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Re-analysis of public genetic data reveals a rare X-chromosomal variant associated with type 2 diabetes

NATURE COMMUNICATIONS 2018年第1期9卷 1页

作者： Bonas-Guarch, Silvia Guindo-Martinez, Marta Miguel-Escalada, Irene Grarup, Niels Sebastian, David Rodriguez-Fos, Elias Sanchez, Friman Planas-Felix, Merce Cortes-Sanchez, Paula Gonzalez, Santi Timshel, Pascal Pers, Tune H. Morgan, Claire C. Moran, Ignasi Atla, Goutham Gonzalez, Juan R. Puiggros, Montserrat Marti, Jonathan Andersson, Ehm A. Diaz, Carlos Badia, Rosa M. Udler, Miriam Leong, Aaron Kaur, Varindepal Flannick, Jason Jorgensen, Torben Linneberg, Allan Jorgensen, Marit E. Witte, Daniel R. Christensen, Cramer Brandslund, Ivan Appel, Emil V. Scott, Robert A. Luan, Jian'an Langenberg, Claudia Wareham, Nicholas J. Pedersen, Oluf Zorzano, Antonio Florez, Jose C. Hansen, Torben Ferrer, Jorge Maria Mercader, Josep Torrents, David BSC Joint BSC CRG IRB Res Program Computat Biol Barcelona 08034 Spain Inst Invest August Pi & Sunyer IDIBAPS Genom Programming Beta Cells Lab Barcelona 08036 Spain Inst Salud Carlos III Ctr Invest Biomed Red Diabet & Enfermedades Metab Madrid 28029 Spain Imperial Coll London Dept Med Sect Epigenom & Dis London W12 0NN England Univ Copenhagen Novo Nordisk Fdn Ctr Basic Metab Res Sect Metab GenetFac Hlth & Med Sci DK-2100 Copenhagen Denmark Barcelona Inst Sci & Technol Inst Res Biomed IRB Barcelona Baldiri Reixac 10-12 Barcelona 08028 Spain Univ Barcelona Fac Biol Dept Bioquim & Biomed Mol E-08028 Barcelona Spain Barcelona Supercomp Ctr BSC CNS Comp Sci Dept Barcelona 08034 Spain Statens Serum Inst Dept Epidemiol Res DK-2300 Copenhagen Denmark Boston Childrens Hosp Div Endocrinol Boston MA 02116 USA Boston Childrens Hosp Ctr Basic & Translat Obes Res Boston MA 02116 USA Broad Inst MIT & Harvard Med & Populat Genet Program Cambridge MA 02142 USA Ctr Res Environm Epidemiol CREAL ISGlobal Barcelona 08003 Spain CIBERESP Madrid 28029 Spain UPF Barcelona 08003 Spain Spanish Council Sci Res CSIC Artificial Intelligence Res Inst IIIA Madrid 28006 Spain Broad Inst Harvard & MIT Program Metab Cambridge MA 02142 USA Broad Inst Harvard & MIT Program Med & Populat Genet Cambridge MA 02142 USA Massachusetts Gen Hosp Diabet Unit Boston MA 02114 USA Massachusetts Gen Hosp Ctr Genom Med Boston MA 02114 USA Massachusetts Gen Hosp Div Gen Internal Med Boston MA 02114 USA Harvard Med Sch Dept Mol Biol Boston MA 02114 USA Capital Reg Denmark Res Ctr Prevent & Hlth DK-2600 Glostrup Denmark Univ Copenhagen Fac Hlth & Med Sci DK-2200 Copenhagen Denmark Aalborg Univ Fac Med DK-9220 Aalborg Denmark Rigshosp Dept Clin Expt Res DK-2100 Copenhagen Denmark Univ Copenhagen Fac Hlth & Med Sci Dept Clin Med DK-2200 Copenhagen Denmark Steno Diabet Ctr DK-2820 Gentofte Denmark Southern Denmark Univ Natl Inst Publ Hlth DK-5230 Odense M Denmark Aarhus Univ Dept

The reanalysis of existing GWAS data represents a powerful and cost-effective opportunity to gain insights into the genetics of complex diseases. By reanalyzing publicly available type 2 diabetes (T2D) genome-wide association studies (GWAS) data for 70,127 subjects, we identify seven novel associated regions, five driven by common variants (LYPLAL1, NEUROG3, CAMKK2, ABO, and GIP genes), one by a low-frequency (EHMT2), and one driven by a rare variant in chromosome Xq23, rs146662057, associated with a twofold increased risk for T2D in males. rs146662057 is located within an active enhancer associated with the expression of Angiotensin II Receptor type 2 gene (AGTR2), a modulator of insulin sensitivity, and exhibits allelic specific activity in muscle cells. Beyond providing insights into the genetics and pathophysiology of T2D, these results also underscore the value of reanalyzing publicly available data using novel genetic resources and analytical approaches.

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Weaning Gives β Cells License to Regenerate

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DEVELOPMENTAL CELL 2015年第5期32卷 531-+页

作者： Rovira, Meritxell Ferrer, Jorge Inst Invest August Pi i Sunyer IDIBAPS Genom Programming Beta Cells Lab Barcelona 08036 Spain CIBER Diabet & Enfermedades Metab Asociadas CIBER Barcelona 08036 Spain Univ London Imperial Coll Sci Technol & Med Dept Med London W12 0NN England

Pancreatic beta cell proliferation is high at birth and then rapidly declines. In this issue of Developmental Cell, Stolovich-Rain etal. (2015) show that β cells’ capacity to increase proliferation in response to injury is unexpectedly not acquired until after weaning-related nutritional changes trigger a metabolic and regenerative competence program.

关键词： Regeneration Weaning Licence Insulin-Secreting Cells

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Transcriptional enhancers: functional insights and role in human disease

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CURRENT OPINION IN GENETICS & DEVELOPMENT 2015年 33卷 71-76页

作者： Miguel-Escalada, Irene Pasquali, Lorenzo Ferrer, Jorge Univ London Imperial Coll Sci Technol & Med Dept Med London W12 0NN England Inst Invest August Pi & Sunyer IDIBAPS Genom Programming Beta Cells Lab Barcelona 08036 Spain CIBER Diabet & Enfermedades Metab Asociadas CIBER Barcelona 08036 Spain Germans Trias & Pujol Univ Hosp & Res Inst Div Endocrinol Barcelona 08036 Spain Josep Carreras Leukaemia Res Inst Barcelona 08036 Spain

In recent years, studies of cis-regulatory mechanisms have evolved from a predominant focus on promoter regions to the realization that spatial and temporal gene regulation is frequently driven by long-range enhancer clusters that operate within chromosomal compartments. This increased understanding of genome function, together with the emergence of technologies that enable whole-genome sequencing of patients' DNAs, open the prospect of dissecting the role of cis-regulatory defects in human disease. In this review we discuss how recent epigenomic studies have provided insights into the function of transcriptional enhancers. We then present examples that illustrate how integrative genomics can help uncover enhancer sequence variants underlying Mendelian and common polygenic human disease.

关键词： Gene regulation Enhancer maladjustment promoter regions Enhancer (genetic element)

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Fast Plasma Investigation for Magnetospheric Multiscale

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SPACE SCIENCE REVIEWS 2016年第1-4期199卷 331-406页

作者： Pollock, C. Moore, T. Jacques, A. Burch, J. Gliese, U. Saito, Y. Omoto, T. Avanov, L. Barrie, A. Coffey, V. Dorelli, J. Gershman, D. Giles, B. Rosnack, T. Salo, C. Yokota, S. Adrian, M. Aoustin, C. Auletti, C. Aung, S. Bigio, V. Cao, N. Chandler, M. Chornay, D. Christian, K. Clark, G. Collinson, G. Corris, T. De Los Santos, A. Devlin, R. Diaz, T. Dickerson, T. Dickson, C. Diekmann, A. Diggs, F. Duncan, C. Figueroa-Vinas, A. Firman, C. Freeman, M. Galassi, N. Garcia, K. Goodhart, G. Guererro, D. Hageman, J. Hanley, J. Hemminger, E. Holland, M. Hutchins, M. James, T. Jones, W. Kreisler, S. Kujawski, J. Lavu, V. Lobell, J. LeCompte, E. Lukemire, A. MacDonald, E. Mariano, A. Mukai, T. Narayanan, K. Nguyan, Q. Onizuka, M. Paterson, W. Persyn, S. Piepgrass, B. Cheney, F. Rager, A. Raghuram, T. Ramil, A. Reichenthal, L. Rodriguez, H. Rouzaud, J. Rucker, A. Saito, Y. Samara, M. Sauvaud, J. -A. Schuster, D. Shappirio, M. Shelton, K. Sher, D. Smith, D. Smith, K. Smith, S. Steinfeld, D. Szymkiewicz, R. Tanimoto, K. Taylor, J. Tucker, C. Tull, K. Uhl, A. Vloet, J. Walpole, P. Weidner, S. White, D. Winkert, G. Yeh, P. -S. Zeuch, M. NASA Goddard Space Flight Ctr Greenbelt MD USA SW Res Inst San Antonio TX USA SGT Inc Greenbelt MD USA Inst Space & Astronaut Sci 3-1-1 Yoshinodai Sagamihara Kanagawa 229 Japan Meisei Elect Co Ltd Isesaki Japan Univ Maryland College Pk MD 20742 USA Millenium Engn Arlington VA USA NASA Marshall Space Flight Ctr Huntsville AL USA Oak Ridge Associated Univ Oak Ridge TN USA Orbital Sci Corp Beltsville MD USA Stellar Solut Inc Chantilly VA USA Inst Res Astrophys & Planetol Toulouse France Northrup Grumman Hyattsville MD USA Florez Engn LLC Laurel MD USA MEI Technol Houston TX USA Global Programming Solut Fairfax VA USA Catholic Univ Amer Washington DC 20064 USA Johns Hopkins Appl Phys Lab Laurel MD USA ASRC AS & D Inc Beltsville MD USA Jacobs ESSSA Grp Huntsville AL USA Prototype Prod Inc Ashburn VA USA Ares Tech Serv Corp Greenbelt MD USA Bandwidth Solut Inc Mclean VA USA Hammers Co Greenbelt MD USA Siena Coll Loudonville NY USA Space Power Elect Inc Kathleen GA USA Teledyne Brown Engn Inc Huntsville AL 35807 USA NASA Headquarders Washington DC USA YS Design Tokyo Japan Vantage Syst Inc Lanham MD USA Design Amer Inc College Pk MD USA Global Sci & Technol Inc Greenbelt MD USA Jackson & Tull Greenbelt MD USA

The Fast Plasma Investigation (FPI) was developed for flight on the Magnetospheric Multiscale (MMS) mission to measure the differential directional flux of magnetospheric electrons and ions with unprecedented time resolution to resolve kinetic-scale plasma dynamics. This increased resolution has been accomplished by placing four dual 180-degree top hat spectrometers for electrons and four dual 180-degree top hat spectrometers for ions around the periphery of each of four MMS spacecraft. Using electrostatic field-of-view deflection, the eight spectrometers for each species together provide 4pi-sr field-of-view with, at worst, 11.25-degree sample spacing. Energy/charge sampling is provided by swept electrostatic energy/charge selection over the range from 10 eV/q to 30000 eV/q. The eight dual spectrometers on each spacecraft are controlled and interrogated by a single block redundant Instrument Data Processing Unit, which in turn interfaces to the observatory's Instrument Suite Central Instrument Data Processor. This paper describes the design of FPI, its ground and in-flight calibration, its operational concept, and its data products.

关键词： Magnetospheric Multiscale Magnetic reconnection Particle instrumentation Electron spectrometer Ion spectrometer Instrument characterization and calibration

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Perfectly Load-Balanced, Stable, Synchronization-Free Parallel Merge

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PARALLEL PROCESSING LETTERS 2014年第1期24卷 1450005-1-1450005-11页

作者： Siebert, Christian Traeff, Jesper Larsson Rhein Westfal TH Aachen Dept Comp Sci Lab Parallel Programming Schinkel Str 2a D-52062 Aachen Germany Vienna Univ Technol Inst Informat Syst Res Grp Parallel Comp A-1040 Vienna Austria

We present a simple, work-optimal and synchronization-free solution to the problem of stably merging in parallel two given, ordered arrays of m and n elements into an ordered array of m+n elements. The main contribution is a new, simple, fast and direct algorithm that determines, for any prefix of the stably merged output array, the exact prefixes of each of the two input arrays needed to produce this output prefix. More precisely, for any given index in the resulting, but not yet constructed output array, representing the desired output prefix, the algorithm computes the indices (called co-ranks) in each of the two input arrays representing the required input prefixes without having to merge the input arrays. The co-ranking algorithm takes O(log min(m,n)) time steps, and uses 0(1) space. Co-ranking is used in parallel to partition the input arrays into a collection of as many pairs as desired, each pair with exactly the same number of elements. Any stable, sequential merge algorithm can be used to merge pairs independently. The result is a perfectly load-balanced, stable, parallel merge algorithm. Co-ranking and sequential merging of pairs can be done without synchronization. Compared to other, linear speedup approaches to the parallel merge problem, the algorithm is considerably simpler and can be up to a factor of two faster. Compared to previous algorithms for solving the co-ranking problem, the new algorithm works for arbitrary output array indices and maintains stability in the presence of repeated elements at no extra space or time cost. When the number of processing elements p does not exceed (m n)/ log min(m, n), the parallel merge algorithm has perfect, linear speedup p. Furthermore, it is easy to implement on both shared and distributed memory systems.

关键词： Merge problem Parallel merging Stable merging

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A Socially-Intelligent Multi-Robot Service Team for In-Home Monitoring

A Socially-Intelligent Multi-Robot Service Team for In-Home ...

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5th International Conference on Information, Intelligence, Systems and Applications (IISA)

作者： Drossos, Konstantinos Floros, Andreas Potirakis, Stelios Tatlas, Nikolas-Alexander Tuna, Gurkan Ionian Univ Dept Audiovisual Arts Audiovisual Signal Proc Lab Corfu Greece Technol Educ Inst Piraeus Dept Elect Egaleo Greece Trakya Univ Dept Comp Programming Edirne Turkey

ISBN: (纸本)9781479961726

The objective of this study is to develop a socially-intelligent service team comprised of multiple robots with sophisticated sonic interaction capabilities that aims to transparently collaborate towards efficient and robust monitoring by close interaction. In the distributed scenario proposed in this study, the robots share any acoustic data extracted from the environment and act in-sync with the events occurring in their living environment in order to provide potential means for efficient monitoring and decision-making within a typical home enclosure. Although each robot acts as an individual recognizer using a novel emotionally-enriched word recognition system, the final decision is social in nature and is followed by all. Moreover, the social decision stage triggers actions that are algorithmically distributed among the robots' population and enhances the overall approach with the potential advantages of the team work within specific communities through collaboration.

关键词： Acoustics Emotion recognition Robot kinematics Robot sensing systems Service robots Stress

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Guest editors' preface to special issue on interval temporal logics

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ANNALS OF MATHEMATICS AND ARTIFICIAL INTELLIGENCE 2014年第1-3期71卷 1-9页

作者： Moszkowski, Ben Guelev, Dimitar Leucker, Martin De Montfort Univ Software Technol Res Lab Leicester LE1 9BH Leics England Inst Math & Informat Dept Algebra & Log Sofia Bulgaria Med Univ Lubeck Inst Software Engn & Programming Languages D-23538 Lubeck Germany

An introduction is presented in which the editors discuss various reports within the issue on topics including the theory and application of interval temporal logics, computational complexity and duration calculus.

关键词： COMPUTATIONAL complexity CALCULUS REASONING (Logic)

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How File Access Patterns Influence Interference Among Cluster Applications 16

How File Access Patterns Influence Interference Among Cluste...

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16th IEEE International Conference on Cluster Computing (CLUSTER)

作者： Kuo, Chih-Song Shah, Aamer Nomura, Akihiro Matsuoka, Satoshi Wolf, Felix Rhein Westfal TH Aachen Dept Comp Sci Aachen Germany German Res Sch Simulat Sci Lab Parallel Programming Aachen Germany Tokyo Inst Technol Global Sci Informat & Comp Ctr Tokyo Japan

ISBN: (纸本)9781479955480

On large-scale clusters, tens to hundreds of applications can simultaneously access a parallel file system, leading to contention and in its wake to degraded application performance. However, the degree of interference depends on the specific file access pattern. On the basis of synchronized time-slice profiles, we compare the interference potential of different file access patterns. We consider both micro-benchmarks, to study the effects of certain patterns in isolation, and realistic applications to gauge the severity of such interference under production conditions. In particular, we found that writing large files simultaneously with small files can slow down the latter at small chunk sizes but the former at larger chunk sizes. We further show that such effects can seriously affect the runtime of real applicationsup to a factor of five in one instance. In the future, both our insights and profiling techniques can be used to automatically classify the interference potential between applications and to adjust scheduling decisions accordingly.

关键词： Benchmarking

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Automated Verification of Feature Model Configuration Processes based on Workflow Petri Nets 14

Automated Verification of Feature Model Configuration Proces...

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18th International Software Product Line Conference (SPLC)

作者： Mennicke, Stephan Lochau, Malte Schroeter, Julia Winkelmann, Tim TU Braunschweig Inst Programming & React Syst Braunschweig Germany Tech Univ Darmstadt Real Time Syst Lab Darmstadt Germany Tech Univ Dresden Inst Software & Multimedia Technol Dresden Germany TU Braunschweig Inst Software Engn & Automat Informat Braunschweig Germany

ISBN: (纸本)9781450327404

Modern software systems are highly configurable in order to satisfy diverse customer requirements and application contexts. Feature models provide a well-established formalism for tailoring configuration spaces of applications. Thereupon, multi-view staged configuration approaches modularize feature models for separation of concerns and apply work-flow modeling for scheduling configuration decisions. However, the complex, often oblivious and even cyclic logical dependencies among configuration decisions obstruct compositional semantics of feature model views thus spoiling intuitive modeling and rigorous analysis of staged configuration processes. In this paper, we apply workflow Petri nets (WPNs) as a formal operational model for staged configuration that makes explicit causal dependencies among feature selections. For the internal separation into composable configuration stages we further adopt the principles of open workflow nets. It is shown that the soundness notion of WPNs naturally coincides with fundamental correctness and liveness properties to be verified for staged configuration processes. We present a prototype implementation for an automated computation of staged configuration processes and provide experimental results concerning scalability properties.

关键词： workflows analysis and synthesis of Petri nets configuration management domain feature model staged configuration

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A Reliability-Aware Address Mapping Strategy for NAND Flash Memory Storage Systems

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IEEE TRANSACTIONS ON COMPUTER-AIDED DESIGN OF INTEGRATED CIRCUITS AND SYSTEMS 2014年第11期33卷 1623-1631页

作者： Wang, Yi Huang, Min Shao, Zili Chan, Henry C. B. Bathen, Luis Angel D. Dutt, Nikil D. Shenzhen Univ Guangdong Prov Key Lab Popular High Performance C Shenzhen 518060 Peoples R China Hong Kong Polytech Univ Dept Comp Hong Kong Hong Kong Peoples R China Harbin Inst Technol Automat Test & Control Inst Harbin 150001 Peoples R China Hong Kong Polytech Univ Embedded Syst & CPS Lab Dept Comp Hong Kong Hong Kong Peoples R China Intel Corp Programming Syst Lab Santa Clara CA 95052 USA Univ Calif Irvine Ctr Embedded Comp Syst Irvine CA 92697 USA

The increasing density of NAND flash memory leads to a dramatic increase in the bit error rate of flash, which greatly reduces the ability of error correcting codes (ECC) to handle multibit errors. NAND flash memory is normally used to store the file system metadata and page mapping information. Thus, a broken physical page containing metadata may cause an unintended and severe change in functionality of the entire flash. This paper presents Meta-Cure, a novel hardware and file system interface that transparently protects metadata in the presence of multibit faults. Meta-Cure exploits built-in ECC and replication in order to protect pages containing critical data, such as file system metadata. Redundant pairs are formed at run time and distributed to different physical pages to protect against failures. Meta-Cure requires no changes to the file system, on-chip hierarchy, or hardware implementation of flash memory chip. We evaluate Meta-Cure under a real-embedded platform using a variety of I/O traces. The evaluation platform adopts dual ARM Cortex A9 processor cores with 64 Gb NAND flash memory. We have evaluated the effectiveness of Meta-Cure on the new technology file system file system. Experimental results show that the proposed technique can reduce uncorrectable page errors by 70.38% with less than 7.86% time overhead in comparison with conventional error correction techniques.

关键词： Error correcting codes (ECC) memory management metadata NAND flash memory redundancy reliability

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