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Sample records for pairwise covariance adds

  1. Covariance of maximum likelihood evolutionary distances between sequences aligned pairwise.

    PubMed

    Dessimoz, Christophe; Gil, Manuel

    2008-06-23

    The estimation of a distance between two biological sequences is a fundamental process in molecular evolution. It is usually performed by maximum likelihood (ML) on characters aligned either pairwise or jointly in a multiple sequence alignment (MSA). Estimators for the covariance of pairs from an MSA are known, but we are not aware of any solution for cases of pairs aligned independently. In large-scale analyses, it may be too costly to compute MSAs every time distances must be compared, and therefore a covariance estimator for distances estimated from pairs aligned independently is desirable. Knowledge of covariances improves any process that compares or combines distances, such as in generalized least-squares phylogenetic tree building, orthology inference, or lateral gene transfer detection. In this paper, we introduce an estimator for the covariance of distances from sequences aligned pairwise. Its performance is analyzed through extensive Monte Carlo simulations, and compared to the well-known variance estimator of ML distances. Our covariance estimator can be used together with the ML variance estimator to form covariance matrices. The estimator performs similarly to the ML variance estimator. In particular, it shows no sign of bias when sequence divergence is below 150 PAM units (i.e. above ~29% expected sequence identity). Above that distance, the covariances tend to be underestimated, but then ML variances are also underestimated.

  2. Fast and accurate estimation of the covariance between pairwise maximum likelihood distances

    PubMed Central

    2014-01-01

    Pairwise evolutionary distances are a model-based summary statistic for a set of molecular sequences. They represent the leaf-to-leaf path lengths of the underlying phylogenetic tree. Estimates of pairwise distances with overlapping paths covary because of shared mutation events. It is desirable to take these covariance structure into account to increase precision in any process that compares or combines distances. This paper introduces a fast estimator for the covariance of two pairwise maximum likelihood distances, estimated under general Markov models. The estimator is based on a conjecture (going back to Nei & Jin, 1989) which links the covariance to path lengths. It is proven here under a simple symmetric substitution model. A simulation shows that the estimator outperforms previously published ones in terms of the mean squared error. PMID:25279263

  3. Kv7 channels regulate pairwise spiking covariability in health and disease.

    PubMed

    Ocker, Gabriel Koch; Doiron, Brent

    2014-07-15

    Low-threshold M currents are mediated by the Kv7 family of potassium channels. Kv7 channels are important regulators of spiking activity, having a direct influence on the firing rate, spike time variability, and filter properties of neurons. How Kv7 channels affect the joint spiking activity of populations of neurons is an important and open area of study. Using a combination of computational simulations and analytic calculations, we show that the activation of Kv7 conductances reduces the covariability between spike trains of pairs of neurons driven by common inputs. This reduction is beyond that explained by the lowering of firing rates and involves an active cancellation of common fluctuations in the membrane potentials of the cell pair. Our theory shows that the excess covariance reduction is due to a Kv7-induced shift from low-pass to band-pass filtering of the single neuron spike train response. Dysfunction of Kv7 conductances is related to a number of neurological diseases characterized by both elevated firing rates and increased network-wide correlations. We show how changes in the activation or strength of Kv7 conductances give rise to excess correlations that cannot be compensated for by synaptic scaling or homeostatic modulation of passive membrane properties. In contrast, modulation of Kv7 activation parameters consistent with pharmacological treatments for certain hyperactivity disorders can restore normal firing rates and spiking correlations. Our results provide key insights into how regulation of a ubiquitous potassium channel class can control the coordination of population spiking activity.

  4. SNPs as Supplements in Simple Kinship Analysis or as Core Markers in Distant Pairwise Relationship Tests: When Do SNPs Add Value or Replace Well-Established and Powerful STR Tests?

    PubMed

    Phillips, Christopher; García-Magariños, Manuel; Salas, Antonio; Carracedo, Angel; Lareu, Maria Victoria

    2012-06-01

    BACKGROUND: Genetic tests for kinship testing routinely reach likelihoods that provide virtual proof of the claimed relationship by typing microsatellites-commonly consisting of 12-15 standard forensic short tandem repeats (STRs). Single nucleotide polymorphisms (SNPs) have also been applied to kinship testing but these binary markers are required in greater numbers than multiple-allele STRs. However SNPs offer certain advantageous characteristics not found in STRs, including, much higher mutational stability, good performance typing highly degraded DNA, and the ability to be readily up-scaled to very high marker numbers reaching over a million loci. This article outlines kinship testing applications where SNPs markedly improve the genetic data obtained. In particular we explore the minimum number of SNPs that will be required to confirm pairwise relationship claims in deficient pedigrees that typify missing persons' identification or war grave investigations where commonly few surviving relatives are available for comparison and the DNA is highly degraded. METHODS: We describe the application of SNPs alongside STRs when incomplete profiles or allelic instability in STRs create ambiguous results, we review the use of high density SNP arrays when the relationship claim is very distant, and we outline simulations of kinship analyses with STRs supplemented with SNPs in order to estimate the practical limit of pairwise relationships that can be differentiated from random unrelated pairs from the same population. RESULTS: The minimum number of SNPs for robust statistical inference of parent-offspring relationships through to those of second cousins (S-3-3) is estimated for both simple, single multiplex SNP sets and for subsets of million-SNP arrays. CONCLUSIONS: There is considerable scope for resolving ambiguous STR results and for improving the statistical power of kinship analysis by adding small-scale SNP sets but where the pedigree is deficient the pairwise

  5. Pairwise-Comparison Software

    NASA Technical Reports Server (NTRS)

    Ricks, Wendell R.

    1995-01-01

    Pairwise comparison (PWC) is computer program that collects data for psychometric scaling techniques now used in cognitive research. It applies technique of pairwise comparisons, which is one of many techniques commonly used to acquire the data necessary for analyses. PWC administers task, collects data from test subject, and formats data for analysis. Written in Turbo Pascal v6.0.

  6. Online Pairwise Learning Algorithms.

    PubMed

    Ying, Yiming; Zhou, Ding-Xuan

    2016-04-01

    Pairwise learning usually refers to a learning task that involves a loss function depending on pairs of examples, among which the most notable ones are bipartite ranking, metric learning, and AUC maximization. In this letter we study an online algorithm for pairwise learning with a least-square loss function in an unconstrained setting of a reproducing kernel Hilbert space (RKHS) that we refer to as the Online Pairwise lEaRning Algorithm (OPERA). In contrast to existing works (Kar, Sriperumbudur, Jain, & Karnick, 2013 ; Wang, Khardon, Pechyony, & Jones, 2012 ), which require that the iterates are restricted to a bounded domain or the loss function is strongly convex, OPERA is associated with a non-strongly convex objective function and learns the target function in an unconstrained RKHS. Specifically, we establish a general theorem that guarantees the almost sure convergence for the last iterate of OPERA without any assumptions on the underlying distribution. Explicit convergence rates are derived under the condition of polynomially decaying step sizes. We also establish an interesting property for a family of widely used kernels in the setting of pairwise learning and illustrate the convergence results using such kernels. Our methodology mainly depends on the characterization of RKHSs using its associated integral operators and probability inequalities for random variables with values in a Hilbert space.

  7. Pairwise comparison device

    NASA Technical Reports Server (NTRS)

    Verber, Carl M. (Inventor); Kenan, Richard P. (Inventor)

    1982-01-01

    Apparatus for comparing first and second sets of voltages having one-to-one correspondence, and providing an indication responsive to the magnitudes of the pairwise differences of the voltages; typically comprising a plurality of channel waveguides (11), each having a first electrode (12) on one side of the channel (11) and a second electrode (13) on the opposite side of the channel (11); contacts (14) and conductors (16) for connecting each voltage of the first set to the first electrode (12) of one waveguide (11); contacts (b 15) and conductors (17) for connecting each voltage of the second set to the second electrode (13) of the waveguide (11) to the first electrode (12) of which the corresponding voltage of the first set is connected; a coupling prism (18), a beam splitter (19), and a waveguide portion (20) for directing to the input end (21,22) of each waveguide (11) a substantially plane wave of coherent light (as indicated at 23,24,25) having predetermined relative intensity and phase; and a detector (51) and associated circuitry (52,58) responsive to the light emerging (as indicated at 26) from the output end (28,29) of the waveguides (11) (via a beam splitter 44 and a coupling prism 45) for providing an indication that is a function of the pairwise relative magnitudes of the first set of voltages and the second set of voltages.

  8. Exact likelihood ratio calculations for pairwise cases.

    PubMed

    Egeland, Thore; Pinto, Nádia; Amorim, António

    2017-07-01

    Some practical and theoretical aspects of evaluation of evidence based on the likelihood ratio (LR) in kinship cases are discussed. If relationships are complex or if complicating factors like mutation, correction for population structure or silent alleles need to be accounted for, available software may fail. We present an explicit general formula for non-inbred pairwise cases. Equipped with this formula it is possible to evaluate, say, how strongly a shared rare allele, points towards a specific relationship. Moreover, a general expression as the one presented, adds to the understanding of models and the underlying biological mechanisms. It is also useful for checking software and defining the limitations of programs. Some ideas for improving software may also be generated by the derivation of exact expressions. We argue that a proportional mutation model is well suited from a pragmatic point of view and derive some theoretical properties of this model. Several examples based on the general pairwise formula and its implementation in the freely available R package mut are presented. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. Earth Observing System Covariance Realism

    NASA Technical Reports Server (NTRS)

    Zaidi, Waqar H.; Hejduk, Matthew D.

    2016-01-01

    The purpose of covariance realism is to properly size a primary object's covariance in order to add validity to the calculation of the probability of collision. The covariance realism technique in this paper consists of three parts: collection/calculation of definitive state estimates through orbit determination, calculation of covariance realism test statistics at each covariance propagation point, and proper assessment of those test statistics. An empirical cumulative distribution function (ECDF) Goodness-of-Fit (GOF) method is employed to determine if a covariance is properly sized by comparing the empirical distribution of Mahalanobis distance calculations to the hypothesized parent 3-DoF chi-squared distribution. To realistically size a covariance for collision probability calculations, this study uses a state noise compensation algorithm that adds process noise to the definitive epoch covariance to account for uncertainty in the force model. Process noise is added until the GOF tests pass a group significance level threshold. The results of this study indicate that when outliers attributed to persistently high or extreme levels of solar activity are removed, the aforementioned covariance realism compensation method produces a tuned covariance with up to 80 to 90% of the covariance propagation timespan passing (against a 60% minimum passing threshold) the GOF tests-a quite satisfactory and useful result.

  10. Hybrid pairwise likelihood analysis of animal behavior experiments.

    PubMed

    Cattelan, Manuela; Varin, Cristiano

    2013-12-01

    The study of the determinants of fights between animals is an important issue in understanding animal behavior. For this purpose, tournament experiments among a set of animals are often used by zoologists. The results of these tournament experiments are naturally analyzed by paired comparison models. Proper statistical analysis of these models is complicated by the presence of dependence between the outcomes of fights because the same animal is involved in different contests. This paper discusses two different model specifications to account for between-fights dependence. Models are fitted through the hybrid pairwise likelihood method that iterates between optimal estimating equations for the regression parameters and pairwise likelihood inference for the association parameters. This approach requires the specification of means and covariances only. For this reason, the method can be applied also when the computation of the joint distribution is difficult or inconvenient. The proposed methodology is investigated by simulation studies and applied to real data about adult male Cape Dwarf Chameleons.

  11. Optimal Arrangement of Components Via Pairwise Rearrangements.

    DTIC Science & Technology

    1987-10-01

    reliability function under component pairwise rearrangement. They use this property to find the optimal component arrangement. Worked examples illustrate the methods proposed. Keywords: Optimization; Permutations; Nodes.

  12. A pairwise interaction model for multivariate functional and longitudinal data.

    PubMed

    Chiou, Jeng-Min; Müller, Hans-Georg

    2016-06-01

    Functional data vectors consisting of samples of multivariate data where each component is a random function are encountered increasingly often but have not yet been comprehensively investigated. We introduce a simple pairwise interaction model that leads to an interpretable and straightforward decomposition of multivariate functional data and of their variation into component-specific processes and pairwise interaction processes. The latter quantify the degree of pairwise interactions between the components of the functional data vectors, while the component-specific processes reflect the functional variation of a particular functional vector component that cannot be explained by the other components. Thus the proposed model provides an extension of the usual notion of a covariance or correlation matrix for multivariate vector data to functional data vectors and generates an interpretable functional interaction map. The decomposition provided by the model can also serve as a basis for subsequent analysis, such as study of the network structure of functional data vectors. The decomposition of the total variance into componentwise and interaction contributions can be quantified by an [Formula: see text]-like decomposition. We provide consistency results for the proposed methods and illustrate the model by applying it to sparsely sampled longitudinal data from the Baltimore Longitudinal Study of Aging, examining the relationships between body mass index and blood fats.

  13. Generalized Linear Covariance Analysis

    NASA Technical Reports Server (NTRS)

    Carpenter, J. Russell; Markley, F. Landis

    2008-01-01

    We review and extend in two directions the results of prior work on generalized covariance analysis methods. This prior work allowed for partitioning of the state space into "solve-for" and "consider" parameters, allowed for differences between the formal values and the true values of the measurement noise, process noise, and a priori solve-for and consider covariances, and explicitly partitioned the errors into subspaces containing only the influence of the measurement noise, process noise, and a priori solve-for and consider covariances. In this work, we explicitly add sensitivity analysis to this prior work, and relax an implicit assumption that the batch estimator s anchor time occurs prior to the definitive span. We also apply the method to an integrated orbit and attitude problem, in which gyro and accelerometer errors, though not estimated, influence the orbit determination performance. We illustrate our results using two graphical presentations, which we call the "variance sandpile" and the "sensitivity mosaic," and we compare the linear covariance results to confidence intervals associated with ensemble statistics from a Monte Carlo analysis.

  14. Generalized Linear Covariance Analysis

    NASA Technical Reports Server (NTRS)

    Carpenter, James R.; Markley, F. Landis

    2014-01-01

    This talk presents a comprehensive approach to filter modeling for generalized covariance analysis of both batch least-squares and sequential estimators. We review and extend in two directions the results of prior work that allowed for partitioning of the state space into solve-for'' and consider'' parameters, accounted for differences between the formal values and the true values of the measurement noise, process noise, and textita priori solve-for and consider covariances, and explicitly partitioned the errors into subspaces containing only the influence of the measurement noise, process noise, and solve-for and consider covariances. In this work, we explicitly add sensitivity analysis to this prior work, and relax an implicit assumption that the batch estimator's epoch time occurs prior to the definitive span. We also apply the method to an integrated orbit and attitude problem, in which gyro and accelerometer errors, though not estimated, influence the orbit determination performance. We illustrate our results using two graphical presentations, which we call the variance sandpile'' and the sensitivity mosaic,'' and we compare the linear covariance results to confidence intervals associated with ensemble statistics from a Monte Carlo analysis.

  15. Combining Multiple Pairwise Structure-based Alignments

    SciTech Connect

    2014-11-12

    CombAlign is a new Python code that generates a gapped, one-to-many, multiple structure-based sequence alignment(MSSA) given a set of pairwise structure-based alignments. In order to better define regions of similarity among related protein structures, it is useful to detect the residue-residue correspondences among a set of pairwise structure alignments. Few codes exist for constructing a one-to-many, multiple sequence alignment derived from a set of structure alignments, and we perceived a need for creating a new tool for combing pairwise structure alignments that would allow for insertion of gaps in the reference structure.

  16. Combining Multiple Pairwise Structure-based Alignments

    SciTech Connect

    2014-11-12

    CombAlign is a new Python code that generates a gapped, one-to-many, multiple structure-based sequence alignment(MSSA) given a set of pairwise structure-based alignments. In order to better define regions of similarity among related protein structures, it is useful to detect the residue-residue correspondences among a set of pairwise structure alignments. Few codes exist for constructing a one-to-many, multiple sequence alignment derived from a set of structure alignments, and we perceived a need for creating a new tool for combing pairwise structure alignments that would allow for insertion of gaps in the reference structure.

  17. Market structure explained by pairwise interactions

    NASA Astrophysics Data System (ADS)

    Bury, Thomas

    2013-03-01

    Financial markets are a typical example of complex systems where interactions between constituents lead to many remarkable features. Here we give empirical evidence, by making as few assumptions as possible, that the market microstructure capturing almost all of the available information in the data of stock markets does not involve higher order than pairwise interactions. We give an economic interpretation of this pairwise model. We show that it accurately recovers the empirical correlation coefficients; thus the collective behaviors are quantitatively described by models that capture the observed pairwise correlations but no higher-order interactions. Furthermore, we show that an order-disorder transition occurs, as predicted by the pairwise model. Last, we make the link with the graph-theoretic description of stock markets recovering the non-random and scale-free topology, shrinking length during crashes and meaningful clustering features, as expected.

  18. Statistical Physics of Pairwise Probability Models

    PubMed Central

    Roudi, Yasser; Aurell, Erik; Hertz, John A.

    2009-01-01

    Statistical models for describing the probability distribution over the states of biological systems are commonly used for dimensional reduction. Among these models, pairwise models are very attractive in part because they can be fit using a reasonable amount of data: knowledge of the mean values and correlations between pairs of elements in the system is sufficient. Not surprisingly, then, using pairwise models for studying neural data has been the focus of many studies in recent years. In this paper, we describe how tools from statistical physics can be employed for studying and using pairwise models. We build on our previous work on the subject and study the relation between different methods for fitting these models and evaluating their quality. In particular, using data from simulated cortical networks we study how the quality of various approximate methods for inferring the parameters in a pairwise model depends on the time bin chosen for binning the data. We also study the effect of the size of the time bin on the model quality itself, again using simulated data. We show that using finer time bins increases the quality of the pairwise model. We offer new ways of deriving the expressions reported in our previous work for assessing the quality of pairwise models. PMID:19949460

  19. Lotka-Volterra pairwise modeling fails to capture diverse pairwise microbial interactions.

    PubMed

    Momeni, Babak; Xie, Li; Shou, Wenying

    2017-03-28

    Pairwise models are commonly used to describe many-species communities. In these models, an individual receives additive fitness effects from pairwise interactions with each species in the community ('additivity assumption'). All pairwise interactions are typically represented by a single equation where parameters reflect signs and strengths of fitness effects ('universality assumption'). Here, we show that a single equation fails to qualitatively capture diverse pairwise microbial interactions. We build mechanistic reference models for two microbial species engaging in commonly-found chemical-mediated interactions, and attempt to derive pairwise models. Different equations are appropriate depending on whether a mediator is consumable or reusable, whether an interaction is mediated by one or more mediators, and sometimes even on quantitative details of the community (e.g. relative fitness of the two species, initial conditions). Our results, combined with potential violation of the additivity assumption in many-species communities, suggest that pairwise modeling will often fail to predict microbial dynamics.

  20. Pairwise constrained concept factorization for data representation.

    PubMed

    He, Yangcheng; Lu, Hongtao; Huang, Lei; Xie, Saining

    2014-04-01

    Concept factorization (CF) is a variant of non-negative matrix factorization (NMF). In CF, each concept is represented by a linear combination of data points, and each data point is represented by a linear combination of concepts. More specifically, each concept is represented by more than one data point with different weights, and each data point carries various weights called membership to represent their degrees belonging to that concept. However, CF is actually an unsupervised method without making use of prior information of the data. In this paper, we propose a novel semi-supervised concept factorization method, called Pairwise Constrained Concept Factorization (PCCF), which incorporates pairwise constraints into the CF framework. We expect that data points which have pairwise must-link constraints should have the same class label as much as possible, while data points with pairwise cannot-link constraints will have different class labels as much as possible. Due to the incorporation of the pairwise constraints, the learning quality of the CF has been significantly enhanced. Experimental results show the effectiveness of our proposed novel method in comparison to the state-of-the-art algorithms on several real world applications.

  1. Tukey-Like Pairwise Comparisons among Proportions.

    ERIC Educational Resources Information Center

    Williams, Richard H.

    1992-01-01

    A QuickBASIC microcomputer program for conducting Tukey-like pairwise comparisons on "k" independent sample proportions is described. The program can accommodate applications involving equal or unequal sample sizes. Studentized range values are computed and displayed on a computer monitor, each of which represents a simple comparison…

  2. PAIRWISE BLENDING OF HIGH LEVEL WASTE (HLW)

    SciTech Connect

    CERTA, P.J.

    2006-02-22

    The primary objective of this study is to demonstrate a mission scenario that uses pairwise and incidental blending of high level waste (HLW) to reduce the total mass of HLW glass. Secondary objectives include understanding how recent refinements to the tank waste inventory and solubility assumptions affect the mass of HLW glass and how logistical constraints may affect the efficacy of HLW blending.

  3. Design, Implementation and Deployment of PAIRwise

    ERIC Educational Resources Information Center

    Knight, Allan; Almeroth, Kevin; Bimber, Bruce

    2008-01-01

    Increased access to the Internet has dramatically increased the sources from which students can deliberately or accidentally copy information. This article discusses our motivation to design, implement, and deploy an Internet based plagiarism detection system, called PAIRwise, to address this growing problem. We give details as to how we detect…

  4. Pairwise Document Classification for Relevance Feedback

    DTIC Science & Technology

    2009-11-01

    Pairwise Document Classification for Relevance Feedback Jonathan L. Elsas, Pinar Donmez, Jamie Callan, Jaime G. Carbonell Language Technologies...Collins-Thompson and J. Callan. Query expansion using random walk models. In CIKM ’05, page 711. ACM, 2005. [5] P. Donmez and J. Carbonell . Paired

  5. Lotka-Volterra pairwise modeling fails to capture diverse pairwise microbial interactions

    PubMed Central

    Momeni, Babak; Xie, Li; Shou, Wenying

    2017-01-01

    Pairwise models are commonly used to describe many-species communities. In these models, an individual receives additive fitness effects from pairwise interactions with each species in the community ('additivity assumption'). All pairwise interactions are typically represented by a single equation where parameters reflect signs and strengths of fitness effects ('universality assumption'). Here, we show that a single equation fails to qualitatively capture diverse pairwise microbial interactions. We build mechanistic reference models for two microbial species engaging in commonly-found chemical-mediated interactions, and attempt to derive pairwise models. Different equations are appropriate depending on whether a mediator is consumable or reusable, whether an interaction is mediated by one or more mediators, and sometimes even on quantitative details of the community (e.g. relative fitness of the two species, initial conditions). Our results, combined with potential violation of the additivity assumption in many-species communities, suggest that pairwise modeling will often fail to predict microbial dynamics. DOI: http://dx.doi.org/10.7554/eLife.25051.001 PMID:28350295

  6. ADD: How Does It Add Up in the Classroom?

    ERIC Educational Resources Information Center

    Sumpter, R. David; Kidd, Libby

    1998-01-01

    Gives a short history of attention-deficit disorder (ADD), describes characteristics of ADD, discusses a four-step plan for identification of ADD, and presents four types of management techniques: medical, environmental, classroom activity, and behavioral management. Stresses importance of cooperation and communication among teacher, parent, and…

  7. Unjamming in models with analytic pairwise potentials

    NASA Astrophysics Data System (ADS)

    Kooij, Stefan; Lerner, Edan

    2017-06-01

    Canonical models for studying the unjamming scenario in systems of soft repulsive particles assume pairwise potentials with a sharp cutoff in the interaction range. The sharp cutoff renders the potential nonanalytic but makes it possible to describe many properties of the solid in terms of the coordination number z , which has an unambiguous definition in these cases. Pairwise potentials without a sharp cutoff in the interaction range have not been studied in this context, but should in fact be considered to understand the relevance of the unjamming phenomenology in systems where such a cutoff is not present. In this work we explore two systems with such interactions: an inverse power law and an exponentially decaying pairwise potential, with the control parameters being the exponent (of the inverse power law) for the former and the number density for the latter. Both systems are shown to exhibit the characteristic features of the unjamming transition, among which are the vanishing of the shear-to-bulk modulus ratio and the emergence of an excess of low-frequency vibrational modes. We establish a relation between the pressure-to-bulk modulus ratio and the distance to unjamming in each of our model systems. This allows us to predict the dependence of other key observables on the distance to unjamming. Our results provide the means for a quantitative estimation of the proximity of generic glass-forming models to the unjamming transition in the absence of a clear-cut definition of the coordination number and highlight the general irrelevance of nonaffine contributions to the bulk modulus.

  8. Partial covariance based functional connectivity computation using Ledoit-Wolf covariance regularization

    PubMed Central

    Brier, Matthew R.; Mitra, Anish; McCarthy, John E.; Ances, Beau M.; Snyder, Abraham Z.

    2015-01-01

    Functional connectivity refers to shared signals among brain regions and is typically assessed in a task free state. Functional connectivity commonly is quantified between signal pairs using Pearson correlation. However, resting-state fMRI is a multivariate process exhibiting a complicated covariance structure. Partial covariance assesses the unique variance shared between two brain regions excluding any widely shared variance, hence is appropriate for the analysis of multivariate fMRI datasets. However, calculation of partial covariance requires inversion of the covariance matrix, which, in most functional connectivity studies, is not invertible owing to rank deficiency. Here we apply Ledoit-Wolf shrinkage (L2 regularization) to invert the high dimensional BOLD covariance matrix. We investigate the network organization and brain-state dependence of partial covariance-based functional connectivity. Although RSNs are conventionally defined in terms of shared variance, removal of widely shared variance, surprisingly, improved the separation of RSNs in a spring embedded graphical model. This result suggests that pair-wise unique shared variance plays a heretofore unrecognized role in RSN covariance organization. In addition, application of partial correlation to fMRI data acquired in the eyes open vs. eyes closed states revealed focal changes in uniquely shared variance between the thalamus and visual cortices. This result suggests that partial correlation of resting state BOLD time series reflect functional processes in addition to structural connectivity. PMID:26208872

  9. Partial covariance based functional connectivity computation using Ledoit-Wolf covariance regularization.

    PubMed

    Brier, Matthew R; Mitra, Anish; McCarthy, John E; Ances, Beau M; Snyder, Abraham Z

    2015-11-01

    Functional connectivity refers to shared signals among brain regions and is typically assessed in a task free state. Functional connectivity commonly is quantified between signal pairs using Pearson correlation. However, resting-state fMRI is a multivariate process exhibiting a complicated covariance structure. Partial covariance assesses the unique variance shared between two brain regions excluding any widely shared variance, hence is appropriate for the analysis of multivariate fMRI datasets. However, calculation of partial covariance requires inversion of the covariance matrix, which, in most functional connectivity studies, is not invertible owing to rank deficiency. Here we apply Ledoit-Wolf shrinkage (L2 regularization) to invert the high dimensional BOLD covariance matrix. We investigate the network organization and brain-state dependence of partial covariance-based functional connectivity. Although RSNs are conventionally defined in terms of shared variance, removal of widely shared variance, surprisingly, improved the separation of RSNs in a spring embedded graphical model. This result suggests that pair-wise unique shared variance plays a heretofore unrecognized role in RSN covariance organization. In addition, application of partial correlation to fMRI data acquired in the eyes open vs. eyes closed states revealed focal changes in uniquely shared variance between the thalamus and visual cortices. This result suggests that partial correlation of resting state BOLD time series reflect functional processes in addition to structural connectivity. Copyright © 2015 Elsevier Inc. All rights reserved.

  10. Pairwise network information and nonlinear correlations

    NASA Astrophysics Data System (ADS)

    Martin, Elliot A.; Hlinka, Jaroslav; Davidsen, Jörn

    2016-10-01

    Reconstructing the structural connectivity between interacting units from observed activity is a challenge across many different disciplines. The fundamental first step is to establish whether or to what extent the interactions between the units can be considered pairwise and, thus, can be modeled as an interaction network with simple links corresponding to pairwise interactions. In principle, this can be determined by comparing the maximum entropy given the bivariate probability distributions to the true joint entropy. In many practical cases, this is not an option since the bivariate distributions needed may not be reliably estimated or the optimization is too computationally expensive. Here we present an approach that allows one to use mutual informations as a proxy for the bivariate probability distributions. This has the advantage of being less computationally expensive and easier to estimate. We achieve this by introducing a novel entropy maximization scheme that is based on conditioning on entropies and mutual informations. This renders our approach typically superior to other methods based on linear approximations. The advantages of the proposed method are documented using oscillator networks and a resting-state human brain network as generic relevant examples.

  11. Pairwise Trajectory Management (PTM): Concept Overview

    NASA Technical Reports Server (NTRS)

    Jones, Kenneth M.; Graff, Thomas J.; Chartrand, Ryan C.; Carreno, Victor; Kibler, Jennifer L.

    2017-01-01

    Pairwise Trajectory Management (PTM) is an Interval Management (IM) concept that utilizes airborne and ground-based capabilities to enable the implementation of airborne pairwise spacing capabilities in oceanic regions. The goal of PTM is to use airborne surveillance and tools to manage an "at or greater than" inter-aircraft spacing. Due to the precision of Automatic Dependent Surveillance-Broadcast (ADS-B) information and the use of airborne spacing guidance, the PTM minimum spacing distance will be less than distances a controller can support with current automation systems that support oceanic operations. Ground tools assist the controller in evaluating the traffic picture and determining appropriate PTM clearances to be issued. Avionics systems provide guidance information that allows the flight crew to conform to the PTM clearance issued by the controller. The combination of a reduced minimum distance and airborne spacing management will increase the capacity and efficiency of aircraft operations at a given altitude or volume of airspace. This paper provides an overview of the proposed application, description of a few key scenarios, high level discussion of expected air and ground equipment and procedure changes, overview of a potential flight crew human-machine interface that would support PTM operations and some initial PTM benefits results.

  12. Pairwise network information and nonlinear correlations.

    PubMed

    Martin, Elliot A; Hlinka, Jaroslav; Davidsen, Jörn

    2016-10-01

    Reconstructing the structural connectivity between interacting units from observed activity is a challenge across many different disciplines. The fundamental first step is to establish whether or to what extent the interactions between the units can be considered pairwise and, thus, can be modeled as an interaction network with simple links corresponding to pairwise interactions. In principle, this can be determined by comparing the maximum entropy given the bivariate probability distributions to the true joint entropy. In many practical cases, this is not an option since the bivariate distributions needed may not be reliably estimated or the optimization is too computationally expensive. Here we present an approach that allows one to use mutual informations as a proxy for the bivariate probability distributions. This has the advantage of being less computationally expensive and easier to estimate. We achieve this by introducing a novel entropy maximization scheme that is based on conditioning on entropies and mutual informations. This renders our approach typically superior to other methods based on linear approximations. The advantages of the proposed method are documented using oscillator networks and a resting-state human brain network as generic relevant examples.

  13. Pairwise Linkage for Point Cloud Segmentation

    NASA Astrophysics Data System (ADS)

    Lu, Xiaohu; Yao, Jian; Tu, Jinge; Li, Kai; Li, Li; Liu, Yahui

    2016-06-01

    In this paper, we first present a novel hierarchical clustering algorithm named Pairwise Linkage (P-Linkage), which can be used for clustering any dimensional data, and then effectively apply it on 3D unstructured point cloud segmentation. The P-Linkage clustering algorithm first calculates a feature value for each data point, for example, the density for 2D data points and the flatness for 3D point clouds. Then for each data point a pairwise linkage is created between itself and its closest neighboring point with a greater feature value than its own. The initial clusters can further be discovered by searching along the linkages in a simple way. After that, a cluster merging procedure is applied to obtain the finally refined clustering result, which can be designed for specialized applications. Based on the P-Linkage clustering, we develop an efficient segmentation algorithm for 3D unstructured point clouds, in which the flatness of the estimated surface of a 3D point is used as its feature value. For each initial cluster a slice is created, then a novel and robust slicemerging method is proposed to get the final segmentation result. The proposed P-Linkage clustering and 3D point cloud segmentation algorithms require only one input parameter in advance. Experimental results on different dimensional synthetic data from 2D to 4D sufficiently demonstrate the efficiency and robustness of the proposed P-Linkage clustering algorithm and a large amount of experimental results on the Vehicle-Mounted, Aerial and Stationary Laser Scanner point clouds illustrate the robustness and efficiency of our proposed 3D point cloud segmentation algorithm.

  14. Galaxy Pairwise Velocity Distributions on Nonlinear Scales

    NASA Astrophysics Data System (ADS)

    Diaferio, Antonaldo; Geller, Margaret J.

    1996-08-01

    The redshift-space correlation function ξ_s_ for projected galaxy separations <~ 1 h^-1^ Mpc can be expressed as the convolution of the real-space correlation function with the galaxy pairwise velocity distribution function (PVDF). An exponential PVDF yields the best fit to the ξ_s_ measured from galaxy samples of different redshift surveys. We show that this exponential PVDF is not merely a fitting function but arises from well-defined gravitational processes. Two ingredients conspire to yield a PVDF with a nearly exponential shape: (1) the number density n(σ) of systems with velocity dispersion σ and (2) the unrelaxed dynamical state of most galaxy systems. The former ingredient determines the exponential tail, and the latter determines the central peak of the PVDF. We examine a third issue: the transfer of orbital kinetic energy to galaxy internal degrees of freedom. Although this effect is of secondary importance for the PVDF exponential shape, it is detectable in galaxy groups, which indicates that galaxy merging is an ongoing process in the present universe. We compare the ξ_s_ measured on nonlinear scales from galaxy samples of the Center for Astrophysics redshift surveys with different models of the PVDF convolved with the measured real-space correlation function. This preliminary comparison indicates that the agreement between model and observations depends strongly on both the underlying cosmological model and the internal dynamics of galaxy systems. Neither parameter dominates. Moreover, the agreement depends sensitively on the accuracy of the galaxy position and velocity measurements. We expect that ξ_s_ will pose further constraints on the model of the universe and will improve the knowledge of the dynamics of galaxy systems on very small scales if we improve (1) the galaxy coordinate determination and (2) the measurement of relative velocities of galaxies with small projected separation. In fact, the redshift-space correlation function

  15. ADD: Does It Really Exist?

    ERIC Educational Resources Information Center

    Armstrong, Thomas

    1996-01-01

    Questions the existence of attention deficit disorder (ADD), a commonly diagnosed "disease" based on behavioral characteristics. There may be no medical or physiological basis for ADD. The National Association of School Psychologists deplores labeling children and creating categories of exclusion. Instead, educators should respond to individual…

  16. Statistical pairwise interaction model of stock market

    NASA Astrophysics Data System (ADS)

    Bury, Thomas

    2013-03-01

    Financial markets are a classical example of complex systems as they are compound by many interacting stocks. As such, we can obtain a surprisingly good description of their structure by making the rough simplification of binary daily returns. Spin glass models have been applied and gave some valuable results but at the price of restrictive assumptions on the market dynamics or they are agent-based models with rules designed in order to recover some empirical behaviors. Here we show that the pairwise model is actually a statistically consistent model with the observed first and second moments of the stocks orientation without making such restrictive assumptions. This is done with an approach only based on empirical data of price returns. Our data analysis of six major indices suggests that the actual interaction structure may be thought as an Ising model on a complex network with interaction strengths scaling as the inverse of the system size. This has potentially important implications since many properties of such a model are already known and some techniques of the spin glass theory can be straightforwardly applied. Typical behaviors, as multiple equilibria or metastable states, different characteristic time scales, spatial patterns, order-disorder, could find an explanation in this picture.

  17. Predicting community composition from pairwise interactions

    NASA Astrophysics Data System (ADS)

    Friedman, Jonathan; Higgins, Logan; Gore, Jeff

    The ability to predict the structure of complex, multispecies communities is crucial for understanding the impact of species extinction and invasion on natural communities, as well as for engineering novel, synthetic communities. Communities are often modeled using phenomenological models, such as the classical generalized Lotka-Volterra (gLV) model. While a lot of our intuition comes from such models, their predictive power has rarely been tested experimentally. To directly assess the predictive power of this approach, we constructed synthetic communities comprised of up to 8 soil bacteria. We measured the outcome of competition between all species pairs, and used these measurements to predict the composition of communities composed of more than 2 species. The pairwise competitions resulted in a diverse set of outcomes, including coexistence, exclusion, and bistability, and displayed evidence for both interference and facilitation. Most pair outcomes could be captured by the gLV framework, and the composition of multispecies communities could be predicted for communities composed solely of such pairs. Our results demonstrate the predictive ability and utility of simple phenomenology, which enables accurate predictions in the absence of mechanistic details.

  18. Signatures of Synchrony in Pairwise Count Correlations

    PubMed Central

    Tchumatchenko, Tatjana; Geisel, Theo; Volgushev, Maxim; Wolf, Fred

    2009-01-01

    Concerted neural activity can reflect specific features of sensory stimuli or behavioral tasks. Correlation coefficients and count correlations are frequently used to measure correlations between neurons, design synthetic spike trains and build population models. But are correlation coefficients always a reliable measure of input correlations? Here, we consider a stochastic model for the generation of correlated spike sequences which replicate neuronal pairwise correlations in many important aspects. We investigate under which conditions the correlation coefficients reflect the degree of input synchrony and when they can be used to build population models. We find that correlation coefficients can be a poor indicator of input synchrony for some cases of input correlations. In particular, count correlations computed for large time bins can vanish despite the presence of input correlations. These findings suggest that network models or potential coding schemes of neural population activity need to incorporate temporal properties of correlated inputs and take into consideration the regimes of firing rates and correlation strengths to ensure that their building blocks are an unambiguous measures of synchrony. PMID:20422044

  19. Disequilibrium mapping: Composite likelihood for pairwise disequilibrium

    SciTech Connect

    Devlin, B.; Roeder, K.; Risch, N.

    1996-08-15

    The pattern of linkage disequilibrium between a disease locus and a set of marker loci has been shown to be a useful tool for geneticists searching for disease genes. Several methods have been advanced to utilize the pairwise disequilibrium between the disease locus and each of a set of marker loci. However, none of the methods take into account the information from all pairs simultaneously while also modeling the variability in the disequilibrium values due to the evolutionary dynamics of the population. We propose a Composite Likelihood CL model that has these features when the physical distances between the marker loci are known or can be approximated. In this instance, and assuming that there is a single disease mutation, the CL model depends on only three parameters, the recombination fraction between the disease locus and an arbitrary marker locus, {theta}, the age of the mutation, and a variance parameter. When the CL is maximized over a grid of {theta}, it provides a graph that can direct the search for the disease locus. We also show how the CL model can be generalized to account for multiple disease mutations. Evolutionary simulations demonstrate the power of the analyses, as well as their potential weaknesses. Finally, we analyze the data from two mapped diseases, cystic fibrosis and diastrophic dysplasia, finding that the CL method performs well in both cases. 28 refs., 6 figs., 4 tabs.

  20. Local Submodularization for Binary Pairwise Energies.

    PubMed

    Gorelick, Lena; Boykov, Yuri; Veksler, Olga; Ayed, Ismail Ben; Delong, Andrew

    2017-10-01

    Many computer vision problems require optimization of binary non-submodular energies. We propose a general optimization framework based on local submodular approximations (LSA). Unlike standard LP relaxation methods that linearize the whole energy globally, our approach iteratively approximates the energy locally. On the other hand, unlike standard local optimization methods (e.g., gradient descent or projection techniques) we use non-linear submodular approximations and optimize them without leaving the domain of integer solutions. We discuss two specific LSA algorithms based on trust region and auxiliary function principles, LSA-TR and LSA-AUX. The proposed methods obtain state-of-the-art results on a wide range of applications such as binary deconvolution, curvature regularization, inpainting, segmentation with repulsion and two types of shape priors. Finally, we discuss a move-making extension to the LSA-TR approach. While our paper is focused on pairwise energies, our ideas extend to higher-order problems. The code is available online.

  1. Pairwise polymer blends for oral drug delivery.

    PubMed

    Marks, Joyann A; Wegiel, Lindsay A; Taylor, Lynne S; Edgar, Kevin J

    2014-09-01

    Blends of polymers with complementary properties hold promise for addressing the diverse, demanding polymer performance requirements in amorphous solid dispersions (ASDs), but we lack comprehensive property understanding for blends of important ASD polymers. Herein, we prepare pairwise blends of commercially available polymers polyvinylpyrrolidone (PVP), the cationic acrylate copolymer Eudragit 100 (E100), hydroxypropyl methylcellulose acetate succinate (HPMCAS), carboxymethyl cellulose acetate butyrate (CMCAB), hydroxypropyl methylcellulose (HPMC), and the new derivative cellulose acetate adipate propionate (CAAdP). This study identifies miscible binary blends that may find use, for example, in ASDs for solubility and bioavailability enhancement of poorly water-soluble drugs. Differential scanning calorimetry, FTIR spectroscopy, and film clarity were used to determine blend miscibility. Several polymer combinations including HPMCAS/PVP, HPMC/CMCAB, and PVP/HPMC appear to be miscible in all proportions. In contrast, blends of E100/PVP and E100/HPMC showed a miscibility gap. Combinations of water-soluble and hydrophobic polymers like these may permit effective balancing of ASD performance criteria such as release rate and polymer-drug interaction to prevent nucleation and crystal growth of poorly soluble drugs. Miscible polymer combinations described herein will enable further study of their drug delivery capabilities, and provide a potentially valuable set of ASD formulation tools. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.

  2. Auto covariance computer

    NASA Technical Reports Server (NTRS)

    Hepner, T. E.; Meyers, J. F. (Inventor)

    1985-01-01

    A laser velocimeter covariance processor which calculates the auto covariance and cross covariance functions for a turbulent flow field based on Poisson sampled measurements in time from a laser velocimeter is described. The device will process a block of data that is up to 4096 data points in length and return a 512 point covariance function with 48-bit resolution along with a 512 point histogram of the interarrival times which is used to normalize the covariance function. The device is designed to interface and be controlled by a minicomputer from which the data is received and the results returned. A typical 4096 point computation takes approximately 1.5 seconds to receive the data, compute the covariance function, and return the results to the computer.

  3. SVM-dependent pairwise HMM: an application to Protein pairwise alignments.

    PubMed

    Orlando, Gabriele; Raimondi, Daniele; Khan, Taushif; Lenaerts, Tom; Vranken, Wim

    2017-06-28

    Methods able to provide reliable protein alignments are crucial for many bioinformatics applications. In the last years many different algorithms have been developed and various kinds of information, from sequence conservation to secondary structure, have been used to improve the alignment performances. This is especially relevant for proteins with highly divergent sequences. However, recent works suggest that different features may have different importance in diverse protein classes and it would be an advantage to have more customizable approaches, capable to deal with different alignment definitions. Here we present Rigapollo, a highly flexible pairwise alignment method based on a pairwise HMM-SVM that can use any type of information to build alignments. Rigapollo lets the user decide the optimal features to align their protein class of interest. It outperforms current state of the art methods on two well known benchmark datasets when aligning highly divergent sequences. A Python implementation of the algorithm is available at http://ibsquare.be/rigapollo. wim.vranken@vub.be. Supplementary data are available at Bioinformatics online.

  4. Galilean covariant harmonic oscillator

    NASA Technical Reports Server (NTRS)

    Horzela, Andrzej; Kapuscik, Edward

    1993-01-01

    A Galilean covariant approach to classical mechanics of a single particle is described. Within the proposed formalism, all non-covariant force laws defining acting forces which become to be defined covariantly by some differential equations are rejected. Such an approach leads out of the standard classical mechanics and gives an example of non-Newtonian mechanics. It is shown that the exactly solvable linear system of differential equations defining forces contains the Galilean covariant description of harmonic oscillator as its particular case. Additionally, it is demonstrated that in Galilean covariant classical mechanics the validity of the second Newton law of dynamics implies the Hooke law and vice versa. It is shown that the kinetic and total energies transform differently with respect to the Galilean transformations.

  5. Prior event rate ratio adjustment for hidden confounding in observational studies of treatment effectiveness: a pairwise Cox likelihood approach.

    PubMed

    Lin, Nan Xuan; Henley, William Edward

    2016-12-10

    Observational studies provide a rich source of information for assessing effectiveness of treatment interventions in many situations where it is not ethical or practical to perform randomized controlled trials. However, such studies are prone to bias from hidden (unmeasured) confounding. A promising approach to identifying and reducing the impact of unmeasured confounding is prior event rate ratio (PERR) adjustment, a quasi-experimental analytic method proposed in the context of electronic medical record database studies. In this paper, we present a statistical framework for using a pairwise approach to PERR adjustment that removes bias inherent in the original PERR method. A flexible pairwise Cox likelihood function is derived and used to demonstrate the consistency of the simple and convenient alternative PERR (PERR-ALT) estimator. We show how to estimate standard errors and confidence intervals for treatment effect estimates based on the observed information and provide R code to illustrate how to implement the method. Assumptions required for the pairwise approach (as well as PERR) are clarified, and the consequences of model misspecification are explored. Our results confirm the need for researchers to consider carefully the suitability of the method in the context of each problem. Extensions of the pairwise likelihood to more complex designs involving time-varying covariates or more than two periods are considered. We illustrate the application of the method using data from a longitudinal cohort study of enzyme replacement therapy for lysosomal storage disorders. © 2016 The Authors. Statistics in Medicine Published by John Wiley & Sons Ltd.

  6. PWC - PAIRWISE COMPARISON SOFTWARE: SOFTWARE PROGRAM FOR PAIRWISE COMPARISON TASK FOR PSYCHOMETRIC SCALING AND COGNITIVE RESEARCH

    NASA Technical Reports Server (NTRS)

    Ricks, W. R.

    1994-01-01

    PWC is used for pair-wise comparisons in both psychometric scaling techniques and cognitive research. The cognitive tasks and processes of a human operator of automated systems are now prominent considerations when defining system requirements. Recent developments in cognitive research have emphasized the potential utility of psychometric scaling techniques, such as multidimensional scaling, for representing human knowledge and cognitive processing structures. Such techniques involve collecting measurements of stimulus-relatedness from human observers. When data are analyzed using this scaling approach, an n-dimensional representation of the stimuli is produced. This resulting representation is said to describe the subject's cognitive or perceptual view of the stimuli. PWC applies one of the many techniques commonly used to acquire the data necessary for these types of analyses: pair-wise comparisons. PWC administers the task, collects the data from the test subject, and formats the data for analysis. It therefore addresses many of the limitations of the traditional "pen-and-paper" methods. By automating the data collection process, subjects are prevented from going back to check previous responses, the possibility of erroneous data transfer is eliminated, and the burden of the administration and taking of the test is eased. By using randomization, PWC ensures that subjects see the stimuli pairs presented in random order, and that each subject sees pairs in a different random order. PWC is written in Turbo Pascal v6.0 for IBM PC compatible computers running MS-DOS. The program has also been successfully compiled with Turbo Pascal v7.0. A sample executable is provided. PWC requires 30K of RAM for execution. The standard distribution medium for this program is a 5.25 inch 360K MS-DOS format diskette. Two electronic versions of the documentation are included on the diskette: one in ASCII format and one in MS Word for Windows format. PWC was developed in 1993.

  7. PWC - PAIRWISE COMPARISON SOFTWARE: SOFTWARE PROGRAM FOR PAIRWISE COMPARISON TASK FOR PSYCHOMETRIC SCALING AND COGNITIVE RESEARCH

    NASA Technical Reports Server (NTRS)

    Ricks, W. R.

    1994-01-01

    PWC is used for pair-wise comparisons in both psychometric scaling techniques and cognitive research. The cognitive tasks and processes of a human operator of automated systems are now prominent considerations when defining system requirements. Recent developments in cognitive research have emphasized the potential utility of psychometric scaling techniques, such as multidimensional scaling, for representing human knowledge and cognitive processing structures. Such techniques involve collecting measurements of stimulus-relatedness from human observers. When data are analyzed using this scaling approach, an n-dimensional representation of the stimuli is produced. This resulting representation is said to describe the subject's cognitive or perceptual view of the stimuli. PWC applies one of the many techniques commonly used to acquire the data necessary for these types of analyses: pair-wise comparisons. PWC administers the task, collects the data from the test subject, and formats the data for analysis. It therefore addresses many of the limitations of the traditional "pen-and-paper" methods. By automating the data collection process, subjects are prevented from going back to check previous responses, the possibility of erroneous data transfer is eliminated, and the burden of the administration and taking of the test is eased. By using randomization, PWC ensures that subjects see the stimuli pairs presented in random order, and that each subject sees pairs in a different random order. PWC is written in Turbo Pascal v6.0 for IBM PC compatible computers running MS-DOS. The program has also been successfully compiled with Turbo Pascal v7.0. A sample executable is provided. PWC requires 30K of RAM for execution. The standard distribution medium for this program is a 5.25 inch 360K MS-DOS format diskette. Two electronic versions of the documentation are included on the diskette: one in ASCII format and one in MS Word for Windows format. PWC was developed in 1993.

  8. Skewed exponential pairwise velocities from Gaussian initial conditions

    SciTech Connect

    Juszkiewicz, R.; Fisher, K. B.; Szapudi, I.

    1998-09-01

    Using an Eulerian perturbative calculation, we show that the distribution of relative pairwise velocities which arises from gravitational instability of Gaussian density fluctuations has asymmetric (skewed) exponential tails. The negative skewness is induced by the negative mean streaming velocity of pairs (the infall prevails over expansion), while the exponential tails arise because the relative pairwise velocity is a number, not volume weighted statistic. The derived probability distribution is compared with N-body simulations and shown to provide a reasonable fit.

  9. Covariant mutually unbiased bases

    NASA Astrophysics Data System (ADS)

    Carmeli, Claudio; Schultz, Jussi; Toigo, Alessandro

    2016-06-01

    The connection between maximal sets of mutually unbiased bases (MUBs) in a prime-power dimensional Hilbert space and finite phase-space geometries is well known. In this article, we classify MUBs according to their degree of covariance with respect to the natural symmetries of a finite phase-space, which are the group of its affine symplectic transformations. We prove that there exist maximal sets of MUBs that are covariant with respect to the full group only in odd prime-power dimensional spaces, and in this case, their equivalence class is actually unique. Despite this limitation, we show that in dimension 2r covariance can still be achieved by restricting to proper subgroups of the symplectic group, that constitute the finite analogues of the oscillator group. For these subgroups, we explicitly construct the unitary operators yielding the covariance.

  10. Covariant Noncommutative Field Theory

    SciTech Connect

    Estrada-Jimenez, S.; Garcia-Compean, H.; Obregon, O.; Ramirez, C.

    2008-07-02

    The covariant approach to noncommutative field and gauge theories is revisited. In the process the formalism is applied to field theories invariant under diffeomorphisms. Local differentiable forms are defined in this context. The lagrangian and hamiltonian formalism is consistently introduced.

  11. A General Pairwise Interaction Model Provides an Accurate Description of In Vivo Transcription Factor Binding Sites

    PubMed Central

    Santolini, Marc; Mora, Thierry; Hakim, Vincent

    2014-01-01

    The identification of transcription factor binding sites (TFBSs) on genomic DNA is of crucial importance for understanding and predicting regulatory elements in gene networks. TFBS motifs are commonly described by Position Weight Matrices (PWMs), in which each DNA base pair contributes independently to the transcription factor (TF) binding. However, this description ignores correlations between nucleotides at different positions, and is generally inaccurate: analysing fly and mouse in vivo ChIPseq data, we show that in most cases the PWM model fails to reproduce the observed statistics of TFBSs. To overcome this issue, we introduce the pairwise interaction model (PIM), a generalization of the PWM model. The model is based on the principle of maximum entropy and explicitly describes pairwise correlations between nucleotides at different positions, while being otherwise as unconstrained as possible. It is mathematically equivalent to considering a TF-DNA binding energy that depends additively on each nucleotide identity at all positions in the TFBS, like the PWM model, but also additively on pairs of nucleotides. We find that the PIM significantly improves over the PWM model, and even provides an optimal description of TFBS statistics within statistical noise. The PIM generalizes previous approaches to interdependent positions: it accounts for co-variation of two or more base pairs, and predicts secondary motifs, while outperforming multiple-motif models consisting of mixtures of PWMs. We analyse the structure of pairwise interactions between nucleotides, and find that they are sparse and dominantly located between consecutive base pairs in the flanking region of TFBS. Nonetheless, interactions between pairs of non-consecutive nucleotides are found to play a significant role in the obtained accurate description of TFBS statistics. The PIM is computationally tractable, and provides a general framework that should be useful for describing and predicting TFBSs beyond

  12. Reliable clock estimation using linear weighted fusion based on pairwise broadcast synchronization

    SciTech Connect

    Shi, Xin Zhao, Xiangmo Hui, Fei Ma, Junyan Yang, Lan

    2014-10-06

    Clock synchronization in wireless sensor networks (WSNs) has been studied extensively in recent years and many protocols are put forward based on the point of statistical signal processing, which is an effective way to optimize accuracy. However, the accuracy derived from the statistical data can be improved mainly by sufficient packets exchange, which will consume the limited power resources greatly. In this paper, a reliable clock estimation using linear weighted fusion based on pairwise broadcast synchronization is proposed to optimize sync accuracy without expending additional sync packets. As a contribution, a linear weighted fusion scheme for multiple clock deviations is constructed with the collaborative sensing of clock timestamp. And the fusion weight is defined by the covariance of sync errors for different clock deviations. Extensive simulation results show that the proposed approach can achieve better performance in terms of sync overhead and sync accuracy.

  13. To Covary or Not to Covary, That is the Question

    NASA Astrophysics Data System (ADS)

    Oehlert, A. M.; Swart, P. K.

    2016-12-01

    The meaning of covariation between the δ13C values of carbonate carbon and that of organic material is classically interpreted as reflecting original variations in the δ13C values of the dissolved inorganic carbon in the depositional environment. However, recently it has been shown by the examination of a core from Great Bahama Bank (Clino) that during exposure not only do the rocks become altered acquiring a negative δ13C value, but at the same time terrestrial vegetation adds organic carbon to the system masking the original marine values. These processes yield a strong positive covariation between δ13Corg and δ13Ccar values even though the signals are clearly not original and unrelated to the marine δ13C values. Examining the correlation between the organic and inorganic system in a stratigraphic sense at Clino and in a second more proximally located core (Unda) using a windowed correlation coefficient technique reveals that the correlation is even more complex. Changes in slope and the magnitude of the correlation are associated with exposure surfaces, facies changes, dolomitized bodies, and non-depositional surfaces. Finally other isotopic systems such as the δ13C value of specific organic compounds as well as δ15N values of bulk and individual compounds can provide additional information. In the case of δ15N values, decreases reflect a changes in the influence of terrestrial organic material and an increase contribution of organic material from the platform surface where the main source of nitrogen is derived from the activities of cyanobacteria.

  14. Covariant Bardeen perturbation formalism

    NASA Astrophysics Data System (ADS)

    Vitenti, S. D. P.; Falciano, F. T.; Pinto-Neto, N.

    2014-05-01

    In a previous work we obtained a set of necessary conditions for the linear approximation in cosmology. Here we discuss the relations of this approach with the so-called covariant perturbations. It is often argued in the literature that one of the main advantages of the covariant approach to describe cosmological perturbations is that the Bardeen formalism is coordinate dependent. In this paper we will reformulate the Bardeen approach in a completely covariant manner. For that, we introduce the notion of pure and mixed tensors, which yields an adequate language to treat both perturbative approaches in a common framework. We then stress that in the referred covariant approach, one necessarily introduces an additional hypersurface choice to the problem. Using our mixed and pure tensors approach, we are able to construct a one-to-one map relating the usual gauge dependence of the Bardeen formalism with the hypersurface dependence inherent to the covariant approach. Finally, through the use of this map, we define full nonlinear tensors that at first order correspond to the three known gauge invariant variables Φ, Ψ and Ξ, which are simultaneously foliation and gauge invariant. We then stress that the use of the proposed mixed tensors allows one to construct simultaneously gauge and hypersurface invariant variables at any order.

  15. Covariance mapping techniques

    NASA Astrophysics Data System (ADS)

    Frasinski, Leszek J.

    2016-08-01

    Recent technological advances in the generation of intense femtosecond pulses have made covariance mapping an attractive analytical technique. The laser pulses available are so intense that often thousands of ionisation and Coulomb explosion events will occur within each pulse. To understand the physics of these processes the photoelectrons and photoions need to be correlated, and covariance mapping is well suited for operating at the high counting rates of these laser sources. Partial covariance is particularly useful in experiments with x-ray free electron lasers, because it is capable of suppressing pulse fluctuation effects. A variety of covariance mapping methods is described: simple, partial (single- and multi-parameter), sliced, contingent and multi-dimensional. The relationship to coincidence techniques is discussed. Covariance mapping has been used in many areas of science and technology: inner-shell excitation and Auger decay, multiphoton and multielectron ionisation, time-of-flight and angle-resolved spectrometry, infrared spectroscopy, nuclear magnetic resonance imaging, stimulated Raman scattering, directional gamma ray sensing, welding diagnostics and brain connectivity studies (connectomics). This review gives practical advice for implementing the technique and interpreting the results, including its limitations and instrumental constraints. It also summarises recent theoretical studies, highlights unsolved problems and outlines a personal view on the most promising research directions.

  16. Evaluation of pairwise distances among orthogonal grid points in hypercube

    NASA Astrophysics Data System (ADS)

    Sadílek, Václav; Vořechovský, Miroslav; Šmídová, Magdalena

    2017-07-01

    This article describes an effective evaluation of pairwise distances among points that form a regular orthogonal grid inside a unit hypercube. Such an regular arrangement of points have many applications one of which is the Design of Experiments - the arrangement is known as the Full Factorial Design. The proposed process of calculation exploits the repeated point projections. Using combinatorial rules, the paper presents a closed-form exact formula that enables faster evaluation of pairwise distances and their counts compared to naive approach that enumerates the list of all possible pairs of points.

  17. Improving Predictions in Imbalanced Data Using Pairwise Expanded Logistic Regression

    PubMed Central

    Jiang, Xiaoqian; El-Kareh, Robert; Ohno-Machado, Lucila

    2011-01-01

    Building classifiers for medical problems often involves dealing with rare, but important events. Imbalanced datasets pose challenges to ordinary classification algorithms such as Logistic Regression (LR) and Support Vector Machines (SVM). The lack of effective strategies for dealing with imbalanced training data often results in models that exhibit poor discrimination. We propose a novel approach to estimate class memberships based on the evaluation of pairwise relationships in the training data. The method we propose, Pairwise Expanded Logistic Regression, improved discrimination and had higher accuracy when compared to existing methods in two imbalanced datasets, thus showing promise as a potential remedy for this problem. PMID:22195118

  18. Covariance Applications with Kiwi

    NASA Astrophysics Data System (ADS)

    Mattoon, C. M.; Brown, D.; Elliott, J. B.

    2012-05-01

    The Computational Nuclear Physics group at Lawrence Livermore National Laboratory (LLNL) is developing a new tool, named `Kiwi', that is intended as an interface between the covariance data increasingly available in major nuclear reaction libraries (including ENDF and ENDL) and large-scale Uncertainty Quantification (UQ) studies. Kiwi is designed to integrate smoothly into large UQ studies, using the covariance matrix to generate multiple variations of nuclear data. The code has been tested using critical assemblies as a test case, and is being integrated into LLNL's quality assurance and benchmarking for nuclear data.

  19. Covariant canonical superstrings

    SciTech Connect

    Aratyn, H.; Ingermanson, R.; Niemi, A.J.

    1987-12-01

    A covariant canonical formulation of generic superstrings is presented. The (super)geometry emerges dynamically and supergravity transformations are identified with particular canonical transformations. By construction these transformations are off-shell closed, and the necessary auxiliary fields can be identified with canonical momenta.

  20. Detection of the pairwise kinematic Sunyaev-Zel'dovich effect with BOSS DR11 and the Atacama Cosmology Telescope

    NASA Astrophysics Data System (ADS)

    De Bernardis, F.; Aiola, S.; Vavagiakis, E. M.; Battaglia, N.; Niemack, M. D.; Beall, J.; Becker, D. T.; Bond, J. R.; Calabrese, E.; Cho, H.; Coughlin, K.; Datta, R.; Devlin, M.; Dunkley, J.; Dunner, R.; Ferraro, S.; Fox, A.; Gallardo, P. A.; Halpern, M.; Hand, N.; Hasselfield, M.; Henderson, S. W.; Hill, J. C.; Hilton, G. C.; Hilton, M.; Hincks, A. D.; Hlozek, R.; Hubmayr, J.; Huffenberger, K.; Hughes, J. P.; Irwin, K. D.; Koopman, B. J.; Kosowsky, A.; Li, D.; Louis, T.; Lungu, M.; Madhavacheril, M. S.; Maurin, L.; McMahon, J.; Moodley, K.; Naess, S.; Nati, F.; Newburgh, L.; Nibarger, J. P.; Page, L. A.; Partridge, B.; Schaan, E.; Schmitt, B. L.; Sehgal, N.; Sievers, J.; Simon, S. M.; Spergel, D. N.; Staggs, S. T.; Stevens, J. R.; Thornton, R. J.; van Engelen, A.; Van Lanen, J.; Wollack, E. J.

    2017-03-01

    We present a new measurement of the kinematic Sunyaev-Zel'dovich effect using data from the Atacama Cosmology Telescope (ACT) and the Baryon Oscillation Spectroscopic Survey (BOSS). Using 600 square degrees of overlapping sky area, we evaluate the mean pairwise baryon momentum associated with the positions of 50,000 bright galaxies in the BOSS DR11 Large Scale Structure catalog. A non-zero signal arises from the large-scale motions of halos containing the sample galaxies. The data fits an analytical signal model well, with the optical depth to microwave photon scattering as a free parameter determining the overall signal amplitude. We estimate the covariance matrix of the mean pairwise momentum as a function of galaxy separation, using microwave sky simulations, jackknife evaluation, and bootstrap estimates. The most conservative simulation-based errors give signal-to-noise estimates between 3.6 and 4.1 for varying galaxy luminosity cuts. We discuss how the other error determinations can lead to higher signal-to-noise values, and consider the impact of several possible systematic errors. Estimates of the optical depth from the average thermal Sunyaev-Zel'dovich signal at the sample galaxy positions are broadly consistent with those obtained from the mean pairwise momentum signal.

  1. Detection of the Pairwise Kinematic Sunyaev-Zel'dovich Effect with BOSS DR11 and the Atacama Cosmology Telescope

    NASA Technical Reports Server (NTRS)

    De Bernardis, F.; Aiola, S.; Vavagiakis, E. M.; Battaglia, N.; Niemack, M. D.; Beall, J.; Becker, D. T.; Bond, J. R.; Calabrese, E.; Cho, H.; hide

    2017-01-01

    We present a new measurement of the kinematic Sunyaev-Zel'dovich effect using data from the Atacama Cosmology Telescope (ACT) and the Baryon Oscillation Spectroscopic Survey (BOSS). Using 600 square degrees of overlapping sky area, we evaluate the mean pairwise baryon momentum associated with the positions of 50,000 bright galaxies in the BOSS DR11 Large Scale Structure catalog. A non-zero signal arises from the large-scale motions of halos containing the sample galaxies. The data fits an analytical signal model well, with the optical depth to microwave photon scattering as a free parameter determining the overall signal amplitude. We estimate the covariance matrix of the mean pairwise momentum as a function of galaxy separation, using microwave sky simulations, jackknife evaluation, and bootstrap estimates. The most conservative simulation-based errors give signal-to-noise estimates between 3.6 and 4.1 for varying galaxy luminosity cuts. We discuss how the other error determinations can lead to higher signal-to-noise values, and consider the impact of several possible systematic errors. Estimates of the optical depth from the average thermal Sunyaev-Zel'dovich signal at the sample galaxy positions are broadly consistent with those obtained from the mean pairwise momentum signal.

  2. Pairwise Identity Verification via Linear Concentrative Metric Learning.

    PubMed

    Zheng, Lilei; Duffner, Stefan; Idrissi, Khalid; Garcia, Christophe; Baskurt, Atilla

    2016-12-16

    This paper presents a study of metric learning systems on pairwise identity verification, including pairwise face verification and pairwise speaker verification, respectively. These problems are challenging because the individuals in training and testing are mutually exclusive, and also due to the probable setting of limited training data. For such pairwise verification problems, we present a general framework of metric learning systems and employ the stochastic gradient descent algorithm as the optimization solution. We have studied both similarity metric learning and distance metric learning systems, of either a linear or shallow nonlinear model under both restricted and unrestricted training settings. Extensive experiments demonstrate that with limited training pairs, learning a linear system on similar pairs only is preferable due to its simplicity and superiority, i.e., it generally achieves competitive performance on both the labeled faces in the wild face dataset and the NIST speaker dataset. It is also found that a pretrained deep nonlinear model helps to improve the face verification results significantly.

  3. Analysis of Pairwise Preference Data Using Integrated B-SPLINES.

    ERIC Educational Resources Information Center

    Winsberg, Suzanne; Ramsay, James O.

    1981-01-01

    A general method of scaling pairwise preference data is presented that may be used without prior knowledge about the nature of the relationship between an observation and the process giving rise to it. The method involves a monotone transformation and is similar to the B-SPLINE approach. (Author/JKS)

  4. Five key factors determining pairwise correlations in visual cortex

    PubMed Central

    Sahani, Maneesh; Carandini, Matteo

    2015-01-01

    The responses of cortical neurons to repeated presentation of a stimulus are highly variable, yet correlated. These “noise correlations” reflect a low-dimensional structure of population dynamics. Here, we examine noise correlations in 22,705 pairs of neurons in primary visual cortex (V1) of anesthetized cats, during ongoing activity and in response to artificial and natural visual stimuli. We measured how noise correlations depend on 11 factors. Because these factors are themselves not independent, we distinguished their influences using a nonlinear additive model. The model revealed that five key factors play a predominant role in determining pairwise correlations. Two of these are distance in cortex and difference in sensory tuning: these are known to decrease correlation. A third factor is firing rate: confirming most earlier observations, it markedly increased pairwise correlations. A fourth factor is spike width: cells with a broad spike were more strongly correlated amongst each other. A fifth factor is spike isolation: neurons with worse isolation were more correlated, even if they were recorded on different electrodes. For pairs of neurons with poor isolation, this last factor was the main determinant of correlations. These results were generally independent of stimulus type and timescale of analysis, but there were exceptions. For instance, pairwise correlations depended on difference in orientation tuning more during responses to gratings than to natural stimuli. These results consolidate disjoint observations in a vast literature on pairwise correlations and point towards regularities of population coding in sensory cortex. PMID:26019310

  5. Discovering Pair-wise Synergies in Microarray Data

    PubMed Central

    Chen, Yuan; Cao, Dan; Gao, Jun; Yuan, Zheming

    2016-01-01

    Informative gene selection can have important implications for the improvement of cancer diagnosis and the identification of new drug targets. Individual-gene-ranking methods ignore interactions between genes. Furthermore, popular pair-wise gene evaluation methods, e.g. TSP and TSG, are helpless for discovering pair-wise interactions. Several efforts to discover pair-wise synergy have been made based on the information approach, such as EMBP and FeatKNN. However, the methods which are employed to estimate mutual information, e.g. binarization, histogram-based and KNN estimators, depend on known data or domain characteristics. Recently, Reshef et al. proposed a novel maximal information coefficient (MIC) measure to capture a wide range of associations between two variables that has the property of generality. An extension from MIC(X; Y) to MIC(X1; X2; Y) is therefore desired. We developed an approximation algorithm for estimating MIC(X1; X2; Y) where Y is a discrete variable. MIC(X1; X2; Y) is employed to detect pair-wise synergy in simulation and cancer microarray data. The results indicate that MIC(X1; X2; Y) also has the property of generality. It can discover synergic genes that are undetectable by reference feature selection methods such as MIC(X; Y) and TSG. Synergic genes can distinguish different phenotypes. Finally, the biological relevance of these synergic genes is validated with GO annotation and OUgene database. PMID:27470995

  6. Dynamics of pairwise motions in the Cosmic Web

    NASA Astrophysics Data System (ADS)

    Hellwing, Wojciech A.

    2016-10-01

    We present results of analysis of the dark matter (DM) pairwise velocity statistics in different Cosmic Web environments. We use the DM velocity and density field from the Millennium 2 simulation together with the NEXUS+ algorithm to segment the simulation volume into voxels uniquely identifying one of the four possible environments: nodes, filaments, walls or cosmic voids. We show that the PDFs of the mean infall velocities v 12 as well as its spatial dependence together with the perpendicular and parallel velocity dispersions bear a significant signal of the large-scale structure environment in which DM particle pairs are embedded. The pairwise flows are notably colder and have smaller mean magnitude in wall and voids, when compared to much denser environments of filaments and nodes. We discuss on our results, indicating that they are consistent with a simple theoretical predictions for pairwise motions as induced by gravitational instability mechanism. Our results indicate that the Cosmic Web elements are coherent dynamical entities rather than just temporal geometrical associations. In addition it should be possible to observationally test various Cosmic Web finding algorithms by segmenting available peculiar velocity data and studying resulting pairwise velocity statistics.

  7. Pairwise comparison versus Likert scale for biomedical image assessment.

    PubMed

    Phelps, Andrew S; Naeger, David M; Courtier, Jesse L; Lambert, Jack W; Marcovici, Peter A; Villanueva-Meyer, Javier E; MacKenzie, John D

    2015-01-01

    Biomedical imaging research relies heavily on the subjective and semi-quantitative reader analysis of images. Current methods are limited by interreader variability and fixed upper and lower limits. The purpose of this study was to compare the performance of two assessment methods, pairwise comparison and Likert scale, for improved analysis of biomedical images. A set of 10 images with varying degrees of image sharpness was created by digitally blurring a normal clinical chest radiograph. Readers assessed the degree of image sharpness using two different methods: pairwise comparison and a 10-point Likert scale. Reader agreement with actual chest radiograph sharpness was calculated for each method by use of the Lin concordance correlation coefficient (CCC). Reader accuracy was highest for pairwise comparison (CCC, 1.0) and ranked Likert (CCC, 0.99) scores and lowest for nonranked Likert scores (CCC, 0.83). Accuracy improved slightly when readers repeated their assessments (CCC, 0.87) or had reference images available (CCC, 0.91). Pairwise comparison and ranked Likert scores yield more accurate reader assessments than nonranked Likert scores.

  8. Beyond connectedness: why pairwise metrics cannot capture community stability.

    PubMed

    Neutel, Anje-Margriet; Thorne, Michael A S

    2016-10-01

    The connectedness of species in a trophic web has long been a key structural characteristic for both theoreticians and empiricists in their understanding of community stability. In the past decades, there has been a shift from focussing on determining the number of interactions to taking into account their relative strengths. The question is: How do the strengths of the interactions determine the stability of a community? Recently, a metric has been proposed which compares the stability of observed communities in terms of the strength of three- and two-link feedback loops (cycles of interaction strengths). However, it has also been suggested that we do not need to go beyond the pairwise structure of interactions to capture stability. Here, we directly compare the performance of the feedback and pairwise metrics. Using observed food-web structures, we show that the pairwise metric does not work as a comparator of stability and is many orders of magnitude away from the actual stability values. We argue that metrics based on pairwise-strength information cannot capture the complex organization of strong and weak links in a community, which is essential for system stability.

  9. Prospects for inferring pairwise relationships with single nucleotide polymorphisms

    Treesearch

    Jeffery C. Glaubitz; O. Eugene, Jr. Rhodes; J. Andrew DeWoody

    2003-01-01

    An extraordinarily large number of single nucleotide polymorphisms (SNPs) are now available in humans as well as in other model organisms. Technological advancements may soon make it feasible to assay hundreds of SNPs in virtually any organism of interest. One potential application of SNPs is the determination of pairwise genetic relationships in populations without...

  10. Pairwise Multiple Comparisons in Single Group Repeated Measures Analysis.

    ERIC Educational Resources Information Center

    Barcikowski, Robert S.; Elliott, Ronald S.

    Research was conducted to provide educational researchers with a choice of pairwise multiple comparison procedures (P-MCPs) to use with single group repeated measures designs. The following were studied through two Monte Carlo (MC) simulations: (1) The T procedure of J. W. Tukey (1953); (2) a modification of Tukey's T (G. Keppel, 1973); (3) the…

  11. Correlated binary regression with covariates specific to each binary observation.

    PubMed

    Prentice, R L

    1988-12-01

    Regression methods are considered for the analysis of correlated binary data when each binary observation may have its own covariates. It is argued that binary response models that condition on some or all binary responses in a given "block" are useful for studying certain types of dependencies, but not for the estimation of marginal response probabilities or pairwise correlations. Fully parametric approaches to these latter problems appear to be unduly complicated except in such special cases as the analysis of paired binary data. Hence, a generalized estimating equation approach is advocated for inference on response probabilities and correlations. Illustrations involving both small and large block sizes are provided.

  12. Measurements of the pairwise kinematic Sunyaev-Zel'dovich effect with the Atacama Cosmology Telescope and future surveys

    NASA Astrophysics Data System (ADS)

    Vavagiakis, Eve Marie; De Bernardis, Francesco; Aiola, Simone; Battaglia, Nicholas; Niemack, Michael D.; ACTPol Collaboration

    2017-06-01

    We have made improved measurements of the kinematic Sunyaev-Zel’dovich (kSZ) effect using data from the Atacama Cosmology Telescope (ACT) and the Baryon Oscillation Spectroscopic Survey (BOSS). We used a map of the Cosmic Microwave Background (CMB) from two seasons of observations each by ACT and the Atacama Cosmology Telescope Polarimeter (ACTPol) receiver. We evaluated the mean pairwise baryon momentum associated with the positions of 50,000 bright galaxies in the BOSS DR11 Large Scale Structure catalog via 600 square degrees of overlapping sky area. The measurement of the kSZ signal arising from the large-scale motions of clusters was made by fitting data to an analytical model. The free parameter of the fit determined the optical depth to microwave photon scattering for the cluster sample. We estimated the covariance matrix of the mean pairwise momentum as a function of galaxy separation using CMB simulations, jackknife evaluation, and bootstrap estimates. The most conservative simulation-based uncertainties gave signal-to-noise estimates between 3.6 and 4.1 for various luminosity cuts. Additionally, we explored a novel approach to estimating cluster optical depths from the average thermal Sunyaev-Zel’dovich (tSZ) signal at the BOSS DR11 catalog positions. Our results were broadly consistent with those obtained from the kSZ signal. In the future, the tSZ signal may provide a valuable probe of cluster optical depths, enabling the extraction of velocities from the kSZ sourced mean pairwise momenta. New CMB maps from three seasons of ACTPol observations with multi-frequency coverage overlap with nearly four times as many DR11 sources and promise to improve statistics and systematics for SZ measurements. With these and other upcoming data, the pairwise kSZ signal is poised to become a powerful new cosmological tool, able to probe large physical scales to inform neutrino physics and test models of modified gravity and dark energy.

  13. Covariant approximation averaging

    NASA Astrophysics Data System (ADS)

    Shintani, Eigo; Arthur, Rudy; Blum, Thomas; Izubuchi, Taku; Jung, Chulwoo; Lehner, Christoph

    2015-06-01

    We present a new class of statistical error reduction techniques for Monte Carlo simulations. Using covariant symmetries, we show that correlation functions can be constructed from inexpensive approximations without introducing any systematic bias in the final result. We introduce a new class of covariant approximation averaging techniques, known as all-mode averaging (AMA), in which the approximation takes account of contributions of all eigenmodes through the inverse of the Dirac operator computed from the conjugate gradient method with a relaxed stopping condition. In this paper we compare the performance and computational cost of our new method with traditional methods using correlation functions and masses of the pion, nucleon, and vector meson in Nf=2 +1 lattice QCD using domain-wall fermions. This comparison indicates that AMA significantly reduces statistical errors in Monte Carlo calculations over conventional methods for the same cost.

  14. Using Analysis of Covariance (ANCOVA) with Fallible Covariates

    ERIC Educational Resources Information Center

    Culpepper, Steven Andrew; Aguinis, Herman

    2011-01-01

    Analysis of covariance (ANCOVA) is used widely in psychological research implementing nonexperimental designs. However, when covariates are fallible (i.e., measured with error), which is the norm, researchers must choose from among 3 inadequate courses of action: (a) know that the assumption that covariates are perfectly reliable is violated but…

  15. Using Analysis of Covariance (ANCOVA) with Fallible Covariates

    ERIC Educational Resources Information Center

    Culpepper, Steven Andrew; Aguinis, Herman

    2011-01-01

    Analysis of covariance (ANCOVA) is used widely in psychological research implementing nonexperimental designs. However, when covariates are fallible (i.e., measured with error), which is the norm, researchers must choose from among 3 inadequate courses of action: (a) know that the assumption that covariates are perfectly reliable is violated but…

  16. Covariant deformed oscillator algebras

    NASA Technical Reports Server (NTRS)

    Quesne, Christiane

    1995-01-01

    The general form and associativity conditions of deformed oscillator algebras are reviewed. It is shown how the latter can be fulfilled in terms of a solution of the Yang-Baxter equation when this solution has three distinct eigenvalues and satisfies a Birman-Wenzl-Murakami condition. As an example, an SU(sub q)(n) x SU(sub q)(m)-covariant q-bosonic algebra is discussed in some detail.

  17. Graph theory for analyzing pair-wise data: application to geophysical model parameters estimated from interferometric synthetic aperture radar data at Okmok volcano, Alaska

    NASA Astrophysics Data System (ADS)

    Reinisch, Elena C.; Cardiff, Michael; Feigl, Kurt L.

    2017-01-01

    Graph theory is useful for analyzing time-dependent model parameters estimated from interferometric synthetic aperture radar (InSAR) data in the temporal domain. Plotting acquisition dates (epochs) as vertices and pair-wise interferometric combinations as edges defines an incidence graph. The edge-vertex incidence matrix and the normalized edge Laplacian matrix are factors in the covariance matrix for the pair-wise data. Using empirical measures of residual scatter in the pair-wise observations, we estimate the relative variance at each epoch by inverting the covariance of the pair-wise data. We evaluate the rank deficiency of the corresponding least-squares problem via the edge-vertex incidence matrix. We implement our method in a MATLAB software package called GraphTreeTA available on GitHub (https://github.com/feigl/gipht). We apply temporal adjustment to the data set described in Lu et al. (Geophys Res Solid Earth 110, 2005) at Okmok volcano, Alaska, which erupted most recently in 1997 and 2008. The data set contains 44 differential volumetric changes and uncertainties estimated from interferograms between 1997 and 2004. Estimates show that approximately half of the magma volume lost during the 1997 eruption was recovered by the summer of 2003. Between June 2002 and September 2003, the estimated rate of volumetric increase is (6.2 ± 0.6) × 10^6 m^3/year . Our preferred model provides a reasonable fit that is compatible with viscoelastic relaxation in the five years following the 1997 eruption. Although we demonstrate the approach using volumetric rates of change, our formulation in terms of incidence graphs applies to any quantity derived from pair-wise differences, such as range change, range gradient, or atmospheric delay.

  18. Attention Deficit Disorder (ADD). Digest #445.

    ERIC Educational Resources Information Center

    Scott, Mary E.

    The term "attention deficit disorder" (ADD) is defined, criteria used by the American Psychiatric Association in diagnosing ADD are listed, and possible causes noted. Remediation needs of children with ADD include attention skills, self-esteem, and social skills. Early diagnosis is important, and teachers and parents need to identify…

  19. The Bayesian Covariance Lasso

    PubMed Central

    Khondker, Zakaria S; Zhu, Hongtu; Chu, Haitao; Lin, Weili; Ibrahim, Joseph G.

    2012-01-01

    Estimation of sparse covariance matrices and their inverse subject to positive definiteness constraints has drawn a lot of attention in recent years. The abundance of high-dimensional data, where the sample size (n) is less than the dimension (d), requires shrinkage estimation methods since the maximum likelihood estimator is not positive definite in this case. Furthermore, when n is larger than d but not sufficiently larger, shrinkage estimation is more stable than maximum likelihood as it reduces the condition number of the precision matrix. Frequentist methods have utilized penalized likelihood methods, whereas Bayesian approaches rely on matrix decompositions or Wishart priors for shrinkage. In this paper we propose a new method, called the Bayesian Covariance Lasso (BCLASSO), for the shrinkage estimation of a precision (covariance) matrix. We consider a class of priors for the precision matrix that leads to the popular frequentist penalties as special cases, develop a Bayes estimator for the precision matrix, and propose an efficient sampling scheme that does not precalculate boundaries for positive definiteness. The proposed method is permutation invariant and performs shrinkage and estimation simultaneously for non-full rank data. Simulations show that the proposed BCLASSO performs similarly as frequentist methods for non-full rank data. PMID:24551316

  20. Temporal pairwise spike correlations fully capture single-neuron information

    PubMed Central

    Dettner, Amadeus; Münzberg, Sabrina; Tchumatchenko, Tatjana

    2016-01-01

    To crack the neural code and read out the information neural spikes convey, it is essential to understand how the information is coded and how much of it is available for decoding. To this end, it is indispensable to derive from first principles a minimal set of spike features containing the complete information content of a neuron. Here we present such a complete set of coding features. We show that temporal pairwise spike correlations fully determine the information conveyed by a single spiking neuron with finite temporal memory and stationary spike statistics. We reveal that interspike interval temporal correlations, which are often neglected, can significantly change the total information. Our findings provide a conceptual link between numerous disparate observations and recommend shifting the focus of future studies from addressing firing rates to addressing pairwise spike correlation functions as the primary determinants of neural information. PMID:27976717

  1. A piecewise lookup table for calculating nonbonded pairwise atomic interactions.

    PubMed

    Luo, Jinping; Liu, Lijun; Su, Peng; Duan, Pengbo; Lu, Daihui

    2015-11-01

    A critical challenge for molecular dynamics simulations of chemical or biological systems is to improve the calculation efficiency while retaining sufficient accuracy. The main bottleneck in improving the efficiency is the evaluation of nonbonded pairwise interactions. We propose a new piecewise lookup table method for rapid and accurate calculation of interatomic nonbonded pairwise interactions. The piecewise lookup table allows nonuniform assignment of table nodes according to the slope of the potential function and the pair interaction distribution. The proposed method assigns the nodes more reasonably than in general lookup tables, and thus improves the accuracy while requiring fewer nodes. To obtain the same level of accuracy, our piecewise lookup table accelerates the calculation via the efficient usage of cache memory. This new method is straightforward to implement and should be broadly applicable. Graphical Abstract Illustration of piecewise lookup table method.

  2. A Pairwise Preferential Interaction Model for Understanding Peptide Aggregation

    PubMed Central

    Kang, Myungshim

    2010-01-01

    A pairwise preferential interaction model (PPIM), based on Kirkwood–Buff integrals, is developed to quantify and characterize the interactions between some of the functional groups commonly observed in peptides. The existing experimental data are analyzed to determine the preferential interaction (PI) parameters for different amino acid and small peptide systems in aqueous solutions. The PIs between the different functional groups present in the peptides are then isolated and quantified by assuming simple pairwise additivity. The PPIM approach provides consistent estimates for the pair interactions between the same functional groups obtained from different solute molecules. Furthermore, these interactions appear to be chemically intuitive. It is argued that this type of approach can provide valuable information concerning specific functional group correlations which could give rise to peptide aggregation. PMID:20694045

  3. Simulations of the pairwise kinematic Sunyaev-Zel'dovich signal

    SciTech Connect

    Flender, Samuel; Bleem, Lindsey; Finkel, Hal; Habib, Salman; Heitmann, Katrin; Holder, Gilbert

    2016-05-26

    The pairwise kinematic Sunyaev–Zel'dovich (kSZ) signal from galaxy clusters is a probe of their line of sight momenta, and thus a potentially valuable source of cosmological information. In addition to the momenta, the amplitude of the measured signal depends on the properties of the intracluster gas and observational limitations such as errors in determining cluster centers and redshifts. In this work, we simulate the pairwise kSZ signal of clusters at $z\\lt 1$, using the output from a cosmological N-body simulation and including the properties of the intracluster gas via a model that can be varied in post-processing. We find that modifications to the gas profile due to star formation and feedback reduce the pairwise kSZ amplitude of clusters by $\\sim 50\\%$, relative to the naive "gas traces mass" assumption. We demonstrate that miscentering can reduce the overall amplitude of the pairwise kSZ signal by up to 10%, while redshift errors can lead to an almost complete suppression of the signal at small separations. We confirm that a high-significance detection is expected from the combination of data from current generation, high-resolution cosmic microwave background experiments, such as the South Pole Telescope, and cluster samples from optical photometric surveys, such as the Dark Energy Survey. As a result, we forecast that future experiments such as Advanced ACTPol in conjunction with data from the Dark Energy Spectroscopic Instrument will yield detection significances of at least $20\\sigma $, and up to $57\\sigma $ in an optimistic scenario.

  4. Simulations of the Pairwise Kinematic Sunyaev-Zel’dovich Signal

    NASA Astrophysics Data System (ADS)

    Flender, Samuel; Bleem, Lindsey; Finkel, Hal; Habib, Salman; Heitmann, Katrin; Holder, Gilbert

    2016-06-01

    The pairwise kinematic Sunyaev-Zel’dovich (kSZ) signal from galaxy clusters is a probe of their line of sight momenta, and thus a potentially valuable source of cosmological information. In addition to the momenta, the amplitude of the measured signal depends on the properties of the intracluster gas and observational limitations such as errors in determining cluster centers and redshifts. In this work, we simulate the pairwise kSZ signal of clusters at z\\lt 1, using the output from a cosmological N-body simulation and including the properties of the intracluster gas via a model that can be varied in post-processing. We find that modifications to the gas profile due to star formation and feedback reduce the pairwise kSZ amplitude of clusters by ˜ 50%, relative to the naive “gas traces mass” assumption. We demonstrate that miscentering can reduce the overall amplitude of the pairwise kSZ signal by up to 10%, while redshift errors can lead to an almost complete suppression of the signal at small separations. We confirm that a high-significance detection is expected from the combination of data from current generation, high-resolution cosmic microwave background experiments, such as the South Pole Telescope, and cluster samples from optical photometric surveys, such as the Dark Energy Survey. Furthermore, we forecast that future experiments such as Advanced ACTPol in conjunction with data from the Dark Energy Spectroscopic Instrument will yield detection significances of at least 20σ , and up to 57σ in an optimistic scenario. Our simulated maps are publicly available at http://www.hep.anl.gov/cosmology/ksz.html.

  5. Simulations of the pairwise kinematic Sunyaev-Zel'dovich signal

    DOE PAGES

    Flender, Samuel; Bleem, Lindsey; Finkel, Hal; ...

    2016-05-26

    The pairwise kinematic Sunyaev–Zel'dovich (kSZ) signal from galaxy clusters is a probe of their line of sight momenta, and thus a potentially valuable source of cosmological information. In addition to the momenta, the amplitude of the measured signal depends on the properties of the intracluster gas and observational limitations such as errors in determining cluster centers and redshifts. In this work, we simulate the pairwise kSZ signal of clusters atmore » $$z\\lt 1$$, using the output from a cosmological N-body simulation and including the properties of the intracluster gas via a model that can be varied in post-processing. We find that modifications to the gas profile due to star formation and feedback reduce the pairwise kSZ amplitude of clusters by $$\\sim 50\\%$$, relative to the naive "gas traces mass" assumption. We demonstrate that miscentering can reduce the overall amplitude of the pairwise kSZ signal by up to 10%, while redshift errors can lead to an almost complete suppression of the signal at small separations. We confirm that a high-significance detection is expected from the combination of data from current generation, high-resolution cosmic microwave background experiments, such as the South Pole Telescope, and cluster samples from optical photometric surveys, such as the Dark Energy Survey. As a result, we forecast that future experiments such as Advanced ACTPol in conjunction with data from the Dark Energy Spectroscopic Instrument will yield detection significances of at least $$20\\sigma $$, and up to $$57\\sigma $$ in an optimistic scenario.« less

  6. Simulations of the pairwise kinematic Sunyaev-Zel'dovich signal

    SciTech Connect

    Flender, Samuel; Bleem, Lindsey; Finkel, Hal; Habib, Salman; Heitmann, Katrin; Holder, Gilbert

    2016-05-26

    The pairwise kinematic Sunyaev–Zel'dovich (kSZ) signal from galaxy clusters is a probe of their line of sight momenta, and thus a potentially valuable source of cosmological information. In addition to the momenta, the amplitude of the measured signal depends on the properties of the intracluster gas and observational limitations such as errors in determining cluster centers and redshifts. In this work, we simulate the pairwise kSZ signal of clusters at $z\\lt 1$, using the output from a cosmological N-body simulation and including the properties of the intracluster gas via a model that can be varied in post-processing. We find that modifications to the gas profile due to star formation and feedback reduce the pairwise kSZ amplitude of clusters by $\\sim 50\\%$, relative to the naive "gas traces mass" assumption. We demonstrate that miscentering can reduce the overall amplitude of the pairwise kSZ signal by up to 10%, while redshift errors can lead to an almost complete suppression of the signal at small separations. We confirm that a high-significance detection is expected from the combination of data from current generation, high-resolution cosmic microwave background experiments, such as the South Pole Telescope, and cluster samples from optical photometric surveys, such as the Dark Energy Survey. As a result, we forecast that future experiments such as Advanced ACTPol in conjunction with data from the Dark Energy Spectroscopic Instrument will yield detection significances of at least $20\\sigma $, and up to $57\\sigma $ in an optimistic scenario.

  7. Inadequacy of internal covariance estimation for super-sample covariance

    NASA Astrophysics Data System (ADS)

    Lacasa, Fabien; Kunz, Martin

    2017-08-01

    We give an analytical interpretation of how subsample-based internal covariance estimators lead to biased estimates of the covariance, due to underestimating the super-sample covariance (SSC). This includes the jackknife and bootstrap methods as estimators for the full survey area, and subsampling as an estimator of the covariance of subsamples. The limitations of the jackknife covariance have been previously presented in the literature because it is effectively a rescaling of the covariance of the subsample area. However we point out that subsampling is also biased, but for a different reason: the subsamples are not independent, and the corresponding lack of power results in SSC underprediction. We develop the formalism in the case of cluster counts that allows the bias of each covariance estimator to be exactly predicted. We find significant effects for a small-scale area or when a low number of subsamples is used, with auto-redshift biases ranging from 0.4% to 15% for subsampling and from 5% to 75% for jackknife covariance estimates. The cross-redshift covariance is even more affected; biases range from 8% to 25% for subsampling and from 50% to 90% for jackknife. Owing to the redshift evolution of the probe, the covariances cannot be debiased by a simple rescaling factor, and an exact debiasing has the same requirements as the full SSC prediction. These results thus disfavour the use of internal covariance estimators on data itself or a single simulation, leaving analytical prediction and simulations suites as possible SSC predictors.

  8. Pairwise KLT-Based Compression for Multispectral Images

    NASA Astrophysics Data System (ADS)

    Nian, Yongjian; Liu, Yu; Ye, Zhen

    2016-12-01

    This paper presents a pairwise KLT-based compression algorithm for multispectral images. Although the KLT has been widely employed for spectral decorrelation, its complexity is high if it is performed on the global multispectral images. To solve this problem, this paper presented a pairwise KLT for spectral decorrelation, where KLT is only performed on two bands every time. First, KLT is performed on the first two adjacent bands and two principle components are obtained. Secondly, one remainning band and the principal component (PC) with the larger eigenvalue is selected to perform a KLT on this new couple. This procedure is repeated until the last band is reached. Finally, the optimal truncation technique of post-compression rate-distortion optimization is employed for the rate allocation of all the PCs, followed by embedded block coding with optimized truncation to generate the final bit-stream. Experimental results show that the proposed algorithm outperforms the algorithm based on global KLT. Moreover, the pairwise KLT structure can significantly reduce the complexity compared with a global KLT.

  9. A fast pairwise evaluation of molecular surface area.

    PubMed

    Vasilyev, Vladislav; Purisima, Enrico O

    2002-05-01

    A fast and general analytical approach was developed for the calculation of the approximate van der Waals and solvent-accessible surface areas. The method is based on three basic ideas: the use of the Lorentz transformation formula, a rigid-geometry approximation, and a single fitting parameter that can be refitted on the fly during a simulation. The Lorentz transformation equation is used for the summation of the areas of an atom buried by its neighboring contacting atoms, and implies that a sum of the buried pairwise areas cannot be larger than the surface area of the isolated spherical atom itself. In a rigid-geometry approximation we numerically calculate and keep constant the surface of each atom buried by the atoms involved in 1-2 and 1-3 interactions. Only the contributions from the nonbonded atoms (1-4 and higher interactions) are considered in terms of the pairwise approximation. The accuracy and speed of the method is competitive with other pairwise algorithms. A major strength of the method is the ease of parametrization.

  10. Optimal covariant quantum networks

    NASA Astrophysics Data System (ADS)

    Chiribella, Giulio; D'Ariano, Giacomo Mauro; Perinotti, Paolo

    2009-04-01

    A sequential network of quantum operations is efficiently described by its quantum comb [1], a non-negative operator with suitable normalization constraints. Here we analyze the case of networks enjoying symmetry with respect to the action of a given group of physical transformations, introducing the notion of covariant combs and testers, and proving the basic structure theorems for these objects. As an application, we discuss the optimal alignment of reference frames (without pre-established common references) with multiple rounds of quantum communication, showing that i) allowing an arbitrary amount of classical communication does not improve the alignment, and ii) a single round of quantum communication is sufficient.

  11. Covariant magnetic connection hypersurfaces

    NASA Astrophysics Data System (ADS)

    Pegoraro, F.

    2016-04-01

    > In the single fluid, non-relativistic, ideal magnetohydrodynamic (MHD) plasma description, magnetic field lines play a fundamental role by defining dynamically preserved `magnetic connections' between plasma elements. Here we show how the concept of magnetic connection needs to be generalized in the case of a relativistic MHD description where we require covariance under arbitrary Lorentz transformations. This is performed by defining 2-D magnetic connection hypersurfaces in the 4-D Minkowski space. This generalization accounts for the loss of simultaneity between spatially separated events in different frames and is expected to provide a powerful insight into the 4-D geometry of electromagnetic fields when .

  12. Weak signal detection in hyperspectral imagery using sparse matrix transform (SMT) covariance estimation

    SciTech Connect

    Theiler, James P; Cao, Guangzhi; Bouman, Charles A

    2009-01-01

    Many detection algorithms in hyperspectral image analysis, from well-characterized gaseous and solid targets to deliberately uncharacterized anomalies and anomlous changes, depend on accurately estimating the covariance matrix of the background. In practice, the background covariance is estimated from samples in the image, and imprecision in this estimate can lead to a loss of detection power. In this paper, we describe the sparse matrix transform (SMT) and investigate its utility for estimating the covariance matrix from a limited number of samples. The SMT is formed by a product of pairwise coordinate (Givens) rotations, which can be efficiently estimated using greedy optimization. Experiments on hyperspectral data show that the estimate accurately reproduces even small eigenvalues and eigenvectors. In particular, we find that using the SMT to estimate the covariance matrix used in the adaptive matched filter leads to consistently higher signal-to-noise ratios.

  13. Revision of Begomovirus taxonomy based on pairwise sequence comparisons.

    PubMed

    Brown, Judith K; Zerbini, F Murilo; Navas-Castillo, Jesús; Moriones, Enrique; Ramos-Sobrinho, Roberto; Silva, José C F; Fiallo-Olivé, Elvira; Briddon, Rob W; Hernández-Zepeda, Cecilia; Idris, Ali; Malathi, V G; Martin, Darren P; Rivera-Bustamante, Rafael; Ueda, Shigenori; Varsani, Arvind

    2015-06-01

    Viruses of the genus Begomovirus (family Geminiviridae) are emergent pathogens of crops throughout the tropical and subtropical regions of the world. By virtue of having a small DNA genome that is easily cloned, and due to the recent innovations in cloning and low-cost sequencing, there has been a dramatic increase in the number of available begomovirus genome sequences. Even so, most of the available sequences have been obtained from cultivated plants and are likely a small and phylogenetically unrepresentative sample of begomovirus diversity, a factor constraining taxonomic decisions such as the establishment of operationally useful species demarcation criteria. In addition, problems in assigning new viruses to established species have highlighted shortcomings in the previously recommended mechanism of species demarcation. Based on the analysis of 3,123 full-length begomovirus genome (or DNA-A component) sequences available in public databases as of December 2012, a set of revised guidelines for the classification and nomenclature of begomoviruses are proposed. The guidelines primarily consider a) genus-level biological characteristics and b) results obtained using a standardized classification tool, Sequence Demarcation Tool, which performs pairwise sequence alignments and identity calculations. These guidelines are consistent with the recently published recommendations for the genera Mastrevirus and Curtovirus of the family Geminiviridae. Genome-wide pairwise identities of 91 % and 94 % are proposed as the demarcation threshold for begomoviruses belonging to different species and strains, respectively. Procedures and guidelines are outlined for resolving conflicts that may arise when assigning species and strains to categories wherever the pairwise identity falls on or very near the demarcation threshold value.

  14. CSA: comprehensive comparison of pairwise protein structure alignments.

    PubMed

    Wohlers, Inken; Malod-Dognin, Noël; Andonov, Rumen; Klau, Gunnar W

    2012-07-01

    CSA is a web server for the computation, evaluation and comprehensive comparison of pairwise protein structure alignments. Its exact alignment engine computes either optimal, top-scoring alignments or heuristic alignments with quality guarantee for the inter-residue distance-based scorings of contact map overlap, PAUL, DALI and MATRAS. These and additional, uploaded alignments are compared using a number of quality measures and intuitive visualizations. CSA brings new insight into the structural relationship of the protein pairs under investigation and is a valuable tool for studying structural similarities. It is available at http://csa.project.cwi.nl.

  15. CSA: comprehensive comparison of pairwise protein structure alignments

    PubMed Central

    Wohlers, Inken; Malod-Dognin, Noël; Andonov, Rumen; Klau, Gunnar W.

    2012-01-01

    CSA is a web server for the computation, evaluation and comprehensive comparison of pairwise protein structure alignments. Its exact alignment engine computes either optimal, top-scoring alignments or heuristic alignments with quality guarantee for the inter-residue distance-based scorings of contact map overlap, PAUL, DALI and MATRAS. These and additional, uploaded alignments are compared using a number of quality measures and intuitive visualizations. CSA brings new insight into the structural relationship of the protein pairs under investigation and is a valuable tool for studying structural similarities. It is available at http://csa.project.cwi.nl. PMID:22553365

  16. Stardust Navigation Covariance Analysis

    NASA Technical Reports Server (NTRS)

    Menon, Premkumar R.

    2000-01-01

    The Stardust spacecraft was launched on February 7, 1999 aboard a Boeing Delta-II rocket. Mission participants include the National Aeronautics and Space Administration (NASA), the Jet Propulsion Laboratory (JPL), Lockheed Martin Astronautics (LMA) and the University of Washington. The primary objective of the mission is to collect in-situ samples of the coma of comet Wild-2 and return those samples to the Earth for analysis. Mission design and operational navigation for Stardust is performed by the Jet Propulsion Laboratory (JPL). This paper will describe the extensive JPL effort in support of the Stardust pre-launch analysis of the orbit determination component of the mission covariance study. A description of the mission and it's trajectory will be provided first, followed by a discussion of the covariance procedure and models. Predicted accuracy's will be examined as they relate to navigation delivery requirements for specific critical events during the mission. Stardust was launched into a heliocentric trajectory in early 1999. It will perform an Earth Gravity Assist (EGA) on January 15, 2001 to acquire an orbit for the eventual rendezvous with comet Wild-2. The spacecraft will fly through the coma (atmosphere) on the dayside of Wild-2 on January 2, 2004. At that time samples will be obtained using an aerogel collector. After the comet encounter Stardust will return to Earth when the Sample Return Capsule (SRC) will separate and land at the Utah Test Site (UTTR) on January 15, 2006. The spacecraft will however be deflected off into a heliocentric orbit. The mission is divided into three phases for the covariance analysis. They are 1) Launch to EGA, 2) EGA to Wild-2 encounter and 3) Wild-2 encounter to Earth reentry. Orbit determination assumptions for each phase are provided. These include estimated and consider parameters and their associated a-priori uncertainties. Major perturbations to the trajectory include 19 deterministic and statistical maneuvers

  17. Deriving covariant holographic entanglement

    NASA Astrophysics Data System (ADS)

    Dong, Xi; Lewkowycz, Aitor; Rangamani, Mukund

    2016-11-01

    We provide a gravitational argument in favour of the covariant holographic entanglement entropy proposal. In general time-dependent states, the proposal asserts that the entanglement entropy of a region in the boundary field theory is given by a quarter of the area of a bulk extremal surface in Planck units. The main element of our discussion is an implementation of an appropriate Schwinger-Keldysh contour to obtain the reduced density matrix (and its powers) of a given region, as is relevant for the replica construction. We map this contour into the bulk gravitational theory, and argue that the saddle point solutions of these replica geometries lead to a consistent prescription for computing the field theory Rényi entropies. In the limiting case where the replica index is taken to unity, a local analysis suffices to show that these saddles lead to the extremal surfaces of interest. We also comment on various properties of holographic entanglement that follow from this construction.

  18. Stardust Navigation Covariance Analysis

    NASA Technical Reports Server (NTRS)

    Menon, Premkumar R.

    2000-01-01

    The Stardust spacecraft was launched on February 7, 1999 aboard a Boeing Delta-II rocket. Mission participants include the National Aeronautics and Space Administration (NASA), the Jet Propulsion Laboratory (JPL), Lockheed Martin Astronautics (LMA) and the University of Washington. The primary objective of the mission is to collect in-situ samples of the coma of comet Wild-2 and return those samples to the Earth for analysis. Mission design and operational navigation for Stardust is performed by the Jet Propulsion Laboratory (JPL). This paper will describe the extensive JPL effort in support of the Stardust pre-launch analysis of the orbit determination component of the mission covariance study. A description of the mission and it's trajectory will be provided first, followed by a discussion of the covariance procedure and models. Predicted accuracy's will be examined as they relate to navigation delivery requirements for specific critical events during the mission. Stardust was launched into a heliocentric trajectory in early 1999. It will perform an Earth Gravity Assist (EGA) on January 15, 2001 to acquire an orbit for the eventual rendezvous with comet Wild-2. The spacecraft will fly through the coma (atmosphere) on the dayside of Wild-2 on January 2, 2004. At that time samples will be obtained using an aerogel collector. After the comet encounter Stardust will return to Earth when the Sample Return Capsule (SRC) will separate and land at the Utah Test Site (UTTR) on January 15, 2006. The spacecraft will however be deflected off into a heliocentric orbit. The mission is divided into three phases for the covariance analysis. They are 1) Launch to EGA, 2) EGA to Wild-2 encounter and 3) Wild-2 encounter to Earth reentry. Orbit determination assumptions for each phase are provided. These include estimated and consider parameters and their associated a-priori uncertainties. Major perturbations to the trajectory include 19 deterministic and statistical maneuvers

  19. Covariant genetic dynamics.

    PubMed

    Chryssomalakos, Chryssomalis; Stephens, Christopher R

    2007-01-01

    We present a covariant form for the dynamics of a canonical GA of arbitrary cardinality, showing how each genetic operator can be uniquely represented by a mathematical object - a tensor - that transforms simply under a general linear coordinate transformation. For mutation and recombination these tensors can be written as tensor products of the analogous tensors for one-bit strings thus giving a greatly simplified formulation of the dynamics. We analyze the three most well known coordinate systems -- string, Walsh and Building Block - discussing their relative advantages and disadvantages with respect to the different operators, showing how one may transform from one to the other, and that the associated coordinate transformation matrices can be written as a tensor product of the corresponding one-bit matrices. We also show that in the Building Block basis the dynamical equations for all Building Blocks can be generated from the equation for the most fine-grained block (string) by a certain projection ("zapping").

  20. Covariantly quantum Galileon

    NASA Astrophysics Data System (ADS)

    Saltas, Ippocratis D.; Vitagliano, Vincenzo

    2017-05-01

    We derive the 1-loop effective action of the cubic Galileon coupled to quantum-gravitational fluctuations in a background and gauge-independent manner, employing the covariant framework of DeWitt and Vilkovisky. Although the bare action respects shift symmetry, the coupling to gravity induces an effective mass to the scalar, of the order of the cosmological constant, as a direct result of the nonflat field-space metric, the latter ensuring the field-reparametrization invariance of the formalism. Within a gauge-invariant regularization scheme, we discover novel, gravitationally induced non-Galileon higher-derivative interactions in the effective action. These terms, previously unnoticed within standard, noncovariant frameworks, are not Planck suppressed. Unless tuned to be subdominant, their presence could have important implications for the classical and quantum phenomenology of the theory.

  1. Survival ensembles by the sum of pairwise differences with application to lung cancer microarray studies.

    PubMed

    Johnson, Brent A; Long, Qi

    2011-06-01

    Lung cancer is among the most common cancers in the United States, in terms of incidence and mortality. In 2009, it is estimated that more than 150,000 deaths will result from lung cancer alone. Genetic information is an extremely valuable data source in characterizing the personal nature of cancer. Over the past several years, investigators have conducted numerous association studies where intensive genetic data is collected on relatively few patients compared to the numbers of gene predictors, with one scientific goal being to identify genetic features associated with cancer recurrence or survival. In this note, we propose high-dimensional survival analysis through a new application of boosting, a powerful tool in machine learning. Our approach is based on an accelerated lifetime model and minimizing the sum of pairwise differences in residuals. We apply our method to a recent microarray study of lung adenocarcinoma and find that our ensemble is composed of 19 genes while a proportional hazards (PH) ensemble is composed of nine genes, a proper subset of the 19-gene panel. In one of our simulation scenarios, we demonstrate that PH boosting in a misspecified model tends to underfit and ignore moderately-sized covariate effects, on average. Diagnostic analyses suggest that the PH assumption is not satisfied in the microarray data and may explain, in part, the discrepancy in the sets of active coefficients. Our simulation studies and comparative data analyses demonstrate how statistical learning by PH models alone is insufficient.

  2. General Galilei Covariant Gaussian Maps

    NASA Astrophysics Data System (ADS)

    Gasbarri, Giulio; Toroš, Marko; Bassi, Angelo

    2017-09-01

    We characterize general non-Markovian Gaussian maps which are covariant under Galilean transformations. In particular, we consider translational and Galilean covariant maps and show that they reduce to the known Holevo result in the Markovian limit. We apply the results to discuss measures of macroscopicity based on classicalization maps, specifically addressing dissipation, Galilean covariance and non-Markovianity. We further suggest a possible generalization of the macroscopicity measure defined by Nimmrichter and Hornberger [Phys. Rev. Lett. 110, 16 (2013)].

  3. Covariance Manipulation for Conjunction Assessment

    NASA Technical Reports Server (NTRS)

    Hejduk, M. D.

    2016-01-01

    Use of probability of collision (Pc) has brought sophistication to CA. Made possible by JSpOC precision catalogue because provides covariance. Has essentially replaced miss distance as basic CA parameter. Embrace of Pc has elevated methods to 'manipulate' covariance to enable/improve CA calculations. Two such methods to be examined here; compensation for absent or unreliable covariances through 'Maximum Pc' calculation constructs, projection (not propagation) of epoch covariances forward in time to try to enable better risk assessments. Two questions to be answered about each; situations to which such approaches are properly applicable, amount of utility that such methods offer.

  4. ADD Teacher Inservice Project. Final Grant Report.

    ERIC Educational Resources Information Center

    Edwards, Mark C.; Schulz, Eldon G.

    The report describes activities and achievements of the Attention Deficit Disorder (ADD) Teacher Inservice Project. The inservice program was developed using a formal process to identify the critical issues related to ADD awareness, assessment, and intervention. Program content was designed to address critical issues identified in the research…

  5. Inviting Calm Within: ADD, Neurology, and Mindfulness

    ERIC Educational Resources Information Center

    Riner, Phillip S.; Tanase, Madalina

    2014-01-01

    The fourth edition of the "Diagnostic and Statistical Manual of Mental Disorders" ("DSM IV") describes ADD as behaviorally observed impairments in attention, impulsivity, and hyperactivity. Officially known as AD/HD, we use ADD here because we are dealing primarily with attention, organizational, and impulsivity issues. A more…

  6. ADD: Acronym for Any Dysfunction or Difficulty.

    ERIC Educational Resources Information Center

    Goodman, Gay; Poillion, Mary Jo

    1992-01-01

    Review of 48 articles and books on attention deficit disorder (ADD) found a total of 69 characteristics and 38 causes cited, evidencing no clearcut pattern for identifying the condition and little agreement for what causes ADD. The label appears to have limited value for communication, planning, decision making, or research efforts. (Author/DB)

  7. Inviting Calm Within: ADD, Neurology, and Mindfulness

    ERIC Educational Resources Information Center

    Riner, Phillip S.; Tanase, Madalina

    2014-01-01

    The fourth edition of the "Diagnostic and Statistical Manual of Mental Disorders" ("DSM IV") describes ADD as behaviorally observed impairments in attention, impulsivity, and hyperactivity. Officially known as AD/HD, we use ADD here because we are dealing primarily with attention, organizational, and impulsivity issues. A more…

  8. Pairwise velocities in the "Running FLRW" cosmological model

    NASA Astrophysics Data System (ADS)

    Bibiano, Antonio; Croton, Darren J.

    2017-01-01

    We present an analysis of the pairwise velocity statistics from a suite of cosmological N-body simulations describing the "Running Friedmann-Lemaître-Robertson-Walker" (R-FLRW) cosmological model. This model is based on quantum field theory in a curved space-time and extends ΛCDM with a time-evolving vacuum energy density, ρ _Λ. To enforce local conservation of matter a time-evolving gravitational coupling is also included. Our results constitute the first study of velocities in the R-FLRW cosmology, and we also compare with other dark energy simulations suites, repeating the same analysis. We find a strong degeneracy between the pairwise velocity and σ8 at z = 0 for almost all scenarios considered, which remains even when we look back to epochs as early as z = 2. We also investigate various Coupled Dark Energy models, some of which show minimal degeneracy, and reveal interesting deviations from ΛCDM which could be readily exploited by future cosmological observations to test and further constrain our understanding of dark energy.

  9. Pairwise velocities in the "Running FLRW" cosmological model

    NASA Astrophysics Data System (ADS)

    Bibiano, Antonio; Croton, Darren J.

    2017-05-01

    We present an analysis of the pairwise velocity statistics from a suite of cosmological N-body simulations describing the 'Running Friedmann-Lemaître-Robertson-Walker' (R-FLRW) cosmological model. This model is based on quantum field theory in a curved space-time and extends Λ cold dark matter (CDM) with a time-evolving vacuum energy density, ρ _Λ. To enforce local conservation of matter, a time-evolving gravitational coupling is also included. Our results constitute the first study of velocities in the R-FLRW cosmology, and we also compare with other dark energy simulations suites, repeating the same analysis. We find a strong degeneracy between the pairwise velocity and σ8 at z = 0 for almost all scenarios considered, which remains even when we look back to epochs as early as z = 2. We also investigate various coupled dark energy models, some of which show minimal degeneracy, and reveal interesting deviations from ΛCDM that could be readily exploited by future cosmological observations to test and further constrain our understanding of dark energy.

  10. Measuring pair-wise molecular interactions in a complex mixture

    NASA Astrophysics Data System (ADS)

    Chakraborty, Krishnendu; Varma, Manoj M.; Venkatapathi, Murugesan

    2016-03-01

    Complex biological samples such as serum contain thousands of proteins and other molecules spanning up to 13 orders of magnitude in concentration. Present measurement techniques do not permit the analysis of all pair-wise interactions between the components of such a complex mixture to a given target molecule. In this work we explore the use of nanoparticle tags which encode the identity of the molecule to obtain the statistical distribution of pair-wise interactions using their Localized Surface Plasmon Resonance (LSPR) signals. The nanoparticle tags are chosen such that the binding between two molecules conjugated to the respective nanoparticle tags can be recognized by the coupling of their LSPR signals. This numerical simulation is done by DDA to investigate this approach using a reduced system consisting of three nanoparticles (a gold ellipsoid with aspect ratio 2.5 and short axis 16 nm, and two silver ellipsoids with aspect ratios 3 and 2 and short axes 8 nm and 10 nm respectively) and the set of all possible dimers formed between them. Incident light was circularly polarized and all possible particle and dimer orientations were considered. We observed that minimum peak separation between two spectra is 5 nm while maximum is 184nm.

  11. N -term pairwise-correlation inequalities, steering, and joint measurability

    NASA Astrophysics Data System (ADS)

    Karthik, H. S.; Devi, A. R. Usha; Tej, J. Prabhu; Rajagopal, A. K.; Sudha, Narayanan, A.

    2017-05-01

    Chained inequalities involving pairwise correlations of qubit observables in the equatorial plane are constructed based on the positivity of a sequence of moment matrices. When a jointly measurable set of positive-operator-valued measures (POVMs) is employed in the first measurement of every pair of sequential measurements, the chained pairwise correlations do not violate the classical bound imposed by the moment matrix positivity. We find that incompatibility of the set of POVMs employed in first measurements is only necessary, but not sufficient, in general, for the violation of the inequality. On the other hand, there exists a one-to-one equivalence between the degree of incompatibility (which quantifies the joint measurability) of the equatorial qubit POVMs and the optimal violation of a nonlocal steering inequality, proposed by Jones and Wiseman [S. J. Jones and H. M. Wiseman, Phys. Rev. A 84, 012110 (2011), 10.1103/PhysRevA.84.012110]. To this end, we construct a local analog of this steering inequality in a single-qubit system and show that its violation is a mere reflection of measurement incompatibility of equatorial qubit POVMs, employed in first measurements in the sequential unsharp-sharp scheme.

  12. Covariant electromagnetic field lines

    NASA Astrophysics Data System (ADS)

    Hadad, Y.; Cohen, E.; Kaminer, I.; Elitzur, A. C.

    2017-08-01

    Faraday introduced electric field lines as a powerful tool for understanding the electric force, and these field lines are still used today in classrooms and textbooks teaching the basics of electromagnetism within the electrostatic limit. However, despite attempts at generalizing this concept beyond the electrostatic limit, such a fully relativistic field line theory still appears to be missing. In this work, we propose such a theory and define covariant electromagnetic field lines that naturally extend electric field lines to relativistic systems and general electromagnetic fields. We derive a closed-form formula for the field lines curvature in the vicinity of a charge, and show that it is related to the world line of the charge. This demonstrates how the kinematics of a charge can be derived from the geometry of the electromagnetic field lines. Such a theory may also provide new tools in modeling and analyzing electromagnetic phenomena, and may entail new insights regarding long-standing problems such as radiation-reaction and self-force. In particular, the electromagnetic field lines curvature has the attractive property of being non-singular everywhere, thus eliminating all self-field singularities without using renormalization techniques.

  13. Congruence of Behavioral Symptomatology in Children with ADD/H, ADD/WO, and Learning Disabilities.

    ERIC Educational Resources Information Center

    Stanford, Lisa D.; Hynd, George W.

    1994-01-01

    This study compared parent and teacher behavioral ratings for 77 children (ages 5-16) diagnosed as having attention deficit disorder with hyperactivity (ADD/H), attention deficit disorder without hyperactivity (ADD/WO), or learning disabilities (LD). ADD/WO and LD children were rated similarly on symptoms of withdrawal and impulsivity but differed…

  14. Covariant harmonic oscillators: 1973 revisited

    NASA Technical Reports Server (NTRS)

    Noz, M. E.

    1993-01-01

    Using the relativistic harmonic oscillator, a physical basis is given to the phenomenological wave function of Yukawa which is covariant and normalizable. It is shown that this wave function can be interpreted in terms of the unitary irreducible representations of the Poincare group. The transformation properties of these covariant wave functions are also demonstrated.

  15. Covariance hypotheses for LANDSAT data

    NASA Technical Reports Server (NTRS)

    Decell, H. P.; Peters, C.

    1983-01-01

    Two covariance hypotheses are considered for LANDSAT data acquired by sampling fields, one an autoregressive covariance structure and the other the hypothesis of exchangeability. A minimum entropy approximation of the first structure by the second is derived and shown to have desirable properties for incorporation into a mixture density estimation procedure. Results of a rough test of the exchangeability hypothesis are presented.

  16. A Statistically Justified Pairwise ML Method for Incomplete Nonnormal Data: A Comparison With Direct ML and Pairwise ADF

    ERIC Educational Resources Information Center

    Savalei, Victoria; Bentler, Peter M.

    2005-01-01

    This article proposes a new approach to the statistical analysis of pairwisepresent covariance structure data. The estimator is based on maximizing the complete data likelihood function, and the associated test statistic and standard errors are corrected for misspecification using Satorra-Bentler corrections. A Monte Carlo study was conducted to…

  17. A Statistically Justified Pairwise ML Method for Incomplete Nonnormal Data: A Comparison With Direct ML and Pairwise ADF

    ERIC Educational Resources Information Center

    Savalei, Victoria; Bentler, Peter M.

    2005-01-01

    This article proposes a new approach to the statistical analysis of pairwisepresent covariance structure data. The estimator is based on maximizing the complete data likelihood function, and the associated test statistic and standard errors are corrected for misspecification using Satorra-Bentler corrections. A Monte Carlo study was conducted to…

  18. Assessing the consistency assumption by exploring treatment by covariate interactions in mixed treatment comparison meta-analysis: individual patient-level covariates versus aggregate trial-level covariates.

    PubMed

    Donegan, Sarah; Williamson, Paula; D'Alessandro, Umberto; Tudur Smith, Catrin

    2012-12-20

    Mixed treatment comparison (MTC) meta-analysis allows several treatments to be compared in a single analysis while utilising direct and indirect evidence. Treatment by covariate interactions can be included in MTC models to explore how the covariate modifies the treatment effects. If interactions exist, the assumptions underlying MTCs may be invalidated. For conventional pair-wise meta-analysis, important benefits regarding the investigation of such interactions, gained from using individual patient data (IPD) rather than aggregate data (AD), have been described. We aim to compare IPD MTC models including patient-level covariates with AD MTC models including study-level covariates. IPD and AD random-effects MTC models for dichotomous outcomes are specified. Three assumptions are made regarding the interactions (i.e. independent, exchangeable and common interactions). The models are applied to a dataset to compare four drugs for treating malaria (i.e. amodiaquine-artesunate, dihydroartemisinin-piperaquine (DHAPQ), artemether-lumefantrine and chlorproguanil-dapsone plus artesunate) using the outcome unadjusted treatment success at day 28. The treatment effects and regression coefficients for interactions from the IPD models were more precise than those from AD models. Using IPD, assuming independent or exchangeable interactions, the regression coefficient for chlorproguanil-dapsone plus artesunate versus DHAPQ was statistically significant and assuming common interactions, the common coefficient was significant; whereas using AD, no coefficients were significant. Using IPD, DHAPQ was the best drug; whereas using AD, the best drug varied. Using AD models, there was no evidence that the consistency assumption was invalid; whereas, the assumption was questionable based on the IPD models. The AD analyses were misleading.

  19. On the early epidemic dynamics for pairwise models.

    PubMed

    Llensa, Carlos; Juher, David; Saldaña, Joan

    2014-07-07

    The relationship between the basic reproduction number R0 and the exponential growth rate, specific to pair approximation models, is derived for the SIS, SIR and SEIR deterministic models without demography. These models are extended by including a random rewiring of susceptible individuals from infectious (and exposed) neighbours. The derived relationship between the exponential growth rate and R0 appears as formally consistent with those derived from homogeneous mixing models, enabling us to measure the transmission potential using the early growth rate of cases. On the other hand, the algebraic expression of R0 for the SEIR pairwise model shows that its value is affected by the average duration of the latent period, in contrast to what happens for the homogeneous mixing SEIR model. Numerical simulations on complex contact networks are performed to check the analytical assumptions and predictions.

  20. Prediction of Spatiotemporal Patterns of Neural Activity from Pairwise Correlations

    SciTech Connect

    Marre, O.; El Boustani, S.; Fregnac, Y.; Destexhe, A.

    2009-04-03

    We designed a model-based analysis to predict the occurrence of population patterns in distributed spiking activity. Using a maximum entropy principle with a Markovian assumption, we obtain a model that accounts for both spatial and temporal pairwise correlations among neurons. This model is tested on data generated with a Glauber spin-glass system and is shown to correctly predict the occurrence probabilities of spatiotemporal patterns significantly better than Ising models only based on spatial correlations. This increase of predictability was also observed on experimental data recorded in parietal cortex during slow-wave sleep. This approach can also be used to generate surrogates that reproduce the spatial and temporal correlations of a given data set.

  1. Hash subgraph pairwise kernel for protein-protein interaction extraction.

    PubMed

    Zhang, Yijia; Lin, Hongfei; Yang, Zhihao; Wang, Jian; Li, Yanpeng

    2012-01-01

    Extracting protein-protein interaction (PPI) from biomedical literature is an important task in biomedical text mining (BioTM). In this paper, we propose a hash subgraph pairwise (HSP) kernel-based approach for this task. The key to the novel kernel is to use the hierarchical hash labels to express the structural information of subgraphs in a linear time. We apply the graph kernel to compute dependency graphs representing the sentence structure for protein-protein interaction extraction task, which can efficiently make use of full graph structural information, and particularly capture the contiguous topological and label information ignored before. We evaluate the proposed approach on five publicly available PPI corpora. The experimental results show that our approach significantly outperforms all-path kernel approach on all five corpora and achieves state-of-the-art performance.

  2. Calibration of Smartphone-Based Weather Measurements Using Pairwise Gossip.

    PubMed

    Zamora, Jane Louie Fresco; Kashihara, Shigeru; Yamaguchi, Suguru

    2015-01-01

    Accurate and reliable daily global weather reports are necessary for weather forecasting and climate analysis. However, the availability of these reports continues to decline due to the lack of economic support and policies in maintaining ground weather measurement systems from where these reports are obtained. Thus, to mitigate data scarcity, it is required to utilize weather information from existing sensors and built-in smartphone sensors. However, as smartphone usage often varies according to human activity, it is difficult to obtain accurate measurement data. In this paper, we present a heuristic-based pairwise gossip algorithm that will calibrate smartphone-based pressure sensors with respect to fixed weather stations as our referential ground truth. Based on actual measurements, we have verified that smartphone-based readings are unstable when observed during movement. Using our calibration algorithm on actual smartphone-based pressure readings, the updated values were significantly closer to the ground truth values.

  3. Calibration of Smartphone-Based Weather Measurements Using Pairwise Gossip

    PubMed Central

    Zamora, Jane Louie Fresco; Kashihara, Shigeru; Yamaguchi, Suguru

    2015-01-01

    Accurate and reliable daily global weather reports are necessary for weather forecasting and climate analysis. However, the availability of these reports continues to decline due to the lack of economic support and policies in maintaining ground weather measurement systems from where these reports are obtained. Thus, to mitigate data scarcity, it is required to utilize weather information from existing sensors and built-in smartphone sensors. However, as smartphone usage often varies according to human activity, it is difficult to obtain accurate measurement data. In this paper, we present a heuristic-based pairwise gossip algorithm that will calibrate smartphone-based pressure sensors with respect to fixed weather stations as our referential ground truth. Based on actual measurements, we have verified that smartphone-based readings are unstable when observed during movement. Using our calibration algorithm on actual smartphone-based pressure readings, the updated values were significantly closer to the ground truth values. PMID:26421312

  4. Pairwise cobalt doping of boron carbides with cobaltocene

    SciTech Connect

    Ignatov, A. Yu.; Losovyj, Ya. B.; Carlson, L.; LaGraffe, D.; Brand, J. I.; Dowben, P. A.

    2007-10-15

    We have performed Co K-edge x-ray absorption fine structure and x-ray absorption near edge structure measurements of Co-doped plasma enhanced chemical vapor phase deposition (PECVD) grown 'C{sub 2}B{sub 10}H{sub x}' semiconducting boron carbides, using cobaltocene. Cobalt does not dope PECVD grown boron carbides as a random fragment of the cobaltocene source gas. The Co atoms are fivefold boron coordinated (R=2.10{+-}0.02 A) and are chemically bonded to the icosahedral cages of B{sub 10}CH{sub x} or B{sub 9}C{sub 2}H{sub y}. Pairwise Co doping occurs, with the cobalt atoms favoring sites some 5.28{+-}0.02 A apart.

  5. Time-Frequency Analysis Reveals Pairwise Interactions in Insect Swarms

    NASA Astrophysics Data System (ADS)

    Puckett, James G.; Ni, Rui; Ouellette, Nicholas T.

    2015-06-01

    The macroscopic emergent behavior of social animal groups is a classic example of dynamical self-organization, and is thought to arise from the local interactions between individuals. Determining these interactions from empirical data sets of real animal groups, however, is challenging. Using multicamera imaging and tracking, we studied the motion of individual flying midges in laboratory mating swarms. By performing a time-frequency analysis of the midge trajectories, we show that the midge behavior can be segmented into two distinct modes: one that is independent and composed of low-frequency maneuvers, and one that consists of higher-frequency nearly harmonic oscillations conducted in synchrony with another midge. We characterize these pairwise interactions, and make a hypothesis as to their biological function.

  6. Weighing Portions Adds Up to Weight Loss

    MedlinePlus

    ... fullstory_167159.html Weighing Portions Adds Up to Weight Loss Put an end to guesstimating calories with simple ... of calories a day. And that can slow weight loss to a snail's pace. The answer is to ...

  7. Covariance Manipulation for Conjunction Assessment

    NASA Technical Reports Server (NTRS)

    Hejduk, M. D.

    2016-01-01

    The manipulation of space object covariances to try to provide additional or improved information to conjunction risk assessment is not an uncommon practice. Types of manipulation include fabricating a covariance when it is missing or unreliable to force the probability of collision (Pc) to a maximum value ('PcMax'), scaling a covariance to try to improve its realism or see the effect of covariance volatility on the calculated Pc, and constructing the equivalent of an epoch covariance at a convenient future point in the event ('covariance forecasting'). In bringing these methods to bear for Conjunction Assessment (CA) operations, however, some do not remain fully consistent with best practices for conducting risk management, some seem to be of relatively low utility, and some require additional information before they can contribute fully to risk analysis. This study describes some basic principles of modern risk management (following the Kaplan construct) and then examines the PcMax and covariance forecasting paradigms for alignment with these principles; it then further examines the expected utility of these methods in the modern CA framework. Both paradigms are found to be not without utility, but only in situations that are somewhat carefully circumscribed.

  8. General Galilei Covariant Gaussian Maps.

    PubMed

    Gasbarri, Giulio; Toroš, Marko; Bassi, Angelo

    2017-09-08

    We characterize general non-Markovian Gaussian maps which are covariant under Galilean transformations. In particular, we consider translational and Galilean covariant maps and show that they reduce to the known Holevo result in the Markovian limit. We apply the results to discuss measures of macroscopicity based on classicalization maps, specifically addressing dissipation, Galilean covariance and non-Markovianity. We further suggest a possible generalization of the macroscopicity measure defined by Nimmrichter and Hornberger [Phys. Rev. Lett. 110, 16 (2013)PRLTAO0031-9007].

  9. Covariance Models for Hydrological Applications

    NASA Astrophysics Data System (ADS)

    Hristopulos, Dionissios

    2014-05-01

    This methodological contribution aims to present some new covariance models with applications in the stochastic analysis of hydrological processes. More specifically, we present explicit expressions for radially symmetric, non-differentiable, Spartan covariance functions in one, two, and three dimensions. The Spartan covariance parameters include a characteristic length, an amplitude coefficient, and a rigidity coefficient which determines the shape of the covariance function. Different expressions are obtained depending on the value of the rigidity coefficient and the dimensionality. If the value of the rigidity coefficient is much larger than one, the Spartan covariance function exhibits multiscaling. Spartan covariance models are more flexible than the classical geostatatistical models (e.g., spherical, exponential). Their non-differentiability makes them suitable for modelling the properties of geological media. We also present a family of radially symmetric, infinitely differentiable Bessel-Lommel covariance functions which are valid in any dimension. These models involve combinations of Bessel and Lommel functions. They provide a generalization of the J-Bessel covariance function, and they can be used to model smooth processes with an oscillatory decay of correlations. We discuss the dependence of the integral range of the Spartan and Bessel-Lommel covariance functions on the parameters. We point out that the dependence is not uniquely specified by the characteristic length, unlike the classical geostatistical models. Finally, we define and discuss the use of the generalized spectrum for characterizing different correlation length scales; the spectrum is defined in terms of an exponent α. We show that the spectrum values obtained for exponent values less than one can be used to discriminate between mean-square continuous but non-differentiable random fields. References [1] D. T. Hristopulos and S. Elogne, 2007. Analytic properties and covariance functions of

  10. Consistency of crisp and fuzzy pairwise comparison matrix using fuzzy preference programming

    NASA Astrophysics Data System (ADS)

    Aminuddin, Adam Shariff Adli; Nawawi, Mohd Kamal Mohd

    2014-12-01

    In this paper, the consistency of crisp pairwise comparison matrix is compared with the fuzzy pairwise comparison matrix of Analytic Network Process (ANP). The fuzzy input in the form of triangular membership function is converted into crisp value using Fuzzy Preference Programming (FPP) method which is implemented using MATLAB. The consistency ratio (CR) for both of the crisp and fuzzy pairwise comparison matrix is calculated using SuperDecisions. Main finding shows that the involvement of fuzzy elements into the decision maker's judgment can reduce the inconsistency of the pairwise comparison matrix compared with the crisp judgment.

  11. Covariation neglect among novice investors.

    PubMed

    Hedesström, Ted Martin; Svedsäter, Henrik; Gärling, Tommy

    2006-09-01

    In 4 experiments, undergraduates made hypothetical investment choices. In Experiment 1, participants paid more attention to the volatility of individual assets than to the volatility of aggregated portfolios. The results of Experiment 2 show that most participants diversified even when this increased risk because of covariation between the returns of individual assets. In Experiment 3, nearly half of those who seemingly attempted to minimize risk diversified even when this increased risk. These results indicate that novice investors neglect covariation when diversifying across investment alternatives. Experiment 4 established that naive diversification follows from motivation to minimize risk and showed that covariation neglect was not significantly reduced by informing participants about how covariation affects portfolio risk but was reduced by making participants systematically calculate aggregate returns for diversified portfolios. In order to counteract naive diversification, novice investors need to be better informed about the rationale underlying recommendations to diversify.

  12. Hawking radiation and covariant anomalies

    SciTech Connect

    Banerjee, Rabin; Kulkarni, Shailesh

    2008-01-15

    Generalizing the method of Wilczek and collaborators we provide a derivation of Hawking radiation from charged black holes using only covariant gauge and gravitational anomalies. The reliability and universality of the anomaly cancellation approach to Hawking radiation is also discussed.

  13. Relative-Error-Covariance Algorithms

    NASA Technical Reports Server (NTRS)

    Bierman, Gerald J.; Wolff, Peter J.

    1991-01-01

    Two algorithms compute error covariance of difference between optimal estimates, based on data acquired during overlapping or disjoint intervals, of state of discrete linear system. Provides quantitative measure of mutual consistency or inconsistency of estimates of states. Relative-error-covariance concept applied, to determine degree of correlation between trajectories calculated from two overlapping sets of measurements and construct real-time test of consistency of state estimates based upon recently acquired data.

  14. Impact of Mucolytic Agents on COPD Exacerbations: A Pair-wise and Network Meta-analysis.

    PubMed

    Cazzola, Mario; Rogliani, Paola; Calzetta, Luigino; Hanania, Nicola A; Matera, Maria Gabriella

    2017-10-01

    Mucolytics are potentially useful for the management of chronic obstructive pulmonary disease (COPD), although there is conflicting advice on their use in different guideline documents. Furthermore, there is paucity of data comparing the efficacy of the different mucolytic agents in reducing the odds of COPD exacerbations. We performed pair-wise and network meta-analyses to evaluate the impact of mucoly-tics in COPD. Randomized clinical trials lasting at least 3 months and investigating the effects of mucolytics on COPD exacerbations were identified from published studies and repository databases. Mucolytics significantly reduced the odds of exacerbation vs. placebo (11 studies analyzed: odds ratio (OR) 0.51, 95% confidence interval (CI) 0.39-0.67; p < 0.001). The most effective drugs were carbocysteine, erdosteine, and N-acetylcysteine 1,200 mg/day (SUCRA 68.0-79.0%), whereas the OR was similar to placebo for ambroxol and N-acetylcysteine 600 mg/day. Only N-acetylcysteine 1,200 mg/day significantly protected against exacerbations vs. placebo (2 studies analyzed: OR 0.56, 95% CI 0.35-0.92; p < 0.05; high quality of evidence). A signal of effectiveness was detected for carbocysteine (2 studies analyzed: OR 0.45, 95% CI 0.20-1.01; p ≥ 0.05; moderate quality of evidence). Specific differences in study designs and patient-related characteristics, such as history of exacerbations and ethnicity, were potential effect modifiers for our statistical models, whereas neither respiratory function nor the use of corticosteroids influenced the analysis. This meta-analysis demonstrates that mucolytics are useful in preventing COPD exacerbations as maintenance add-on therapy to patients with frequent exacerbations. The effectiveness of mucolytics is independent of the severity of airway obstruction and the use of inhaled corticosteroids.

  15. Accelerated Learning-Based Interactive Image Segmentation using Pairwise Constraints

    PubMed Central

    Sourati, Jamshid; Erdogmus, Deniz; Dy, Jennifer G.; Brooks, Dana H.

    2014-01-01

    Algorithms for fully automatic segmentation of images are often not sufficiently generic with suitable accuracy, and fully manual segmentation is not practical in many settings. There is a need for semi-automatic algorithms which are capable of interacting with the user and taking into account the collected feedback. Typically such methods have simply incorporated user feedback directly. Here we employ active learning of optimal queries to guide user interaction. Our work in this paper is based on constrained spectral clustering that iteratively incorporates user feedback by propagating it through the calculated affinities [17]. The original framework does not scale well to large data sets, and hence is not straightforward to apply to interactive image segmentation. In order to address this issue, we adopt advanced numerical methods for eigen-decomposition implemented over a subsampling scheme. Our key innovation, however, is an active learning strategy that chooses pairwise queries to present to the user in order to increase the rate of learning from the feedback. Performance evaluation is carried out on the Berkeley segmentation and Graz-02 image data sets, confirming that convergence to high accuracy levels is realizable in relatively few iterations. PMID:24860031

  16. Characterization of pairwise and multiple sequence alignment errors.

    PubMed

    Landan, Giddy; Graur, Dan

    2009-07-15

    We characterize pairwise and multiple sequence alignment (MSA) errors by comparing true alignments from simulations of sequence evolution with reconstructed alignments. The vast majority of reconstructed alignments contain many errors. Error rates rapidly increase with sequence divergence, thus, for even intermediate degrees of sequence divergence, more than half of the columns of a reconstructed alignment may be expected to be erroneous. In closely related sequences, most errors consist of the erroneous positioning of a single indel event and their effect is local. As sequences diverge, errors become more complex as a result of the simultaneous mis-reconstruction of many indel events, and the lengths of the affected MSA segments increase dramatically. We found a systematic bias towards underestimation of the number of gaps, which leads to the reconstructed MSA being on average shorter than the true one. Alignment errors are unavoidable even when the evolutionary parameters are known in advance. Correct reconstruction can only be guaranteed when the likelihood of true alignment is uniquely optimal. However, true alignment features are very frequently sub-optimal or co-optimal, with the result that optimal albeit erroneous features are incorporated into the reconstructed MSA. Progressive MSA utilizes a guide-tree in the reconstruction of MSAs. The quality of the guide-tree was found to affect MSA error levels only marginally.

  17. A pairwise alignment algorithm which favors clusters of blocks.

    PubMed

    Nédélec, Elodie; Moncion, Thomas; Gassiat, Elisabeth; Bossard, Bruno; Duchateau-Nguyen, Guillemette; Denise, Alain; Termier, Michel

    2005-01-01

    Pairwise sequence alignments aim to decide whether two sequences are related and, if so, to exhibit their related domains. Recent works have pointed out that a significant number of true homologous sequences are missed when using classical comparison algorithms. This is the case when two homologous sequences share several little blocks of homology, too small to lead to a significant score. On the other hand, classical alignment algorithms, when detecting homologies, may fail to recognize all the significant biological signals. The aim of the paper is to give a solution to these two problems. We propose a new scoring method which tends to increase the score of an alignment when "blocks" are detected. This so-called Block-Scoring algorithm, which makes use of dynamic programming, is worth being used as a complementary tool to classical exact alignments methods. We validate our approach by applying it on a large set of biological data. Finally, we give a limit theorem for the score statistics of the algorithm.

  18. Nonreciprocal photonic crystal add-drop filter

    SciTech Connect

    Tao, Keyu; Xiao, Jun-Jun; Yin, Xiaobo

    2014-11-24

    We present a versatile add-drop integrated photonic filter (ADF) consisting of nonreciprocal waveguides in which the propagation of light is restricted in one predetermined direction. With the bus and add/drop waveguides symmetrically coupled through a cavity, the four-port device allows each individual port to add and/or drop a signal of the same frequency. The scheme is general and we demonstrate the nonreciprocal ADF with magneto-optical photonic crystals. The filter is immune to waveguide defects, allowing straightforward implementation of multi-channel ADFs by cascading the four-port designs. The results should find applications in wavelength-division multiplexing and related integrated photonic techniques.

  19. Shift-and-add for astronomical imaging

    NASA Technical Reports Server (NTRS)

    Ribak, Erez; Hege, E. Keith; Strobel, Nicolas V.; Christou, Julian C.

    1989-01-01

    Diffraction-limited astronomical images have been obtained utilizing a variant of the shift-and-add method. It is shown that the matched filter approach for extending the weighted shift-and-add method reduces specklegrams from extended objects and from an object dominated by photon noise. The method is aberration-insensitive and yields very high dynamic range results. The iterative method for arriving at the matched filter does not automatically converge in the case of photon-noisy specklegrams for objects with more than one maximum.

  20. Shift-and-add for astronomical imaging

    NASA Technical Reports Server (NTRS)

    Ribak, Erez; Hege, E. Keith; Strobel, Nicolas V.; Christou, Julian C.

    1989-01-01

    Diffraction-limited astronomical images have been obtained utilizing a variant of the shift-and-add method. It is shown that the matched filter approach for extending the weighted shift-and-add method reduces specklegrams from extended objects and from an object dominated by photon noise. The method is aberration-insensitive and yields very high dynamic range results. The iterative method for arriving at the matched filter does not automatically converge in the case of photon-noisy specklegrams for objects with more than one maximum.

  1. Equating a Large-Scale Writing Assessment Using Pairwise Comparisons of Performances

    ERIC Educational Resources Information Center

    Humphry, Stephen M.; McGrane, Joshua A.

    2015-01-01

    This paper presents a method for equating writing assessments using pairwise comparisons which does not depend upon conventional common-person or common-item equating designs. Pairwise comparisons have been successfully applied in the assessment of open-ended tasks in English and other areas such as visual art and philosophy. In this paper,…

  2. Differential Item Functioning Detection across Two Methods of Defining Group Comparisons: Pairwise and Composite Group Comparisons

    ERIC Educational Resources Information Center

    Sari, Halil Ibrahim; Huggins, Anne Corinne

    2015-01-01

    This study compares two methods of defining groups for the detection of differential item functioning (DIF): (a) pairwise comparisons and (b) composite group comparisons. We aim to emphasize and empirically support the notion that the choice of pairwise versus composite group definitions in DIF is a reflection of how one defines fairness in DIF…

  3. Differential Item Functioning Detection across Two Methods of Defining Group Comparisons: Pairwise and Composite Group Comparisons

    ERIC Educational Resources Information Center

    Sari, Halil Ibrahim; Huggins, Anne Corinne

    2015-01-01

    This study compares two methods of defining groups for the detection of differential item functioning (DIF): (a) pairwise comparisons and (b) composite group comparisons. We aim to emphasize and empirically support the notion that the choice of pairwise versus composite group definitions in DIF is a reflection of how one defines fairness in DIF…

  4. Equating a Large-Scale Writing Assessment Using Pairwise Comparisons of Performances

    ERIC Educational Resources Information Center

    Humphry, Stephen M.; McGrane, Joshua A.

    2015-01-01

    This paper presents a method for equating writing assessments using pairwise comparisons which does not depend upon conventional common-person or common-item equating designs. Pairwise comparisons have been successfully applied in the assessment of open-ended tasks in English and other areas such as visual art and philosophy. In this paper,…

  5. Post Hoc Pair-Wise Comparisons for the Chi-Square Test of Homogeneity of Proportions.

    ERIC Educational Resources Information Center

    Cox, Myron K.; Key, Coretta H.

    1993-01-01

    A model is presented for multiple pairwise comparisons of selected categories (cells) of a contingency table after the chi-square test has rejected the null hypothesis of equality of population proportions. The model determines which, if any, pairwise proportions have led to the rejection. (SLD)

  6. Using analysis of covariance (ANCOVA) with fallible covariates.

    PubMed

    Culpepper, Steven Andrew; Aguinis, Herman

    2011-06-01

    Analysis of covariance (ANCOVA) is used widely in psychological research implementing nonexperimental designs. However, when covariates are fallible (i.e., measured with error), which is the norm, researchers must choose from among 3 inadequate courses of action: (a) know that the assumption that covariates are perfectly reliable is violated but use ANCOVA anyway (and, most likely, report misleading results); (b) attempt to employ 1 of several measurement error models with the understanding that no research has examined their relative performance and with the added practical difficulty that several of these models are not available in commonly used statistical software; or (c) not use ANCOVA at all. First, we discuss analytic evidence to explain why using ANCOVA with fallible covariates produces bias and a systematic inflation of Type I error rates that may lead to the incorrect conclusion that treatment effects exist. Second, to provide a solution for this problem, we conduct 2 Monte Carlo studies to compare 4 existing approaches for adjusting treatment effects in the presence of covariate measurement error: errors-in-variables (EIV; Warren, White, & Fuller, 1974), Lord's (1960) method, Raaijmakers and Pieters's (1987) method (R&P), and structural equation modeling methods proposed by Sörbom (1978) and Hayduk (1996). Results show that EIV models are superior in terms of parameter accuracy, statistical power, and keeping Type I error close to the nominal value. Finally, we offer a program written in R that performs all needed computations for implementing EIV models so that ANCOVA can be used to obtain accurate results even when covariates are measured with error. © 2011 American Psychological Association

  7. Covariate-free and Covariate-dependent Reliability.

    PubMed

    Bentler, Peter M

    2016-12-01

    Classical test theory reliability coefficients are said to be population specific. Reliability generalization, a meta-analysis method, is the main procedure for evaluating the stability of reliability coefficients across populations. A new approach is developed to evaluate the degree of invariance of reliability coefficients to population characteristics. Factor or common variance of a reliability measure is partitioned into parts that are, and are not, influenced by control variables, resulting in a partition of reliability into a covariate-dependent and a covariate-free part. The approach can be implemented in a single sample and can be applied to a variety of reliability coefficients.

  8. Levy Matrices and Financial Covariances

    NASA Astrophysics Data System (ADS)

    Burda, Zdzislaw; Jurkiewicz, Jerzy; Nowak, Maciej A.; Papp, Gabor; Zahed, Ismail

    2003-10-01

    In a given market, financial covariances capture the intra-stock correlations and can be used to address statistically the bulk nature of the market as a complex system. We provide a statistical analysis of three SP500 covariances with evidence for raw tail distributions. We study the stability of these tails against reshuffling for the SP500 data and show that the covariance with the strongest tails is robust, with a spectral density in remarkable agreement with random Lévy matrix theory. We study the inverse participation ratio for the three covariances. The strong localization observed at both ends of the spectral density is analogous to the localization exhibited in the random Lévy matrix ensemble. We discuss two competitive mechanisms responsible for the occurrence of an extensive and delocalized eigenvalue at the edge of the spectrum: (a) the Lévy character of the entries of the correlation matrix and (b) a sort of off-diagonal order induced by underlying inter-stock correlations. (b) can be destroyed by reshuffling, while (a) cannot. We show that the stocks with the largest scattering are the least susceptible to correlations, and likely candidates for the localized states. We introduce a simple model for price fluctuations which captures behavior of the SP500 covariances. It may be of importance for assets diversification.

  9. Educational Interventions for Students with ADD.

    ERIC Educational Resources Information Center

    Salend, Spencer J.; Elhoweris, Hala; van Garderen, Delinda

    2003-01-01

    Principles of educational interventions for students with attention deficit disorder (ADD) include: (1) giving complete and thorough directions; (2) individualizing in-class and homework assignments; (3) motivating students; (4) promoting active responding and monitoring understanding; (5) employing content enhancements; (6) offering learning…

  10. Selected Perspectives on ADD and ADHD.

    ERIC Educational Resources Information Center

    Porter, Louise

    1997-01-01

    Offers an overview of ADD and ADHD, their causes and long-term prognoses, including the complexities of the conditions, the incomplete knowledge about them, and the difficulties of diagnosis during early childhood. Summarizes assessment and treatment options and concludes that the conditions have so many secondary effects that designing an…

  11. Selected Perspectives on ADD and ADHD.

    ERIC Educational Resources Information Center

    Porter, Louise

    1997-01-01

    Offers an overview of ADD and ADHD, their causes and long-term prognoses, including the complexities of the conditions, the incomplete knowledge about them, and the difficulties of diagnosis during early childhood. Summarizes assessment and treatment options and concludes that the conditions have so many secondary effects that designing an…

  12. 76 FR 49508 - ``Add Us In'' Initiative

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-08-10

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF LABOR Office of Disability Employment Program ``Add Us In'' Initiative AGENCY: Office of Disability Employment.... SUMMARY: The Office of Disability Employment Policy, Department of Labor is correcting the New Notice of...

  13. Shift Would Add Burden on Principals

    ERIC Educational Resources Information Center

    Killion, Joellen

    2004-01-01

    In this article, the author describes how the transition from district-centered to school-based staff development can add to the burden on principals. This column first presents a brief review of the efforts of Braxton Hinsdale, a staff development director who advocated for moving professional development resources from the district level to the…

  14. Probabilistic pairwise Markov models: application to prostate cancer detection

    NASA Astrophysics Data System (ADS)

    Monaco, James; Tomaszewski, John E.; Feldman, Michael D.; Moradi, Mehdi; Mousavi, Parvin; Boag, Alexander; Davidson, Chris; Abolmaesumi, Purang; Madabhushi, Anant

    2009-02-01

    Markov Random Fields (MRFs) provide a tractable means for incorporating contextual information into a Bayesian framework. This contextual information is modeled using multiple local conditional probability density functions (LCPDFs) which the MRF framework implicitly combines into a single joint probability density function (JPDF) that describes the entire system. However, only LCPDFs of certain functional forms are consistent, meaning they reconstitute a valid JPDF. These forms are specified by the Gibbs-Markov equivalence theorem which indicates that the JPDF, and hence the LCPDFs, should be representable as a product of potential functions (i.e. Gibbs distributions). Unfortunately, potential functions are mathematical abstractions that lack intuition; and consequently, constructing LCPDFs through their selection becomes an ad hoc procedure, usually resulting in generic and/or heuristic models. In this paper we demonstrate that under certain conditions the LCDPFs can be formulated in terms of quantities that are both meaningful and descriptive: probability distributions. Using probability distributions instead of potential functions enables us to construct consistent LCPDFs whose modeling capabilities are both more intuitive and expansive than typical MRF models. As an example, we compare the efficacy of our so-called probabilistic pairwise Markov models (PPMMs) to the prevalent Potts model by incorporating both into a novel computer aided diagnosis (CAD) system for detecting prostate cancer in whole-mount histological sections. Using the Potts model the CAD system is able to detection cancerous glands with a specificity of 0.82 and sensitivity of 0.71; its area under the receiver operator characteristic (AUC) curve is 0.83. If instead the PPMM model is employed the sensitivity (specificity is held fixed) and AUC increase to 0.77 and 0.87.

  15. A class of covariate-dependent spatiotemporal covariance functions.

    PubMed

    Reich, Brian J; Eidsvik, Jo; Guindani, Michele; Nail, Amy J; Schmidt, Alexandra M

    2011-12-01

    In geostatistics, it is common to model spatially distributed phenomena through an underlying stationary and isotropic spatial process. However, these assumptions are often untenable in practice because of the influence of local effects in the correlation structure. Therefore, it has been of prolonged interest in the literature to provide flexible and effective ways to model non-stationarity in the spatial effects. Arguably, due to the local nature of the problem, we might envision that the correlation structure would be highly dependent on local characteristics of the domain of study, namely the latitude, longitude and altitude of the observation sites, as well as other locally defined covariate information. In this work, we provide a flexible and computationally feasible way for allowing the correlation structure of the underlying processes to depend on local covariate information. We discuss the properties of the induced covariance functions and discuss methods to assess its dependence on local covariate information by means of a simulation study and the analysis of data observed at ozone-monitoring stations in the Southeast United States.

  16. A relativistically covariant random walk

    NASA Astrophysics Data System (ADS)

    Almaguer, J.; Larralde, H.

    2007-08-01

    In this work we present and analyze an extremely simple relativistically covariant random walk model. In our approach, the probability density and the flow of probability arise naturally as the components of a four-vector and they are related to one another via a tensorial constitutive equation. We show that the system can be described in terms of an underlying invariant space time random walk parameterized by the number of sojourns. Finally, we obtain explicit expressions for the moments of the covariant random walk as well as for the underlying invariant random walk.

  17. REFINING GENETICALLY INFERRED RELATIONSHIPS USING TREELET COVARIANCE SMOOTHING1

    PubMed Central

    Crossett, Andrew; Lee, Ann B.; Klei, Lambertus; Devlin, Bernie; Roeder, Kathryn

    2013-01-01

    Recent technological advances coupled with large sample sets have uncovered many factors underlying the genetic basis of traits and the predisposition to complex disease, but much is left to discover. A common thread to most genetic investigations is familial relationships. Close relatives can be identified from family records, and more distant relatives can be inferred from large panels of genetic markers. Unfortunately these empirical estimates can be noisy, especially regarding distant relatives. We propose a new method for denoising genetically—inferred relationship matrices by exploiting the underlying structure due to hierarchical groupings of correlated individuals. The approach, which we call Treelet Covariance Smoothing, employs a multiscale decomposition of covariance matrices to improve estimates of pairwise relationships. On both simulated and real data, we show that smoothing leads to better estimates of the relatedness amongst distantly related individuals. We illustrate our method with a large genome-wide association study and estimate the “heritability” of body mass index quite accurately. Traditionally heritability, defined as the fraction of the total trait variance attributable to additive genetic effects, is estimated from samples of closely related individuals using random effects models. We show that by using smoothed relationship matrices we can estimate heritability using population-based samples. Finally, while our methods have been developed for refining genetic relationship matrices and improving estimates of heritability, they have much broader potential application in statistics. Most notably, for error-in-variables random effects models and settings that require regularization of matrices with block or hierarchical structure. PMID:24587841

  18. REFINING GENETICALLY INFERRED RELATIONSHIPS USING TREELET COVARIANCE SMOOTHING.

    PubMed

    Crossett, Andrew; Lee, Ann B; Klei, Lambertus; Devlin, Bernie; Roeder, Kathryn

    2013-06-27

    Recent technological advances coupled with large sample sets have uncovered many factors underlying the genetic basis of traits and the predisposition to complex disease, but much is left to discover. A common thread to most genetic investigations is familial relationships. Close relatives can be identified from family records, and more distant relatives can be inferred from large panels of genetic markers. Unfortunately these empirical estimates can be noisy, especially regarding distant relatives. We propose a new method for denoising genetically-inferred relationship matrices by exploiting the underlying structure due to hierarchical groupings of correlated individuals. The approach, which we call Treelet Covariance Smoothing, employs a multiscale decomposition of covariance matrices to improve estimates of pairwise relationships. On both simulated and real data, we show that smoothing leads to better estimates of the relatedness amongst distantly related individuals. We illustrate our method with a large genome-wide association study and estimate the "heritability" of body mass index quite accurately. Traditionally heritability, defined as the fraction of the total trait variance attributable to additive genetic effects, is estimated from samples of closely related individuals using random effects models. We show that by using smoothed relationship matrices we can estimate heritability using population-based samples. Finally, while our methods have been developed for refining genetic relationship matrices and improving estimates of heritability, they have much broader potential application in statistics. Most notably, for error-in-variables random effects models and settings that require regularization of matrices with block or hierarchical structure.

  19. Condition Number Regularized Covariance Estimation.

    PubMed

    Won, Joong-Ho; Lim, Johan; Kim, Seung-Jean; Rajaratnam, Bala

    2013-06-01

    Estimation of high-dimensional covariance matrices is known to be a difficult problem, has many applications, and is of current interest to the larger statistics community. In many applications including so-called the "large p small n" setting, the estimate of the covariance matrix is required to be not only invertible, but also well-conditioned. Although many regularization schemes attempt to do this, none of them address the ill-conditioning problem directly. In this paper, we propose a maximum likelihood approach, with the direct goal of obtaining a well-conditioned estimator. No sparsity assumption on either the covariance matrix or its inverse are are imposed, thus making our procedure more widely applicable. We demonstrate that the proposed regularization scheme is computationally efficient, yields a type of Steinian shrinkage estimator, and has a natural Bayesian interpretation. We investigate the theoretical properties of the regularized covariance estimator comprehensively, including its regularization path, and proceed to develop an approach that adaptively determines the level of regularization that is required. Finally, we demonstrate the performance of the regularized estimator in decision-theoretic comparisons and in the financial portfolio optimization setting. The proposed approach has desirable properties, and can serve as a competitive procedure, especially when the sample size is small and when a well-conditioned estimator is required.

  20. Condition Number Regularized Covariance Estimation*

    PubMed Central

    Won, Joong-Ho; Lim, Johan; Kim, Seung-Jean; Rajaratnam, Bala

    2012-01-01

    Estimation of high-dimensional covariance matrices is known to be a difficult problem, has many applications, and is of current interest to the larger statistics community. In many applications including so-called the “large p small n” setting, the estimate of the covariance matrix is required to be not only invertible, but also well-conditioned. Although many regularization schemes attempt to do this, none of them address the ill-conditioning problem directly. In this paper, we propose a maximum likelihood approach, with the direct goal of obtaining a well-conditioned estimator. No sparsity assumption on either the covariance matrix or its inverse are are imposed, thus making our procedure more widely applicable. We demonstrate that the proposed regularization scheme is computationally efficient, yields a type of Steinian shrinkage estimator, and has a natural Bayesian interpretation. We investigate the theoretical properties of the regularized covariance estimator comprehensively, including its regularization path, and proceed to develop an approach that adaptively determines the level of regularization that is required. Finally, we demonstrate the performance of the regularized estimator in decision-theoretic comparisons and in the financial portfolio optimization setting. The proposed approach has desirable properties, and can serve as a competitive procedure, especially when the sample size is small and when a well-conditioned estimator is required. PMID:23730197

  1. Covariation Neglect among Novice Investors

    ERIC Educational Resources Information Center

    Hedesstrom, Ted Martin; Svedsater, Henrik; Garling, Tommy

    2006-01-01

    In 4 experiments, undergraduates made hypothetical investment choices. In Experiment 1, participants paid more attention to the volatility of individual assets than to the volatility of aggregated portfolios. The results of Experiment 2 show that most participants diversified even when this increased risk because of covariation between the returns…

  2. Covariation Neglect among Novice Investors

    ERIC Educational Resources Information Center

    Hedesstrom, Ted Martin; Svedsater, Henrik; Garling, Tommy

    2006-01-01

    In 4 experiments, undergraduates made hypothetical investment choices. In Experiment 1, participants paid more attention to the volatility of individual assets than to the volatility of aggregated portfolios. The results of Experiment 2 show that most participants diversified even when this increased risk because of covariation between the returns…

  3. Covariant Formulations of Superstring Theories.

    NASA Astrophysics Data System (ADS)

    Mikovic, Aleksandar Radomir

    1990-01-01

    Chapter 1 contains a brief introduction to the subject of string theory, and tries to motivate the study of superstrings and covariant formulations. Chapter 2 describes the Green-Schwarz formulation of the superstrings. The Hamiltonian and BRST structure of the theory is analysed in the case of the superparticle. Implications for the superstring case are discussed. Chapter 3 describes the Siegel's formulation of the superstring, which contains only the first class constraints. It is shown that the physical spectrum coincides with that of the Green-Schwarz formulation. In chapter 4 we analyse the BRST structure of the Siegel's formulation. We show that the BRST charge has the wrong cohomology, and propose a modification, called first ilk, which gives the right cohomology. We also propose another superparticle model, called second ilk, which has infinitely many coordinates and constraints. We construct the complete BRST charge for it, and show that it gives the correct cohomology. In chapter 5 we analyse the properties of the covariant vertex operators and the corresponding S-matrix elements by using the Siegel's formulation. We conclude that the knowledge of the ghosts is necessary, even at the tree level, in order to obtain the correct S-matrix. In chapter 6 we attempt to calculate the superstring loops, in a covariant gauge. We calculate the vacuum-to -vacuum amplitude, which is also the cosmological constant. We show that it vanishes to all loop orders, under the assumption that the free covariant gauge-fixed action exists. In chapter 7 we present our conclusions, and briefly discuss the random lattice approach to the string theory, as a possible way of resolving the problem of the covariant quantization and the nonperturbative definition of the superstrings.

  4. Canadian reactor delays add to agency's troubles

    NASA Astrophysics Data System (ADS)

    Howell, Elizabeth

    2009-08-01

    A plan to replace two aging nuclear reactors in Ontario, Canada, with Advanced CANDU Reactors (ACR) has been rejected by the provincial government due to concerns over ballooning costs. The rejected bid, which was made by the state-owned Atomic Energy of Canada Limited (AECL), adds to the woes of an agency that is already facing rumoured privatization of its business to build and maintain nuclear reactors.

  5. Cross-Section Covariance Data Processing with the AMPX Module PUFF-IV

    SciTech Connect

    Wiarda, Dorothea; Leal, Luiz C; Dunn, Michael E

    2011-01-01

    The ENDF community is endeavoring to release an updated version of the ENDF/B-VII library (ENDF/B-VII.1). In the new release several new evaluations containing covariance information have been added, as the community strives to add covariance information for use in programs like the TSUNAMI (Tools for Sensitivity and Uncertainty Analysis Methodology Implementation) sequence of SCALE (Ref 1). The ENDF/B formatted files are processed into libraries to be used in transport calculations using the AMPX code system (Ref 2) or the NJOY code system (Ref 3). Both codes contain modules to process covariance matrices: PUFF-IV for AMPX and ERRORR in the case of NJOY. While the cross section processing capability between the two code systems has been widely compared, the same is not true for the covariance processing. This paper compares the results for the two codes using the pre-release version of ENDF/B-VII.1.

  6. Generalization of Pairwise Models to non-Markovian Epidemics on Networks

    NASA Astrophysics Data System (ADS)

    Kiss, Istvan Z.; Röst, Gergely; Vizi, Zsolt

    2015-08-01

    In this Letter, a generalization of pairwise models to non-Markovian epidemics on networks is presented. For the case of infectious periods of fixed length, the resulting pairwise model is a system of delay differential equations, which shows excellent agreement with results based on stochastic simulations. Furthermore, we analytically compute a new R0 -like threshold quantity and an analytical relation between this and the final epidemic size. Additionally, we show that the pairwise model and the analytic results can be generalized to an arbitrary distribution of the infectious times, using integro-differential equations, and this leads to a general expression for the final epidemic size. By showing the rigorous link between non-Markovian dynamics and pairwise delay differential equations, we provide the framework for a more systematic understanding of non-Markovian dynamics.

  7. Manipulation of Karyotype in Caenorhabditis elegans Reveals Multiple Inputs Driving Pairwise Chromosome Synapsis During Meiosis

    PubMed Central

    Roelens, Baptiste; Schvarzstein, Mara; Villeneuve, Anne M.

    2015-01-01

    Meiotic chromosome segregation requires pairwise association between homologs, stabilized by the synaptonemal complex (SC). Here, we investigate factors contributing to pairwise synapsis by investigating meiosis in polyploid worms. We devised a strategy, based on transient inhibition of cohesin function, to generate polyploid derivatives of virtually any Caenorhabditis elegans strain. We exploited this strategy to investigate the contribution of recombination to pairwise synapsis in tetraploid and triploid worms. In otherwise wild-type polyploids, chromosomes first sort into homolog groups, then multipartner interactions mature into exclusive pairwise associations. Pairwise synapsis associations still form in recombination-deficient tetraploids, confirming a propensity for synapsis to occur in a strictly pairwise manner. However, the transition from multipartner to pairwise association was perturbed in recombination-deficient triploids, implying a role for recombination in promoting this transition when three partners compete for synapsis. To evaluate the basis of synapsis partner preference, we generated polyploid worms heterozygous for normal sequence and rearranged chromosomes sharing the same pairing center (PC). Tetraploid worms had no detectable preference for identical partners, indicating that PC-adjacent homology drives partner choice in this context. In contrast, triploid worms exhibited a clear preference for identical partners, indicating that homology outside the PC region can influence partner choice. Together, our findings, suggest a two-phase model for C. elegans synapsis: an early phase, in which initial synapsis interactions are driven primarily by recombination-independent assessment of homology near PCs and by a propensity for pairwise SC assembly, and a later phase in which mature synaptic interactions are promoted by recombination. PMID:26500263

  8. An IRT Approach to Constructing and Scoring Pairwise Preference Items Involving Stimuli on Different Dimensions: The Multi-Unidimensional Pairwise-Preference Model

    ERIC Educational Resources Information Center

    Stark, Stephen; Chernyshenko, Oleksandr S.; Drasgow, Fritz

    2005-01-01

    This article proposes an item response theory (IRT) approach to constructing and scoring multidimensional pairwise preference items. Individual statements are administered and calibrated using a unidimensional single-stimulus model. Tests are created by combining multidimensional items with a small number of unidimensional pairings needed to…

  9. Szekeres models: a covariant approach

    NASA Astrophysics Data System (ADS)

    Apostolopoulos, Pantelis S.

    2017-05-01

    We exploit the 1  +  1  +  2 formalism to covariantly describe the inhomogeneous and anisotropic Szekeres models. It is shown that an average scale length can be defined covariantly which satisfies a 2d equation of motion driven from the effective gravitational mass (EGM) contained in the dust cloud. The contributions to the EGM are encoded to the energy density of the dust fluid and the free gravitational field E ab . We show that the quasi-symmetric property of the Szekeres models is justified through the existence of 3 independent intrinsic Killing vector fields (IKVFs). In addition the notions of the apparent and absolute apparent horizons are briefly discussed and we give an alternative gauge-invariant form to define them in terms of the kinematical variables of the spacelike congruences. We argue that the proposed program can be used in order to express Sachs’ optical equations in a covariant form and analyze the confrontation of a spatially inhomogeneous irrotational overdense fluid model with the observational data.

  10. Towards an accurate model of redshift-space distortions: a bivariate Gaussian description for the galaxy pairwise velocity distributions

    NASA Astrophysics Data System (ADS)

    Bianchi, Davide; Chiesa, Matteo; Guzzo, Luigi

    2016-10-01

    As a step towards a more accurate modelling of redshift-space distortions (RSD) in galaxy surveys, we develop a general description of the probability distribution function of galaxy pairwise velocities within the framework of the so-called streaming model. For a given galaxy separation , such function can be described as a superposition of virtually infinite local distributions. We characterize these in terms of their moments and then consider the specific case in which they are Gaussian functions, each with its own mean μ and variance σ2. Based on physical considerations, we make the further crucial assumption that these two parameters are in turn distributed according to a bivariate Gaussian, with its own mean and covariance matrix. Tests using numerical simulations explicitly show that with this compact description one can correctly model redshift-space distorsions on all scales, fully capturing the overall linear and nonlinear dynamics of the galaxy flow at different separations. In particular, we naturally obtain Gaussian/exponential, skewed/unskewed distribution functions, depending on separation as observed in simulations and data. Also, the recently proposed single-Gaussian description of redshift-space distortions is included in this model as a limiting case, when the bivariate Gaussian is collapsed to a two-dimensional Dirac delta function. More work is needed, but these results indicate a very promising path to make definitive progress in our program to improve RSD estimators.

  11. Understanding covariate shift in model performance

    PubMed Central

    McGaughey, Georgia; Walters, W. Patrick; Goldman, Brian

    2016-01-01

    Three (3) different methods (logistic regression, covariate shift and k-NN) were applied to five (5) internal datasets and one (1) external, publically available dataset where covariate shift existed. In all cases, k-NN’s performance was inferior to either logistic regression or covariate shift. Surprisingly, there was no obvious advantage for using covariate shift to reweight the training data in the examined datasets. PMID:27803797

  12. Lorentz-covariant dissipative Lagrangian systems

    NASA Technical Reports Server (NTRS)

    Kaufman, A. N.

    1985-01-01

    The concept of dissipative Hamiltonian system is converted to Lorentz-covariant form, with evolution generated jointly by two scalar functionals, the Lagrangian action and the global entropy. A bracket formulation yields the local covariant laws of energy-momentum conservation and of entropy production. The formalism is illustrated by a derivation of the covariant Landau kinetic equation.

  13. Are Maxwell's equations Lorentz-covariant?

    NASA Astrophysics Data System (ADS)

    Redžić, D. V.

    2017-01-01

    It is stated in many textbooks that Maxwell's equations are manifestly covariant when written down in tensorial form. We recall that tensorial form of Maxwell's equations does not secure their tensorial contents; they become covariant by postulating certain transformation properties of field functions. That fact should be stressed when teaching about the covariance of Maxwell's equations.

  14. Lorentz-covariant dissipative Lagrangian systems

    NASA Technical Reports Server (NTRS)

    Kaufman, A. N.

    1985-01-01

    The concept of dissipative Hamiltonian system is converted to Lorentz-covariant form, with evolution generated jointly by two scalar functionals, the Lagrangian action and the global entropy. A bracket formulation yields the local covariant laws of energy-momentum conservation and of entropy production. The formalism is illustrated by a derivation of the covariant Landau kinetic equation.

  15. Testing the equivalence of modern human cranial covariance structure: Implications for bioarchaeological applications.

    PubMed

    von Cramon-Taubadel, Noreen; Schroeder, Lauren

    2016-10-01

    Estimation of the variance-covariance (V/CV) structure of fragmentary bioarchaeological populations requires the use of proxy extant V/CV parameters. However, it is currently unclear whether extant human populations exhibit equivalent V/CV structures. Random skewers (RS) and hierarchical analyses of common principal components (CPC) were applied to a modern human cranial dataset. Cranial V/CV similarity was assessed globally for samples of individual populations (jackknifed method) and for pairwise population sample contrasts. The results were examined in light of potential explanatory factors for covariance difference, such as geographic region, among-group distance, and sample size. RS analyses showed that population samples exhibited highly correlated multivariate responses to selection, and that differences in RS results were primarily a consequence of differences in sample size. The CPC method yielded mixed results, depending upon the statistical criterion used to evaluate the hierarchy. The hypothesis-testing (step-up) approach was deemed problematic due to sensitivity to low statistical power and elevated Type I errors. In contrast, the model-fitting (lowest AIC) approach suggested that V/CV matrices were proportional and/or shared a large number of CPCs. Pairwise population sample CPC results were correlated with cranial distance, suggesting that population history explains some of the variability in V/CV structure among groups. The results indicate that patterns of covariance in human craniometric samples are broadly similar but not identical. These findings have important implications for choosing extant covariance matrices to use as proxy V/CV parameters in evolutionary analyses of past populations. © 2016 Wiley Periodicals, Inc.

  16. User's manual for Axisymmetric Diffuser Duct (ADD) code. Volume 3: ADD code coordinate generator

    NASA Technical Reports Server (NTRS)

    Anderson, O. L.; Hankins, G. B., Jr.; Edwards, D. E.

    1982-01-01

    This User's Manual contains a complete description of the computer codes known as the Axisymmetric Diffuser Duct (ADD) code. It includes a list of references which describe the formulation of the ADD code and comparisons of calculation with experimental flows. The input/output and general use of the code is described in the first volume. The second volume contains a detailed description of the code including the global structure of the code, list of FORTRAN variables, and descriptions of the subroutines. The third volume contains a detailed description of the CODUCT code which generates coordinate systems for arbitrary axisymmetric ducts.

  17. User's manual for Axisymmetric Diffuser Duct (ADD) code. Volume 1: General ADD code description

    NASA Technical Reports Server (NTRS)

    Anderson, O. L.; Hankins, G. B., Jr.; Edwards, D. E.

    1982-01-01

    This User's Manual contains a complete description of the computer codes known as the AXISYMMETRIC DIFFUSER DUCT code or ADD code. It includes a list of references which describe the formulation of the ADD code and comparisons of calculation with experimental flows. The input/output and general use of the code is described in the first volume. The second volume contains a detailed description of the code including the global structure of the code, list of FORTRAN variables, and descriptions of the subroutines. The third volume contains a detailed description of the CODUCT code which generates coordinate systems for arbitrary axisymmetric ducts.

  18. Covariance Evaluation Methodology for Neutron Cross Sections

    SciTech Connect

    Herman,M.; Arcilla, R.; Mattoon, C.M.; Mughabghab, S.F.; Oblozinsky, P.; Pigni, M.; Pritychenko, b.; Songzoni, A.A.

    2008-09-01

    We present the NNDC-BNL methodology for estimating neutron cross section covariances in thermal, resolved resonance, unresolved resonance and fast neutron regions. The three key elements of the methodology are Atlas of Neutron Resonances, nuclear reaction code EMPIRE, and the Bayesian code implementing Kalman filter concept. The covariance data processing, visualization and distribution capabilities are integral components of the NNDC methodology. We illustrate its application on examples including relatively detailed evaluation of covariances for two individual nuclei and massive production of simple covariance estimates for 307 materials. Certain peculiarities regarding evaluation of covariances for resolved resonances and the consistency between resonance parameter uncertainties and thermal cross section uncertainties are also discussed.

  19. Phase-covariant quantum benchmarks

    SciTech Connect

    Calsamiglia, J.; Aspachs, M.; Munoz-Tapia, R.; Bagan, E.

    2009-05-15

    We give a quantum benchmark for teleportation and quantum storage experiments suited for pure and mixed test states. The benchmark is based on the average fidelity over a family of phase-covariant states and certifies that an experiment cannot be emulated by a classical setup, i.e., by a measure-and-prepare scheme. We give an analytical solution for qubits, which shows important differences with standard state estimation approach, and compute the value of the benchmark for coherent and squeezed states, both pure and mixed.

  20. Using Joint Interviews to Add Analytic Value.

    PubMed

    Polak, Louisa; Green, Judith

    2016-10-01

    Joint interviewing has been frequently used in health research, and is the subject of a growing methodological literature. We review this literature, and build on it by drawing on a case study of how people make decisions about taking statins. This highlights two ways in which a dyadic approach to joint interviewing can add analytic value compared with individual interviewing. First, the analysis of interaction within joint interviews can help to explicate tacit knowledge and to illuminate the range of often hard-to-access resources that are drawn upon in making decisions. Second, joint interviews mitigate some of the weaknesses of interviewing as a method for studying practices; we offer a cautious defense of the often-tacit assumption that the "naturalness" of joint interviews strengthens their credibility as the basis for analytic inferences. We suggest that joint interviews are a particularly appropriate method for studying complex shared practices such as making health decisions.

  1. Independents add gas reserves, forego romance

    SciTech Connect

    Gill, D.

    1981-08-01

    Incentive pricing for low-permeability reservoirs and tax advantages for drilling them are 2 big reasons why more independents may start making a special effort to add gas reserves to their inventories. If so, it will be a change from past practices, which saw independents build up big gas positions by circumstance rather than by intention. There are always major refiners ready and willing to buy whole crude oil reservoirs from small producers, but purchasers willing to take gas fields in a single investment are few and far between. Lower-than-normal return on equity during the first 20 years, plus the heavy front-end cost of a frac necessary to produce the tight gas might dissuade independents from drilling tight gas sands, but those liabilities are offset by the higher price tight gas gets and the peculiar tax advantages of exploring for it that make a nice fit with the small operator's way of doing business.

  2. NASA Adds Leap Second to Master Clock

    NASA Image and Video Library

    2017-09-28

    On Dec. 31, 2016, official clocks around the world will add a leap second just before midnight Coordinated Universal Time — which corresponds to 6:59:59 p.m. EST. NASA missions will also have to make the switch, including the Solar Dynamics Observatory, or SDO, which watches the sun 24/7. Clocks do this to keep in sync with Earth's rotation, which gradually slows down over time. When the dinosaurs roamed Earth, for example, our globe took only 23 hours to make a complete rotation. In space, millisecond accuracy is crucial to understanding how satellites orbit. "SDO moves about 1.9 miles every second," said Dean Pesnell, the project scientist for SDO at NASA's Goddard Space Flight Center in Greenbelt, Maryland. "So does every other object in orbit near SDO. We all have to use the same time to make sure our collision avoidance programs are accurate. So we all add a leap second to the end of 2016, delaying 2017 by one second." The leap second is also key to making sure that SDO is in sync with the Coordinated Universal Time, or UTC, used to label each of its images. SDO has a clock that counts the number of seconds since the beginning of the mission. To convert that count to UTC requires knowing just how many leap seconds have been added to Earth-bound clocks since the mission started. When the spacecraft wants to provide a time in UTC, it calls a software module that takes into consideration both the mission's second count and the number of leap seconds — and then returns a time in UTC.

  3. Improving efficiency of inferences in randomized clinical trials using auxiliary covariates

    PubMed Central

    Zhang, Min; Tsiatis, Anastasios A.; Davidian, Marie

    2008-01-01

    Summary The primary goal of a randomized clinical trial is to make comparisons among two or more treatments. For example, in a two-arm trial with continuous response, the focus may be on the difference in treatment means; with more than two treatments, the comparison may be based on pairwise differences. With binary outcomes, pairwise odds-ratios or log-odds ratios may be used. In general, comparisons may be based on meaningful parameters in a relevant statistical model. Standard analyses for estimation and testing in this context typically are based on the data collected on response and treatment assignment only. In many trials, auxiliary baseline covariate information may also be available, and it is of interest to exploit these data to improve the efficiency of inferences. Taking a semiparametric theory perspective, we propose a broadly-applicable approach to adjustment for auxiliary covariates to achieve more efficient estimators and tests for treatment parameters in the analysis of randomized clinical trials. Simulations and applications demonstrate the performance of the methods. PMID:18190618

  4. Pairwise diversity and tMRCA as potential markers for HIV infection recency

    PubMed Central

    Moyo, Sikhulile; Wilkinson, Eduan; Vandormael, Alain; Wang, Rui; Weng, Jia; Kotokwe, Kenanao P.; Gaseitsiwe, Simani; Musonda, Rosemary; Makhema, Joseph; Essex, Max; Engelbrecht, Susan; de Oliveira, Tulio; Novitsky, Vladimir

    2017-01-01

    Abstract Intrahost human immunodeficiency virus (HIV)-1 diversity increases linearly over time. We assessed the extent to which mean pairwise distances and the time to the most recent common ancestor (tMRCA) inferred from intrahost HIV-1C env sequences were associated with the estimated time of HIV infection. Data from a primary HIV-1C infection study in Botswana were used for this analysis (N = 42). A total of 2540 HIV-1C env gp120 variable loop region 1 to conserved region 5 (V1C5) of the HIV-1 envelope gp120 viral sequences were generated by single genome amplification and sequencing, with an average of 61 viral sequences per participant and 11 sequences per time point per participant. Raw pairwise distances were calculated for each time point and participant using the ape package in R software. The tMRCA was estimated using phylogenetic inference implemented in Bayesian Evolutionary Analysis by Sampling Trees v1.8.2. Pairwise distances and tMRCA were significantly associated with the estimated time since HIV infection (both P < 0.001). Taking into account multiplicity of HIV infection strengthened these associations. HIV-1C env-based pairwise distances and tMRCA can be used as potential markers for HIV recency. However, the tMRCA estimates demonstrated no advantage over the pairwise distances estimates. PMID:28178146

  5. Non-pairwise additivity of the leading-order dispersion energy.

    PubMed

    Hollett, Joshua W

    2015-02-28

    The leading-order (i.e., dipole-dipole) dispersion energy is calculated for one-dimensional (1D) and two-dimensional (2D) infinite lattices, and an infinite 1D array of infinitely long lines, of doubly occupied locally harmonic wells. The dispersion energy is decomposed into pairwise and non-pairwise additive components. By varying the force constant and separation of the wells, the non-pairwise additive contribution to the dispersion energy is shown to depend on the overlap of density between neighboring wells. As well separation is increased, the non-pairwise additivity of the dispersion energy decays. The different rates of decay for 1D and 2D lattices of wells is explained in terms of a Jacobian effect that influences the number of nearest neighbors. For an array of infinitely long lines of wells spaced 5 bohrs apart, and an inter-well spacing of 3 bohrs within a line, the non-pairwise additive component of the leading-order dispersion energy is -0.11 kJ mol(-1) well(-1), which is 7% of the total. The polarizability of the wells and the density overlap between them are small in comparison to that of the atomic densities that arise from the molecular density partitioning used in post-density-functional theory (DFT) damped dispersion corrections, or DFT-D methods. Therefore, the nonadditivity of the leading-order dispersion observed here is a conservative estimate of that in molecular clusters.

  6. Single versus pairwise interpretation of cardiotochography, a comparative study from six Swedish delivery units.

    PubMed

    Åmark, Hanna; Millde-Luthander, Charlotte; Ajne, Gunilla; Högberg, Ulf; Pettersson, Hans; Wiklund, Ingela; Grunewald, Charlotta

    2014-12-01

    The aim of the study was to evaluate whether interpreting CTG pairwise brings about a higher level of correctly classified CTG recordings in a non-selected population of midwives and physicians. A comparative study. Five delivery units in Stockholm and one delivery unit in Uppsala, with 1589, 3740, 3908, 4539, 6438, and 7331 deliveries in 2011, respectively. 536 midwives and physicians classified one randomly selected CTG recording individually followed by a pairwise classification. The pairs consisted of two midwives (119 pairs) or one midwife and one physician (149 pairs), a total of 268 pairs. The proportion of individually correctly classified CTG recordings versus the proportion of pairwise correctly classified CTG recordings. The proportion of individually correctly classified CTG's was 75% and the proportion of pairwise correctly classified CTG's was 80% (difference 5%, p = 0.12). There was no statistically significant difference when CTG's were classified pairwise compared to individual classifications. The proportion of individually correctly classified CTG's was high (75%). There were differences in the proportion of correctly classified CTG recordings between the delivery units, indicating potential areas of improvement. Copyright © 2014 Elsevier B.V. All rights reserved.

  7. Relativistic covariance of Ohm's law

    NASA Astrophysics Data System (ADS)

    Starke, R.; Schober, G. A. H.

    2016-04-01

    The derivation of Lorentz-covariant generalizations of Ohm's law has been a long-term issue in theoretical physics with deep implications for the study of relativistic effects in optical and atomic physics. In this article, we propose an alternative route to this problem, which is motivated by the tremendous progress in first-principles materials physics in general and ab initio electronic structure theory in particular. We start from the most general, Lorentz-covariant first-order response law, which is written in terms of the fundamental response tensor χμ ν relating induced four-currents to external four-potentials. By showing the equivalence of this description to Ohm's law, we prove the validity of Ohm's law in every inertial frame. We further use the universal relation between χμ ν and the microscopic conductivity tensor σkℓ to derive a fully relativistic transformation law for the latter, which includes all effects of anisotropy and relativistic retardation. In the special case of a constant, scalar conductivity, this transformation law can be used to rederive a standard textbook generalization of Ohm's law.

  8. Equivalence of kernel machine regression and kernel distance covariance for multidimensional phenotype association studies.

    PubMed

    Hua, Wen-Yu; Ghosh, Debashis

    2015-09-01

    Associating genetic markers with a multidimensional phenotype is an important yet challenging problem. In this work, we establish the equivalence between two popular methods: kernel-machine regression (KMR), and kernel distance covariance (KDC). KMR is a semiparametric regression framework that models covariate effects parametrically and genetic markers non-parametrically, while KDC represents a class of methods that include distance covariance (DC) and Hilbert-Schmidt independence criterion (HSIC), which are nonparametric tests of independence. We show that the equivalence between the score test of KMR and the KDC statistic under certain conditions can lead to a novel generalization of the KDC test that incorporates covariates. Our contributions are 3-fold: (1) establishing the equivalence between KMR and KDC; (2) showing that the principles of KMR can be applied to the interpretation of KDC; (3) the development of a broader class of KDC statistics, where the class members are statistics corresponding to different kernel combinations. Finally, we perform simulation studies and an analysis of real data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) study. The ADNI study suggest that SNPs of FLJ16124 exhibit pairwise interaction effects that are strongly correlated to the changes of brain region volumes. © 2015, The International Biometric Society.

  9. Children with Attention Deficit Disorders. ADD Fact Sheet.

    ERIC Educational Resources Information Center

    Parker, Harvey C.

    This fact sheet summarizes basic information on Attention Deficit Disorders (ADD), including prevalence and characteristics, causes, identification, treatment, outcomes, and suggestions. Children with ADD comprise approximately 3-5 percent of the school age population, with boys significantly outnumbering girls. Of 14 characteristics of ADD, the…

  10. Pairwise Force Smoothed Particle Hydrodynamics model for multiphase flow: Surface tension and contact line dynamics

    SciTech Connect

    Tartakovsky, Alexandre M.; Panchenko, Alexander

    2016-01-01

    We present a novel formulation of the Pairwise Force Smoothed Particle Hydrodynamics Model (PF-SPH) and use it to simulate two- and three-phase flows in bounded domains. In the PF-SPH model, the Navier-Stokes equations are discretized with the Smoothed Particle Hydrodynamics (SPH) method and the Young-Laplace boundary condition at the fluid-fluid interface and the Young boundary condition at the fluid-fluid-solid interface are replaced with pairwise forces added into the Navier-Stokes equations. We derive a relationship between the parameters in the pairwise forces and the surface tension and static contact angle. Next, we demonstrate the accuracy of the model under static and dynamic conditions. Finally, to demonstrate the capabilities and robustness of the model we use it to simulate flow of three fluids in a porous material.

  11. Pairwise Force Smoothed Particle Hydrodynamics model for multiphase flow: Surface tension and contact line dynamics

    NASA Astrophysics Data System (ADS)

    Tartakovsky, Alexandre M.; Panchenko, Alexander

    2016-01-01

    We present a novel formulation of the Pairwise Force Smoothed Particle Hydrodynamics (PF-SPH) model and use it to simulate two- and three-phase flows in bounded domains. In the PF-SPH model, the Navier-Stokes equations are discretized with the Smoothed Particle Hydrodynamics (SPH) method, and the Young-Laplace boundary condition at the fluid-fluid interface and the Young boundary condition at the fluid-fluid-solid interface are replaced with pairwise forces added into the Navier-Stokes equations. We derive a relationship between the parameters in the pairwise forces and the surface tension and static contact angle. Next, we demonstrate the model's accuracy under static and dynamic conditions. Finally, we use the Pf-SPH model to simulate three phase flow in a porous medium.

  12. COVARIANCE ASSISTED SCREENING AND ESTIMATION

    PubMed Central

    Ke, By Tracy; Jin, Jiashun; Fan, Jianqing

    2014-01-01

    Consider a linear model Y = X β + z, where X = Xn,p and z ~ N(0, In). The vector β is unknown and it is of interest to separate its nonzero coordinates from the zero ones (i.e., variable selection). Motivated by examples in long-memory time series (Fan and Yao, 2003) and the change-point problem (Bhattacharya, 1994), we are primarily interested in the case where the Gram matrix G = X′X is non-sparse but sparsifiable by a finite order linear filter. We focus on the regime where signals are both rare and weak so that successful variable selection is very challenging but is still possible. We approach this problem by a new procedure called the Covariance Assisted Screening and Estimation (CASE). CASE first uses a linear filtering to reduce the original setting to a new regression model where the corresponding Gram (covariance) matrix is sparse. The new covariance matrix induces a sparse graph, which guides us to conduct multivariate screening without visiting all the submodels. By interacting with the signal sparsity, the graph enables us to decompose the original problem into many separated small-size subproblems (if only we know where they are!). Linear filtering also induces a so-called problem of information leakage, which can be overcome by the newly introduced patching technique. Together, these give rise to CASE, which is a two-stage Screen and Clean (Fan and Song, 2010; Wasserman and Roeder, 2009) procedure, where we first identify candidates of these submodels by patching and screening, and then re-examine each candidate to remove false positives. For any procedure β̂ for variable selection, we measure the performance by the minimax Hamming distance between the sign vectors of β̂ and β. We show that in a broad class of situations where the Gram matrix is non-sparse but sparsifiable, CASE achieves the optimal rate of convergence. The results are successfully applied to long-memory time series and the change-point model. PMID:25541567

  13. Pairwise FCM based feature weighting for improved classification of vertebral column disorders.

    PubMed

    Unal, Yavuz; Polat, Kemal; Erdinc Kocer, H

    2014-03-01

    In this paper, an innovative data pre-processing method to improve the classification performance and to determine automatically the vertebral column disorders including disk hernia (DH), spondylolisthesis (SL) and normal (NO) groups has been proposed. In the classification of vertebral column disorders' dataset with three classes, a pairwise fuzzy C-means (FCM) based feature weighting method has been proposed. In this method, first of all, the vertebral column dataset has been grouped as pairwise (DH-SL, DH-NO, and SL-NO) and then these pairwise groups have been weighted using a FCM based feature set. These weighted groups have been classified using classifier algorithms including multilayer perceptron (MLP), k-nearest neighbor (k-NN), Naive Bayes, and support vector machine (SVM). The general classification performance has been obtained by averaging of classification accuracies obtained from pairwise classifier algorithms. To evaluate the performance of the proposed method, the classification accuracy, sensitivity, specificity, ROC curves, and f-measure have been used. Without the proposed feature weighting, the obtained f-measure values were 0.7738 for MLP classifier, 0.7021 for k-NN, 0.7263 for Naive Bayes, and 0.7298 for SVM classifier algorithms in the classification of vertebral column disorders' dataset with three classes. With the pairwise fuzzy C-means based feature weighting method, the obtained f-measure values were 0.9509 for MLP, 0.9313 for k-NN, 0.9603 for Naive Bayes, and 0.9468 for SVM classifier algorithms. The experimental results demonstrated that the proposed pairwise fuzzy C-means based feature weighting method is robust and effective in the classification of vertebral column disorders' dataset. In the future, this method could be used confidently for medical datasets with more classes.

  14. SDT: a virus classification tool based on pairwise sequence alignment and identity calculation.

    PubMed

    Muhire, Brejnev Muhizi; Varsani, Arvind; Martin, Darren Patrick

    2014-01-01

    The perpetually increasing rate at which viral full-genome sequences are being determined is creating a pressing demand for computational tools that will aid the objective classification of these genome sequences. Taxonomic classification approaches that are based on pairwise genetic identity measures are potentially highly automatable and are progressively gaining favour with the International Committee on Taxonomy of Viruses (ICTV). There are, however, various issues with the calculation of such measures that could potentially undermine the accuracy and consistency with which they can be applied to virus classification. Firstly, pairwise sequence identities computed based on multiple sequence alignments rather than on multiple independent pairwise alignments can lead to the deflation of identity scores with increasing dataset sizes. Also, when gap-characters need to be introduced during sequence alignments to account for insertions and deletions, methodological variations in the way that these characters are introduced and handled during pairwise genetic identity calculations can cause high degrees of inconsistency in the way that different methods classify the same sets of sequences. Here we present Sequence Demarcation Tool (SDT), a free user-friendly computer program that aims to provide a robust and highly reproducible means of objectively using pairwise genetic identity calculations to classify any set of nucleotide or amino acid sequences. SDT can produce publication quality pairwise identity plots and colour-coded distance matrices to further aid the classification of sequences according to ICTV approved taxonomic demarcation criteria. Besides a graphical interface version of the program for Windows computers, command-line versions of the program are available for a variety of different operating systems (including a parallel version for cluster computing platforms).

  15. Perceptron learning of pairwise contact energies for proteins incorporating the amino acid environment

    NASA Astrophysics Data System (ADS)

    Heo, Muyoung; Kim, Suhkmann; Moon, Eun-Joung; Cheon, Mookyung; Chung, Kwanghoon; Chang, Iksoo

    2005-07-01

    Although a coarse-grained description of proteins is a simple and convenient way to attack the protein folding problem, the construction of a global pairwise energy function which can simultaneously recognize the native folds of many proteins has resulted in partial success. We have sought the possibility of a systematic improvement of this pairwise-contact energy function as we extended the parameter space of amino acids, incorporating local environments of amino acids, beyond a 20×20 matrix. We have studied the pairwise contact energy functions of 20×20 , 60×60 , and 180×180 matrices depending on the extent of parameter space, and compared their effect on the learnability of energy parameters in the context of a gapless threading, bearing in mind that a 20×20 pairwise contact matrix has been shown to be too simple to recognize the native folds of many proteins. In this paper, we show that the construction of a global pairwise energy function was achieved using 1006 training proteins of a homology of less than 30%, which include all representatives of different protein classes. After parametrizing the local environments of the amino acids into nine categories depending on three secondary structures and three kinds of hydrophobicity (desolvation), the 16290 pairwise contact energies (scores) of the amino acids could be determined by perceptron learning and protein threading. These could simultaneously recognize all the native folds of the 1006 training proteins. When these energy parameters were tested on the 382 test proteins of a homology of less than 90%, 370 (96.9%) proteins could recognize their native folds. We set up a simple thermodynamic framework in the conformational space of decoys to calculate the unfolded fraction and the specific heat of real proteins. The different thermodynamic stabilities of E.coli ribonuclease H (RNase H) and its mutants were well described in our calculation, agreeing with the experiment.

  16. Frailty models with missing covariates.

    PubMed

    Herring, Amy H; Ibrahim, Joseph G; Lipsitz, Stuart R

    2002-03-01

    We present a method for estimating the parameters in random effects models for survival data when covariates are subject to missingness. Our method is more general than the usual frailty model as it accommodates a wide range of distributions for the random effects, which are included as an offset in the linear predictor in a manner analogous to that used in generalized linear mixed models. We propose using a Monte Carlo EM algorithm along with the Gibbs sampler to obtain parameter estimates. This method is useful in reducing the bias that may be incurred using complete-case methods in this setting. The methodology is applied to data from Eastern Cooperative Oncology Group melanoma clinical trials in which observations were believed to be clustered and several tumor characteristics were not always observed.

  17. Effects of pairwise versus many-body forces on high-stress plastic deformation

    NASA Astrophysics Data System (ADS)

    Holian, B. L.; Voter, A. F.; Wagner, N. J.; Ravelo, R. J.; Chen, S. P.; Hoover, W. G.; Hoover, C. G.; Hammerberg, J. E.; Dontje, T. D.

    1991-03-01

    We propose a model embedded-atom (many-body) potential and test it against an effective, density-independent, pairwise-additive potential in a variety of nonequilibrium molecular-dynamics simulations of plastic deformation under high stress. Even though both kinds of interactions have nearly the same equilibrium equation of state, the defect energies (i.e., vacancy formation and surface energies) are quite different. As a result, we observe significant qualitative differences in flow behavior between systems characterized by purely pairwise interactions versus higher-order many-body forces.

  18. Comparing Robustness of Pairwise and Multiclass Neural-Network Systems for Face Recognition

    NASA Astrophysics Data System (ADS)

    Uglov, J.; Jakaite, L.; Schetinin, V.; Maple, C.

    2007-12-01

    Noise, corruptions, and variations in face images can seriously hurt the performance of face-recognition systems. To make these systems robust to noise and corruptions in image data, multiclass neural networks capable of learning from noisy data have been suggested. However on large face datasets such systems cannot provide the robustness at a high level. In this paper, we explore a pairwise neural-network system as an alternative approach to improve the robustness of face recognition. In our experiments, the pairwise recognition system is shown to outperform the multiclass-recognition system in terms of the predictive accuracy on the test face images.

  19. Covariant diagrams for one-loop matching

    DOE PAGES

    Zhang, Zhengkang

    2017-05-30

    Here, we present a diagrammatic formulation of recently-revived covariant functional approaches to one-loop matching from an ultraviolet (UV) theory to a low-energy effective fi eld theory. Various terms following from a covariant derivative expansion (CDE) are represented by diagrams which, unlike conventional Feynman diagrams, involve gauge-covariant quantities and are thus dubbed "covariant diagrams." The use of covariant diagrams helps organize and simplify one-loop matching calculations, which we illustrate with examples. Of particular interest is the derivation of UV model-independent universal results, which reduce matching calculations of specifi c UV models to applications of master formulas. We also show how suchmore » derivation can be done in a more concise manner than the previous literature, and discuss how additional structures that are not directly captured by existing universal results, including mixed heavy-light loops, open covariant derivatives, and mixed statistics, can be easily accounted for.« less

  20. Covariant diagrams for one-loop matching

    NASA Astrophysics Data System (ADS)

    Zhang, Zhengkang

    2017-05-01

    We present a diagrammatic formulation of recently-revived covariant functional approaches to one-loop matching from an ultraviolet (UV) theory to a low-energy effective field theory. Various terms following from a covariant derivative expansion (CDE) are represented by diagrams which, unlike conventional Feynman diagrams, involve gauge-covariant quantities and are thus dubbed "covariant diagrams." The use of covariant diagrams helps organize and simplify one-loop matching calculations, which we illustrate with examples. Of particular interest is the derivation of UV model-independent universal results, which reduce matching calculations of specific UV models to applications of master formulas. We show how such derivation can be done in a more concise manner than the previous literature, and discuss how additional structures that are not directly captured by existing universal results, including mixed heavy-light loops, open covariant derivatives, and mixed statistics, can be easily accounted for.

  1. Covariant density functional theory: The role of the pion

    SciTech Connect

    Lalazissis, G. A.; Karatzikos, S.; Serra, M.; Otsuka, T.; Ring, P.

    2009-10-15

    We investigate the role of the pion in covariant density functional theory. Starting from conventional relativistic mean field (RMF) theory with a nonlinear coupling of the {sigma} meson and without exchange terms we add pions with a pseudovector coupling to the nucleons in relativistic Hartree-Fock approximation. In order to take into account the change of the pion field in the nuclear medium the effective coupling constant of the pion is treated as a free parameter. It is found that the inclusion of the pion to this sort of density functionals does not destroy the overall description of the bulk properties by RMF. On the other hand, the noncentral contribution of the pion (tensor coupling) does have effects on single particle energies and on binding energies of certain nuclei.

  2. Shrinkage approach for EEG covariance matrix estimation.

    PubMed

    Beltrachini, Leandro; von Ellenrieder, Nicolas; Muravchik, Carlos H

    2010-01-01

    We present a shrinkage estimator for the EEG spatial covariance matrix of the background activity. We show that such an estimator has some advantages over the maximum likelihood and sample covariance estimators when the number of available data to carry out the estimation is low. We find sufficient conditions for the consistency of the shrinkage estimators and results concerning their numerical stability. We compare several shrinkage schemes and show how to improve the estimator by incorporating known structure of the covariance matrix.

  3. ANL Critical Assembly Covariance Matrix Generation - Addendum

    SciTech Connect

    McKnight, Richard D.; Grimm, Karl N.

    2014-01-13

    In March 2012, a report was issued on covariance matrices for Argonne National Laboratory (ANL) critical experiments. That report detailed the theory behind the calculation of covariance matrices and the methodology used to determine the matrices for a set of 33 ANL experimental set-ups. Since that time, three new experiments have been evaluated and approved. This report essentially updates the previous report by adding in these new experiments to the preceding covariance matrix structure.

  4. Balancing continuous covariates based on Kernel densities.

    PubMed

    Ma, Zhenjun; Hu, Feifang

    2013-03-01

    The balance of important baseline covariates is essential for convincing treatment comparisons. Stratified permuted block design and minimization are the two most commonly used balancing strategies, both of which require the covariates to be discrete. Continuous covariates are typically discretized in order to be included in the randomization scheme. But breakdown of continuous covariates into subcategories often changes the nature of the covariates and makes distributional balance unattainable. In this article, we propose to balance continuous covariates based on Kernel density estimations, which keeps the continuity of the covariates. Simulation studies show that the proposed Kernel-Minimization can achieve distributional balance of both continuous and categorical covariates, while also keeping the group size well balanced. It is also shown that the Kernel-Minimization is less predictable than stratified permuted block design and minimization. Finally, we apply the proposed method to redesign the NINDS trial, which has been a source of controversy due to imbalance of continuous baseline covariates. Simulation shows that imbalances such as those observed in the NINDS trial can be generally avoided through the implementation of the new method. Copyright © 2012 Elsevier Inc. All rights reserved.

  5. Lorentz covariant {kappa}-Minkowski spacetime

    SciTech Connect

    DaPbrowski, Ludwik; Godlinski, Michal; Piacitelli, Gherardo

    2010-06-15

    In recent years, different views on the interpretation of Lorentz covariance of noncommuting coordinates have been discussed. By a general procedure, we construct the minimal canonical central covariantization of the {kappa}-Minkowski spacetime. Here, undeformed Lorentz covariance is implemented by unitary operators, in the presence of two dimensionful parameters. We then show that, though the usual {kappa}-Minkowski spacetime is covariant under deformed (or twisted) Lorentz action, the resulting framework is equivalent to taking a noncovariant restriction of the covariantized model. We conclude with some general comments on the approach of deformed covariance.

  6. Improving the modelling of redshift-space distortions - I. A bivariate Gaussian description for the galaxy pairwise velocity distributions

    NASA Astrophysics Data System (ADS)

    Bianchi, Davide; Chiesa, Matteo; Guzzo, Luigi

    2015-01-01

    As a step towards a more accurate modelling of redshift-space distortions (RSD) in galaxy surveys, we develop a general description of the probability distribution function of galaxy pairwise velocities within the framework of the so-called streaming model. For a given galaxy separation r, such function can be described as a superposition of virtually infinite local distributions. We characterize these in terms of their moments and then consider the specific case in which they are Gaussian functions, each with its own mean μ and dispersion σ. Based on physical considerations, we make the further crucial assumption that these two parameters are in turn distributed according to a bivariate Gaussian, with its own mean and covariance matrix. Tests using numerical simulations explicitly show that with this compact description one can correctly model redshift-space distortions on all scales, fully capturing the overall linear and non-linear dynamics of the galaxy flow at different separations. In particular, we naturally obtain Gaussian/exponential, skewed/unskewed distribution functions, depending on separation as observed in simulations and data. Also, the recently proposed single-Gaussian description of RSD is included in this model as a limiting case, when the bivariate Gaussian is collapsed to a two-dimensional Dirac delta function. We also show how this description naturally allows for the Taylor expansion of 1 + ξS(s) around 1 + ξR(r), which leads to the Kaiser linear formula when truncated to second order, explicating its connection with the moments of the velocity distribution functions. More work is needed, but these results indicate a very promising path to make definitive progress in our programme to improve RSD estimators.

  7. A Scaling Study by Pair-Wise Comparison Method: Friend Choosing in Adolescents

    ERIC Educational Resources Information Center

    Özmercan, Esra Eminoglu; Kumandas, Hatice

    2016-01-01

    This study aims to identify the perception levels of characteristics considered important to choose friends by adolescents from secondary education and to scale them with pair-wise comparison judgements. In this respect, this study was conducted with 100 10th grade students from a state vocational high school located in Marmara region in Turkey.…

  8. Input nonlinearities can shape beyond-pairwise correlations and improve information transmission by neural populations

    NASA Astrophysics Data System (ADS)

    Zylberberg, Joel; Shea-Brown, Eric

    2015-12-01

    While recent recordings from neural populations show beyond-pairwise, or higher-order, correlations (HOC), we have little understanding of how HOC arise from network interactions and of how they impact encoded information. Here, we show that input nonlinearities imply HOC in spin-glass-type statistical models. We then discuss one such model with parametrized pairwise- and higher-order interactions, revealing conditions under which beyond-pairwise interactions increase the mutual information between a given stimulus type and the population responses. For jointly Gaussian stimuli, coding performance is improved by shaping output HOC only when neural firing rates are constrained to be low. For stimuli with skewed probability distributions (like natural image luminances), performance improves for all firing rates. Our work suggests surprising connections between nonlinear integration of neural inputs, stimulus statistics, and normative theories of population coding. Moreover, it suggests that the inclusion of beyond-pairwise interactions could improve the performance of Boltzmann machines for machine learning and signal processing applications.

  9. Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints

    PubMed Central

    Dowell, Robin D; Eddy, Sean R

    2006-01-01

    Background We are interested in the problem of predicting secondary structure for small sets of homologous RNAs, by incorporating limited comparative sequence information into an RNA folding model. The Sankoff algorithm for simultaneous RNA folding and alignment is a basis for approaches to this problem. There are two open problems in applying a Sankoff algorithm: development of a good unified scoring system for alignment and folding and development of practical heuristics for dealing with the computational complexity of the algorithm. Results We use probabilistic models (pair stochastic context-free grammars, pairSCFGs) as a unifying framework for scoring pairwise alignment and folding. A constrained version of the pairSCFG structural alignment algorithm was developed which assumes knowledge of a few confidently aligned positions (pins). These pins are selected based on the posterior probabilities of a probabilistic pairwise sequence alignment. Conclusion Pairwise RNA structural alignment improves on structure prediction accuracy relative to single sequence folding. Constraining on alignment is a straightforward method of reducing the runtime and memory requirements of the algorithm. Five practical implementations of the pairwise Sankoff algorithm – this work (Consan), David Mathews' Dynalign, Ian Holmes' Stemloc, Ivo Hofacker's PMcomp, and Jan Gorodkin's FOLDALIGN – have comparable overall performance with different strengths and weaknesses. PMID:16952317

  10. SVM-based detection of distant protein structural relationships using pairwise probabilistic suffix trees.

    PubMed

    Oğul, Hasan; Mumcuoğlu, Erkan U

    2006-08-01

    A new method based on probabilistic suffix trees (PSTs) is defined for pairwise comparison of distantly related protein sequences. The new definition is adopted in a discriminative framework for protein classification using pairwise sequence similarity scores in feature encoding. The framework uses support vector machines (SVMs) to separate structurally similar and dissimilar examples. The new discriminative system, which we call as SVM-PST, has been tested for SCOP family classification task, and compared with existing discriminative methods SVM-BLAST and SVM-Pairwise, which use BLAST similarity scores and dynamic-programming-based alignment scores, respectively. Results have shown that SVM-PST is more accurate than SVM-BLAST and competitive with SVM-Pairwise. In terms of computational efficiency, PST-based comparison is much better than dynamic-programming-based alignment. We also compared our results with the original family-based PST approach from which we were inspired. The present method provides a significantly better solution for protein classification in comparison with the family-based PST model.

  11. Document Level Assessment of Document Retrieval Systems in a Pairwise System Evaluation

    ERIC Educational Resources Information Center

    Rajagopal, Prabha; Ravana, Sri Devi

    2017-01-01

    Introduction: The use of averaged topic-level scores can result in the loss of valuable data and can cause misinterpretation of the effectiveness of system performance. This study aims to use the scores of each document to evaluate document retrieval systems in a pairwise system evaluation. Method: The chosen evaluation metrics are document-level…

  12. Hyperbolic Cosine Latent Trait Models for Unfolding Direct Responses and Pairwise Preferences.

    ERIC Educational Resources Information Center

    Andrich, David

    1995-01-01

    The hyperbolic cosine unfolding model for direct responses (HCMDR) of persons to individual stimuli is elaborated in three ways. The specialization of the second parameter is shown to be a property of the data, and not arbitrary. The HCMDR is used to construct an elegant model for pairwise preferences. (SLD)

  13. From Markovian to pairwise epidemic models and the performance of moment closure approximations.

    PubMed

    Taylor, Michael; Simon, Péter L; Green, Darren M; House, Thomas; Kiss, Istvan Z

    2012-05-01

    Many if not all models of disease transmission on networks can be linked to the exact state-based Markovian formulation. However the large number of equations for any system of realistic size limits their applicability to small populations. As a result, most modelling work relies on simulation and pairwise models. In this paper, for a simple SIS dynamics on an arbitrary network, we formalise the link between a well known pairwise model and the exact Markovian formulation. This involves the rigorous derivation of the exact ODE model at the level of pairs in terms of the expected number of pairs and triples. The exact system is then closed using two different closures, one well established and one that has been recently proposed. A new interpretation of both closures is presented, which explains several of their previously observed properties. The closed dynamical systems are solved numerically and the results are compared to output from individual-based stochastic simulations. This is done for a range of networks with the same average degree and clustering coefficient but generated using different algorithms. It is shown that the ability of the pairwise system to accurately model an epidemic is fundamentally dependent on the underlying large-scale network structure. We show that the existing pairwise models are a good fit for certain types of network but have to be used with caution as higher-order network structures may compromise their effectiveness.

  14. Intransitivity is infrequent and fails to promote annual plant coexistence without pairwise niche differences.

    PubMed

    Godoy, Oscar; Stouffer, Daniel B; Kraft, Nathan J B; Levine, Jonathan M

    2017-02-27

    Intransitive competition is often projected to be a widespread mechanism of species coexistence in ecological communities. However, it is unknown how much of the coexistence we observe in nature results from this mechanism when species interactions are also stabilized by pairwise niche differences. We combined field-parameterized models of competition among 18 annual plant species with tools from network theory to quantify the prevalence of intransitive competitive relationships. We then analyzed the predicted outcome of competitive interactions with and without pairwise niche differences. Intransitive competition was found for just 15 to 19% of the 816 possible triplets, and this mechanism was never sufficient to stabilize the coexistence of the triplet when the pair-wise niche differences between competitors were removed. Of the transitive and intransitive triplets, only four were predicted to coexist and these were more similar in multidimensional trait space defined by 11 functional traits than non-coexisting triplets. Our results argue that intransitive competition may be less frequent than recently posed, and that even when it does operate, pairwise niche differences may be key to possible coexistence. This article is protected by copyright. All rights reserved.

  15. Input nonlinearities can shape beyond-pairwise correlations and improve information transmission by neural populations.

    PubMed

    Zylberberg, Joel; Shea-Brown, Eric

    2015-12-01

    While recent recordings from neural populations show beyond-pairwise, or higher-order, correlations (HOC), we have little understanding of how HOC arise from network interactions and of how they impact encoded information. Here, we show that input nonlinearities imply HOC in spin-glass-type statistical models. We then discuss one such model with parametrized pairwise- and higher-order interactions, revealing conditions under which beyond-pairwise interactions increase the mutual information between a given stimulus type and the population responses. For jointly Gaussian stimuli, coding performance is improved by shaping output HOC only when neural firing rates are constrained to be low. For stimuli with skewed probability distributions (like natural image luminances), performance improves for all firing rates. Our work suggests surprising connections between nonlinear integration of neural inputs, stimulus statistics, and normative theories of population coding. Moreover, it suggests that the inclusion of beyond-pairwise interactions could improve the performance of Boltzmann machines for machine learning and signal processing applications.

  16. Pairwise beta diversity resolves an underappreciated source of confusion in calculating species turnover.

    PubMed

    Marion, Zachary H; Fordyce, James A; Fitzpatrick, Benjamin M

    2017-01-30

    Beta diversity is an important metric in ecology quantifying differentiation or disparity in composition among communities, ecosystems, or phenotypes. To compare systems with different sizes (N, number of units within a system), beta diversity is often converted to related indices such as turnover or local/regional differentiation. Here we use simulations to demonstrate that these naive measures of dissimilarity depend on sample size and design. We show that when N is the number of sampled units (e.g., quadrats) rather than the "true" number of communities in the system (if such exists), these differentiation measures are biased estimators. We propose using average pairwise dissimilarity as an intuitive solution. That is, instead of attempting to estimate an N-community measure, we advocate estimating the expected dissimilarity between any random pairs of communities (or sampling units)-especially when the "true" N is unknown or undefined. Fortunately, measures of pairwise dissimilarity or overlap have been used in ecology for decades, and their properties are well known. Using the same simulations, we show that average pairwise metrics give consistent and unbiased estimates regardless of the number of survey units sampled. We advocate pairwise dissimilarity as a general standardization to ensure commensurability of different study systems. This article is protected by copyright. All rights reserved.

  17. Covariant chiral kinetic equation in the Wigner function approach

    NASA Astrophysics Data System (ADS)

    Gao, Jian-hua; Pu, Shi; Wang, Qun

    2017-07-01

    The covariant chiral kinetic equation (CCKE) is derived from the four-dimensional Wigner function by an improved perturbative method under the static equilibrium conditions. The chiral kinetic equation in three dimensions can be obtained by integration over the time component of the four-momentum. There is freedom to add more terms to the CCKE allowed by conservation laws. In the derivation of the three-dimensional equation, there is also freedom to choose coefficients of some terms in d x0/d τ and d x /d τ [τ is a parameter along the worldline, and (x0,x ) denotes the time-space position of a particle] whose three-momentum integrals are vanishing. So the three-dimensional chiral kinetic equation derived from the CCKE is not uniquely determined in the current approach. The key assumption of our approach is the perturbation in powers of space-time derivative and constant electromagnetic field strength tensor under the static equilibrium conditions. To go beyond the current approach and overcome these problems one needs a new way of building up the three-dimensional chiral kinetic equation from the CCKE or directly from covariant Wigner equations.

  18. Covariation of Color and Luminance Facilitate Object Individuation in Infancy

    PubMed Central

    Woods, Rebecca J.; Wilcox, Teresa

    2013-01-01

    The ability to individuate objects is one of our most fundamental cognitive capacities. Recent research has revealed that when objects vary in color or luminance alone, infants fail to individuate those objects until 11.5 months. However, color and luminance frequently covary in the natural environment, thus providing a more salient and reliable indicator of distinct objects. For this reason, we propose that infants may be more likely to individuate when objects vary in both color and luminance. Using the narrow-screen task of Wilcox and Baillargeon (1998a), in Experiment 1 we assessed 7.5-month-old infants' ability to individuate uniformly colored objects that varied in both color and luminance or luminance alone. Experiment 2 further explored the link between color and luminance by assessing infants' ability to use pattern differences that included luminance or color to individuate objects. Results indicated that infants individuated objects only when covariations in color and luminance were used. These studies add to a growing body of literature investigating the interaction of color and luminance in object processing in infants and have implications for developmental changes in the nature and content of infants' object representations. PMID:20438179

  19. A Covariance Generation Methodology for Fission Product Yields

    NASA Astrophysics Data System (ADS)

    Terranova, N.; Serot, O.; Archier, P.; Vallet, V.; De Saint Jean, C.; Sumini, M.

    2016-03-01

    Recent safety and economical concerns for modern nuclear reactor applications have fed an outstanding interest in basic nuclear data evaluation improvement and completion. It has been immediately clear that the accuracy of our predictive simulation models was strongly affected by our knowledge on input data. Therefore strong efforts have been made to improve nuclear data and to generate complete and reliable uncertainty information able to yield proper uncertainty propagation on integral reactor parameters. Since in modern nuclear data banks (such as JEFF-3.1.1 and ENDF/BVII.1) no correlations for fission yields are given, in the present work we propose a covariance generation methodology for fission product yields. The main goal is to reproduce the existing European library and to add covariance information to allow proper uncertainty propagation in depletion and decay heat calculations. To do so, we adopted the Generalized Least Square Method (GLSM) implemented in CONRAD (COde for Nuclear Reaction Analysis and Data assimilation), developed at CEA-Cadarache. Theoretical values employed in the Bayesian parameter adjustment are delivered thanks to a convolution of different models, representing several quantities in fission yield calculations: the Brosa fission modes for pre-neutron mass distribution, a simplified Gaussian model for prompt neutron emission probability, theWahl systematics for charge distribution and the Madland-England model for the isomeric ratio. Some results will be presented for the thermal fission of U-235, Pu-239 and Pu-241.

  20. Non-pairwise additivity of the leading-order dispersion energy

    SciTech Connect

    Hollett, Joshua W.

    2015-02-28

    The leading-order (i.e., dipole-dipole) dispersion energy is calculated for one-dimensional (1D) and two-dimensional (2D) infinite lattices, and an infinite 1D array of infinitely long lines, of doubly occupied locally harmonic wells. The dispersion energy is decomposed into pairwise and non-pairwise additive components. By varying the force constant and separation of the wells, the non-pairwise additive contribution to the dispersion energy is shown to depend on the overlap of density between neighboring wells. As well separation is increased, the non-pairwise additivity of the dispersion energy decays. The different rates of decay for 1D and 2D lattices of wells is explained in terms of a Jacobian effect that influences the number of nearest neighbors. For an array of infinitely long lines of wells spaced 5 bohrs apart, and an inter-well spacing of 3 bohrs within a line, the non-pairwise additive component of the leading-order dispersion energy is −0.11 kJ mol{sup −1} well{sup −1}, which is 7% of the total. The polarizability of the wells and the density overlap between them are small in comparison to that of the atomic densities that arise from the molecular density partitioning used in post-density-functional theory (DFT) damped dispersion corrections, or DFT-D methods. Therefore, the nonadditivity of the leading-order dispersion observed here is a conservative estimate of that in molecular clusters.

  1. Robust covariance estimation of galaxy-galaxy weak lensing: validation and limitation of jackknife covariance

    NASA Astrophysics Data System (ADS)

    Shirasaki, Masato; Takada, Masahiro; Miyatake, Hironao; Takahashi, Ryuichi; Hamana, Takashi; Nishimichi, Takahiro; Murata, Ryoma

    2017-09-01

    We develop a method to simulate galaxy-galaxy weak lensing by utilizing all-sky, light-cone simulations and their inherent halo catalogues. Using the mock catalogue to study the error covariance matrix of galaxy-galaxy weak lensing, we compare the full covariance with the 'jackknife' (JK) covariance, the method often used in the literature that estimates the covariance from the resamples of the data itself. We show that there exists the variation of JK covariance over realizations of mock lensing measurements, while the average JK covariance over mocks can give a reasonably accurate estimation of the true covariance up to separations comparable with the size of JK subregion. The scatter in JK covariances is found to be ∼10 per cent after we subtract the lensing measurement around random points. However, the JK method tends to underestimate the covariance at the larger separations, more increasingly for a survey with a higher number density of source galaxies. We apply our method to the Sloan Digital Sky Survey (SDSS) data, and show that the 48 mock SDSS catalogues nicely reproduce the signals and the JK covariance measured from the real data. We then argue that the use of the accurate covariance, compared to the JK covariance, allows us to use the lensing signals at large scales beyond a size of the JK subregion, which contains cleaner cosmological information in the linear regime.

  2. Group Theory of Covariant Harmonic Oscillators

    ERIC Educational Resources Information Center

    Kim, Y. S.; Noz, Marilyn E.

    1978-01-01

    A simple and concrete example for illustrating the properties of noncompact groups is presented. The example is based on the covariant harmonic-oscillator formalism in which the relativistic wave functions carry a covariant-probability interpretation. This can be used in a group theory course for graduate students who have some background in…

  3. Quality Quantification of Evaluated Cross Section Covariances

    SciTech Connect

    Varet, S.; Dossantos-Uzarralde, P.

    2015-01-15

    Presently, several methods are used to estimate the covariance matrix of evaluated nuclear cross sections. Because the resulting covariance matrices can be different according to the method used and according to the assumptions of the method, we propose a general and objective approach to quantify the quality of the covariance estimation for evaluated cross sections. The first step consists in defining an objective criterion. The second step is computation of the criterion. In this paper the Kullback-Leibler distance is proposed for the quality quantification of a covariance matrix estimation and its inverse. It is based on the distance to the true covariance matrix. A method based on the bootstrap is presented for the estimation of this criterion, which can be applied with most methods for covariance matrix estimation and without the knowledge of the true covariance matrix. The full approach is illustrated on the {sup 85}Rb nucleus evaluations and the results are then used for a discussion on scoring and Monte Carlo approaches for covariance matrix estimation of the cross section evaluations.

  4. Covariance Structure Analysis of Ordinal Ipsative Data.

    ERIC Educational Resources Information Center

    Chan, Wai; Bentler, Peter M.

    1998-01-01

    Proposes a two-stage estimation method for the analysis of covariance structure models with ordinal ipsative data (OID). A goodness-of-fit statistic is given for testing the hypothesized covariance structure matrix, and simulation results show that the method works well with a large sample. (SLD)

  5. Group Theory of Covariant Harmonic Oscillators

    ERIC Educational Resources Information Center

    Kim, Y. S.; Noz, Marilyn E.

    1978-01-01

    A simple and concrete example for illustrating the properties of noncompact groups is presented. The example is based on the covariant harmonic-oscillator formalism in which the relativistic wave functions carry a covariant-probability interpretation. This can be used in a group theory course for graduate students who have some background in…

  6. Position Error Covariance Matrix Validation and Correction

    NASA Technical Reports Server (NTRS)

    Frisbee, Joe, Jr.

    2016-01-01

    In order to calculate operationally accurate collision probabilities, the position error covariance matrices predicted at times of closest approach must be sufficiently accurate representations of the position uncertainties. This presentation will discuss why the Gaussian distribution is a reasonable expectation for the position uncertainty and how this assumed distribution type is used in the validation and correction of position error covariance matrices.

  7. Adjoints and Low-rank Covariance Representation

    NASA Technical Reports Server (NTRS)

    Tippett, Michael K.; Cohn, Stephen E.

    2000-01-01

    Quantitative measures of the uncertainty of Earth System estimates can be as important as the estimates themselves. Second moments of estimation errors are described by the covariance matrix, whose direct calculation is impractical when the number of degrees of freedom of the system state is large. Ensemble and reduced-state approaches to prediction and data assimilation replace full estimation error covariance matrices by low-rank approximations. The appropriateness of such approximations depends on the spectrum of the full error covariance matrix, whose calculation is also often impractical. Here we examine the situation where the error covariance is a linear transformation of a forcing error covariance. We use operator norms and adjoints to relate the appropriateness of low-rank representations to the conditioning of this transformation. The analysis is used to investigate low-rank representations of the steady-state response to random forcing of an idealized discrete-time dynamical system.

  8. Spatio-temporal covariability in coho salmon ( Oncorhynchus kisutch) survival, from California to southeast Alaska

    NASA Astrophysics Data System (ADS)

    Teo, Steven L. H.; Botsford, Louis W.; Hastings, Alan

    2009-12-01

    One of the motivations of the GLOBEC Northeast Pacific program is to understand the apparent inverse relationship between the increase in salmon catches in the Gulf of Alaska and concurrent declines in the California Current System (CCS). We therefore used coded wire tag (CWT) data to examine the spatial and temporal patterns of covariability in the survival of hatchery coho salmon along the coast from California to southeast Alaska between release years 1980 and 2004. There is substantial covariability in coho salmon survival between neighboring regions along the coast, and there is clear evidence for increased covariability within two main groups - a northern and southern group. The dividing line between the groups lies approximately at the north end of Vancouver Island. However, CWT survivals do not support inverse covariability in hatchery coho salmon survival between southeast Alaska and the CCS over this 25 year time span. Instead, the hatchery coho survival in southeast Alaska is relatively uncorrelated with coho survival in the California Current System on inter-annual time scales. The 50% correlation and e-folding scales (distances at which magnitude of correlations decreases to 50% and e -1 (32.8%), respectively) of pairwise correlations between individual hatcheries were 150 and 217 km, which are smaller than that reported for sockeye, pink, and chum salmon. The 50% correlation scale of coho salmon is also substantially smaller than those reported for upwelling indices and sea surface temperature. There are also periods of 5-10 years with high covariability between adjacent regions on the scale of hundreds of km, which may be of biological and physical significance.

  9. Genetic diversity and species diversity of stream fishes covary across a land-use gradient.

    PubMed

    Blum, Michael J; Bagley, Mark J; Walters, David M; Jackson, Suzanne A; Daniel, F Bernard; Chaloud, Deborah J; Cade, Brian S

    2012-01-01

    Genetic diversity and species diversity are expected to covary according to area and isolation, but may not always covary with environmental heterogeneity. In this study, we examined how patterns of genetic and species diversity in stream fishes correspond to local and regional environmental conditions. To do so, we compared population size, genetic diversity and divergence in central stonerollers (Campostoma anomalum) to measures of species diversity and turnover in stream fish assemblages among similarly sized watersheds across an agriculture-forest land-use gradient in the Little Miami River basin (Ohio, USA). Significant correlations were found in many, but not all, pair-wise comparisons. Allelic richness and species richness were strongly correlated, for example, but diversity measures based on allele frequencies and assemblage structure were not. In-stream conditions related to agricultural land use were identified as significant predictors of genetic diversity and species diversity. Comparisons to population size indicate, however, that genetic diversity and species diversity are not necessarily independent and that variation also corresponds to watershed location and glaciation history in the drainage basin. Our findings demonstrate that genetic diversity and species diversity can covary in stream fish assemblages, and illustrate the potential importance of scaling observations to capture responses to hierarchical environmental variation. More comparisons according to life history variation could further improve understanding of conditions that give rise to parallel variation in genetic diversity and species diversity, which in turn could improve diagnosis of anthropogenic influences on aquatic ecosystems.

  10. Genetic diversity and species diversity of stream fishes covary across a land-use gradient

    USGS Publications Warehouse

    Blum, M.J.; Bagley, M.J.; Walters, D.M.; Jackson, S.A.; Daniel, F.B.; Chaloud, D.J.; Cade, B.S.

    2012-01-01

    Genetic diversity and species diversity are expected to covary according to area and isolation, but may not always covary with environmental heterogeneity. In this study, we examined how patterns of genetic and species diversity in stream fishes correspond to local and regional environmental conditions. To do so, we compared population size, genetic diversity and divergence in central stonerollers (Campostoma anomalum) to measures of species diversity and turnover in stream fish assemblages among similarly sized watersheds across an agriculture-forest land-use gradient in the Little Miami River basin (Ohio, USA). Significant correlations were found in many, but not all, pair-wise comparisons. Allelic richness and species richness were strongly correlated, for example, but diversity measures based on allele frequencies and assemblage structure were not. In-stream conditions related to agricultural land use were identified as significant predictors of genetic diversity and species diversity. Comparisons to population size indicate, however, that genetic diversity and species diversity are not necessarily independent and that variation also corresponds to watershed location and glaciation history in the drainage basin. Our findings demonstrate that genetic diversity and species diversity can covary in stream fish assemblages, and illustrate the potential importance of scaling observations to capture responses to hierarchical environmental variation. More comparisons according to life history variation could further improve understanding of conditions that give rise to parallel variation in genetic diversity and species diversity, which in turn could improve diagnosis of anthropogenic influences on aquatic ecosystems. ?? 2011 Springer-Verlag.

  11. Characterizing conserved structural contacts by pair-wise relative contacts and relative packing groups.

    PubMed

    Holmes, J Bradley; Tsai, Jerry

    2005-12-02

    To adequately deal with the inherent complexity of interactions between protein side-chains, we develop and describe here a novel method for characterizing protein packing within a fold family. Instead of approaching side-chain interactions absolutely from one residue to another, we instead consider the relative interactions of contacting residue pairs. The basic element, the pair-wise relative contact, is constructed from a sequence alignment and contact analysis of a set of structures and consists of a cluster of similarly oriented, interacting, side-chain pairs. To demonstrate this construct's usefulness in analyzing protein structure, we used the pair-wise relative contacts to analyze two sets of protein structures as defined by SCOP: the diverse globin-like superfamily (126 structures) and the more uniform heme binding globin family (a 94 structure subset of the globin-like superfamily). The superfamily structure set produced 1266 unique pair-wise relative contacts, whereas the family structure subset gave 1001 unique pair-wise relative contacts. For both sets, we show that these constructs can be used to accurately and automatically differentiate between fold classes. Furthermore, these pair-wise relative contacts correlate well with sequence identity and thus provide a direct relationship between changes in sequence and changes in structure. To capture the complexity of protein packing, these pair-wise relative contacts can be superimposed around a single residue to create a multi-body construct called a relative packing group. Construction of convex hulls around the individual packing groups provides a measure of the variation in packing around a residue and defines an approximate volume of space occupied by the groups interacting with a residue. We find that these relative packing groups are useful in understanding the structural quality of sequence or structure alignments. Moreover, they provide context to calculate a value for structural randomness

  12. Global multiple protein-protein interaction network alignment by combining pairwise network alignments

    PubMed Central

    2015-01-01

    Background A wealth of protein interaction data has become available in recent years, creating an urgent need for powerful analysis techniques. In this context, the problem of finding biologically meaningful correspondences between different protein-protein interaction networks (PPIN) is of particular interest. The PPIN of a species can be compared with that of other species through the process of PPIN alignment. Such an alignment can provide insight into basic problems like species evolution and network component function determination, as well as translational problems such as target identification and elucidation of mechanisms of disease spread. Furthermore, multiple PPINs can be aligned simultaneously, expanding the analytical implications of the result. While there are several pairwise network alignment algorithms, few methods are capable of multiple network alignment. Results We propose SMAL, a MNA algorithm based on the philosophy of scaffold-based alignment. SMAL is capable of converting results from any global pairwise alignment algorithms into a MNA in linear time. Using this method, we have built multiple network alignments based on combining pairwise alignments from a number of publicly available (pairwise) network aligners. We tested SMAL using PPINs of eight species derived from the IntAct repository and employed a number of measures to evaluate performance. Additionally, as part of our experimental investigations, we compared the effectiveness of SMAL while aligning up to eight input PPINs, and examined the effect of scaffold network choice on the alignments. Conclusions A key advantage of SMAL lies in its ability to create MNAs through the use of pairwise network aligners for which native MNA implementations do not exist. Experiments indicate that the performance of SMAL was comparable to that of the native MNA implementation of established methods such as IsoRankN and SMETANA. However, in terms of computational time, SMAL was significantly faster

  13. Concordance between criteria for covariate model building.

    PubMed

    Hennig, Stefanie; Karlsson, Mats O

    2014-04-01

    When performing a population pharmacokinetic modelling analysis covariates are often added to the model. Such additions are often justified by improved goodness of fit and/or decreased in unexplained (random) parameter variability. Increased goodness of fit is most commonly measured by the decrease in the objective function value. Parameter variability can be defined as the sum of unexplained (random) and explained (predictable) variability. Increase in magnitude of explained parameter variability could be another possible criterion for judging improvement in the model. The agreement between these three criteria in diagnosing covariate-parameter relationships of different strengths and nature using stochastic simulations and estimations as well as assessing covariate-parameter relationships in four previously published real data examples were explored. Total estimated parameter variability was found to vary with the number of covariates introduced on the parameter. In the simulated examples and two real examples, the parameter variability increased with increasing number of included covariates. For the other real examples parameter variability decreased or did not change systematically with the addition of covariates. The three criteria were highly correlated, with the decrease in unexplained variability being more closely associated with changes in objective function values than increases in explained parameter variability were. The often used assumption that inclusion of covariates in models only shifts unexplained parameter variability to explained parameter variability appears not to be true, which may have implications for modelling decisions.

  14. Dyslexia and ADD: 20 Questions Parents Ask. Children with Disabilities.

    ERIC Educational Resources Information Center

    Pickering, Joyce S.

    2002-01-01

    This article uses a question-answer format to present information for parents on dyslexia and attention deficit disorders (ADD). Information includes typical behaviors and skills of children with dyslexia or ADD, how parents can help their children, and the use of medication to control hyperactivity. (KB)

  15. Discovering Focus: Helping Students with ADD (Attention Deficit Disorder)

    ERIC Educational Resources Information Center

    Valkenburg, Jim

    2012-01-01

    Attention Deficit Disorder (ADD) is a neurological disorder which effects learning and that has a confusing set of diagnostic symptoms and an even more confusing set of remedies ranging from medication to meditation to nothing at all. Current neurological research suggests, however, that there are strategies that the individual with ADD can use to…

  16. Discovering Focus: Helping Students with ADD (Attention Deficit Disorder)

    ERIC Educational Resources Information Center

    Valkenburg, Jim

    2012-01-01

    Attention Deficit Disorder (ADD) is a neurological disorder which effects learning and that has a confusing set of diagnostic symptoms and an even more confusing set of remedies ranging from medication to meditation to nothing at all. Current neurological research suggests, however, that there are strategies that the individual with ADD can use to…

  17. Social Capital: Does It Add to the Health Inequalities Debate?

    ERIC Educational Resources Information Center

    Chappell, Neena L.; Funk, Laura M.

    2010-01-01

    This paper empirically examines the relationship between advantage, social capital and health status to assess (a) whether social capital adds explanatory power to what we already know about the relationship between advantage and health and (b) whether social capital adds anything beyond its component parts, namely social participation and trust.…

  18. Social Capital: Does It Add to the Health Inequalities Debate?

    ERIC Educational Resources Information Center

    Chappell, Neena L.; Funk, Laura M.

    2010-01-01

    This paper empirically examines the relationship between advantage, social capital and health status to assess (a) whether social capital adds explanatory power to what we already know about the relationship between advantage and health and (b) whether social capital adds anything beyond its component parts, namely social participation and trust.…

  19. Reliability-based covariance control design

    SciTech Connect

    Field, R.V. Jr.; Bergman, L.A.

    1997-03-01

    An extension to classical covariance control methods, introduced by Skelton and co-workers, is proposed specifically for application to the control of civil engineering structures subjected to random dynamic excitations. The covariance structure of the system is developed directly from specification of its reliability via the assumption of independent (Poisson) outcrossings of its stationary response process from a polyhedral safe region. This leads to a set of state covariance controllers, each of which guarantees that the closed-loop system will possess the specified level of reliability. An example civil engineering structure is considered.

  20. Conformal Covariance and the Split Property

    NASA Astrophysics Data System (ADS)

    Morinelli, Vincenzo; Tanimoto, Yoh; Weiner, Mihály

    2017-08-01

    We show that for a conformal local net of observables on the circle, the split property is automatic. Both full conformal covariance (i.e., diffeomorphism covariance) and the circle-setting play essential roles in this fact, while by previously constructed examples it was already known that even on the circle, Möbius covariance does not imply the split property. On the other hand, here we also provide an example of a local conformal net living on the 2-dimensional Minkowski space, which—although being diffeomorphism covariant—does not have the split property.

  1. Pairwise entanglement and critical behavior of an anisotropic ferrimagnetic spin chain

    NASA Astrophysics Data System (ADS)

    Solano-Carrillo, E.; Franco, R.; Silva-Valencia, J.

    2011-02-01

    We studied the quantum phase transition revealed to occur in the ferrimagnetic mixed-spin (S,s)=(1,1/2) chain with positive crystal-field anisotropy D under an external magnetic field by using concepts from quantum information theory such as pairwise entanglement and purity, incorporated into the density matrix renormalization group algorithm. In this system, a magnetization plateau appears at 1/3 of the saturation magnetization for all values of D except for a critical value Dc where it vanishes. We obtained this value Dc=1.11445±0.00065 within the thermodynamic limit as local minima of the pairwise entanglement and the purity. Moreover, using this procedure we were able to investigate the second-order (or continuous) character of the quantum phase transition.

  2. Pairwise adaptive thermostats for improved accuracy and stability in dissipative particle dynamics

    NASA Astrophysics Data System (ADS)

    Leimkuhler, Benedict; Shang, Xiaocheng

    2016-11-01

    We examine the formulation and numerical treatment of dissipative particle dynamics (DPD) and momentum-conserving molecular dynamics. We show that it is possible to improve both the accuracy and the stability of DPD by employing a pairwise adaptive Langevin thermostat that precisely matches the dynamical characteristics of DPD simulations (e.g., autocorrelation functions) while automatically correcting thermodynamic averages using a negative feedback loop. In the low friction regime, it is possible to replace DPD by a simpler momentum-conserving variant of the Nosé-Hoover-Langevin method based on thermostatting only pairwise interactions; we show that this method has an extra order of accuracy for an important class of observables (a superconvergence result), while also allowing larger timesteps than alternatives. All the methods mentioned in the article are easily implemented. Numerical experiments are performed in both equilibrium and nonequilibrium settings; using Lees-Edwards boundary conditions to induce shear flow.

  3. NgsRelate: a software tool for estimating pairwise relatedness from next-generation sequencing data.

    PubMed

    Korneliussen, Thorfinn Sand; Moltke, Ida

    2015-12-15

    Pairwise relatedness estimation is important in many contexts such as disease mapping and population genetics. However, all existing estimation methods are based on called genotypes, which is not ideal for next-generation sequencing (NGS) data of low depth from which genotypes cannot be called with high certainty. We present a software tool, NgsRelate, for estimating pairwise relatedness from NGS data. It provides maximum likelihood estimates that are based on genotype likelihoods instead of genotypes and thereby takes the inherent uncertainty of the genotypes into account. Using both simulated and real data, we show that NgsRelate provides markedly better estimates for low-depth NGS data than two state-of-the-art genotype-based methods. NgsRelate is implemented in C++ and is available under the GNU license at www.popgen.dk/software. © The Author 2015. Published by Oxford University Press.

  4. NgsRelate: a software tool for estimating pairwise relatedness from next-generation sequencing data

    PubMed Central

    Korneliussen, Thorfinn Sand; Moltke, Ida

    2015-01-01

    Motivation: Pairwise relatedness estimation is important in many contexts such as disease mapping and population genetics. However, all existing estimation methods are based on called genotypes, which is not ideal for next-generation sequencing (NGS) data of low depth from which genotypes cannot be called with high certainty. Results: We present a software tool, NgsRelate, for estimating pairwise relatedness from NGS data. It provides maximum likelihood estimates that are based on genotype likelihoods instead of genotypes and thereby takes the inherent uncertainty of the genotypes into account. Using both simulated and real data, we show that NgsRelate provides markedly better estimates for low-depth NGS data than two state-of-the-art genotype-based methods. Availability: NgsRelate is implemented in C++ and is available under the GNU license at www.popgen.dk/software. Contact: ida@binf.ku.dk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26323718

  5. A Ranking Procedure by Incomplete Pairwise Comparisons Using Information Entropy and Dempster-Shafer Evidence Theory

    PubMed Central

    Pan, Dongbo; Lu, Xi; Liu, Juan; Deng, Yong

    2014-01-01

    Decision-making, as a way to discover the preference of ranking, has been used in various fields. However, owing to the uncertainty in group decision-making, how to rank alternatives by incomplete pairwise comparisons has become an open issue. In this paper, an improved method is proposed for ranking of alternatives by incomplete pairwise comparisons using Dempster-Shafer evidence theory and information entropy. Firstly, taking the probability assignment of the chosen preference into consideration, the comparison of alternatives to each group is addressed. Experiments verified that the information entropy of the data itself can determine the different weight of each group's choices objectively. Numerical examples in group decision-making environments are used to test the effectiveness of the proposed method. Moreover, the divergence of ranking mechanism is analyzed briefly in conclusion section. PMID:25250393

  6. Pairwise Classifier Ensemble with Adaptive Sub-Classifiers for fMRI Pattern Analysis.

    PubMed

    Kim, Eunwoo; Park, HyunWook

    2017-02-01

    The multi-voxel pattern analysis technique is applied to fMRI data for classification of high-level brain functions using pattern information distributed over multiple voxels. In this paper, we propose a classifier ensemble for multiclass classification in fMRI analysis, exploiting the fact that specific neighboring voxels can contain spatial pattern information. The proposed method converts the multiclass classification to a pairwise classifier ensemble, and each pairwise classifier consists of multiple sub-classifiers using an adaptive feature set for each class-pair. Simulated and real fMRI data were used to verify the proposed method. Intra- and inter-subject analyses were performed to compare the proposed method with several well-known classifiers, including single and ensemble classifiers. The comparison results showed that the proposed method can be generally applied to multiclass classification in both simulations and real fMRI analyses.

  7. Pairwise adaptive thermostats for improved accuracy and stability in dissipative particle dynamics

    SciTech Connect

    Leimkuhler, Benedict Shang, Xiaocheng

    2016-11-01

    We examine the formulation and numerical treatment of dissipative particle dynamics (DPD) and momentum-conserving molecular dynamics. We show that it is possible to improve both the accuracy and the stability of DPD by employing a pairwise adaptive Langevin thermostat that precisely matches the dynamical characteristics of DPD simulations (e.g., autocorrelation functions) while automatically correcting thermodynamic averages using a negative feedback loop. In the low friction regime, it is possible to replace DPD by a simpler momentum-conserving variant of the Nosé–Hoover–Langevin method based on thermostatting only pairwise interactions; we show that this method has an extra order of accuracy for an important class of observables (a superconvergence result), while also allowing larger timesteps than alternatives. All the methods mentioned in the article are easily implemented. Numerical experiments are performed in both equilibrium and nonequilibrium settings; using Lees–Edwards boundary conditions to induce shear flow.

  8. Accounting for pairwise distance restraints in FFT-based protein-protein docking.

    PubMed

    Xia, Bing; Vajda, Sandor; Kozakov, Dima

    2016-11-01

    ClusPro is a heavily used protein-protein docking server based on the fast Fourier transform (FFT) correlation approach. While FFT enables global docking, accounting for pairwise distance restraints using penalty terms in the scoring function is computationally expensive. We use a different approach and directly select low energy solutions that also satisfy the given restraints. As expected, accounting for restraints generally improves the rank of near native predictions, while retaining or even improving the numerical efficiency of FFT based docking.

  9. Improvements to pairwise sequence comparison (PASC): a genome-based web tool for virus classification.

    PubMed

    Bao, Yiming; Chetvernin, Vyacheslav; Tatusova, Tatiana

    2014-12-01

    The number of viral genome sequences in the public databases is increasing dramatically, and these sequences are playing an important role in virus classification. Pairwise sequence comparison is a sequence-based virus classification method. A program using this method calculates the pairwise identities of virus sequences within a virus family and displays their distribution, and visual analysis helps to determine demarcations at different taxonomic levels such as strain, species, genus and subfamily. Subsequent comparison of new sequences against existing ones allows viruses from which the new sequences were derived to be classified. Although this method cannot be used as the only criterion for virus classification in some cases, it is a quantitative method and has many advantages over conventional virus classification methods. It has been applied to several virus families, and there is an increasing interest in using this method for other virus families/groups. The Pairwise Sequence Comparison (PASC) classification tool was created at the National Center for Biotechnology Information. The tool's database stores pairwise identities for complete genomes/segments of 56 virus families/groups. Data in the system are updated every day to reflect changes in virus taxonomy and additions of new virus sequences to the public database. The web interface of the tool ( http://www.ncbi.nlm.nih.gov/sutils/pasc/ ) makes it easy to navigate and perform analyses. Multiple new viral genome sequences can be tested simultaneously with this system to suggest the taxonomic position of virus isolates in a specific family. PASC eliminates potential discrepancies in the results caused by different algorithms and/or different data used by researchers.

  10. PTM Along Track Algorithm to Maintain Spacing During Same Direction Pair-Wise Trajectory Management Operations

    NASA Technical Reports Server (NTRS)

    Carreno, Victor A.

    2015-01-01

    Pair-wise Trajectory Management (PTM) is a cockpit based delegated responsibility separation standard. When an air traffic service provider gives a PTM clearance to an aircraft and the flight crew accepts the clearance, the flight crew will maintain spacing and separation from a designated aircraft. A PTM along track algorithm will receive state information from the designated aircraft and from the own ship to produce speed guidance for the flight crew to maintain spacing and separation

  11. Pairwise Kinship Analysis by the Index of Chromosome Sharing Using High-Density Single Nucleotide Polymorphisms.

    PubMed

    Morimoto, Chie; Manabe, Sho; Kawaguchi, Takahisa; Kawai, Chihiro; Fujimoto, Shuntaro; Hamano, Yuya; Yamada, Ryo; Matsuda, Fumihiko; Tamaki, Keiji

    2016-01-01

    We developed a new approach for pairwise kinship analysis in forensic genetics based on chromosomal sharing between two individuals. Here, we defined "index of chromosome sharing" (ICS) calculated using 174,254 single nucleotide polymorphism (SNP) loci typed by SNP microarray and genetic length of the shared segments from the genotypes of two individuals. To investigate the expected ICS distributions from first- to fifth-degree relatives and unrelated pairs, we used computationally generated genotypes to consider the effect of linkage disequilibrium and recombination. The distributions were used for probabilistic evaluation of the pairwise kinship analysis, such as likelihood ratio (LR) or posterior probability, without allele frequencies and haplotype frequencies. Using our method, all actual sample pairs from volunteers showed significantly high LR values (i.e., ≥ 108); therefore, we can distinguish distant relationships (up to the fifth-degree) from unrelated pairs based on LR. Moreover, we can determine accurate degrees of kinship in up to third-degree relationships with a probability of > 80% using the criterion of posterior probability ≥ 0.90, even if the kinship of the pair is totally unpredictable. This approach greatly improves pairwise kinship analysis of distant relationships, specifically in cases involving identification of disaster victims or missing persons.

  12. A Simple Mechanism for Beyond-Pairwise Correlations in Integrate-and-Fire Neurons.

    PubMed

    Leen, David A; Shea-Brown, Eric

    2015-12-01

    The collective dynamics of neural populations are often characterized in terms of correlations in the spike activity of different neurons. We have developed an understanding of the circuit mechanisms that lead to correlations among cell pairs, but little is known about what determines the population firing statistics among larger groups of cells. Here, we examine this question for a simple, but ubiquitous, circuit feature: common fluctuating input arriving to spiking neurons of integrate-and-fire type. We show that this leads to strong beyond-pairwise correlations-that is, correlations that cannot be captured by maximum entropy models that extrapolate from pairwise statistics-as for earlier work with discrete threshold crossing (dichotomous Gaussian) models. Moreover, we find that the same is true for another widely used, doubly stochastic model of neural spiking, the linear-nonlinear cascade. We demonstrate the strong connection between the collective dynamics produced by integrate-and-fire and dichotomous Gaussian models, and show that the latter is a surprisingly accurate model of the former. Our conclusion is that beyond-pairwise correlations can be both broadly expected and possible to describe by simplified (and tractable) statistical models.

  13. Using Incidence Sampling to Estimate Covariances.

    ERIC Educational Resources Information Center

    Knapp, Thomas R.

    1979-01-01

    This paper presents the generalized symmetric means approach to the estimation of population covariances, complete with derivations and examples. Particular attention is paid to the problem of missing data, which is handled very naturally in the incidence sampling framework. (CTM)

  14. Conformally covariant parametrizations for relativistic initial data

    NASA Astrophysics Data System (ADS)

    Delay, Erwann

    2017-01-01

    We revisit the Lichnerowicz-York method, and an alternative method of York, in order to obtain some conformally covariant systems. This type of parametrization is certainly more natural for non constant mean curvature initial data.

  15. Earth Observing System Covariance Realism Updates

    NASA Technical Reports Server (NTRS)

    Ojeda Romero, Juan A.; Miguel, Fred

    2017-01-01

    This presentation will be given at the International Earth Science Constellation Mission Operations Working Group meetings June 13-15, 2017 to discuss the Earth Observing System Covariance Realism updates.

  16. Covariance Spectroscopy for Fissile Material Detection

    SciTech Connect

    Rusty Trainham, Jim Tinsley, Paul Hurley, Ray Keegan

    2009-06-02

    Nuclear fission produces multiple prompt neutrons and gammas at each fission event. The resulting daughter nuclei continue to emit delayed radiation as neutrons boil off, beta decay occurs, etc. All of the radiations are causally connected, and therefore correlated. The correlations are generally positive, but when different decay channels compete, so that some radiations tend to exclude others, negative correlations could also be observed. A similar problem of reduced complexity is that of cascades radiation, whereby a simple radioactive decay produces two or more correlated gamma rays at each decay. Covariance is the usual means for measuring correlation, and techniques of covariance mapping may be useful to produce distinct signatures of special nuclear materials (SNM). A covariance measurement can also be used to filter data streams because uncorrelated signals are largely rejected. The technique is generally more effective than a coincidence measurement. In this poster, we concentrate on cascades and the covariance filtering problem.

  17. Covariation bias in panic-prone individuals.

    PubMed

    Pauli, P; Montoya, P; Martz, G E

    1996-11-01

    Covariation estimates between fear-relevant (FR; emergency situations) or fear-irrelevant (FI; mushrooms and nudes) stimuli and an aversive outcome (electrical shock) were examined in 10 high-fear (panic-prone) and 10 low-fear respondents. When the relation between slide category and outcome was random (illusory correlation), only high-fear participants markedly overestimated the contingency between FR slides and shocks. However, when there was a high contingency of shocks following FR stimuli (83%) and a low contingency of shocks following FI stimuli (17%), the group difference vanished. Reversal of contingencies back to random induced a covariation bias for FR slides in high- and low-fear respondents. Results indicate that panic-prone respondents show a covariation bias for FR stimuli and that the experience of a high contingency between FR slides and aversive outcomes may foster such a covariation bias even in low-fear respondents.

  18. Pairwise statistical significance of local sequence alignment using sequence-specific and position-specific substitution matrices.

    PubMed

    Agrawal, Ankit; Huang, Xiaoqiu

    2011-01-01

    Pairwise sequence alignment is a central problem in bioinformatics, which forms the basis of various other applications. Two related sequences are expected to have a high alignment score, but relatedness is usually judged by statistical significance rather than by alignment score. Recently, it was shown that pairwise statistical significance gives promising results as an alternative to database statistical significance for getting individual significance estimates of pairwise alignment scores. The improvement was mainly attributed to making the statistical significance estimation process more sequence-specific and database-independent. In this paper, we use sequence-specific and position-specific substitution matrices to derive the estimates of pairwise statistical significance, which is expected to use more sequence-specific information in estimating pairwise statistical significance. Experiments on a benchmark database with sequence-specific substitution matrices at different levels of sequence-specific contribution were conducted, and results confirm that using sequence-specific substitution matrices for estimating pairwise statistical significance is significantly better than using a standard matrix like BLOSUM62, and than database statistical significance estimates reported by popular database search programs like BLAST, PSI-BLAST (without pretrained PSSMs), and SSEARCH on a benchmark database, but with pretrained PSSMs, PSI-BLAST results are significantly better. Further, using position-specific substitution matrices for estimating pairwise statistical significance gives significantly better results even than PSI-BLAST using pretrained PSSMs.

  19. Noncommutative Gauge Theory with Covariant Star Product

    SciTech Connect

    Zet, G.

    2010-08-04

    We present a noncommutative gauge theory with covariant star product on a space-time with torsion. In order to obtain the covariant star product one imposes some restrictions on the connection of the space-time. Then, a noncommutative gauge theory is developed applying this product to the case of differential forms. Some comments on the advantages of using a space-time with torsion to describe the gravitational field are also given.

  20. Breeding curvature from extended gauge covariance

    NASA Astrophysics Data System (ADS)

    Aldrovandi, R.

    1991-05-01

    Independence between spacetime and “internal” space in gauge theories is related to the adjoint-covariant behaviour of the gauge potential. The usual gauge scheme is modified to allow a coupling between both spaces. Gauging spacetime translations produce field equations similar to Einstein equations. A curvature-like quantity of mixed differential-algebraic character emerges. Enlarged conservation laws are present, pointing to the presence of an covariance.

  1. Covariate analysis of bivariate survival data

    SciTech Connect

    Bennett, L.E.

    1992-01-01

    The methods developed are used to analyze the effects of covariates on bivariate survival data when censoring and ties are present. The proposed method provides models for bivariate survival data that include differential covariate effects and censored observations. The proposed models are based on an extension of the univariate Buckley-James estimators which replace censored data points by their expected values, conditional on the censoring time and the covariates. For the bivariate situation, it is necessary to determine the expectation of the failure times for one component conditional on the failure or censoring time of the other component. Two different methods have been developed to estimate these expectations. In the semiparametric approach these expectations are determined from a modification of Burke's estimate of the bivariate empirical survival function. In the parametric approach censored data points are also replaced by their conditional expected values where the expected values are determined from a specified parametric distribution. The model estimation will be based on the revised data set, comprised of uncensored components and expected values for the censored components. The variance-covariance matrix for the estimated covariate parameters has also been derived for both the semiparametric and parametric methods. Data from the Demographic and Health Survey was analyzed by these methods. The two outcome variables are post-partum amenorrhea and breastfeeding; education and parity were used as the covariates. Both the covariate parameter estimates and the variance-covariance estimates for the semiparametric and parametric models will be compared. In addition, a multivariate test statistic was used in the semiparametric model to examine contrasts. The significance of the statistic was determined from a bootstrap distribution of the test statistic.

  2. Combining biomarkers for classification with covariate adjustment.

    PubMed

    Kim, Soyoung; Huang, Ying

    2017-03-09

    Combining multiple markers can improve classification accuracy compared with using a single marker. In practice, covariates associated with markers or disease outcome can affect the performance of a biomarker or biomarker combination in the population. The covariate-adjusted receiver operating characteristic (ROC) curve has been proposed as a tool to tease out the covariate effect in the evaluation of a single marker; this curve characterizes the classification accuracy solely because of the marker of interest. However, research on the effect of covariates on the performance of marker combinations and on how to adjust for the covariate effect when combining markers is still lacking. In this article, we examine the effect of covariates on classification performance of linear marker combinations and propose to adjust for covariates in combining markers by maximizing the nonparametric estimate of the area under the covariate-adjusted ROC curve. The proposed method provides a way to estimate the best linear biomarker combination that is robust to risk model assumptions underlying alternative regression-model-based methods. The proposed estimator is shown to be consistent and asymptotically normally distributed. We conduct simulations to evaluate the performance of our estimator in cohort and case/control designs and compare several different weighting strategies during estimation with respect to efficiency. Our estimator is also compared with alternative regression-model-based estimators or estimators that maximize the empirical area under the ROC curve, with respect to bias and efficiency. We apply the proposed method to a biomarker study from an human immunodeficiency virus vaccine trial. Copyright © 2017 John Wiley & Sons, Ltd.

  3. Covariant action for type IIB supergravity

    NASA Astrophysics Data System (ADS)

    Sen, Ashoke

    2016-07-01

    Taking clues from the recent construction of the covariant action for type II and heterotic string field theories, we construct a manifestly Lorentz covariant action for type IIB supergravity, and discuss its gauge fixing maintaining manifest Lorentz invariance. The action contains a (non-gravitating) free 4-form field besides the usual fields of type IIB supergravity. This free field, being completely decoupled from the interacting sector, has no physical consequence.

  4. Vector Meson Property in Covariant Classification Scheme

    NASA Astrophysics Data System (ADS)

    Oda, Masuho

    2004-08-01

    Recently our collaboration group has proposed the covariant classification shceme of hadrons, leading to possible existence of two ground state vector mesons. One is corresponding to ordinary ρ nonet and the other is extra ρ nonet. We investigate the decay property of ω(1250) and ρ(1250) in the covariant classification scheme. And it is shown that ω(1250) is promising candidate of our extra ω meson.

  5. Phase-covariant quantum cloning of qudits

    SciTech Connect

    Fan Heng; Imai, Hiroshi; Matsumoto, Keiji; Wang, Xiang-Bin

    2003-02-01

    We study the phase-covariant quantum cloning machine for qudits, i.e., the input states in a d-level quantum system have complex coefficients with arbitrary phase but constant module. A cloning unitary transformation is proposed. After optimizing the fidelity between input state and single qudit reduced density operator of output state, we obtain the optimal fidelity for 1 to 2 phase-covariant quantum cloning of qudits and the corresponding cloning transformation.

  6. Covariance Modifications to Subspace Bases

    SciTech Connect

    Harris, D B

    2008-11-19

    Adaptive signal processing algorithms that rely upon representations of signal and noise subspaces often require updates to those representations when new data become available. Subspace representations frequently are estimated from available data with singular value (SVD) decompositions. Subspace updates require modifications to these decompositions. Updates can be performed inexpensively provided they are low-rank. A substantial literature on SVD updates exists, frequently focusing on rank-1 updates (see e.g. [Karasalo, 1986; Comon and Golub, 1990, Badeau, 2004]). In these methods, data matrices are modified by addition or deletion of a row or column, or data covariance matrices are modified by addition of the outer product of a new vector. A recent paper by Brand [2006] provides a general and efficient method for arbitrary rank updates to an SVD. The purpose of this note is to describe a closely-related method for applications where right singular vectors are not required. This note also describes the SVD updates to a particular scenario of interest in seismic array signal processing. The particular application involve updating the wideband subspace representation used in seismic subspace detectors [Harris, 2006]. These subspace detectors generalize waveform correlation algorithms to detect signals that lie in a subspace of waveforms of dimension d {ge} 1. They potentially are of interest because they extend the range of waveform variation over which these sensitive detectors apply. Subspace detectors operate by projecting waveform data from a detection window into a subspace specified by a collection of orthonormal waveform basis vectors (referred to as the template). Subspace templates are constructed from a suite of normalized, aligned master event waveforms that may be acquired by a single sensor, a three-component sensor, an array of such sensors or a sensor network. The template design process entails constructing a data matrix whose columns contain the

  7. Low-dimensional Representation of Error Covariance

    NASA Technical Reports Server (NTRS)

    Tippett, Michael K.; Cohn, Stephen E.; Todling, Ricardo; Marchesin, Dan

    2000-01-01

    Ensemble and reduced-rank approaches to prediction and assimilation rely on low-dimensional approximations of the estimation error covariances. Here stability properties of the forecast/analysis cycle for linear, time-independent systems are used to identify factors that cause the steady-state analysis error covariance to admit a low-dimensional representation. A useful measure of forecast/analysis cycle stability is the bound matrix, a function of the dynamics, observation operator and assimilation method. Upper and lower estimates for the steady-state analysis error covariance matrix eigenvalues are derived from the bound matrix. The estimates generalize to time-dependent systems. If much of the steady-state analysis error variance is due to a few dominant modes, the leading eigenvectors of the bound matrix approximate those of the steady-state analysis error covariance matrix. The analytical results are illustrated in two numerical examples where the Kalman filter is carried to steady state. The first example uses the dynamics of a generalized advection equation exhibiting nonmodal transient growth. Failure to observe growing modes leads to increased steady-state analysis error variances. Leading eigenvectors of the steady-state analysis error covariance matrix are well approximated by leading eigenvectors of the bound matrix. The second example uses the dynamics of a damped baroclinic wave model. The leading eigenvectors of a lowest-order approximation of the bound matrix are shown to approximate well the leading eigenvectors of the steady-state analysis error covariance matrix.

  8. Generating Covariance Data with Nuclear Models

    NASA Astrophysics Data System (ADS)

    Koning, A. J.

    2006-04-01

    A reliable assessment of the uncertainties in calculated integral reactor parameters depends directly on the uncertainties of the underlying nuclear data. Unfortunately, covariance nuclear data are scarce, not only because a significant experimental database for the isotope under consideration must be available, but also because the covariance evaluation process can be rather complex and time-consuming. We attack this problem with a systematical approach and developed, following the initial ideas of D. Smith (ANL), a method to produce a complete covariance matrix for evaluated data files on the basis of uncertainties of nuclear model parameters. This is accomplished by subjecting the nuclear model code TALYS to a Monte Carlo method for perturbing input parameters, an approach that is now possible with the available computer power. After establishing uncertainties for parameters of the optical model, level densities, gamma-ray strength functions, fission barriers etc., we produce random input files for the TALYS code. These deliver, provided enough calculations (samples) are performed, uncertainties + all off-diagonal elements for all open reaction channels. The uncertainties of the nuclear model parameter are tuned such that the calculated cross section uncertainties coincide, to a reasonable extent, with uncertainties obtained from covariance evaluations based on experimental data. If this method proves to be successful, and we will show here that we are not too far off, it will enable mass production of credible covariance data for isotopes for which no covariance data exists……and this constitutes a very significant part of the periodic table of elements.

  9. Sequential BART for imputation of missing covariates

    PubMed Central

    Xu, Dandan; Daniels, Michael J.; Winterstein, Almut G.

    2016-01-01

    To conduct comparative effectiveness research using electronic health records (EHR), many covariates are typically needed to adjust for selection and confounding biases. Unfortunately, it is typical to have missingness in these covariates. Just using cases with complete covariates will result in considerable efficiency losses and likely bias. Here, we consider the covariates missing at random with missing data mechanism either depending on the response or not. Standard methods for multiple imputation can either fail to capture nonlinear relationships or suffer from the incompatibility and uncongeniality issues. We explore a flexible Bayesian nonparametric approach to impute the missing covariates, which involves factoring the joint distribution of the covariates with missingness into a set of sequential conditionals and applying Bayesian additive regression trees to model each of these univariate conditionals. Using data augmentation, the posterior for each conditional can be sampled simultaneously. We provide details on the computational algorithm and make comparisons to other methods, including parametric sequential imputation and two versions of multiple imputation by chained equations. We illustrate the proposed approach on EHR data from an affiliated tertiary care institution to examine factors related to hyperglycemia. PMID:26980459

  10. Lorentz covariance of loop quantum gravity

    NASA Astrophysics Data System (ADS)

    Rovelli, Carlo; Speziale, Simone

    2011-05-01

    The kinematics of loop gravity can be given a manifestly Lorentz-covariant formulation: the conventional SU(2)-spin-network Hilbert space can be mapped to a space K of SL(2,C) functions, where Lorentz covariance is manifest. K can be described in terms of a certain subset of the projected spin networks studied by Livine, Alexandrov and Dupuis. It is formed by SL(2,C) functions completely determined by their restriction on SU(2). These are square-integrable in the SU(2) scalar product, but not in the SL(2,C) one. Thus, SU(2)-spin-network states can be represented by Lorentz-covariant SL(2,C) functions, as two-component photons can be described in the Lorentz-covariant Gupta-Bleuler formalism. As shown by Wolfgang Wieland in a related paper, this manifestly Lorentz-covariant formulation can also be directly obtained from canonical quantization. We show that the spinfoam dynamics of loop quantum gravity is locally SL(2,C)-invariant in the bulk, and yields states that are precisely in K on the boundary. This clarifies how the SL(2,C) spinfoam formalism yields an SU(2) theory on the boundary. These structures define a tidy Lorentz-covariant formalism for loop gravity.

  11. Avoidant Personality Disorder in Individuals with Generalized Social Anxiety Disorder: What Does It Add?

    PubMed Central

    Marques, Luana; Porter, Eliora; Keshaviah, Aparna; Pollack, Mark H.; Van Ameringen, Michael; Stein, Murray B.; Simon, Naomi M.

    2012-01-01

    Avoidant Personality Disorder (AvPD) has a high level of symptom overlap and comorbidity with Generalized Social Anxiety Disorder (GSAD). We examined whether the presence of comorbid AvPD adds significant clinically relevant information for individuals seeking treatment for GSAD. Results suggested that AvPD was significantly associated with poorer quality of life and greater disability in univariate, but not multivariate analyses. Endorsement of more AvPD symptoms was associated with increased disability, increased risk of intimacy, and lower social support, even after covariate adjustment. Specifically, AvPD item 3, hard to be “open” even with people you are close to, was most strongly correlated with quality of life and disability. A binary diagnosis of AvPD alone adds little beyond a marker of greater GSAD severity and depression among patients with GSAD, while a specific feature of AvPD not captured by the GSAD diagnosis, namely emotional guardedness, may be associated with greater impairment. PMID:22705954

  12. Avoidant personality disorder in individuals with generalized social anxiety disorder: what does it add?

    PubMed

    Marques, Luana; Porter, Eliora; Keshaviah, Aparna; Pollack, Mark H; Van Ameringen, Michael; Stein, Murray B; Simon, Naomi M

    2012-08-01

    Avoidant personality disorder (AvPD) has a high level of symptom overlap and comorbidity with generalized social anxiety disorder (GSAD). We examined whether the presence of comorbid AvPD adds significant clinically relevant information for individuals seeking treatment for GSAD. Results suggested that AvPD was significantly associated with poorer quality of life and greater disability in univariate, but not multivariate analyses. Endorsement of more AvPD symptoms was associated with increased disability, increased risk of intimacy, and lower social support, even after covariate adjustment. Specifically, AvPD item 3, hard to be "open" even with people you are close to, was most strongly correlated with quality of life and disability. A binary diagnosis of AvPD alone adds little beyond a marker of greater GSAD severity and depression among patients with GSAD, while a specific feature of AvPD not captured by the GSAD diagnosis, namely emotional guardedness, may be associated with greater impairment. Published by Elsevier Ltd.

  13. Covariation in the human masticatory apparatus.

    PubMed

    Noback, Marlijn L; Harvati, Katerina

    2015-01-01

    Many studies have described shape variation of the modern human cranium in relation to subsistence; however, patterns of covariation within the masticatory apparatus (MA) remain largely unexplored. The patterns and intensity of shape covariation, and how this is related to diet, are essential for understanding the evolution of functional masticatory adaptations of the human cranium. Within a worldwide sample (n = 255) of 15 populations with different modes of subsistence, we use partial least squares analysis to study the relationships between three components of the MA: upper dental arch, masseter muscle, and temporalis muscle attachments. We show that the shape of the masseter muscle and the shape of the temporalis muscle clearly covary with one another, but that the shape of the dental arch seems to be rather independent of the masticatory muscles. On the contrary, when relative positioning, orientation, and size of the masticatory components is included in the analysis, the dental arch shows the highest covariation with the other cranial parts, indicating that these additional factors are more important than just shape with regard to covariation within the MA. Covariation patterns among these cranial regions differ mainly between hunting-fishing and gathering-agriculture groups, possibly relating to greater masticatory strains resulting from a large meat component in the diet. High-strain groups show stronger covariation between upper dental arch and masticatory muscle shape when compared with low-strain groups. These results help to provide a clearer understanding of constraints and interlinkage of shape variation within the human MA and allow for more realistic modeling and predictions in future biomechanical studies. © 2014 Wiley Periodicals, Inc.

  14. Top 5 Ways to Help Students with ADD/ADHD

    ERIC Educational Resources Information Center

    Johnson, Kathy

    2011-01-01

    This article suggests five ways to help students with ADD/ADHD. These are: (1) Integrate the primitive reflexes; (2) Diet; (3) Visual attention; (4) Help for auditory attention; and (5) Cognitive training.

  15. Top 5 Ways to Help Students with ADD/ADHD

    ERIC Educational Resources Information Center

    Johnson, Kathy

    2011-01-01

    This article suggests five ways to help students with ADD/ADHD. These are: (1) Integrate the primitive reflexes; (2) Diet; (3) Visual attention; (4) Help for auditory attention; and (5) Cognitive training.

  16. 'Pokemon Go' Players Add 2,000 Steps a Day

    MedlinePlus

    ... Pokemon Go' Players Add 2,000 Steps a Day Smartphone game benefits overweight, sedentary people most, researchers ... as likely to walk 10,000 steps a day than they were before taking up the game, ...

  17. TDRS-K to Add to Vital Space Network

    NASA Image and Video Library

    NASA officials discuss the launch of the TDRS-K spacecraft to add to the space network that enables communications between the International Space Station and Earth-orbiting satellites and ground c...

  18. Contamination vs. harm-relevant outcome expectancies and covariation bias in spider phobia.

    PubMed

    de Jong, Peter J; Peters, Madelon L

    2007-06-01

    There is increasing evidence that spiders are not feared because of harmful outcome expectancies but because of disgust and contamination-relevant outcome expectancies. This study investigated the relative strength of contamination- and harm-relevant UCS expectancies and covariation bias in spider phobia. High (n=25) and low (n=24) spider fearful individuals saw a series of slides comprising spiders, pitbulls, maggots, and rabbits. Slides were randomly paired with either a harm-relevant outcome (electrical shock), a contamination-related outcome (drinking of a distasting fluid), or nothing. Spider fearful individuals displayed a contamination-relevant UCS expectancy bias associated with spiders, whereas controls displayed a harm-relevant expectancy bias. There was no evidence for a (differential) postexperimental covariation bias; thus the biased expectancies were not robust against refutation. The present findings add to the evidence that contamination ideation is critically involved in spider phobia.

  19. Convex Banding of the Covariance Matrix

    PubMed Central

    Bien, Jacob; Bunea, Florentina; Xiao, Luo

    2016-01-01

    We introduce a new sparse estimator of the covariance matrix for high-dimensional models in which the variables have a known ordering. Our estimator, which is the solution to a convex optimization problem, is equivalently expressed as an estimator which tapers the sample covariance matrix by a Toeplitz, sparsely-banded, data-adaptive matrix. As a result of this adaptivity, the convex banding estimator enjoys theoretical optimality properties not attained by previous banding or tapered estimators. In particular, our convex banding estimator is minimax rate adaptive in Frobenius and operator norms, up to log factors, over commonly-studied classes of covariance matrices, and over more general classes. Furthermore, it correctly recovers the bandwidth when the true covariance is exactly banded. Our convex formulation admits a simple and efficient algorithm. Empirical studies demonstrate its practical effectiveness and illustrate that our exactly-banded estimator works well even when the true covariance matrix is only close to a banded matrix, confirming our theoretical results. Our method compares favorably with all existing methods, in terms of accuracy and speed. We illustrate the practical merits of the convex banding estimator by showing that it can be used to improve the performance of discriminant analysis for classifying sound recordings. PMID:28042189

  20. A sparse Ising model with covariates.

    PubMed

    Cheng, Jie; Levina, Elizaveta; Wang, Pei; Zhu, Ji

    2014-12-01

    There has been a lot of work fitting Ising models to multivariate binary data in order to understand the conditional dependency relationships between the variables. However, additional covariates are frequently recorded together with the binary data, and may influence the dependence relationships. Motivated by such a dataset on genomic instability collected from tumor samples of several types, we propose a sparse covariate dependent Ising model to study both the conditional dependency within the binary data and its relationship with the additional covariates. This results in subject-specific Ising models, where the subject's covariates influence the strength of association between the genes. As in all exploratory data analysis, interpretability of results is important, and we use ℓ1 penalties to induce sparsity in the fitted graphs and in the number of selected covariates. Two algorithms to fit the model are proposed and compared on a set of simulated data, and asymptotic results are established. The results on the tumor dataset and their biological significance are discussed in detail.

  1. Convex Banding of the Covariance Matrix.

    PubMed

    Bien, Jacob; Bunea, Florentina; Xiao, Luo

    2016-01-01

    We introduce a new sparse estimator of the covariance matrix for high-dimensional models in which the variables have a known ordering. Our estimator, which is the solution to a convex optimization problem, is equivalently expressed as an estimator which tapers the sample covariance matrix by a Toeplitz, sparsely-banded, data-adaptive matrix. As a result of this adaptivity, the convex banding estimator enjoys theoretical optimality properties not attained by previous banding or tapered estimators. In particular, our convex banding estimator is minimax rate adaptive in Frobenius and operator norms, up to log factors, over commonly-studied classes of covariance matrices, and over more general classes. Furthermore, it correctly recovers the bandwidth when the true covariance is exactly banded. Our convex formulation admits a simple and efficient algorithm. Empirical studies demonstrate its practical effectiveness and illustrate that our exactly-banded estimator works well even when the true covariance matrix is only close to a banded matrix, confirming our theoretical results. Our method compares favorably with all existing methods, in terms of accuracy and speed. We illustrate the practical merits of the convex banding estimator by showing that it can be used to improve the performance of discriminant analysis for classifying sound recordings.

  2. A Nonparametric Prior for Simultaneous Covariance Estimation

    PubMed Central

    Gaskins, Jeremy T.; Daniels, Michael J.

    2013-01-01

    Summary In the modeling of longitudinal data from several groups, appropriate handling of the dependence structure is of central importance. Standard methods include specifying a single covariance matrix for all groups or independently estimating the covariance matrix for each group without regard to the others, but when these model assumptions are incorrect, these techniques can lead to biased mean effects or loss of efficiency, respectively. Thus, it is desirable to develop methods to simultaneously estimate the covariance matrix for each group that will borrow strength across groups in a way that is ultimately informed by the data. In addition, for several groups with covariance matrices of even medium dimension, it is difficult to manually select a single best parametric model among the huge number of possibilities given by incorporating structural zeros and/or commonality of individual parameters across groups. In this paper we develop a family of nonparametric priors using the matrix stick-breaking process of Dunson et al. (2008) that seeks to accomplish this task by parameterizing the covariance matrices in terms of the parameters of their modified Cholesky decomposition (Pourahmadi, 1999). We establish some theoretic properties of these priors, examine their effectiveness via a simulation study, and illustrate the priors using data from a longitudinal clinical trial. PMID:24324281

  3. Bistability, non-ergodicity, and inhibition in pairwise maximum-entropy models.

    PubMed

    Rostami, Vahid; Porta Mana, PierGianLuca; Grün, Sonja; Helias, Moritz

    2017-10-02

    Pairwise maximum-entropy models have been used in neuroscience to predict the activity of neuronal populations, given only the time-averaged correlations of the neuron activities. This paper provides evidence that the pairwise model, applied to experimental recordings, would produce a bimodal distribution for the population-averaged activity, and for some population sizes the second mode would peak at high activities, that experimentally would be equivalent to 90% of the neuron population active within time-windows of few milliseconds. Several problems are connected with this bimodality: 1. The presence of the high-activity mode is unrealistic in view of observed neuronal activity and on neurobiological grounds. 2. Boltzmann learning becomes non-ergodic, hence the pairwise maximum-entropy distribution cannot be found: in fact, Boltzmann learning would produce an incorrect distribution; similarly, common variants of mean-field approximations also produce an incorrect distribution. 3. The Glauber dynamics associated with the model is unrealistically bistable and cannot be used to generate realistic surrogate data. This bimodality problem is first demonstrated for an experimental dataset from 159 neurons in the motor cortex of macaque monkey. Evidence is then provided that this problem affects typical neural recordings of population sizes of a couple of hundreds or more neurons. The cause of the bimodality problem is identified as the inability of standard maximum-entropy distributions with a uniform reference measure to model neuronal inhibition. To eliminate this problem a modified maximum-entropy model is presented, which reflects a basic effect of inhibition in the form of a simple but non-uniform reference measure. This model does not lead to unrealistic bimodalities, can be found with Boltzmann learning, and has an associated Glauber dynamics which incorporates a minimal asymmetric inhibition.

  4. Pair-wise multicomparison and OPLS analyses of cold-acclimation phases in Siberian spruce.

    PubMed

    Shiryaeva, Liudmila; Antti, Henrik; Schröder, Wolfgang P; Strimbeck, Richard; Shiriaev, Anton S

    2012-06-01

    Analysis of metabolomics data often goes beyond the task of discovering biomarkers and can be aimed at recovering other important characteristics of observed metabolomic changes. In this paper we explore different methods to detect the presence of distinctive phases in seasonal-responsive changes of metabolomic patterns of Siberian spruce (Picea obovata) during cold acclimation occurred in the period from mid-August to January. Multivariate analysis, specifically orthogonal projection to latent structures discriminant analysis (OPLS-DA), identified time points where the metabolomic patterns underwent substantial modifications as a whole, revealing four distinctive phases during acclimation. This conclusion was re-examined by a univariate analysis consisting of multiple pair-wise comparisons to identify homogeneity intervals for each metabolite. These tests complemented OPLS-DA, clarifying biological interpretation of the classification: about 60% of metabolites found responsive to the cold stress indeed changed at one or more of the time points predicted by OPLS-DA. However, the univariate approach did not support the proposed division of the acclimation period into four phases: less than 10% of metabolites altered during the acclimation had homogeneous levels predicted by OPLS-DA. This demonstrates that coupling the classification found by OPLS-DA and the analysis of dynamics of individual metabolites obtained by pair-wise multicomparisons reveals a more correct characterization of biochemical processes in freezing tolerant trees and leads to interpretations that cannot be deduced by either method alone. The combined analysis can be used in other 'omics'-studies, where response factors have a causal dependence (like the time in the present work) and pair-wise multicomparisons are not conservative. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11306-011-0304-5) contains supplementary material, which is available to authorized

  5. Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign

    PubMed Central

    2007-01-01

    Background Joint alignment and secondary structure prediction of two RNA sequences can significantly improve the accuracy of the structural predictions. Methods addressing this problem, however, are forced to employ constraints that reduce computation by restricting the alignments and/or structures (i.e. folds) that are permissible. In this paper, a new methodology is presented for the purpose of establishing alignment constraints based on nucleotide alignment and insertion posterior probabilities. Using a hidden Markov model, posterior probabilities of alignment and insertion are computed for all possible pairings of nucleotide positions from the two sequences. These alignment and insertion posterior probabilities are additively combined to obtain probabilities of co-incidence for nucleotide position pairs. A suitable alignment constraint is obtained by thresholding the co-incidence probabilities. The constraint is integrated with Dynalign, a free energy minimization algorithm for joint alignment and secondary structure prediction. The resulting method is benchmarked against the previous version of Dynalign and against other programs for pairwise RNA structure prediction. Results The proposed technique eliminates manual parameter selection in Dynalign and provides significant computational time savings in comparison to prior constraints in Dynalign while simultaneously providing a small improvement in the structural prediction accuracy. Savings are also realized in memory. In experiments over a 5S RNA dataset with average sequence length of approximately 120 nucleotides, the method reduces computation by a factor of 2. The method performs favorably in comparison to other programs for pairwise RNA structure prediction: yielding better accuracy, on average, and requiring significantly lesser computational resources. Conclusion Probabilistic analysis can be utilized in order to automate the determination of alignment constraints for pairwise RNA structure prediction

  6. Pairwise contact energy statistical potentials can help to find probability of point mutations.

    PubMed

    Saravanan, K M; Suvaithenamudhan, S; Parthasarathy, S; Selvaraj, S

    2017-01-01

    To adopt a particular fold, a protein requires several interactions between its amino acid residues. The energetic contribution of these residue-residue interactions can be approximated by extracting statistical potentials from known high resolution structures. Several methods based on statistical potentials extracted from unrelated proteins are found to make a better prediction of probability of point mutations. We postulate that the statistical potentials extracted from known structures of similar folds with varying sequence identity can be a powerful tool to examine probability of point mutation. By keeping this in mind, we have derived pairwise residue and atomic contact energy potentials for the different functional families that adopt the (α/β)8 TIM-Barrel fold. We carried out computational point mutations at various conserved residue positions in yeast Triose phosphate isomerase enzyme for which experimental results are already reported. We have also performed molecular dynamics simulations on a subset of point mutants to make a comparative study. The difference in pairwise residue and atomic contact energy of wildtype and various point mutations reveals probability of mutations at a particular position. Interestingly, we found that our computational prediction agrees with the experimental studies of Silverman et al. (Proc Natl Acad Sci 2001;98:3092-3097) and perform better prediction than iMutant and Cologne University Protein Stability Analysis Tool. The present work thus suggests deriving pairwise contact energy potentials and molecular dynamics simulations of functionally important folds could help us to predict probability of point mutations which may ultimately reduce the time and cost of mutation experiments. Proteins 2016; 85:54-64. © 2016 Wiley Periodicals, Inc.

  7. Progress on Nuclear Data Covariances: AFCI-1.2 Covariance Library

    SciTech Connect

    Oblozinsky,P.; Oblozinsky,P.; Mattoon,C.M.; Herman,M.; Mughabghab,S.F.; Pigni,M.T.; Talou,P.; Hale,G.M.; Kahler,A.C.; Kawano,T.; Little,R.C.; Young,P.G

    2009-09-28

    Improved neutron cross section covariances were produced for 110 materials including 12 light nuclei (coolants and moderators), 78 structural materials and fission products, and 20 actinides. Improved covariances were organized into AFCI-1.2 covariance library in 33-energy groups, from 10{sup -5} eV to 19.6 MeV. BNL contributed improved covariance data for the following materials: {sup 23}Na and {sup 55}Mn where more detailed evaluation was done; improvements in major structural materials {sup 52}Cr, {sup 56}Fe and {sup 58}Ni; improved estimates for remaining structural materials and fission products; improved covariances for 14 minor actinides, and estimates of mubar covariances for {sup 23}Na and {sup 56}Fe. LANL contributed improved covariance data for {sup 235}U and {sup 239}Pu including prompt neutron fission spectra and completely new evaluation for {sup 240}Pu. New R-matrix evaluation for {sup 16}O including mubar covariances is under completion. BNL assembled the library and performed basic testing using improved procedures including inspection of uncertainty and correlation plots for each material. The AFCI-1.2 library was released to ANL and INL in August 2009.

  8. Mathematics Teachers' Covariational Reasoning Levels and Predictions about Students' Covariational Reasoning Abilities

    ERIC Educational Resources Information Center

    Zeytun, Aysel Sen; Cetinkaya, Bulent; Erbas, Ayhan Kursat

    2010-01-01

    Various studies suggest that covariational reasoning plays an important role on understanding the fundamental ideas of calculus and modeling dynamic functional events. The purpose of this study was to investigate a group of mathematics teachers' covariational reasoning abilities and predictions about their students. Data were collected through…

  9. Symmetry, topology and the maximum number of mutually pairwise-touching infinite cylinders: configuration classification

    PubMed Central

    Pikhitsa, Stanislaw

    2017-01-01

    We provide a complete classification of possible configurations of mutually pairwise-touching infinite cylinders in Euclidian three-dimensional space. It turns out that there is a maximum number of such cylinders possible in three dimensions independently of the shape of the cylinder cross-sections. We give the explanation of the uniqueness of the non-trivial configuration of seven equal mutually touching round infinite cylinders found earlier. Some results obtained for the chirality matrix, which is equivalent to the Seidel adjacency matrix, may be found useful for the theory of graphs. PMID:28280575

  10. Pairwise mode entanglement in Schwinger production of particle-antiparticle pairs in an electric field

    NASA Astrophysics Data System (ADS)

    Li, Yujie; Dai, Yue; Shi, Yu

    2017-02-01

    Quantum entanglement is the characteristic quantum correlation. Here, we use this concept to analyze the quantum entanglement generated by Schwinger production of particle-antiparticle pairs in an electric field, as well as the change of entanglement as a consequence of the electric field effect on a pre-existing entangled pair of particles. The system is partitioned by using momentum modes. Various kinds of pairwise mode entanglement are calculated as functions of the electric field. Both constant and pulsed electric fields are considered. The use of entanglement exposes information beyond that in particle number distributions.

  11. Twist-boundary energies for metals with long-range pairwise interatomic potentials

    SciTech Connect

    Brokman, A.; Linial, N.; Balluffi, R.W.

    1983-04-01

    The recent calculation of Devlin predicting that the energy of rigid (001) twist boundaries in a central force pairwise interaction model with a long-ranged potential increases linearly with ..sigma.. (for 5 less than or equal to ..sigma.. less than or equal to 37) is considered. By use of a general argument based on the Geometry of Numbers it is shown that this linear increase of the energy is too strong to be physically reasonable. Instead, the energy approaches a constant asymptotic value in this range, and any variations can be represented by a higher order term which varies as the order of ..sigma../sup -//sup 3/4/.

  12. Improving pairwise sequence alignment accuracy using near-optimal protein sequence alignments

    PubMed Central

    2010-01-01

    Background While the pairwise alignments produced by sequence similarity searches are a powerful tool for identifying homologous proteins - proteins that share a common ancestor and a similar structure; pairwise sequence alignments often fail to represent accurately the structural alignments inferred from three-dimensional coordinates. Since sequence alignment algorithms produce optimal alignments, the best structural alignments must reflect suboptimal sequence alignment scores. Thus, we have examined a range of suboptimal sequence alignments and a range of scoring parameters to understand better which sequence alignments are likely to be more structurally accurate. Results We compared near-optimal protein sequence alignments produced by the Zuker algorithm and a set of probabilistic alignments produced by the probA program with structural alignments produced by four different structure alignment algorithms. There is significant overlap between the solution spaces of structural alignments and both the near-optimal sequence alignments produced by commonly used scoring parameters for sequences that share significant sequence similarity (E-values < 10-5) and the ensemble of probA alignments. We constructed a logistic regression model incorporating three input variables derived from sets of near-optimal alignments: robustness, edge frequency, and maximum bits-per-position. A ROC analysis shows that this model more accurately classifies amino acid pairs (edges in the alignment path graph) according to the likelihood of appearance in structural alignments than the robustness score alone. We investigated various trimming protocols for removing incorrect edges from the optimal sequence alignment; the most effective protocol is to remove matches from the semi-global optimal alignment that are outside the boundaries of the local alignment, although trimming according to the model-generated probabilities achieves a similar level of improvement. The model can also be used to

  13. Benefits of Using Pairwise Trajectory Management in the Central East Pacific

    NASA Technical Reports Server (NTRS)

    Chartrand, Ryan; Ballard, Kathryn

    2017-01-01

    Pairwise Trajectory Management (PTM) is a concept that utilizes airborne and ground-based capabilities to enable airborne spacing operations in procedural airspace. This concept makes use of updated ground automation, Automatic Dependent Surveillance-Broadcast (ADS-B) and on board avionics generating real time guidance. An experiment was conducted to examine the potential benefits of implementing PTM in the Central East Pacific oceanic region. An explanation of the experiment and some of the results are included in this paper. The PTM concept allowed for an increase in the average time an aircraft is able to spend at its desired flight level and a reduction in fuel burn.

  14. Geometric measure of pairwise quantum discord for superpositions of multipartite generalized coherent states

    NASA Astrophysics Data System (ADS)

    Daoud, M.; Ahl Laamara, R.

    2012-07-01

    We give the explicit expressions of the pairwise quantum correlations present in superpositions of multipartite coherent states. A special attention is devoted to the evaluation of the geometric quantum discord. The dynamics of quantum correlations under a dephasing channel is analyzed. A comparison of geometric measure of quantum discord with that of concurrence shows that quantum discord in multipartite coherent states is more resilient to dissipative environments than is quantum entanglement. To illustrate our results, we consider some special superpositions of Weyl-Heisenberg, SU(2) and SU(1,1) coherent states which interpolate between Werner and Greenberger-Horne-Zeilinger states.

  15. Covariant Lyapunov vectors for rigid disk systems.

    PubMed

    Bosetti, Hadrien; Posch, Harald A

    2010-10-05

    We carry out extensive computer simulations to study the Lyapunov instability of a two-dimensional hard-disk system in a rectangular box with periodic boundary conditions. The system is large enough to allow the formation of Lyapunov modes parallel to the x-axis of the box. The Oseledec splitting into covariant subspaces of the tangent space is considered by computing the full set of covariant perturbation vectors co-moving with the flow in tangent space. These vectors are shown to be transversal, but generally not orthogonal to each other. Only the angle between covariant vectors associated with immediate adjacent Lyapunov exponents in the Lyapunov spectrum may become small, but the probability of this angle to vanish approaches zero. The stable and unstable manifolds are transverse to each other and the system is hyperbolic.

  16. Incorporating covariates in skewed functional data models.

    PubMed

    Li, Meng; Staicu, Ana-Maria; Bondell, Howard D

    2015-07-01

    We introduce a class of covariate-adjusted skewed functional models (cSFM) designed for functional data exhibiting location-dependent marginal distributions. We propose a semi-parametric copula model for the pointwise marginal distributions, which are allowed to depend on covariates, and the functional dependence, which is assumed covariate invariant. The proposed cSFM framework provides a unifying platform for pointwise quantile estimation and trajectory prediction. We consider a computationally feasible procedure that handles densely as well as sparsely observed functional data. The methods are examined numerically using simulations and is applied to a new tractography study of multiple sclerosis. Furthermore, the methodology is implemented in the R package cSFM, which is publicly available on CRAN.

  17. FAST NEUTRON COVARIANCES FOR EVALUATED DATA FILES.

    SciTech Connect

    HERMAN, M.; OBLOZINSKY, P.; ROCHMAN, D.; KAWANO, T.; LEAL, L.

    2006-06-05

    We describe implementation of the KALMAN code in the EMPIRE system and present first covariance data generated for Gd and Ir isotopes. A complete set of covariances, in the full energy range, was produced for the chain of 8 Gadolinium isotopes for total, elastic, capture, total inelastic (MT=4), (n,2n), (n,p) and (n,alpha) reactions. Our correlation matrices, based on combination of model calculations and experimental data, are characterized by positive mid-range and negative long-range correlations. They differ from the model-generated covariances that tend to show strong positive long-range correlations and those determined solely from experimental data that result in nearly diagonal matrices. We have studied shapes of correlation matrices obtained in the calculations and interpreted them in terms of the underlying reaction models. An important result of this study is the prediction of narrow energy ranges with extremely small uncertainties for certain reactions (e.g., total and elastic).

  18. Covariant Lyapunov vectors for rigid disk systems

    PubMed Central

    Bosetti, Hadrien; Posch, Harald A.

    2010-01-01

    We carry out extensive computer simulations to study the Lyapunov instability of a two-dimensional hard-disk system in a rectangular box with periodic boundary conditions. The system is large enough to allow the formation of Lyapunov modes parallel to the x-axis of the box. The Oseledec splitting into covariant subspaces of the tangent space is considered by computing the full set of covariant perturbation vectors co-moving with the flow in tangent space. These vectors are shown to be transversal, but generally not orthogonal to each other. Only the angle between covariant vectors associated with immediate adjacent Lyapunov exponents in the Lyapunov spectrum may become small, but the probability of this angle to vanish approaches zero. The stable and unstable manifolds are transverse to each other and the system is hyperbolic. PMID:21151326

  19. Gram-Schmidt algorithms for covariance propagation

    NASA Technical Reports Server (NTRS)

    Thornton, C. L.; Bierman, G. J.

    1977-01-01

    This paper addresses the time propagation of triangular covariance factors. Attention is focused on the square-root free factorization, P = UD(transpose of U), where U is unit upper triangular and D is diagonal. An efficient and reliable algorithm for U-D propagation is derived which employs Gram-Schmidt orthogonalization. Partitioning the state vector to distinguish bias and coloured process noise parameters increase mapping efficiency. Cost comparisons of the U-D, Schmidt square-root covariance and conventional covariance propagation methods are made using weighted arithmetic operation counts. The U-D time update is shown to be less costly than the Schmidt method; and, except in unusual circumstances, it is within 20% of the cost of conventional propagation.

  20. Covariance for Cone and Wedge Complete Filling

    NASA Astrophysics Data System (ADS)

    Rascón, C.; Parry, A. O.

    2005-03-01

    Interfacial phenomena associated with fluid adsorption in two dimensional systems have recently been shown to exhibit hidden symmetries, or covariances, which precisely relate local adsorption properties in different confining geometries. We show that covariance also occurs in three-dimensional systems and is likely to be verifiable experimentally and in Ising model simulations studies. Specifically, we study complete wetting in wedge (W) and cone (C) geometries as bulk coexistence is approached and show that the equilibrium midpoint heights satisfy lc(h,α)=lw(h/2,α), where h measures the partial pressure and α is the tilt angle. This covariance is valid for both short-ranged and long-ranged intermolecular forces and identifies both leading and next-to-leading-order critical exponents and amplitudes in the confining geometries.

  1. Matrix of the covariance of covariance of acceleration responses for damage detection from ambient vibration measurements

    NASA Astrophysics Data System (ADS)

    Li, X. Y.; Law, S. S.

    2010-05-01

    A new matrix on the covariance of covariance is formed from the auto/cross-correlation function of acceleration responses of a structure under white noise ambient excitation. The components of the covariance matrix are proved to be function of the modal parameters (modal frequency, mode shape, and damping parameter) of the structure. Information from all the vibration modes of the structure limited by the sampling frequency contributes to these components. The formulated covariance matrix contains more information on the vibration modes of the structure that cannot be obtained by the general methods for extracting modal parameters. When the component of the covariance matrix is used for damage detection, it is found more sensitive to local stiffness reduction than the first few modal frequencies and mode shapes obtained from ambient excitation. A simply supported 31 bar plane truss structure is studied numerically where a multiple damage scenario with different noise levels is identified with satisfactory results.

  2. Structural damage detection based on covariance of covariance matrix with general white noise excitation

    NASA Astrophysics Data System (ADS)

    Hui, Yi; Law, Siu Seong; Ku, Chiu Jen

    2017-02-01

    Covariance of the auto/cross-covariance matrix based method is studied for the damage identification of a structure with illustrations on its advantages and limitations. The original method is extended for structures under direct white noise excitations. The auto/cross-covariance function of the measured acceleration and its corresponding derivatives are formulated analytically, and the method is modified in two new strategies to enable successful identification with much fewer sensors. Numerical examples are adopted to illustrate the improved method, and the effects of sampling frequency and sampling duration are discussed. Results show that the covariance of covariance calculated from responses of higher order modes of a structure play an important role to the accurate identification of local damage in a structure.

  3. Covariance based outlier detection with feature selection.

    PubMed

    Zwilling, Chris E; Wang, Michelle Y

    2016-08-01

    The present covariance based outlier detection algorithm selects from a candidate set of feature vectors that are best at identifying outliers. Features extracted from biomedical and health informatics data can be more informative in disease assessment and there are no restrictions on the nature and number of features that can be tested. But an important challenge for an algorithm operating on a set of features is for it to winnow the effective features from the ineffective ones. The powerful algorithm described in this paper leverages covariance information from the time series data to identify features with the highest sensitivity for outlier identification. Empirical results demonstrate the efficacy of the method.

  4. Covariance Analysis of Gamma Ray Spectra

    SciTech Connect

    Trainham, R.; Tinsley, J.

    2013-01-01

    The covariance method exploits fluctuations in signals to recover information encoded in correlations which are usually lost when signal averaging occurs. In nuclear spectroscopy it can be regarded as a generalization of the coincidence technique. The method can be used to extract signal from uncorrelated noise, to separate overlapping spectral peaks, to identify escape peaks, to reconstruct spectra from Compton continua, and to generate secondary spectral fingerprints. We discuss a few statistical considerations of the covariance method and present experimental examples of its use in gamma spectroscopy.

  5. Covariance analysis of gamma ray spectra

    SciTech Connect

    Trainham, R.; Tinsley, J.

    2013-01-15

    The covariance method exploits fluctuations in signals to recover information encoded in correlations which are usually lost when signal averaging occurs. In nuclear spectroscopy it can be regarded as a generalization of the coincidence technique. The method can be used to extract signal from uncorrelated noise, to separate overlapping spectral peaks, to identify escape peaks, to reconstruct spectra from Compton continua, and to generate secondary spectral fingerprints. We discuss a few statistical considerations of the covariance method and present experimental examples of its use in gamma spectroscopy.

  6. Parametric number covariance in quantum chaotic spectra.

    PubMed

    Vinayak; Kumar, Sandeep; Pandey, Akhilesh

    2016-03-01

    We study spectral parametric correlations in quantum chaotic systems and introduce the number covariance as a measure of such correlations. We derive analytic results for the classical random matrix ensembles using the binary correlation method and obtain compact expressions for the covariance. We illustrate the universality of this measure by presenting the spectral analysis of the quantum kicked rotors for the time-reversal invariant and time-reversal noninvariant cases. A local version of the parametric number variance introduced earlier is also investigated.

  7. Covariant version of Verlinde's emergent gravity

    NASA Astrophysics Data System (ADS)

    Hossenfelder, Sabine

    2017-06-01

    A generally covariant version of Erik Verlinde's emergent gravity model is proposed. The Lagrangian constructed here allows an improved interpretation of the underlying mechanism. It suggests that de Sitter space is filled with a vector field that couples to baryonic matter and, by dragging on it, creates an effect similar to dark matter. We solve the covariant equation of motion in the background of a Schwarzschild space-time and obtain correction terms to the noncovariant expression. Furthermore, we demonstrate that the vector field can also mimic dark energy.

  8. Determination of Ensemble-Average Pairwise Root Mean-Square Deviation from Experimental B-Factors

    PubMed Central

    Kuzmanic, Antonija; Zagrovic, Bojan

    2010-01-01

    Abstract Root mean-square deviation (RMSD) after roto-translational least-squares fitting is a measure of global structural similarity of macromolecules used commonly. On the other hand, experimental x-ray B-factors are used frequently to study local structural heterogeneity and dynamics in macromolecules by providing direct information about root mean-square fluctuations (RMSF) that can also be calculated from molecular dynamics simulations. We provide a mathematical derivation showing that, given a set of conservative assumptions, a root mean-square ensemble-average of an all-against-all distribution of pairwise RMSD for a single molecular species, 1/2, is directly related to average B-factors () and 1/2. We show this relationship and explore its limits of validity on a heterogeneous ensemble of structures taken from molecular dynamics simulations of villin headpiece generated using distributed-computing techniques and the Folding@Home cluster. Our results provide a basis for quantifying global structural diversity of macromolecules in crystals directly from x-ray experiments, and we show this on a large set of structures taken from the Protein Data Bank. In particular, we show that the ensemble-average pairwise backbone RMSD for a microscopic ensemble underlying a typical protein x-ray structure is ∼1.1 Å, under the assumption that the principal contribution to experimental B-factors is conformational variability. PMID:20197040

  9. Multilevel summation with B-spline interpolation for pairwise interactions in molecular dynamics simulations

    PubMed Central

    Wolff, Matthew A.; Xia, Jianlin; Schulten, Klaus

    2016-01-01

    The multilevel summation method for calculating electrostatic interactions in molecular dynamics simulations constructs an approximation to a pairwise interaction kernel and its gradient, which can be evaluated at a cost that scales linearly with the number of atoms. The method smoothly splits the kernel into a sum of partial kernels of increasing range and decreasing variability with the longer-range parts interpolated from grids of increasing coarseness. Multilevel summation is especially appropriate in the context of dynamics and minimization, because it can produce continuous gradients. This article explores the use of B-splines to increase the accuracy of the multilevel summation method (for nonperiodic boundaries) without incurring additional computation other than a preprocessing step (whose cost also scales linearly). To obtain accurate results efficiently involves technical difficulties, which are overcome by a novel preprocessing algorithm. Numerical experiments demonstrate that the resulting method offers substantial improvements in accuracy and that its performance is competitive with an implementation of the fast multipole method in general and markedly better for Hamiltonian formulations of molecular dynamics. The improvement is great enough to establish multilevel summation as a serious contender for calculating pairwise interactions in molecular dynamics simulations. In particular, the method appears to be uniquely capable for molecular dynamics in two situations, nonperiodic boundary conditions and massively parallel computation, where the fast Fourier transform employed in the particle–mesh Ewald method falls short. PMID:27004867

  10. COLLECTIVE PAIRWISE CLASSIFICATION FOR MULTI-WAY ANALYSIS OF DISEASE AND DRUG DATA.

    PubMed

    Zitnik, Marinka; Zupan, Blaz

    2016-01-01

    Interactions between drugs, drug targets or diseases can be predicted on the basis of molecular, clinical and genomic features by, for example, exploiting similarity of disease pathways, chemical structures, activities across cell lines or clinical manifestations of diseases. A successful way to better understand complex interactions in biomedical systems is to employ collective relational learning approaches that can jointly model diverse relationships present in multiplex data. We propose a novel collective pairwise classification approach for multi-way data analysis. Our model leverages the superiority of latent factor models and classifies relationships in a large relational data domain using a pairwise ranking loss. In contrast to current approaches, our method estimates probabilities, such that probabilities for existing relationships are higher than for assumed-to-be-negative relationships. Although our method bears correspondence with the maximization of non-differentiable area under the ROC curve, we were able to design a learning algorithm that scales well on multi-relational data encoding interactions between thousands of entities.We use the new method to infer relationships from multiplex drug data and to predict connections between clinical manifestations of diseases and their underlying molecular signatures. Our method achieves promising predictive performance when compared to state-of-the-art alternative approaches and can make "category-jumping" predictions about diseases from genomic and clinical data generated far outside the molecular context.

  11. PIPER: an FFT-based protein docking program with pairwise potentials.

    PubMed

    Kozakov, Dima; Brenke, Ryan; Comeau, Stephen R; Vajda, Sandor

    2006-11-01

    The Fast Fourier Transform (FFT) correlation approach to protein-protein docking can evaluate the energies of billions of docked conformations on a grid if the energy is described in the form of a correlation function. Here, this restriction is removed, and the approach is efficiently used with pairwise interaction potentials that substantially improve the docking results. The basic idea is approximating the interaction matrix by its eigenvectors corresponding to the few dominant eigenvalues, resulting in an energy expression written as the sum of a few correlation functions, and solving the problem by repeated FFT calculations. In addition to describing how the method is implemented, we present a novel class of structure-based pairwise intermolecular potentials. The DARS (Decoys As the Reference State) potentials are extracted from structures of protein-protein complexes and use large sets of docked conformations as decoys to derive atom pair distributions in the reference state. The current version of the DARS potential works well for enzyme-inhibitor complexes. With the new FFT-based program, DARS provides much better docking results than the earlier approaches, in many cases generating 50% more near-native docked conformations. Although the potential is far from optimal for antibody-antigen pairs, the results are still slightly better than those given by an earlier FFT method. The docking program PIPER is freely available for noncommercial applications.

  12. Pairwise and edge-based models of epidemic dynamics on correlated weighted networks.

    PubMed

    Rattana, P; Miller, J C; Kiss, I Z

    2014-04-24

    In this paper we explore the potential of the pairwise-type modelling approach to be extended to weighted networks where nodal degree and weights are not independent. As a baseline or null model for weighted networks, we consider undirected, heterogenous networks where edge weights are randomly distributed. We show that the pairwise model successfully captures the extra complexity of the network, but does this at the cost of limited analytical tractability due the high number of equations. To circumvent this problem, we employ the edge-based modelling approach to derive models corresponding to two different cases, namely for degree-dependent and randomly distributed weights. These models are more amenable to compute important epidemic descriptors, such as early growth rate and final epidemic size, and produce similarly excellent agreement with simulation. Using a branching process approach we compute the basic reproductive ratio for both models and discuss the implication of random and correlated weight distributions on this as well as on the time evolution and final outcome of epidemics. Finally, we illustrate that the two seemingly different modelling approaches, pairwsie and edge-based, operate on similar assumptions and it is possible to formally link the two.

  13. Experimental evidence rejects pairwise modelling approach to coexistence in plant communities

    PubMed Central

    Dormann, Carsten F; Roxburgh, Stephen H

    2005-01-01

    Competition is often invoked as the cause of plant species loss with increasing system productivity. Experimental results for multispecies assemblages are virtually absent and mathematical models are thus used to explore the relationship between competition and coexistence. Modelling approaches to coexistence and diversity in competitive communities commonly employ Lotka–Volterra-type (LV) models with additive pairwise competitive effects. Using pairwise plant competition experiments, we calibrate the LV system and use it to predict plant biomass and coexistence in six three-species and one seven-species experimental mixture. Our results show that five out of the six three-species sets and the seven-species set deviate significantly from LV model predictions. Fitting an additional non-additive competition coefficient resulted in predictions that more closely matched the experimental results, with stable coexistence suggested in all but one case. These results are discussed with particular reference to the possible underlying mechanisms of coexistence in our experimental community. Modelling the effect of competition intensity on stability indicates that if non-additive effects occur, they will be relevant over a wide range of community sizes. Our findings caution against relying on coexistence predictions based on LV models. PMID:16024393

  14. Pairwise Operator Learning for Patch Based Single-image Super-resolution.

    PubMed

    Tang, Yi; Shao, Ling

    2016-12-14

    Motivated by the fact that image patches could be inherently represented by matrices, single-image super-resolution is treated as a problem of learning regression operators in a matrix space in this paper. The regression operators that map low-resolution image patches to high-resolution image patches are generally defined by left and right multiplication operators. The pairwise operators are respectively used to extract the raw and column information of low-resolution image patches for recovering high-resolution estimations. The patch based regression algorithm possesses three favorable properties. Firstly, the proposed super-resolution algorithm is efficient during both training and testing, because image patches are treated as matrices. Secondly, the data storage requirement of the optimal pairwise operator is far less than most popular single-image super-resolution algorithms because only two small sized matrices need to be stored. Lastly, the super-resolution performance is competitive with most popular single-image super-resolution algorithms because both raw and column information of image patches is considered. Experimental results show the efficiency and effectiveness of the proposed patch-based single-image superresolution algorithm.

  15. Genomic fingerprinting using arbitrarily primed PCR and a matrix of pairwise combinations of primers.

    PubMed Central

    Welsh, J; McClelland, M

    1991-01-01

    Polymorphisms in genomic fingerprints generated by arbitrarily primed PCR (AP-PCR) can distinguish between slightly divergent strains of any organism. Single oligodeoxyribonucleotide (oligo) primers have been used to generate such fingerprints, with the same primer being present at the 5' end of both strands for every PCR product. We used three arbitrary oligos, individually and in pairs, to generate six different genomic fingerprints of the same mouse genomic DNAs. Fewer than half of the products in genomic fingerprints generated using the oligos in pairs were the same as those produced by AP-PCR using one of the three oligos alone. Thus, a few oligos could be used in a very large number of single and pairwise combinations, each producing a distinct AP-PCR fingerprint with the potential to identify new polymorphisms. For example, 50 oligos can be used in a matrix of pairwise combinations to produce 2,500 fingerprints, in which at least half the data can be expected to be unique to each pair. We demonstrate this principle by using two oligos, alone and together, to generate three sets of fingerprints and map thirteen polymorphisms in the C57BL/6J x DBA/2J set of recombinant inbred mice. Images PMID:1923811

  16. Evaluation of Jackknife and Bootstrap for Defining Confidence Intervals for Pairwise Agreement Measures

    PubMed Central

    Severiano, Ana; Carriço, João A.; Robinson, D. Ashley; Ramirez, Mário; Pinto, Francisco R.

    2011-01-01

    Several research fields frequently deal with the analysis of diverse classification results of the same entities. This should imply an objective detection of overlaps and divergences between the formed clusters. The congruence between classifications can be quantified by clustering agreement measures, including pairwise agreement measures. Several measures have been proposed and the importance of obtaining confidence intervals for the point estimate in the comparison of these measures has been highlighted. A broad range of methods can be used for the estimation of confidence intervals. However, evidence is lacking about what are the appropriate methods for the calculation of confidence intervals for most clustering agreement measures. Here we evaluate the resampling techniques of bootstrap and jackknife for the calculation of the confidence intervals for clustering agreement measures. Contrary to what has been shown for some statistics, simulations showed that the jackknife performs better than the bootstrap at accurately estimating confidence intervals for pairwise agreement measures, especially when the agreement between partitions is low. The coverage of the jackknife confidence interval is robust to changes in cluster number and cluster size distribution. PMID:21611165

  17. Crystal Structure of the lamda Repressor and a Model for Pairwise Cooperative Operator Binding

    SciTech Connect

    Stayrook,S.; Jaru-Ampornpan, P.; Ni, J.; Hochschild, A.; Lewis, M.

    2008-01-01

    Bacteriophage {lambda} has for many years been a model system for understanding mechanisms of gene regulation1. A 'genetic switch' enables the phage to transition from lysogenic growth to lytic development when triggered by specific environmental conditions. The key component of the switch is the cI repressor, which binds to two sets of three operator sites on the chromosome that are separated by about 2,400 base pairs (bp)2, 3. A hallmark of the system is the pairwise cooperativity of repressor binding4. In the absence of detailed structural information, it has been difficult to understand fully how repressor molecules establish the cooperativity complex. Here we present the X-ray crystal structure of the intact cI repressor dimer bound to a DNA operator site. The structure of the repressor, determined by multiple isomorphous replacement methods, reveals an unusual overall architecture that allows it to adopt a conformation that appears to facilitate pairwise cooperative binding to adjacent operator sites.

  18. Determination of ensemble-average pairwise root mean-square deviation from experimental B-factors.

    PubMed

    Kuzmanic, Antonija; Zagrovic, Bojan

    2010-03-03

    Root mean-square deviation (RMSD) after roto-translational least-squares fitting is a measure of global structural similarity of macromolecules used commonly. On the other hand, experimental x-ray B-factors are used frequently to study local structural heterogeneity and dynamics in macromolecules by providing direct information about root mean-square fluctuations (RMSF) that can also be calculated from molecular dynamics simulations. We provide a mathematical derivation showing that, given a set of conservative assumptions, a root mean-square ensemble-average of an all-against-all distribution of pairwise RMSD for a single molecular species, (1/2), is directly related to average B-factors () and (1/2). We show this relationship and explore its limits of validity on a heterogeneous ensemble of structures taken from molecular dynamics simulations of villin headpiece generated using distributed-computing techniques and the Folding@Home cluster. Our results provide a basis for quantifying global structural diversity of macromolecules in crystals directly from x-ray experiments, and we show this on a large set of structures taken from the Protein Data Bank. In particular, we show that the ensemble-average pairwise backbone RMSD for a microscopic ensemble underlying a typical protein x-ray structure is approximately 1.1 A, under the assumption that the principal contribution to experimental B-factors is conformational variability.

  19. Canonical Force Distributions in Pairwise Interatomic Interactions from the Perspective of the Hellmann-Feynman Theorem.

    PubMed

    Walton, Jay R; Rivera-Rivera, Luis A; Lucchese, Robert R; Bevan, John W

    2016-05-26

    Force-based canonical approaches have recently given a unified but different viewpoint on the nature of bonding in pairwise interatomic interactions. Differing molecular categories (covalent, ionic, van der Waals, hydrogen, and halogen bonding) of representative interatomic interactions with binding energies ranging from 1.01 to 1072.03 kJ/mol have been modeled canonically giving a rigorous semiempirical verification to high accuracy. However, the fundamental physical basis expected to provide the inherent characteristics of these canonical transformations has not yet been elucidated. Subsequently, it was shown through direct numerical differentiation of these potentials that their associated force curves have canonical shapes. However, this approach to analyzing force results in inherent loss of accuracy coming from numerical differentiation of the potentials. We now show that this serious obstruction can be avoided by directly demonstrating the canonical nature of force distributions from the perspective of the Hellmann-Feynman theorem. This requires only differentiation of explicitly known Coulombic potentials, and we discuss how this approach to canonical forces can be used to further explain the nature of chemical bonding in pairwise interatomic interactions. All parameter values used in the canonical transformation are determined through explicit physical based algorithms, and it does not require direct consideration of electron correlation effects.

  20. Evaluating the use of pairwise dissimilarity metrics in paleoanthropology.

    PubMed

    Gordon, Adam D; Wood, Bernard

    2013-10-01

    Questions of alpha taxonomy are best addressed by comparing unknown specimens to samples of the taxa to which they might belong. However, analysis of the hominin fossil record is riddled with methods that claim to evaluate whether pairs of individual fossils belong to the same species. Two such methods, log sem and the related STET method, have been introduced and used in studies of fossil hominins. Both methods attempt to quantify morphological dissimilarity for a pair of fossils and then evaluate a null hypothesis of conspecificity using the assumption that pairs of fossils that fall beneath a predefined dissimilarity threshold are likely to belong to the same species, whereas pairs of fossils above that threshold are likely to belong to different species. In this contribution, we address (1) whether these particular methods do what they claim to do, and (2) whether such approaches can ever reliably address the question of conspecificity. We show that log sem and STET do not reliably measure deviations from shape similarity, and that values of these measures for any pair of fossils are highly dependent upon the number of variables compared. To address these issues we develop a measure of shape dissimilarity, the Standard Deviation of Logged Ratios (sLR). We suggest that while pairwise dissimilarity metrics that accurately measure deviations from isometry (e.g., sLR) may be useful for addressing some questions that relate to morphological variation, no pairwise method can reliably answer the question of whether two fossils are conspecific.

  1. A Pairwise Naïve Bayes Approach to Bayesian Classification

    PubMed Central

    Betensky, Rebecca A.

    2016-01-01

    Despite the relatively high accuracy of the naïve Bayes (NB) classifier, there may be several instances where it is not optimal, i.e. does not have the same classification performance as the Bayes classifier utilizing the joint distribution of the examined attributes. However, the Bayes classifier can be computationally intractable due to its required knowledge of the joint distribution. Therefore, we introduce a “pairwise naïve” Bayes (PNB) classifier that incorporates all pairwise relationships among the examined attributes, but does not require specification of the joint distribution. In this paper, we first describe the necessary and sufficient conditions under which the PNB classifier is optimal. We then discuss sufficient conditions for which the PNB classifier, and not NB, is optimal for normal attributes. Through simulation and actual studies, we evaluate the performance of our proposed classifier relative to the Bayes and NB classifiers, along with the HNB, AODE, LBR and TAN classifiers, using normal density and empirical estimation methods. Our applications show that the PNB classifier using normal density estimation yields the highest accuracy for data sets containing continuous attributes. We conclude that it offers a useful compromise between the Bayes and NB classifiers. PMID:27087730

  2. Pairwise antibiotic interactions in Escherichia coli: triclosan, rifampicin and aztreonam with nine other classes of antibiotics.

    PubMed

    Nguyen, Caroline; Zhou, Alice; Khan, Ayesha; Miller, Jeffrey H; Yeh, Pamela

    2016-11-01

    Previous investigations have shown that analyzing pairwise interactions between 22 antibiotics in Escherichia coli enable the grouping of drugs into nine functional classes. Our aim is to significantly expand this drug network by adding three clinically relevant antibiotics, two of which have distinct mechanisms of action not previously represented. Here, we examine triclosan, rifampicin and aztreonam, by testing them pairwise against themselves and one antibiotic from each of the nine classes. Network analysis shows that triclosan, rifampicin and aztreonam each form distinct functional groups of their own. This is particularly surprising for aztreonam, which is a cell wall synthesis inhibitor but did not cluster with other cell wall synthesis inhibitors. Furthermore, of the 30 pairs tested, we found several previously unreported synergies that could potentially be used in multidrug therapies. The distinct functional groups suggest that there may be properties of these drugs that are different from other drugs even with similar mechanism of action, and that, when considering drug combinations, aztreonam in particular is not simply interchangeable with other cell wall synthesis inhibitors.

  3. A water market simulator considering pair-wise trades between agents

    NASA Astrophysics Data System (ADS)

    Huskova, I.; Erfani, T.; Harou, J. J.

    2012-04-01

    In many basins in England no further water abstraction licences are available. Trading water between water rights holders has been recognized as a potentially effective and economically efficient strategy to mitigate increasing scarcity. A screening tool that could assess the potential for trade through realistic simulation of individual water rights holders would help assess the solution's potential contribution to local water management. We propose an optimisation-driven water market simulator that predicts pair-wise trade in a catchment and represents its interaction with natural hydrology and engineered infrastructure. A model is used to emulate licence-holders' willingness to engage in short-term trade transactions. In their simplest form agents are represented using an economic benefit function. The working hypothesis is that trading behaviour can be partially predicted based on differences in marginal values of water over space and time and estimates of transaction costs on pair-wise trades. We discuss the further possibility of embedding rules, norms and preferences of the different water user sectors to more realistically represent the behaviours, motives and constraints of individual licence holders. The potential benefits and limitations of such a social simulation (agent-based) approach is contrasted with our simulator where agents are driven by economic optimization. A case study based on the Dove River Basin (UK) demonstrates model inputs and outputs. The ability of the model to suggest impacts of water rights policy reforms on trading is discussed.

  4. COLLECTIVE PAIRWISE CLASSIFICATION FOR MULTI-WAY ANALYSIS OF DISEASE AND DRUG DATA

    PubMed Central

    ZITNIK, MARINKA; ZUPAN, BLAZ

    2015-01-01

    Interactions between drugs, drug targets or diseases can be predicted on the basis of molecular, clinical and genomic features by, for example, exploiting similarity of disease pathways, chemical structures, activities across cell lines or clinical manifestations of diseases. A successful way to better understand complex interactions in biomedical systems is to employ collective relational learning approaches that can jointly model diverse relationships present in multiplex data. We propose a novel collective pairwise classification approach for multi-way data analysis. Our model leverages the superiority of latent factor models and classifies relationships in a large relational data domain using a pairwise ranking loss. In contrast to current approaches, our method estimates probabilities, such that probabilities for existing relationships are higher than for assumed-to-be-negative relationships. Although our method bears correspondence with the maximization of non-differentiable area under the ROC curve, we were able to design a learning algorithm that scales well on multi-relational data encoding interactions between thousands of entities. We use the new method to infer relationships from multiplex drug data and to predict connections between clinical manifestations of diseases and their underlying molecular signatures. Our method achieves promising predictive performance when compared to state-of-the-art alternative approaches and can make “category-jumping” predictions about diseases from genomic and clinical data generated far outside the molecular context. PMID:26776175

  5. Statistical properties of pairwise distances between leaves on a random Yule tree.

    PubMed

    Sheinman, Michael; Massip, Florian; Arndt, Peter F

    2015-01-01

    A Yule tree is the result of a branching process with constant birth and death rates. Such a process serves as an instructive null model of many empirical systems, for instance, the evolution of species leading to a phylogenetic tree. However, often in phylogeny the only available information is the pairwise distances between a small fraction of extant species representing the leaves of the tree. In this article we study statistical properties of the pairwise distances in a Yule tree. Using a method based on a recursion, we derive an exact, analytic and compact formula for the expected number of pairs separated by a certain time distance. This number turns out to follow a increasing exponential function. This property of a Yule tree can serve as a simple test for empirical data to be well described by a Yule process. We further use this recursive method to calculate the expected number of the n-most closely related pairs of leaves and the number of cherries separated by a certain time distance. To make our results more useful for realistic scenarios, we explicitly take into account that the leaves of a tree may be incompletely sampled and derive a criterion for poorly sampled phylogenies. We show that our result can account for empirical data, using two families of birds species.

  6. Statistical Properties of Pairwise Distances between Leaves on a Random Yule Tree

    PubMed Central

    Sheinman, Michael; Massip, Florian; Arndt, Peter F.

    2015-01-01

    A Yule tree is the result of a branching process with constant birth and death rates. Such a process serves as an instructive null model of many empirical systems, for instance, the evolution of species leading to a phylogenetic tree. However, often in phylogeny the only available information is the pairwise distances between a small fraction of extant species representing the leaves of the tree. In this article we study statistical properties of the pairwise distances in a Yule tree. Using a method based on a recursion, we derive an exact, analytic and compact formula for the expected number of pairs separated by a certain time distance. This number turns out to follow a increasing exponential function. This property of a Yule tree can serve as a simple test for empirical data to be well described by a Yule process. We further use this recursive method to calculate the expected number of the n-most closely related pairs of leaves and the number of cherries separated by a certain time distance. To make our results more useful for realistic scenarios, we explicitly take into account that the leaves of a tree may be incompletely sampled and derive a criterion for poorly sampled phylogenies. We show that our result can account for empirical data, using two families of birds species. PMID:25826216

  7. A framework for understanding the architecture of collective movements using pairwise analyses of animal movement data

    PubMed Central

    Polansky, Leo; Wittemyer, George

    2011-01-01

    The study of collective or group-level movement patterns can provide insight regarding the socio-ecological interface, the evolution of self-organization and mechanisms of inter-individual information exchange. The suite of drivers influencing coordinated movement trajectories occur across scales, resulting from regular annual, seasonal and circadian stimuli and irregular intra- or interspecific interactions and environmental encounters acting on individuals. Here, we promote a conceptual framework with an associated statistical machinery to quantify the type and degree of synchrony, spanning absence to complete, in pairwise movements. The application of this framework offers a foundation for detailed understanding of collective movement patterns and causes. We emphasize the use of Fourier and wavelet approaches of measuring pairwise movement properties and illustrate them with simulations that contain different types of complexity in individual movement, correlation in movement stochasticity, and transience in movement relatedness. Application of this framework to movements of free-ranging African elephants (Loxodonta africana) provides unique insight on the separate roles of sociality and ecology in the fission–fusion society of these animals, quantitatively characterizing the types of bonding that occur at different levels of social relatedness in a movement context. We conclude with a discussion about expanding this framework to the context of larger (greater than three) groups towards understanding broader population and interspecific collective movement patterns and their mechanisms. PMID:20826473

  8. Pairwise Interaction Extended Point Particle (PIEP) Model for a Random Array of Spheres

    NASA Astrophysics Data System (ADS)

    Akiki, Georges; Jackson, Thomas; Balachandar, Sivaramakrishnan; CenterCompressible Multiphase Turbulence Team

    2016-11-01

    This study investigates a flow past random array of spherical particles. The understanding of the governing forces within these arrays is crucial for obtaining accurate models used in particle-laden simulations. These models have to faithfully reflect the sub-grid interactions between the particles and the continuous phase. The models being used today assumes an average force on all particles within the array based on the mean volume fraction and Reynolds number. Here, we develop a model which can compute the drag and lateral forces on each particle by accounting for the precise location of few surrounding neighbors. A pairwise interaction is assumed where the perturbation flow induced by each neighbor is considered separately, then the effect of all neighbors are linearly superposed to obtain the total perturbation. Faxén correction is used to quantify the force perturbation due to the presence of the neighbors. The single neighbor perturbations are mapped in the vicinity of a reference sphere and stored as libraries. We test the Pairwise Interaction Extended Point-Particle (PIEP) model for random arrays at two different volume fractions of ϕ = 0 . 1 and 0.21 and Reynolds number in the range 16 <= Re <= 170 . The PIEP model predictions are compared against drag and lift forces obtained from fully-resolved DNS performed using immersed boundary method. We observe the PIEP model prediction to correlate much better with the DNS results than the classical mean drag model prediction.

  9. Multilevel summation with B-spline interpolation for pairwise interactions in molecular dynamics simulations.

    PubMed

    Hardy, David J; Wolff, Matthew A; Xia, Jianlin; Schulten, Klaus; Skeel, Robert D

    2016-03-21

    The multilevel summation method for calculating electrostatic interactions in molecular dynamics simulations constructs an approximation to a pairwise interaction kernel and its gradient, which can be evaluated at a cost that scales linearly with the number of atoms. The method smoothly splits the kernel into a sum of partial kernels of increasing range and decreasing variability with the longer-range parts interpolated from grids of increasing coarseness. Multilevel summation is especially appropriate in the context of dynamics and minimization, because it can produce continuous gradients. This article explores the use of B-splines to increase the accuracy of the multilevel summation method (for nonperiodic boundaries) without incurring additional computation other than a preprocessing step (whose cost also scales linearly). To obtain accurate results efficiently involves technical difficulties, which are overcome by a novel preprocessing algorithm. Numerical experiments demonstrate that the resulting method offers substantial improvements in accuracy and that its performance is competitive with an implementation of the fast multipole method in general and markedly better for Hamiltonian formulations of molecular dynamics. The improvement is great enough to establish multilevel summation as a serious contender for calculating pairwise interactions in molecular dynamics simulations. In particular, the method appears to be uniquely capable for molecular dynamics in two situations, nonperiodic boundary conditions and massively parallel computation, where the fast Fourier transform employed in the particle-mesh Ewald method falls short.

  10. Estimating the transition/transversion ratio from independent pairwise comparisons with an assumed phylogeny.

    PubMed

    Purvis, A; Bromham, L

    1997-01-01

    A method is presented for estimating the transition/transversion ratio (TI/TV), based on phylogenetically independent comparisons. TI/TV is a parameter of some models used in phylogeny estimation intended to reflect the fact that nucleotide substitutions are not all equally likely. Previous attempts to estimate TI/TV have commonly faced three problems: (1) few taxa; (2) nonindependence among pairwise comparisons; and (3) multiple hits make the apparent TI/TV between two sequences decrease over time since their divergence, giving a misleading impression of relative substitution probabilities. We have made use of the time dependency, modeling how the observed TI/TV changes over time and extrapolating to estimate the "instantaneous" TI/TV-the relevant parameter for phylogenetic inference. To illustrate our method, TI/TV was estimated for two mammalian mitochondrial genes. For 26 pairs of cytochrome b sequences, the estimate of TI/TV was 5.5; 16 pairs of 12s rRNA yielded an estimate of 9.5. These estimates are higher than those given by the maximum likelihood method and than those obtained by averaging all possible pairwise comparisons (with or without a two-parameter correction for multiple substitutions). We discuss strengths, weaknesses, and further uses of our method.

  11. A framework for understanding the architecture of collective movements using pairwise analyses of animal movement data.

    PubMed

    Polansky, Leo; Wittemyer, George

    2011-03-06

    The study of collective or group-level movement patterns can provide insight regarding the socio-ecological interface, the evolution of self-organization and mechanisms of inter-individual information exchange. The suite of drivers influencing coordinated movement trajectories occur across scales, resulting from regular annual, seasonal and circadian stimuli and irregular intra- or interspecific interactions and environmental encounters acting on individuals. Here, we promote a conceptual framework with an associated statistical machinery to quantify the type and degree of synchrony, spanning absence to complete, in pairwise movements. The application of this framework offers a foundation for detailed understanding of collective movement patterns and causes. We emphasize the use of Fourier and wavelet approaches of measuring pairwise movement properties and illustrate them with simulations that contain different types of complexity in individual movement, correlation in movement stochasticity, and transience in movement relatedness. Application of this framework to movements of free-ranging African elephants (Loxodonta africana) provides unique insight on the separate roles of sociality and ecology in the fission-fusion society of these animals, quantitatively characterizing the types of bonding that occur at different levels of social relatedness in a movement context. We conclude with a discussion about expanding this framework to the context of larger (greater than three) groups towards understanding broader population and interspecific collective movement patterns and their mechanisms.

  12. Pairwise and edge-based models of epidemic dynamics on correlated weighted networks

    PubMed Central

    Rattana, P.; Miller, J.C.; Kiss, I.Z.

    2014-01-01

    In this paper we explore the potential of the pairwise-type modelling approach to be extended to weighted networks where nodal degree and weights are not independent. As a baseline or null model for weighted networks, we consider undirected, heterogenous networks where edge weights are randomly distributed. We show that the pairwise model successfully captures the extra complexity of the network, but does this at the cost of limited analytical tractability due the high number of equations. To circumvent this problem, we employ the edge-based modelling approach to derive models corresponding to two different cases, namely for degree-dependent and randomly distributed weights. These models are more amenable to compute important epidemic descriptors, such as early growth rate and final epidemic size, and produce similarly excellent agreement with simulation. Using a branching process approach we compute the basic reproductive ratio for both models and discuss the implication of random and correlated weight distributions on this as well as on the time evolution and final outcome of epidemics. Finally, we illustrate that the two seemingly different modelling approaches, pairwsie and edge-based, operate on similar assumptions and it is possible to formally link the two. PMID:25580064

  13. Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments

    SciTech Connect

    Daily, Jeffrey A.

    2016-02-10

    Sequence alignment algorithms are a key component of many bioinformatics applications. Though various fast Smith-Waterman local sequence alignment implementations have been developed for x86 CPUs, most are embedded into larger database search tools. In addition, fast implementations of Needleman-Wunsch global sequence alignment and its semi-global variants are not as widespread. This article presents the first software library for local, global, and semi-global pairwise intra-sequence alignments and improves the performance of previous intra-sequence implementations. As a result, a faster intra-sequence pairwise alignment implementation is described and benchmarked. Using a 375 residue query sequence a speed of 136 billion cell updates per second (GCUPS) was achieved on a dual Intel Xeon E5-2670 12-core processor system, the highest reported for an implementation based on Farrar’s ’striped’ approach. When using only a single thread, parasail was 1.7 times faster than Rognes’s SWIPE. For many score matrices, parasail is faster than BLAST. The software library is designed for 64 bit Linux, OS X, or Windows on processors with SSE2, SSE41, or AVX2. Source code is available from https://github.com/jeffdaily/parasail under the Battelle BSD-style license. In conclusion, applications that require optimal alignment scores could benefit from the improved performance. For the first time, SIMD global, semi-global, and local alignments are available in a stand-alone C library.

  14. Hierarchical ordering with partial pairwise hierarchical relationships on the macaque brain data sets

    PubMed Central

    Lee, Jungsoo; Lim, Yongsub; Bae, Doo-Hwan; Park, Haesun; Kim, Dae-Shik; Jung, Kyomin

    2017-01-01

    Hierarchical organizations of information processing in the brain networks have been known to exist and widely studied. To find proper hierarchical structures in the macaque brain, the traditional methods need the entire pairwise hierarchical relationships between cortical areas. In this paper, we present a new method that discovers hierarchical structures of macaque brain networks by using partial information of pairwise hierarchical relationships. Our method uses a graph-based manifold learning to exploit inherent relationship, and computes pseudo distances of hierarchical levels for every pair of cortical areas. Then, we compute hierarchy levels of all cortical areas by minimizing the sum of squared hierarchical distance errors with the hierarchical information of few cortical areas. We evaluate our method on the macaque brain data sets whose true hierarchical levels are known as the FV91 model. The experimental results show that hierarchy levels computed by our method are similar to the FV91 model, and its errors are much smaller than the errors of hierarchical clustering approaches. PMID:28545042

  15. Observed Score Linear Equating with Covariates

    ERIC Educational Resources Information Center

    Branberg, Kenny; Wiberg, Marie

    2011-01-01

    This paper examined observed score linear equating in two different data collection designs, the equivalent groups design and the nonequivalent groups design, when information from covariates (i.e., background variables correlated with the test scores) was included. The main purpose of the study was to examine the effect (i.e., bias, variance, and…

  16. Covariant formulation of pion-nucleon scattering

    NASA Astrophysics Data System (ADS)

    Lahiff, A. D.; Afnan, I. R.

    A covariant model of elastic pion-nucleon scattering based on the Bethe-Salpeter equation is presented. The kernel consists of s- and u-channel nucleon and delta poles, along with rho and sigma exchange in the t-channel. A good fit is obtained to the s- and p-wave phase shifts up to the two-pion production threshold.

  17. Observed Score Linear Equating with Covariates

    ERIC Educational Resources Information Center

    Branberg, Kenny; Wiberg, Marie

    2011-01-01

    This paper examined observed score linear equating in two different data collection designs, the equivalent groups design and the nonequivalent groups design, when information from covariates (i.e., background variables correlated with the test scores) was included. The main purpose of the study was to examine the effect (i.e., bias, variance, and…

  18. Scale covariant gravitation. V. Kinetic theory

    SciTech Connect

    Hsieh, S.; Canuto, V.M.

    1981-09-01

    In this paper we construct a scale covariant kinetic theory for particles and photons. The mathematical framework of the theory is given by the tangent bundle of a Weyl manifold. The Liouville equation is then derived. Solutions corresponding to equilibrium distributions are presented and shown to yield thermodynamic results identical to the ones obtained previously.

  19. Analysis of Covariance: A Proposed Algorithm.

    ERIC Educational Resources Information Center

    Frigon, Jean-Yves; Laurencelle, Louis

    1993-01-01

    The statistical power of analysis of covariance (ANCOVA) and its advantages over simple analysis of variance are examined in some experimental situations, and an algorithm is proposed for its proper application. In nonrandomized experiments, an ANCOVA is generally not a good approach. (SLD)

  20. Economical phase-covariant cloning of qudits

    SciTech Connect

    Buscemi, Francesco; D'Ariano, Giacomo Mauro; Macchiavello, Chiara

    2005-04-01

    We derive the optimal N{yields}M phase-covariant quantum cloning for equatorial states in dimension d with M=kd+N, k integer. The cloning maps are optimal for both global and single-qudit fidelity. The map is achieved by an 'economical' cloning machine, which works without ancilla.

  1. Covariant brackets for particles and fields

    NASA Astrophysics Data System (ADS)

    Asorey, M.; Ciaglia, M.; di Cosmo, F.; Ibort, A.

    2017-06-01

    A geometrical approach to the covariant formulation of the dynamics of relativistic systems is introduced. A realization of Peierls brackets by means of a bivector field over the space of solutions of the Euler-Lagrange equations of a variational principle is presented. The method is illustrated with some relevant examples.

  2. Covariance modeling in geodetic applications of collocation

    NASA Astrophysics Data System (ADS)

    Barzaghi, Riccardo; Cazzaniga, Noemi; De Gaetani, Carlo; Reguzzoni, Mirko

    2014-05-01

    Collocation method is widely applied in geodesy for estimating/interpolating gravity related functionals. The crucial problem of this approach is the correct modeling of the empirical covariance functions of the observations. Different methods for getting reliable covariance models have been proposed in the past by many authors. However, there are still problems in fitting the empirical values, particularly when different functionals of T are used and combined. Through suitable linear combinations of positive degree variances a model function that properly fits the empirical values can be obtained. This kind of condition is commonly handled by solver algorithms in linear programming problems. In this work the problem of modeling covariance functions has been dealt with an innovative method based on the simplex algorithm. This requires the definition of an objective function to be minimized (or maximized) where the unknown variables or their linear combinations are subject to some constraints. The non-standard use of the simplex method consists in defining constraints on model covariance function in order to obtain the best fit on the corresponding empirical values. Further constraints are applied so to have coherence with model degree variances to prevent possible solutions with no physical meaning. The fitting procedure is iterative and, in each iteration, constraints are strengthened until the best possible fit between model and empirical functions is reached. The results obtained during the test phase of this new methodology show remarkable improvements with respect to the software packages available until now. Numerical tests are also presented to check for the impact that improved covariance modeling has on the collocation estimate.

  3. ProADD: A database on Protein Aggregation Diseases

    PubMed Central

    Shobana, Ramesh; Pandaranayaka, Eswari PJ

    2014-01-01

    ProADD, a database for protein aggregation diseases, is developed to organize the data under a single platform to facilitate easy access for researchers. Diseases caused due to protein aggregation and the proteins involved in each of these diseases are integrated. The database helps in classification of proteins involved in the protein aggregation diseases based on sequence and structural analysis. Analysis of proteins can be done to mine patterns prevailing among the aggregating proteins. Availability http://bicmku.in/ProADD PMID:25097386

  4. A covariance NMR toolbox for MATLAB and OCTAVE.

    PubMed

    Short, Timothy; Alzapiedi, Leigh; Brüschweiler, Rafael; Snyder, David

    2011-03-01

    The Covariance NMR Toolbox is a new software suite that provides a streamlined implementation of covariance-based analysis of multi-dimensional NMR data. The Covariance NMR Toolbox uses the MATLAB or, alternatively, the freely available GNU OCTAVE computer language, providing a user-friendly environment in which to apply and explore covariance techniques. Covariance methods implemented in the toolbox described here include direct and indirect covariance processing, 4D covariance, generalized indirect covariance (GIC), and Z-matrix transform. In order to provide compatibility with a wide variety of spectrometer and spectral analysis platforms, the Covariance NMR Toolbox uses the NMRPipe format for both input and output files. Additionally, datasets small enough to fit in memory are stored as arrays that can be displayed and further manipulated in a versatile manner within MATLAB or OCTAVE.

  5. Potential of 13 linked autosomal short tandem repeat loci in pairwise kinship analysis.

    PubMed

    Liu, Qiu-Ling; Xue, Li; Wu, Wei-Wei; He, Xin; Liu, Kai-Yan; Zhao, Hu; Lu, De-Jian

    2016-10-01

    In this study, a panel of 13 STR loci locate on chromosome 3, 4, and 17 (D3S2402, D3S2452, D3S1766, D3S4554, D3S2388, D3S3051, D3S3053, D4S2404, D4S2364, AC001348A, AC001348B, D17S975, and D17S1294) were assessed for pairwise kinship analysis. Map distances between these STR loci ranged from 0.07 cM to 97.03 cM. The population genetic study of Chinese Han population showed that linkage disequilibrium exists in two clusters of closely linked markers (D4S2404-D4S2364 and D17S975-D17S1294), in which the recombination fractions were 0.0026 and 0.0001, respectively. The recombination fractions derived from the Rutgers Map for the closely linked markers (genetic distance < 0.5 cM) were significant underestimates in comparison to those of direct observation of STR transmissions in families. When effect of linkage on pairwise kinship testing was evaluated by comparing likelihood ratio (LR) values taking linkage into account, overall LR values increased. But extremely low LRs were also observed. Finally, the power of the 13 STR loci to discriminate relationship among full-sibs, half-sibs, grandparent-grandchild, uncle-niece, and unrelated pairs was assessed with a category fraction. The results showed that about 72.64% of full-sib pairs and about 82.84% of unrelated pairs could be classified correctly. But the category fractions of second-degree relationships drastically reduced to 7.34-35.48%. If only pairs of grandparent-grandchild, half-sibs, and uncle-niece were distinguished, the category fraction was 0.5512, 0.1147, and 0.4362, respectively. Our study results demonstrated that linked STRs were helpful to differentiate the most frequent relationships in pairwise kinship analysis.

  6. Adjusting for covariate effects on classification accuracy using the covariate-adjusted receiver operating characteristic curve.

    PubMed

    Janes, Holly; Pepe, Margaret S

    2009-06-01

    Recent scientific and technological innovations have produced an abundance of potential markers that are being investigated for their use in disease screening and diagnosis. In evaluating these markers, it is often necessary to account for covariates associated with the marker of interest. Covariates may include subject characteristics, expertise of the test operator, test procedures or aspects of specimen handling. In this paper, we propose the covariate-adjusted receiver operating characteristic curve, a measure of covariate-adjusted classification accuracy. Nonparametric and semiparametric estimators are proposed, asymptotic distribution theory is provided and finite sample performance is investigated. For illustration we characterize the age-adjusted discriminatory accuracy of prostate-specific antigen as a biomarker for prostate cancer.

  7. ADD and ADHD: An Overview for School Counselors. ERIC Digest.

    ERIC Educational Resources Information Center

    Pledge, Deanna S.

    School counselors are often consultants for parents and teachers on problems that children and adolescents face. Attention deficit disorder (ADD) is one such problem. It is frequently misunderstood, presenting a challenge for parents and teachers alike. The counselor is a resource for initial identification and interventions at home and in the…

  8. Serving Students Diagnosed with ADD: Avoiding Deficits in Professional Attention.

    ERIC Educational Resources Information Center

    Stoner, Gary; Carey, Sean P.

    1992-01-01

    Responds to previous article (Hakola, this issue) on legal rights of students with Attention Deficit Disorder (ADD). Presents contrasting perspective on educational services for children diagnosed with Attention Deficit Hyperactivity Disorder, linked more closely to professional research and practice than to law. Concerns discussed are grounded in…

  9. Meeting Learning Challenges: Working with the Child Who Has ADD

    ERIC Educational Resources Information Center

    Greenspan, Stanley I.

    2006-01-01

    The terms ADD (Attention Deficit Disorder) and ADHD (Attention Deficit Hyperactivity Disorder) are applied to several symptoms, including: difficulty in paying attention, distractibility, having a hard time following through on things, and sometimes over-activity and impulsivity. There are many different reasons why children have these symptoms.…

  10. Four Simple Ways to Add Movement in Daily Lessons

    ERIC Educational Resources Information Center

    Helgeson, John

    2011-01-01

    Adding movement to classroom activities not only engages students, but also may improve the classroom climate and reduce disruptions. In this article, the author discusses four simple activities to add movement in daily lessons. These activities are: (1) Vocabulary/Notes around the Room; (2) Cooperative Learning: Posting Task Assignments; (3)…

  11. Water Softeners: How Much Sodium Do They Add?

    MedlinePlus

    ... healthy eating I'm trying to watch the sodium in my diet. Should I be concerned about sodium from water softeners? Answers from Sheldon G. Sheps, M.D. Regular tap water contains very little sodium. The amount of sodium a water softener adds ...

  12. Face equipment lighting: integrated vs. add-on

    SciTech Connect

    Scott, F.E.

    1982-10-01

    The problems of providing lighting on face equipment are examined. In the US, some equipment manufacturers are building-in lighting systems to their machinery; others will install lighting systems as add-on or retrofitted items. The pros and cons of each method are examined and the views of manufacturers are quoted.

  13. Digging Postholes Adds Depth and Authenticity to a Shallow Curriculum

    ERIC Educational Resources Information Center

    Virtue, David C.; Buchanan, Anne; Vogler, Kenneth E.

    2012-01-01

    In the current era of high-stakes testing and accountability, many social studies teachers struggle to find creative ways to add depth and authenticity to a broad, shallow curriculum. Teachers can use the time after tests are administered for students to reflect back on the social studies curriculum and select topics they want to study more deeply…

  14. Mode-routed fiber-optic add-drop filter

    NASA Technical Reports Server (NTRS)

    Moslehi, Behzad (Inventor); Black, Richard James (Inventor); Shaw, Herbert John (Inventor)

    2000-01-01

    New elements mode-converting two-mode grating and mode-filtering two-mode coupler are disclosed and used as elements in a system for communications, add-drop filtering, and strain sensing. Methods of fabrication for these new two-mode gratings and mode-filtering two-mode couplers are also disclosed.

  15. Accommodating College Students with Learning Disabilities: ADD, ADHD, and Dyslexia

    ERIC Educational Resources Information Center

    Vickers, Melana Zyla

    2010-01-01

    Universities are providing extra time on tests, quiet exam rooms, in-class note-takers, and other assistance to college students with modest learning disabilities. But these policies are shrouded in secrecy. This paper, "Accommodating College Students with Learning Disabilities: ADD, ADHD, and Dyslexia," by Melana Zyla Vickers, examines…

  16. Four Simple Ways to Add Movement in Daily Lessons

    ERIC Educational Resources Information Center

    Helgeson, John

    2011-01-01

    Adding movement to classroom activities not only engages students, but also may improve the classroom climate and reduce disruptions. In this article, the author discusses four simple activities to add movement in daily lessons. These activities are: (1) Vocabulary/Notes around the Room; (2) Cooperative Learning: Posting Task Assignments; (3)…

  17. Medicalised Pupils: The Case of ADD/ADHD

    ERIC Educational Resources Information Center

    Kristjansson, Kristjan

    2009-01-01

    Recent decades have seen an increasing number of life's problems conceptualised and interpreted through the prism of disease; among them are those affecting pupils at school. Witness the cases of hyperactivity and deficient attention, so often diagnosed as ADD/ADHD. Research indicates that there is at least some tendency towards overdiagnosis of…

  18. How HR Leaders Can Add Value to an Organization

    ERIC Educational Resources Information Center

    Smallwood, Norm; Ulrich, Dave

    2006-01-01

    Generally speaking, it is safe to say that human resource leaders whole-heartedly believe that the HR function should add value to an organization. However, many wonder where to start. In this article, the authors outline three ways in which the HR function, and the HR leader, can create sustained value for an organization and its stakeholders.

  19. Enhancing Teaching using MATLAB Add-Ins for Excel

    ERIC Educational Resources Information Center

    Hamilton, Paul V.

    2004-01-01

    In this paper I will illustrate how to extend the capabilities of Microsoft Excel spreadsheets with add-ins created by MATLAB. Excel provides a broad array of fundamental tools but often comes up short when more sophisticated scenarios are involved. To overcome this short-coming of Excel while retaining its ease of use, I will describe how…

  20. Non-parametric estimation for baseline hazards function and covariate effects with time-dependent covariates.

    PubMed

    Gao, Feng; Manatunga, Amita K; Chen, Shande

    2007-02-20

    Often in many biomedical and epidemiologic studies, estimating hazards function is of interest. The Breslow's estimator is commonly used for estimating the integrated baseline hazard, but this estimator requires the functional form of covariate effects to be correctly specified. It is generally difficult to identify the true functional form of covariate effects in the presence of time-dependent covariates. To provide a complementary method to the traditional proportional hazard model, we propose a tree-type method which enables simultaneously estimating both baseline hazards function and the effects of time-dependent covariates. Our interest will be focused on exploring the potential data structures rather than formal hypothesis testing. The proposed method approximates the baseline hazards and covariate effects with step-functions. The jump points in time and in covariate space are searched via an algorithm based on the improvement of the full log-likelihood function. In contrast to most other estimating methods, the proposed method estimates the hazards function rather than integrated hazards. The method is applied to model the risk of withdrawal in a clinical trial that evaluates the anti-depression treatment in preventing the development of clinical depression. Finally, the performance of the method is evaluated by several simulation studies.

  1. ALP & FALP: C++ libraries for pairwise local alignment E-values.

    PubMed

    Sheetlin, Sergey; Park, Yonil; Frith, Martin C; Spouge, John L

    2016-01-15

    Pairwise local alignment is an indispensable tool for molecular biologists. In real time (i.e. in about 1 s), ALP (Ascending Ladder Program) calculates the E-values for protein-protein or DNA-DNA local alignments of random sequences, for arbitrary substitution score matrix, gap costs and letter abundances; and FALP (Frameshift Ascending Ladder Program) performs a similar task, although more slowly, for frameshifting DNA-protein alignments. To permit other C++ programmers to implement the computational efficiencies in ALP and FALP directly within their own programs, C++ source codes are available in the public domain at http://go.usa.gov/3GTSW under 'ALP' and 'FALP', along with the standalone programs ALP and FALP. spouge@nih.gov Supplementary data are available at Bioinformatics online. Published by Oxford University Press 2015. This work is written by US Government employees and is in the public domain in the US.

  2. General parity between trio and pairwise breeding of laboratory mice in static caging.

    PubMed

    Kedl, Ross M; Wysocki, Lawrence J; Janssen, William J; Born, Willi K; Rosenbaum, Matthew D; Granowski, Julia; Kench, Jennifer A; Fong, Derek L; Switzer, Lisa A; Cruse, Margaret; Huang, Hua; Jakubzick, Claudia V; Kosmider, Beata; Takeda, Katsuyuki; Stranova, Thomas J; Klumm, Randal C; Delgado, Christine; Tummala, Saigiridhar; De Langhe, Stijn; Cambier, John; Haskins, Katherine; Lenz, Laurel L; Curran-Everett, Douglas

    2014-11-15

    Changes made in the 8th edition of the Guide for the Care and Use of Laboratory Animals included new recommendations for the amount of space for breeding female mice. Adopting the new recommendations required, in essence, the elimination of trio breeding practices for all institutions. Both public opinion and published data did not readily support the new recommendations. In response, the National Jewish Health Institutional Animal Care and Use Committee established a program to directly compare the effects of breeding format on mouse pup survival and growth. Our study showed an overall parity between trio and pairwise breeding formats on the survival and growth of the litters, suggesting that the housing recommendations for breeding female mice as stated in the current Guide for the Care and Use of Laboratory Animals should be reconsidered.

  3. PAirwise Sequence Comparison (PASC) and its application in the classification of filoviruses.

    PubMed

    Bao, Yiming; Chetvernin, Vyacheslav; Tatusova, Tatiana

    2012-08-01

    PAirwise Sequence Comparison (PASC) is a tool that uses genome sequence similarity to help with virus classification. The PASC tool at NCBI uses two methods: local alignment based on BLAST and global alignment based on Needleman-Wunsch algorithm. It works for complete genomes of viruses of several families/groups, and for the family of Filoviridae, it currently includes 52 complete genomes available in GenBank. It has been shown that BLAST-based alignment approach works better for filoviruses, and therefore is recommended for establishing taxon demarcations criteria. When more genome sequences with high divergence become available, these demarcation will most likely become more precise. The tool can compare new genome sequences of filoviruses with the ones already in the database, and propose their taxonomic classification.

  4. Video-based depression detection using local Curvelet binary patterns in pairwise orthogonal planes.

    PubMed

    Pampouchidou, Anastasia; Marias, Kostas; Tsiknakis, Manolis; Simos, Panagiotis; Fan Yang; Lemaitre, Guillaume; Meriaudeau, Fabrice

    2016-08-01

    Depression is an increasingly prevalent mood disorder. This is the reason why the field of computer-based depression assessment has been gaining the attention of the research community during the past couple of years. The present work proposes two algorithms for depression detection, one Frame-based and the second Video-based, both employing Curvelet transform and Local Binary Patterns. The main advantage of these methods is that they have significantly lower computational requirements, as the extracted features are of very low dimensionality. This is achieved by modifying the previously proposed algorithm which considers Three-Orthogonal-Planes, to only Pairwise-Orthogonal-Planes. Performance of the algorithms was tested on the benchmark dataset provided by the Audio/Visual Emotion Challenge 2014, with the person-specific system achieving 97.6% classification accuracy, and the person-independed one yielding promising preliminary results of 74.5% accuracy. The paper concludes with open issues, proposed solutions, and future plans.

  5. Consensus formation simulation in a social network modeling controversial opinion dynamics with pairwise interactions

    NASA Astrophysics Data System (ADS)

    Medina-Guevara, María G.; Macías-Díaz, Jorge E.; Gallegos, Armando; Vargas-Rodríguez, Héctor

    In this work, we consider a system of coupled finite-difference equations which incorporates a variety of opinion formation models, and use it to describe the dynamics of opinions on controversial subjects. The social network consists of a finite number of agents with pairwise interactions at discrete times. Meanwhile, the opinion of each agent is updated following a general nonlinear law which considers parameters identified as the personal constants of each of the members. We establish conditions that guarantee the existence of global attracting points (strong consensus) and intervals (weak consensus). Moreover, we note that these conditions are independent of the weight matrix and the number of agents of the network. Two particular scenarios are investigated numerically in order to confirm the validity of the analytical results.

  6. Pairwise Velocities of Galaxies in the CfA and SSRS2 Redshift Surveys

    NASA Astrophysics Data System (ADS)

    Marzke, Ronald O.; Geller, Margaret J.; da Costa, L. N.; Huchra, John P.

    1995-08-01

    We combine the CfA Redshift Survey (CfA2) and the Southern Sky Redshift Survey (SSRS2) to estimate the pairwise velocity dispersion of galaxies σ_12_ on a scale of ~1 h^-1^ Mpc. Both surveys are complete to an apparent magnitude limit B(0) = 15.5. Our sample includes 12812 galaxies distributed in a volume 1.8 x 10^6^ h^-3^ Mpc^3^. We conclude: (1) The pairwise velocity dispersion of galaxies in the combined CfA2+SSRS2 redshift survey is σ_12_ = 540 +/- 180 km s^-1^. Both the estimate and the variance of σ_12_ significantly exceed the canonical values σ_12_ = 340 +/- 40 measured by Davis & Peebles (1983) using CfA1. (2) We derive the uncertainty in σ_12_ from the variation among subsamples with volumes on the order of 7 x 10^5^h^-3^ Mpc^3^. This variation is nearly an order of magnitude larger than the formal error, 36 km s^-1^, derived using least-squares fits to the CfA2+SSRS2 correlation function. This variation among samples is consistent with the conclusions of Mo et al. (1993) for a number of smaller surveys and with the analysis of CfA1 by Zurek et al. (1994). (3) When we remove Abell clusters with R > 1 from our sample, the pairwise velocity dispersion of the remaining galaxies drops to 295 +/- 99 km s^-1^. (4) The dominant source of variance in σ_12_ is the shot noise contributed by dense virialised systems. Because σ_12_ is pair weighted, the statistic is sensitive to the few richest systems in the volume. This sensitivity has two consequences. First, σ_12_ is biased low in small volumes, where the number of clusters is small. Second, we can estimate the variance in σ_12_ as a function of survey volume from the distribution of cluster and group velocity dispersions n (σ). For either a COBE-normalized CDM universe or for the observed distribution of Abell cluster velocity dispersions, the volume required for σ_12_ to converge (δσ_12_/σ_12_ < 0.1) is ~5 x 10^6^h^-3^ Mpc^3^, larger than the volume of CfA2+SSRS2. (5) The distribution of pairwise

  7. On the Sufficiency of Pairwise Interactions in Maximum Entropy Models of Networks

    NASA Astrophysics Data System (ADS)

    Merchan, Lina; Nemenman, Ilya

    2016-03-01

    Biological information processing networks consist of many components, which are coupled by an even larger number of complex multivariate interactions. However, analyses of data sets from fields as diverse as neuroscience, molecular biology, and behavior have reported that observed statistics of states of some biological networks can be approximated well by maximum entropy models with only pairwise interactions among the components. Based on simulations of random Ising spin networks with p-spin (p>2) interactions, here we argue that this reduction in complexity can be thought of as a natural property of densely interacting networks in certain regimes, and not necessarily as a special property of living systems. By connecting our analysis to the theory of random constraint satisfaction problems, we suggest a reason for why some biological systems may operate in this regime.

  8. Inferring Pairwise Interactions from Biological Data Using Maximum-Entropy Probability Models

    PubMed Central

    Stein, Richard R.; Marks, Debora S.; Sander, Chris

    2015-01-01

    Maximum entropy-based inference methods have been successfully used to infer direct interactions from biological datasets such as gene expression data or sequence ensembles. Here, we review undirected pairwise maximum-entropy probability models in two categories of data types, those with continuous and categorical random variables. As a concrete example, we present recently developed inference methods from the field of protein contact prediction and show that a basic set of assumptions leads to similar solution strategies for inferring the model parameters in both variable types. These parameters reflect interactive couplings between observables, which can be used to predict global properties of the biological system. Such methods are applicable to the important problems of protein 3-D structure prediction and association of gene–gene networks, and they enable potential applications to the analysis of gene alteration patterns and to protein design. PMID:26225866

  9. Matrix multiplication operations using pair-wise load and splat operations

    DOEpatents

    Eichenberger, Alexandre E.; Gschwind, Michael K.; Gunnels, John A.; Salapura, Valentina

    2017-03-21

    Mechanisms for performing a matrix multiplication operation are provided. A vector load operation is performed to load a first vector operand of the matrix multiplication operation to a first target vector register. A pair-wise load and splat operation is performed to load a pair of scalar values of a second vector operand and replicate the pair of scalar values within a second target vector register. An operation is performed on elements of the first target vector register and elements of the second target vector register to generate a partial product of the matrix multiplication operation. The partial product is accumulated with other partial products and a resulting accumulated partial product is stored. This operation may be repeated for a second pair of scalar values of the second vector operand.

  10. KISSa: a strategy to build multiple sequence alignments from pairwise comparisons of very closely related sequences.

    PubMed

    Marass, Francesco; Upton, Chris

    2009-05-20

    The volume of viral genomic sequence data continues to increase rapidly. This is especially true for the smaller RNA viruses, which are relatively easy to sequence in large numbers. The data volumes cause a number of significant problems for research applications that require large multiple alignments of essentially complete genomes, which are of the order of 10 kb. We present a simple strategy to enable the creation of large quasi-multiple sequence alignments from pairwise alignment data. This process is suitable for large, closely related sequences such as the polyproteins of dengue viruses, which need the insertion of very few indels. The quasi-multiple sequence alignments generated by KISSa are sufficiently accurate to support tree-based genome selection for interactive bioinformatics analysis tools. The speed of this process is critical to providing an interactive experience for the user.

  11. On the sufficiency of pairwise interactions in maximum entropy models of networks

    NASA Astrophysics Data System (ADS)

    Nemenman, Ilya; Merchan, Lina

    Biological information processing networks consist of many components, which are coupled by an even larger number of complex multivariate interactions. However, analyses of data sets from fields as diverse as neuroscience, molecular biology, and behavior have reported that observed statistics of states of some biological networks can be approximated well by maximum entropy models with only pairwise interactions among the components. Based on simulations of random Ising spin networks with p-spin (p > 2) interactions, here we argue that this reduction in complexity can be thought of as a natural property of some densely interacting networks in certain regimes, and not necessarily as a special property of living systems. This work was supported in part by James S. McDonnell Foundation Grant No. 220020321.

  12. Solution to urn models of pairwise interaction with application to social, physical, and biological sciences

    NASA Astrophysics Data System (ADS)

    Pickering, William; Lim, Chjan

    2017-07-01

    We investigate a family of urn models that correspond to one-dimensional random walks with quadratic transition probabilities that have highly diverse applications. Well-known instances of these two-urn models are the Ehrenfest model of molecular diffusion, the voter model of social influence, and the Moran model of population genetics. We also provide a generating function method for diagonalizing the corresponding transition matrix that is valid if and only if the underlying mean density satisfies a linear differential equation and express the eigenvector components as terms of ordinary hypergeometric functions. The nature of the models lead to a natural extension to interaction between agents in a general network topology. We analyze the dynamics on uncorrelated heterogeneous degree sequence networks and relate the convergence times to the moments of the degree sequences for various pairwise interaction mechanisms.

  13. A fast, scalable method for the parallel evaluation of distance-limited pairwise particle interactions.

    PubMed

    Shaw, David E

    2005-10-01

    Classical molecular dynamics simulations of biological macromolecules in explicitly modeled solvent typically require the evaluation of interactions between all pairs of atoms separated by no more than some distance R, with more distant interactions handled using some less expensive method. Performing such simulations for periods on the order of a millisecond is likely to require the use of massive parallelism. The extent to which such simulations can be efficiently parallelized, however, has historically been limited by the time required for interprocessor communication. This article introduces a new method for the parallel evaluation of distance-limited pairwise particle interactions that significantly reduces the amount of data transferred between processors by comparison with traditional methods. Specifically, the amount of data transferred into and out of a given processor scales as O(R(3/2)p(-1/2)), where p is the number of processors, and with constant factors that should yield a substantial performance advantage in practice.

  14. a General Transformation to Canonical Form for Potentials in Pairwise Intermolecular Interactions

    NASA Astrophysics Data System (ADS)

    Walton, Jay R.; Rivera-Rivera, Luis A.; Lucchese, Robert R.; Bevan, John W.

    2015-06-01

    A generalized formulation of explicit transformations is introduced to investigate the concept of a canonical potential in both fundamental chemical and intermolecular bonding. Different classes of representative ground electronic state pairwise interatomic interactions are referenced to a single canonical potential illustrating application of explicit transformations. Specifically, accurately determined potentials of the diatomic molecules H_2, H_2^+, HF, LiH, argon dimer, and one-dimensional dissociative coordinates in Ar-HBr, OC-HF, and OC-Cl_2 are investigated throughout their bound potentials. The advantages of the current formulation for accurately evaluating equilibrium dissociation energies and a fundamentally different unified perspective on nature of intermolecular interactions will be emphasized. In particular, this canonical approach has relevance to previous assertions that there is no very fundamental distinction between van der Waals bonding and covalent bonding or for that matter hydrogen and halogen bonds.

  15. Pairwise frictional profile between particles determines discontinuous shear thickening transition in non-colloidal suspensions

    PubMed Central

    Comtet, Jean; Chatté, Guillaume; Niguès, Antoine; Bocquet, Lydéric; Siria, Alessandro; Colin, Annie

    2017-01-01

    The process by which sheared suspensions go through a dramatic change in viscosity is known as discontinuous shear thickening. Although well-characterized on the macroscale, the microscopic mechanisms at play in this transition are still poorly understood. Here, by developing new experimental procedures based on quartz-tuning fork atomic force microscopy, we measure the pairwise frictional profile between approaching pairs of polyvinyl chloride and cornstarch particles in solvent. We report a clear transition from a low-friction regime, where pairs of particles support a finite normal load, while interacting purely hydrodynamically, to a high-friction regime characterized by hard repulsive contact between the particles and sliding friction. Critically, we show that the normal stress needed to enter the frictional regime at nanoscale matches the critical stress at which shear thickening occurs for macroscopic suspensions. Our experiments bridge nano and macroscales and provide long needed demonstration of the role of frictional forces in discontinuous shear thickening. PMID:28561032

  16. Pairwise frictional profile between particles determines discontinuous shear thickening transition in non-colloidal suspensions.

    PubMed

    Comtet, Jean; Chatté, Guillaume; Niguès, Antoine; Bocquet, Lydéric; Siria, Alessandro; Colin, Annie

    2017-05-31

    The process by which sheared suspensions go through a dramatic change in viscosity is known as discontinuous shear thickening. Although well-characterized on the macroscale, the microscopic mechanisms at play in this transition are still poorly understood. Here, by developing new experimental procedures based on quartz-tuning fork atomic force microscopy, we measure the pairwise frictional profile between approaching pairs of polyvinyl chloride and cornstarch particles in solvent. We report a clear transition from a low-friction regime, where pairs of particles support a finite normal load, while interacting purely hydrodynamically, to a high-friction regime characterized by hard repulsive contact between the particles and sliding friction. Critically, we show that the normal stress needed to enter the frictional regime at nanoscale matches the critical stress at which shear thickening occurs for macroscopic suspensions. Our experiments bridge nano and macroscales and provide long needed demonstration of the role of frictional forces in discontinuous shear thickening.

  17. Market Competitiveness Evaluation of Mechanical Equipment with a Pairwise Comparisons Hierarchical Model.

    PubMed

    Hou, Fujun

    2016-01-01

    This paper provides a description of how market competitiveness evaluations concerning mechanical equipment can be made in the context of multi-criteria decision environments. It is assumed that, when we are evaluating the market competitiveness, there are limited number of candidates with some required qualifications, and the alternatives will be pairwise compared on a ratio scale. The qualifications are depicted as criteria in hierarchical structure. A hierarchical decision model called PCbHDM was used in this study based on an analysis of its desirable traits. Illustration and comparison shows that the PCbHDM provides a convenient and effective tool for evaluating the market competitiveness of mechanical equipment. The researchers and practitioners might use findings of this paper in application of PCbHDM.

  18. Market Competitiveness Evaluation of Mechanical Equipment with a Pairwise Comparisons Hierarchical Model

    PubMed Central

    Hou, Fujun

    2016-01-01

    This paper provides a description of how market competitiveness evaluations concerning mechanical equipment can be made in the context of multi-criteria decision environments. It is assumed that, when we are evaluating the market competitiveness, there are limited number of candidates with some required qualifications, and the alternatives will be pairwise compared on a ratio scale. The qualifications are depicted as criteria in hierarchical structure. A hierarchical decision model called PCbHDM was used in this study based on an analysis of its desirable traits. Illustration and comparison shows that the PCbHDM provides a convenient and effective tool for evaluating the market competitiveness of mechanical equipment. The researchers and practitioners might use findings of this paper in application of PCbHDM. PMID:26783751

  19. tuple_plot: fast pairwise nucleotide sequence comparison with noise suppression.

    PubMed

    Szafranski, Karol; Jahn, Niels; Platzer, Matthias

    2006-08-01

    The program tuple_plot identifies and visualizes local similarities between two genomic sequences, typically 100 kb or longer, by applying the well-known dotplot principle. A dictionary of sequence words built from the input sequences serves to construct a task-specific expectancy model that is used to attribute significance values to pairwise word hits. The dictionary-based approach allows fast computation, the computation time scaling to O(N log N), depending on the size of the input sequences. The proposed scoring scheme appreciably increases the signal-to-noise ratio and may help to improve other word-based sequence comparison approaches. tuple_plot is available at http://genome.fli-leibniz.de/software.html and may be used under GNU public license.

  20. The pairwise velocity difference of over 2000 BHB stars in the Milky Way halo

    NASA Astrophysics Data System (ADS)

    Xue, Xiang-Xiang; Rix, Hans-Walter; Zhao, Gang

    2009-11-01

    Models of hierarchical galaxy formation predict that the extended stellar halos of galaxies like our Milky Way show a great deal of sub-structure, arising from disrupted satellites. Spatial sub-structure is directly observed, and has been quantified, in the Milky Way's stellar halo. Phase-space conservation implies that there should be sub-structure in position-velocity space. Here, we aim to quantify such position-velocity sub-structure, using a state-of-the art data set having over 2000 blue horizontal branch (BHB) stars with photometry and spectroscopy from SDSS. For stars in dynamically cold streams (“young" streams), we expect that pairs of objects that are physically close also have similar velocities. Therefore, we apply the well-established “pairwise velocity difference" (PVD) statistic <|ΔVlos|> (Δr), where we expect <|ΔVlod|> to drop for small separations Δr. We calculate the PVD for the SDSS BHB sample and find <|ΔVlos|> (Δr) approx const., i.e. no such signal. By making mock-observations of the simulations by Bullock & Johnston and applying the same statistic, we show that for individual, dynamically young streams, or assemblages of such streams, <|ΔVlod|> drops for small distance separations Δr, as qualitatively expected. However, for a realistic complete set of halo streams, the pair-wise velocity difference shows no signal, as the simulated halos are dominated by “dynamically old" phase-mixed streams. Our findings imply that the sparse sampling and the sample sizes in SDSS DR6 are still insufficient to use the position-velocity sub-structure for a stringent quantitative data-model comparison. Therefore, alternate statistics must be explored and much more densely sampled surveys, dedicated to the structure of the Milky Way, such as LAMOST, are needed.

  1. Analysis of Geographic and Pairwise Distances among Chinese Cashmere Goat Populations

    PubMed Central

    Liu, Jian-Bin; Wang, Fan; Lang, Xia; Zha, Xi; Sun, Xiao-Ping; Yue, Yao-Jing; Feng, Rui-Lin; Yang, Bo-Hui; Guo, Jian

    2013-01-01

    This study investigated the geographic and pairwise distances of nine Chinese local Cashmere goat populations through the analysis of 20 microsatellite DNA markers. Fluorescence PCR was used to identify the markers, which were selected based on their significance as identified by the Food and Agriculture Organization of the United Nations (FAO) and the International Society for Animal Genetics (ISAG). In total, 206 alleles were detected; the average allele number was 10.30; the polymorphism information content of loci ranged from 0.5213 to 0.7582; the number of effective alleles ranged from 4.0484 to 4.6178; the observed heterozygosity was from 0.5023 to 0.5602 for the practical sample; the expected heterozygosity ranged from 0.5783 to 0.6464; and Allelic richness ranged from 4.7551 to 8.0693. These results indicated that Chinese Cashmere goat populations exhibited rich genetic diversity. Further, the Wright’s F-statistics of subpopulation within total (FST) was 0.1184; the genetic differentiation coefficient (GST) was 0.0940; and the average gene flow (Nm) was 2.0415. All pairwise FST values among the populations were highly significant (p<0.01 or p<0.001), suggesting that the populations studied should all be considered to be separate breeds. Finally, the clustering analysis divided the Chinese Cashmere goat populations into at least four clusters, with the Hexi and Yashan goat populations alone in one cluster. These results have provided useful, practical, and important information for the future of Chinese Cashmere goat breeding. PMID:25049794

  2. Feature-based pairwise retinal image registration by radial distortion correction

    NASA Astrophysics Data System (ADS)

    Lee, Sangyeol; Abràmoff, Michael D.; Reinhardt, Joseph M.

    2007-03-01

    Fundus camera imaging is widely used to document disorders such as diabetic retinopathy and macular degeneration. Multiple retinal images can be combined together through a procedure known as mosaicing to form an image with a larger field of view. Mosaicing typically requires multiple pairwise registrations of partially overlapped images. We describe a new method for pairwise retinal image registration. The proposed method is unique in that the radial distortion due to image acquisition is corrected prior to the geometric transformation. Vessel lines are detected using the Hessian operator and are used as input features to the registration. Since the overlapping region is typically small in a retinal image pair, only a few correspondences are available, thus limiting the applicable model to an afine transform at best. To recover the distortion due to curved-surface of retina and lens optics, a combined approach of an afine model with a radial distortion correction is proposed. The parameters of the image acquisition and radial distortion models are estimated during an optimization step that uses Powell's method driven by the vessel line distance. Experimental results using 20 pairs of green channel images acquired from three subjects with a fundus camera confirmed that the afine model with distortion correction could register retinal image pairs to within 1.88+/-0.35 pixels accuracy (mean +/- standard deviation) assessed by vessel line error, which is 17% better than the afine-only approach. Because the proposed method needs only two correspondences, it can be applied to obtain good registration accuracy even in the case of small overlap between retinal image pairs.

  3. Infinite Boundary Terms of Ewald Sums and Pairwise Interactions for Electrostatics in Bulk and at Interfaces.

    PubMed

    Hu, Zhonghan

    2014-12-09

    We present a unified derivation of the Ewald sum for electrostatics in a three-dimensional infinite system that is periodic in one, two, or three dimensions. The derivation leads to the Ewald3D sum being expressed as a sum of a real space contribution and a reciprocal space contribution, as in previous work. However, the k → 0 term in the reciprocal space contribution is analyzed further and found to give an additional contribution that is not part of previous reciprocal space contributions. The transparent derivation provides a unified view of the existing conducting infinite boundary term, the vacuum spherical infinite boundary term and the vacuum planar infinite boundary term for the Ewald3D sum. The derivation further explains that the infinite boundary term is conditional for the Ewald3D sum because it depends on the asymptotic behavior that the system approaches the infinite in 3D but it becomes a definite term for the Ewald2D or Ewald1D sum irrespective of the asymptotic behavior in the reduced dimensions. Moreover, the unified derivation yields two formulas for the Ewald sum in one-dimensional periodicity, and we rigorously prove that the two formulas are equivalent. These formulas might be useful for simulations of organic crystals with wirelike shapes or liquids confined in uniform cylinders. More importantly, the Ewald3D, Ewald2D, and Ewald1D sums are further written as sums of well-defined pairwise potentials overcoming the difficulty in splitting the total Coulomb potential energy into contributions from each individual group of charges. The pairwise interactions with their clear physical meaning of the explicit presence of the periodic images thus can be used to consistently perform analysis based on the trajectories from computer simulations of bulk or interfaces.

  4. Understanding molecular crystals with dispersion-inclusive density functional theory: pairwise corrections and beyond.

    PubMed

    Kronik, Leeor; Tkatchenko, Alexandre

    2014-11-18

    CONSPECTUS: Molecular crystals are ubiquitous in many areas of science and engineering, including biology and medicine. Until recently, our ability to understand and predict their structure and properties using density functional theory was severely limited by the lack of approximate exchange-correlation functionals able to achieve sufficient accuracy. Here we show that there are many cases where the simple, minimally empirical pairwise correction scheme of Tkatchenko and Scheffler provides a useful prediction of the structure and properties of molecular crystals. After a brief introduction of the approach, we demonstrate its strength through some examples taken from our recent work. First, we show the accuracy of the approach using benchmark data sets of molecular complexes. Then we show its efficacy for structural determination using the hemozoin crystal, a challenging system possessing a wide range of strong and weak binding scenarios. Next, we show that it is equally useful for response properties by considering the elastic constants exhibited by the supramolecular diphenylalanine peptide solid and the infrared signature of water libration movements in brushite. Throughout, we emphasize lessons learned not only for the methodology but also for the chemistry and physics of the crystals in question. We further show that in many other scenarios where the simple pairwise correction scheme is not sufficiently accurate, one can go beyond it by employing a computationally inexpensive many-body dispersive approach that results in useful, quantitative accuracy, even in the presence of significant screening and/or multibody contributions to the dispersive energy. We explain the principles of the many-body approach and demonstrate its accuracy for benchmark data sets of small and large molecular complexes and molecular solids.

  5. Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments

    DOE PAGES

    Daily, Jeffrey A.

    2016-02-10

    Sequence alignment algorithms are a key component of many bioinformatics applications. Though various fast Smith-Waterman local sequence alignment implementations have been developed for x86 CPUs, most are embedded into larger database search tools. In addition, fast implementations of Needleman-Wunsch global sequence alignment and its semi-global variants are not as widespread. This article presents the first software library for local, global, and semi-global pairwise intra-sequence alignments and improves the performance of previous intra-sequence implementations. As a result, a faster intra-sequence pairwise alignment implementation is described and benchmarked. Using a 375 residue query sequence a speed of 136 billion cell updates permore » second (GCUPS) was achieved on a dual Intel Xeon E5-2670 12-core processor system, the highest reported for an implementation based on Farrar’s ’striped’ approach. When using only a single thread, parasail was 1.7 times faster than Rognes’s SWIPE. For many score matrices, parasail is faster than BLAST. The software library is designed for 64 bit Linux, OS X, or Windows on processors with SSE2, SSE41, or AVX2. Source code is available from https://github.com/jeffdaily/parasail under the Battelle BSD-style license. In conclusion, applications that require optimal alignment scores could benefit from the improved performance. For the first time, SIMD global, semi-global, and local alignments are available in a stand-alone C library.« less

  6. Cellular and Circuit Mechanisms Maintain Low Spike Co-Variability and Enhance Population Coding in Somatosensory Cortex

    PubMed Central

    Ly, Cheng; Middleton, Jason W.; Doiron, Brent

    2012-01-01

    The responses of cortical neurons are highly variable across repeated presentations of a stimulus. Understanding this variability is critical for theories of both sensory and motor processing, since response variance affects the accuracy of neural codes. Despite this influence, the cellular and circuit mechanisms that shape the trial-to-trial variability of population responses remain poorly understood. We used a combination of experimental and computational techniques to uncover the mechanisms underlying response variability of populations of pyramidal (E) cells in layer 2/3 of rat whisker barrel cortex. Spike trains recorded from pairs of E-cells during either spontaneous activity or whisker deflected responses show similarly low levels of spiking co-variability, despite large differences in network activation between the two states. We developed network models that show how spike threshold non-linearities dilute E-cell spiking co-variability during spontaneous activity and low velocity whisker deflections. In contrast, during high velocity whisker deflections, cancelation mechanisms mediated by feedforward inhibition maintain low E-cell pairwise co-variability. Thus, the combination of these two mechanisms ensure low E-cell population variability over a wide range of whisker deflection velocities. Finally, we show how this active decorrelation of population variability leads to a drastic increase in the population information about whisker velocity. The prevalence of spiking non-linearities and feedforward inhibition in the nervous system suggests that the mechanisms for low network variability presented in our study may generalize throughout the brain. PMID:22408615

  7. Cellular and circuit mechanisms maintain low spike co-variability and enhance population coding in somatosensory cortex.

    PubMed

    Ly, Cheng; Middleton, Jason W; Doiron, Brent

    2012-01-01

    The responses of cortical neurons are highly variable across repeated presentations of a stimulus. Understanding this variability is critical for theories of both sensory and motor processing, since response variance affects the accuracy of neural codes. Despite this influence, the cellular and circuit mechanisms that shape the trial-to-trial variability of population responses remain poorly understood. We used a combination of experimental and computational techniques to uncover the mechanisms underlying response variability of populations of pyramidal (E) cells in layer 2/3 of rat whisker barrel cortex. Spike trains recorded from pairs of E-cells during either spontaneous activity or whisker deflected responses show similarly low levels of spiking co-variability, despite large differences in network activation between the two states. We developed network models that show how spike threshold non-linearities dilute E-cell spiking co-variability during spontaneous activity and low velocity whisker deflections. In contrast, during high velocity whisker deflections, cancelation mechanisms mediated by feedforward inhibition maintain low E-cell pairwise co-variability. Thus, the combination of these two mechanisms ensure low E-cell population variability over a wide range of whisker deflection velocities. Finally, we show how this active decorrelation of population variability leads to a drastic increase in the population information about whisker velocity. The prevalence of spiking non-linearities and feedforward inhibition in the nervous system suggests that the mechanisms for low network variability presented in our study may generalize throughout the brain.

  8. RNA sequence analysis using covariance models.

    PubMed Central

    Eddy, S R; Durbin, R

    1994-01-01

    We describe a general approach to several RNA sequence analysis problems using probabilistic models that flexibly describe the secondary structure and primary sequence consensus of an RNA sequence family. We call these models 'covariance models'. A covariance model of tRNA sequences is an extremely sensitive and discriminative tool for searching for additional tRNAs and tRNA-related sequences in sequence databases. A model can be built automatically from an existing sequence alignment. We also describe an algorithm for learning a model and hence a consensus secondary structure from initially unaligned example sequences and no prior structural information. Models trained on unaligned tRNA examples correctly predict tRNA secondary structure and produce high-quality multiple alignments. The approach may be applied to any family of small RNA sequences. Images PMID:8029015

  9. Lorentz Covariant Distributions with Spectral Conditions

    SciTech Connect

    Zinoviev, Yury M.

    2007-11-14

    The properties of the vacuum expectation values of products of the quantum fields are formulated in the book [1]. The vacuum expectation values of quantum fields products would be the Fourier transforms of the Lorentz covariant tempered distributions with supports in the product of the closed upper light cones. Lorentz invariant distributions are studied in the papers [2]--[4]. The authors of these papers wanted to describe Lorentz invariant distributions in terms of distributions given on the Lorentz group orbit space. This orbit space has a complicated structure. It is noted [5] that a tempered distribution with support in the closed upper light cone may be represented as the action of the wave operator in some power on a differentiable function with support in the closed upper light cone. For the description of the Lorentz covariant differentiable functions the boundary of the closed upper light cone is not important. The measure of this boundary is zero.

  10. On covariance structure in noisy, big data

    NASA Astrophysics Data System (ADS)

    Paffenroth, Randy C.; Nong, Ryan; Du Toit, Philip C.

    2013-09-01

    Herein we describe theory and algorithms for detecting covariance structures in large, noisy data sets. Our work uses ideas from matrix completion and robust principal component analysis to detect the presence of low-rank covariance matrices, even when the data is noisy, distorted by large corruptions, and only partially observed. In fact, the ability to handle partial observations combined with ideas from randomized algorithms for matrix decomposition enables us to produce asymptotically fast algorithms. Herein we will provide numerical demonstrations of the methods and their convergence properties. While such methods have applicability to many problems, including mathematical finance, crime analysis, and other large-scale sensor fusion problems, our inspiration arises from applying these methods in the context of cyber network intrusion detection.

  11. Linear transformations of variance/covariance matrices.

    PubMed

    Parois, Pascal; Lutz, Martin

    2011-07-01

    Many applications in crystallography require the use of linear transformations on parameters and their standard uncertainties. While the transformation of the parameters is textbook knowledge, the transformation of the standard uncertainties is more complicated and needs the full variance/covariance matrix. For the transformation of second-rank tensors it is suggested that the 3 × 3 matrix is re-written into a 9 × 1 vector. The transformation of the corresponding variance/covariance matrix is then straightforward and easily implemented into computer software. This method is applied in the transformation of anisotropic displacement parameters, the calculation of equivalent isotropic displacement parameters, the comparison of refinements in different space-group settings and the calculation of standard uncertainties of eigenvalues.

  12. Covariant approach to parametrized cosmological perturbations

    NASA Astrophysics Data System (ADS)

    Tattersall, Oliver J.; Lagos, Macarena; Ferreira, Pedro G.

    2017-09-01

    We present a covariant formulation for constructing general quadratic actions for cosmological perturbations, invariant under a given set of gauge symmetries for a given field content. This approach allows us to analyze scalar, vector, and tensor perturbations at the same time in a straightforward manner. We apply the procedure to diffeomorphism invariant single-tensor, scalar-tensor, and vector-tensor theories and show explicitly the full covariant form of the quadratic actions in such cases, in addition to the actions determining the evolution of vector and tensor perturbations. We also discuss the role of the symmetry of the background in identifying the set of cosmologically relevant free parameters describing these classes of theories, including calculating the relevant free parameters for an axisymmetric Bianchi-I vacuum universe.

  13. Chiral four-dimensional heterotic covariant lattices

    NASA Astrophysics Data System (ADS)

    Beye, Florian

    2014-11-01

    In the covariant lattice formalism, chiral four-dimensional heterotic string vacua are obtained from certain even self-dual lattices which completely decompose into a left-mover and a right-mover lattice. The main purpose of this work is to classify all right-mover lattices that can appear in such a chiral model, and to study the corresponding left-mover lattices using the theory of lattice genera. In particular, the Smith-Minkowski-Siegel mass formula is employed to calculate a lower bound on the number of left-mover lattices. Also, the known relationship between asymmetric orbifolds and covariant lattices is considered in the context of our classification.

  14. Construction of Covariance Functions with Variable Length Fields

    NASA Technical Reports Server (NTRS)

    Gaspari, Gregory; Cohn, Stephen E.; Guo, Jing; Pawson, Steven

    2005-01-01

    This article focuses on construction, directly in physical space, of three-dimensional covariance functions parametrized by a tunable length field, and on an application of this theory to reproduce the Quasi-Biennial Oscillation (QBO) in the Goddard Earth Observing System, Version 4 (GEOS-4) data assimilation system. These Covariance models are referred to as multi-level or nonseparable, to associate them with the application where a multi-level covariance with a large troposphere to stratosphere length field gradient is used to reproduce the QBO from sparse radiosonde observations in the tropical lower stratosphere. The multi-level covariance functions extend well-known single level covariance functions depending only on a length scale. Generalizations of the first- and third-order autoregressive covariances in three dimensions are given, providing multi-level covariances with zero and three derivatives at zero separation, respectively. Multi-level piecewise rational covariances with two continuous derivatives at zero separation are also provided. Multi-level powerlaw covariances are constructed with continuous derivatives of all orders. Additional multi-level covariance functions are constructed using the Schur product of single and multi-level covariance functions. A multi-level powerlaw covariance used to reproduce the QBO in GEOS-4 is described along with details of the assimilation experiments. The new covariance model is shown to represent the vertical wind shear associated with the QBO much more effectively than in the baseline GEOS-4 system.

  15. Inverse covariance simplification for efficient uncertainty management

    NASA Astrophysics Data System (ADS)

    Jalobeanu, A.; Gutiérrez, J. A.

    2007-11-01

    When it comes to manipulating uncertain knowledge such as noisy observations of physical quantities, one may ask how to do it in a simple way. Processing corrupted signals or images always propagates the uncertainties from the data to the final results, whether these errors are explicitly computed or not. When such error estimates are provided, it is crucial to handle them in such a way that their interpretation, or their use in subsequent processing steps, remain user-friendly and computationally tractable. A few authors follow a Bayesian approach and provide uncertainties as an inverse covariance matrix. Despite its apparent sparsity, this matrix contains many small terms that carry little information. Methods have been developed to select the most significant entries, through the use of information-theoretic tools for instance. One has to find a Gaussian pdf that is close enough to the posterior pdf, and with a small number of non-zero coefficients in the inverse covariance matrix. We propose to restrict the search space to Markovian models (where only neighbors can interact), well-suited to signals or images. The originality of our approach is in conserving the covariances between neighbors while setting to zero the entries of the inverse covariance matrix for all other variables. This fully constrains the solution, and the computation is performed via a fast, alternate minimization scheme involving quadratic forms. The Markovian structure advantageously reduces the complexity of Bayesian updating (where the simplified pdf is used as a prior). Moreover, uncertainties exhibit the same temporal or spatial structure as the data.

  16. Covariance expressions for eigenvalue and eigenvector problems

    NASA Astrophysics Data System (ADS)

    Liounis, Andrew J.

    There are a number of important scientific and engineering problems whose solutions take the form of an eigenvalue--eigenvector problem. Some notable examples include solutions to linear systems of ordinary differential equations, controllability of linear systems, finite element analysis, chemical kinetics, fitting ellipses to noisy data, and optimal estimation of attitude from unit vectors. In many of these problems, having knowledge of the eigenvalue and eigenvector Jacobians is either necessary or is nearly as important as having the solution itself. For instance, Jacobians are necessary to find the uncertainty in a computed eigenvalue or eigenvector estimate. This uncertainty, which is usually represented as a covariance matrix, has been well studied for problems similar to the eigenvalue and eigenvector problem, such as singular value decomposition. There has been substantially less research on the covariance of an optimal estimate originating from an eigenvalue-eigenvector problem. In this thesis we develop two general expressions for the Jacobians of eigenvalues and eigenvectors with respect to the elements of their parent matrix. The expressions developed make use of only the parent matrix and the eigenvalue and eigenvector pair under consideration. In addition, they are applicable to any general matrix (including complex valued matrices, eigenvalues, and eigenvectors) as long as the eigenvalues are simple. Alongside this, we develop expressions that determine the uncertainty in a vector estimate obtained from an eigenvalue-eigenvector problem given the uncertainty of the terms of the matrix. The Jacobian expressions developed are numerically validated with forward finite, differencing and the covariance expressions are validated using Monte Carlo analysis. Finally, the results from this work are used to determine covariance expressions for a variety of estimation problem examples and are also applied to the design of a dynamical system.

  17. A covariant Lagrangian for stable nonsingular bounce

    NASA Astrophysics Data System (ADS)

    Cai, Yong; Piao, Yun-Song

    2017-09-01

    The nonsingular bounce models usually suffer from the ghost or gradient instabilities, as has been proved recently. In this paper, we propose a covariant effective theory for stable nonsingular bounce, which has the quadratic order of the second order derivative of the field ϕ but the background set only by P ( ϕ, X). With it, we explicitly construct a fully stable nonsingular bounce model for the ekpyrotic scenario.

  18. Covariant quantization of the CBS superparticle

    NASA Astrophysics Data System (ADS)

    Grassi, P. A.; Policastro, G.; Porrati, M.

    2001-07-01

    The quantization of the Casalbuoni-Brink-Schwarz superparticle is performed in an explicitly covariant way using the antibracket formalism. Since an infinite number of ghost fields are required, within a suitable off-shell twistor-like formalism, we are able to fix the gauge of each ghost sector without modifying the physical content of the theory. The computation reveals that the antibracket cohomology contains only the physical degrees of freedom.

  19. Linear Covariance Analysis for a Lunar Lander

    NASA Technical Reports Server (NTRS)

    Jang, Jiann-Woei; Bhatt, Sagar; Fritz, Matthew; Woffinden, David; May, Darryl; Braden, Ellen; Hannan, Michael

    2017-01-01

    A next-generation lunar lander Guidance, Navigation, and Control (GNC) system, which includes a state-of-the-art optical sensor suite, is proposed in a concept design cycle. The design goal is to allow the lander to softly land within the prescribed landing precision. The achievement of this precision landing requirement depends on proper selection of the sensor suite. In this paper, a robust sensor selection procedure is demonstrated using a Linear Covariance (LinCov) analysis tool developed by Draper.

  20. Discrete symmetries in covariant loop quantum gravity

    NASA Astrophysics Data System (ADS)

    Rovelli, Carlo; Wilson-Ewing, Edward

    2012-09-01

    We study time-reversal and parity—on the physical manifold and in internal space—in covariant loop gravity. We consider a minor modification of the Holst action which makes it transform coherently under such transformations. The classical theory is not affected but the quantum theory is slightly different. In particular, the simplicity constraints are slightly modified and this restricts orientation flips in a spin foam to occur only across degenerate regions, thus reducing the sources of potential divergences.

  1. Twisted covariant noncommutative self-dual gravity

    SciTech Connect

    Estrada-Jimenez, S.; Garcia-Compean, H.; Obregon, O.; Ramirez, C.

    2008-12-15

    A twisted covariant formulation of noncommutative self-dual gravity is presented. The formulation for constructing twisted noncommutative Yang-Mills theories is used. It is shown that the noncommutative torsion is solved at any order of the {theta} expansion in terms of the tetrad and some extra fields of the theory. In the process the first order expansion in {theta} for the Plebanski action is explicitly obtained.

  2. Torsion and geometrostasis in covariant superstrings

    SciTech Connect

    Zachos, C.

    1985-01-01

    The covariant action for freely propagating heterotic superstrings consists of a metric and a torsion term with a special relative strength. It is shown that the strength for which torsion flattens the underlying 10-dimensional superspace geometry is precisely that which yields free oscillators on the light cone. This is in complete analogy with the geometrostasis of two-dimensional sigma-models with Wess-Zumino interactions. 13 refs.

  3. Low-Fidelity Covariances: Neutron Cross Section Covariance Estimates for 387 Materials

    DOE Data Explorer

    The Low-fidelity Covariance Project (Low-Fi) was funded in FY07-08 by DOEÆs Nuclear Criticality Safety Program (NCSP). The project was a collaboration among ANL, BNL, LANL, and ORNL. The motivation for the Low-Fi project stemmed from an imbalance in supply and demand of covariance data. The interest in, and demand for, covariance data has been in a continual uptrend over the past few years. Requirements to understand application-dependent uncertainties in simulated quantities of interest have led to the development of sensitivity / uncertainty and data adjustment software such as TSUNAMI [1] at Oak Ridge. To take full advantage of the capabilities of TSUNAMI requires general availability of covariance data. However, the supply of covariance data has not been able to keep up with the demand. This fact is highlighted by the observation that the recent release of the much-heralded ENDF/B-VII.0 included covariance data for only 26 of the 393 neutron evaluations (which is, in fact, considerably less covariance data than was included in the final ENDF/B-VI release).[Copied from R.C. Little et al., "Low-Fidelity Covariance Project", Nuclear Data Sheets 109 (2008) 2828-2833] The Low-Fi covariance data are now available at the National Nuclear Data Center. They are separate from ENDF/B-VII.0 and the NNDC warns that this information is not approved by CSEWG. NNDC describes the contents of this collection as: "Covariance data are provided for radiative capture (or (n,ch.p.) for light nuclei), elastic scattering (or total for some actinides), inelastic scattering, (n,2n) reactions, fission and nubars over the energy range from 10(-5{super}) eV to 20 MeV. The library contains 387 files including almost all (383 out of 393) materials of the ENDF/B-VII.0. Absent are data for (7{super})Li, (232{super})Th, (233,235,238{super})U and (239{super})Pu as well as (223,224,225,226{super})Ra, while (nat{super})Zn is replaced by (64,66,67,68,70{super})Zn

  4. Development of covariance capabilities in EMPIRE code

    SciTech Connect

    Herman,M.; Pigni, M.T.; Oblozinsky, P.; Mughabghab, S.F.; Mattoon, C.M.; Capote, R.; Cho, Young-Sik; Trkov, A.

    2008-06-24

    The nuclear reaction code EMPIRE has been extended to provide evaluation capabilities for neutron cross section covariances in the thermal, resolved resonance, unresolved resonance and fast neutron regions. The Atlas of Neutron Resonances by Mughabghab is used as a primary source of information on uncertainties at low energies. Care is taken to ensure consistency among the resonance parameter uncertainties and those for thermal cross sections. The resulting resonance parameter covariances are formatted in the ENDF-6 File 32. In the fast neutron range our methodology is based on model calculations with the code EMPIRE combined with experimental data through several available approaches. The model-based covariances can be obtained using deterministic (Kalman) or stochastic (Monte Carlo) propagation of model parameter uncertainties. We show that these two procedures yield comparable results. The Kalman filter and/or the generalized least square fitting procedures are employed to incorporate experimental information. We compare the two approaches analyzing results for the major reaction channels on {sup 89}Y. We also discuss a long-standing issue of unreasonably low uncertainties and link it to the rigidity of the model.

  5. Shrinkage covariance matrix approach for microarray data

    NASA Astrophysics Data System (ADS)

    Karjanto, Suryaefiza; Aripin, Rasimah

    2013-04-01

    Microarray technology was developed for the purpose of monitoring the expression levels of thousands of genes. A microarray data set typically consists of tens of thousands of genes (variables) from just dozens of samples due to various constraints including the high cost of producing microarray chips. As a result, the widely used standard covariance estimator is not appropriate for this purpose. One such technique is the Hotelling's T2 statistic which is a multivariate test statistic for comparing means between two groups. It requires that the number of observations (n) exceeds the number of genes (p) in the set but in microarray studies it is common that n < p. This leads to a biased estimate of the covariance matrix. In this study, the Hotelling's T2 statistic with the shrinkage approach is proposed to estimate the covariance matrix for testing differential gene expression. The performance of this approach is then compared with other commonly used multivariate tests using a widely analysed diabetes data set as illustrations. The results across the methods are consistent, implying that this approach provides an alternative to existing techniques.

  6. Using Covariance Analysis to Assess Pointing Performance

    NASA Technical Reports Server (NTRS)

    Bayard, David; Kang, Bryan

    2009-01-01

    A Pointing Covariance Analysis Tool (PCAT) has been developed for evaluating the expected performance of the pointing control system for NASA s Space Interferometry Mission (SIM). The SIM pointing control system is very complex, consisting of multiple feedback and feedforward loops, and operating with multiple latencies and data rates. The SIM pointing problem is particularly challenging due to the effects of thermomechanical drifts in concert with the long camera exposures needed to image dim stars. Other pointing error sources include sensor noises, mechanical vibrations, and errors in the feedforward signals. PCAT models the effects of finite camera exposures and all other error sources using linear system elements. This allows the pointing analysis to be performed using linear covariance analysis. PCAT propagates the error covariance using a Lyapunov equation associated with time-varying discrete and continuous-time system matrices. Unlike Monte Carlo analysis, which could involve thousands of computational runs for a single assessment, the PCAT analysis performs the same assessment in a single run. This capability facilitates the analysis of parametric studies, design trades, and "what-if" scenarios for quickly evaluating and optimizing the control system architecture and design.

  7. Covariant equations for the NN-πNN system

    NASA Astrophysics Data System (ADS)

    Phillips, D. R.; Afnan, I. R.

    1995-05-01

    We explain the deficiencies of the current NN-πNN equations, sketch the derivation of a set of covariant NN-πNN equations and describe the ways in which these equations differ from previous sets of covariant equations.

  8. Covariant balance laws in continua with microstructure

    NASA Astrophysics Data System (ADS)

    Yavari, Arash; Marsden, Jerrold E.

    2009-02-01

    The purpose of this paper is to extend the Green-Naghdi-Rivlin balance of energy method to continua with microstructure. The key idea is to replace the group of Galilean transformations with the group of diffeomorphisms of the ambient space. A key advantage is that one obtains in a natural way all the needed balance laws on both the macro and micro levels along with two Doyle-Erickson formulas. We model a structured continuum as a triplet of Riemannian manifolds: a material manifold, the ambient space manifold of material particles and a director field manifold. The Green-Naghdi-Rivlin theorem and its extensions for structured continua are critically reviewed. We show that when the ambient space is Euclidean and when the microstructure manifold is the tangent space of the ambient space manifold, postulating a single balance of energy law and its invariance under time-dependent isometries of the ambient space, one obtains conservation of mass, balances of linear and angular momenta but not a separate balance of linear momentum. We develop a covariant elasticity theory for structured continua by postulating that energy balance is invariant under time-dependent spatial diffeomorphisms of the ambient space, which in this case is the product of two Riemannian manifolds. We then introduce two types of constrained continua in which microstructure manifold is linked to the reference and ambient space manifolds. In the case when at every material point, the microstructure manifold is the tangent space of the ambient space manifold at the image of the material point, we show that the assumption of covariance leads to balances of linear and angular momenta with contributions from both forces and micro-forces along with two Doyle-Ericksen formulas. We show that generalized covariance leads to two balances of linear momentum and a single coupled balance of angular momentum. Using this theory, we covariantly obtain the balance laws for two specific examples, namely elastic

  9. Eigenvalue-eigenvector decomposition (EED) analysis of dissimilarity and covariance matrix obtained from total synchronous fluorescence spectral (TSFS) data sets of herbal preparations: Optimizing the classification approach.

    PubMed

    Tarai, Madhumita; Kumar, Keshav; Divya, O; Bairi, Partha; Mishra, Kishor Kumar; Mishra, Ashok Kumar

    2017-09-05

    The present work compares the dissimilarity and covariance based unsupervised chemometric classification approaches by taking the total synchronous fluorescence spectroscopy data sets acquired for the cumin and non-cumin based herbal preparations. The conventional decomposition method involves eigenvalue-eigenvector analysis of the covariance of the data set and finds the factors that can explain the overall major sources of variation present in the data set. The conventional approach does this irrespective of the fact that the samples belong to intrinsically different groups and hence leads to poor class separation. The present work shows that classification of such samples can be optimized by performing the eigenvalue-eigenvector decomposition on the pair-wise dissimilarity matrix. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. Eigenvalue-eigenvector decomposition (EED) analysis of dissimilarity and covariance matrix obtained from total synchronous fluorescence spectral (TSFS) data sets of herbal preparations: Optimizing the classification approach

    NASA Astrophysics Data System (ADS)

    Tarai, Madhumita; Kumar, Keshav; Divya, O.; Bairi, Partha; Mishra, Kishor Kumar; Mishra, Ashok Kumar

    2017-09-01

    The present work compares the dissimilarity and covariance based unsupervised chemometric classification approaches by taking the total synchronous fluorescence spectroscopy data sets acquired for the cumin and non-cumin based herbal preparations. The conventional decomposition method involves eigenvalue-eigenvector analysis of the covariance of the data set and finds the factors that can explain the overall major sources of variation present in the data set. The conventional approach does this irrespective of the fact that the samples belong to intrinsically different groups and hence leads to poor class separation. The present work shows that classification of such samples can be optimized by performing the eigenvalue-eigenvector decomposition on the pair-wise dissimilarity matrix.

  11. Factorization of the Discrete Noise Covariance Matrix for Plans,

    DTIC Science & Technology

    1991-02-01

    rapport prdsente la formulation exacte de la matrice de covariance Qk necessaire pour la propagation de la matrice de covariance du filtre Kalman ...approximation la d6composition necessaire pour utiliser la formulation Biermann-Agee-Turner du filtre Kalman . Cette decomposition approximative est...form of the discrete driving noise covariance matrix Qk which is needed to propagate the covariance matrix in the Kalman filter used by PLANS. It is

  12. Earth Observation System Flight Dynamics System Covariance Realism

    NASA Technical Reports Server (NTRS)

    Zaidi, Waqar H.; Tracewell, David

    2016-01-01

    This presentation applies a covariance realism technique to the National Aeronautics and Space Administration (NASA) Earth Observation System (EOS) Aqua and Aura spacecraft based on inferential statistics. The technique consists of three parts: collection calculation of definitive state estimates through orbit determination, calculation of covariance realism test statistics at each covariance propagation point, and proper assessment of those test statistics.

  13. Covariate Imbalance and Precision in Measuring Treatment Effects

    ERIC Educational Resources Information Center

    Liu, Xiaofeng Steven

    2011-01-01

    Covariate adjustment can increase the precision of estimates by removing unexplained variance from the error in randomized experiments, although chance covariate imbalance tends to counteract the improvement in precision. The author develops an easy measure to examine chance covariate imbalance in randomization by standardizing the average…

  14. Covariate Selection in Propensity Scores Using Outcome Proxies

    ERIC Educational Resources Information Center

    Kelcey, Ben

    2011-01-01

    This study examined the practical problem of covariate selection in propensity scores (PSs) given a predetermined set of covariates. Because the bias reduction capacity of a confounding covariate is proportional to the concurrent relationships it has with the outcome and treatment, particular focus is set on how we might approximate…

  15. Hidden Covariation Detection Produces Faster, Not Slower, Social Judgments

    ERIC Educational Resources Information Center

    Barker, Lynne A.; Andrade, Jackie

    2006-01-01

    In P. Lewicki's (1986b) demonstration of hidden covariation detection (HCD), responses of participants were slower to faces that corresponded with a covariation encountered previously than to faces with novel covariations. This slowing contrasts with the typical finding that priming leads to faster responding and suggests that HCD is a unique type…

  16. Add Control: plant virtualization for control solutions in WWTP.

    PubMed

    Maiza, M; Bengoechea, A; Grau, P; De Keyser, W; Nopens, I; Brockmann, D; Steyer, J P; Claeys, F; Urchegui, G; Fernández, O; Ayesa, E

    2013-01-01

    This paper summarizes part of the research work carried out in the Add Control project, which proposes an extension of the wastewater treatment plant (WWTP) models and modelling architectures used in traditional WWTP simulation tools, addressing, in addition to the classical mass transformations (transport, physico-chemical phenomena, biological reactions), all the instrumentation, actuation and automation & control components (sensors, actuators, controllers), considering their real behaviour (signal delays, noise, failures and power consumption of actuators). Its ultimate objective is to allow a rapid transition from the simulation of the control strategy to its implementation at full-scale plants. Thus, this paper presents the application of the Add Control simulation platform for the design and implementation of new control strategies at the WWTP of Mekolalde.

  17. Stereovision Imaging in Smart Mobile Phone Using Add on Prisms

    NASA Astrophysics Data System (ADS)

    Bar-Magen Numhauser, Jonathan; Zalevsky, Zeev

    2014-03-01

    In this work we present the use of a prism-based add on component installed on top of a smart phone to achieve stereovision capabilities using iPhone mobile operating system. Through these components and the combination of the appropriate application programming interface and mathematical algorithms the obtained results will permit the analysis of possible enhancements for new uses to such system, in a variety of areas including medicine and communications.

  18. Family nurse practitioners: "value add" in outpatient chronic disease management.

    PubMed

    Stephens, Lynn

    2012-12-01

    Nurse practitioners are capable leaders in primary care design as practices nationwide move to consider and adopt the patient-centered medical home. The chronic care model provides a structure to enhance the care of chronic illness. Nurse practitioners are instrumental in many areas of this model as both leaders and caregivers. Safety and quality are basic medical home goals; nurse practitioners enhance both. The addition of a nurse practitioner to a practice is an effective "value add" in every way.

  19. Higher Curvature Effects in the ADD and RS Models

    SciTech Connect

    Rizzo, Thomas G.; /SLAC

    2006-07-05

    Over the last few years several extra-dimensional models have been introduced in attempt to deal with the hierarchy problem. These models can lead to rather unique and spectacular signatures at Terascale colliders such as the LHC and ILC. The ADD and RS models, though quite distinct, have many common feature including a constant curvature bulk, localized Standard Model(SM) fields and the assumption of the validity of the EH action as a description of gravitational interactions.

  20. Randomized Controlled Trials of Add-On Antidepressants in Schizophrenia.

    PubMed

    Terevnikov, Viacheslav; Joffe, Grigori; Stenberg, Jan-Henry

    2015-05-19

    Despite adequate treatment with antipsychotics, a substantial number of patients with schizophrenia demonstrate only suboptimal clinical outcome. To overcome this challenge, various psychopharmacological combination strategies have been used, including antidepressants added to antipsychotics. To analyze the efficacy of add-on antidepressants for the treatment of negative, positive, cognitive, depressive, and antipsychotic-induced extrapyramidal symptoms in schizophrenia, published randomized controlled trials assessing the efficacy of adjunctive antidepressants in schizophrenia were reviewed using the following parameters: baseline clinical characteristics and number of patients, their on-going antipsychotic treatment, dosage of the add-on antidepressants, duration of the trial, efficacy measures, and outcomes. There were 36 randomized controlled trials reported in 41 journal publications (n=1582). The antidepressants used were the selective serotonin reuptake inhibitors, duloxetine, imipramine, mianserin, mirtazapine, nefazodone, reboxetin, trazodone, and bupropion. Mirtazapine and mianserin showed somewhat consistent efficacy for negative symptoms and both seemed to enhance neurocognition. Trazodone and nefazodone appeared to improve the antipsychotics-induced extrapyramidal symptoms. Imipramine and duloxetine tended to improve depressive symptoms. No clear evidence supporting selective serotonin reuptake inhibitors' efficacy on any clinical domain of schizophrenia was found. Add-on antidepressants did not worsen psychosis. Despite a substantial number of randomized controlled trials, the overall efficacy of add-on antidepressants in schizophrenia remains uncertain mainly due to methodological issues. Some differences in efficacy on several schizophrenia domains seem, however, to exist and to vary by the antidepressant subgroups--plausibly due to differences in the mechanisms of action. Antidepressants may not worsen the course of psychosis. Better designed

  1. Randomized Controlled Trials of Add-On Antidepressants in Schizophrenia

    PubMed Central

    Joffe, Grigori; Stenberg, Jan-Henry

    2015-01-01

    Background: Despite adequate treatment with antipsychotics, a substantial number of patients with schizophrenia demonstrate only suboptimal clinical outcome. To overcome this challenge, various psychopharmacological combination strategies have been used, including antidepressants added to antipsychotics. Methods: To analyze the efficacy of add-on antidepressants for the treatment of negative, positive, cognitive, depressive, and antipsychotic-induced extrapyramidal symptoms in schizophrenia, published randomized controlled trials assessing the efficacy of adjunctive antidepressants in schizophrenia were reviewed using the following parameters: baseline clinical characteristics and number of patients, their on-going antipsychotic treatment, dosage of the add-on antidepressants, duration of the trial, efficacy measures, and outcomes. Results: There were 36 randomized controlled trials reported in 41 journal publications (n=1582). The antidepressants used were the selective serotonin reuptake inhibitors, duloxetine, imipramine, mianserin, mirtazapine, nefazodone, reboxetin, trazodone, and bupropion. Mirtazapine and mianserin showed somewhat consistent efficacy for negative symptoms and both seemed to enhance neurocognition. Trazodone and nefazodone appeared to improve the antipsychotics-induced extrapyramidal symptoms. Imipramine and duloxetine tended to improve depressive symptoms. No clear evidence supporting selective serotonin reuptake inhibitors’ efficacy on any clinical domain of schizophrenia was found. Add-on antidepressants did not worsen psychosis. Conclusions: Despite a substantial number of randomized controlled trials, the overall efficacy of add-on antidepressants in schizophrenia remains uncertain mainly due to methodological issues. Some differences in efficacy on several schizophrenia domains seem, however, to exist and to vary by the antidepressant subgroups—plausibly due to differences in the mechanisms of action. Antidepressants may not worsen

  2. Add-on unidirectional elastic metamaterial plate cloak.

    PubMed

    Lee, Min Kyung; Kim, Yoon Young

    2016-02-10

    Metamaterial cloaks control the propagation of waves to make an object invisible or insensible. To manipulate elastic waves in space, a metamaterial cloak is typically embedded in a base system that includes or surrounds a target object. The embedding is undesirable because it structurally weakens or permanently alters the base system. In this study, we propose a new add-on metamaterial elastic cloak that can be placed over and mechanically coupled with a base structure without embedding. We designed an add-on type annular metamaterial plate cloak through conformal mapping, fabricated it and performed cloaking experiments in a thin-plate with a hole. Experiments were performed in a thin plate by using the lowest symmetric Lamb wave centered at 100 kHz. As a means to check the cloaking performance of the add-on elastic plate cloak, possibly as a temporary stress reliever or a so-called "stress bandage", the degree of stress concentration mitigation and the recovery from the perturbed wave field due to a hole were investigated.

  3. Optical add/drop filter for wavelength division multiplexed systems

    DOEpatents

    Deri, Robert J.; Strand, Oliver T.; Garrett, Henry E.

    2002-01-01

    An optical add/drop filter for wavelength division multiplexed systems and construction methods are disclosed. The add/drop filter includes a first ferrule having a first pre-formed opening for receiving a first optical fiber; an interference filter oriented to pass a first set of wavelengths along the first optical fiber and reflect a second set of wavelengths; and, a second ferrule having a second pre-formed opening for receiving the second optical fiber, and the reflected second set of wavelengths. A method for constructing the optical add/drop filter consists of the steps of forming a first set of openings in a first ferrule; inserting a first set of optical fibers into the first set of openings; forming a first set of guide pin openings in the first ferrule; dividing the first ferrule into a first ferrule portion and a second ferrule portion; forming an interference filter on the first ferrule portion; inserting guide pins through the first set of guide pin openings in the first ferrule portion and second ferrule portion to passively align the first set of optical fibers; removing material such that light reflected from the interference filter from the first set of optical fibers is accessible; forming a second set of openings in a second ferrule; inserting a second set of optical fibers into the second set of openings; and positioning the second ferrule with respect to the first ferrule such that the second set of optical fibers receive the light reflected from the interference filter.

  4. Add-on unidirectional elastic metamaterial plate cloak

    PubMed Central

    Lee, Min Kyung; Kim, Yoon Young

    2016-01-01

    Metamaterial cloaks control the propagation of waves to make an object invisible or insensible. To manipulate elastic waves in space, a metamaterial cloak is typically embedded in a base system that includes or surrounds a target object. The embedding is undesirable because it structurally weakens or permanently alters the base system. In this study, we propose a new add-on metamaterial elastic cloak that can be placed over and mechanically coupled with a base structure without embedding. We designed an add-on type annular metamaterial plate cloak through conformal mapping, fabricated it and performed cloaking experiments in a thin-plate with a hole. Experiments were performed in a thin plate by using the lowest symmetric Lamb wave centered at 100 kHz. As a means to check the cloaking performance of the add-on elastic plate cloak, possibly as a temporary stress reliever or a so-called “stress bandage”, the degree of stress concentration mitigation and the recovery from the perturbed wave field due to a hole were investigated. PMID:26860896

  5. 40 CFR 75.34 - Units with add-on emission controls.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 17 2014-07-01 2014-07-01 false Units with add-on emission controls... add-on emission controls. (a) The owner or operator of an affected unit equipped with add-on SO2 and... which the add-on emission controls are documented to be operating properly, as described in the...

  6. 40 CFR 75.34 - Units with add-on emission controls.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 17 2012-07-01 2012-07-01 false Units with add-on emission controls... add-on emission controls. (a) The owner or operator of an affected unit equipped with add-on SO2 and... which the add-on emission controls are documented to be operating properly, as described in the...

  7. 40 CFR 75.34 - Units with add-on emission controls.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 17 2013-07-01 2013-07-01 false Units with add-on emission controls... add-on emission controls. (a) The owner or operator of an affected unit equipped with add-on SO2 and... which the add-on emission controls are documented to be operating properly, as described in the...

  8. 24 CFR 990.190 - Other formula expenses (add-ons).

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 24 Housing and Urban Development 4 2014-04-01 2014-04-01 false Other formula expenses (add-ons... formula expenses (add-ons). In addition to calculating operating subsidy based on the PEL and UEL, a PHA's eligible formula expenses shall be increased by add-ons. The allowed add-ons are: (a) Self-sufficiency....

  9. 24 CFR 990.190 - Other formula expenses (add-ons).

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 24 Housing and Urban Development 4 2011-04-01 2011-04-01 false Other formula expenses (add-ons... formula expenses (add-ons). In addition to calculating operating subsidy based on the PEL and UEL, a PHA's eligible formula expenses shall be increased by add-ons. The allowed add-ons are: (a) Self-sufficiency....

  10. Classification of forest-based ecotourism areas in Pocahontas County of West Virginia using GIS and pairwise comparison method

    Treesearch

    Ishwar Dhami; Jinyang. Deng

    2012-01-01

    Many previous studies have examined ecotourism primarily from the perspective of tourists while largely ignoring ecotourism destinations. This study used geographical information system (GIS) and pairwise comparison to identify forest-based ecotourism areas in Pocahontas County, West Virginia. The study adopted the criteria and scores developed by Boyd and Butler (1994...

  11. Pair-Wise Trajectory Management-Oceanic (PTM-O) . [Concept of Operations—Version 3.9

    NASA Technical Reports Server (NTRS)

    Jones, Kenneth M.

    2014-01-01

    This document describes the Pair-wise Trajectory Management-Oceanic (PTM-O) Concept of Operations (ConOps). Pair-wise Trajectory Management (PTM) is a concept that includes airborne and ground-based capabilities designed to enable and to benefit from, airborne pair-wise distance-monitoring capability. PTM includes the capabilities needed for the controller to issue a PTM clearance that resolves a conflict for a specific pair of aircraft. PTM avionics include the capabilities needed for the flight crew to manage their trajectory relative to specific designated aircraft. Pair-wise Trajectory Management PTM-Oceanic (PTM-O) is a regional specific application of the PTM concept. PTM is sponsored by the National Aeronautics and Space Administration (NASA) Concept and Technology Development Project (part of NASA's Airspace Systems Program). The goal of PTM is to use enhanced and distributed communications and surveillance along with airborne tools to permit reduced separation standards for given aircraft pairs, thereby increasing the capacity and efficiency of aircraft operations at a given altitude or volume of airspace.

  12. Pairwise Maximum Entropy Models for Studying Large Biological Systems: When They Can Work and When They Can't

    PubMed Central

    Roudi, Yasser; Nirenberg, Sheila; Latham, Peter E.

    2009-01-01

    One of the most critical problems we face in the study of biological systems is building accurate statistical descriptions of them. This problem has been particularly challenging because biological systems typically contain large numbers of interacting elements, which precludes the use of standard brute force approaches. Recently, though, several groups have reported that there may be an alternate strategy. The reports show that reliable statistical models can be built without knowledge of all the interactions in a system; instead, pairwise interactions can suffice. These findings, however, are based on the analysis of small subsystems. Here, we ask whether the observations will generalize to systems of realistic size, that is, whether pairwise models will provide reliable descriptions of true biological systems. Our results show that, in most cases, they will not. The reason is that there is a crossover in the predictive power of pairwise models: If the size of the subsystem is below the crossover point, then the results have no predictive power for large systems. If the size is above the crossover point, then the results may have predictive power. This work thus provides a general framework for determining the extent to which pairwise models can be used to predict the behavior of large biological systems. Applied to neural data, the size of most systems studied so far is below the crossover point. PMID:19424487

  13. Quantum energy inequalities and local covariance II: categorical formulation

    NASA Astrophysics Data System (ADS)

    Fewster, Christopher J.

    2007-11-01

    We formulate quantum energy inequalities (QEIs) in the framework of locally covariant quantum field theory developed by Brunetti, Fredenhagen and Verch, which is based on notions taken from category theory. This leads to a new viewpoint on the QEIs, and also to the identification of a new structural property of locally covariant quantum field theory, which we call local physical equivalence. Covariant formulations of the numerical range and spectrum of locally covariant fields are given and investigated, and a new algebra of fields is identified, in which fields are treated independently of their realisation on particular spacetimes and manifestly covariant versions of the functional calculus may be formulated.

  14. Linear Covariance Analysis and Epoch State Estimators

    NASA Technical Reports Server (NTRS)

    Markley, F. Landis; Carpenter, J. Russell

    2012-01-01

    This paper extends in two directions the results of prior work on generalized linear covariance analysis of both batch least-squares and sequential estimators. The first is an improved treatment of process noise in the batch, or epoch state, estimator with an epoch time that may be later than some or all of the measurements in the batch. The second is to account for process noise in specifying the gains in the epoch state estimator. We establish the conditions under which the latter estimator is equivalent to the Kalman filter.

  15. Inferring Meta-covariates in Classification

    NASA Astrophysics Data System (ADS)

    Harris, Keith; McMillan, Lisa; Girolami, Mark

    This paper develops an alternative method for gene selection that combines model based clustering and binary classification. By averaging the covariates within the clusters obtained from model based clustering, we define “meta-covariates” and use them to build a probit regression model, thereby selecting clusters of similarly behaving genes, aiding interpretation. This simultaneous learning task is accomplished by an EM algorithm that optimises a single likelihood function which rewards good performance at both classification and clustering. We explore the performance of our methodology on a well known leukaemia dataset and use the Gene Ontology to interpret our results.

  16. Covariant constraints in ghost free massive gravity

    SciTech Connect

    Deffayet, C.; Mourad, J.; Zahariade, G. E-mail: mourad@apc.univ-paris7.fr

    2013-01-01

    We show that the reformulation of the de Rham-Gabadadze-Tolley massive gravity theory using vielbeins leads to a very simple and covariant way to count constraints, and hence degrees of freedom. Our method singles out a subset of theories, in the de Rham-Gabadadze-Tolley family, where an extra constraint, needed to eliminate the Boulware Deser ghost, is easily seen to appear. As a side result, we also introduce a new method, different from the Stuckelberg trick, to extract kinetic terms for the polarizations propagating in addition to those of the massless graviton.

  17. Cosmology of a covariant Galilean field.

    PubMed

    De Felice, Antonio; Tsujikawa, Shinji

    2010-09-10

    We study the cosmology of a covariant scalar field respecting a Galilean symmetry in flat space-time. We show the existence of a tracker solution that finally approaches a de Sitter fixed point responsible for cosmic acceleration today. The viable region of model parameters is clarified by deriving conditions under which ghosts and Laplacian instabilities of scalar and tensor perturbations are absent. The field equation of state exhibits a peculiar phantomlike behavior along the tracker, which allows a possibility to observationally distinguish the Galileon gravity from the cold dark matter model with a cosmological constant.

  18. Covariant harmonic oscillators and coupled harmonic oscillators

    NASA Technical Reports Server (NTRS)

    Han, Daesoo; Kim, Young S.; Noz, Marilyn E.

    1995-01-01

    It is shown that the system of two coupled harmonic oscillators shares the basic symmetry properties with the covariant harmonic oscillator formalism which provides a concise description of the basic features of relativistic hadronic features observed in high-energy laboratories. It is shown also that the coupled oscillator system has the SL(4,r) symmetry in classical mechanics, while the present formulation of quantum mechanics can accommodate only the Sp(4,r) portion of the SL(4,r) symmetry. The possible role of the SL(4,r) symmetry in quantum mechanics is discussed.

  19. Covariant change of signature in classical relativity

    NASA Astrophysics Data System (ADS)

    Ellis, G. F. R.

    1992-10-01

    This paper gives a covariant formalism enabling investigation of the possibility of change of signature in classical General Relativity, when the geometry is that of a Robertson-Walker universe. It is shown that such changes are compatible with the Einstein field equations, both in the case of a barotropic fluid and of a scalar field. A criterion is given for when such a change of signature should take place in the scalar field case. Some examples show the kind of resulting exact solutions of the field equations.

  20. Linear Covariance Analysis and Epoch State Estimators

    NASA Technical Reports Server (NTRS)

    Markley, F. Landis; Carpenter, J. Russell

    2014-01-01

    This paper extends in two directions the results of prior work on generalized linear covariance analysis of both batch least-squares and sequential estimators. The first is an improved treatment of process noise in the batch, or epoch state, estimator with an epoch time that may be later than some or all of the measurements in the batch. The second is to account for process noise in specifying the gains in the epoch state estimator. We establish the conditions under which the latter estimator is equivalent to the Kalman filter.

  1. Minimal covariant observables identifying all pure states

    NASA Astrophysics Data System (ADS)

    Carmeli, Claudio; Heinosaari, Teiko; Toigo, Alessandro

    2013-09-01

    It has been recently shown by Heinosaari, Mazzarella and Wolf (2013) [1] that an observable that identifies all pure states of a d-dimensional quantum system has minimally 4d-4 outcomes or slightly less (the exact number depending on d). However, no simple construction of this type of minimal observable is known. We investigate covariant observables that identify all pure states and have minimal number of outcomes. It is shown that the existence of this kind of observables depends on the dimension of the Hilbert space.

  2. Phase-covariant cloning of coherent states

    NASA Astrophysics Data System (ADS)

    Sacchi, Massimiliano F.

    2007-04-01

    We consider the problem of phase-covariant cloning for coherent states. We show that an experimental scheme based on ideal phase measurement and feedforward outperforms the semiclassical procedure of ideal phase measurement and preparation in terms of fidelity. A realistic scheme where the ideal phase measurement is replaced with double-homodyne detection is shown to be unable to overcome the semiclassical cloning strategy. On the other hand, such a realistic scheme is better than semiclassical cloning based on double-homodyne phase measurement and preparation.

  3. Coupled nucleotide covariations reveal dynamic RNA interaction patterns.

    PubMed Central

    Gultyaev, A P; Franch, T; Gerdes, K

    2000-01-01

    Evolutionarily conserved structures in related RNA molecules contain coordinated variations (covariations) of paired nucleotides. Analysis of covariations is a very powerful approach to deduce phylogenetically conserved (i.e., functional) conformations, including tertiary interactions. Here we discuss conserved RNA folding pathways that are revealed by covariation patterns. In such pathways, structural requirements for alternative pairings cause some nucleotides to covary with two different partners. Such "coupled" covariations between three or more nucleotides were found in various types of RNAs. The analysis of coupled covariations can unravel important features of RNA folding dynamics and improve phylogeny reconstruction in some cases. Importantly, it is necessary to distinguish between multiple covariations determined by mutually exclusive structures and those determined by tertiary contacts. PMID:11105748

  4. An efficient algorithm for pairwise local alignment of protein interaction networks

    DOE PAGES

    Chen, Wenbin; Schmidt, Matthew; Tian, Wenhong; ...

    2015-04-01

    Recently, researchers seeking to understand, modify, and create beneficial traits in organisms have looked for evolutionarily conserved patterns of protein interactions. Their conservation likely means that the proteins of these conserved functional modules are important to the trait's expression. In this paper, we formulate the problem of identifying these conserved patterns as a graph optimization problem, and develop a fast heuristic algorithm for this problem. We compare the performance of our network alignment algorithm to that of the MaWISh algorithm [Koyuturk M, Kim Y, Topkara U, Subramaniam S, Szpankowski W, Grama A, Pairwise alignment of protein interaction networks, J Computmore » Biol 13(2): 182-199, 2006.], which bases its search algorithm on a related decision problem formulation. We find that our algorithm discovers conserved modules with a larger number of proteins in an order of magnitude less time. In conclusion, the protein sets found by our algorithm correspond to known conserved functional modules at comparable precision and recall rates as those produced by the MaWISh algorithm.« less

  5. OxfordGrid: a web interface for pairwise comparative map views.

    PubMed

    Yang, Hongyu; Gingle, Alan R

    2005-12-01

    OxfordGrid is a web application and database schema for storing and interactively displaying genetic map data in a comparative, dot-plot, fashion. Its display is composed of a matrix of cells, each representing a pairwise comparison of mapped probe data for two linkage groups or chromosomes. These are arranged along the axes with one forming grid columns and the other grid rows with the degree and pattern of synteny/colinearity between the two linkage groups manifested in the cell's dot density and structure. A mouse click over the selected grid cell launches an image map-based display for the selected cell. Both individual and linear groups of mapped probes can be selected and displayed. Also, configurable links can be used to access other web resources for mapped probe information. OxfordGrid is implemented in C#/ASP.NET and the package, including MySQL schema creation scripts, is available at ftp://cggc.agtec.uga.edu/OxfordGrid/.

  6. EpiGPU: exhaustive pairwise epistasis scans parallelized on consumer level graphics cards.

    PubMed

    Hemani, Gibran; Theocharidis, Athanasios; Wei, Wenhua; Haley, Chris

    2011-06-01

    Hundreds of genome-wide association studies have been performed over the last decade, but as single nucleotide polymorphism (SNP) chip density has increased so has the computational burden to search for epistasis [for n SNPs the computational time resource is O(n(n-1)/2)]. While the theoretical contribution of epistasis toward phenotypes of medical and economic importance is widely discussed, empirical evidence is conspicuously absent because its analysis is often computationally prohibitive. To facilitate resolution in this field, tools must be made available that can render the search for epistasis universally viable in terms of hardware availability, cost and computational time. By partitioning the 2D search grid across the multicore architecture of a modern consumer graphics processing unit (GPU), we report a 92× increase in the speed of an exhaustive pairwise epistasis scan for a quantitative phenotype, and we expect the speed to increase as graphics cards continue to improve. To achieve a comparable computational improvement without a graphics card would require a large compute-cluster, an option that is often financially non-viable. The implementation presented uses OpenCL--an open-source library designed to run on any commercially available GPU and on any operating system. The software is free, open-source, platformindependent and GPU-vendor independent. It can be downloaded from http://sourceforge.net/projects/epigpu/.

  7. Serial-position effects in preference construction: a sensitivity analysis of the pairwise-competition model.

    PubMed

    Canic, Emina; Pachur, Thorsten

    2014-01-01

    People have a stronger preference for options encountered earlier or later in a sequence than for options in the middle of the sequence. To account for these primacy and recency effects, Mantonakis et al. (2009) sketched a sequential updating mechanism, the pairwise-competition model. We propose a formal instantiation of the model and, using computer simulations, examine how the sizes of the predicted primacy and recency effects are affected by (a) variability in the quality of the options; (b) the number of options presented (sequence length); (c) the level of choice inertia (i.e., the tendency to stick with the current favorite); and (d) whether choice inertia dynamically increases over the sequence. We find that recency effects are reduced and primacy effects are increased with variability in quality as compared to without, and that this holds regardless of sequence length. A sizeable primacy effect occurs only with relatively short sequences or rather high levels of choice inertia. Dynamic inertia increases primacy effects and reduces recency effects, and the impact increases with higher inertia levels. We relate these results to empirical findings and derive novel predictions from the model.

  8. Serial-position effects in preference construction: a sensitivity analysis of the pairwise-competition model

    PubMed Central

    Canic, Emina; Pachur, Thorsten

    2014-01-01

    People have a stronger preference for options encountered earlier or later in a sequence than for options in the middle of the sequence. To account for these primacy and recency effects, Mantonakis et al. (2009) sketched a sequential updating mechanism, the pairwise-competition model. We propose a formal instantiation of the model and, using computer simulations, examine how the sizes of the predicted primacy and recency effects are affected by (a) variability in the quality of the options; (b) the number of options presented (sequence length); (c) the level of choice inertia (i.e., the tendency to stick with the current favorite); and (d) whether choice inertia dynamically increases over the sequence. We find that recency effects are reduced and primacy effects are increased with variability in quality as compared to without, and that this holds regardless of sequence length. A sizeable primacy effect occurs only with relatively short sequences or rather high levels of choice inertia. Dynamic inertia increases primacy effects and reduces recency effects, and the impact increases with higher inertia levels. We relate these results to empirical findings and derive novel predictions from the model. PMID:25202288

  9. Detection of prostate cancer on histopathology using color fractals and Probabilistic Pairwise Markov models.

    PubMed

    Yu, Elaine; Monaco, James P; Tomaszewski, John; Shih, Natalie; Feldman, Michael; Madabhushi, Anant

    2011-01-01

    In this paper we present a system for detecting regions of carcinoma of the prostate (CaP) in H&E stained radical prostatectomy specimens using the color fractal dimension. Color textural information is known to be a valuable characteristic to distinguish CaP from benign tissue. In addition to color information, we know that cancer tends to form contiguous regions. Our system leverages the color staining information of histology as well as spatial dependencies. The color and textural information is first captured using color fractal dimension. To incorporate spatial dependencies, we combine the probability map constructed via color fractal dimension with a novel Markov prior called the Probabilistic Pairwise Markov Model (PPMM). To demonstrate the capability of this CaP detection system, we applied the algorithm to 27 radical prostatectomy specimens from 10 patients. A per pixel evaluation was conducted with ground truth provided by an expert pathologist using only the color fractal feature first, yielding an area under the receiver operator characteristic curve (AUC) curve of 0.790. In conjunction with a Markov prior, the resultant color fractal dimension + Markov random field (MRF) classifier yielded an AUC of 0.831.

  10. A fast and powerful W-test for pairwise epistasis testing.

    PubMed

    Wang, Maggie Haitian; Sun, Rui; Guo, Junfeng; Weng, Haoyi; Lee, Jack; Hu, Inchi; Sham, Pak Chung; Zee, Benny Chung-Ying

    2016-07-08

    Epistasis plays an essential role in the development of complex diseases. Interaction methods face common challenge of seeking a balance between persistent power, model complexity, computation efficiency, and validity of identified bio-markers. We introduce a novel W-test to identify pairwise epistasis effect, which measures the distributional difference between cases and controls through a combined log odds ratio. The test is model-free, fast, and inherits a Chi-squared distribution with data adaptive degrees of freedom. No permutation is needed to obtain the P-values. Simulation studies demonstrated that the W-test is more powerful in low frequency variants environment than alternative methods, which are the Chi-squared test, logistic regression and multifactor-dimensionality reduction (MDR). In two independent real bipolar disorder genome-wide associations (GWAS) datasets, the W-test identified significant interactions pairs that can be replicated, including SLIT3-CENPN, SLIT3-TMEM132D, CNTNAP2-NDST4 and CNTCAP2-RTN4R The genes in the pairs play central roles in neurotransmission and synapse formation. A majority of the identified loci are undiscoverable by main effect and are low frequency variants. The proposed method offers a powerful alternative tool for mapping the genetic puzzle underlying complex disorders.

  11. Evaluation of a Pair-Wise Conflict Detection and Resolution Algorithm in a Multiple Aircraft Scenario

    NASA Technical Reports Server (NTRS)

    Carreno, Victor A.

    2002-01-01

    The KB3D algorithm is a pairwise conflict detection and resolution (CD&R) algorithm. It detects and generates trajectory vectoring for an aircraft which has been predicted to be in an airspace minima violation within a given look-ahead time. It has been proven, using mechanized theorem proving techniques, that for a pair of aircraft, KB3D produces at least one vectoring solution and that all solutions produced are correct. Although solutions produced by the algorithm are mathematically correct, they might not be physically executable by an aircraft or might not solve multiple aircraft conflicts. This paper describes a simple solution selection method which assesses all solutions generated by KB3D and determines the solution to be executed. The solution selection method and KB3D are evaluated using a simulation in which N aircraft fly in a free-flight environment and each aircraft in the simulation uses KB3D to maintain separation. Specifically, the solution selection method filters KB3D solutions which are procedurally undesirable or physically not executable and uses a predetermined criteria for selection.

  12. Net2Align: An Algorithm For Pairwise Global Alignment of Biological Networks

    PubMed Central

    Wadhwab, Gulshan; Upadhyayaa, K. C.

    2016-01-01

    The amount of data on molecular interactions is growing at an enormous pace, whereas the progress of methods for analysing this data is still lacking behind. Particularly, in the area of comparative analysis of biological networks, where one wishes to explore the similarity between two biological networks, this holds a potential problem. In consideration that the functionality primarily runs at the network level, it advocates the need for robust comparison methods. In this paper, we describe Net2Align, an algorithm for pairwise global alignment that can perform node-to-node correspondences as well as edge-to-edge correspondences into consideration. The uniqueness of our algorithm is in the fact that it is also able to detect the type of interaction, which is essential in case of directed graphs. The existing algorithm is only able to identify the common nodes but not the common edges. Another striking feature of the algorithm is that it is able to remove duplicate entries in case of variable datasets being aligned. This is achieved through creation of a local database which helps exclude duplicate links. In a pervasive computational study on gene regulatory network, we establish that our algorithm surpasses its counterparts in its results. Net2Align has been implemented in Java 7 and the source code is available as supplementary files. PMID:28356678

  13. Benefits of Using Pairwise Trajectory Management in the Central East Pacific

    NASA Technical Reports Server (NTRS)

    Chartrand, Ryan; Ballard, Kathryn

    2016-01-01

    Pairwise Trajectory Management (PTM) is a concept that utilizes airborne and ground-based capabilities to enable airborne spacing operations in oceanic regions. The goal of PTM is to use enhanced surveillance, along with airborne tools, to manage the spacing between aircraft. Due to the enhanced airborne surveillance of Automatic Dependent Surveillance-Broadcast (ADS-B) information and reduced communication, the PTM minimum spacing distance will be less than distances currently required of an air traffic controller. Reduced minimum distance will increase the capacity of aircraft operations at a given altitude or volume of airspace, thereby increasing time on desired trajectory and overall flight efficiency. PTM is designed to allow a flight crew to resolve a specific traffic conflict (or conflicts), identified by the air traffic controller, while maintaining the flight crew's desired altitude. The air traffic controller issues a PTM clearance to a flight crew authorized to conduct PTM operations in order to resolve a conflict for the pair (or pairs) of aircraft (i.e., the PTM aircraft and a designated target aircraft). This clearance requires the flight crew of the PTM aircraft to use their ADS-B-enabled onboard equipment to manage their spacing relative to the designated target aircraft to ensure spacing distances that are no closer than the PTM minimum distance. When the air traffic controller determines that PTM is no longer required, the controller issues a clearance to cancel the PTM operation.

  14. Advancing health-related cluster analysis methodology: quantification of pairwise activity cluster similarities.

    PubMed

    Ferrar, Katia; Maher, Carol; Petkov, John; Olds, Tim

    2015-03-01

    To date, most health-related time-use research has investigated behaviors in isolation; more recently, however, researchers have begun to conceptualize behaviors in the form of multidimensional patterns or clusters. The study employed 2 techniques: radar graphs and centroid vector length, angles and distance to quantify pairwise time-use cluster similarities among adolescents living in Australia (N = 1853) and in New Zealand (N = 679). Based on radar graph shape, 2 pairs of clusters were similar for both boys and girls. Using vector angles (VA), vector length (VL) and centroid distances (CD), 1 pair for each sex was considered most similar (boys: VA = 63°, VL = 44 and 50 units, and CD = 48 units; girls: VA = 23°, VL = 65 and 85 units, and CD = 36 units). Both methods employed to determine similarity had strengths and weaknesses. The description and quantification of cluster similarity is an important step in the research process. An ability to track and compare clusters may provide greater understanding of complex multidimensional relationships, and in relation to health behavior clusters, present opportunities to monitor and to intervene.

  15. Reconstructing Protein Structures by Neural Network Pairwise Interaction Fields and Iterative Decoy Set Construction

    PubMed Central

    Mirabello, Claudio; Adelfio, Alessandro; Pollastri, Gianluca

    2014-01-01

    Predicting the fold of a protein from its amino acid sequence is one of the grand problems in computational biology. While there has been progress towards a solution, especially when a protein can be modelled based on one or more known structures (templates), in the absence of templates, even the best predictions are generally much less reliable. In this paper, we present an approach for predicting the three-dimensional structure of a protein from the sequence alone, when templates of known structure are not available. This approach relies on a simple reconstruction procedure guided by a novel knowledge-based evaluation function implemented as a class of artificial neural networks that we have designed: Neural Network Pairwise Interaction Fields (NNPIF). This evaluation function takes into account the contextual information for each residue and is trained to identify native-like conformations from non-native-like ones by using large sets of decoys as a training set. The training set is generated and then iteratively expanded during successive folding simulations. As NNPIF are fast at evaluating conformations, thousands of models can be processed in a short amount of time, and clustering techniques can be adopted for model selection. Although the results we present here are very preliminary, we consider them to be promising, with predictions being generated at state-of-the-art levels in some of the cases. PMID:24970210

  16. Pairwise selection assembly for sequence-independent construction of long-length DNA.

    PubMed

    Blake, William J; Chapman, Brad A; Zindal, Anuradha; Lee, Michael E; Lippow, Shaun M; Baynes, Brian M

    2010-05-01

    The engineering of biological components has been facilitated by de novo synthesis of gene-length DNA. Biological engineering at the level of pathways and genomes, however, requires a scalable and cost-effective assembly of DNA molecules that are longer than approximately 10 kb, and this remains a challenge. Here we present the development of pairwise selection assembly (PSA), a process that involves hierarchical construction of long-length DNA through the use of a standard set of components and operations. In PSA, activation tags at the termini of assembly sub-fragments are reused throughout the assembly process to activate vector-encoded selectable markers. Marker activation enables stringent selection for a correctly assembled product in vivo, often obviating the need for clonal isolation. Importantly, construction via PSA is sequence-independent, and does not require primary sequence modification (e.g. the addition or removal of restriction sites). The utility of PSA is demonstrated in the construction of a completely synthetic 91-kb chromosome arm from Saccharomyces cerevisiae.

  17. A fast and powerful W-test for pairwise epistasis testing

    PubMed Central

    Wang, Maggie Haitian; Sun, Rui; Guo, Junfeng; Weng, Haoyi; Lee, Jack; Hu, Inchi; Sham, Pak Chung; Zee, Benny Chung-Ying

    2016-01-01

    Epistasis plays an essential role in the development of complex diseases. Interaction methods face common challenge of seeking a balance between persistent power, model complexity, computation efficiency, and validity of identified bio-markers. We introduce a novel W-test to identify pairwise epistasis effect, which measures the distributional difference between cases and controls through a combined log odds ratio. The test is model-free, fast, and inherits a Chi-squared distribution with data adaptive degrees of freedom. No permutation is needed to obtain the P-values. Simulation studies demonstrated that the W-test is more powerful in low frequency variants environment than alternative methods, which are the Chi-squared test, logistic regression and multifactor-dimensionality reduction (MDR). In two independent real bipolar disorder genome-wide associations (GWAS) datasets, the W-test identified significant interactions pairs that can be replicated, including SLIT3-CENPN, SLIT3-TMEM132D, CNTNAP2-NDST4 and CNTCAP2-RTN4R. The genes in the pairs play central roles in neurotransmission and synapse formation. A majority of the identified loci are undiscoverable by main effect and are low frequency variants. The proposed method offers a powerful alternative tool for mapping the genetic puzzle underlying complex disorders. PMID:27112568

  18. Pairwise entanglement and the Mott transition for correlated electrons in nanochains

    NASA Astrophysics Data System (ADS)

    Rycerz, Adam

    2017-05-01

    Pairwise entanglement, calculated separately for charge and spin degrees of freedom, is proposed as a ground-state signature of the Mott transition in correlated nanoscopic systems. Utilizing the exact diagonalization—ab initio, for chains containing N≤slant 16 hydrogenic-like atoms (at the half filling), we find that the vanishing of the nearest-neighbor charge concurrence indicates the crossover from a partly-localized quantum liquid to the Mott insulator. Spin concurrence remains nonzero at the insulating phase, showing that the decopling of spin and charge degrees of freedom may manifest itself by wavefunctions entangled in spin, but separable in charge coordinates. At the quarter filling, the analysis for N≤slant 20 shows that spin concurrence vanishes immediately when the charge-energy gap obtained from the scaling with 1/N\\to 0 vanishes, constituting a finite-system version of the Mott transition. Analytic derivations of the formulas expressing either charge or spin concurrence in terms of ground-state correlation functions are also provided.

  19. Evaluation of advanced multiplex short tandem repeat systems in pairwise kinship analysis.

    PubMed

    Tamura, Tomonori; Osawa, Motoki; Ochiai, Eriko; Suzuki, Takanori; Nakamura, Takashi

    2015-09-01

    The AmpFLSTR Identifiler Kit, comprising 15 autosomal short tandem repeat (STR) loci, is commonly employed in forensic practice for calculating match probabilities and parentage testing. The conventional system exhibits insufficient estimation for kinship analysis such as sibship testing because of shortness of examined loci. This study evaluated the power of the PowerPlex Fusion System, GlobalFiler Kit, and PowerPlex 21 System, which comprise more than 20 autosomal STR loci, to estimate pairwise blood relatedness (i.e., parent-child, full siblings, second-degree relatives, and first cousins). The genotypes of all 24 STR loci in 10,000 putative pedigrees were constructed by simulation. The likelihood ratio for each locus was calculated from joint probabilities for relatives and non-relatives. The combined likelihood ratio was calculated according to the product rule. The addition of STR loci improved separation between relatives and non-relatives. However, these systems were less effectively extended to the inference for first cousins. In conclusion, these advanced systems will be useful in forensic personal identification, especially in the evaluation of full siblings and second-degree relatives. Moreover, the additional loci may give rise to two major issues of more frequent mutational events and several pairs of linked loci on the same chromosome.

  20. Hydrostatic pressure effect on hydrophobic hydration and pairwise hydrophobic interaction of methane

    NASA Astrophysics Data System (ADS)

    Graziano, Giuseppe

    2014-03-01

    At room temperature, the Ben-Naim standard hydration Gibbs energy of methane is a positive quantity that increases markedly with hydrostatic pressure [M. S. Moghaddam and H. S. Chan, J. Chem. Phys. 126, 114507 (2007)]. This finding is rationalized by showing that the magnitude of the reversible work to create a suitable cavity in water increases with pressure due to both the increase in the volume packing density of water and the contribution of the pressure-volume work. According to the present approach, at room temperature, the Gibbs energy of the contact-minimum configuration of two methane molecules is a negative quantity that increases in magnitude with hydrostatic pressure. This result is not in line with the results of several computer simulation studies [T. Ghosh, A. E. Garcia, and S. Garde, J. Am. Chem. Soc. 123, 10997-11003 (2001)], and emerges because pairwise association causes a decrease in solvent-excluded volume that produces a gain of configurational/translational entropy of water molecules, whose magnitude increases with the volume packing density of the liquid phase.

  1. pyRMSD: a Python package for efficient pairwise RMSD matrix calculation and handling.

    PubMed

    Gil, Víctor A; Guallar, Víctor

    2013-09-15

    We introduce pyRMSD, an open source standalone Python package that aims at offering an integrative and efficient way of performing Root Mean Square Deviation (RMSD)-related calculations of large sets of structures. It is specially tuned to do fast collective RMSD calculations, as pairwise RMSD matrices, implementing up to three well-known superposition algorithms. pyRMSD provides its own symmetric distance matrix class that, besides the fact that it can be used as a regular matrix, helps to save memory and increases memory access speed. This last feature can dramatically improve the overall performance of any Python algorithm using it. In addition, its extensibility, testing suites and documentation make it a good choice to those in need of a workbench for developing or testing new algorithms. The source code (under MIT license), installer, test suites and benchmarks can be found at https://pele.bsc.es/ under the tools section. victor.guallar@bsc.es Supplementary data are available at Bioinformatics online.

  2. Pairwise alignment of interaction networks by fast identification of maximal conserved patterns.

    PubMed

    Tian, Wenhong; Samatova, Nagiza F

    2009-01-01

    A number of tools for the alignment of protein-protein interaction (PPI) networks have laid the foundation for PPI network analysis. They typically find conserved interaction patterns by various local or global search algorithms, and then validate the results using genome annotation. The improvement of the speed, scalability and accuracy of network alignment is still the target of ongoing research. In view of this, we introduce a connected-components based algorithm, called HopeMap for pairwise network alignment with the focus on fast identification of maximal conserved patterns across species. Observing that the number of true homologs across species is relatively small compared to the total number of proteins in all species, we start with highly homologous groups across species, find maximal conserved interaction patterns globally with a generic scoring system, and validate the results across multiple known functional annotations. The results are evaluated in terms of statistical enrichment of gene ontology (GO) terms and KEGG ortholog groups (KO) within conserved interaction patters. HopeMap is fast, with linear computational cost, accurate in terms of KO groups and GO terms specificity and sensitivity, and extensible to multiple network alignment.

  3. A pairwise likelihood augmented Cox estimator for left-truncated data.

    PubMed

    Wu, Fan; Kim, Sehee; Qin, Jing; Saran, Rajiv; Li, Yi

    2017-08-29

    Survival data collected from a prevalent cohort are subject to left truncation and the analysis is challenging. Conditional approaches for left-truncated data could be inefficient as they ignore the information in the marginal likelihood of the truncation times. Length-biased sampling methods may improve the estimation efficiency but only when the underlying truncation time is uniform; otherwise, they may generate biased estimates. We propose a semiparametric method for left-truncated data under the Cox model with no parametric distributional assumption about the truncation times. Our approach is to make inference based on the conditional likelihood augmented with a pairwise likelihood, which eliminates the truncation distribution, yet retains the information about the regression coefficients and the baseline hazard function in the marginal likelihood. An iterative algorithm is provided to solve for the regression coefficients and the baseline hazard function simultaneously. By empirical process and U-process theories, it has been shown that the proposed estimator is consistent and asymptotically normal with a closed-form consistent variance estimator. Simulation studies show substantial efficiency gain of our estimator in both the regression coefficients and the cumulative baseline hazard function over the conditional approach estimator. When the uniform truncation assumption holds, our estimator enjoys smaller biases and efficiency comparable to that of the full maximum likelihood estimator. An application to the analysis of a chronic kidney disease cohort study illustrates the utility of the method. © 2017, The International Biometric Society.

  4. A new graph-based method for pairwise global network alignment

    PubMed Central

    Klau, Gunnar W

    2009-01-01

    Background In addition to component-based comparative approaches, network alignments provide the means to study conserved network topology such as common pathways and more complex network motifs. Yet, unlike in classical sequence alignment, the comparison of networks becomes computationally more challenging, as most meaningful assumptions instantly lead to NP-hard problems. Most previous algorithmic work on network alignments is heuristic in nature. Results We introduce the graph-based maximum structural matching formulation for pairwise global network alignment. We relate the formulation to previous work and prove NP-hardness of the problem. Based on the new formulation we build upon recent results in computational structural biology and present a novel Lagrangian relaxation approach that, in combination with a branch-and-bound method, computes provably optimal network alignments. The Lagrangian algorithm alone is a powerful heuristic method, which produces solutions that are often near-optimal and – unlike those computed by pure heuristics – come with a quality guarantee. Conclusion Computational experiments on the alignment of protein-protein interaction networks and on the classification of metabolic subnetworks demonstrate that the new method is reasonably fast and has advantages over pure heuristics. Our software tool is freely available as part of the LISA library. PMID:19208162

  5. The distribution of pairwise genetic distances: a tool for investigating disease transmission.

    PubMed

    Worby, Colin J; Chang, Hsiao-Han; Hanage, William P; Lipsitch, Marc

    2014-12-01

    Whole-genome sequencing of pathogens has recently been used to investigate disease outbreaks and is likely to play a growing role in real-time epidemiological studies. Methods to analyze high-resolution genomic data in this context are still lacking, and inferring transmission dynamics from such data typically requires many assumptions. While recent studies have proposed methods to infer who infected whom based on genetic distance between isolates from different individuals, the link between epidemiological relationship and genetic distance is still not well understood. In this study, we investigated the distribution of pairwise genetic distances between samples taken from infected hosts during an outbreak. We proposed an analytically tractable approximation to this distribution, which provides a framework to evaluate the likelihood of particular transmission routes. Our method accounts for the transmission of a genetically diverse inoculum, a possibility overlooked in most analyses. We demonstrated that our approximation can provide a robust estimation of the posterior probability of transmission routes in an outbreak and may be used to rule out transmission events at a particular probability threshold. We applied our method to data collected during an outbreak of methicillin-resistant Staphylococcus aureus, ruling out several potential transmission links. Our study sheds light on the accumulation of mutations in a pathogen during an epidemic and provides tools to investigate transmission dynamics, avoiding the intensive computation necessary in many existing methods.

  6. Visualization of pairwise and multilocus linkage disequilibrium structure using latent forests.

    PubMed

    Mourad, Raphaël; Sinoquet, Christine; Dina, Christian; Leray, Philippe

    2011-01-01

    Linkage disequilibrium study represents a major issue in statistical genetics as it plays a fundamental role in gene mapping and helps us to learn more about human history. The linkage disequilibrium complex structure makes its exploratory data analysis essential yet challenging. Visualization methods, such as the triangular heat map implemented in Haploview, provide simple and useful tools to help understand complex genetic patterns, but remain insufficient to fully describe them. Probabilistic graphical models have been widely recognized as a powerful formalism allowing a concise and accurate modeling of dependences between variables. In this paper, we propose a method for short-range, long-range and chromosome-wide linkage disequilibrium visualization using forests of hierarchical latent class models. Thanks to its hierarchical nature, our method is shown to provide a compact view of both pairwise and multilocus linkage disequilibrium spatial structures for the geneticist. Besides, a multilocus linkage disequilibrium measure has been designed to evaluate linkage disequilibrium in hierarchy clusters. To learn the proposed model, a new scalable algorithm is presented. It constrains the dependence scope, relying on physical positions, and is able to deal with more than one hundred thousand single nucleotide polymorphisms. The proposed algorithm is fast and does not require phase genotypic data.

  7. Visualization of Pairwise and Multilocus Linkage Disequilibrium Structure Using Latent Forests

    PubMed Central

    Mourad, Raphaël; Sinoquet, Christine; Dina, Christian; Leray, Philippe

    2011-01-01

    Linkage disequilibrium study represents a major issue in statistical genetics as it plays a fundamental role in gene mapping and helps us to learn more about human history. The linkage disequilibrium complex structure makes its exploratory data analysis essential yet challenging. Visualization methods, such as the triangular heat map implemented in Haploview, provide simple and useful tools to help understand complex genetic patterns, but remain insufficient to fully describe them. Probabilistic graphical models have been widely recognized as a powerful formalism allowing a concise and accurate modeling of dependences between variables. In this paper, we propose a method for short-range, long-range and chromosome-wide linkage disequilibrium visualization using forests of hierarchical latent class models. Thanks to its hierarchical nature, our method is shown to provide a compact view of both pairwise and multilocus linkage disequilibrium spatial structures for the geneticist. Besides, a multilocus linkage disequilibrium measure has been designed to evaluate linkage disequilibrium in hierarchy clusters. To learn the proposed model, a new scalable algorithm is presented. It constrains the dependence scope, relying on physical positions, and is able to deal with more than one hundred thousand single nucleotide polymorphisms. The proposed algorithm is fast and does not require phase genotypic data. PMID:22174739

  8. Allowing for uncertainty due to missing continuous outcome data in pairwise and network meta-analysis.

    PubMed

    Mavridis, Dimitris; White, Ian R; Higgins, Julian P T; Cipriani, Andrea; Salanti, Georgia

    2015-02-28

    Missing outcome data are commonly encountered in randomized controlled trials and hence may need to be addressed in a meta-analysis of multiple trials. A common and simple approach to deal with missing data is to restrict analysis to individuals for whom the outcome was obtained (complete case analysis). However, estimated treatment effects from complete case analyses are potentially biased if informative missing data are ignored. We develop methods for estimating meta-analytic summary treatment effects for continuous outcomes in the presence of missing data for some of the individuals within the trials. We build on a method previously developed for binary outcomes, which quantifies the degree of departure from a missing at random assumption via the informative missingness odds ratio. Our new model quantifies the degree of departure from missing at random using either an informative missingness difference of means or an informative missingness ratio of means, both of which relate the mean value of the missing outcome data to that of the observed data. We propose estimating the treatment effects, adjusted for informative missingness, and their standard errors by a Taylor series approximation and by a Monte Carlo method. We apply the methodology to examples of both pairwise and network meta-analysis with multi-arm trials.

  9. An efficient algorithm for pairwise local alignment of protein interaction networks

    SciTech Connect

    Chen, Wenbin; Schmidt, Matthew; Tian, Wenhong; Samatova, Nagiza F.; Zhang, Shaohong

    2015-04-01

    Recently, researchers seeking to understand, modify, and create beneficial traits in organisms have looked for evolutionarily conserved patterns of protein interactions. Their conservation likely means that the proteins of these conserved functional modules are important to the trait's expression. In this paper, we formulate the problem of identifying these conserved patterns as a graph optimization problem, and develop a fast heuristic algorithm for this problem. We compare the performance of our network alignment algorithm to that of the MaWISh algorithm [Koyuturk M, Kim Y, Topkara U, Subramaniam S, Szpankowski W, Grama A, Pairwise alignment of protein interaction networks, J Comput Biol 13(2): 182-199, 2006.], which bases its search algorithm on a related decision problem formulation. We find that our algorithm discovers conserved modules with a larger number of proteins in an order of magnitude less time. In conclusion, the protein sets found by our algorithm correspond to known conserved functional modules at comparable precision and recall rates as those produced by the MaWISh algorithm.

  10. Spatiotemporal noise covariance estimation from limited empirical magnetoencephalographic data

    NASA Astrophysics Data System (ADS)

    Jun, Sung C.; Plis, Sergey M.; Ranken, Doug M.; Schmidt, David M.

    2006-11-01

    The performance of parametric magnetoencephalography (MEG) and electroencephalography (EEG) source localization approaches can be degraded by the use of poor background noise covariance estimates. In general, estimation of the noise covariance for spatiotemporal analysis is difficult mainly due to the limited noise information available. Furthermore, its estimation requires a large amount of storage and a one-time but very large (and sometimes intractable) calculation or its inverse. To overcome these difficulties, noise covariance models consisting of one pair or a sum of multi-pairs of Kronecker products of spatial covariance and temporal covariance have been proposed. However, these approaches cannot be applied when the noise information is very limited, i.e., the amount of noise information is less than the degrees of freedom of the noise covariance models. A common example of this is when only averaged noise data are available for a limited prestimulus region (typically at most a few hundred milliseconds duration). For such cases, a diagonal spatiotemporal noise covariance model consisting of sensor variances with no spatial or temporal correlation has been the common choice for spatiotemporal analysis. In this work, we propose a different noise covariance model which consists of diagonal spatial noise covariance and Toeplitz temporal noise covariance. It can easily be estimated from limited noise information, and no time-consuming optimization and data-processing are required. Thus, it can be used as an alternative choice when one-pair or multi-pair noise covariance models cannot be estimated due to lack of noise information. To verify its capability we used Bayesian inference dipole analysis and a number of simulated and empirical datasets. We compared this covariance model with other existing covariance models such as conventional diagonal covariance, one-pair and multi-pair noise covariance models, when noise information is sufficient to estimate them. We

  11. Spatiotemporal noise covariance estimation from limited empirical magnetoencephalographic data.

    PubMed

    Jun, Sung C; Plis, Sergey M; Ranken, Doug M; Schmidt, David M

    2006-11-07

    The performance of parametric magnetoencephalography (MEG) and electroencephalography (EEG) source localization approaches can be degraded by the use of poor background noise covariance estimates. In general, estimation of the noise covariance for spatiotemporal analysis is difficult mainly due to the limited noise information available. Furthermore, its estimation requires a large amount of storage and a one-time but very large (and sometimes intractable) calculation or its inverse. To overcome these difficulties, noise covariance models consisting of one pair or a sum of multi-pairs of Kronecker products of spatial covariance and temporal covariance have been proposed. However, these approaches cannot be applied when the noise information is very limited, i.e., the amount of noise information is less than the degrees of freedom of the noise covariance models. A common example of this is when only averaged noise data are available for a limited prestimulus region (typically at most a few hundred milliseconds duration). For such cases, a diagonal spatiotemporal noise covariance model consisting of sensor variances with no spatial or temporal correlation has been the common choice for spatiotemporal analysis. In this work, we propose a different noise covariance model which consists of diagonal spatial noise covariance and Toeplitz temporal noise covariance. It can easily be estimated from limited noise information, and no time-consuming optimization and data-processing are required. Thus, it can be used as an alternative choice when one-pair or multi-pair noise covariance models cannot be estimated due to lack of noise information. To verify its capability we used Bayesian inference dipole analysis and a number of simulated and empirical datasets. We compared this covariance model with other existing covariance models such as conventional diagonal covariance, one-pair and multi-pair noise covariance models, when noise information is sufficient to estimate them. We

  12. Sharpening bounds on principal effects with covariates.

    PubMed

    Long, Dustin M; Hudgens, Michael G

    2013-12-01

    Estimation of treatment effects in randomized studies is often hampered by possible selection bias induced by conditioning on or adjusting for a variable measured post-randomization. One approach to obviate such selection bias is to consider inference about treatment effects within principal strata, that is, principal effects. A challenge with this approach is that without strong assumptions principal effects are not identifiable from the observable data. In settings where such assumptions are dubious, identifiable large sample bounds may be the preferred target of inference. In practice these bounds may be wide and not particularly informative. In this work we consider whether bounds on principal effects can be improved by adjusting for a categorical baseline covariate. Adjusted bounds are considered which are shown to never be wider than the unadjusted bounds. Necessary and sufficient conditions are given for which the adjusted bounds will be sharper (i.e., narrower) than the unadjusted bounds. The methods are illustrated using data from a recent, large study of interventions to prevent mother-to-child transmission of HIV through breastfeeding. Using a baseline covariate indicating low birth weight, the estimated adjusted bounds for the principal effect of interest are 63% narrower than the estimated unadjusted bounds. © 2013, The International Biometric Society.

  13. Modeling Covariance Matrices via Partial Autocorrelations

    PubMed Central

    Daniels, M.J.; Pourahmadi, M.

    2009-01-01

    Summary We study the role of partial autocorrelations in the reparameterization and parsimonious modeling of a covariance matrix. The work is motivated by and tries to mimic the phenomenal success of the partial autocorrelations function (PACF) in model formulation, removing the positive-definiteness constraint on the autocorrelation function of a stationary time series and in reparameterizing the stationarity-invertibility domain of ARMA models. It turns out that once an order is fixed among the variables of a general random vector, then the above properties continue to hold and follows from establishing a one-to-one correspondence between a correlation matrix and its associated matrix of partial autocorrelations. Connections between the latter and the parameters of the modified Cholesky decomposition of a covariance matrix are discussed. Graphical tools similar to partial correlograms for model formulation and various priors based on the partial autocorrelations are proposed. We develop frequentist/Bayesian procedures for modelling correlation matrices, illustrate them using a real dataset, and explore their properties via simulations. PMID:20161018

  14. Noisy covariance matrices and portfolio optimization

    NASA Astrophysics Data System (ADS)

    Pafka, S.; Kondor, I.

    2002-05-01

    According to recent findings [#!bouchaud!#,#!stanley!#], empirical covariance matrices deduced from financial return series contain such a high amount of noise that, apart from a few large eigenvalues and the corresponding eigenvectors, their structure can essentially be regarded as random. In [#!bouchaud!#], e.g., it is reported that about 94% of the spectrum of these matrices can be fitted by that of a random matrix drawn from an appropriately chosen ensemble. In view of the fundamental role of covariance matrices in the theory of portfolio optimization as well as in industry-wide risk management practices, we analyze the possible implications of this effect. Simulation experiments with matrices having a structure such as described in [#!bouchaud!#,#!stanley!#] lead us to the conclusion that in the context of the classical portfolio problem (minimizing the portfolio variance under linear constraints) noise has relatively little effect. To leading order the solutions are determined by the stable, large eigenvalues, and the displacement of the solution (measured in variance) due to noise is rather small: depending on the size of the portfolio and on the length of the time series, it is of the order of 5 to 15%. The picture is completely different, however, if we attempt to minimize the variance under non-linear constraints, like those that arise e.g. in the problem of margin accounts or in international capital adequacy regulation. In these problems the presence of noise leads to a serious instability and a high degree of degeneracy of the solutions.

  15. Stochastic precipitation generator with hidden state covariates

    NASA Astrophysics Data System (ADS)

    Kim, Yongku; Lee, GyuWon

    2017-08-01

    Time series of daily weather such as precipitation, minimum temperature and maximum temperature are commonly required for various fields. Stochastic weather generators constitute one of the techniques to produce synthetic daily weather. The recently introduced approach for stochastic weather generators is based on generalized linear modeling (GLM) with covariates to account for seasonality and teleconnections (e.g., with the El Niño). In general, stochastic weather generators tend to underestimate the observed interannual variance of seasonally aggregated variables. To reduce this overdispersion, we incorporated time series of seasonal dry/wet indicators in the GLM weather generator as covariates. These seasonal time series were local (or global) decodings obtained by a hidden Markov model of seasonal total precipitation and implemented in the weather generator. The proposed method is applied to time series of daily weather from Seoul, Korea and Pergamino, Argentina. This method provides a straightforward translation of the uncertainty of the seasonal forecast to the corresponding conditional daily weather statistics.

  16. Covariant perturbations in a multifluid cosmological medium

    NASA Astrophysics Data System (ADS)

    Dunsby, Peter K. S.; Bruni, Marco; Ellis, George F. R.

    1992-08-01

    In a series of recent papers, a new covariant formalism was introduced to treat inhomogeneities in any spacetime. The variables introduced in these papers are gauge-invariant with respect to a Robertson-Walker background spacetime because they vanish identically in such models, and they have a transparent physical meaning. Exact evolution equations were found for these variables, and the linearized form of these equations were obtained, showing that they give the standard results for a barotropic perfect fluid. In this paper we extend this formalism to the general case of multicomponent fluid sources with interactions between them. We show, using the tilted formalism of King and Ellis, (1973) that choosing either the energy frame or the particle frame gives rise to a set of physically well-defined covariant and gauge-invariant variables which describe density and velocity perturbations, both for the total fluid and its constituent components. We then derive a complete set of equations for these variables and show, through harmonic analysis, that they are equivalent to those of Bardeen (1980) and of Kodama and Sasaki (1984). We discuss a number of interesting applications, including the case where the universe is filled with a mixture of baryons and radiation, coupled through Thomson scattering, and we derive solutions for the density and velocity perturbations in the large-scale limit. We also correct a number of errors in the previous literature.

  17. Hierarchical multivariate covariance analysis of metabolic connectivity.

    PubMed

    Carbonell, Felix; Charil, Arnaud; Zijdenbos, Alex P; Evans, Alan C; Bedell, Barry J

    2014-12-01

    Conventional brain connectivity analysis is typically based on the assessment of interregional correlations. Given that correlation coefficients are derived from both covariance and variance, group differences in covariance may be obscured by differences in the variance terms. To facilitate a comprehensive assessment of connectivity, we propose a unified statistical framework that interrogates the individual terms of the correlation coefficient. We have evaluated the utility of this method for metabolic connectivity analysis using [18F]2-fluoro-2-deoxyglucose (FDG) positron emission tomography (PET) data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) study. As an illustrative example of the utility of this approach, we examined metabolic connectivity in angular gyrus and precuneus seed regions of mild cognitive impairment (MCI) subjects with low and high β-amyloid burdens. This new multivariate method allowed us to identify alterations in the metabolic connectome, which would not have been detected using classic seed-based correlation analysis. Ultimately, this novel approach should be extensible to brain network analysis and broadly applicable to other imaging modalities, such as functional magnetic resonance imaging (MRI).

  18. Hierarchical multivariate covariance analysis of metabolic connectivity

    PubMed Central

    Carbonell, Felix; Charil, Arnaud; Zijdenbos, Alex P; Evans, Alan C; Bedell, Barry J

    2014-01-01

    Conventional brain connectivity analysis is typically based on the assessment of interregional correlations. Given that correlation coefficients are derived from both covariance and variance, group differences in covariance may be obscured by differences in the variance terms. To facilitate a comprehensive assessment of connectivity, we propose a unified statistical framework that interrogates the individual terms of the correlation coefficient. We have evaluated the utility of this method for metabolic connectivity analysis using [18F]2-fluoro-2-deoxyglucose (FDG) positron emission tomography (PET) data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) study. As an illustrative example of the utility of this approach, we examined metabolic connectivity in angular gyrus and precuneus seed regions of mild cognitive impairment (MCI) subjects with low and high β-amyloid burdens. This new multivariate method allowed us to identify alterations in the metabolic connectome, which would not have been detected using classic seed-based correlation analysis. Ultimately, this novel approach should be extensible to brain network analysis and broadly applicable to other imaging modalities, such as functional magnetic resonance imaging (MRI). PMID:25294129

  19. A Class of Population Covariance Matrices in the Bootstrap Approach to Covariance Structure Analysis

    ERIC Educational Resources Information Center

    Yuan, Ke-Hai; Hayashi, Kentaro; Yanagihara, Hirokazu

    2007-01-01

    Model evaluation in covariance structure analysis is critical before the results can be trusted. Due to finite sample sizes and unknown distributions of real data, existing conclusions regarding a particular statistic may not be applicable in practice. The bootstrap procedure automatically takes care of the unknown distribution and, for a given…

  20. A Class of Population Covariance Matrices in the Bootstrap Approach to Covariance Structure Analysis

    ERIC Educational Resources Information Center

    Yuan, Ke-Hai; Hayashi, Kentaro; Yanagihara, Hirokazu

    2007-01-01

    Model evaluation in covariance structure analysis is critical before the results can be trusted. Due to finite sample sizes and unknown distributions of real data, existing conclusions regarding a particular statistic may not be applicable in practice. The bootstrap procedure automatically takes care of the unknown distribution and, for a given…

  1. Image restoration by the shift-and-add algorithm.

    PubMed

    Bagnuolo, W G

    1985-05-01

    A new method for image restoration based on the shift-and-add (SAA) algorithm is presented, the main advantages of which appear to be speed and simplicity. The SAA pattern produced by an object is given by the object correlated by a nonlinear replica of itself whose intensity distribution is strongly weighted toward the brighter pixels. A method of successive substitutions analogous to Fienup's algorithm can then be used to decorrelate the SAA pattern and recover the object. The method is applied to the case of the extended chromosphere of Betelgeuse.

  2. Astronomical imaging by filtered weighted-shift-and-add technique

    NASA Technical Reports Server (NTRS)

    Ribak, Erez

    1986-01-01

    The weighted-shift-and-add speckle imaging technique is analyzed using simple assumptions. The end product is shown to be a convolution of the object with a typical point-spread function (psf) that is similar in shape to the telescope psf and depends marginally on the speckle psf. A filter can be applied to each data frame before locating the maxima, either to identify the speckle locations (matched filter) or to estimate the instantaneous atmospheric psf (Wiener filter). Preliminary results show the power of the technique when applied to photon-limited data and to extended objects.

  3. Add/Compare/Select Circuit For Rapid Decoding

    NASA Technical Reports Server (NTRS)

    Budinger, James M.; Becker, Neal D.; Johnson, Peter N.

    1993-01-01

    Prototype decoding system operates at 200 Mb/s. ACS (add/compare/select) gate array is highly integrated emitter-coupled-logic circuit implementing arithmetic operations essential to Viterbi decoding of convolutionally encoded data signals. Principal advantage of circuit is speed. Operates as single unit performing eight additions and finds minimum of eight sums, or operates as two independent units, each performing four additions and finding minimum of four sums. Flexibility enables application to variety of different codes. Includes built-in self-testing circuitry, enabling unit to be tested at full speed with help of only simple test fixture.

  4. Can the default-mode network be described with one spatial-covariance network?

    PubMed

    Habeck, Christian; Steffener, Jason; Rakitin, Brian; Stern, Yaakov

    2012-08-15

    The default-mode network (DMN) has become a well accepted concept in cognitive and clinical neuroscience over the last decade, and perusal of the recent literature attests to a stimulating research field of cognitive and diagnostic applications (for example, (Andrews-Hanna et al., 2010; Koch et al., 2010; Sheline et al., 2009a; Sheline et al., 2009b; Uddin et al., 2008; Uddin et al., 2009; Weng et al., 2009; Yan et al., 2009)). However, a formal definition of what exactly constitutes a functional brain network is difficult to come by. In recent contributions, some researchers argue that the DMN is best understood as multiple interacting subsystems (Buckner et al., 2008) and have explored modular components of the DMN that have different functional specialization and could to some extent be identified separately (Fox et al., 2005; Uddin et al., 2009). Such conception of modularity seems to imply an opposite construct of a 'unified whole', but it is difficult to locate proponents of the idea of a DMN who are supplying constraints that can be brought to bear on data in rigorous tests. Our aim in this paper is to present a principled way of deriving a single covariance pattern as the neural substrate of the DMN, test to what extent its behavior tracks the coupling strength between critical seed regions, and investigate to what extent our stricter concept of a network is consistent with the already established findings about the DMN in the literature. We show that our approach leads to a functional covariance pattern whose pattern scores are a good proxy for the integrity of the connections between a medioprefrontal, posterior cingulate and parietal seed regions. Our derived DMN network thus has potential for diagnostic applications that are simpler to perform than computation of pairwise correlational strengths or seed maps.

  5. Impact of the 235U Covariance Data in Benchmark Calculations

    SciTech Connect

    Leal, Luiz C; Mueller, Don; Arbanas, Goran; Wiarda, Dorothea; Derrien, Herve

    2008-01-01

    The error estimation for calculated quantities relies on nuclear data uncertainty information available in the basic nuclear data libraries such as the U.S. Evaluated Nuclear Data File (ENDF/B). The uncertainty files (covariance matrices) in the ENDF/B library are generally obtained from analysis of experimental data. In the resonance region, the computer code SAMMY is used for analyses of experimental data and generation of resonance parameters. In addition to resonance parameters evaluation, SAMMY also generates resonance parameter covariance matrices (RPCM). SAMMY uses the generalized least-squares formalism (Bayes method) together with the resonance formalism (R-matrix theory) for analysis of experimental data. Two approaches are available for creation of resonance-parameter covariance data. (1) During the data-evaluation process, SAMMY generates both a set of resonance parameters that fit the experimental data and the associated resonance-parameter covariance matrix. (2) For existing resonance-parameter evaluations for which no resonance-parameter covariance data are available, SAMMY can retroactively create a resonance-parameter covariance matrix. The retroactive method was used to generate covariance data for 235U. The resulting 235U covariance matrix was then used as input to the PUFF-IV code, which processed the covariance data into multigroup form, and to the TSUNAMI code, which calculated the uncertainty in the multiplication factor due to uncertainty in the experimental cross sections. The objective of this work is to demonstrate the use of the 235U covariance data in calculations of critical benchmark systems.

  6. Evaluating covariance in prognostic and system health management applications

    NASA Astrophysics Data System (ADS)

    Menon, Sandeep; Jin, Xiaohang; Chow, Tommy W. S.; Pecht, Michael

    2015-06-01

    Developing a diagnostic and prognostic health management system involves analyzing system parameters monitored during the lifetime of the system. This data analysis may involve multiple steps, including data reduction, feature extraction, clustering and classification, building control charts, identification of anomalies, and modeling and predicting parameter degradation in order to evaluate the state of health for the system under investigation. Evaluating the covariance between the monitored system parameters allows for better understanding of the trends in monitored system data, and therefore it is an integral part of the data analysis. Typically, a sample covariance matrix is used to evaluate the covariance between monitored system parameters. The monitored system data are often sensor data, which are inherently noisy. The noise in sensor data can lead to inaccurate evaluation of the covariance in data using a sample covariance matrix. This paper examines approaches to evaluate covariance, including the minimum volume ellipsoid, the minimum covariance determinant, and the nearest neighbor variance estimation. When the performance of these approaches was evaluated on datasets with increasing percentage of Gaussian noise, it was observed that the nearest neighbor variance estimation exhibited the most stable estimates of covariance. To improve the accuracy of covariance estimates using nearest neighbor-based methodology, a modified approach for the nearest neighbor variance estimation technique is developed in this paper. Case studies based on data analysis steps involved in prognostic solutions are developed in order to compare the performance of the covariance estimation methodologies discussed in the paper.

  7. The Impact of Covariate Measurement Error on Risk Prediction

    PubMed Central

    Khudyakov, Polyna; Gorfine, Malka; Zucker, David; Spiegelman, Donna

    2015-01-01

    In the development of risk prediction models, predictors are often measured with error. In this paper, we investigate the impact of covariate measurement error on risk prediction. We compare the prediction performance using a costly variable measured without error, along with error-free covariates, to that of a model based on an inexpensive surrogate along with the error-free covariates. We consider continuous error-prone covariates with homoscedastic and heteroscedastic errors, and also a discrete misclassified covariate. Prediction performance is evaluated by the area under the receiver operating characteristic curve (AUC), the Brier score (BS), and the ratio of the observed to the expected number of events (calibration). In an extensive numerical study, we show that (i) the prediction model with the error-prone covariate is very well calibrated, even when it is mis-specified; (ii) using the error-prone covariate instead of the true covariate can reduce the AUC and increase the BS dramatically; (iii) adding an auxiliary variable, which is correlated with the error-prone covariate but conditionally independent of the outcome given all covariates in the true model, can improve the AUC and BS substantially. We conclude that reducing measurement error in covariates will improve the ensuing risk prediction, unless the association between the error-free and error-prone covariates is very high. Finally, we demonstrate how a validation study can be used to assess the effect of mismeasured covariates on risk prediction. These concepts are illustrated in a breast cancer risk prediction model developed in the Nurses’ Health Study. PMID:25865315

  8. Fast Estimation of Covariance Parameters in Least-Squares Collocation by Fisher Scoring with Levenberg-Marquardt Optimization

    NASA Astrophysics Data System (ADS)

    Jarmołowski, Wojciech

    2017-07-01

    Maximum likelihood (ML) and restricted maximum likelihood (REML) are nowadays very popular in geophysics, geodesy and many other fields. There is also a growing number of investigations into how to calculate covariance parameters by ML/REML accurately and fast, and assure the convergence of the iteration steps in derivative-based approaches. The latter condition is not satisfied in many solutions, as it requires composed procedures or takes an unacceptable amount of time. The article implements efficient Fisher scoring (FS) to covariance parameter estimation in least-squares collocation (LSC). FS is optimized through Levenberg-Marquardt (LM) optimization, which provides stability in convergence when estimating two covariance parameters necessary for LSC. The motivation for this work was a very large number of non-optimized FS in the literature, as well as a deficiency of its scientific and engineering applications. The example work adds some usefulness to maximum likelihood estimation (ML) and FS and shows a new application—an alternative approach to LSC—a parametrization with no empirical covariance estimation. The results of LM damping applied to FS (FSLM) require some additional research related with optimal LM parameter. However, the method appears to be a milestone in relation to non-optimized FS, in terms of convergence. The FS with LM provides a reliable convergence, whose speed can be adjusted by manipulating the LM parameter.

  9. Field Performance Verification of Carbon Dioxide, Water, and Nitrous Oxide Closed-Path Eddy Covariance Systems with Vortex Intakes

    NASA Astrophysics Data System (ADS)

    Burgon, R. P., Jr.; Sargent, S.; Zha, T.; Jia, X.

    2015-12-01

    Closed-path eddy covariance systems measure the flux of greenhouse gasses such as carbon dioxide, water vapor, and nitrous oxide. The challenge is to make accurate field measurements at sites around the world, even in extreme environmental conditions. Sites with dirty air present a particular challenge. Gas concentration measurements may be degraded as dust or debris is deposited on the optical windows in the sample cell. The traditional solution has been to add an in-line filter upstream of the sample cell to keep the windows clean. However, these filters clog over time and must be changed periodically. An in-line filter also acts as a mixing volume and in some cases limits the frequency response of the analyzer. A novel eddy-covariance system that includes a vortex air cleaner at the inlet has been developed and field tested. This new system eliminates the need for a traditional in-line filter to keep the sample cell windows clean. The new system reduces system maintenance and down time. Eddy covariance systems with the vortex intake were tested at several sites ranging from sites with extremely dirty urban air to sites with relatively clean mountain air, and in agricultural areas. These flux systems were monitoring either CO2 and H2O, or N2O. Results show that the closed-path eddy covariance systems with a vortex intake perform very well and require lower maintenance compared to similar systems with in-line filters.

  10. Noisy covariance matrices and portfolio optimization II

    NASA Astrophysics Data System (ADS)

    Pafka, Szilárd; Kondor, Imre

    2003-03-01

    Recent studies inspired by results from random matrix theory (Galluccio et al.: Physica A 259 (1998) 449; Laloux et al.: Phys. Rev. Lett. 83 (1999) 1467; Risk 12 (3) (1999) 69; Plerou et al.: Phys. Rev. Lett. 83 (1999) 1471) found that covariance matrices determined from empirical financial time series appear to contain such a high amount of noise that their structure can essentially be regarded as random. This seems, however, to be in contradiction with the fundamental role played by covariance matrices in finance, which constitute the pillars of modern investment theory and have also gained industry-wide applications in risk management. Our paper is an attempt to resolve this embarrassing paradox. The key observation is that the effect of noise strongly depends on the ratio r= n/ T, where n is the size of the portfolio and T the length of the available time series. On the basis of numerical experiments and analytic results for some toy portfolio models we show that for relatively large values of r (e.g. 0.6) noise does, indeed, have the pronounced effect suggested by Galluccio et al. (1998), Laloux et al. (1999) and Plerou et al. (1999) and illustrated later by Laloux et al. (Int. J. Theor. Appl. Finance 3 (2000) 391), Plerou et al. (Phys. Rev. E, e-print cond-mat/0108023) and Rosenow et al. (Europhys. Lett., e-print cond-mat/0111537) in a portfolio optimization context, while for smaller r (around 0.2 or below), the error due to noise drops to acceptable levels. Since the length of available time series is for obvious reasons limited in any practical application, any bound imposed on the noise-induced error translates into a bound on the size of the portfolio. In a related set of experiments we find that the effect of noise depends also on whether the problem arises in asset allocation or in a risk measurement context: if covariance matrices are used simply for measuring the risk of portfolios with a fixed composition rather than as inputs to optimization, the

  11. Identifying sources of uncertainty using covariance analysis

    NASA Astrophysics Data System (ADS)

    Hyslop, N. P.; White, W. H.

    2010-12-01

    Atmospheric aerosol monitoring often includes performing multiple analyses on a collected sample. Some common analyses resolve suites of elements or compounds (e.g., spectrometry, chromatography). Concentrations are determined through multi-step processes involving sample collection, physical or chemical analysis, and data reduction. Uncertainties in the individual steps propagate into uncertainty in the calculated concentration. The assumption in most treatments of measurement uncertainty is that errors in the various species concentrations measured in a sample are random and therefore independent of each other. This assumption is often not valid in speciated aerosol data because some errors can be common to multiple species. For example, an error in the sample volume will introduce a common error into all species concentrations determined in the sample, and these errors will correlate with each other. Measurement programs often use paired (collocated) measurements to characterize the random uncertainty in their measurements. Suites of paired measurements provide an opportunity to go beyond the characterization of measurement uncertainties in individual species to examine correlations amongst the measurement uncertainties in multiple species. This additional information can be exploited to distinguish sources of uncertainty that affect all species from those that only affect certain subsets or individual species. Data from the Interagency Monitoring of Protected Visual Environments (IMPROVE) program are used to illustrate these ideas. Nine analytes commonly detected in the IMPROVE network were selected for this analysis. The errors in these analytes can be reasonably modeled as multiplicative, and the natural log of the ratio of concentrations measured on the two samplers provides an approximation of the error. Figure 1 shows the covariation of these log ratios among the different analytes for one site. Covariance is strongest amongst the dust element (Fe, Ca, and

  12. Does Chiropractic ‘Add Years to Life’?

    PubMed Central

    Morgan, Lon

    2004-01-01

    The chiropractic cliché “Chiropractic Adds Life to Years and Years to Life” was examined for validity. It was assumed that chiropractors themselves would be the best informed about the health benefits of chiropractic care. Chiropractors would therefore be most likely to receive some level of chiropractic care, and do so on a long-term basis. If chiropractic care significantly improves general health then chiropractors themselves should demonstrate longer life spans than the general population. Two separate data sources were used to examine chiropractic mortality rates. One source used obituary notices from past issues of Dynamic Chiropractic from 1990 to mid-2003. The second source used biographies from Who Was Who in Chiropractic – A Necrology covering a ten year period from 1969–1979. The two sources yielded a mean age at death for chiropractors of 73.4 and 74.2 years respectively. The mean ages at death of chiropractors is below the national average of 76.9 years and is below their medical doctor counterparts of 81.5. This review of mortality date found no evidence to support the claim that chiropractic care “Adds Years to Life.” PMID:17549121

  13. A note on two methods for estimating missing pairwise preference values.

    PubMed

    Chiclana, Francisco; Herrera-Viedma, Enrique; Alonso, Sergio

    2009-12-01

    This note analyzes two methods for calculating missing values of an incomplete reciprocal fuzzy preference relation. The first method by Herrera-Viedma appeared in the IEEE Transactions on Systems, Man, and Cybernetics-Part B: Cybernetics [vol. 37, no. 1 (2007) 176-189], while the second one by Fedrizzi and Giove appeared later in the European Journal of Operational Research [vol. 183 (2007) 303-313]. The underlying concept driving both methods is the additive consistency property. We show that both methods, although different, are very similar. Both methods derive the same estimated values for the independent-missing-comparison case, while they differ in the dependent-missing-comparison case. However, it is shown that a modification of the first method coincides with the second one. Regarding the total reconstruction of an incomplete preference relation, it is true that the second method performs worse than the first one. When Herrera-Viedma 's method is unsuccessful, Fedrizzi-Giove's method is as well. However, in those cases when Fedrizzi-Giove's method cannot guarantee the successful reconstruction of an incomplete preference relation, we have that Herrera-Viedma 's method can. These results lead us to claim that both methods should be seen as complementary rather than competitors in their application, and as such, we propose a reconstruction policy of incomplete fuzzy preference relations using both methods. By doing this, the only unsuccessful reconstruction case is when there is a chain of missing pairwise comparisons involving each one of the feasible alternatives at least once.

  14. Distance dependence and salt sensitivity of pairwise, coulombic interactions in a protein

    PubMed Central

    Lee, Kelly K.; Fitch, Carolyn A.; García-Moreno E., Bertrand

    2002-01-01

    Histidine pKa values were measured in charge-reversal (K78E, K97E, K127E, and K97E/K127E) and charge-neutralization (E10A, E101A, and R35A) mutants of staphylococcal nuclease (SNase) by 1H-NMR spectroscopy. Energies of interaction between pairs of charges (ΔGij) were obtained from the shifts in pKa values relative to wild-type values. The data describe the distance dependence and salt sensitivity of pairwise coulombic interactions. Calculations with a continuum electrostatics method captured the experimental ΔGij when static structures were used and when the protein interior was treated empirically with a dielectric constant of 20. The ΔGij when rij ≤ 10 Å were exaggerated slightly in the calculations. Coulomb's law with a dielectric constant near 80 and a Debye-Hückel term to account for screening by the ionic strength reproduced the salt sensitivity and distance dependence of ΔGij as well as the structure-based method. In their interactions with each other, surface charges behave as if immersed in water; the Debye length describes realistically the distance where interactions become negligible at a given ionic strength. On average, charges separated by distances (rij) ≈5 Å interacted with ΔGij ≈ 0.6 kcal/mole in 0.01 M KCl, but ΔGij decayed to ≤0.10 kcal/mole when rij = 20 Å. In 0.10 M KCl, ΔGij ≈ 0.10 kcal/mole when rij = 10 Å. In 1.5 M KCl, only short-range interactions with rij ≤ 5 Å persisted. Although at physiological ionic strengths the interactions between charges separated by more than 10 Å are extremely weak, in situations where charge imbalance exists many weak interactions can cumulatively produce substantial effects. PMID:11967358

  15. Pairwise additivity in the nuclear magnetic resonance interactions of atomic xenon.

    PubMed

    Hanni, Matti; Lantto, Perttu; Vaara, Juha

    2009-04-14

    Nuclear magnetic resonance (NMR) of atomic (129/131)Xe is used as a versatile probe of the structure and dynamics of various host materials, due to the sensitivity of the Xe NMR parameters to intermolecular interactions. The principles governing this sensitivity can be investigated using the prototypic system of interacting Xe atoms. In the pairwise additive approximation (PAA), the binary NMR chemical shift, nuclear quadrupole coupling (NQC), and spin-rotation (SR) curves for the xenon dimer are utilized for fast and efficient evaluation of the corresponding NMR tensors in small xenon clusters Xe(n) (n = 2-12). If accurate, the preparametrized PAA enables the analysis of the NMR properties of xenon clusters, condensed xenon phases, and xenon gas without having to resort to electronic structure calculations of instantaneous configurations for n > 2. The binary parameters for Xe(2) at different internuclear distances were obtained at the nonrelativistic Hartree-Fock level of theory. Quantum-chemical (QC) calculations at the corresponding level were used to obtain the NMR parameters of the Xe(n) (n = 2-12) clusters at the equilibrium geometries. Comparison of PAA and QC data indicates that the direct use of the binary property curves of Xe(2) can be expected to be well-suited for the analysis of Xe NMR in the gaseous phase dominated by binary collisions. For use in condensed phases where many-body effects should be considered, effective binary property functions were fitted using the principal components of QC tensors from Xe(n) clusters. Particularly, the chemical shift in Xe(n) is strikingly well-described by the effective PAA. The coordination number Z of the Xe site is found to be the most important factor determining the chemical shift, with the largest shifts being found for high-symmetry sites with the largest Z. This is rationalized in terms of the density of virtual electronic states available for response to magnetic perturbations.

  16. Numerical simulation of the pairwise interaction of deformable cells during migration in a microchannel.

    PubMed

    Lan, Hongzhi; Khismatullin, Damir B

    2014-07-01

    Leukocytes and other circulating cells deform and move relatively to the channel flow in the lateral and translational directions. Their migratory property is important in immune response, hemostasis, cancer progression, delivery of nutrients, and microfluidic technologies such as cell separation and enrichment, and flow cytometry. Using our three-dimensional computational algorithm for multiphase viscoelastic flow, we have investigated the effect of pairwise interaction on the lateral and translational migration of circulating cells in a microchannel. The numerical simulation data show that when two cells with the same size and small separation distance interact, repulsive interaction take place until they reach the same lateral equilibrium position. During this process, they undergo swapping or passing, depending on the initial separation distance between each other. The threshold value of this distance increases with cell deformation, indicating that the cells experiencing larger deformation are more likely to swap. When a series of closely spaced cells with the same size are considered, they generally undergo damped oscillation in both lateral and translational directions until they reach equilibrium positions where they become evenly distributed in the flow direction (self-assembly phenomenon). A series of cells with a large lateral separation distance could collide repeatedly with each other, eventually crossing the centerline and entering the other side of the channel. For a series of cells with different deformability, more deformable cells, upon impact with less deformable cells, move to an equilibrium position closer to the centerline. The results of our study show that the bulk deformation of circulating cells plays a key role in their migration in a microchannel.

  17. Extracting multiple structural alignments from pairwise alignments: a comparison of a rigorous and a heuristic approach.

    PubMed

    Sandelin, Erik

    2005-04-01

    Multiple structural alignments (MSTAs) provide position-specific information on the sequence variability allowed by protein folds. This information can be exploited to better understand the evolution of proteins and the physical chemistry of polypeptide folding. Most MSTA methods rely on a pre-computed library of pairwise alignments. This library will in general contain conflicting residue equivalences not all of which can be realized in the final MSTA. Hence to build a consistent MSTA, these methods have to select a conflict-free subset of equivalences. Using a dataset with 327 families from SCOP 1.63 we compare the ability of two different methods to select an optimal conflict-free subset of equivalences. One is an implementation of Reinert et al.'s integer linear programming formulation (ILP) of the maximum weight trace problem (Reinert et al., 1997, Proc. 1st Ann. Int. Conf. Comput. Mol. Biol. (RECOMB-97), ACM Press, New York). This ILP formulation is a rigorous approach but its complexity is difficult to predict. The other method is T-Coffee (Notredame et al., 2000) which uses a heuristic enhancement of the equivalence weights which allow it to use the speed and simplicity of the progressive alignment approach while still incorporating information of all alignments in each step of building the MSTA. We find that although the ILP formulation consistently selects a more optimal set of conflict-free equivalences, the differences are small and the quality of the resulting MSTAs are essentially the same for both methods. Given its speed and predictable complexity, our results show that T-Coffee is an attractive alternative for producing high-quality MSTAs.

  18. Mapping of the interaction sites of galanthamine: a quantitative analysis through pairwise potentials and quantum chemistry.

    PubMed

    Galland, Nicolas; Kone, Soleymane; Le Questel, Jean-Yves

    2012-10-01

    A quantitative analysis of the interaction sites of the anti-Alzheimer drug galanthamine with molecular probes (water and benzene molecules) representative of its surroundings in the binding site of acetylcholinesterase (AChE) has been realized through pairwise potentials calculations and quantum chemistry. This strategy allows a full and accurate exploration of the galanthamine potential energy surface of interaction. Significantly different results are obtained according to the distances of approaches between the various molecular fragments and the conformation of the galanthamine N-methyl substituent. The geometry of the most relevant complexes has then been fully optimized through MPWB1K/6-31 + G(d,p) calculations, final energies being recomputed at the LMP2/aug-cc-pVTZ(-f) level of theory. Unexpectedly, galanthamine is found to interact mainly from its hydrogen-bond donor groups. Among those, CH groups in the vicinity of the ammonium group are prominent. The trends obtained provide rationales to the predilection of the equatorial orientation of the galanthamine N-methyl substituent for binding to AChE. The analysis of the interaction energies pointed out the independence between the various interaction sites and the rigid character of galanthamine. The comparison between the cluster calculations and the crystallographic observations in galanthamine-AChE co-crystals allows the validation of the theoretical methodology. In particular, the positions of several water molecules appearing as strongly conserved in galanthamine-AChE co-crystals are predicted by the calculations. Moreover, the experimental position and orientation of lateral chains of functionally important aminoacid residues are in close agreement with the ones predicted theoretically. Our study provides relevant information for a rational drug design of galanthamine based AChE inhibitors.

  19. Fast Pairwise Structural RNA Alignments by Pruning of the Dynamical Programming Matrix

    PubMed Central

    Havgaard, Jakob H; Torarinsson, Elfar; Gorodkin, Jan

    2007-01-01

    It has become clear that noncoding RNAs (ncRNA) play important roles in cells, and emerging studies indicate that there might be a large number of unknown ncRNAs in mammalian genomes. There exist computational methods that can be used to search for ncRNAs by comparing sequences from different genomes. One main problem with these methods is their computational complexity, and heuristics are therefore employed. Two heuristics are currently very popular: pre-folding and pre-aligning. However, these heuristics are not ideal, as pre-aligning is dependent on sequence similarity that may not be present and pre-folding ignores the comparative information. Here, pruning of the dynamical programming matrix is presented as an alternative novel heuristic constraint. All subalignments that do not exceed a length-dependent minimum score are discarded as the matrix is filled out, thus giving the advantage of providing the constraints dynamically. This has been included in a new implementation of the FOLDALIGN algorithm for pairwise local or global structural alignment of RNA sequences. It is shown that time and memory requirements are dramatically lowered while overall performance is maintained. Furthermore, a new divide and conquer method is introduced to limit the memory requirement during global alignment and backtrack of local alignment. All branch points in the computed RNA structure are found and used to divide the structure into smaller unbranched segments. Each segment is then realigned and backtracked in a normal fashion. Finally, the FOLDALIGN algorithm has also been updated with a better memory implementation and an improved energy model. With these improvements in the algorithm, the FOLDALIGN software package provides the molecular biologist with an efficient and user-friendly tool for searching for new ncRNAs. The software package is available for download at http://foldalign.ku.dk. PMID:17937495

  20. Numerical simulation of the pairwise interaction of deformable cells during migration in a microchannel

    NASA Astrophysics Data System (ADS)

    Lan, Hongzhi; Khismatullin, Damir B.

    2014-07-01

    Leukocytes and other circulating cells deform and move relatively to the channel flow in the lateral and translational directions. Their migratory property is important in immune response, hemostasis, cancer progression, delivery of nutrients, and microfluidic technologies such as cell separation and enrichment, and flow cytometry. Using our three-dimensional computational algorithm for multiphase viscoelastic flow, we have investigated the effect of pairwise interaction on the lateral and translational migration of circulating cells in a microchannel. The numerical simulation data show that when two cells with the same size and small separation distance interact, repulsive interaction take place until they reach the same lateral equilibrium position. During this process, they undergo swapping or passing, depending on the initial separation distance between each other. The threshold value of this distance increases with cell deformation, indicating that the cells experiencing larger deformation are more likely to swap. When a series of closely spaced cells with the same size are considered, they generally undergo damped oscillation in both lateral and translational directions until they reach equilibrium positions where they become evenly distributed in the flow direction (self-assembly phenomenon). A series of cells with a large lateral separation distance could collide repeatedly with each other, eventually crossing the centerline and entering the other side of the channel. For a series of cells with different deformability, more deformable cells, upon impact with less deformable cells, move to an equilibrium position closer to the centerline. The results of our study show that the bulk deformation of circulating cells plays a key role in their migration in a microchannel.