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Human genome meeting 2016 : Houston, TX, USA. 28 February - 2 March 2016

Human genomics 2016年第1期10 Suppl 1卷 12页

作者： A. K. Srivastava Y. Wang R. Huang C. Skinner T. Thompson L. Pollard T. Wood F. Luo R. Stevenson R. Polimanti J. Gelernter X. Lin I. Y. Lim Y. Wu A. L. Teh L. Chen I. M. Aris S. E. Soh M. T. Tint J. L. MacIsaac F. Yap K. Kwek S. M. Saw M. S. Kobor M. J. Meaney K. M. Godfrey Y. S. Chong J. D. Holbrook Y. S. Lee P. D. Gluckman N. Karnani A. Kapoor D. Lee A. Chakravarti C. Maercker F. Graf M. Boutros G. Stamoulis F. Santoni P. Makrythanasis A. Letourneau M. Guipponi N. Panousis M. Garieri P. Ribaux E. Falconnet C. Borel S. E. Antonarakis S. Kumar J. Curran J. Blangero S. Chatterjee J. Akiyama D. Auer C. Berrios L. Pennacchio T. R. Donti G. Cappuccio M. Miller P. Atwal A. Kennedy A. Cardon C. Bacino L. Emrick J. Hertecant F. Baumer B. Porter M. Bainbridge P. Bonnen B. Graham R. Sutton Q. Sun S. Elsea Z. Hu P. Wang Y. Zhu J. Zhao M. Xiong David A. Bennett A. Hidalgo-Miranda S. Romero-Cordoba S. Rodriguez-Cuevas R. Rebollar-Vega E. Tagliabue M. Iorio E. D’Ippolito S. Baroni B. Kaczkowski Y. Tanaka H. Kawaji A. Sandelin R. Andersson M. Itoh T. Lassmann Y. Hayashizaki P. Carninci A. R. R. Forrest C. A. Semple E. A. Rosenthal B. Shirts L. Amendola C. Gallego M. Horike-Pyne A. Burt P. Robertson P. Beyers C. Nefcy D. Veenstra F. Hisama R. Bennett M. Dorschner D. Nickerson J. Smith K. Patterson D. Crosslin R. Nassir N. Zubair T. Harrison U. Peters G. Jarvik F. Menghi K. Inaki X. Woo P. Kumar K. Grzeda A. Malhotra H. Kim D. Ucar P. Shreckengast K. Karuturi J. Keck J. Chuang E. T. Liu B. Ji A. Tyler G. Ananda G. Carter H. Nikbakht M. Montagne M. Zeinieh A. Harutyunyan M. Mcconechy N. Jabado P. Lavigne J. Majewski J. B. Goldstein M. Overman G. Varadhachary R. Shroff R. Wolff M. Javle A. Futreal D. Fogelman L. Bravo W. Fajardo H. Gomez C. Castaneda C. Rolfo J. A. Pinto K. C. Akdemir L. Chin S. Patterson C. Statz S. Mockus S. N. Nikolaev X. I. Bonilla L. Parmentier B. King F. Bezrukov G. Kaya V. Zoete V. Seplyarskiy H. Sharpe T. McKee K. Popadin N. Basset-Seguin R. Ben Chaabene M. Andrianova C. Verdan K. Grosdemange O. Sumara M. E JCSRI Greenwood Genetic Center Greenwood USA School of Computing Clemson University Clemson USA Biochemical Genetics Laboratory Greenwood Genetic Center Greenwood USA Department Psychiatry Yale Sch Med and VA CT Healthcare Center West Haven USA Department Genetics Yale Sch Med and VA CT Healthcare Center West Haven USA Department Neurobiology Yale Sch Med and VA CT Healthcare Center West Haven USA Singapore Institute for Clinical Sciences Singapore Singapore National University of Singapore Singapore Singapore University of British Columbia Vancouver Canada KK Women’s and Children’s Hospital Singapore Singapore University of Southampton and University Hospital Southampton NHS Foundation Trust Southampton UK University of Auckland Auckland New Zealand McKusick-Nathans Institute of Genetic Medicine Johns Hopkins University School of Medicine Baltimore USA Esslingen University of Applied Sciences Esslingen Germany German Cancer Research Center Heidelberg Germany Department of Genetic Medicine and Development University of Geneva Medical School Geneva Switzerland Geneva University Hospitals-HUG Service of Genetic Medicine Geneva Switzerland GE3 Institute of Genetics and Genomics of Geneva University of Geneva Medical School Geneva Switzerland South Texas Diabetes and Obesity Institute School of Medicine University of Texas Rio-Grande Valley Edinburg USA South Texas Diabetes and Obesity Institute School of Medicine University of Texas Rio-Grande Valley Brownsville USA Institute of Genetic Medicine Johns Hopkins University Baltimore USA Genomics Division Lawrence Berkeley National Laboratory Berkeley USA Molecular and Human Genetics Baylor College of Medicine Houston USA Department of Translational Medical Sciences Federico II University Naples Italy Metabolon Inc Durham USA Section of Pediatric Neurology and Neuroscience Baylor College of Medicine Houston USA Tawam Hospital Abu Dhabi United Arab Emirates Stanford Medical School Stanford USA Sch

O1 The metabolomics approach to autism: identification of biomarkers for early detection of autism spectrum disorder A. K. Srivastava, Y. Wang, R. Huang, C. Skinner, T. Thompson, L. Pollard, T. Wood, F. Luo, R. Stevenson O2 Phenome-wide association study for smoking- and drinking-associated genes in 26,394 American women with African, Asian, European, and Hispanic descents R. Polimanti, J. Gelernter O3 Effects of prenatal environment, genotype and DNA methylation on birth weight and subsequent postnatal outcomes: findings from GUSTO, an Asian birth cohort X. Lin, I. Y. Lim, Y. Wu, A. L. Teh, L. Chen, I. M. Aris, S. E. Soh, M. T. Tint, J. L. MacIsaac, F. Yap, K. Kwek, S. M. Saw, M. S. Kobor, M. J. Meaney, K. M. Godfrey, Y. S. Chong, J. D. Holbrook, Y. S. Lee, P. D. Gluckman, N. Karnani, GUSTO study group O4 High-throughput identification of specific qt interval modulating enhancers at the SCN5A locus A. Kapoor, D. Lee, A. Chakravarti O5 Identification of extracellular matrix components inducing cancer cell migration in the supernatant of cultivated mesenchymal stem cells C. Maercker, F. Graf, M. Boutros O6 Single cell allele specific expression (ASE) IN T21 and common trisomies: a novel approach to understand DOWN syndrome and other aneuploidies G. Stamoulis, F. Santoni, P. Makrythanasis, A. Letourneau, M. Guipponi, N. Panousis, M. Garieri, P. Ribaux, E. Falconnet, C. Borel, S. E. Antonarakis O7 Role of microRNA in LCL to IPSC reprogramming S. Kumar, J. Curran, J. Blangero O8 Multiple enhancer variants disrupt gene regulatory network in Hirschsprung disease S. Chatterjee, A. Kapoor, J. Akiyama, D. Auer, C. Berrios, L. Pennacchio, A. Chakravarti O9 Metabolomic profiling for the diagnosis of neurometabolic disorders T. R. Donti, G. Cappuccio, M. Miller, P. Atwal, A. Kennedy, A. Cardon, C. Bacino, L. Emrick, J. Hertecant, F. Baumer, B. Porter, M. Bainbridge, P. Bonnen, B. Graham, R. Sutton, Q. Sun, S. Elsea O10 A novel causal methylation network approach to Alzheimer’s

关键词： Pulmonary Arterial Hypertension Oral Squamous Cell Carcinoma Deep Neural Network Autosomal Recessive Polycystic Kidney Disease Whole Genome Bisulfite Sequencing

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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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Modeling the breakage-fusion-bridge mechanism: Combinatorics and cancer genomics

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16th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2012

作者： Kinsella, Marcus Bafna, Vineet Bioinformatics and Systems Biology Program University of California San Diego San Diego CA 92093 United States Department of Computer Science and Engineering University of California San Diego San Diego CA 92093 United States

ISBN: (纸本)9783642296260

The breakage-fusion-bridge (BFB) mechanism was proposed over seven decades ago and is a source of genomic variability and gene amplification in cancer. Here we formally model and analyze the BFB mechanism, to our knowledge this first time this has been undertaken. We show that BFB can be modeled as successive inverted prefix duplications of a string. Using this model, we show that BFB can achieve a surprisingly broad range of amplification patterns. We find that a sequence of BFB operations can be found that nearly fits most patterns of copy number increases along a chromosome. We conclude that this limits the usefulness of methods like array CGH for detecting BFB and discuss other implications for understanding mechanisms of genomic instability. © 2012 Springer-Verlag Berlin Heidelberg.

关键词： Pattern matching

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Towards a formal model to reason about context-aware exception handling

Towards a formal model to reason about context-aware excepti...

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International Workshop on Exception Handling (WEH)

作者： Lincoln S. Rocha Rossana M. C. Andrade Group of Computer Networks Software Engineering and Systems Graduate Program in Computer Science Federal University of Ceará Fortaleza Ceara Brazil

The context-awareness is a central aspect in the design of pervasive systems, characterizing their ability to adapt its structure and behavior. The context-aware exception handling (CAEH) is an existing approach employed to design exception handling in pervasive systems. In this approach, the context is used to define, detect, propagate, and handle exceptions. CAEH is a complex and error prone activity, needing designers' insights and domain expertise to identify and characterize contextual exceptions. However, despite the existence of formal methods to analyze the adaptive behavior of pervasive systems, such methods lack specific support to specify the CAEH behavior. In this paper, we propose a formal model to reason about the CAEH behavior. It comprises an extension of the Kripke Structure to model the context evolution of a pervasive system and a transformation function that derivates the CAEH control flow from that proposed structure.

关键词： Context Context modeling Adaptation models Middleware Computational modeling Engines Cognition

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Formalizing the situation of a business process activity

Formalizing the situation of a business process activity

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International Conference on computer Supported Cooperative Work in Design

作者： Talita da Cunha Mattos Flávia Maria Santoro Kate Revoredo Vanessa Tavares Nunes Postgraduate Information Systems Program UNIRIO Rio de Janeiro Brazil COPPE/PESC-Systems Engineering and Computer Science Program UFRJ Rio de Janeiro Brazil

Business processes are dynamic and constantly evolving. Contextual elements that had not yet been identified and represented can arise and influence the execution of each process instance in diverse manners. In this scenario, the identification of these elements is considered of great importance. This paper proposes a formalism for context associated with business processes that intends to identify the situation of an activity in order to subsidize decisions to be taken within the execution of a process.

关键词： Computational modeling Context Psychology Media Navigation

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A solution to the state estimation problem of systems with unknown inputs

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Recent Patents on Mechanical engineering 2012年第2期5卷 102-112页

作者： Bolandhemmat, Hamidreza Clark, Christopher Golnaraghi, Farid MicroPilot Inc 72067 Road 8E Sturgeon Rd. Stony Mountain Manitoba R0C 3A0 Canada Computer Science Program Cal Poly State University San Luis Obispo CA 93407 United States Mechatronics Systems Engineering Simon Fraser University Surrey BC Canada

A solution to the state estimation problem of systems with unmeasurable non-zero mean inputs/disturbances, which do not satisfy the disturbance decoupling conditions, is given using the Kalman filtering and Bayesian estimation theory. The proposed estimation algorithm, named Supervisory Kalman Filter (SKF), consists of a Kalman filter with an extra update step which is inspired by the particle filtering technique. The extra step, called supervisory layer, numerically solves the measurement equations for the portion of the state vector that cannot be estimated by the Kalman filter. First, it produces N randomly generated state vectors, the particles, which are distributed based on the Kalman filter's last updated estimate. Then, the estimated measurement vector associated with each particle is compared to the actual measurement vector to identify the particle's probability to be a solution. Finally, a so-called resampling stage is implemented to refine the particles with higher likelihoods. The effectiveness of the SKF is demonstrated by comparing its estimation performance with that of the standard Kalman Filter and the particle filter for a vehicle state estimation problem. The estimation results confirm that the SKF precisely estimates those states of the vehicle that cannot be estimated by either the Kalman filter or the particle filter, regardless of the unknown disturbances from the road. The filtering methodology offered in the article has a potential to improve performance of the systems presented in the patents WO2011115960, WO2010024751, US8073528, and US20110299730. © 2012 Bentham science Publishers.

关键词： State estimation

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Low-frequency noise in "graphene-like" exfoliated thin films of topological insulators

Low-frequency noise in "graphene-like" exfoliated thin films...

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2011 MRS Spring Meeting

作者： Hossain, M.Z. Rumyantsev, S.L. Shahil, K.M.F. Teweldebrhan, D. Shur, M. Balandin, A.A. Nano-Device Laboratory Department of Electrical Engineering and Materials Science and Engineering Program University of California Riverside CA 92521 United States Department of Electrical Computer and Systems Engineering Center for Integrated Electronics Rensselaer Polytechnic Institute Troy NY 12180 United States Ioffe Institute Russian Academy of Sciences St. Petersburg 194021 Russia

ISBN: (纸本)9781605113210

We report results of the study of the low-frequency noise in thin films of bismuth selenide topological insulators, which were mechanically exfoliated from bulk crystals via "graphene-like" procedures. From the resistance dependence on the film thickness, it was established that the surface conduction contributions to electron transport were dominant. It was found that the current fluctuations have the noise spectral density S1 ∞ l/f (where f is the frequency) for the frequency range up to 10 kHz. The obtained noise data are important for transport experiments with topological insulators and for any proposed device applications of these materials. © 2011 Materials Research Society.

关键词： Thin films

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Introducing Software Process Tailoring to BPMN: BPMNt

Introducing Software Process Tailoring to BPMN: BPMNt

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International Conference on Software and System Process (ICSSP)

作者： Raquel M. Pillat Toacy C. Oliveira Fabio L. Fonseca Systems Engineering and Computer Science Program-PESC / COPPE Federal University of Rio de Janeiro Rio de Janeiro Brazil

BPMN 2.0 is a widely used notation to model business process that has associated tools and techniques to facilitate process management, execution and monitoring. As a result using BPMN to model Software Development Process (SDP) can leverage on the BPMN's infrastructure to improve SDP quality. Nevertheless, when using BPMN to model Software Processes one can observe the lack of an important feature: means to represent process tailoring. This article introduces the BPMNt, a conservative extension to BPMN that aims at aggregating a tailoring representation mechanism as the one found at SPEM 2.0. BPMNt uses the extensibility classes already present in the BPMN meta-model. Our work also presents an example to illustrate the approach.

关键词： Software Business Unified modeling language programming Adaptation models Standards Semantics

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Accelerating the artificial bee colony algorithm by hardware parallel implementations

Accelerating the artificial bee colony algorithm by hardware...

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2012 IEEE 3rd Latin American Symposium on Circuits and systems, LASCAS 2012

作者： Muñoz, Daniel M. Llanos, Carlos H. Coelho, Leandro Dos S. Ayala-Rincón, Mauricio Department of Mechanical Engineering Automation and Control Group/GRACO University of Brasilia Brasilia D.F. Brazil Industrial and Systems Engineering Graduate Program LAS/PPGEPS Pontifical Catholic University of Parana Curitiba Parana Brazil Department of Computer Science and Mathematics University of Brasilia Brasilia D.F. Brazil

ISBN: (纸本)9781467312080

Artificial bee colony (ABC) is an optimization algorithm inspired on the intelligent behavior of honey bee swarms. It is suitable to be applied when mathematical techniques are impractical or provide suboptimal solutions. As a population-based algorithm, the ABC suffers on large execution times specifically for embedded optimization problems with computational limitations. For that we propose a hardware parallel architecture of the opposition-based ABC algorithm (HPOABC) that facilitates the implementation in Field programmable Gate Arrays (FPGAs). Numerical simulations using four well-known benchmark problems demonstrate that the opposition-based approach allows the algorithm to improve its functionality, preserving the swarm diversity. Additionally, synthesis results point outs that the HPOABC architecture is effectively mapped in hardware and is suitable for embedded applications. © 2012 IEEE.

关键词： Global optimization

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Mediating process adaptation through a goal-oriented context-aware approach

Mediating process adaptation through a goal-oriented context...

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International Conference on computer Supported Cooperative Work in Design

作者： Vanessa Tavares Nunes Cláudia M. Lima Werner Flávia Maria Santoro COPPE/PESC-Systems Engineering and Computer Science Program UFRJ Rio de Janeiro Brazil NP2Tec and Postgraduate Information Systems Program UNIRIO Rio de Janeiro Brazil

Complexity and dynamism of day-to-day activities in organizations are inextricably linked, one impacting the other, increasing the challenges for constant adaptation on the way to organize work to address emerging demands. Market is demanding systems that are aware of organizations processes and able to evolve and adapt to new situations in everyday working activities. We argue that flexibility in processes could be managed in real time, by PAIS (Process-aware Information systems), using context information collected in the work environment. This paper proposes CGAdapt, a context management architecture approach that aims to improve and automate dynamic process adaptation. We explain how process adaptation may occur in real time through an existent scenario using this proposal and discuss the value of context-awareness to reason about process alternative adaptations in a goal oriented approach.

关键词： Context Materials Business Adaptation models Analytical models

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