hematopoietic stem cells, fetal liver cells, embryonic stem cells, induced pluripotent stem cells, NF-E2-transduced fibroblasts, and preadipocytes. Here, among these cells preadipocytes, especially in the subcutaneous adipose tissue, could be ideal candidate cells for manufacturing megakaryocytes (MKs) and platelets, because (1) they are relatively easy to obtain large quantities and have ability to proliferate in vitro, (2) their differentiation does not require gene transfer, as they possess genes in relation to megakaryopoiesis and thrombopoiesis, such as p45NF-E2 and c-mpl, and (3) they differentiate into MKs and platelets using an endogenous thrombopoietin. Thus, to clarify the usefulness of preadipocytes as a donor-independent source for platelet transfusion, we compared both number and function between platelets derived from mouse subcutaneous preadipocytes and those from bone marrow mononuclear cells (BMMNCs), the established cell source for manufacturing platelets. First, BMMNCs were not feasible for their expansion in vitro and therefore the cells were directly seeded in MK lineage induction media. In contrast, preadipocytes were to be passaged 6 times without any morphological changes, and then cultured in MK lineage induction media for their differentiation into platelets. Thus, as assessed by CD41-positive platelet-sized cells, 106.2±5.0 ×105 or 3.9±1.0 ×105 platelets were obtained from 106 preadipocytes or 106 BMMNCs, respectively (p<0.01). To next analyze platelet function, the binding of Alexa Fluor 488-labaled fibrinogen to CD41-positive platelet-sized cells, as assessed by mean fluor

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Analysis of Fluconazole in Human Urine Sample by High Performance Liquid Chromatography Method

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Journal of Physics: Conference Series 2013年第1期423卷

作者： D Hermawan N A Md Ali W A Wan Ibrahim M M Sanagi Separation Science and Technology Group Ibnu Sina Institute for Fundamental Sciences Studies Faculty of Science Universiti Teknologi Malaysia 81310 Johor Bahru Malaysia Chemistry Study Program Faculty of Science and Engineering Jenderal Soedirman University Purwokerto Indonesia

A method for determination of fluconazole, antifungal drug in human urine by using reversed-phased high performance liquid chromatography (RP-HPLC) with ultraviolet (UV) detector was developed. Optimization HPLC conditions were carried out by changing the flow rate and composition of mobile phase. The optimum separation conditions at a flow rate 0.85 mL/min with a composition of mobile phase containing methanol:water (70:30, v/v) with UV detection at a wavelength 254 nm was able to analyze fluconazole within 3 min. The excellent linearity was obtained in the range of concentration 1 to 10 μg/mL with r2 = 0.998. The limit of detection (LOD) and limit of quantitation (LOQ) were 0.39 μg/mL and 1.28 μg/mL, respectively. Solid phase extraction (SPE) method using octadecylsilane (C18) as a sorbent was used to clean-up and pre-concentrated of the urine sample prior to HPLC analysis. The average recoveries of fluconazole in spiked urine sample was 72.4% with RSD of 3.21% (n=3).

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An efficient parallel architecture for ray-tracing

An efficient parallel architecture for ray-tracing

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作者： Nery, Alexandre S. Nedjah, Nadia França, Felipe M.G. LAM - Computer Architecture and Microeletronics Laboratory Systems Engineering and Computer Science Program COPPE Universidade Federal Do Rio de Janeiro Rio de Janeiro RJ Brazil Department of Electronics Engineering and Telecommunications Faculty of Engineering Universidade Do Estado Do Rio de Janeiro Rio de Janeiro RJ Brazil

Real time rendering of three-dimensional scenes in high photorealistic details is a hard task, such as in the ray tracing rendering algorithm. In general, the performance achieved by a sequential software-based implementation of ray tracing is far from satisfactory. However, parallel implementations of ray tracing have been enabling reasonable real time performance, as the algorithm is embarrassingly parallel. Thus, a custom parallel design in hardware is likely to achieve an even higher performance. In this paper, we propose a hardware parallel architecture capable of dealing with the main desirable features of ray tracing, such as shadows and reflection effects, imposing low area cost and a promising rendering performance. Such architecture, called GridRT, is based on the Uniform Grid acceleration structure and is intended to deliver massive parallelism through parallel ray-triangle intersection tests as well as parallel processing of many rays. A hardware implementation of the proposed architecture is presented, together with some performance results and resources requirements. The rendering is reduced by 80% using a grid configuration of eight processing elements. © Springer science+Business Media, LLC 2011.

关键词： Field programmable gate arrays (FPGA)

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Development Model for Knowledge Management System (KMS) to Improve University's Performance (Case Studies in Indonesia University of Education)

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International Journal of Computer science Issues 2012年第1 1-1期9卷 1-6页

作者： Munir Rohendi, Dedi Study Program of Computer Science Faculty of Mathematics and Sciences Education Indonesia University of Education Bandung Indonesia Mechanical Engineering Education Department Faculty of Technology and Vocational Education Indonesia University of Education Bandung Indonesia

Knowledge Management System (KMS) is one way to organize and documented the knowledge of institution. The purpose of this study is to develop a prototype KMS in organizing and documenting the knowledge in the university and to do a document aggregation based on the total number, subjects and writers (lecturers). The development method of KMS prototype is using sharepoints which are able to collect, store and publish all digital data available at the university which can be accessed online. Aggregation is using the percentage between the number of documents, subjects, and writers (lecturers). The aggregation's result between the number of digital files compared to the number of courses and the number of lecturers are each below 10%. In the future, the university still needs to encourage all lecturers or academic community to increase the collection of digital files that can indirectly improve the quality and educational services. © 2012 International Journal of Computer science Issues.

关键词： Knowledge based systems

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Comparison between conventional system and displacement ventilation system with ceiling supply openings by CFD and experiments: Commercial kitchen ventilation in casual restaurants (Part 1)

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Journal of Environmental engineering (Japan) 2012年第682期77卷 977-986页

作者： Kondo, Yasushi Ogita, Shunsuke Yoshino, Hajime Fujita, Miwako Ogasawara, Takeshi Department of Architecture Faculty of Engineering Tokyo City University Japan Technical Research Institute Tonets Co. Japan Technical Research Institute Tonets Co. Tokyo City University Japan Energy Applications Research and Development Center Chubu Electric Power Co. Japan Program in Architecture School of Science and Engineering Meisei University Japan

Previous research works, such as CFD simulation and laboratory tests, show that displacement ventilation system (hereafter DV system) is suitable for electrical commercial kitchens because DV system does not disturb thermal plume over electrical cooking appliances. The DV system with ceiling mounted supply openings was also studied to apply to Japanese small kitchens in the previous papers. After the research stage, the DV system with ceiling openings was installed in a real kitchen of a casual restaurant. This paper shows the results of CFD simulation and experiments conducted when the DV system was applied to the real kitchens. In the experiments, a full scale mock-up kitchen model including a moving panel to simulate cooking disturbance was made to compare the DV system with the conventional local ventilation system. The CFD simulation was carried out to decide to detail of the system such as position of ceiling opening etc. The subsequent paper will show that the DV system can improve thermal environment in the real kitchen and can save energy consumption on the basis of field measurements.

关键词： Kitchens

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Comparative analysis of design-bid-build and design-build from the standpoint of claims

Comparative analysis of design-bid-build and design-build fr...

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Construction Research Congress 2012: Construction Challenges in a Flat World

作者： Pishdad-Bozorgi, Pardis De La Garza, Jesus M. Department of Building Construction Myers-Lawson School of Construction Virginia Polytechnic Institute and State University 501 W. Durango Blvd. San Antonio TX 78207 United States Faculty of Construction Science and Management Program College of Architecture University of Texas at San Antonio 501 W. Durango Blvd. San Antonio TX 78207 United States Department of Civil and Environmental Engineering Virginia Polytechnic Institute and State University 200 Patton Hall Blacksburg VA 24061 United States

ISBN: (纸本)9780784412329

The traditional project delivery method known as design-bid-build (DBB) has been known to give rise to adversarial relationships amongst and between project participants, and, as a result, litigation amongst and between such parties. It has been suggested that the design/build (DB) project delivery method has reduced the number of claims from the contractor to the owner since the designer is now a member of the contractor's project team. It is also suggested that the number of claims from the owner to the design-builder has been increased as a result of owner's dissatisfaction with the actual performance of the project. This research conducts a literature review and interviews with experienced project participants to gather information on DBB and DB with respect to claims. The key categories of claims and the underlying influential factors leading to those claims are identified. Qualitative data analysis is performed to determine how the DB approach has affected the typical influential factors leading to claims under the DBB model. This paper presents the result of the data analysis both in a framework and textual format. © 2012 ASCE.

关键词： Contractors

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A parallel Ray Tracing architecture suitable for application-specific hardware and GPGPU implementations

A parallel Ray Tracing architecture suitable for application...

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2011 14th Euromicro Conference on Digital System Design: architectures, Methods and Tools, DSD 2011

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

ISBN: (纸本)9780769544946

The Ray Tracing rendering algorithm can produce high-fidelity images of 3-D scenes, including shadow effects, as well as reflections and transparencies. This is currently done at a processing speed of at most 30 frames per second. Therefore, actual implementations of the algorithm are not yet suitable for interactive real-time rendering, which is required in games and virtual reality based applications. Fortunately, the algorithm allows for massive parallelization of its computations. In this paper, we present a parallel architecture for ray tracing based on a uniform spatial subdivision of the scene and exploiting an embedded computation of ray-triangle intersections. This approach allows for a significant acceleration of intersection computations, as well as, a reduction of the total number of the required intersections checks. Furthermore, it allows for these checks to be performed in parallel and in advance for each ray. In this paper we discuss and analyze an ASIP-based implementation using FPGAs and a GPGPU-based parallel implementation of the proposed architecture. The performance of both implementations are reported and compared." © 2011 IEEE.

关键词： Ray tracing

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Hardware reuse in modern application-specific processors and accelerators

Hardware reuse in modern application-specific processors and...

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2011 14th Euromicro Conference on Digital System Design: architectures, Methods and Tools, DSD 2011

作者： Nery, Alexandre S. Jozwiak, Lech Lindwer, Menno Cocco, Mauro Nedjah, Nadia França, Felipe M.G. LAM - Computer Architecture and Microelectronics Laboratory Systems Engineering and Computer Science Program COPPE Universidade Federal do Rio de Janeiro Brazil Department of Electronics Engineering and Telecommunications Faculty of Engineering Universidade do Estado do Rio de Janeiro Brazil Department of Electrical Engineering - Electronic Systems Eindhoven University of Technology Netherlands Silicon Hive - Intel UMG Netherlands

ISBN: (纸本)9780769544946

Effective exploitation of the application-specific parallel patterns and computation operations through their direct implementation in hardware is the base for construction of high-quality application-specific (re-) configurable application specific instruction set processors (ASIPs) and hardware accelerators for modern highly-demanding applications. Although it receives a lot of attention from the researchers and practitioners, a very important problem of hardware reuse in ASIP and accelerator synthesis is clearly underestimated and does not get enough attention in the published research. This paper is an effect of an industry and academic collaborative research. It analyses the problem of hardware sharing, shows its high practical relevance, as well as a big influence of hardware sharing on the major circuit and system parameters, and its importance for the multi-objective optimization and tradeoff exploitation. It also demonstrates that the state-of-the-art synthesis tools do not sufficiently address this problem and gives several guidelines related to enhancement of the hardware reuse. © 2011 IEEE.

关键词： Multiobjective optimization

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A parallel architecture for ray-tracing with an embedded intersection algorithm

A parallel architecture for ray-tracing with an embedded int...

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IEEE International Symposium on Circuits and Systems (ISCAS)

作者： Alexandre S. Nery Nadia Nedjah Felipe M.G. França Lech Jozwiak LAM-Computer Architecture and Microelectronics Laboratory Systems Engineering and Computer Science Program COPPE Universidade Federal do Rio de Janeiro Brazil Department of Electrical Engineering-Electronic Systems Eindhovan University of Technology Netherlands Department of Electronics Engineering and Telecommunications-Faculty of Engineering Universidade do Estado do Rio de Janeiro (UERJ) Brazil

Real time rendering of three-dimensional scenes in Ray Tracing is a hard problem. However, parallel implementations have been enabling real time performance, as the algorithm can be highly parallelized. Thus, a custom parallel design in hardware is likely to achieve a good performance. In this paper, we further improve the GridRT architecture overall performance by embedding the ray-triangle intersection computation into the precessing elements that form the architecture. Low cost and high rendering performance are the main concerns in this novel design. The results show that the execution time of each intersection computation is reduced by at least 50%, while the area cost is practically unchanged or even reduced when compared to the original GridRT implementation.

关键词： Ray tracing Registers Equations USA Councils Mathematical model Parallel architectures

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