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An integrative approach to investigate the respective roles of single-nucleotide variants and copy-number variants in Attention-Deficit/Hyperactivity Disorder (vol 6, 22851, 2016)

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SCIENTIFIC REPORTS 2016年第1期6卷 1-14页

作者： Lima, Leandro de Araujo Feio-dos-Santos, Ana Cecilia Belangero, Sintia Iole Gadelha, Ary Bressan, Rodrigo Affonseca Salum, Giovanni Abrahao Pan, Pedro Mario Moriyama, Tais Silveira Graeff-Martins, Ana Soledade Tamanaha, Ana Carina Alvarenga, Pedro Krieger, Fernanda Valle Fleitlich-Bilyk, Bacy Jackowski, Andrea Parolin Brietzke, Elisa Sato, Joao Ricardo Polanczyk, Guilherme Vanoni Mari, Jair de Jesus Manfro, Gisele Gus do Rosario, Maria Conceiao Miguel, Euripedes Constantino Puga, Renato David Tahira, Ana Carolina Souza, Viviane Neri Chile, Thais Gouveia, Gisele Rodrigues Simoes, Sergio Nery Chang, Xiao Pellegrino, Renata Tian, Lifeng Glessner, Joseph T. Hashimoto, Ronaldo Fumio Rohde, Luis Augusto Sleiman, Patrick M. A. Hakonarson, Hakon Brentani, Helena Inter-institutional Grad Program on Bioinformatics University of São Paulo São Paulo SP Brazil. Center for Applied Genomics The Children's Hospital of Philadelphia Philadelphia PA USA. Department &Institute of Psychiatry University of São Paulo Medical School São Paulo SP Brazil. National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq) São Paulo SP Brazil. Department of Psychiatry Federal University of São Paulo São Paulo SP Brazil. Department of Psychiatry Hospital de Clínicas de Porto Alegre Federal University of Rio Grande do Sul Porto Alegre RS Brazil. Center of Mathematics Computation and Cognition. Universidade Federal do ABC Santo André Brazil. Hospital Israelita Albert Einstein Clinical Research São Paulo SP Brazil. Federal Institute of Espírito Santo Serra ES Brazil. Mathematics &Statistics Institute University of São Paulo São Paulo SP Brazil. Department of Pediatrics The Perelman School of Medicine University of Pennsylvania Philadelphia PA USA.

Many studies have attempted to investigate the genetic susceptibility of Attention-Deficit/Hyperactivity Disorder (ADHD), but without much success. The present study aimed to analyze both single-nucleotide and copy-number variants contributing to the genetic architecture of ADHD. We generated exome data from 30 Brazilian trios with sporadic ADHD. We also analyzed a Brazilian sample of 503 children/adolescent controls from a High Risk Cohort Study for the Development of Childhood Psychiatric Disorders, and also previously published results of five CNV studies and one GWAS meta-analysis of ADHD involving children/adolescents. The results from the Brazilian trios showed that cases with de novo SNVs tend not to have de novo CNVs and vice-versa. Although the sample size is small, we could also see that various comorbidities are more frequent in cases with only inherited variants. Moreover, using only genes expressed in brain, we constructed two "in silico" protein-protein interaction networks, one with genes from any analysis, and other with genes with hits in two analyses. Topological and functional analyses of genes in this network uncovered genes related to synapse, cell adhesion, glutamatergic and serotoninergic pathways, both confirming findings of previous studies and capturing new genes and genetic variants in these pathways.

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Reliability and Precision Are Optimal for Non-Uniform Distributions of Presynaptic Release Probability

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Journal of Biomedical Science and Engineering 2015年第3期8卷 170-183页

作者： Jean-Marc Fellous Nadia S. Corral-Frías Graduate Interdisciplinary Program in Neuroscience University of Arizona Tucson USA Department of Psychology and Applied Mathematics University of Arizona Tucson USA

Most conceptual and computational models assume that synaptic transmission is reliable, a simplification rarely substantiated by data. The functional consequences of the recruitment of high and low initial release probability synapses on the reliability and precision of their postsynaptic targets are studied in a multi-compartmental model of a hippocampal CA1 pyramidal cell. We show that changes in the firing rate of CA3 afferent inputs (rate remapping) are not reflected in the firing rate of the CA1 cell but in the reliability and precise timing of some of its action potentials, suggesting that a signature of remapping may be found in the precise spike timing of CA1. Our results suggest that about half of the action potentials produced by a CA1 cell can potentially carry reliable information in their precise timing with about 25 ms precision, a time scale on the order of the gamma cycle. We show further that reliable events were primarily elicited by CA3 synapses in a state of low probability of release. Overall, our results suggest that the non-uniform distribution of initial release probabilities observed experimentally achieves an optimum yielding simultaneously high precision and high reliability, and allows large populations of CA3 synapses to contribute to the production of reliable CA1 spiking events.

关键词： Spike Timing Hippocampus Computational Model Synapses

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Comparison of Polarized Radiative Transfer Codes Used by the EHT Collaboration

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The Astrophysical Journal 2023年第1期950卷 35-35页

作者： Ben S. Prather Jason Dexter Monika Moscibrodzka Hung-Yi Pu Thomas Bronzwaer Jordy Davelaar Ziri Younsi Charles F. Gammie Roman Gold George N. Wong Kazunori Akiyama Antxon Alberdi Walter Alef Juan Carlos Algaba Richard Anantua Keiichi Asada Rebecca Azulay Uwe Bach Anne-Kathrin Baczko David Ball Mislav Baloković John Barrett Michi Bauböck Bradford A. Benson Dan Bintley Lindy Blackburn Raymond Blundell Katherine L. Bouman Geoffrey C. Bower Hope Boyce Michael Bremer Christiaan D. Brinkerink Roger Brissenden Silke Britzen Avery E. Broderick Dominique Broguiere Sandra Bustamante Do-Young Byun John E. Carlstrom Chiara Ceccobello Andrew Chael Chi-kwan Chan Dominic O. Chang Koushik Chatterjee Shami Chatterjee Ming-Tang Chen Yongjun Chen Xiaopeng Cheng Ilje Cho Pierre Christian Nicholas S. Conroy John E. Conway James M. Cordes Thomas M. Crawford Geoffrey B. Crew Alejandro Cruz-Osorio Yuzhu Cui Mariafelicia De Laurentis Roger Deane Jessica Dempsey Gregory Desvignes Vedant Dhruv Sheperd S. Doeleman Sean Dougal Sergio A. Dzib Ralph P. Eatough Razieh Emami Heino Falcke Joseph Farah Vincent L. Fish Ed Fomalont H. Alyson Ford Raquel Fraga-Encinas William T. Freeman Per Friberg Christian M. Fromm Antonio Fuentes Peter Galison Roberto García Olivier Gentaz Boris Georgiev Ciriaco Goddi Arturo I. Gómez-Ruiz José L. Gómez Minfeng Gu Mark Gurwell Kazuhiro Hada Daryl Haggard Kari Haworth Michael H. Hecht Ronald Hesper Dirk Heumann Luis C. Ho Paul Ho Mareki Honma Chih-Wei L. Huang Lei Huang David H. Hughes Shiro Ikeda C. M. Violette Impellizzeri Makoto Inoue Sara Issaoun David J. James Buell T. Jannuzi Michael Janssen Britton Jeter Wu Jiang Alejandra Jiménez-Rosales Michael D. Johnson Svetlana Jorstad Abhishek V. Joshi Taehyun Jung Mansour Karami Ramesh Karuppusamy Tomohisa Kawashima Garrett K. Keating Mark Kettenis Dong-Jin Kim Jae-Young Kim Jongsoo Kim Junhan Kim Motoki Kino Jun Yi Koay Prashant Kocherlakota Yutaro Kofuji Shoko Koyama Carsten Kramer Michael Kramer Thomas P. Krichbaum Cheng-Yu Kuo Noemi La Bella Tod R. Lauer Daeyoung L CCS-2 Los Alamos National Laboratory P.O. Box 1663 Los Alamos NM 87545 USA bprather@lanl.gov JILA and Department of Astrophysical and Planetary Sciences University of Colorado Boulder CO 80309 USA Department of Astrophysics/IMAPP Radboud University P.O. Box 9010 6500 GL Nijmegen The Netherlands Department of Physics National Taiwan Normal University No. 88 Sec.4 Tingzhou Road Taipei 116 Taiwan R.O.C. Center of Astronomy and Gravitation National Taiwan Normal University No. 88 Sec. 4 Tingzhou Road Taipei 116 Taiwan R.O.C. Institute of Astronomy and Astrophysics Academia Sinica 11F of Astronomy-Mathematics Building AS/NTU No. 1 Sec. 4 Roosevelt Road Taipei 10617 Taiwan R.O.C. Department of Astronomy and Columbia Astrophysics Laboratory Columbia University 550 W. 120th Street New York NY 10027 USA Center for Computational Astrophysics Flatiron Institute 162 Fifth Avenue New York NY 10010 USA Department of Astrophysics Institute for Mathematics Astrophysics and Particle Physics (IMAPP) Radboud University P.O. Box 9010 6500 GL Nijmegen The Netherlands Mullard Space Science Laboratory University College London Holmbury St. Mary Dorking Surrey RH5 6NT UK Institut für Theoretische Physik Goethe-Universität Frankfurt Max-von-Laue-Straße 1 D-60438 Frankfurt am Main Germany Department of Physics University of Illinois 1110 West Green Street Urbana IL 61801 USA Department of Astronomy University of Illinois at Urbana-Champaign 1002 West Green Street Urbana IL 61801 USA NCSA University of Illinois 1205 W. Clark Street Urbana IL 61801 USA CP3-Origins University of Southern Denmark Campusvej 55 DK-5230 Odense M Denmark School of Natural Sciences Institute for Advanced Study 1 Einstein Drive Princeton NJ 08540 USA Princeton Gravity Initiative Princeton University Princeton NJ 08544 USA Massachusetts Institute of Technology Haystack Observatory 99 Millstone Road Westford MA 01886 USA National Astronomical Observatory of Japan 2-21-1 Osaw

Interpretation of resolved polarized images of black holes by the Event Horizon Telescope (EHT) requires predictions of the polarized emission observable by an Earth-based instrument for a particular model of the black hole accretion system. Such predictions are generated by general relativistic radiative transfer (GRRT) codes, which integrate the equations of polarized radiative transfer in curved spacetime. A selection of ray-tracing GRRT codes used within the EHT Collaboration is evaluated for accuracy and consistency in producing a selection of test images, demonstrating that the various methods and implementations of radiative transfer calculations are highly consistent. When imaging an analytic accretion model, we find that all codes produce images similar within a pixel-wise normalized mean squared error (NMSE) of 0.012 in the worst case. When imaging a snapshot from a cell-based magnetohydrodynamic simulation, we find all test images to be similar within NMSEs of 0.02, 0.04, 0.04, and 0.12 in Stokes I, Q, U, and V, respectively. We additionally find the values of several image metrics relevant to published EHT results to be in agreement to much better precision than measurement uncertainties.

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Climate Precipitation Prediction by Neural Network

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Journal of mathematics and System Science 2015年第5期5卷 207-213页

作者： Juliana Aparecida Anochi Haroldo Fraga de Campos Velho Applied Computing Graduate Program National Institute for Space Research (INPE) Brazil. Associated Laboratory for Computing and Applied Mathematics National Institute for Space Research (INPE).

In this work a neural network model for climate forecasting is presented. The model is built by training a neural network with available reanalysis data. In order to assess the model, the development methodology considers the use of data reduction strategies that eliminate data redundancy thus reducing the complexity of the models. The results presented in this paper considered the use of Rough Sets Theory principles in extracting relevant information from the available data to achieve the reduction of redundancy among the variables used for forecasting purposes. The paper presents results of climate prediction made with the use of the neural network based model. The results obtained in the conducted experiments show the effectiveness of the methodology, presenting estimates similar to observations.

关键词： Climate Prediction Neural Networks Rough Sets Theory

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Inverse design of disordered stealthy hyperuniform spin chains

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Physical Review B 2016年第6期93卷 064201-064201页

作者： Eli Chertkov Robert A. DiStasio, Jr. Ge Zhang Roberto Car Salvatore Torquato Department of Physics Princeton University Princeton New Jersey 08544 USA Department of Chemistry Princeton University Princeton New Jersey 08544 USA Department of Chemistry and Chemical Biology Cornell University Ithaca New York 14853 USA Princeton Institute for the Science and Technology of Materials Princeton University Princeton New Jersey 08544 USA Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA

Positioned between crystalline solids and liquids, disordered many-particle systems which are stealthy and hyperuniform represent new states of matter that are endowed with novel physical and thermodynamic properties. Such stealthy and hyperuniform states are unique in that they are transparent to radiation for a range of wave numbers around the origin. In this work, we employ recently developed inverse statistical-mechanical methods, which seek to obtain the optimal set of interactions that will spontaneously produce a targeted structure or configuration as a unique ground state, to investigate the spin-spin interaction potentials required to stabilize disordered stealthy hyperuniform one-dimensional (1D) Ising-type spin chains. By performing an exhaustive search over the spin configurations that can be enumerated on periodic 1D integer lattices containing N=2,3,...,36 sites, we were able to identify and structurally characterize all stealthy hyperuniform spin chains in this range of system sizes. Within this pool of stealthy hyperuniform spin configurations, we then utilized such inverse optimization techniques to demonstrate that stealthy hyperuniform spin chains can be realized as either unique or degenerate disordered ground states of radial long-ranged (relative to the spin-chain length) spin-spin interactions. Such exotic ground states appear to be distinctly different from spin glasses in both their inherent structural properties and the nature of the spin-spin interactions required to stabilize them. As such, the implications and significance of the existence of these disordered stealthy hyperuniform ground-state spin systems warrants further study, including whether their bulk physical properties and excited states, like their many-particle system counterparts, are singularly remarkable, and can be experimentally realized.

关键词： Optimization problems Ising model Spin chains

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Wall to wall optimal transport 15

Wall to wall optimal transport

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15th European Turbulence Conference, ETC 2015

作者： Doering, Charles R. Souza, Andre N. Chini, Gregory P. Hassanzadeh, Pedram Department of Physics University of Michigan United States Department of Mathematics University of Michigan United States Center for the Study of Complex Systems University of Michigan United States Department of Mechanical Engineering Program in Integrated Applied Mathematics and Center for Fluid Physics University of New Hampshire United States Centre for the Environment Department of Earth and Planetary Sciences Harvard University United States

The calculus of variations is employed to find steady divergence-free velocity fields that maximize transport of a tracer between two parallel walls held at fixed concentration for one of two constraints on flow strength: a fixed value of the kinetic energy or a fixed value of the enstrophy (the mean square rate of strain in this situation). The optimizing flows realize upper limits on convective transport in this scenario. We interpret the results in the context of buoyancy-driven Rayleigh–Bénard convection problems that satisfy the flow intensity constraints, enabling us to investigate how optimal transport scalings compare with upper bounds on Nu expressed as a function of the Rayleigh number Ra. © TU Delft.

关键词： Kinetic energy

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Preconditioning techniques for reduced basis methods for parameterized elliptic partial differential equations

Preconditioning techniques for reduced basis methods for par...

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作者： Elman, Howard C. Forstall, Virginia Department of Computer Science Institute for Advanced Computer Studies University of Maryland College ParkMD20742 United States Applied Mathematics and Statistics and Scientific Computation Program University of Maryland College ParkMD20742 United States

The reduced basis methodology is an efficient approach to solve parameterized discrete partial differential equations when the solution is needed at many parameter values. An offline step approximates the solution space, and an online step utilizes this approximation, the reduced basis, to solve a smaller reduced problem, which provides an accurate estimate of the solution. Traditionally, the reduced problem is solved using direct methods. However, the size of the reduced system needed to produce solutions of a given accuracy depends on the characteristics of the problem, and it may happen that the size is significantly smaller than that of the original discrete problem but large enough to make direct solution costly. In this scenario, it may be more effective to use iterative methods to solve the reduced problem. We construct preconditioners for reduced iterative methods which are derived from preconditioners for the full problem. This approach permits reduced basis methods to be practical for larger bases than direct methods allow. We illustrate the effectiveness of iterative methods for solving reduced problems by considering two examples, the steady-state diffusion and convection-diffusion-reaction equations. © 2015 Society for Industrial and applied mathematics.

关键词： Iterative methods

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Confined disordered strictly jammed binary sphere packings

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Physical Review E 2015年第6期92卷 062207-062207页

作者： D. Chen S. Torquato Department of Chemistry Department of Physics Princeton Institute for the Science and Technology of Materials and Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA

Disordered jammed packings under confinement have received considerably less attention than their bulk counterparts and yet arise in a variety of practical situations. In this work, we study binary sphere packings that are confined between two parallel hard planes and generalize the Torquato-Jiao (TJ) sequential linear programming algorithm [Phys. Rev. E 82, 061302 (2010)] to obtain putative maximally random jammed (MRJ) packings that are exactly isostatic with high fidelity over a large range of plane separation distances H, small to large sphere radius ratio α, and small sphere relative concentration x. We find that packing characteristics can be substantially different from their bulk analogs, which is due to what we term “confinement frustration.” Rattlers in confined packings are generally more prevalent than those in their bulk counterparts. We observe that packing fraction, rattler fraction, and degree of disorder of MRJ packings generally increase with H, though exceptions exist. Discontinuities in the packing characteristics as H varies in the vicinity of certain values of H are due to associated discontinuous transitions between different jammed states. When the plane separation distance is on the order of two large-sphere diameters or less, the packings exhibit salient two-dimensional features; when the plane separation distance exceeds about 30 large-sphere diameters, the packings approach three-dimensional bulk packings. As the size contrast increases (as α decreases), the rattler fraction dramatically increases due to what we call “size-disparity” frustration. We find that at intermediate α and when x is about 0.5 (50-50 mixture), the disorder of packings is maximized, as measured by an order metric ψ that is based on the number density fluctuations in the direction perpendicular to the hard walls. We also apply the local volume-fraction variance στ2(R) to characterize confined packings and find that these packings possess essentially the same level of

关键词： Packing

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Ground states of stealthy hyperuniform potentials. II. Stacked-slider phases

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Physical Review E 2015年第2期92卷 022120-022120页

作者： G. Zhang F. H. Stillinger S. Torquato Department of Chemistry Department of Physics Princeton Institute for the Science and Technology of Materials and Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA

Stealthy potentials, a family of long-range isotropic pair potentials, produce infinitely degenerate disordered ground states at high densities and crystalline ground states at low densities in d-dimensional Euclidean space Rd. In the previous paper in this series, we numerically studied the entropically favored ground states in the canonical ensemble in the zero-temperature limit across the first three Euclidean space dimensions. In this paper, we investigate using both numerical and theoretical techniques metastable stacked-slider phases, which are part of the ground-state manifold of stealthy potentials at densities in which crystal ground states are favored entropically. Our numerical results enable us to devise analytical models of this phase in two, three, and higher dimensions. Utilizing this model, we estimated the size of the feasible region in configuration space of the stacked-slider phase, finding it to be smaller than that of crystal structures in the infinite-system-size limit, which is consistent with our recent previous work. In two dimensions, we also determine exact expressions for the pair correlation function and structure factor of the analytical model of stacked-slider phases and analyze the connectedness of the ground-state manifold of stealthy potentials in this density regime. We demonstrate that stacked-slider phases are distinguishable states of matter; they are nonperiodic, statistically anisotropic structures that possess long-range orientational order but have zero shear modulus. We outline some possible future avenues of research to elucidate our understanding of this unusual phase of matter.

关键词： Ground state

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Ground states of stealthy hyperuniform potentials: I. Entropically favored configurations

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Physical Review E 2015年第2期92卷 022119-022119页

Systems of particles interacting with “stealthy” pair potentials have been shown to possess infinitely degenerate disordered hyperuniform classical ground states with novel physical properties. Previous attempts to sample the infinitely degenerate ground states used energy minimization techniques, introducing algorithmic dependence that is artificial in nature. Recently, an ensemble theory of stealthy hyperuniform ground states was formulated to predict the structure and thermodynamics that was shown to be in excellent agreement with corresponding computer simulation results in the canonical ensemble (in the zero-temperature limit). In this paper, we provide details and justifications of the simulation procedure, which involves performing molecular dynamics simulations at sufficiently low temperatures and minimizing the energy of the snapshots for both the high-density disordered regime, where the theory applies, as well as lower densities. We also use numerical simulations to extend our study to the lower-density regime. We report results for the pair correlation functions, structure factors, and Voronoi cell statistics. In the high-density regime, we verify the theoretical ansatz that stealthy disordered ground states behave like “pseudo” disordered equilibrium hard-sphere systems in Fourier space. The pair statistics obey certain exact integral conditions with very high accuracy. These results show that as the density decreases from the high-density limit, the disordered ground states in the canonical ensemble are characterized by an increasing degree of short-range order and eventually the system undergoes a phase transition to crystalline ground states. In the crystalline regime (low densities), there exist aperiodic structures that are part of the ground-state manifold but yet are not entropically favored. We also provide numerical evidence suggesting that different forms of stealthy pair potentials produce the same ground-state ensemble in the zero-temperatur

关键词： Ground state

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