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Gene expression imputation across multiple brain regions provides insights into schizophrenia risk (vol 51, pg 659, 2019)

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NATURE GENETICS 2019年第6期51卷 1068-1068页

作者： Huckins, Laura M. Dobbyn, Amanda Ruderfer, Douglas M. Hoffman, Gabriel Wang, Weiqing Pardinas, Antonio F. Rajagopal, Veera M. Als, Thomas D. Nguyen, Hoang T. Girdhar, Kiran Boocock, James Roussos, Panos Fromer, Menachem Kramer, Robin Domenici, Enrico Gamazon, Eric R. Purcell, Shaun Demontis, Ditte Borglum, Anders D. Walters, James T. R. O'Donovan, Michael C. Sullivan, Patrick Owen, Michael J. Devlin, Bernie Sieberts, Solveig K. Cox, Nancy J. Im, Hae Kyung Sklar, Pamela Stahl, Eli A. Pamela Sklar Division of Psychiatric Genomics Icahn School of Medicine at Mount Sinai New York NY USA Department of Genetics and Genomics Icahn School of Medicine at Mount Sinai New York NY USA Department of Psychiatry Icahn School of Medicine at Mount Sinai New York NY USA Icahn Institute for Genomics and Multiscale Biology Icahn School of Medicine at Mount Sinai New York NY USA Vanderbilt University Medical Center Nashville TN USA MRC Centre for Neuropsychiatric Genetics and Genomics Cardiff University Cardiff UK Department of Biomedicine Aarhus University Aarhus Denmark The Lundbeck Foundation Initiative for Integrative Psychiatric Research iPSYCH Denmark Center for Integrative Sequencing Aarhus University Aarhus Denmark Department of Human Genetics David Geffen School of Medicine University of California Los Angeles Los Angeles CA USA Human Brain Collection Core National Institute of Mental Health Bethesda MD USA Laboratory of Neurogenomic Biomarkers Centre for Integrative Biology (CIBIO) University of Trento Trento Italy Clare Hall University of Cambridge Cambridge UK University of North Carolina at Chapel Hill Chapel Hill NC USA Karolinska Institutet Stockholm Sweden Department of Psychiatry University of Pittsburgh Pittsburgh PA USA Systems Biology Sage Bionetworks Seattle WA USA Section of Genetic Medicine Department of Medicine University of Chicago Chicago IL USA Integrated Technology Research Laboratories Pharmaceutical Research Division Takeda Pharmaceutical Company Limited Fujisawa Japan Neuropsychiatry Section Department of Psychiatry Perelman School of Medicine University of Pennsylvania Philadelphia PA USA Neuropsychiatric Signaling Program Department of Psychiatry Perelman School of Medicine University of Pennsylvania Philadelphia PA USA Psychiatry JJ Peters Virginia Medical Center Bronx NY USA Department of Neuroscience Icahn School of Medicine at Mount Sinai New York New York NY USA Friedman Brain Institute

Transcriptomic imputation approaches combine eQTL reference panels with large-scale genotype data in order to test associations between disease and gene expression. These genic associations could elucidate signals in complex genome-wide association study (GWAS) loci and may disentangle the role of different tissues in disease development. We used the largest eQTL reference panel for the dorso-lateral prefrontal cortex (DLPFC) to create a set of gene expression predictors and demonstrate their utility. We applied DLPFC and 12 GTEx-brain predictors to 40,299 schizophrenia cases and 65,264 matched controls for a large transcriptomic imputation study of schizophrenia. We identified 413 genic associations across 13 brain regions. Stepwise conditioning identified 67 non-MHC genes, of which 14 did not fall within previous GWAS loci. We identified 36 significantly enriched pathways, including hexosaminidase-A deficiency, and multiple porphyric disorder pathways. We investigated developmental expression patterns among the 67 non-MHC genes and identified specific groups of pre- and postnatal expression.

关键词： Gene expression Genome-wide association studies Schizophrenia Transcriptomics

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Reactive High-level Behavior Synthesis for an Atlas Humanoid Robot

Reactive High-level Behavior Synthesis for an Atlas Humanoid...

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IEEE International Conference on Robotics and Automation

作者： Spyros Maniatopoulos Philipp Schillinger Vitchyr Pong David C. Conner Hadas Kress-Gazit Verifiable Robotics Research Group Sibley School of Mechanical and Aerospace Engineering Cornell University Ithaca NY 14853 USA Robert Bosch GmbH Corporate Research Department for Cognitive Systems 70442 Stuttgart Germany Capable Humanitarian Robotics & Intelligent Systems Lab Department of Physics Computer Science and Engineering Christopher Newport University Newport News VA 23606 USA

ISBN: (纸本)9781467380270

In this work, we take a step towards bridging the gap between the theory of formal synthesis and its application to real-world, complex, robotic systems. In particular, we present an end-to-end approach for the automatic generation of code that implements high-level robot behaviors in a verifiably correct manner, including reaction to the possible failures of low-level actions. We start with a description of the system defined a priori. Thus, a non-expert user need only specify a high-level task. We automatically construct a formal specification, in a fragment of Linear Temporal Logic (LTL), that encodes the system's capabilities and constraints, the task, and the desired reaction to low-level failures. We then synthesize a reactive mission plan that is guaranteed to satisfy the formal specification, i.e., achieve the task's goals or correctly react to failures. Lastly, we automatically generate a state machine that instantiates the synthesized symbolic plan in software. We showcase our approach using Team ViGIR's software and Atlas humanoid robot and present lab experiments, thus demonstrating the application of formal synthesis techniques to complex robotic systems. The proposed approach has been implemented and open-sourced as a collection of Robot Operating System (ROS) packages, which are adaptable to other systems.

关键词： Atlas Humanoid Robot formal synthesis ROS

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People counting in crowded and outdoor scenes using a hybrid multi-camera approach

arXiv

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arXiv 2017年

作者： Dittrich, Fabio De Oliveira, Luiz E. S. Britto, Alceu S. Koerich, Alessandro L. Laboratoire d'Imagerie Vision et Intelligence Artificielle Ecole de Technologie Superieure 1100 Notre-Dame West MontrealQCH3A 1E3 Canada Federal University of Paraná Department of Informatics Centro Politécnico Curitiba PR81531-970 Brazil Pontifical Catholic University of Paraná Postgraduate Program in Computer Science R. Imaculada Conceiç aõ 1155 Curitiba PR80215-901 Brazil Ecole de Technologie Supérieure Department of Software and IT Engineering 1100 Notre-Dame West MontrealQCH3A 1E3 Canada

This paper presents two novel approaches for people counting in crowded and open environments that combine the information gathered by multiple views. Multiple camera are used to expand the field of view as well as to mitigate the problem of occlusion that commonly affects the performance of counting methods using single cameras. The first approach is regarded as a direct approach and it attempts to segment and count each individual in the crowd. For such an aim, two head detectors trained with head images are employed: One based on support vector machines and another based on Adaboost perceptron. The second approach, regarded as an indirect approach employs learning algorithms and statistical analysis on the whole crowd to achieve counting. For such an aim, corner points are extracted from groups of people in a foreground image and computed by a learning algorithm which estimates the number of people in the scene. Both approaches count the number of people on the scene and not only on a given image or video frame of the scene. The experimental results obtained on the benchmark PETS2009 video dataset show that proposed indirect method surpasses other methods with improvements of up to 46.7% and provides accurate counting results for the crowded scenes. On the other hand, the direct method shows high error rates due to the fact that the latter has much more complex problems to solve, such as segmentation of heads. Copyright © 2017, The Authors. All rights reserved.

关键词： Cameras

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Origin of life in a digital microcosm

arXiv

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arXiv 2017年

作者： Nitash, C.G. LaBar, Thomas Hintze, Arend Adami, Christoph Department of Computer Science & Engineering Michigan State University East LansingMI48824 United States BEACON Center for the Study of Evolution in Action Michigan State University East LansingMI48824 Department of Microbiology & Molecular Genetics Michigan State University East LansingMI48824 United States Program in Ecology Evolutionary Biology and Behavior Michigan State University East LansingMI48824 United States Department of Integrative Biology Michigan State University East LansingMI48824 United States Department of Physics and Astronomy Michigan State University East LansingMI48824 United States

While all organisms on Earth descend from a common ancestor, there is no consensus on whether the origin of this ancestral self-replicator was a one-off event or whether it was only the final survivor of multiple origins. Here we use the digital evolution system Avida to study the origin of self-replicating computer programs. By using a computational system, we avoid many of the uncertainties inherent in any biochemical system of self-replicators (while running the risk of ignoring a fundamental aspect of biochemistry). We generated the exhaustive set of minimal-genome self-replicators and analyzed the network structure of this fitness landscape. We further examined the evolvability of these self-replicators and found that the evolvability of a self-replicator is dependent on its genomic architecture. We studied the differential ability of replicators to take over the population when competed against each other (akin to a primordial-soup model of biogenesis) and found that the probability of a self-replicator out-competing the others is not uniform. Instead, progenitor (most-recent common ancestor) genotypes are clustered in a small region of the replicator space. Our results demonstrate how computational systems can be used as test systems for hypotheses concerning the origin of life. Copyright © 2017, The Authors. All rights reserved.

关键词： Biochemistry

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Light, the universe, and everything-12 Herculean tasks for quantum cowboys and black diamond skiers

arXiv

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arXiv 2018年

作者： Agarwal, Girish Allen, Roland E. Bezdìková, Iva Boyd, Robert W. Chen, Goong Hanson, Ronald Hawthorne, Dean L. Hemmer, Philip Kim, Moochan B. Kocharovskaya, Olga Lee, David M. Lidström, Sebastian K. Lidström, Suzy Losert, Harald Maier, Helmut Neuberger, John W. Padgett, Miles J. Raizen, Mark Rajendran, Surjeet Rasel, Ernst Schleich, Wolfgang P. Scully, Marlan O. Shchedrin, Gavriil Shvets, Gennady Sokolov, Alexei Svidzinsky, Anatoly Walsworth, Ronald L. Weiss, Rainer Wilczek, Frank Willner, Alan E. Yablonovich, Eli Zheludev, Nikolay Department of Physics and Astronomy Texas A&M University College StationTX77843 United States Department of Physics Faculty of Nuclear Sciences and Physical Engineering Czech Technical University in Prague Brehova 7 Praha 1-Staré mìsto11519 Czech Republic Department of Physics Technical University of Ostrava 17 Listopadu 15 Ostrava-Poruba70833 Czech Republic Department of Physics School of Electrical Engineering and Computer Science University of Ottawa OttawaONK1N6N5 Canada Institute of Optics Department of Physics and Astronomy University of Rochester RochesterNY14627 United States School of Physics and Astronomy University of Glasgow GlasgowG128QQ United Kingdom Department of Mathematics Texas A&M University College StationTX77843 United States Science Program Texas A&M University at Qatar Education City Doha Qatar Texas A&M University College StationTX77843 United States QuTech and Kavli Institute of Nanoscience Delft University of Technology P.O. Box 5046 Delft2600 GA Netherlands Cornell Laboratory of Ornithology Cornell University IthacaNY14850 United States Laboratory of Atomic and Solid State Physics Cornell University IthacaNY14853 United States Department of Electrical & Computer Engineering Texas A&M Energy Institute Texas A&M University TX77843 United States Department of Physics Strathclyde University GlasgowG11XJ United Kingdom Physica Scripta Royal Swedish Academy of Sciences StockholmSE-10405 Sweden Universität Ulm Albert-Einstein-Allee 11 Ulm89081 Germany Institut für Zahlentheorie und Wahrscheinlichkeitstheorie Universität Ulm Albert-Einstein-Allee 11 Ulm89081 Germany Department of Mathematics University of North Texas DentonTX76203-5017 United States College of Natural Sciences University of Texas AustinTX78712 United States Department of Physics University of California BerkeleyCA94720-7300 United States Institut fuer Quantenoptik QUEST-LFS Welfengarten 1 Hannover30167 Germany Hagler Insti

The Winter Colloquium on the Physics of Quantum Electronics (PQE) has been a seminal force in quantum optics and related areas since 1971. It is rather mindboggling to recognize how the concepts presented at these conferences have transformed scientific understanding and human society. In January, 2017, the participants of PQE were asked to consider the equally important prospects for the future, and to formulate a set of questions representing some of the greatest aspirations in this broad field. The result is this multi-authored paper, in which many of the world's leading experts address the following fundamental questions: (1) What is the future of gravitational wave astronomy? (2) Are there new quantum phases of matter away from equilibrium that can be found and exploited-such as the time crystal? (3) Quantum theory in uncharted territory: What can we learn? (4) What are the ultimate limits for laser photon energies? (5) What are the ultimate limits to temporal, spatial, and optical resolution? (6) What novel roles will atoms play in technology? (7) What applications lie ahead for nitrogen-vacancy centers in diamond? (8) What is the future of quantum coherence, squeezing, and entanglement for enhanced superresolution and sensing? (9) How can we solve (some of) humanity's biggest problems through new quantum technologies? (10) What new understanding of materials and biological molecules will result from their dynamical characterization with free electron lasers? (11) What new technologies and fundamental discoveries might quantum optics achieve by the end of this century? (12) What novel topological structures can be created and employed in quantum optics? Copyright © 2018, The Authors. All rights reserved.

关键词： Quantum optics

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Ancestral reconstruction with duplications using binary encoding and probabilistic model 7

Ancestral reconstruction with duplications using binary enco...

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7th International Conference on Bioinformatics and Computational Biology, BICOB 2015

作者： Zhou, Lingxi Feng, Bing Yang, Ning Tang, Jijun Tianjin Key Laboratory of Cognitive Computing and Application Tianjin University China Department of Computer Science and Engineering University of South Carolina United States School of Automation Northwestern Polytechnical University China

ISBN: (纸本)9781880843994

A number of approaches have been developed using gene order data to conduct research on both ancestral genomic inference and phylogenetic reconstruction. When investigating species divergence and evolution, gene order data has several inherent advantages that enable researchers to determine a more detailed evolutionary scenario. In this study, we propose a framework to integrate free gene and whole genome duplications with gene additions and losses and rearrangements under probabilistic models to infer the gene order of an ancestor and name it PMAG++. We configured a series of experiments to evaluate the performance of PMAG++ on simulated data and we concluded that it can reconstruct ancestral genome content and orientation with high accuracy and efficiency. Copyright ISCA, BICOB 2015.

关键词： Genes

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Effect of active learning using program visualization in technology-constrained college classrooms

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Research and Practice in Technology Enhanced Learning 2015年第1期10卷 1-25页

作者： Banerjee, Gargi Murthy, Sahana Iyer, Sridhar Interdisciplinary Program in Educational Technology Indian Institute of Technology Bombay Mumbai 400076 India Department of Computer Science and Engineering Indian Institute of Technology Bombay Mumbai 400076 India

Multiple studies report that computer science (CS) instructors face problems on how to integrate visualizations in their teaching. This problem gets compounded for instructors in technology-constrained classrooms that are common in developing countries. In these classrooms, students are not able to interact with visualization directly;instead, their interaction is mediated by the instructor who alone may have access to the visualization. In the current study, we contrasted learning outcome from integrating program visualization at two different engagement levels in instructor-mediated classroom setting. The two levels were “Responding” (prediction activity with visualization) and “Viewing” (watching visualization with instructor commentary) as per Naps’ taxonomy. The study was conducted for a programming topic of medium complexity. We found the strategy of prediction with visualization (“Responding”) led to statistically significant higher active behavioral engagement and higher perception of learning among students than the strategy of watching the visualization with instructor commentary (“Viewing”). We also found statistically significant higher cognitive achievement in terms of the rate of problem solving for the “Responding” group, if the students had prior training in active learning. This study can serve as a reference guide to design effective integration of visualizations in instructor-mediated classrooms. © 2015, The Author(s).

关键词： Active learning Engagement levels Prediction program visualization Viewing

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Self-assembly of colloidal particles in deformation landscapes of electrically driven layer undulations in cholesteric liquid crystals

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Physical Review E 2016年第4期94卷 042709-042709页

作者： Michael C. M. Varney Qiaoxuan Zhang Bohdan Senyuk Ivan I. Smalyukh Department of Physics and Soft Materials Research Center University of Colorado at Boulder Boulder Colorado 80309 USA Materials Science and Engineering Program University of Colorado at Boulder Boulder Colorado 80309 USA Department of Electrical Computer and Energy Engineering University of Colorado at Boulder Boulder Colorado 80309 USA Renewable and Sustainable Energy Institute National Renewable Energy Laboratory and University of Colorado at Boulder Boulder Colorado 80309 USA

We study elastic interactions between colloidal particles and deformation landscapes of undulations in a cholesteric liquid crystal under an electric field applied normal to cholesteric layers. The onset of undulation instability is influenced by the presence of colloidal inclusions and, in turn, layers’ undulations mediate the spatial patterning of particle locations. We find that the bending of cholesteric layers around a colloidal particle surface prompts the local nucleation of an undulations lattice at electric fields below the well-defined threshold known for liquid crystals without inclusions, and that the onset of the resulting lattice is locally influenced, both dimensionally and orientationally, by the initial arrangements of colloids defined using laser tweezers. Spherical particles tend to spatially localize in the regions of strong distortions of the cholesteric layers, while colloidal nanowires exhibit an additional preference for multistable alignment offset along various vectors of the undulations lattice. Magnetic rotation of superparamagnetic colloidal particles couples with the locally distorted helical axis and undulating cholesteric layers in a manner that allows for a controlled three-dimensional translation of these particles. These interaction modes lend insight into the physics of liquid crystal structure-colloid elastic interactions, as well as point the way towards guided self-assembly of reconfigurable colloidal composites with potential applications in diffraction optics and photonics.

关键词： Distortions & defects Elastic forces Electric field alignment Electric field effects Magnetic field alignment Pattern formation Patterning Self-assembly

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Causes of blindness and vision impairment in 2020 and trends over 30 years, and prevalence of avoidable blindness in relation to VISION 2020: the Right to Sight: an analysis for the Global Burden of Disease Study (vol 2, pg 144, 2021)

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LANCET GLOBAL HEALTH 2021年第4期9卷 E408-E408页

作者： Steinmetz, Jaimie D. Vision and Eye Research Institute Anglia Ruskin University Cambridge United Kingdom Biomedical Informatics Seoul National University Hospital Seoul South Korea Institute for Health Metrics and Evaluation University of Washington Seattle WA United States Department of Health Metrics Sciences School of Medicine University of Washington Seattle WA United States Institute of Health Services Research Yonsei University Seoul South Korea Department of Ophthalmology University of Washington Seattle WA United States Department of Mathematics Imperial College London London United Kingdom WHO Collaborating Centre for Public Health Education and Training Imperial College London London United Kingdom Department of Primary Care and Public Health Imperial College London London United Kingdom School of Population and Global Health University of Melbourne Carlton VIC Australia School of Optometry and Vision Science UNSW Sydney NSW Australia Brien Holden Vision Institute Sydney Australia Department of Ophthalmology University of Adelaide Adelaide SA Australia Department of Parasitology and Mycology Jahrom University of Medical Sciences Jahrom Iran Department of Clinical Sciences University of Sharjah Sharjah United Arab Emirates Ophthalmic Research Center Shahid Beheshti University of Medical Sciences Tehran Iran Department of Ophthalmology Shahid Beheshti University of Medical Sciences Tehran Iran Research Institute for Endocrine Sciences Shahid Beheshti University of Medical Sciences Tehran Iran Ophthalmic Epidemiology Research Center Shahid Beheshti University of Medical Sciences Tehran Iran Health Services Management Department Qazvin University of Medical Sciences Qazvin Iran Department of Systems Populations and Leadership University of Michigan Ann Arbor MI United States Department of Medicine Sofia Ismail Memorial Medical Centre Bogura Bangladesh The Fred Hollows Foundation Sydney NSW Australia Berhan Public Health & Eye Care Consultancy Addis A

Hospital El Salvador: a novel paradigm of intensive care in response to COVID-19 in central America. Lancet Glob Health 2021;9: e241?42?In this Comment, the conflict of interest statement should have included the following: ?By virtue of their roles within a public hospital or the Ministry of Health, MB, LC, WH, and XS are government employees. The findings and conclusions in the Comment are only those of the authors.? This correction has been made as of Feb 26, 2021.

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A real-time moving objects detection and classification approach for static cameras

A real-time moving objects detection and classification appr...

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IEEE International Conference on Consumer Electronics-Taiwan (ICCE-TW)

作者： Hong-Son Vu Jia-Xian Guo Kuan-Hung Chen Shu-Jui Hsieh De-Sheng Chen Ph.D. Program of Electrical and Communications Engineering Feng Chia University Taichung Taiwan R.O.C Department of Electronic Engineering Feng Chia University Taichung Taiwan R.O.C Department of Information Engineering and Computer Science Feng Chia University Taichung Taiwan R.O.C

ISBN: (纸本)9781509020744

Moving objects recognition plays an important role in camera-only active safety systems and intelligent autonomous vehicles. For these applications, reliable detection performance is required; however, pedestrian detection is challenging due to their divergent dressing and action variety. Besides, real-time detection and recognition performance is also critical. This paper aims to optimize the pedestrian detection and recognition by combining both temporal-domain and spatial-domain methods. Accordingly, we first use Background Subtraction (BS) technique to detect moving objects. Then, we use AdaBoost algorithm to classify the detected moving objects into their categories. Experimental results on our datasets show that the proposed approach can speed up 3.3 times in terms of processing rate, with significantly improved detection performance, i.e., at least 17% detection rate increment and 38% false alarm decrement for daytime out-door applications.

关键词： Classification algorithms Object detection Real-time systems Object recognition Lighting Training Histograms

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