Science.gov

Sample records for pairwise covariance adds

  1. A Basic Computer Program for Calculating Simultaneous Pairwise Comparisons in Analysis of Covariance.

    ERIC Educational Resources Information Center

    Powers, Stephen; Jones, Patricia

    1986-01-01

    This paper describes a computer program which tests all pairwise comparisons of adjusted means in analysis of covariance by using Tukey-Kramer Test. The program contains: means of covariate, adjusted means of the criterion measure, sample size, mean square error, and the desired percentile point on the Studentized range distribution. (JAZ)

  2. 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.

  3. Pareto optimal pairwise sequence alignment.

    PubMed

    DeRonne, Kevin W; Karypis, George

    2013-01-01

    Sequence alignment using evolutionary profiles is a commonly employed tool when investigating a protein. Many profile-profile scoring functions have been developed for use in such alignments, but there has not yet been a comprehensive study of Pareto optimal pairwise alignments for combining multiple such functions. We show that the problem of generating Pareto optimal pairwise alignments has an optimal substructure property, and develop an efficient algorithm for generating Pareto optimal frontiers of pairwise alignments. All possible sets of two, three, and four profile scoring functions are used from a pool of 11 functions and applied to 588 pairs of proteins in the ce_ref data set. The performance of the best objective combinations on ce_ref is also evaluated on an independent set of 913 protein pairs extracted from the BAliBASE RV11 data set. Our dynamic-programming-based heuristic approach produces approximated Pareto optimal frontiers of pairwise alignments that contain comparable alignments to those on the exact frontier, but on average in less than 1/58th the time in the case of four objectives. Our results show that the Pareto frontiers contain alignments whose quality is better than the alignments obtained by single objectives. However, the task of identifying a single high-quality alignment among those in the Pareto frontier remains challenging.

  4. Generalized Linear Covariance Analysis

    NASA Astrophysics Data System (ADS)

    Markley, F. Landis; Carpenter, J. Russell

    2009-01-01

    This paper 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 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 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.

  5. 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.

  6. 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.

  7. 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.

  8. Combining Multiple Pairwise Structure-based Alignments

    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 newmore » tool for combing pairwise structure alignments that would allow for insertion of gaps in the reference structure.« less

  9. 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.

  10. 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…

  11. 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.

  12. On multitarget pairwise-Markov models

    NASA Astrophysics Data System (ADS)

    Mahler, Ronald

    2015-05-01

    Single- and multi-target tracking are both typically based on strong independence assumptions regarding both the target states and sensor measurements. In particular, both are theoretically based on the hidden Markov chain (HMC) model. That is, the target process is a Markov chain that is observed by an independent observation process. Since HMC assumptions are invalid in many practical applications, the pairwise Markov chain (PMC) model has been proposed as a way to weaken those assumptions. In this paper it is shown that the PMC model can be directly generalized to multitarget problems. Since the resulting tracking filters are computationally intractable, the paper investigates generalizations of the cardinalized probability hypothesis density (CPHD) filter to applications with PMC models.

  13. Model Fit after Pairwise Maximum Likelihood

    PubMed Central

    Barendse, M. T.; Ligtvoet, R.; Timmerman, M. E.; Oort, F. J.

    2016-01-01

    Maximum likelihood factor analysis of discrete data within the structural equation modeling framework rests on the assumption that the observed discrete responses are manifestations of underlying continuous scores that are normally distributed. As maximizing the likelihood of multivariate response patterns is computationally very intensive, the sum of the log–likelihoods of the bivariate response patterns is maximized instead. Little is yet known about how to assess model fit when the analysis is based on such a pairwise maximum likelihood (PML) of two–way contingency tables. We propose new fit criteria for the PML method and conduct a simulation study to evaluate their performance in model selection. With large sample sizes (500 or more), PML performs as well the robust weighted least squares analysis of polychoric correlations. PMID:27148136

  14. 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.

  15. 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.

  16. 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.

  17. Optimal pairwise and non-pairwise alchemical pathways for free energy calculations of molecular transformation in solution phase.

    PubMed

    Pham, Tri T; Shirts, Michael R

    2012-03-28

    We estimate the global minimum variance path for computing the free energy insertion into or deletion of small molecules from a dense fluid. We perform this optimization over all pair potentials, irrespective of functional form, using functional optimization with a two-body approximation for the radial distribution function. Surprisingly, the optimal pairwise path obtained via this method is almost identical to the path obtained using a optimized generalized "soft core" potential reported by Pham and Shirts [J. Chem. Phys. 135, 034114 (2011)]. We also derive the lowest variance non-pairwise potential path for molecular insertion or deletion and compare its efficiency to the pairwise path. Under certain conditions, non-pairwise pathways can reduce the total variance by up to 60% compared to optimal pairwise pathways. However, optimal non-pairwise pathways do not appear generally feasible for practical free energy calculations because an accurate estimate of the free energy, the parameter that is itself is desired, is required for constructing this non-pairwise path. Additionally, simulations at most intermediate states of these non-pairwise paths have significantly longer correlation times, often exceeding standard simulation lengths for solvation of bulky molecules. The findings suggest that the previously obtained soft core pathway is the lowest variance pathway for molecular insertion or deletion in practice. The findings also demonstrate the utility of functional optimization for determining the efficiency of thermodynamic processes performed with molecular simulation.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. Predicting coiled coils by use of pairwise residue correlations.

    PubMed Central

    Berger, B; Wilson, D B; Wolf, E; Tonchev, T; Milla, M; Kim, P S

    1995-01-01

    A method is presented that predicts coiled-coil domains in protein sequences by using pairwise residue correlations obtained from a (two-stranded) coiled-coil database of 58,217 amino acid residues. A program called PAIRCOIL implements this method and is significantly better than existing methods at distinguishing coiled coils from alpha-helices that are not coiled coils. The database of pairwise residue correlations suggests structural features that stabilize or destabilize coiled coils. Images Fig. 1 Fig. 2 PMID:7667278

  5. The covariant chiral ring

    NASA Astrophysics Data System (ADS)

    Bourget, Antoine; Troost, Jan

    2016-03-01

    We construct a covariant generating function for the spectrum of chiral primaries of symmetric orbifold conformal field theories with N = (4 , 4) supersymmetry in two dimensions. For seed target spaces K3 and T 4, the generating functions capture the SO(21) and SO(5) representation theoretic content of the chiral ring respectively. Via string dualities, we relate the transformation properties of the chiral ring under these isometries of the moduli space to the Lorentz covariance of perturbative string partition functions in flat space.

  6. 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

  7. 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.

  8. Discovering Pair-wise Synergies in Microarray Data.

    PubMed

    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

  9. Unequal Covariate Group Means and the Analysis of Covariance.

    ERIC Educational Resources Information Center

    Hsu, Tse-Chi; Sebatane, E. Molapi

    1979-01-01

    A Monte Carlo technique was used to investigate the effect of the differences in covariate means among treatment groups on the significance level and the power of the F-test of the analysis of covariance. (Author/GDC)

  10. 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.

    2016-07-01

    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.

  11. 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…

  12. 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.

  13. Constraints on Gravity and Dark Energy from the Pairwise Kinematic Sunyaev-Zel'dovich Effect

    NASA Astrophysics Data System (ADS)

    Mueller, Eva-Maria; de Bernardis, Francesco; Bean, Rachel; Niemack, Michael D.

    2015-07-01

    We calculate the constraints on dark energy and cosmic modifications to gravity achievable with upcoming cosmic microwave background (CMB) surveys sensitive to the Sunyaev-Zel’dovich (SZ) effects. The analysis focuses on using the mean pairwise velocity of clusters as observed through the kinematic SZ effect (kSZ), an approach based on the same methods used for the first detection of the kSZ effect, and includes a detailed derivation and discussion of this statistic’s covariance under a variety of different survey assumptions. The potential of current, Stage II, and upcoming, Stages III and IV, CMB observations are considered, in combination with contemporaneous spectroscopic and photometric galaxy observations. A detailed assessment is made of the sensitivity to the assumed statistical and systematic uncertainties in the optical depth determination, the magnitude and uncertainty in the minimum detectable mass, and the importance of pairwise velocity correlations at small separations, where nonlinear effects can start to arise. In combination with Stage III constraints on the expansion history, such as those projected by the Dark Energy Task Force, we forecast 5% and 3% for fractional errors on the growth factor, γ, for Stage III and IV surveys, respectively, and 2% constraints on the growth rate, fg, for a Stage IV survey for 0.2\\lt z\\lt 0.6. The results suggest that kSZ measurements of cluster peculiar velocities, obtained from cross-correlation with upcoming spectroscopic galaxy surveys, could provide robust tests of dark energy and theories of gravity on cosmic scales.

  14. 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. PMID:26481475

  15. 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.

  16. Pairwise correlations in layered close-packed structures.

    PubMed

    Riechers, P M; Varn, D P; Crutchfield, J P

    2015-07-01

    Given a description of the stacking statistics of layered close-packed structures in the form of a hidden Markov model, analytical expressions are developed for the pairwise correlation functions between the layers. These may be calculated analytically as explicit functions of model parameters or the expressions may be used as a fast, accurate and efficient way to obtain numerical values. Several examples are presented, finding agreement with previous work as well as deriving new relations. PMID:26131898

  17. 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.

  18. 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. PMID:11948592

  19. From pairwise to group interactions in games of cyclic dominance

    NASA Astrophysics Data System (ADS)

    Szolnoki, Attila; Vukov, Jeromos; Perc, Matjaž

    2014-06-01

    We study the rock-paper-scissors game in structured populations, where the invasion rates determine individual payoffs that govern the process of strategy change. The traditional version of the game is recovered if the payoffs for each potential invasion stem from a single pairwise interaction. However, the transformation of invasion rates to payoffs also allows the usage of larger interaction ranges. In addition to the traditional pairwise interaction, we therefore consider simultaneous interactions with all nearest neighbors, as well as with all nearest and next-nearest neighbors, thus effectively going from single pair to group interactions in games of cyclic dominance. We show that differences in the interaction range affect not only the stationary fractions of strategies but also their relations of dominance. The transition from pairwise to group interactions can thus decelerate and even revert the direction of the invasion between the competing strategies. Like in evolutionary social dilemmas, in games of cyclic dominance, too, the indirect multipoint interactions that are due to group interactions hence play a pivotal role. Our results indicate that, in addition to the invasion rates, the interaction range is at least as important for the maintenance of biodiversity among cyclically competing strategies.

  20. From pairwise to group interactions in games of cyclic dominance.

    PubMed

    Szolnoki, Attila; Vukov, Jeromos; Perc, Matjaž

    2014-06-01

    We study the rock-paper-scissors game in structured populations, where the invasion rates determine individual payoffs that govern the process of strategy change. The traditional version of the game is recovered if the payoffs for each potential invasion stem from a single pairwise interaction. However, the transformation of invasion rates to payoffs also allows the usage of larger interaction ranges. In addition to the traditional pairwise interaction, we therefore consider simultaneous interactions with all nearest neighbors, as well as with all nearest and next-nearest neighbors, thus effectively going from single pair to group interactions in games of cyclic dominance. We show that differences in the interaction range affect not only the stationary fractions of strategies but also their relations of dominance. The transition from pairwise to group interactions can thus decelerate and even revert the direction of the invasion between the competing strategies. Like in evolutionary social dilemmas, in games of cyclic dominance, too, the indirect multipoint interactions that are due to group interactions hence play a pivotal role. Our results indicate that, in addition to the invasion rates, the interaction range is at least as important for the maintenance of biodiversity among cyclically competing strategies. PMID:25019743

  1. Robust Subjective Visual Property Prediction from Crowdsourced Pairwise Labels.

    PubMed

    Fu, Yanwei; Hospedales, Timothy M; Xiang, Tao; Xiong, Jiechao; Gong, Shaogang; Wang, Yizhou; Yao, Yuan

    2016-03-01

    The problem of estimating subjective visual properties from image and video has attracted increasing interest. A subjective visual property is useful either on its own (e.g. image and video interestingness) or as an intermediate representation for visual recognition (e.g. a relative attribute). Due to its ambiguous nature, annotating the value of a subjective visual property for learning a prediction model is challenging. To make the annotation more reliable, recent studies employ crowdsourcing tools to collect pairwise comparison labels. However, using crowdsourced data also introduces outliers. Existing methods rely on majority voting to prune the annotation outliers/errors. They thus require a large amount of pairwise labels to be collected. More importantly as a local outlier detection method, majority voting is ineffective in identifying outliers that can cause global ranking inconsistencies. In this paper, we propose a more principled way to identify annotation outliers by formulating the subjective visual property prediction task as a unified robust learning to rank problem, tackling both the outlier detection and learning to rank jointly. This differs from existing methods in that (1) the proposed method integrates local pairwise comparison labels together to minimise a cost that corresponds to global inconsistency of ranking order, and (2) the outlier detection and learning to rank problems are solved jointly. This not only leads to better detection of annotation outliers but also enables learning with extremely sparse annotations. PMID:27046498

  2. 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 .

  3. 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.

  4. Introducing a Pairwise Comparison Scale for UX Evaluations with Preschoolers

    NASA Astrophysics Data System (ADS)

    Zaman, Bieke

    This paper describes the development and validation of a pairwise comparison scale for user experience (UX) evaluations with preschoolers. More particularly, the dimensionality, reliability and validity of the scale are discussed. The results of three experiments among almost 170 preschoolers show that user experience cannot be measured quantitatively as a multi-dimensional construct. In contrast, preschoolers’ UX should be measured directly as a one-dimensional higher order construct. This one-dimensional scale encompassing five general items proved to be internally consistent and valid providing evidence of a solid theory-based instrument to measure UX with preschoolers.

  5. Covariant Lyapunov vectors

    NASA Astrophysics Data System (ADS)

    Ginelli, Francesco; Chaté, Hugues; Livi, Roberto; Politi, Antonio

    2013-06-01

    Recent years have witnessed a growing interest in covariant Lyapunov vectors (CLVs) which span local intrinsic directions in the phase space of chaotic systems. Here, we review the basic results of ergodic theory, with a specific reference to the implications of Oseledets’ theorem for the properties of the CLVs. We then present a detailed description of a ‘dynamical’ algorithm to compute the CLVs and show that it generically converges exponentially in time. We also discuss its numerical performance and compare it with other algorithms presented in the literature. We finally illustrate how CLVs can be used to quantify deviations from hyperbolicity with reference to a dissipative system (a chain of Hénon maps) and a Hamiltonian model (a Fermi-Pasta-Ulam chain). This article is part of a special issue of Journal of Physics A: Mathematical and Theoretical devoted to ‘Lyapunov analysis: from dynamical systems theory to applications’.

  6. 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

  7. Pairwise agonist scanning predicts cellular signaling responses to combinatorial stimuli.

    PubMed

    Chatterjee, Manash S; Purvis, Jeremy E; Brass, Lawrence F; Diamond, Scott L

    2010-07-01

    Prediction of cellular response to multiple stimuli is central to evaluating patient-specific clinical status and to basic understanding of cell biology. Cross-talk between signaling pathways cannot be predicted by studying them in isolation and the combinatorial complexity of multiple agonists acting together prohibits an exhaustive exploration of the complete experimental space. Here we describe pairwise agonist scanning (PAS), a strategy that trains a neural network model based on measurements of cellular responses to individual and all pairwise combinations of input signals. We apply PAS to predict calcium signaling responses of human platelets in EDTA-treated plasma to six different agonists (ADP, convulxin, U46619, SFLLRN, AYPGKF and PGE(2)) at three concentrations (0.1, 1 and 10 x EC(50)). The model predicted responses to sequentially added agonists, to ternary combinations of agonists and to 45 different combinations of four to six agonists (R = 0.88). Furthermore, we use PAS to distinguish between the phenotypic responses of platelets from ten donors. Training neural networks with pairs of stimuli across the dose-response regime represents an efficient approach for predicting complex signal integration in a patient-specific disease milieu. PMID:20562863

  8. Genetic structure of Aedes aegypti populations determined using pairwise comparisons.

    PubMed

    Patarro, T de F; Guirado, M M; Ravazzi, L M; Bicudo, H E M de C

    2013-01-01

    The biological characteristics of Aedes aegypti (Diptera, Culicidae), which is a vector of dengue and yellow fever, make this organism a good model for studying population structure and the events that may influence it under the effect of human activity. We assessed the genetic variability of five A. aegypti populations using RAPD-PCR technique and six primers. Four populations were from Brazil and one was from the USA. A total of 165 polymorphic DNA loci were generated. Considering the six primers and the five populations, the mean value of inter-population genetic diversity (Gst) was 0.277, which is considered high according to the Wright classification. However, pairwise comparisons of the populations gave variable Gst values ranging from 0.044 to 0.289. This variation followed the population's geographic distance to some extent but was also influenced by human activity. The lowest Gst values were obtained in the comparison of populations from cities with intensive commercial and medical contacts. These mosquito populations were previously classified as insecticide resistant, susceptible, or with decreased susceptibility; this parameter apparently had an effect on the Gst values obtained in the pairwise comparisons.

  9. Radiance Covariance and Climate Models

    NASA Technical Reports Server (NTRS)

    Haskins, R.; Goody, R.; Chen, L.

    1998-01-01

    Spectral Empirical Orhtogonal Functions (EOFs) derived from the covariance of satellite radiance spectra may be interpreted in terms of the vertical distribution of the covariance of temperature, water vapor, and clouds. The purpose of the investigation is to demonstrate the important constraints that resolved spectral radiances can place upon climate models.

  10. 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.

  11. ADDE: Application Development for the Distributed Enterprise.

    ERIC Educational Resources Information Center

    Franckson, Marcel; Hall, John; Helmerich, Alfred; Canadas, Rafael; Dehn, Martin

    1998-01-01

    Describes the Application Development for the Distributed Enterprise (ADDE) project, a methodological set that supports the design of distributed business processes and information and communication technologies. Discusses principles behind ADDE, guidance on definition and planning of application development, guidance on distributed application…

  12. 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…

  13. 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…

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

    NASA Astrophysics Data System (ADS)

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

    2009-04-01

    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.

  15. 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.

  16. 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.

  17. Galaxy and Mass Assembly (GAMA): galaxy pairwise velocity dispersion

    NASA Astrophysics Data System (ADS)

    Loveday, Jon; Christodoulou, Leonidas

    2016-10-01

    We describe preliminary measurements of the pairwise velocity dispersion (PVD) of galaxies in the Galaxy and Mass Assembly (GAMA) survey as a function of projected separation and galaxy luminosity. Due to the faint magnitude limit (r < 19.8) and highly-complete spectroscopic sampling of the GAMA survey, we are able to measure the PVD to smaller scales and for lower-luminosity galaxies than previous SDSS-based work. We see no strong scale-dependence at most luminosities in the quasi-linear regime. We observe an apparent drop in PVD towards very small scales (below ~ 0.1h -1 Mpc), but this could in part be due to a restriction of the streaming model employed. At intermediate scales, the PVD is highest (~ 500 km/s) at intermediate luminosities, dropping at both fainter and brighter luminosities.

  18. 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

  19. On the early epidemic dynamics for pairwise models.

    PubMed

    Llensa, Carlos; Juher, David; Saldaña, Joan

    2014-07-01

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

    PubMed

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

    2015-06-26

    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. PMID:26197145

  1. 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.

  2. A human platelet calcium calculator trained by pairwise agonist scanning.

    PubMed

    Lee, Mei Yan; Diamond, Scott L

    2015-02-01

    Since platelet intracellular calcium mobilization [Ca(t)]i controls granule release, cyclooxygenase-1 and integrin activation, and phosphatidylserine exposure, blood clotting simulations require prediction of platelet [Ca(t)]i in response to combinatorial agonists. Pairwise Agonist Scanning (PAS) deployed all single and pairwise combinations of six agonists (ADP, convulxin, thrombin, U46619, iloprost and GSNO used at 0.1, 1, and 10xEC50; 154 conditions including a null condition) to stimulate platelet P2Y1/P2Y12 GPVI, PAR1/PAR4, TP, IP receptors, and guanylate cyclase, respectively, in Factor Xa-inhibited (250 nM apixaban), diluted platelet rich plasma that had been loaded with the calcium dye Fluo-4 NW. PAS of 10 healthy donors provided [Ca(t)]i data for training 10 neural networks (NN, 2-layer/12-nodes) per donor. Trinary stimulations were then conducted at all 0.1x and 1xEC50 doses (160 conditions) as was a sampling of 45 higher ordered combinations (four to six agonists). The NN-ensemble average was a calcium calculator that accurately predicted [Ca (t)]i beyond the single and binary training set for trinary stimulations (R = 0.924). The 160 trinary synergy scores, a normalized metric of signaling crosstalk, were also well predicted (R = 0.850) as were the calcium dynamics (R = 0.871) and high-dimensional synergy scores (R = 0.695) for the 45 higher ordered conditions. The calculator even predicted sequential addition experiments (n = 54 conditions, R = 0.921). NN-ensemble is a fast calcium calculator, ideal for multiscale clotting simulations that include spatiotemporal concentrations of ADP, collagen, thrombin, thromboxane, prostacyclin, and nitric oxide.

  3. A human platelet calcium calculator trained by pairwise agonist scanning.

    PubMed

    Lee, Mei Yan; Diamond, Scott L

    2015-02-01

    Since platelet intracellular calcium mobilization [Ca(t)]i controls granule release, cyclooxygenase-1 and integrin activation, and phosphatidylserine exposure, blood clotting simulations require prediction of platelet [Ca(t)]i in response to combinatorial agonists. Pairwise Agonist Scanning (PAS) deployed all single and pairwise combinations of six agonists (ADP, convulxin, thrombin, U46619, iloprost and GSNO used at 0.1, 1, and 10xEC50; 154 conditions including a null condition) to stimulate platelet P2Y1/P2Y12 GPVI, PAR1/PAR4, TP, IP receptors, and guanylate cyclase, respectively, in Factor Xa-inhibited (250 nM apixaban), diluted platelet rich plasma that had been loaded with the calcium dye Fluo-4 NW. PAS of 10 healthy donors provided [Ca(t)]i data for training 10 neural networks (NN, 2-layer/12-nodes) per donor. Trinary stimulations were then conducted at all 0.1x and 1xEC50 doses (160 conditions) as was a sampling of 45 higher ordered combinations (four to six agonists). The NN-ensemble average was a calcium calculator that accurately predicted [Ca (t)]i beyond the single and binary training set for trinary stimulations (R = 0.924). The 160 trinary synergy scores, a normalized metric of signaling crosstalk, were also well predicted (R = 0.850) as were the calcium dynamics (R = 0.871) and high-dimensional synergy scores (R = 0.695) for the 45 higher ordered conditions. The calculator even predicted sequential addition experiments (n = 54 conditions, R = 0.921). NN-ensemble is a fast calcium calculator, ideal for multiscale clotting simulations that include spatiotemporal concentrations of ADP, collagen, thrombin, thromboxane, prostacyclin, and nitric oxide. PMID:25723389

  4. A Human Platelet Calcium Calculator Trained by Pairwise Agonist Scanning

    PubMed Central

    Lee, Mei Yan; Diamond, Scott L.

    2015-01-01

    Since platelet intracellular calcium mobilization [Ca(t)]i controls granule release, cyclooxygenase-1 and integrin activation, and phosphatidylserine exposure, blood clotting simulations require prediction of platelet [Ca(t)]i in response to combinatorial agonists. Pairwise Agonist Scanning (PAS) deployed all single and pairwise combinations of six agonists (ADP, convulxin, thrombin, U46619, iloprost and GSNO used at 0.1, 1, and 10xEC50; 154 conditions including a null condition) to stimulate platelet P2Y1/P2Y12 GPVI, PAR1/PAR4, TP, IP receptors, and guanylate cyclase, respectively, in Factor Xa-inhibited (250 nM apixaban), diluted platelet rich plasma that had been loaded with the calcium dye Fluo-4 NW. PAS of 10 healthy donors provided [Ca(t)]i data for training 10 neural networks (NN, 2-layer/12-nodes) per donor. Trinary stimulations were then conducted at all 0.1x and 1xEC50 doses (160 conditions) as was a sampling of 45 higher ordered combinations (four to six agonists). The NN-ensemble average was a calcium calculator that accurately predicted [Ca (t)]i beyond the single and binary training set for trinary stimulations (R = 0.924). The 160 trinary synergy scores, a normalized metric of signaling crosstalk, were also well predicted (R = 0.850) as were the calcium dynamics (R = 0.871) and high-dimensional synergy scores (R = 0.695) for the 45 higher ordered conditions. The calculator even predicted sequential addition experiments (n = 54 conditions, R = 0.921). NN-ensemble is a fast calcium calculator, ideal for multiscale clotting simulations that include spatiotemporal concentrations of ADP, collagen, thrombin, thromboxane, prostacyclin, and nitric oxide. PMID:25723389

  5. The incredible shrinking covariance estimator

    NASA Astrophysics Data System (ADS)

    Theiler, James

    2012-05-01

    Covariance estimation is a key step in many target detection algorithms. To distinguish target from background requires that the background be well-characterized. This applies to targets ranging from the precisely known chemical signatures of gaseous plumes to the wholly unspecified signals that are sought by anomaly detectors. When the background is modelled by a (global or local) Gaussian or other elliptically contoured distribution (such as Laplacian or multivariate-t), a covariance matrix must be estimated. The standard sample covariance overfits the data, and when the training sample size is small, the target detection performance suffers. Shrinkage addresses the problem of overfitting that inevitably arises when a high-dimensional model is fit from a small dataset. In place of the (overfit) sample covariance matrix, a linear combination of that covariance with a fixed matrix is employed. The fixed matrix might be the identity, the diagonal elements of the sample covariance, or some other underfit estimator. The idea is that the combination of an overfit with an underfit estimator can lead to a well-fit estimator. The coefficient that does this combining, called the shrinkage parameter, is generally estimated by some kind of cross-validation approach, but direct cross-validation can be computationally expensive. This paper extends an approach suggested by Hoffbeck and Landgrebe, and presents efficient approximations of the leave-one-out cross-validation (LOOC) estimate of the shrinkage parameter used in estimating the covariance matrix from a limited sample of data.

  6. 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.

  7. 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.

  8. Covariant Closed String Coherent States

    SciTech Connect

    Hindmarsh, Mark; Skliros, Dimitri

    2011-02-25

    We give the first construction of covariant coherent closed string states, which may be identified with fundamental cosmic strings. We outline the requirements for a string state to describe a cosmic string, and provide an explicit and simple map that relates three different descriptions: classical strings, light cone gauge quantum states, and covariant vertex operators. The resulting coherent state vertex operators have a classical interpretation and are in one-to-one correspondence with arbitrary classical closed string loops.

  9. Covariant closed string coherent states.

    PubMed

    Hindmarsh, Mark; Skliros, Dimitri

    2011-02-25

    We give the first construction of covariant coherent closed string states, which may be identified with fundamental cosmic strings. We outline the requirements for a string state to describe a cosmic string, and provide an explicit and simple map that relates three different descriptions: classical strings, light cone gauge quantum states, and covariant vertex operators. The resulting coherent state vertex operators have a classical interpretation and are in one-to-one correspondence with arbitrary classical closed string loops. PMID:21405564

  10. DNorm: disease name normalization with pairwise learning to rank

    PubMed Central

    Leaman, Robert; Islamaj Doğan, Rezarta; Lu, Zhiyong

    2013-01-01

    Motivation: Despite the central role of diseases in biomedical research, there have been much fewer attempts to automatically determine which diseases are mentioned in a text—the task of disease name normalization (DNorm)—compared with other normalization tasks in biomedical text mining research. Methods: In this article we introduce the first machine learning approach for DNorm, using the NCBI disease corpus and the MEDIC vocabulary, which combines MeSH® and OMIM. Our method is a high-performing and mathematically principled framework for learning similarities between mentions and concept names directly from training data. The technique is based on pairwise learning to rank, which has not previously been applied to the normalization task but has proven successful in large optimization problems for information retrieval. Results: We compare our method with several techniques based on lexical normalization and matching, MetaMap and Lucene. Our algorithm achieves 0.782 micro-averaged F-measure and 0.809 macro-averaged F-measure, an increase over the highest performing baseline method of 0.121 and 0.098, respectively. Availability: The source code for DNorm is available at http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/DNorm, along with a web-based demonstration and links to the NCBI disease corpus. Results on PubMed abstracts are available in PubTator: http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator Contact: zhiyong.lu@nih.gov PMID:23969135

  11. Convergent cross-mapping and pairwise asymmetric inference

    NASA Astrophysics Data System (ADS)

    McCracken, James M.; Weigel, Robert S.

    2014-12-01

    Convergent cross-mapping (CCM) is a technique for computing specific kinds of correlations between sets of times series. It was introduced by Sugihara et al. [Science 338, 496 (2012)., 10.1126/science.1227079] and is reported to be "a necessary condition for causation" capable of distinguishing causality from standard correlation. We show that the relationships between CCM correlations proposed by Sugihara et al. do not, in general, agree with intuitive concepts of "driving" and as such should not be considered indicative of causality. It is shown that the fact that the CCM algorithm implies causality is a function of system parameters for simple linear and nonlinear systems. For example, in a circuit containing a single resistor and inductor, both voltage and current can be identified as the driver depending on the frequency of the source voltage. It is shown that the CCM algorithm, however, can be modified to identify relationships between pairs of time series that are consistent with intuition for the considered example systems for which CCM causality analysis provided nonintuitive driver identifications. This modification of the CCM algorithm is introduced as "pairwise asymmetric inference" (PAI) and examples of its use are presented.

  12. Convergent cross-mapping and pairwise asymmetric inference.

    PubMed

    McCracken, James M; Weigel, Robert S

    2014-12-01

    Convergent cross-mapping (CCM) is a technique for computing specific kinds of correlations between sets of times series. It was introduced by Sugihara et al. [Science 338, 496 (2012).] and is reported to be "a necessary condition for causation" capable of distinguishing causality from standard correlation. We show that the relationships between CCM correlations proposed by Sugihara et al. do not, in general, agree with intuitive concepts of "driving" and as such should not be considered indicative of causality. It is shown that the fact that the CCM algorithm implies causality is a function of system parameters for simple linear and nonlinear systems. For example, in a circuit containing a single resistor and inductor, both voltage and current can be identified as the driver depending on the frequency of the source voltage. It is shown that the CCM algorithm, however, can be modified to identify relationships between pairs of time series that are consistent with intuition for the considered example systems for which CCM causality analysis provided nonintuitive driver identifications. This modification of the CCM algorithm is introduced as "pairwise asymmetric inference" (PAI) and examples of its use are presented. PMID:25615160

  13. 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…

  14. 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.

  15. Covariance evaluation work at LANL

    SciTech Connect

    Kawano, Toshihiko; Talou, Patrick; Young, Phillip; Hale, Gerald; Chadwick, M B; Little, R C

    2008-01-01

    Los Alamos evaluates covariances for nuclear data library, mainly for actinides above the resonance regions and light elements in the enUre energy range. We also develop techniques to evaluate the covariance data, like Bayesian and least-squares fitting methods, which are important to explore the uncertainty information on different types of physical quantities such as elastic scattering angular distribution, or prompt neutron fission spectra. This paper summarizes our current activities of the covariance evaluation work at LANL, including the actinide and light element data mainly for the criticality safety study and transmutation technology. The Bayesian method based on the Kalman filter technique, which combines uncertainties in the theoretical model and experimental data, is discussed.

  16. Posterior covariance versus analysis error covariance in variational data assimilation

    NASA Astrophysics Data System (ADS)

    Shutyaev, Victor; Gejadze, Igor; Le Dimet, Francois-Xavier

    2013-04-01

    The problem of variational data assimilation for a nonlinear evolution model is formulated as an optimal control problem to find the initial condition function (analysis) [1]. The data contain errors (observation and background errors), hence there is an error in the analysis. For mildly nonlinear dynamics, the analysis error covariance can be approximated by the inverse Hessian of the cost functional in the auxiliary data assimilation problem [2], whereas for stronger nonlinearity - by the 'effective' inverse Hessian [3, 4]. However, it has been noticed that the analysis error covariance is not the posterior covariance from the Bayesian perspective. While these two are equivalent in the linear case, the difference may become significant in practical terms with the nonlinearity level rising. For the proper Bayesian posterior covariance a new approximation via the Hessian of the original cost functional is derived and its 'effective' counterpart is introduced. An approach for computing the mentioned estimates in the matrix-free environment using Lanczos method with preconditioning is suggested. Numerical examples which validate the developed theory are presented for the model governed by the Burgers equation with a nonlinear viscous term. The authors acknowledge the funding through the Natural Environment Research Council (NERC grant NE/J018201/1), the Russian Foundation for Basic Research (project 12-01-00322), the Ministry of Education and Science of Russia, the MOISE project (CNRS, INRIA, UJF, INPG) and Région Rhône-Alpes. References: 1. Le Dimet F.X., Talagrand O. Variational algorithms for analysis and assimilation of meteorological observations: theoretical aspects. Tellus, 1986, v.38A, pp.97-110. 2. Gejadze I., Le Dimet F.-X., Shutyaev V. On analysis error covariances in variational data assimilation. SIAM J. Sci. Computing, 2008, v.30, no.4, pp.184-1874. 3. Gejadze I.Yu., Copeland G.J.M., Le Dimet F.-X., Shutyaev V. Computation of the analysis error

  17. Nonreciprocal photonic crystal add-drop filter

    NASA Astrophysics Data System (ADS)

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

    2014-11-01

    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.

  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. 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. Are Eddy Covariance series stationary?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Spectral analysis via a discrete Fourier transform is used often to examine eddy covariance series for cycles (eddies) of interest. Generally the analysis is performed on hourly or half-hourly data sets collected at 10 or 20 Hz. Each original series is often assumed to be stationary. Also automated ...

  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. 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.

  4. 76 FR 49508 - ``Add Us In'' Initiative

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-08-10

    ... Federal Register on August 4, 2011 at 76 FR 150. Specifically, we are correcting the Funding Opportunity... 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...

  5. 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.

  6. Minimal unitary (covariant) scattering theory

    SciTech Connect

    Lindesay, J.V.; Markevich, A.

    1983-06-01

    In the minimal three particle equations developed by Lindesay the two body input amplitude was an on shell relativistic generalization of the non-relativistic scattering model characterized by a single mass parameter ..mu.. which in the two body (m + m) system looks like an s-channel bound state (..mu.. < 2m) or virtual state (..mu.. > 2m). Using this driving term in covariant Faddeev equations generates a rich covariant and unitary three particle dynamics. However, the simplest way of writing the relativisitic generalization of the Faddeev equations can take the on shell Mandelstam parameter s = 4(q/sup 2/ + m/sup 2/), in terms of which the two particle input is expressed, to negative values in the range of integration required by the dynamics. This problem was met in the original treatment by multiplying the two particle input amplitude by THETA(s). This paper provides what we hope to be a more direct way of meeting the problem.

  7. 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.

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

    PubMed

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

    2015-12-01

    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.

  9. 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

  10. Covariant jump conditions in electromagnetism

    NASA Astrophysics Data System (ADS)

    Itin, Yakov

    2012-02-01

    A generally covariant four-dimensional representation of Maxwell's electrodynamics in a generic material medium can be achieved straightforwardly in the metric-free formulation of electromagnetism. In this setup, the electromagnetic phenomena are described by two tensor fields, which satisfy Maxwell's equations. A generic tensorial constitutive relation between these fields is an independent ingredient of the theory. By use of different constitutive relations (local and non-local, linear and non-linear, etc.), a wide area of applications can be covered. In the current paper, we present the jump conditions for the fields and for the energy-momentum tensor on an arbitrarily moving surface between two media. From the differential and integral Maxwell equations, we derive the covariant boundary conditions, which are independent of any metric and connection. These conditions include the covariantly defined surface current and are applicable to an arbitrarily moving smooth curved boundary surface. As an application of the presented jump formulas, we derive a Lorentzian type metric as a condition for existence of the wave front in isotropic media. This result holds for ordinary materials as well as for metamaterials with negative material constants.

  11. 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.

  12. Covariance control of discrete stochastic bilinear systems

    NASA Technical Reports Server (NTRS)

    Skelton, R. E.; Kherat, S. M.; Yaz, E.

    1991-01-01

    The covariances that certain bilinear stochastic discrete time systems may possess are characterized. An explicit parameterization of all controllers that assign such covariances is given. The state feedback assignability and robustness of the system are discussed from a deterministic point of view. This work extends the theory of covariance control for continuous time bilinear systems to a discrete time setting.

  13. Relative error covariance analysis techniques and application

    NASA Technical Reports Server (NTRS)

    Wolff, Peter, J.; Williams, Bobby G.

    1988-01-01

    A technique for computing the error covariance of the difference between two estimators derived from different (possibly overlapping) data arcs is presented. The relative error covariance is useful for predicting the achievable consistency between Kalman-Bucy filtered estimates generated from two (not necessarily disjoint) data sets. The relative error covariance analysis technique is then applied to a Venus Orbiter simulation.

  14. 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.

  15. Structural covariance in schizophrenia and first-episode psychosis: An approach based on graph analysis.

    PubMed

    Zugman, André; Assunção, Idaiane; Vieira, Gilson; Gadelha, Ary; White, Thomas P; Oliveira, Pedro Paulo M; Noto, Cristiano; Crossley, Nicolas; Mcguire, Philip; Cordeiro, Quirino; Belangero, Sintia I O; Bressan, Rodrigo A; Jackowski, Andrea P; Sato, João Ricardo

    2015-12-01

    Schizophrenia is a neurodevelopmental disorder that produces abnormalities across different brain regions. Measuring structural covariance with MRI is a well-established approach to investigate common changes in distinct systems. We investigated structural covariance in schizophrenia in a large Brazilian sample of individuals with chronic schizophrenia (n = 143), First Episode Psychosis (n = 32), and matched healthy controls (n = 82) using a combination of graph analysis and computational neuroanatomy. Firstly, we proposed the connectivity-closeness and integrity-closeness centrality measures and them compared healthy controls with chronic schizophrenia regarding these metrics. We then conducted a second analysis on the mapped regions comparing the pairwise difference between the three groups. Our results show that compared with controls, both patient groups (in pairwise comparisons) had a reduced integrity-closeness in pars orbitalis and insula, suggesting that the relationship between these areas and other brain regions is increased in schizophrenia. No differences were found between the First Episode Psychosis and Schizophrenia groups. Since in schizophrenia the brain is affected as a whole, this may mirror that these regions may be related to the generalized structural alteration seen in schizophrenia.

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

    PubMed

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

    2008-09-01

    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

  17. Structural covariance in schizophrenia and first-episode psychosis: An approach based on graph analysis.

    PubMed

    Zugman, André; Assunção, Idaiane; Vieira, Gilson; Gadelha, Ary; White, Thomas P; Oliveira, Pedro Paulo M; Noto, Cristiano; Crossley, Nicolas; Mcguire, Philip; Cordeiro, Quirino; Belangero, Sintia I O; Bressan, Rodrigo A; Jackowski, Andrea P; Sato, João Ricardo

    2015-12-01

    Schizophrenia is a neurodevelopmental disorder that produces abnormalities across different brain regions. Measuring structural covariance with MRI is a well-established approach to investigate common changes in distinct systems. We investigated structural covariance in schizophrenia in a large Brazilian sample of individuals with chronic schizophrenia (n = 143), First Episode Psychosis (n = 32), and matched healthy controls (n = 82) using a combination of graph analysis and computational neuroanatomy. Firstly, we proposed the connectivity-closeness and integrity-closeness centrality measures and them compared healthy controls with chronic schizophrenia regarding these metrics. We then conducted a second analysis on the mapped regions comparing the pairwise difference between the three groups. Our results show that compared with controls, both patient groups (in pairwise comparisons) had a reduced integrity-closeness in pars orbitalis and insula, suggesting that the relationship between these areas and other brain regions is increased in schizophrenia. No differences were found between the First Episode Psychosis and Schizophrenia groups. Since in schizophrenia the brain is affected as a whole, this may mirror that these regions may be related to the generalized structural alteration seen in schizophrenia. PMID:26458012

  18. 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. PMID:25939365

  19. 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.

  20. Electromagnetics: from Covariance to Cloaking

    NASA Astrophysics Data System (ADS)

    McCall, M. W.

    2008-10-01

    An overview of some topical themes in electromagnetism is presented. Recent interest in metamaterials research has enabled earlier theoretical speculations concerning electromagnetic media displaying a negative refractive index to be experimentally realized. Such media can act as perfect lenses. The mathematical criterion of what signals such unusual electromagnetic behavior is discussed, showing that a covariant (or coordinate free) perspective is essential. Coordinate transformations have also become significant in the theme of transformation optics, where the interplay between a coordinate transformation and metamaterial behavior has led to the concept of an electromagnetic cloak.

  1. Phase-covariant quantum benchmarks

    NASA Astrophysics Data System (ADS)

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

    2009-05-01

    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.

  2. 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.

  3. Improved polarization dependent loss tolerance for polarization multiplexed coherent optical systems by polarization pairwise coding.

    PubMed

    Zhu, Chen; Song, Binhuang; Corcoran, Bill; Zhuang, Leimeng; Lowery, Arthur James

    2015-10-19

    Polarization dependent loss (PDL) causes imbalanced optical signal to noise ratio (OSNR) of the two polarizations, thus remains one of the major bottlenecks for next-generation polarization-division-multiplexed (PDM) coherent optical transmission systems. In this paper, we investigate Pairwise Coding for adaptive PDL mitigation in PDM coherent optical systems. By pre-coding across two polarizations, the PDL-induced performance degradation can be largely mitigated without any coding overhead. We present details of the coding and de-coding design, and also derive the analytical symbol/bit error rate of the Polarization Pairwise Coding scheme, which can be used to predict the performance gain as well as for optimal rotation angle calculation. Simulation results verify that Pairwise Coding achieves substantial system performance gains over a wide range of PDL values. Compared with other digital coding techniques, Polarization Pairwise Coding shows improved performance than Walsh-Hadamard transform since it maximizes the coordinate diversity; and also Pairwise Coding is computationally much simpler to decode compared with the Golden and Silver Codes, therefore is practical for current 100-Gb/s and future 400-Gb/s and 1-Tb/s digital coherent transceivers. PMID:26480404

  4. Beyond Rainbow-Ladder in a covariant three-body Bethe-Salpeter approach: Baryons

    NASA Astrophysics Data System (ADS)

    Sanchis-Alepuz, Hèlios; Kubrak, Stanislav D.; Fischer, Christian S.

    2014-06-01

    We report on recent results of a calculation of the nucleon and delta masses in a covariant bound-state approach, where to the simple rainbow-ladder gluon-exchange interaction kernel we add a pion-exchange contribution to account for pion cloud effects. We observe good agreement with lattice data at large pion masses. At the physical point our masses are too large by about five percent, signaling the need for more structure in the gluon part of the interaction.

  5. 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.

  6. 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.

  7. 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). PMID:25259891

  8. Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA

    PubMed Central

    Kelly, Brendan J.; Gross, Robert; Bittinger, Kyle; Sherrill-Mix, Scott; Lewis, James D.; Collman, Ronald G.; Bushman, Frederic D.; Li, Hongzhe

    2015-01-01

    Motivation: The variation in community composition between microbiome samples, termed beta diversity, can be measured by pairwise distance based on either presence–absence or quantitative species abundance data. PERMANOVA, a permutation-based extension of multivariate analysis of variance to a matrix of pairwise distances, partitions within-group and between-group distances to permit assessment of the effect of an exposure or intervention (grouping factor) upon the sampled microbiome. Within-group distance and exposure/intervention effect size must be accurately modeled to estimate statistical power for a microbiome study that will be analyzed with pairwise distances and PERMANOVA. Results: We present a framework for PERMANOVA power estimation tailored to marker-gene microbiome studies that will be analyzed by pairwise distances, which includes: (i) a novel method for distance matrix simulation that permits modeling of within-group pairwise distances according to pre-specified population parameters; (ii) a method to incorporate effects of different sizes within the simulated distance matrix; (iii) a simulation-based method for estimating PERMANOVA power from simulated distance matrices; and (iv) an R statistical software package that implements the above. Matrices of pairwise distances can be efficiently simulated to satisfy the triangle inequality and incorporate group-level effects, which are quantified by the adjusted coefficient of determination, omega-squared (ω2). From simulated distance matrices, available PERMANOVA power or necessary sample size can be estimated for a planned microbiome study. Availability and implementation: http://github.com/brendankelly/micropower. Contact: brendank@mail.med.upenn.edu or hongzhe@upenn.edu PMID:25819674

  9. 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).

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

    SciTech Connect

    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. )

    1991-03-15

    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.

  11. 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.

  12. 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. PMID:25850721

  13. 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.

  14. 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.

  15. 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.

  16. Computerized Adaptive Testing with the Zinnes and Griggs Pairwise Preference Ideal Point Model

    ERIC Educational Resources Information Center

    Stark, Stephen; Chernyshenko, Oleksandr S.

    2011-01-01

    This article delves into a relatively unexplored area of measurement by focusing on adaptive testing with unidimensional pairwise preference items. The use of such tests is becoming more common in applied non-cognitive assessment because research suggests that this format may help to reduce certain types of rater error and response sets commonly…

  17. 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.

  18. 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. PMID:26764727

  19. Revisiting the classification of curtoviruses based on genome-wide pairwise identity.

    PubMed

    Varsani, Arvind; Martin, Darren P; Navas-Castillo, Jesús; Moriones, Enrique; Hernández-Zepeda, Cecilia; Idris, Ali; Murilo Zerbini, F; Brown, Judith K

    2014-07-01

    Members of the genus Curtovirus (family Geminiviridae) are important pathogens of many wild and cultivated plant species. Until recently, relatively few full curtovirus genomes have been characterised. However, with the 19 full genome sequences now available in public databases, we revisit the proposed curtovirus species and strain classification criteria. Using pairwise identities coupled with phylogenetic evidence, revised species and strain demarcation guidelines have been instituted. Specifically, we have established 77 % genome-wide pairwise identity as a species demarcation threshold and 94 % genome-wide pairwise identity as a strain demarcation threshold. Hence, whereas curtovirus sequences with >77 % genome-wide pairwise identity would be classified as belonging to the same species, those sharing >94 % identity would be classified as belonging to the same strain. We provide step-by-step guidelines to facilitate the classification of newly discovered curtovirus full genome sequences and a set of defined criteria for naming new species and strains. The revision yields three curtovirus species: Beet curly top virus (BCTV), Spinach severe surly top virus (SpSCTV) and Horseradish curly top virus (HrCTV). PMID:24463952

  20. 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.…

  1. 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…

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. The National Longitudinal Study of Adolescent to Adult Health (Add Health) Sibling Pairs Genome-Wide Data

    PubMed Central

    McQueen, Matthew B.; Boardman, Jason D.; Domingue, Benjamin W.; Smolen, Andrew; Tabor, Joyce; Killeya-Jones, Ley; Halpern, Carolyn T.; Whitsel, Eric A.; MullanHarris, Kathleen

    2014-01-01

    Here we provide a detailed description of the genome-wide information available on the National Longitudinal Study of Adolescent to Adult Health (Add Health) sibling pair subsample (Harris et al., 2012). A total of 2020 samples were genotyped (including duplicates) arising from 1946 Add Health individuals from the sibling pairs subsample. After various steps for quality control (QC) and quality assurance (QA), we have high quality genome-wide data available on 1,888 individuals. In this report, we first highlight theQC and QA steps that were taken to prune the data of poorly performing samples and genetic markers. We further estimate the pairwise biological relationships using genome-wide data and compare those estimates to the assumed relationships in Add Health. Additionally, using genome-wide data from knownregional reference populations from Europe, West Africa, North and South America, Japan and China, weestimate the relative genetic ancestry of the respondents. Finally, rather than conducting a traditional cross-sectional genome-wide association study (GWAS) of body mass index (BMI), we opted to utilize the extensivepublicly available genome-wide information to conduct a weighted genome-wide association study (GWAS) of longitudinal BMI while accounting for both family and ethnic variation. PMID:25378290

  7. The National Longitudinal Study of Adolescent to Adult Health (Add Health) sibling pairs genome-wide data.

    PubMed

    McQueen, Matthew B; Boardman, Jason D; Domingue, Benjamin W; Smolen, Andrew; Tabor, Joyce; Killeya-Jones, Ley; Halpern, Carolyn T; Whitsel, Eric A; Harris, Kathleen Mullan

    2015-01-01

    Here we provide a detailed description of the genome-wide information available on the National Longitudinal Study of Adolescent to Adult Health (Add Health) sibling pair subsample (Harris et al. in Twin Res Hum Genet 16:391-398, 2013). A total of 2,020 samples were genotyped (including duplicates) arising from 1946 Add Health individuals from the sibling pairs subsample. After various steps for quality control (QC) and quality assurance (QA), we have high quality genome-wide data available on 1,888 individuals. In this report, we first highlight the QC and QA steps that were taken to prune the data of poorly performing samples and genetic markers. We further estimate the pairwise biological relationships using genome-wide data and compare those estimates to the assumed relationships in Add Health. Additionally, using genome-wide data from known regional reference populations from Europe, West Africa, North and South America, Japan and China, we estimate the relative genetic ancestry of the respondents. Finally, rather than conducting a traditional cross-sectional genome-wide association study (GWAS) of body mass index (BMI), we opted to utilize the extensive publicly available genome-wide information to conduct a weighted GWAS of longitudinal BMI while accounting for both family and ethnic variation.

  8. The covariate-adjusted frequency plot.

    PubMed

    Holling, Heinz; Böhning, Walailuck; Böhning, Dankmar; Formann, Anton K

    2016-04-01

    Count data arise in numerous fields of interest. Analysis of these data frequently require distributional assumptions. Although the graphical display of a fitted model is straightforward in the univariate scenario, this becomes more complex if covariate information needs to be included into the model. Stratification is one way to proceed, but has its limitations if the covariate has many levels or the number of covariates is large. The article suggests a marginal method which works even in the case that all possible covariate combinations are different (i.e. no covariate combination occurs more than once). For each covariate combination the fitted model value is computed and then summed over the entire data set. The technique is quite general and works with all count distributional models as well as with all forms of covariate modelling. The article provides illustrations of the method for various situations and also shows that the proposed estimator as well as the empirical count frequency are consistent with respect to the same parameter.

  9. 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

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

    PubMed

    Holmes, J Bradley; Tsai, Jerry

    2005-12-01

    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

  11. Evaluated Nuclear Data Covariances: The Journey From ENDF/B-VII.0 to ENDF/B-VII.1

    NASA Astrophysics Data System (ADS)

    Smith, Donald L.

    2011-12-01

    detail various aspects of the data producer community's efforts to improve the evaluation methods and to add covariance content to the ENDF/B library. The present paper offers just a brief glimpse of these activities by drawing material from covariance papers presented at meetings, workshops and international conferences during the past five years. Highlighted are: advances in methods for producing and processing covariance data, recently developed covariance visualization capabilities, and the development and implementation of quality assurance (QA) requirements that should be satisfied for covariance data to be included in ENDF/B-VII.1.

  12. Pairwise Variable Selection for High-dimensional Model-based Clustering

    PubMed Central

    Guo, Jian; Levina, Elizaveta; Michailidis, George

    2009-01-01

    SUMMARY Variable selection for clustering is an important and challenging problem in high-dimensional data analysis. Existing variable selection methods for model-based clustering select informative variables in a “one-in-all-out” manner; that is, a variable is selected if at least one pair of clusters is separable by this variable and removed if it cannot separate any of the clusters. In many applications, however, it is of interest to further establish exactly which clusters are separable by each informative variable. To address this question, we propose a pairwise variable selection method for high-dimensional model-based clustering. The method is based on a new pairwise penalty. Results on simulated and real data show that the new method performs better than alternative approaches which use ℓ1 and ℓ∞ penalties and offers better interpretation. PMID:19912170

  13. 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.

  14. Pairwise-Svm for On-Board Urban Road LIDAR Classification

    NASA Astrophysics Data System (ADS)

    Shu, Zhen; Sun, Kai; Qiu, Kaijin; Ding, Kou

    2016-06-01

    The common method of LiDAR classifications is Markov random fields (MRF). Based on construction of MRF energy function, spectral and directional features are extracted for on-board urban point clouds. The MRF energy function is consisted of unary and pairwise potentials. The unary terms are computed by SVM classifictaion. The initial labeling is mainly processed through geometrical shapes. The pairwise potential is estimated by Naïve Bayes. From training data, the probability of adjacent objects is computed by prior knowledge. The final labeling method is reweighted message-passing to minimization the energy function. The MRF model is difficult to process the large-scale misclassification. We propose a super-voxel clustering method for over-segment and grouping segment for large objects. Trees, poles ground, and building are classified in this paper. The experimental results show that this method improves the accuracy of classification and speed of computation.

  15. A ranking procedure by incomplete pairwise comparisons using information entropy and Dempster-Shafer evidence theory.

    PubMed

    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

  16. Pairwise Comparisons of Mitochondrial DNA Sequences in Subdivided Populations and Implications for Early Human Evolution

    PubMed Central

    Marjoram, P.; Donnelly, P.

    1994-01-01

    We consider the effect on the distribution of pairwise differences between mitochondrial DNA sequences of the incorporation into the underlying population genetics model of two particular effects that seem realistic for human populations. The first is that the population size was roughly constant before growing to its current level. The second is that the population is geographically subdivided rather than panmictic. In each case these features tend to encourage multimodal distributions of pairwise differences, in contrast to existing, unimodal datasets. We argue that population genetics models currently used to analyze such data may thus fail to reflect important features of human mitochondrial DNA evolution. These may include selection on the mitochondrial genome, more realistic mutation mechanisms, or special population or migration dynamics. Particularly in view of the variability inherent in the single available human mitochondrial genealogy, it is argued that until these effects are better understood, inferences from such data should be rather cautious. PMID:8150290

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. 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.

  2. 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.

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

    PubMed Central

    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. PMID:27472558

  4. 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. PMID:27472558

  5. 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.

  6. 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.

  7. 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…

  8. 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.…

  9. 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.

  10. O(D, D) covariant Noether currents and global charges in double field theory

    NASA Astrophysics Data System (ADS)

    Park, Jeong-Hyuck; Rey, Soo-Jong; Rim, Woohyun; Sakatani, Yuho

    2015-11-01

    Double field theory is an approach for massless modes of string theory, unifying and geometrizing all gauge invariance in manifest O( D, D) covariant manner. In this approach, we derive off-shell conserved Noether current and corresponding Noether potential associated with unified gauge invariance. We add Wald-type counter two-form to the Noether potential and define conserved global charges as surface integral. We check our O( D, D) covariant formula against various string backgrounds, both geometric and non-geometric. In all cases we examined, we find perfect agreements with previous results. Our formula facilitates to evaluate momenta along not only ordinary spacetime directions but also dual spacetime directions on equal footing. From this, we confirm recent assertion that null wave in doubled spacetime is the same as macroscopic fundamental string in ordinary spacetime.

  11. Upper and lower covariance bounds for perturbed linear systems

    NASA Technical Reports Server (NTRS)

    Xu, J.-H.; Skelton, R. E.; Zhu, G.

    1990-01-01

    Both upper and lower bounds are established for state covariance matrices under parameter perturbations of the plant. The motivation for this study lies in the fact that many robustness properties of linear systems are given explicitly in terms of the state covariance matrix. Moreover, there exists a theory for control by covariance assignment. The results provide robustness properties of these covariance controllers.

  12. 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).

  13. 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.

  14. Gram-Schmidt algorithms for covariance propagation

    NASA Technical Reports Server (NTRS)

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

    1975-01-01

    This paper addresses the time propagation of triangular covariance factors. Attention is focused on the square-root free factorization, P = UDU/T/, 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 colored process noise parameters increases 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.

  15. 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.

  16. 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.

  17. High-dimensional visual analytics: interactive exploration guided by pairwise views of point distributions.

    PubMed

    Wilkinson, Leland; Anand, Anushka; Grossman, Robert

    2006-01-01

    We introduce a method for organizing multivariate displays and for guiding interactive exploration through high-dimensional data. The method is based on nine characterizations of the 2D distributions of orthogonal pairwise projections on a set of points in multidimensional Euclidean space. These characterizations include such measures as density, skewness, shape, outliers, and texture. Statistical analysis of these measures leads to ways for 1) organizing 2D scatterplots of points for coherent viewing, 2) locating unusual (outlying) marginal 2D distributions of points for anomaly detection, and 3) sorting multivariate displays based on high-dimensional data, such as trees, parallel coordinates, and glyphs.

  18. Covariant theory with a confined quantum

    SciTech Connect

    Noyes, H.P.; Pastrana, G.

    1983-06-01

    It has been shown by Lindesay, Noyes and Lindesay, and by Lindesay and Markevich that by using a simple unitary two particle driving term in covariant Faddeev equations a rich covariant and unitary three particle dynamics can be generated, including single quantum exchange and production. The basic observation on which this paper rests is that if the two particle input amplitudes used as driving terms in a three particle Faddeev equation are assumed to be simply bound state poles with no elastic scattering cut, they generate rearrangement collisions, but breakup is impossible.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. TDRS-K to Add to Vital Space Network

    NASA Video Gallery

    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...

  4. Mid-Space-Independent Symmetric Data Term for Pairwise Deformable Image Registration

    PubMed Central

    Aganj, Iman; Iglesias, Juan Eugenio; Reuter, Martin; Sabuncu, Mert Rory; Fischl, Bruce

    2016-01-01

    Aligning a pair of images in a mid-space is a common approach to ensuring that deformable image registration is symmetric – that it does not depend on the arbitrary ordering of the input images. The results are, however, generally dependent on the choice of the mid-space. In particular, the set of possible solutions is typically affected by the constraints that are enforced on the two transformations (that deform the two images), which are to prevent the mid-space from drifting too far from the native image spaces. The use of an implicit atlas has been proposed to define the mid-space for pairwise registration. In this work, we show that by aligning the atlas to each image in the native image space, implicit-atlas-based pairwise registration can be made independent of the mid-space, thereby eliminating the need for anti-drift constraints. We derive a new symmetric cost function that only depends on a single transformation morphing one image to the other, and validate it through diffeomorphic registration experiments on brain magnetic resonance images. PMID:26835520

  5. 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

  6. 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.

  7. 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.

  8. Gene order in rosid phylogeny, inferred from pairwise syntenies among extant genomes

    PubMed Central

    2012-01-01

    Background Ancestral gene order reconstruction for flowering plants has lagged behind developments in yeasts, insects and higher animals, because of the recency of widespread plant genome sequencing, sequencers' embargoes on public data use, paralogies due to whole genome duplication (WGD) and fractionation of undeleted duplicates, extensive paralogy from other sources, and the computational cost of existing methods. Results We address these problems, using the gene order of four core eudicot genomes (cacao, castor bean, papaya and grapevine) that have escaped any recent WGD events, and two others (poplar and cucumber) that descend from independent WGDs, in inferring the ancestral gene order of the rosid clade and those of its main subgroups, the fabids and malvids. We improve and adapt techniques including the OMG method for extracting large, paralogy-free, multiple orthologies from conflated pairwise synteny data among the six genomes and the PATHGROUPS approach for ancestral gene order reconstruction in a given phylogeny, where some genomes may be descendants of WGD events. We use the gene order evidence to evaluate the hypothesis that the order Malpighiales belongs to the malvids rather than as traditionally assigned to the fabids. Conclusions Gene orders of ancestral eudicot species, involving 10,000 or more genes can be reconstructed in an efficient, parsimonious and consistent way, despite paralogies due to WGD and other processes. Pairwise genomic syntenies provide appropriate input to a parameter-free procedure of multiple ortholog identification followed by gene-order reconstruction in solving instances of the "small phylogeny" problem. PMID:22759433

  9. 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.

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

    PubMed

    Kuzmanic, Antonija; Zagrovic, Bojan

    2010-03-01

    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.

  11. 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. PMID:27143175

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

    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.

  13. 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.

  14. Conditional Covariance-Based Nonparametric Multidimensionality Assessment.

    ERIC Educational Resources Information Center

    Stout, William; And Others

    1996-01-01

    Three nonparametric procedures that use estimates of covariances of item-pair responses conditioned on examinee trait level for assessing dimensionality of a test are described. The HCA/CCPROX, DIMTEST, and DETECT are applied to a dimensionality study of the Law School Admission Test. (SLD)

  15. Hawking fluxes, back reaction and covariant anomalies

    NASA Astrophysics Data System (ADS)

    Kulkarni, Shailesh

    2008-11-01

    Starting from the chiral covariant effective action approach of Banerjee and Kulkarni (2008 Phys. Lett. B 659 827), we provide a derivation of the Hawking radiation from a charged black hole in the presence of gravitational back reaction. The modified expressions for charge and energy flux, due to the effect of one-loop back reaction are obtained.

  16. Rasch's Multiplicative Poisson Model with Covariates.

    ERIC Educational Resources Information Center

    Ogasawara, Haruhiko

    1996-01-01

    Rasch's multiplicative Poisson model is extended so that parameters for individuals in the prior gamma distribution have continuous covariates. Parameters for individuals are integrated out, and hyperparameters in the prior distribution are estimated by a numerical method separately from difficulty parameters that are treated as fixed parameters…

  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. A Covariance NMR Toolbox for MATLAB and OCTAVE

    NASA Astrophysics Data System (ADS)

    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.

  19. 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. PMID:21215669

  20. 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.

  1. 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.

  2. Memory-efficient dynamic programming backtrace and pairwise local sequence alignment

    PubMed Central

    Newberg, Lee A.

    2008-01-01

    Motivation: A backtrace through a dynamic programming algorithm's intermediate results in search of an optimal path, or to sample paths according to an implied probability distribution, or as the second stage of a forward–backward algorithm, is a task of fundamental importance in computational biology. When there is insufficient space to store all intermediate results in high-speed memory (e.g. cache) existing approaches store selected stages of the computation, and recompute missing values from these checkpoints on an as-needed basis. Results: Here we present an optimal checkpointing strategy, and demonstrate its utility with pairwise local sequence alignment of sequences of length 10 000. Availability: Sample C++-code for optimal backtrace is available in the Supplementary Materials. Contact: leen@cs.rpi.edu Supplementary information: Supplementary data is available at Bioinformatics online. PMID:18558620

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

    PubMed

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

    2015-07-01

    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

  4. Pairwise Quantum Discord for a Symmetric Multi-Qubit System in Different Types of Noisy Channels

    NASA Astrophysics Data System (ADS)

    Guo, You-Neng; Zeng, Ke; Wang, Guo-You

    2016-06-01

    We study the pairwise quantum discord (QD) for a symmetric multi-qubit system in different types of noisy channels, such as phase-flip, amplitude damping, phase-damping, and depolarizing channels. Using the QD and geometric quantum discord (GMQD) to quantify quantum correlations, some analytical and numerical results are presented. The results show that, the QD dynamics is strongly related to the number of spin particles N as well as the initial parameter 𝜃 of the one-axis twisting collective state. With the number of spin particles N increasing, the amount of the QD increases. However, when the amount of the QD arrives at a stable maximal value, the QD is independence of the number of spin particles N increasing. The behavior of the QD is symmetrical during a period 0 ≤ 𝜃 ≤ 2 π. Moreover, we compare the QD dynamics with the GMQD for a symmetric multi-qubit system in different types of noisy channels.

  5. 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. PMID:26783751

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. A Maximum-Likelihood Method for the Estimation of Pairwise Relatedness in Structured Populations

    PubMed Central

    Anderson, Amy D.; Weir, Bruce S.

    2007-01-01

    A maximum-likelihood estimator for pairwise relatedness is presented for the situation in which the individuals under consideration come from a large outbred subpopulation of the population for which allele frequencies are known. We demonstrate via simulations that a variety of commonly used estimators that do not take this kind of misspecification of allele frequencies into account will systematically overestimate the degree of relatedness between two individuals from a subpopulation. A maximum-likelihood estimator that includes FST as a parameter is introduced with the goal of producing the relatedness estimates that would have been obtained if the subpopulation allele frequencies had been known. This estimator is shown to work quite well, even when the value of FST is misspecified. Bootstrap confidence intervals are also examined and shown to exhibit close to nominal coverage when FST is correctly specified. PMID:17339212

  11. 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

  12. 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

  13. 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. PMID:24901508

  14. 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.

  15. Covariance Spectroscopy Applied to Nuclear Radiation Detection

    SciTech Connect

    Trainham, R., Tinsley, J., Keegan, R., Quam, W.

    2011-09-01

    Covariance spectroscopy is a method of processing second order moments of data to obtain information that is usually absent from average spectra. In nuclear radiation detection it represents a generalization of nuclear coincidence techniques. Correlations and fluctuations in data encode valuable information about radiation sources, transport media, and detection systems. Gaining access to the extra information can help to untangle complicated spectra, uncover overlapping peaks, accelerate source identification, and even sense directionality. Correlations existing at the source level are particularly valuable since many radioactive isotopes emit correlated gammas and neutrons. Correlations also arise from interactions within detector systems, and from scattering in the environment. In particular, correlations from Compton scattering and pair production within a detector array can be usefully exploited in scenarios where direct measurement of source correlations would be unfeasible. We present a covariance analysis of a few experimental data sets to illustrate the utility of the concept.

  16. Covariance and the hierarchy of frame bundles

    NASA Technical Reports Server (NTRS)

    Estabrook, Frank B.

    1987-01-01

    This is an essay on the general concept of covariance, and its connection with the structure of the nested set of higher frame bundles over a differentiable manifold. Examples of covariant geometric objects include not only linear tensor fields, densities and forms, but affinity fields, sectors and sector forms, higher order frame fields, etc., often having nonlinear transformation rules and Lie derivatives. The intrinsic, or invariant, sets of forms that arise on frame bundles satisfy the graded Cartan-Maurer structure equations of an infinite Lie algebra. Reduction of these gives invariant structure equations for Lie pseudogroups, and for G-structures of various orders. Some new results are introduced for prolongation of structure equations, and for treatment of Riemannian geometry with higher-order moving frames. The use of invariant form equations for nonlinear field physics is implicitly advocated.

  17. 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

  18. Covariant quantum mechanics applied to noncommutative geometry

    NASA Astrophysics Data System (ADS)

    Astuti, Valerio

    2015-08-01

    We here report a result obtained in collaboration with Giovanni Amelino-Camelia, first shown in the paper [1]. Applying the manifestly covariant formalism of quantum mechanics to the much studied Snyder spacetime [2] we show how it is trivial in every physical observables, this meaning that every measure in this spacetime gives the same results that would be obtained in the flat Minkowski spacetime.

  19. 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.

  20. Generalized Covariance Analysis For Remote Estimators

    NASA Technical Reports Server (NTRS)

    Boone, Jack N.

    1991-01-01

    Technique developed to predict true covariance of stochastic process at remote location when control applied to process both by autonomous (local-estimator) control subsystem and remote (non-local-estimator) control subsystem. Intended orginally for design and evaluation of ground-based schemes for estimation of gyro parameters of Magellan spacecraft. Applications include variety of remote-control systems with and without delays. Potential terrestrial applications include navigation and control of industrial processes.

  1. 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.

  2. All covariance controllers for linear discrete-time systems

    NASA Technical Reports Server (NTRS)

    Hsieh, Chen; Skelton, Robert E.

    1990-01-01

    The set of covariances that a linear discrete-time plant with a specified-order controller can have is characterized. The controllers that assign such covariances to any linear discrete-time system are given explicitly in closed form. The freedom in these covariance controllers is explicit and is parameterized by two orthogonal matrices. By appropriately choosing these free parameters, additional system objectives can be achieved without altering the state covariance, and the stability of the closed-loop system is guaranteed.

  3. 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.

  4. 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.

  5. Covariance tracking: architecture optimizations for embedded systems

    NASA Astrophysics Data System (ADS)

    Romero, Andrés; Lacassagne, Lionel; Gouiffès, Michèle; Zahraee, Ali Hassan

    2014-12-01

    Covariance matching techniques have recently grown in interest due to their good performances for object retrieval, detection, and tracking. By mixing color and texture information in a compact representation, it can be applied to various kinds of objects (textured or not, rigid or not). Unfortunately, the original version requires heavy computations and is difficult to execute in real time on embedded systems. This article presents a review on different versions of the algorithm and its various applications; our aim is to describe the most crucial challenges and particularities that appeared when implementing and optimizing the covariance matching algorithm on a variety of desktop processors and on low-power processors suitable for embedded systems. An application of texture classification is used to compare different versions of the region descriptor. Then a comprehensive study is made to reach a higher level of performance on multi-core CPU architectures by comparing different ways to structure the information, using single instruction, multiple data (SIMD) instructions and advanced loop transformations. The execution time is reduced significantly on two dual-core CPU architectures for embedded computing: ARM Cortex-A9 and Cortex-A15 and Intel Penryn-M U9300 and Haswell-M 4650U. According to our experiments on covariance tracking, it is possible to reach a speedup greater than ×2 on both ARM and Intel architectures, when compared to the original algorithm, leading to real-time execution.

  6. 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.

    2008-12-15

    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.

  7. 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.

  8. ANALYSIS OF COVARIANCE WITH SPATIALLY CORRELATED SECONDARY VARIABLES

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Data sets which contain measurements on a spatially referenced response and covariate are analyzed using either co-kriging or spatial analysis of covariance. While co-kriging accounts for the correlation structure of the covariate, it is purely a predictive tool. Alternatively, spatial analysis of c...

  9. 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…

  10. 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.

  11. Stealing time. Time management techniques add hours to each day.

    PubMed

    Davis, Nadinia

    2003-06-01

    Time not only flies when we're having fun, but also when we're filing paperwork, checking e-mail, and looking for our car keys. But you can add hours to your day by managing yourself rather than time. Here's how.

  12. 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…

  13. 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.

  14. 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…

  15. Reading Disabled and ADD Children: Similarities and Differences.

    ERIC Educational Resources Information Center

    Dykman, Roscoe A.; And Others

    This paper covers selected findings from three studies that compared different diagnostic groups: boys with attention deficit disorder (ADD) with or without hyperactivity (HY) but normal reading ability; boys with reading disability (RD) but not HY; and boys with both RD and HY. Studies examined an adapted task to assess frontal and temporal lobe…

  16. The Care Tradition: Beyond "Add Women and Stir."

    ERIC Educational Resources Information Center

    Noddings, Nel

    2001-01-01

    Examines problems of curricular inclusion, emphasizing ways of including the interests and contributions of women in social studies curricula. After describing the inadequacy of the "add women and stir" approach to inclusion, the paper discusses the tradition of care long identified with female life, then explores ways to preserve and extend this…

  17. 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.

  18. 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

  19. 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.

  20. Spatiotemporal noise covariance estimation from limited empirical magnetoencephalographic data.

    PubMed

    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

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Boost covariant gluon distributions in large nuclei

    NASA Astrophysics Data System (ADS)

    McLerran, Larry; Venugopalan, Raju

    1998-04-01

    It has been shown recently that there exist analytical solutions of the Yang-Mills equations for non-Abelian Weizsäcker-Williams fields which describe the distribution of gluons in large nuclei at small x. These solutions however depend on the color charge distribution at large rapidities. We here construct a model of the color charge distribution of partons in the fragmentation region and use it to compute the boost covariant momentum distributions of wee gluons. The phenomenological applications of our results are discussed.

  6. 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.

  7. Childhood-onset lupus with clinical neurocognitive dysfunction shows lower streamline density and pairwise connectivity on diffusion tensor imaging

    PubMed Central

    Jones, JT; DiFrancesco, M; Zaal, AI; Klein-Gitelman, MS; Gitelman, D; Ying, J; Brunner, HI

    2015-01-01

    Objectives To use diffusion tensor imaging (DTI) for investigating white matter connectivity changes associated with neurocognitive dysfunction in childhood-onset lupus (cSLE-NCD) as measured by formal neuropsychological testing. Methods DTI was performed in six subjects with (cSLE-NCD) and nine without neurocognitive dysfunction (cSLE-noNCD) as well as 14 healthy controls. Presence of neurocognitive deficits were identified by formal neuropsychological testing. The brain was divided into 116 regions, and pairwise connectivity (defined as the number of streamlines with an endpoint in each of those regions) and streamline density (defined as the number of streamlines passing through a region regardless of endpoints) were evaluated. Group comparisons were made for regional and global measures of streamline density and pairwise connectivity. Results A significant decrease in global streamline density was observed in the cSLE-NCD vs. control group (1189 vs. 1305 p = 0.002) and vs. cSLE-noNCD (1189 vs 1320 p= 0.001). The cSLE-noNCD and control groups had similar streamline density. A similar pattern for pairwise connectivity was observed with significant decrease in the cSLE-NCD group (217) versus the cSLE-noNCD (236; p=0.013) and control group (238; p=0.004). Regional measures of pairwise connectivity displayed mixed results. Conclusions The analysis of DTI in this pilot study shows cSLE-NCD is associated with global loss of streamline density and pairwise connectivity suggesting breakdown of the structural network. These results complement previously reported functional and volumetric findings that suggest cSLE-NCD is associated with measurable changes in gray and white matter. If confirmed in larger cohorts, DTI abnormalities could be used as imaging biomarkers of cSLE-NCD. PMID:25701565

  8. 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.

  9. Contrasting distributions of pairwise entanglement and mutual information in Heisenberg spin systems

    NASA Astrophysics Data System (ADS)

    Subrahmanyam, V.

    2016-08-01

    The correlations between a pair of spins in a many-spin state encoded in the diagonal and off-diagonal spin-spin correlation functions. These spin functions determine the quantum correlation measures, like pair-wise concurrence, quantum discord and other measures of quantum information. We show that for isotropic and translationally invariant states, the quantum correlations depend only on the diagonal spin correlation function. The pair concurrence shows a strict short-ranged behavior. The distribution of concurrence for a random W-like state exhibits a long tail for both time-reversal invariant states and for states that break the time reversal. The quantum discord can be related to the diagonal spin correlation function. As the spin function is long range close to a critical point, analogously the quantum discord exhibits a long range behavior. For the isotropic state, the conditional entropy distribution is a Dirac delta function, whereas it has a twin-peak structure for the anisotropic model.

  10. 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.

  11. 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

  12. Pairwise energies for polypeptide coarse-grained models derived from atomic force fields

    NASA Astrophysics Data System (ADS)

    Betancourt, Marcos R.; Omovie, Sheyore J.

    2009-05-01

    The energy parametrization of geometrically simplified versions of polypeptides, better known as polypeptide or protein coarse-grained models, is obtained from molecular dynamics and statistical methods. Residue pairwise interactions are derived by performing atomic-level simulations in explicit water for all 210 pairs of amino acids, where the amino acids are modified to closer match their structure and charges in polypeptides. Radial density functions are computed from equilibrium simulations for each pair of residues, from which statistical energies are extracted using the Boltzmann inversion method. The resulting models are compared to similar potentials obtained by knowledge based methods and to hydrophobic scales, resulting in significant similarities in spite of the model simplicity. However, it was found that glutamine, asparagine, lysine, and arginine are more attractive to other residues than anticipated, in part, due to their amphiphilic nature. In addition, equally charged residues appear more repulsive than expected. Difficulties in the calculation of knowledge based potentials and hydrophobicity scale for these cases, as well as sensitivity of the force field to polarization effects are suspected to cause this discrepancy. It is also shown that the coarse-grained model can identify native structures in decoy databases nearly as well as more elaborate knowledge based methods, in spite of its resolution limitations. In a test conducted with several proteins and corresponding decoys, the coarse-grained potential was able to identify the native state structure but not the original atomic force field.

  13. Mixed directional false discovery rate control in multiple pairwise comparisons using weighted p-values.

    PubMed

    Zhao, Haibing; Peddada, Shyamal D; Cui, Xinping

    2015-01-01

    In many applications, researchers are interested in making q pairwise comparisons among k test groups on the basis of m outcome variables. Often, m is very large. For example, such situations arise in gene expression microarray studies involving several experimental groups. Researchers are often not only interested in identifying differentially expressed genes between a given pair of experimental groups, but are also interested in making directional inferences such as whether a gene is up- or downregulated in one treatment group relative to another. In such situations, in addition to the usual errors such as false positive (Type I error) and false negative (Type II error), one may commit directional error (Type III error). For example, in a dose response microarray study, a gene may be declared to be upregulated in the high dose group compared to the low dose group when it is not. In this paper, we introduce a mixed directional false discovery rate (mdFDR) controlling procedure using weighted p-values to select positives in different directions. The weights are defined as the inverse of two times the proportion of either positive or negative discoveries. The proposed procedure has been proved mathematically to control the mdFDR at level α and to have a larger power (which is defined as the expected proportion of nontrue null hypotheses) than the GSP10 procedure proposed by Guo et al. (2010). Simulation studies and real data analysis are also conducted to show the outperformance of the proposed procedure than the GSP10 procedure.

  14. 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.

  15. Pairwise energies for polypeptide coarse-grained models derived from atomic force fields.

    PubMed

    Betancourt, Marcos R; Omovie, Sheyore J

    2009-05-21

    The energy parametrization of geometrically simplified versions of polypeptides, better known as polypeptide or protein coarse-grained models, is obtained from molecular dynamics and statistical methods. Residue pairwise interactions are derived by performing atomic-level simulations in explicit water for all 210 pairs of amino acids, where the amino acids are modified to closer match their structure and charges in polypeptides. Radial density functions are computed from equilibrium simulations for each pair of residues, from which statistical energies are extracted using the Boltzmann inversion method. The resulting models are compared to similar potentials obtained by knowledge based methods and to hydrophobic scales, resulting in significant similarities in spite of the model simplicity. However, it was found that glutamine, asparagine, lysine, and arginine are more attractive to other residues than anticipated, in part, due to their amphiphilic nature. In addition, equally charged residues appear more repulsive than expected. Difficulties in the calculation of knowledge based potentials and hydrophobicity scale for these cases, as well as sensitivity of the force field to polarization effects are suspected to cause this discrepancy. It is also shown that the coarse-grained model can identify native structures in decoy databases nearly as well as more elaborate knowledge based methods, in spite of its resolution limitations. In a test conducted with several proteins and corresponding decoys, the coarse-grained potential was able to identify the native state structure but not the original atomic force field.

  16. 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

    2016-07-01

    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

  17. 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.

  18. Pairwise detection of site-specific receptor phosphorylations using single-molecule blotting

    PubMed Central

    Kim, Kyung Lock; Kim, Daehyung; Lee, Seongsil; Kim, Su-Jeong; Noh, Jung Eun; Kim, Joung-Hun; Chae, Young Chan; Lee, Jong-Bong; Ryu, Sung Ho

    2016-01-01

    Post-translational modifications (PTMs) of receptor tyrosine kinases (RTKs) at the plasma membrane (PM) determine the signal transduction efficacy alone and in combination. However, current approaches to identify PTMs provide ensemble results, inherently overlooking combinatorial PTMs in a single polypeptide molecule. Here, we describe a single-molecule blotting (SiMBlot) assay that combines biotinylation of cell surface receptors with single-molecule fluorescence microscopy. This method enables quantitative measurement of the phosphorylation status of individual membrane receptor molecules and colocalization analysis of multiple immunofluorescence signals to directly visualize pairwise site-specific phosphorylation patterns at the single-molecule level. Strikingly, application of SiMBlot to study ligand-dependent epidermal growth factor receptor (EGFR) phosphorylation, which is widely thought to be multi-phosphorylated, reveals that EGFR on cell membranes is hardly multi-phosphorylated, unlike in vitro autophosphorylated EGFR. Therefore, we expect SiMBlot to aid understanding of vast combinatorial PTM patterns, which are concealed in ensemble methods, and to broaden knowledge of RTK signaling. PMID:27009355

  19. Establishing disability weights from pairwise comparisons for a US burden of disease study.

    PubMed

    Rehm, Jürgen; Frick, Ulrich

    2013-06-01

    To determine valid and reliable disability weights for a U.S. burden of disease study, a convenience sample of 68 clinical experts was recruited, including representatives from over 20 NIH institutes and Centers for Disease Control and Prevention. Experts were given various health state valuation tasks including pairwise comparison, ranking, and Person Trade Off. Materials consisted of standardized descriptions of 11 attributes per health state (Classification and Measurement System of Functional Health, CLAMES). Attributes comprised up to 5 ordinal levels of disability. All states were displayed either with or without health state labels. Health state descriptions were taken from an existing comprehensive Canadian system. Conditional Logistic (CLR) and Probit Regression (PR) were used to derive disability weights. CLR and PR converged in yielding stable regression weights to construct disability weights, with a correlation of 0.816. The overall test-retest reliability amounted to 92.5% identical decisions. No significant difference was found for the presentation of health states with or without labels. A comparison of the expert valuations from our study with a standard gamble based valuation in the general population resulted in agreement of r = 0.61. The chosen methodology yielded valid and reliable and disability weights. As it is based on a modularized set of attributes, this methodology will allow derivation of disability weights on the basis of existing descriptions using the CLAMES.

  20. 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.

  1. DIALIGN P: Fast pair-wise and multiple sequence alignment using parallel processors

    PubMed Central

    Schmollinger, Martin; Nieselt, Kay; Kaufmann, Michael; Morgenstern, Burkhard

    2004-01-01

    Background Parallel computing is frequently used to speed up computationally expensive tasks in Bioinformatics. Results Herein, a parallel version of the multi-alignment program DIALIGN is introduced. We propose two ways of dividing the program into independent sub-routines that can be run on different processors: (a) pair-wise sequence alignments that are used as a first step to multiple alignment account for most of the CPU time in DIALIGN. Since alignments of different sequence pairs are completely independent of each other, they can be distributed to multiple processors without any effect on the resulting output alignments. (b) For alignments of large genomic sequences, we use a heuristics by splitting up sequences into sub-sequences based on a previously introduced anchored alignment procedure. For our test sequences, this combined approach reduces the program running time of DIALIGN by up to 97%. Conclusions By distributing sub-routines to multiple processors, the running time of DIALIGN can be crucially improved. With these improvements, it is possible to apply the program in large-scale genomics and proteomics projects that were previously beyond its scope. PMID:15357879

  2. 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

  3. 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.

  4. Covariant constitutive relations and relativistic inhomogeneous plasmas

    SciTech Connect

    Gratus, J.; Tucker, R. W.

    2011-04-15

    The notion of a 2-point susceptibility kernel used to describe linear electromagnetic responses of dispersive continuous media in nonrelativistic phenomena is generalized to accommodate the constraints required of a causal formulation in spacetimes with background gravitational fields. In particular the concepts of spatial material inhomogeneity and temporal nonstationarity are formulated within a fully covariant spacetime framework. This framework is illustrated by recasting the Maxwell-Vlasov equations for a collisionless plasma in a form that exposes a 2-point electromagnetic susceptibility kernel in spacetime. This permits the establishment of a perturbative scheme for nonstationary inhomogeneous plasma configurations. Explicit formulae for the perturbed kernel are derived in both the presence and absence of gravitation using the general solution to the relativistic equations of motion of the plasma constituents. In the absence of gravitation this permits an analysis of collisionless damping in terms of a system of integral equations that reduce to standard Landau damping of Langmuir modes when the perturbation refers to a homogeneous stationary plasma configuration. It is concluded that constitutive modeling in terms of a 2-point susceptibility kernel in a covariant spacetime framework offers a natural extension of standard nonrelativistic descriptions of simple media and that its use for describing linear responses of more general dispersive media has wide applicability in relativistic plasma modeling.

  5. 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. PMID:23863420

  6. 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.

  7. 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…

  8. 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.

  9. 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

  10. 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.

  11. The impact of covariate measurement error on risk prediction.

    PubMed

    Khudyakov, Polyna; Gorfine, Malka; Zucker, David; Spiegelman, Donna

    2015-07-10

    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

  12. 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.

  13. 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

  14. Add-on unidirectional elastic metamaterial plate cloak.

    PubMed

    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

  15. 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.

  16. Add-on unidirectional elastic metamaterial plate cloak

    NASA Astrophysics Data System (ADS)

    Lee, Min Kyung; Kim, Yoon Young

    2016-02-01

    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.

  17. 40 CFR 75.34 - Units with add-on emission controls.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 16 2010-07-01 2010-07-01 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...

  18. Geometric derivation of the microscopic stress: A covariant central force decomposition

    NASA Astrophysics Data System (ADS)

    Torres-Sánchez, Alejandro; Vanegas, Juan M.; Arroyo, Marino

    2016-08-01

    We revisit the derivation of the microscopic stress, linking the statistical mechanics of particle systems and continuum mechanics. The starting point in our geometric derivation is the Doyle-Ericksen formula, which states that the Cauchy stress tensor is the derivative of the free-energy with respect to the ambient metric tensor and which follows from a covariance argument. Thus, our approach to define the microscopic stress tensor does not rely on the statement of balance of linear momentum as in the classical Irving-Kirkwood-Noll approach. Nevertheless, the resulting stress tensor satisfies balance of linear and angular momentum. Furthermore, our approach removes the ambiguity in the definition of the microscopic stress in the presence of multibody interactions by naturally suggesting a canonical and physically motivated force decomposition into pairwise terms, a key ingredient in this theory. As a result, our approach provides objective expressions to compute a microscopic stress for a system in equilibrium and for force-fields expanded into multibody interactions of arbitrarily high order. We illustrate the proposed methodology with molecular dynamics simulations of a fibrous protein using a force-field involving up to 5-body interactions.

  19. Covariates of intravenous paracetamol pharmacokinetics in adults

    PubMed Central

    2014-01-01

    Background Pharmacokinetic estimates for intravenous paracetamol in individual adult cohorts are different to a certain extent, and understanding the covariates of these differences may guide dose individualization. In order to assess covariate effects of intravenous paracetamol disposition in adults, pharmacokinetic data on discrete studies were pooled. Methods This pooled analysis was based on 7 studies, resulting in 2755 time-concentration observations in 189 adults (mean age 46 SD 23 years; weight 73 SD 13 kg) given intravenous paracetamol. The effects of size, age, pregnancy and other clinical settings (intensive care, high dependency, orthopaedic or abdominal surgery) on clearance and volume of distribution were explored using non-linear mixed effects models. Results Paracetamol disposition was best described using normal fat mass (NFM) with allometric scaling as a size descriptor. A three-compartment linear disposition model revealed that the population parameter estimates (between subject variability,%) were central volume (V1) 24.6 (55.5%) L/70 kg with peripheral volumes of distribution V2 23.1 (49.6%) L/70 kg and V3 30.6 (78.9%) L/70 kg. Clearance (CL) was 16.7 (24.6%) L/h/70 kg and inter-compartment clearances were Q2 67.3 (25.7%) L/h/70 kg and Q3 2.04 (71.3%) L/h/70 kg. Clearance and V2 decreased only slightly with age. Sex differences in clearance were minor and of no significance. Clearance, relative to median values, was increased during pregnancy (FPREG = 1.14) and decreased during abdominal surgery (FABDCL = 0.715). Patients undergoing orthopaedic surgery had a reduced V2 (FORTHOV = 0.649), while those in intensive care had increased V2 (FICV = 1.51). Conclusions Size and age are important covariates for paracetamol pharmacokinetics explaining approximately 40% of clearance and V2 variability. Dose individualization in adult subpopulations would achieve little benefit in the scenarios explored. PMID:25342929

  20. 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

  1. Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts

    PubMed Central

    Göke, Jonathan; Schulz, Marcel H.; Lasserre, Julia; Vingron, Martin

    2012-01-01

    Motivation: The identity of cells and tissues is to a large degree governed by transcriptional regulation. A major part is accomplished by the combinatorial binding of transcription factors at regulatory sequences, such as enhancers. Even though binding of transcription factors is sequence-specific, estimating the sequence similarity of two functionally similar enhancers is very difficult. However, a similarity measure for regulatory sequences is crucial to detect and understand functional similarities between two enhancers and will facilitate large-scale analyses like clustering, prediction and classification of genome-wide datasets. Results: We present the standardized alignment-free sequence similarity measure N2, a flexible framework that is defined for word neighbourhoods. We explore the usefulness of adding reverse complement words as well as words including mismatches into the neighbourhood. On simulated enhancer sequences as well as functional enhancers in mouse development, N2 is shown to outperform previous alignment-free measures. N2 is flexible, faster than competing methods and less susceptible to single sequence noise and the occurrence of repetitive sequences. Experiments on the mouse enhancers reveal that enhancers active in different tissues can be separated by pairwise comparison using N2. Conclusion: N2 represents an improvement over previous alignment-free similarity measures without compromising speed, which makes it a good candidate for large-scale sequence comparison of regulatory sequences. Availability: The software is part of the open-source C++ library SeqAn (www.seqan.de) and a compiled version can be downloaded at http://www.seqan.de/projects/alf.html Contact: goeke@molgen.mpg.de; vingron@molgen.mpg.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:22247280

  2. Benchmarking the performance of pairwise homogenization of surface temperatures in the United States

    NASA Astrophysics Data System (ADS)

    Menne, M. J.; Williams, C. N.; Thorne, P. W.

    2013-09-01

    Changes in the circumstances behind in situ temperature measurements often lead to shifts in individual station records that can lead to over or under-estimates of the local and regional temperature trends. Since these shifts are comparable in magnitude to climate change signals, homogeneity "corrections" are necessary to make the records suitable for climate analysis. To quantify the effectiveness of surface temperature homogenization in the United States, a randomized perturbed ensemble of the pairwise homogenization algorithm was run against a suite of benchmark analogs to real monthly temperature data from the United States Cooperative Observer Program, which includes the subset of stations known as the United States Historical Climatology Network (USHCN). Results indicate that all randomized versions of the algorithm consistently produce homogenized data closer to the true climate signal in the presence of widespread systematic shifts in the data. When applied to the real-world observations, the randomized ensemble reinforces previous understanding that the two dominant sources of shifts in the U.S. temperature records are caused by changes to time of observation (spurious cooling in minimum and maximum) and conversion to electronic resistance thermometers (spurious cooling in maximum and warming in minimum). Trend bounds defined by the ensemble output indicate that maximum temperature trends are positive for the past 30, 50 and 100 years, and that these maximums contain pervasive negative shifts that cause the unhomogenized (raw) trends to fall below the lowest of the ensemble of homogenized trends. Moreover, because the residual impact of undetected/uncorrected shifts in the homogenized analogs is one-tailed when the imposed shifts have a positive or negative sign preference, it is likely that maximum temperature trends have been underestimated in the real-world homogenized temperature data from the USHCN. Trends for minimum temperature are also positive

  3. Benchmarking the performance of pairwise homogenization of surface temperatures in the United States

    NASA Astrophysics Data System (ADS)

    Williams, Claude N.; Menne, Matthew J.; Thorne, Peter W.

    2012-03-01

    Changes in the circumstances behind in situ temperature measurements often lead to biases in individual station records that, collectively, can also bias regional temperature trends. Since these biases are comparable in magnitude to climate change signals, homogeneity "corrections" are necessary to make the records suitable for climate analysis. To quantify the effectiveness of U.S. surface temperature homogenization, a randomized perturbed ensemble of the USHCN pairwise homogenization algorithm was run against a suite of benchmark analogs to real monthly temperature data. Results indicate that all randomized versions of the algorithm consistently produce homogenized data closer to the true climate signal in the presence of widespread systematic errors. When applied to the real-world observations, the randomized ensemble reinforces previous understanding that the two dominant sources of bias in the U.S. temperature records are caused by changes to time of observation (spurious cooling in minimum and maximum) and conversion to electronic resistance thermometers (spurious cooling in maximum and warming in minimum). Error bounds defined by the ensemble output indicate that maximum temperature trends are positive for the past 30, 50 and 100 years, and that these maximums contain pervasive negative biases that cause the unhomogenized (raw) trends to fall below the lower limits of uncertainty. Moreover, because residual bias in the homogenized analogs is one-tailed under biased errors, it is likely that maximum temperature trends have been underestimated in the USHCN. Trends for minimum temperature are also positive over the three periods, but the ensemble error bounds encompass trends from the unhomogenized data.

  4. 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.

  5. Generation of phase-covariant quantum cloning

    SciTech Connect

    Karimipour, V.; Rezakhani, A.T.

    2002-11-01

    It is known that in phase-covariant quantum cloning, the equatorial states on the Bloch sphere can be cloned with a fidelity higher than the optimal bound established for universal quantum cloning. We generalize this concept to include other states on the Bloch sphere with a definite z component of spin. It is shown that once we know the z component, we can always clone a state with a fidelity higher than the universal value and that of equatorial states. We also make a detailed study of the entanglement properties of the output copies and show that the equatorial states are the only states that give rise to a separable density matrix for the outputs.

  6. Baryon Spectrum Analysis using Covariant Constraint Dynamics

    NASA Astrophysics Data System (ADS)

    Whitney, Joshua; Crater, Horace

    2012-03-01

    The energy spectrum of the baryons is determined by treating each of them as a three-body system with the interacting forces coming from a set of two-body potentials that depend on both the distance between the quarks and the spin and orbital angular momentum coupling terms. The Two Body Dirac equations of constraint dynamics derived by Crater and Van Alstine, matched with the quasipotential formalism of Todorov as the underlying two-body formalism are used, as well as the three-body constraint formalism of Sazdjian to integrate the three two-body equations into a single relativistically covariant three body equation for the bound state energies. The results are analyzed and compared to experiment using a best fit method and several different algorithms, including a gradient approach, and Monte Carlo method. Results for all well-known baryons are presented and compared to experiment, with good accuracy.

  7. Covariant Lyapunov analysis of chaotic Kolmogorov flows.

    PubMed

    Inubushi, Masanobu; Kobayashi, Miki U; Takehiro, Shin-ichi; Yamada, Michio

    2012-01-01

    Hyperbolicity is an important concept in dynamical system theory; however, we know little about the hyperbolicity of concrete physical systems including fluid motions governed by the Navier-Stokes equations. Here, we study numerically the hyperbolicity of the Navier-Stokes equation on a two-dimensional torus (Kolmogorov flows) using the method of covariant Lyapunov vectors developed by Ginelli et al. [Phys. Rev. Lett. 99, 130601 (2007)]. We calculate the angle between the local stable and unstable manifolds along an orbit of chaotic solution to evaluate the hyperbolicity. We find that the attractor of chaotic Kolmogorov flows is hyperbolic at small Reynolds numbers, but that smaller angles between the local stable and unstable manifolds are observed at larger Reynolds numbers, and the attractor appears to be nonhyperbolic at a certain Reynolds numbers. Also, we observed some relations between these hyperbolic properties and physical properties such as time correlation of the vorticity and the energy dissipation rate.

  8. EMPIRE ULTIMATE EXPANSION: RESONANCES AND COVARIANCES.

    SciTech Connect

    HERMAN,M.; MUGHABGHAB, S.F.; OBLOZINSKY, P.; ROCHMAN, D.; PIGNI, M.T.; KAWANO, T.; CAPOTE, R.; ZERKIN, V.; TRKOV, A.; SIN, M.; CARSON, B.V.; WIENKE, H. CHO, Y.-S.

    2007-04-22

    The EMPIRE code system is being extended to cover the resolved and unresolved resonance region employing proven methodology used for the production of new evaluations in the recent Atlas of Neutron Resonances. Another directions of Empire expansion are uncertainties and correlations among them. These include covariances for cross sections as well as for model parameters. In this presentation we concentrate on the KALMAN method that has been applied in EMPIRE to the fast neutron range as well as to the resonance region. We also summarize role of the EMPIRE code in the ENDF/B-VII.0 development. Finally, large scale calculations and their impact on nuclear model parameters are discussed along with the exciting perspectives offered by the parallel supercomputing.

  9. Covariant chronogeometry and extreme distances: Elementary particles

    PubMed Central

    Segal, I. E.; Jakobsen, H. P.; Ørsted, B.; Paneitz, S. M.; Speh, B.

    1981-01-01

    We study a variant of elementary particle theory in which Minkowski space, M0, is replaced by a natural alternative, the unique four-dimensional manifold ¯M with comparable properties of causality and symmetry. Free particles are considered to be associated (i) with positive-energy representations in bundles of prescribed spin over ¯M of the group of causality-preserving transformations on ¯M (or its mass-conserving subgroup) and (ii) with corresponding wave equations. In this study these bundles, representations, and equations are detailed, and some of their basic features are developed in the cases of spins 0 and ½. Preliminaries to a general study are included; issues of covariance, unitarity, and positivity of the energy are treated; appropriate quantum numbers are indicated; and possible physical applications are discussed. PMID:16593075

  10. Covariant entropy bound and loop quantum cosmology

    SciTech Connect

    Ashtekar, Abhay; Wilson-Ewing, Edward

    2008-09-15

    We examine Bousso's covariant entropy bound conjecture in the context of radiation filled, spatially flat, Friedmann-Robertson-Walker models. The bound is violated near the big bang. However, the hope has been that quantum gravity effects would intervene and protect it. Loop quantum cosmology provides a near ideal setting for investigating this issue. For, on the one hand, quantum geometry effects resolve the singularity and, on the other hand, the wave function is sharply peaked at a quantum corrected but smooth geometry, which can supply the structure needed to test the bound. We find that the bound is respected. We suggest that the bound need not be an essential ingredient for a quantum gravity theory but may emerge from it under suitable circumstances.

  11. Covariance of Lucky Images: Performance analysis

    NASA Astrophysics Data System (ADS)

    Cagigal, Manuel P.; Valle, Pedro J.; Cagigas, Miguel A.; Villó-Pérez, Isidro; Colodro-Conde, Carlos; Ginski, C.; Mugrauer, M.; Seeliger, M.

    2016-09-01

    The covariance of ground-based Lucky Images (COELI) is a robust and easy-to-use algorithm that allows us to detect faint companions surrounding a host star. In this paper we analyze the relevance of the number of processed frames, the frames quality, the atmosphere conditions and the detection noise on the companion detectability. This analysis has been carried out using both experimental and computer simulated imaging data. Although the technique allows us the detection of faint companions, the camera detection noise and the use of a limited number of frames reduce the minimum detectable companion intensity to around 1000 times fainter than that of the host star when placed at an angular distance corresponding to the few first Airy rings. The reachable contrast could be even larger when detecting companions with the assistance of an adaptive optics system.

  12. A covariant treatment of cosmic parallax

    SciTech Connect

    Räsänen, Syksy

    2014-03-01

    The Gaia satellite will soon probe parallax on cosmological distances. Using the covariant formalism and considering the angle between a pair of sources, we find parallax for both spacelike and timelike separation between observation points. Our analysis includes both intrinsic parallax and parallax due to observer motion. We propose a consistency condition that tests the FRW metric using the parallax distance and the angular diameter distance. This test is purely kinematic and relies only on geometrical optics, it is independent of matter content and its relation to the spacetime geometry. We study perturbations around the FRW model, and find that they should be taken into account when analysing observations to determine the parallax distance.

  13. Conformal killing tensors and covariant Hamiltonian dynamics

    SciTech Connect

    Cariglia, M.; Gibbons, G. W.; Holten, J.-W. van; Horvathy, P. A.; Zhang, P.-M.

    2014-12-15

    A covariant algorithm for deriving the conserved quantities for natural Hamiltonian systems is combined with the non-relativistic framework of Eisenhart, and of Duval, in which the classical trajectories arise as geodesics in a higher dimensional space-time, realized by Brinkmann manifolds. Conserved quantities which are polynomial in the momenta can be built using time-dependent conformal Killing tensors with flux. The latter are associated with terms proportional to the Hamiltonian in the lower dimensional theory and with spectrum generating algebras for higher dimensional quantities of order 1 and 2 in the momenta. Illustrations of the general theory include the Runge-Lenz vector for planetary motion with a time-dependent gravitational constant G(t), motion in a time-dependent electromagnetic field of a certain form, quantum dots, the Hénon-Heiles and Holt systems, respectively, providing us with Killing tensors of rank that ranges from one to six.

  14. Covariant density functional theory for magnetic rotation

    NASA Astrophysics Data System (ADS)

    Peng, J.; Meng, J.; Ring, P.; Zhang, S. Q.

    2008-08-01

    The tilted axis cranking formalism is implemented in relativistic mean field (RMF) theory. It is used for a microscopic description of magnetic rotation in the framework of covariant density functional theory. We assume that the rotational axis is in the xz plane and consider systems with the two symmetries P (space reflection) and PyT (a combination of a reflection in the y direction and time reversal). A computer code based on these symmetries is developed, and first applications are discussed for the nucleus Gd142: the rotational band based on the configuration πh11/22⊗νh11/2-2 is investigated in a fully microscopic and self-consistent way. The results are compared with available data, such as spectra and electromagnetic transition ratios B(M1)/B(E2). The relation between rotational velocity and angular momentum are discussed in detail together with the shears mechanism characteristic of magnetic rotation.

  15. Covariant generalization of cosmological perturbation theory

    SciTech Connect

    Enqvist, Kari; Hoegdahl, Janne; Nurmi, Sami; Vernizzi, Filippo

    2007-01-15

    We present an approach to cosmological perturbations based on a covariant perturbative expansion between two worldlines in the real inhomogeneous universe. As an application, at an arbitrary order we define an exact scalar quantity which describes the inhomogeneities in the number of e-folds on uniform density hypersurfaces and which is conserved on all scales for a barotropic ideal fluid. We derive a compact form for its conservation equation at all orders and assign it a simple physical interpretation. To make a comparison with the standard perturbation theory, we develop a method to construct gauge-invariant quantities in a coordinate system at arbitrary order, which we apply to derive the form of the nth order perturbation in the number of e-folds on uniform density hypersurfaces and its exact evolution equation. On large scales, this provides the gauge-invariant expression for the curvature perturbation on uniform density hypersurfaces and its evolution equation at any order.

  16. A covariance analysis algorithm for interconnected systems

    NASA Technical Reports Server (NTRS)

    Cheng, Victor H. L.; Curley, Robert D.; Lin, Ching-An

    1987-01-01

    A covariance analysis algorithm for propagation of signal statistics in arbitrarily interconnected nonlinear systems is presented which is applied to six-degree-of-freedom systems. The algorithm uses statistical linearization theory to linearize the nonlinear subsystems, and the resulting linearized subsystems are considered in the original interconnection framework for propagation of the signal statistics. Some nonlinearities commonly encountered in six-degree-of-freedom space-vehicle models are referred to in order to illustrate the limitations of this method, along with problems not encountered in standard deterministic simulation analysis. Moreover, the performance of the algorithm shall be numerically exhibited by comparing results using such techniques to Monte Carlo analysis results, both applied to a simple two-dimensional space-intercept problem.

  17. A Product Partition Model With Regression on Covariates

    PubMed Central

    Müller, Peter; Quintana, Fernando; Rosner, Gary L.

    2011-01-01

    We propose a probability model for random partitions in the presence of covariates. In other words, we develop a model-based clustering algorithm that exploits available covariates. The motivating application is predicting time to progression for patients in a breast cancer trial. We proceed by reporting a weighted average of the responses of clusters of earlier patients. The weights should be determined by the similarity of the new patient’s covariate with the covariates of patients in each cluster. We achieve the desired inference by defining a random partition model that includes a regression on covariates. Patients with similar covariates are a priori more likely to be clustered together. Posterior predictive inference in this model formalizes the desired prediction. We build on product partition models (PPM). We define an extension of the PPM to include a regression on covariates by including in the cohesion function a new factor that increases the probability of experimental units with similar covariates to be included in the same cluster. We discuss implementations suitable for any combination of continuous, categorical, count, and ordinal covariates. An implementation of the proposed model as R-package is available for download. PMID:21566678

  18. Performance of internal covariance estimators for cosmic shear correlation functions

    SciTech Connect

    Friedrich, O.; Seitz, S.; Eifler, T. F.; Gruen, D.

    2015-12-31

    Data re-sampling methods such as the delete-one jackknife are a common tool for estimating the covariance of large scale structure probes. In this paper we investigate the concepts of internal covariance estimation in the context of cosmic shear two-point statistics. We demonstrate how to use log-normal simulations of the convergence field and the corresponding shear field to carry out realistic tests of internal covariance estimators and find that most estimators such as jackknife or sub-sample covariance can reach a satisfactory compromise between bias and variance of the estimated covariance. In a forecast for the complete, 5-year DES survey we show that internally estimated covariance matrices can provide a large fraction of the true uncertainties on cosmological parameters in a 2D cosmic shear analysis. The volume inside contours of constant likelihood in the $\\Omega_m$-$\\sigma_8$ plane as measured with internally estimated covariance matrices is on average $\\gtrsim 85\\%$ of the volume derived from the true covariance matrix. The uncertainty on the parameter combination $\\Sigma_8 \\sim \\sigma_8 \\Omega_m^{0.5}$ derived from internally estimated covariances is $\\sim 90\\%$ of the true uncertainty.

  19. Performance of internal covariance estimators for cosmic shear correlation functions

    DOE PAGES

    Friedrich, O.; Seitz, S.; Eifler, T. F.; Gruen, D.

    2015-12-31

    Data re-sampling methods such as the delete-one jackknife are a common tool for estimating the covariance of large scale structure probes. In this paper we investigate the concepts of internal covariance estimation in the context of cosmic shear two-point statistics. We demonstrate how to use log-normal simulations of the convergence field and the corresponding shear field to carry out realistic tests of internal covariance estimators and find that most estimators such as jackknife or sub-sample covariance can reach a satisfactory compromise between bias and variance of the estimated covariance. In a forecast for the complete, 5-year DES survey we show that internally estimated covariance matrices can provide a large fraction of the true uncertainties on cosmological parameters in a 2D cosmic shear analysis. The volume inside contours of constant likelihood in themore » $$\\Omega_m$$-$$\\sigma_8$$ plane as measured with internally estimated covariance matrices is on average $$\\gtrsim 85\\%$$ of the volume derived from the true covariance matrix. The uncertainty on the parameter combination $$\\Sigma_8 \\sim \\sigma_8 \\Omega_m^{0.5}$$ derived from internally estimated covariances is $$\\sim 90\\%$$ of the true uncertainty.« less

  20. Study of the Large-Scale Distribution of Gamma-Ray Burst Sources by the Method of Pairwise Distances

    NASA Astrophysics Data System (ADS)

    Gerasim, R. V.; Orlov, V. V.; Raikov, A. A.

    2015-06-01

    The method of pairwise distances developed earlier by the authors is used to study the spatial distribution of 352 sources of gamma-ray bursts with measured redshifts. Three cosmological models are considered: a model with a Euclidean metric, the "tired light" model, and the standard ΛCDM model. It is found that this set has fractal features and may be multifractal. The fractal dimensionalities are estimated.

  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. PMID:19724393

  2. 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.

  3. Methods for estimation of covariance matrices and covariance components for the Hanford Waste Vitrification Plant Process

    SciTech Connect

    Bryan, M.F.; Piepel, G.F.; Simpson, D.B.

    1996-03-01

    The high-level waste (HLW) vitrification plant at the Hanford Site was being designed to transuranic and high-level radioactive waste in borosilicate class. Each batch of plant feed material must meet certain requirements related to plant performance, and the resulting class must meet requirements imposed by the Waste Acceptance Product Specifications. Properties of a process batch and the resultlng glass are largely determined by the composition of the feed material. Empirical models are being developed to estimate some property values from data on feed composition. Methods for checking and documenting compliance with feed and glass requirements must account for various types of uncertainties. This document focuses on the estimation. manipulation, and consequences of composition uncertainty, i.e., the uncertainty inherent in estimates of feed or glass composition. Three components of composition uncertainty will play a role in estimating and checking feed and glass properties: batch-to-batch variability, within-batch uncertainty, and analytical uncertainty. In this document, composition uncertainty and its components are treated in terms of variances and variance components or univariate situations, covariance matrices and covariance components for multivariate situations. The importance of variance and covariance components stems from their crucial role in properly estimating uncertainty In values calculated from a set of observations on a process batch. Two general types of methods for estimating uncertainty are discussed: (1) methods based on data, and (2) methods based on knowledge, assumptions, and opinions about the vitrification process. Data-based methods for estimating variances and covariance matrices are well known. Several types of data-based methods exist for estimation of variance components; those based on the statistical method analysis of variance are discussed, as are the strengths and weaknesses of this approach.

  4. Covariant Spectator Theory: Foundations and Applications A Mini-Review of the Covariant Spectator Theory

    SciTech Connect

    Alfred Stadler, Franz Gross

    2010-10-01

    We provide a short overview of the Covariant Spectator Theory and its applications. The basic ideas are introduced through the example of a {phi}{sup 4}-type theory. High-precision models of the two-nucleon interaction are presented and the results of their use in calculations of properties of the two- and three-nucleon systems are discussed. A short summary of applications of this framework to other few-body systems is also presented.

  5. Assessing Trait Covariation and Morphological Integration on Phylogenies Using Evolutionary Covariance Matrices

    PubMed Central

    Adams, Dean C.; Felice, Ryan N.

    2014-01-01

    Morphological integration describes the degree to which sets of organismal traits covary with one another. Morphological covariation may be evaluated at various levels of biological organization, but when characterizing such patterns across species at the macroevolutionary level, phylogeny must be taken into account. We outline an analytical procedure based on the evolutionary covariance matrix that allows species-level patterns of morphological integration among structures defined by sets of traits to be evaluated while accounting for the phylogenetic relationships among taxa, providing a flexible and robust complement to related phylogenetic independent contrasts based approaches. Using computer simulations under a Brownian motion model we show that statistical tests based on the approach display appropriate Type I error rates and high statistical power for detecting known levels of integration, and these trends remain consistent for simulations using different numbers of species, and for simulations that differ in the number of trait dimensions. Thus, our procedure provides a useful means of testing hypotheses of morphological integration in a phylogenetic context. We illustrate the utility of this approach by evaluating evolutionary patterns of morphological integration in head shape for a lineage of Plethodon salamanders, and find significant integration between cranial shape and mandible shape. Finally, computer code written in R for implementing the procedure is provided. PMID:24728003

  6. Novel fiber bottle microresonator add-drop filters

    NASA Astrophysics Data System (ADS)

    Senthil Murugan, Ganapathy; Wilkinson, James S.; Zervas, Michalis N.

    2010-02-01

    Novel bottle microresonators fabricated from standard telecommunications optical fiber were recently shown to support helical whispering gallery modes (WGMs) extending along the bottle length between the bottle necks. Intensity maxima were observed around the turning points on both sides close to the bottle necks where the WGMs are effectively reflected. Selective excitation on one side of the bottle microresonator leads to strong power localization at a symmetrically located turning point for the WGMs and can potentially be exploited to form effective add-drop filters. Channel dropping characteristics have been studied experimentally for the first time in this novel type of microresonator. A tapered optical fiber (drawn down to 2-3 microns in diameter with effective index of approximately 1.2) was placed on one side of the bottle to excite the bottle WGMs. A similar tapered fiber placed symmetrically on the other side of the bottle acted as a probe to extract the excited modes. We have successfully extracted power from all the resonance wavelengths using the probe placed at appropriate positions along the bottle, leading to the potential to construct efficient all fiber add-drop filters.

  7. Using Patient Lists to Add Value to Integrated Data Repositories

    PubMed Central

    Wade, Ted D.; Zelarney, Pearlanne T.; Hum, Richard C.; McGee, Sylvia; Batson, Deborah H.

    2014-01-01

    Patient lists are project-specific sets of patients that can be queried in integrated data repositories (IDR’s). By allowing a set of patients to be an addition to the qualifying conditions of a query, returned results will refer to, and only to, that set of patients. We report a variety of use cases for such lists, including: restricting retrospective chart review to a defined set of patients; following a set of patients for practice management purposes; distributing “honest-brokered” (deidentified) data; adding phenotypes to biosamples; and enhancing the content of study or registry data. Among the capabilities needed to implement patient lists in an IDR are: capture of patient identifiers from a query and feedback of these into the IDR; the existence of a permanent internal identifier in the IDR that is mappable to external identifiers; the ability to add queryable attributes to the IDR; the ability to merge data from multiple queries; and suitable control over user access and de-identification of results. We implemented patient lists in a custom IDR of our own design. We reviewed capabilities of other published IDRs for focusing on sets of patients. The widely used i2b2 IDR platform has various ways to address patient sets, and it could be modified to add the low-overhead version of patient lists that we describe. PMID:24534444

  8. Covariate Balance in Bayesian Propensity Score Approaches for Observational Studies

    ERIC Educational Resources Information Center

    Chen, Jianshen; Kaplan, David

    2015-01-01

    Bayesian alternatives to frequentist propensity score approaches have recently been proposed. However, few studies have investigated their covariate balancing properties. This article compares a recently developed two-step Bayesian propensity score approach to the frequentist approach with respect to covariate balance. The effects of different…

  9. Alternative Multiple Imputation Inference for Mean and Covariance Structure Modeling

    ERIC Educational Resources Information Center

    Lee, Taehun; Cai, Li

    2012-01-01

    Model-based multiple imputation has become an indispensable method in the educational and behavioral sciences. Mean and covariance structure models are often fitted to multiply imputed data sets. However, the presence of multiple random imputations complicates model fit testing, which is an important aspect of mean and covariance structure…

  10. Universal and phase-covariant superbroadcasting for mixed qubit states

    SciTech Connect

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

    2006-10-15

    We describe a general framework to study covariant symmetric broadcasting maps for mixed qubit states. We explicitly derive the optimal N{yields}M superbroadcasting maps, achieving optimal purification of the single-site output copy, in both the universal and phase-covariant cases. We also study the bipartite entanglement properties of the superbroadcast states.

  11. Handling Correlations between Covariates and Random Slopes in Multilevel Models

    ERIC Educational Resources Information Center

    Bates, Michael David; Castellano, Katherine E.; Rabe-Hesketh, Sophia; Skrondal, Anders

    2014-01-01

    This article discusses estimation of multilevel/hierarchical linear models that include cluster-level random intercepts and random slopes. Viewing the models as structural, the random intercepts and slopes represent the effects of omitted cluster-level covariates that may be correlated with included covariates. The resulting correlations between…

  12. Covariation and Quantifier Polarity: What Determines Causal Attribution in Vignettes?

    ERIC Educational Resources Information Center

    Majid, Asifa; Sanford, Anthony J.; Pickering, Martin J.

    2006-01-01

    Tests of causal attribution often use verbal vignettes, with covariation information provided through statements quantified with natural language expressions. The effect of covariation information has typically been taken to show that set size information affects attribution. However, recent research shows that quantifiers provide information…

  13. The Regression Trunk Approach to Discover Treatment Covariate Interaction

    ERIC Educational Resources Information Center

    Dusseldorp, Elise; Meulman, Jacqueline J.

    2004-01-01

    The regression trunk approach (RTA) is an integration of regression trees and multiple linear regression analysis. In this paper RTA is used to discover treatment covariate interactions, in the regression of one continuous variable on a treatment variable with "multiple" covariates. The performance of RTA is compared to the classical method of…

  14. Covariate-adjusted response-adaptive designs for binary response.

    PubMed

    Rosenberger, W F; Vidyashankar, A N; Agarwal, D K

    2001-11-01

    An adaptive allocation design for phase III clinical trials that incorporates covariates is described. The allocation scheme maps the covariate-adjusted odds ratio from a logistic regression model onto [0, 1]. Simulations assume that both staggered entry and time to response are random and follow a known probability distribution that can depend on the treatment assigned, the patient's response, a covariate, or a time trend. Confidence intervals on the covariate-adjusted odds ratio is slightly anticonservative for the adaptive design under the null hypothesis, but power is similar to equal allocation under various alternatives for n = 200. For similar power, the net savings in terms of expected number of treatment failures is modest, but enough to make this design attractive for certain studies where known covariates are expected to be important and stratification is not desired, and treatment failures have a high ethical cost.

  15. Correcting eddy-covariance flux underestimates over a grassland.

    SciTech Connect

    Twine, T. E.; Kustas, W. P.; Norman, J. M.; Cook, D. R.; Houser, P. R.; Meyers, T. P.; Prueger, J. H.; Starks, P. J.; Wesely, M. L.; Environmental Research; Univ. of Wisconsin at Madison; DOE; National Aeronautics and Space Administration; National Oceanic and Atmospheric Administrationoratory

    2000-06-08

    Independent measurements of the major energy balance flux components are not often consistent with the principle of conservation of energy. This is referred to as a lack of closure of the surface energy balance. Most results in the literature have shown the sum of sensible and latent heat fluxes measured by eddy covariance to be less than the difference between net radiation and soil heat fluxes. This under-measurement of sensible and latent heat fluxes by eddy-covariance instruments has occurred in numerous field experiments and among many different manufacturers of instruments. Four eddy-covariance systems consisting of the same models of instruments were set up side-by-side during the Southern Great Plains 1997 Hydrology Experiment and all systems under-measured fluxes by similar amounts. One of these eddy-covariance systems was collocated with three other types of eddy-covariance systems at different sites; all of these systems under-measured the sensible and latent-heat fluxes. The net radiometers and soil heat flux plates used in conjunction with the eddy-covariance systems were calibrated independently and measurements of net radiation and soil heat flux showed little scatter for various sites. The 10% absolute uncertainty in available energy measurements was considerably smaller than the systematic closure problem in the surface energy budget, which varied from 10 to 30%. When available-energy measurement errors are known and modest, eddy-covariance measurements of sensible and latent heat fluxes should be adjusted for closure. Although the preferred method of energy balance closure is to maintain the Bowen-ratio, the method for obtaining closure appears to be less important than assuring that eddy-covariance measurements are consistent with conservation of energy. Based on numerous measurements over a sorghum canopy, carbon dioxide fluxes, which are measured by eddy covariance, are underestimated by the same factor as eddy covariance evaporation

  16. Supergeometry in Locally Covariant Quantum Field Theory

    NASA Astrophysics Data System (ADS)

    Hack, Thomas-Paul; Hanisch, Florian; Schenkel, Alexander

    2016-03-01

    In this paper we analyze supergeometric locally covariant quantum field theories. We develop suitable categories SLoc of super-Cartan supermanifolds, which generalize Lorentz manifolds in ordinary quantum field theory, and show that, starting from a few representation theoretic and geometric data, one can construct a functor A : SLoc to S* Alg to the category of super-*-algebras, which can be interpreted as a non-interacting super-quantum field theory. This construction turns out to disregard supersymmetry transformations as the morphism sets in the above categories are too small. We then solve this problem by using techniques from enriched category theory, which allows us to replace the morphism sets by suitable morphism supersets that contain supersymmetry transformations as their higher superpoints. We construct super-quantum field theories in terms of enriched functors eA : eSLoc to eS* Alg between the enriched categories and show that supersymmetry transformations are appropriately described within the enriched framework. As examples we analyze the superparticle in 1|1-dimensions and the free Wess-Zumino model in 3|2-dimensions.

  17. Holographic bound in covariant loop quantum gravity

    NASA Astrophysics Data System (ADS)

    Tamaki, Takashi

    2016-07-01

    We investigate puncture statistics based on the covariant area spectrum in loop quantum gravity. First, we consider Maxwell-Boltzmann statistics with a Gibbs factor for punctures. We establish formulas which relate physical quantities such as horizon area to the parameter characterizing holographic degrees of freedom. We also perform numerical calculations and obtain consistency with these formulas. These results tell us that the holographic bound is satisfied in the large area limit and the correction term of the entropy-area law can be proportional to the logarithm of the horizon area. Second, we also consider Bose-Einstein statistics and show that the above formulas are also useful in this case. By applying the formulas, we can understand intrinsic features of Bose-Einstein condensate which corresponds to the case when the horizon area almost consists of punctures in the ground state. When this phenomena occurs, the area is approximately constant against the parameter characterizing the temperature. When this phenomena is broken, the area shows rapid increase which suggests the phase transition from quantum to classical area.

  18. Super-sample covariance in simulations

    NASA Astrophysics Data System (ADS)

    Li, Yin; Hu, Wayne; Takada, Masahiro

    2014-04-01

    Using separate universe simulations, we accurately quantify super-sample covariance (SSC), the typically dominant sampling error for matter power spectrum estimators in a finite volume, which arises from the presence of super survey modes. By quantifying the power spectrum response to a background mode, this approach automatically captures the separate effects of beat coupling in the quasilinear regime, halo sample variance in the nonlinear regime and a new dilation effect which changes scales in the power spectrum coherently across the survey volume, including the baryon acoustic oscillation scale. It models these effects at typically the few percent level or better with a handful of small volume simulations for any survey geometry compared with directly using many thousands of survey volumes in a suite of large-volume simulations. The stochasticity of the response is sufficiently small that in the quasilinear regime, SSC can be alternately included by fitting the mean density in the volume with these fixed templates in parameter estimation. We also test the halo model prescription and find agreement typically at better than the 10% level for the response.

  19. Generalized Covariant Gyrokinetic Dynamics of Magnetoplasmas

    SciTech Connect

    Cremaschini, C.; Tessarotto, M.; Nicolini, P.; Beklemishev, A.

    2008-12-31

    A basic prerequisite for the investigation of relativistic astrophysical magnetoplasmas, occurring typically in the vicinity of massive stellar objects (black holes, neutron stars, active galactic nuclei, etc.), is the accurate description of single-particle covariant dynamics, based on gyrokinetic theory (Beklemishev et al., 1999-2005). Provided radiation-reaction effects are negligible, this is usually based on the assumption that both the space-time metric and the EM fields (in particular the magnetic field) are suitably prescribed and are considered independent of single-particle dynamics, while allowing for the possible presence of gravitational/EM perturbations driven by plasma collective interactions which may naturally arise in such systems. The purpose of this work is the formulation of a generalized gyrokinetic theory based on the synchronous variational principle recently pointed out (Tessarotto et al., 2007) which permits to satisfy exactly the physical realizability condition for the four-velocity. The theory here developed includes the treatment of nonlinear perturbations (gravitational and/or EM) characterized locally, i.e., in the rest frame of a test particle, by short wavelength and high frequency. Basic feature of the approach is to ensure the validity of the theory both for large and vanishing parallel electric field. It is shown that the correct treatment of EM perturbations occurring in the presence of an intense background magnetic field generally implies the appearance of appropriate four-velocity corrections, which are essential for the description of single-particle gyrokinetic dynamics.

  20. Epigenetic Contribution to Covariance Between Relatives

    PubMed Central

    Tal, Omri; Kisdi, Eva; Jablonka, Eva

    2010-01-01

    Recent research has pointed to the ubiquity and abundance of between-generation epigenetic inheritance. This research has implications for assessing disease risk and the responses to ecological stresses and also for understanding evolutionary dynamics. An important step toward a general evaluation of these implications is the identification and estimation of the amount of heritable, epigenetic variation in populations. While methods for modeling the phenotypic heritable variance contributed by culture have already been developed, there are no comparable methods for nonbehavioral epigenetic inheritance systems. By introducing a model that takes epigenetic transmissibility (the probability of transmission of ancestral phenotypes) and environmental induction into account, we provide novel expressions for covariances between relatives. We have combined a classical quantitative genetics approach with information about the number of opportunities for epigenetic reset between generations and assumptions about environmental induction to estimate the heritable epigenetic variance and epigenetic transmissibility for both asexual and sexual populations. This assists us in the identification of phenotypes and populations in which epigenetic transmission occurs and enables a preliminary quantification of their transmissibility, which could then be followed by genomewide association and QTL studies. PMID:20100941

  1. Add-on laser reading device for a camera phone

    NASA Astrophysics Data System (ADS)

    Mäkinen, Jukka-Tapani; Niemelä, Karri; Vasama, Hannu; Mattila, Rauno; Aikio, Mika; Aikio, Sanna; Aikio, Janne

    2005-09-01

    A novel add-on device to a mobile camera phone has been developed. The prototype system contains both laser and LED illumination as well as imaging optics. Main idea behind the device is to have a small printable diffractive ROM (Read Only Memory) element, which can be read by illuminating it with a laser-beam and recording the resulting datamatrix pattern with a camera phone. The element contains information in the same manner as a traditional bar-code, but due to the 2D-pattern and diffractive nature of the tag, a much larger amount of information can be packed on a smaller area. Optical and mechanical designs of the prototype device have been made in such a way that the system can be used in three different modes: as a laser reader, as a telescope and as a microscope.

  2. A subsurface add-on for standard atomic force microscopes.

    PubMed

    Verbiest, G J; van der Zalm, D J; Oosterkamp, T H; Rost, M J

    2015-03-01

    The application of ultrasound in an Atomic Force Microscope (AFM) gives access to subsurface information. However, no commercially AFM exists that is equipped with this technique. The main problems are the electronic crosstalk in the AFM setup and the insufficiently strong excitation of the cantilever at ultrasonic (MHz) frequencies. In this paper, we describe the development of an add-on that provides a solution to these problems by using a special piezo element with a lowest resonance frequency of 2.5 MHz and by separating the electronic connection for this high frequency piezo element from all other connections. In this sense, we support researches with the possibility to perform subsurface measurements with their existing AFMs and hopefully pave also the way for the development of a commercial AFM that is capable of imaging subsurface features with nanometer resolution.

  3. A subsurface add-on for standard atomic force microscopes

    SciTech Connect

    Verbiest, G. J.; Zalm, D. J. van der; Oosterkamp, T. H.; Rost, M. J.

    2015-03-15

    The application of ultrasound in an Atomic Force Microscope (AFM) gives access to subsurface information. However, no commercially AFM exists that is equipped with this technique. The main problems are the electronic crosstalk in the AFM setup and the insufficiently strong excitation of the cantilever at ultrasonic (MHz) frequencies. In this paper, we describe the development of an add-on that provides a solution to these problems by using a special piezo element with a lowest resonance frequency of 2.5 MHz and by separating the electronic connection for this high frequency piezo element from all other connections. In this sense, we support researches with the possibility to perform subsurface measurements with their existing AFMs and hopefully pave also the way for the development of a commercial AFM that is capable of imaging subsurface features with nanometer resolution.

  4. Visualization of species pairwise associations: a case study of surrogacy in bird assemblages

    PubMed Central

    Lane, Peter W; Lindenmayer, David B; Barton, Philip S; Blanchard, Wade; Westgate, Martin J

    2014-01-01

    Quantifying and visualizing species associations are important to many areas of ecology and conservation biology. Species networks are one way to analyze species associations, with a growing number of applications such as food webs, nesting webs, plant–animal mutualisms, and interlinked extinctions. We present a new method for assessing and visualizing patterns of co-occurrence of species. The method depicts interactions and associations in an analogous way with existing network diagrams for studying pollination and trophic interactions, but adds the assessment of sign, strength, and direction of the associations. This provides a distinct advantage over existing methods of quantifying and visualizing co-occurrence. We demonstrate the utility of our new approach by showing differences in associations among woodland bird species found in different habitats and by illustrating the way these can be interpreted in terms of underlying ecological mechanisms. Our new method is computationally feasible for large assemblages and provides readily interpretable effects with standard errors. It has wide applications for quantifying species associations within ecological communities, examining questions about particular species that occur with others, and how their associations can determine the structure and composition of communities. PMID:25473480

  5. Quantification of Covariance in Tropical Cyclone Activity across Teleconnected Basins

    NASA Astrophysics Data System (ADS)

    Tolwinski-Ward, S. E.; Wang, D.

    2015-12-01

    Rigorous statistical quantification of natural hazard covariance across regions has important implications for risk management, and is also of fundamental scientific interest. We present a multivariate Bayesian Poisson regression model for inferring the covariance in tropical cyclone (TC) counts across multiple ocean basins and across Saffir-Simpson intensity categories. Such covariability results from the influence of large-scale modes of climate variability on local environments that can alternately suppress or enhance TC genesis and intensification, and our model also simultaneously quantifies the covariance of TC counts with various climatic modes in order to deduce the source of inter-basin TC covariability. The model explicitly treats the time-dependent uncertainty in observed maximum sustained wind data, and hence the nominal intensity category of each TC. Differences in annual TC counts as measured by different agencies are also formally addressed. The probabilistic output of the model can be probed for probabilistic answers to such questions as: - Does the relationship between different categories of TCs differ statistically by basin? - Which climatic predictors have significant relationships with TC activity in each basin? - Are the relationships between counts in different basins conditionally independent given the climatic predictors, or are there other factors at play affecting inter-basin covariability? - How can a portfolio of insured property be optimized across space to minimize risk? Although we present results of our model applied to TCs, the framework is generalizable to covariance estimation between multivariate counts of natural hazards across regions and/or across peril types.

  6. Modeling spatiotemporal covariance for magnetoencephalography or electroencephalography source analysis

    NASA Astrophysics Data System (ADS)

    Plis, Sergey M.; George, J. S.; Jun, S. C.; Paré-Blagoev, J.; Ranken, D. M.; Wood, C. C.; Schmidt, D. M.

    2007-01-01

    We propose a new model to approximate spatiotemporal noise covariance for use in neural electromagnetic source analysis, which better captures temporal variability in background activity. As with other existing formalisms, our model employs a Kronecker product of matrices representing temporal and spatial covariance. In our model, spatial components are allowed to have differing temporal covariances. Variability is represented as a series of Kronecker products of spatial component covariances and corresponding temporal covariances. Unlike previous attempts to model covariance through a sum of Kronecker products, our model is designed to have a computationally manageable inverse. Despite increased descriptive power, inversion of the model is fast, making it useful in source analysis. We have explored two versions of the model. One is estimated based on the assumption that spatial components of background noise have uncorrelated time courses. Another version, which gives closer approximation, is based on the assumption that time courses are statistically independent. The accuracy of the structural approximation is compared to an existing model, based on a single Kronecker product, using both Frobenius norm of the difference between spatiotemporal sample covariance and a model, and scatter plots. Performance of ours and previous models is compared in source analysis of a large number of single dipole problems with simulated time courses and with background from authentic magnetoencephalography data.

  7. Structural constraints identified with covariation analysis in ribosomal RNA.

    PubMed

    Shang, Lei; Xu, Weijia; Ozer, Stuart; Gutell, Robin R

    2012-01-01

    Covariation analysis is used to identify those positions with similar patterns of sequence variation in an alignment of RNA sequences. These constraints on the evolution of two positions are usually associated with a base pair in a helix. While mutual information (MI) has been used to accurately predict an RNA secondary structure and a few of its tertiary interactions, early studies revealed that phylogenetic event counting methods are more sensitive and provide extra confidence in the prediction of base pairs. We developed a novel and powerful phylogenetic events counting method (PEC) for quantifying positional covariation with the Gutell lab's new RNA Comparative Analysis Database (rCAD). The PEC and MI-based methods each identify unique base pairs, and jointly identify many other base pairs. In total, both methods in combination with an N-best and helix-extension strategy identify the maximal number of base pairs. While covariation methods have effectively and accurately predicted RNAs secondary structure, only a few tertiary structure base pairs have been identified. Analysis presented herein and at the Gutell lab's Comparative RNA Web (CRW) Site reveal that the majority of these latter base pairs do not covary with one another. However, covariation analysis does reveal a weaker although significant covariation between sets of nucleotides that are in proximity in the three-dimensional RNA structure. This reveals that covariation analysis identifies other types of structural constraints beyond the two nucleotides that form a base pair.

  8. Recurrence Analysis of Eddy Covariance Fluxes

    NASA Astrophysics Data System (ADS)

    Lange, Holger; Flach, Milan; Foken, Thomas; Hauhs, Michael

    2015-04-01

    The eddy covariance (EC) method is one key method to quantify fluxes in biogeochemical cycles in general, and carbon and energy transport across the vegetation-atmosphere boundary layer in particular. EC data from the worldwide net of flux towers (Fluxnet) have also been used to validate biogeochemical models. The high resolution data are usually obtained at 20 Hz sampling rate but are affected by missing values and other restrictions. In this contribution, we investigate the nonlinear dynamics of EC fluxes using Recurrence Analysis (RA). High resolution data from the site DE-Bay (Waldstein-Weidenbrunnen) and fluxes calculated at half-hourly resolution from eight locations (part of the La Thuile dataset) provide a set of very long time series to analyze. After careful quality assessment and Fluxnet standard gapfilling pretreatment, we calculate properties and indicators of the recurrent structure based both on Recurrence Plots as well as Recurrence Networks. Time series of RA measures obtained from windows moving along the time axis are presented. Their interpretation is guided by three different questions: (1) Is RA able to discern periods where the (atmospheric) conditions are particularly suitable to obtain reliable EC fluxes? (2) Is RA capable to detect dynamical transitions (different behavior) beyond those obvious from visual inspection? (3) Does RA contribute to an understanding of the nonlinear synchronization between EC fluxes and atmospheric parameters, which is crucial for both improving carbon flux models as well for reliable interpolation of gaps? (4) Is RA able to recommend an optimal time resolution for measuring EC data and for analyzing EC fluxes? (5) Is it possible to detect non-trivial periodicities with a global RA? We will demonstrate that the answers to all five questions is affirmative, and that RA provides insights into EC dynamics not easily obtained otherwise.

  9. Structural covariance networks in the mouse brain.

    PubMed

    Pagani, Marco; Bifone, Angelo; Gozzi, Alessandro

    2016-04-01

    The presence of networks of correlation between regional gray matter volume as measured across subjects in a group of individuals has been consistently described in several human studies, an approach termed structural covariance MRI (scMRI). Complementary to prevalent brain mapping modalities like functional and diffusion-weighted imaging, the approach can provide precious insights into the mutual influence of trophic and plastic processes in health and pathological states. To investigate whether analogous scMRI networks are present in lower mammal species amenable to genetic and experimental manipulation such as the laboratory mouse, we employed high resolution morphoanatomical MRI in a large cohort of genetically-homogeneous wild-type mice (C57Bl6/J) and mapped scMRI networks using a seed-based approach. We show that the mouse brain exhibits robust homotopic scMRI networks in both primary and associative cortices, a finding corroborated by independent component analyses of cortical volumes. Subcortical structures also showed highly symmetric inter-hemispheric correlations, with evidence of distributed antero-posterior networks in diencephalic regions of the thalamus and hypothalamus. Hierarchical cluster analysis revealed six identifiable clusters of cortical and sub-cortical regions corresponding to previously described neuroanatomical systems. Our work documents the presence of homotopic cortical and subcortical scMRI networks in the mouse brain, thus supporting the use of this species to investigate the elusive biological and neuroanatomical underpinnings of scMRI network development and its derangement in neuropathological states. The identification of scMRI networks in genetically homogeneous inbred mice is consistent with the emerging view of a key role of environmental factors in shaping these correlational networks.

  10. Inflation in general covariant theory of gravity

    SciTech Connect

    Huang, Yongqing; Wang, Anzhong; Wu, Qiang E-mail: anzhong_wang@baylor.edu

    2012-10-01

    In this paper, we study inflation in the framework of the nonrelativistic general covariant theory of the Hořava-Lifshitz gravity with the projectability condition and an arbitrary coupling constant λ. We find that the Friedmann-Robterson-Walker (FRW) universe is necessarily flat in such a setup. We work out explicitly the linear perturbations of the flat FRW universe without specifying to a particular gauge, and find that the perturbations are different from those obtained in general relativity, because of the presence of the high-order spatial derivative terms. Applying the general formulas to a single scalar field, we show that in the sub-horizon regions, the metric and scalar field are tightly coupled and have the same oscillating frequencies. In the super-horizon regions, the perturbations become adiabatic, and the comoving curvature perturbation is constant. We also calculate the power spectra and indices of both the scalar and tensor perturbations, and express them explicitly in terms of the slow roll parameters and the coupling constants of the high-order spatial derivative terms. In particular, we find that the perturbations, of both scalar and tensor, are almost scale-invariant, and, with some reasonable assumptions on the coupling coefficients, the spectrum index of the tensor perturbation is the same as that given in the minimum scenario in general relativity (GR), whereas the index for scalar perturbation in general depends on λ and is different from the standard GR value. The ratio of the scalar and tensor power spectra depends on the high-order spatial derivative terms, and can be different from that of GR significantly.

  11. 24 CFR 983.206 - HAP contract amendments (to add or substitute contract units).

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 24 Housing and Urban Development 4 2011-04-01 2011-04-01 false HAP contract amendments (to add or... Contract § 983.206 HAP contract amendments (to add or substitute contract units). (a) Amendment to... substitute unit and must determine the reasonable rent for such unit. (b) Amendment to add contract units....

  12. 24 CFR 983.206 - HAP contract amendments (to add or substitute contract units).

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 24 Housing and Urban Development 4 2010-04-01 2010-04-01 false HAP contract amendments (to add or... Contract § 983.206 HAP contract amendments (to add or substitute contract units). (a) Amendment to... substitute unit and must determine the reasonable rent for such unit. (b) Amendment to add contract units....

  13. 12 CFR 502.60 - When will OTS adjust, add, waive, or eliminate a fee?

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 12 Banks and Banking 5 2010-01-01 2010-01-01 false When will OTS adjust, add, waive, or eliminate... TREASURY ASSESSMENTS AND FEES Fees § 502.60 When will OTS adjust, add, waive, or eliminate a fee? Under unusual circumstances, the Director may deem it necessary or appropriate to adjust, add, waive,...

  14. 12 CFR 502.60 - When will OTS adjust, add, waive, or eliminate a fee?

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 12 Banks and Banking 5 2011-01-01 2011-01-01 false When will OTS adjust, add, waive, or eliminate... TREASURY ASSESSMENTS AND FEES Fees § 502.60 When will OTS adjust, add, waive, or eliminate a fee? Under unusual circumstances, the Director may deem it necessary or appropriate to adjust, add, waive,...

  15. The Source for ADD/ADHD: Attention Deficit Disorder and Attention Deficit/Hyperactivity Disorder.

    ERIC Educational Resources Information Center

    Richard, Gail J.; Russell, Joy L.

    This book is intended for professionals who are responsible for designing and implementing educational programs for children with attention deficit disorders and attention deficit/hyperactivity disorder (ADD/ADHD). Chapters address: (1) myths and realities about ADD/ADHD; (2) definitions, disorders associated with ADD/ADHD, and federal educational…

  16. Pairwise additivity of energy components in protein-ligand binding: the HIV II protease-Indinavir case.

    PubMed

    Ucisik, Melek N; Dashti, Danial S; Faver, John C; Merz, Kenneth M

    2011-08-28

    An energy expansion (binding energy decomposition into n-body interaction terms for n ≥ 2) to express the receptor-ligand binding energy for the fragmented HIV II protease-Indinavir system is described to address the role of cooperativity in ligand binding. The outcome of this energy expansion is compared to the total receptor-ligand binding energy at the Hartree-Fock, density functional theory, and semiempirical levels of theory. We find that the sum of the pairwise interaction energies approximates the total binding energy to ∼82% for HF and to >95% for both the M06-L density functional and PM6-DH2 semiempirical method. The contribution of the three-body interactions amounts to 18.7%, 3.8%, and 1.4% for HF, M06-L, and PM6-DH2, respectively. We find that the expansion can be safely truncated after n=3. That is, the contribution of the interactions involving more than three parties to the total binding energy of Indinavir to the HIV II protease receptor is negligible. Overall, we find that the two-body terms represent a good approximation to the total binding energy of the system, which points to pairwise additivity in the present case. This basic principle of pairwise additivity is utilized in fragment-based drug design approaches and our results support its continued use. The present results can also aid in the validation of non-bonded terms contained within common force fields and in the correction of systematic errors in physics-based score functions. PMID:21895219

  17. Pairwise additivity of energy components in protein-ligand binding: The HIV II protease-Indinavir case

    PubMed Central

    Ucisik, Melek N.; Dashti, Danial S.; Faver, John C.; Merz, Kenneth M.

    2011-01-01

    An energy expansion (binding energy decomposition into n-body interaction terms for n ≥ 2) to express the receptor-ligand binding energy for the fragmented HIV II protease-Indinavir system is described to address the role of cooperativity in ligand binding. The outcome of this energy expansion is compared to the total receptor-ligand binding energy at the Hartree-Fock, density functional theory, and semiempirical levels of theory. We find that the sum of the pairwise interaction energies approximates the total binding energy to ∼82% for HF and to >95% for both the M06-L density functional and PM6-DH2 semiempirical method. The contribution of the three-body interactions amounts to 18.7%, 3.8%, and 1.4% for HF, M06-L, and PM6-DH2, respectively. We find that the expansion can be safely truncated after n = 3. That is, the contribution of the interactions involving more than three parties to the total binding energy of Indinavir to the HIV II protease receptor is negligible. Overall, we find that the two-body terms represent a good approximation to the total binding energy of the system, which points to pairwise additivity in the present case. This basic principle of pairwise additivity is utilized in fragment-based drug design approaches and our results support its continued use. The present results can also aid in the validation of non-bonded terms contained within common force fields and in the correction of systematic errors in physics-based score functions. PMID:21895219

  18. Bispectral pairwise interacting source analysis for identifying systems of cross-frequency interacting brain sources from electroencephalographic or magnetoencephalographic signals

    NASA Astrophysics Data System (ADS)

    Chella, Federico; Pizzella, Vittorio; Zappasodi, Filippo; Nolte, Guido; Marzetti, Laura

    2016-05-01

    Brain cognitive functions arise through the coordinated activity of several brain regions, which actually form complex dynamical systems operating at multiple frequencies. These systems often consist of interacting subsystems, whose characterization is of importance for a complete understanding of the brain interaction processes. To address this issue, we present a technique, namely the bispectral pairwise interacting source analysis (biPISA), for analyzing systems of cross-frequency interacting brain sources when multichannel electroencephalographic (EEG) or magnetoencephalographic (MEG) data are available. Specifically, the biPISA makes it possible to identify one or many subsystems of cross-frequency interacting sources by decomposing the antisymmetric components of the cross-bispectra between EEG or MEG signals, based on the assumption that interactions are pairwise. Thanks to the properties of the antisymmetric components of the cross-bispectra, biPISA is also robust to spurious interactions arising from mixing artifacts, i.e., volume conduction or field spread, which always affect EEG or MEG functional connectivity estimates. This method is an extension of the pairwise interacting source analysis (PISA), which was originally introduced for investigating interactions at the same frequency, to the study of cross-frequency interactions. The effectiveness of this approach is demonstrated in simulations for up to three interacting source pairs and for real MEG recordings of spontaneous brain activity. Simulations show that the performances of biPISA in estimating the phase difference between the interacting sources are affected by the increasing level of noise rather than by the number of the interacting subsystems. The analysis of real MEG data reveals an interaction between two pairs of sources of central mu and beta rhythms, localizing in the proximity of the left and right central sulci.

  19. Decomposed pairwise regression analysis of genetic and geographic distances reveals a metapopulation structure of stream-dwelling Dolly Varden charr.

    PubMed

    Koizumi, Itsuro; Yamamoto, Shoichiro; Maekawa, Koji

    2006-10-01

    Isolation by distance is usually tested by the correlation of genetic and geographic distances separating all pairwise populations' combinations. However, this method can be significantly biased by only a few highly diverged populations and lose the information of individual population. To detect outlier populations and investigate the relative strengths of gene flow and genetic drift for each population, we propose a decomposed pairwise regression analysis. This analysis was applied to the well-described one-dimensional stepping-stone system of stream-dwelling Dolly Varden charr (Salvelinus malma). When genetic and geographic distances were plotted for all pairs of 17 tributary populations, the correlation was significant but weak (r(2) = 0.184). Seven outlier populations were determined based on the systematic bias of the regression residuals, followed by Akaike's information criteria. The best model, 10 populations included, showed a strong pattern of isolation by distance (r(2) = 0.758), suggesting equilibrium between gene flow and genetic drift in these populations. Each outlier population was also analysed by plotting pairwise genetic and geographic distances against the 10 nonoutlier populations, and categorized into one of the three patterns: strong genetic drift, genetic drift with a limited gene flow and a high level of gene flow. These classifications were generally consistent with a priori predictions for each population (physical barrier, population size, anthropogenic impacts). Combined the genetic analysis with field observations, Dolly Varden in this river appeared to form a mainland-island or source-sink metapopulation structure. The generality of the method will merit many types of spatial genetic analyses.

  20. Hawking radiation, covariant boundary conditions, and vacuum states

    SciTech Connect

    Banerjee, Rabin; Kulkarni, Shailesh

    2009-04-15

    The basic characteristics of the covariant chiral current and the covariant chiral energy-momentum tensor are obtained from a chiral effective action. These results are used to justify the covariant boundary condition used in recent approaches of computing the Hawking flux from chiral gauge and gravitational anomalies. We also discuss a connection of our results with the conventional calculation of nonchiral currents and stress tensors in different (Unruh, Hartle-Hawking and Boulware) states.

  1. The importance of covariance in nuclear data uncertainty propagation studies

    SciTech Connect

    Benstead, J.

    2012-07-01

    A study has been undertaken to investigate what proportion of the uncertainty propagated through plutonium critical assembly calculations is due to the covariances between the fission cross section in different neutron energy groups. The uncertainties on k{sub eff} calculated show that the presence of covariances between the cross section in different neutron energy groups accounts for approximately 27-37% of the propagated uncertainty due to the plutonium fission cross section. This study also confirmed the validity of employing the sandwich equation, with associated sensitivity and covariance data, instead of a Monte Carlo sampling approach to calculating uncertainties for linearly varying systems. (authors)

  2. The effective colloid interaction in the Asakura-Oosawa model. Assessment of non-pairwise terms from the virial expansion.

    PubMed

    Santos, Andrés; López de Haro, Mariano; Fiumara, Giacomo; Saija, Franz

    2015-06-14

    The relevance of neglecting three- and four-body interactions in the coarse-grained version of the Asakura-Oosawa model is examined. A mapping between the first few virial coefficients of the binary nonadditive hard-sphere mixture representative of this model and those arising from the coarse-grained (pairwise) depletion potential approximation allows for a quantitative evaluation of the effect of such interactions. This turns out to be especially important for large size ratios and large reservoir polymer packing fractions.

  3. The effective colloid interaction in the Asakura-Oosawa model. Assessment of non-pairwise terms from the virial expansion.

    PubMed

    Santos, Andrés; López de Haro, Mariano; Fiumara, Giacomo; Saija, Franz

    2015-06-14

    The relevance of neglecting three- and four-body interactions in the coarse-grained version of the Asakura-Oosawa model is examined. A mapping between the first few virial coefficients of the binary nonadditive hard-sphere mixture representative of this model and those arising from the coarse-grained (pairwise) depletion potential approximation allows for a quantitative evaluation of the effect of such interactions. This turns out to be especially important for large size ratios and large reservoir polymer packing fractions. PMID:26071727

  4. Empirical State Error Covariance Matrix for Batch Estimation

    NASA Technical Reports Server (NTRS)

    Frisbee, Joe

    2015-01-01

    State estimation techniques effectively provide mean state estimates. However, the theoretical state error covariance matrices provided as part of these techniques often suffer from a lack of confidence in their ability to describe the uncertainty in the estimated states. By a reinterpretation of the equations involved in the weighted batch least squares algorithm, it is possible to directly arrive at an empirical state error covariance matrix. The proposed empirical state error covariance matrix will contain the effect of all error sources, known or not. This empirical error covariance matrix may be calculated as a side computation for each unique batch solution. Results based on the proposed technique will be presented for a simple, two observer and measurement error only problem.

  5. Optimal Estimation and Rank Detection for Sparse Spiked Covariance Matrices

    PubMed Central

    Cai, Tony; Ma, Zongming; Wu, Yihong

    2014-01-01

    This paper considers a sparse spiked covariancematrix model in the high-dimensional setting and studies the minimax estimation of the covariance matrix and the principal subspace as well as the minimax rank detection. The optimal rate of convergence for estimating the spiked covariance matrix under the spectral norm is established, which requires significantly different techniques from those for estimating other structured covariance matrices such as bandable or sparse covariance matrices. We also establish the minimax rate under the spectral norm for estimating the principal subspace, the primary object of interest in principal component analysis. In addition, the optimal rate for the rank detection boundary is obtained. This result also resolves the gap in a recent paper by Berthet and Rigollet [2] where the special case of rank one is considered. PMID:26257453

  6. Covariance Matrix Evaluations for Independent Mass Fission Yields

    SciTech Connect

    Terranova, N.; Serot, O.; Archier, P.; De Saint Jean, C.

    2015-01-15

    Recent needs for more accurate fission product yields include covariance information to allow improved uncertainty estimations of the parameters used by design codes. The aim of this work is to investigate the possibility to generate more reliable and complete uncertainty information on independent mass fission yields. Mass yields covariances are estimated through a convolution between the multi-Gaussian empirical model based on Brosa's fission modes, which describe the pre-neutron mass yields, and the average prompt neutron multiplicity curve. The covariance generation task has been approached using the Bayesian generalized least squared method through the CONRAD code. Preliminary results on mass yields variance-covariance matrix will be presented and discussed from physical grounds in the case of {sup 235}U(n{sub th}, f) and {sup 239}Pu(n{sub th}, f) reactions.

  7. Progress of Covariance Evaluation at the China Nuclear Data Center

    SciTech Connect

    Xu, R.; Zhang, Q.; Zhang, Y.; Liu, T.; Ge, Z.; Lu, H.; Sun, Z.; Yu, B.; Tang, G.

    2015-01-15

    Covariance evaluations at the China Nuclear Data Center focus on the cross sections of structural materials and actinides in the fast neutron energy range. In addition to the well-known Least-squares approach, a method based on the analysis of the sources of experimental uncertainties is especially introduced to generate a covariance matrix for a particular reaction for which multiple measurements are available. The scheme of the covariance evaluation flow is presented, and an example of n+{sup 90}Zr is given to illuminate the whole procedure. It is proven that the accuracy of measurements can be properly incorporated into the covariance and the long-standing small uncertainty problem can be avoided.

  8. True covariance simulation of the EUVE update filter

    NASA Technical Reports Server (NTRS)

    Bar-Itzhack, I. Y.; Harman, R. R.

    1990-01-01

    This paper presents a covariance analysis of the performance and sensitivity of the attitude determination Extended Kalman Filter (EKF) used by the On Board Computer (OBC) of the Extreme Ultra Violet Explorer (EUVE) spacecraft. The linearized dynamics and measurement equations of the error states are used in formulating the 'truth model' describing the real behavior of the systems involved. The 'design model' used by the OBC EKF is then obtained by reducing the order of the truth model. The covariance matrix of the EKF which uses the reduced order model is not the correct covariance of the EKF estimation error. A 'true covariance analysis' has to be carried out in order to evaluate the correct accuracy of the OBC generated estimates. The results of such analysis are presented which indicate both the performance and the sensitivity of the OBC EKF.

  9. True covariance simulation of the EUVE update filter

    NASA Technical Reports Server (NTRS)

    Bar-Itzhack, Itzhack Y.; Harman, R. R.

    1989-01-01

    A covariance analysis of the performance and sensitivity of the attitude determination Extended Kalman Filter (EKF) used by the On Board Computer (OBC) of the Extreme Ultra Violet Explorer (EUVE) spacecraft is presented. The linearized dynamics and measurement equations of the error states are derived which constitute the truth model describing the real behavior of the systems involved. The design model used by the OBC EKF is then obtained by reducing the order of the truth model. The covariance matrix of the EKF which uses the reduced order model is not the correct covariance of the EKF estimation error. A true covariance analysis has to be carried out in order to evaluate the correct accuracy of the OBC generated estimates. The results of such analysis are presented which indicate both the performance and the sensitivity of the OBC EKF.

  10. The effect of mood on detection of covariation.

    PubMed

    Braverman, Julia

    2005-11-01

    The purpose of this research is to explore the effect of mood on the detection of covariation. Predictions were based on an assumption that sad moods facilitate a data-driven information elaboration style and careful data scrutinizing, whereas happy moods predispose individuals toward top-down information processing and decrease the attention given to cognitive tasks. The primary dependent variable involved is the detection of covariation between facial features and personal information and the use of this information for evaluating new target faces. The findings support the view that sad mood facilitates both conscious and unconscious detection of covariation because it increases motivation to engage in the task. Limiting available cognitive resources does not eliminate the effect of mood on the detecting of covariation.

  11. Covariance Matrix Evaluations for Independent Mass Fission Yields

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

    Recent needs for more accurate fission product yields include covariance information to allow improved uncertainty estimations of the parameters used by design codes. The aim of this work is to investigate the possibility to generate more reliable and complete uncertainty information on independent mass fission yields. Mass yields covariances are estimated through a convolution between the multi-Gaussian empirical model based on Brosa's fission modes, which describe the pre-neutron mass yields, and the average prompt neutron multiplicity curve. The covariance generation task has been approached using the Bayesian generalized least squared method through the CONRAD code. Preliminary results on mass yields variance-covariance matrix will be presented and discussed from physical grounds in the case of 235U(nth, f) and 239Pu(nth, f) reactions.

  12. Does aquaculture add resilience to the global food system?

    PubMed

    Troell, Max; Naylor, Rosamond L; Metian, Marc; Beveridge, Malcolm; Tyedmers, Peter H; Folke, Carl; Arrow, Kenneth J; Barrett, Scott; Crépin, Anne-Sophie; Ehrlich, Paul R; Gren, Asa; Kautsky, Nils; Levin, Simon A; Nyborg, Karine; Österblom, Henrik; Polasky, Stephen; Scheffer, Marten; Walker, Brian H; Xepapadeas, Tasos; de Zeeuw, Aart

    2014-09-16

    Aquaculture is the fastest growing food sector and continues to expand alongside terrestrial crop and livestock production. Using portfolio theory as a conceptual framework, we explore how current interconnections between the aquaculture, crop, livestock, and fisheries sectors act as an impediment to, or an opportunity for, enhanced resilience in the global food system given increased resource scarcity and climate change. Aquaculture can potentially enhance resilience through improved resource use efficiencies and increased diversification of farmed species, locales of production, and feeding strategies. However, aquaculture's reliance on terrestrial crops and wild fish for feeds, its dependence on freshwater and land for culture sites, and its broad array of environmental impacts diminishes its ability to add resilience. Feeds for livestock and farmed fish that are fed rely largely on the same crops, although the fraction destined for aquaculture is presently small (∼4%). As demand for high-value fed aquaculture products grows, competition for these crops will also rise, as will the demand for wild fish as feed inputs. Many of these crops and forage fish are also consumed directly by humans and provide essential nutrition for low-income households. Their rising use in aquafeeds has the potential to increase price levels and volatility, worsening food insecurity among the most vulnerable populations. Although the diversification of global food production systems that includes aquaculture offers promise for enhanced resilience, such promise will not be realized if government policies fail to provide adequate incentives for resource efficiency, equity, and environmental protection. PMID:25136111

  13. Does aquaculture add resilience to the global food system?

    PubMed Central

    Troell, Max; Naylor, Rosamond L.; Metian, Marc; Beveridge, Malcolm; Tyedmers, Peter H.; Folke, Carl; Arrow, Kenneth J.; Barrett, Scott; Crépin, Anne-Sophie; Ehrlich, Paul R.; Gren, Åsa; Kautsky, Nils; Levin, Simon A.; Nyborg, Karine; Österblom, Henrik; Polasky, Stephen; Scheffer, Marten; Walker, Brian H.; Xepapadeas, Tasos; de Zeeuw, Aart

    2014-01-01

    Aquaculture is the fastest growing food sector and continues to expand alongside terrestrial crop and livestock production. Using portfolio theory as a conceptual framework, we explore how current interconnections between the aquaculture, crop, livestock, and fisheries sectors act as an impediment to, or an opportunity for, enhanced resilience in the global food system given increased resource scarcity and climate change. Aquaculture can potentially enhance resilience through improved resource use efficiencies and increased diversification of farmed species, locales of production, and feeding strategies. However, aquaculture’s reliance on terrestrial crops and wild fish for feeds, its dependence on freshwater and land for culture sites, and its broad array of environmental impacts diminishes its ability to add resilience. Feeds for livestock and farmed fish that are fed rely largely on the same crops, although the fraction destined for aquaculture is presently small (∼4%). As demand for high-value fed aquaculture products grows, competition for these crops will also rise, as will the demand for wild fish as feed inputs. Many of these crops and forage fish are also consumed directly by humans and provide essential nutrition for low-income households. Their rising use in aquafeeds has the potential to increase price levels and volatility, worsening food insecurity among the most vulnerable populations. Although the diversification of global food production systems that includes aquaculture offers promise for enhanced resilience, such promise will not be realized if government policies fail to provide adequate incentives for resource efficiency, equity, and environmental protection. PMID:25136111

  14. The IRBIT domain adds new functions to the AHCY family.

    PubMed

    Devogelaere, Benoit; Sammels, Eva; De Smedt, Humbert

    2008-07-01

    During the past few years, the IRBIT domain has emerged as an important add-on of S-adenosyl-L-homocystein hydrolase (AHCY), thereby creating the new family of AHCY-like proteins. In this review, we discuss the currently available data on this new family of proteins. We describe the IRBIT domain as a unique part of these proteins and give an overview of its regulation via (de)phosphorylation and proteolysis. The second part of this review is focused on the potential functions of the AHCY-like proteins. We propose that the IRBIT domain serves as an anchor for targeting AHCY-like proteins towards cytoplasmic targets. This leads to regulation of (i) intracellular Ca2+ via the inositol 1,4,5-trisphosphate receptor (IP3R), (ii) intracellular pH via the Na+/HCO3 - cotransporters (NBCs); whereas inactivation of the IRBIT domain induces (iii) nuclear translocation and regulation of AHCY activity. Dysfunction of AHCY-like proteins will disturb these three important functions, with various biological implications. PMID:18536033

  15. The IRBIT domain adds new functions to the AHCY family.

    PubMed

    Devogelaere, Benoit; Sammels, Eva; De Smedt, Humbert

    2008-07-01

    During the past few years, the IRBIT domain has emerged as an important add-on of S-adenosyl-L-homocystein hydrolase (AHCY), thereby creating the new family of AHCY-like proteins. In this review, we discuss the currently available data on this new family of proteins. We describe the IRBIT domain as a unique part of these proteins and give an overview of its regulation via (de)phosphorylation and proteolysis. The second part of this review is focused on the potential functions of the AHCY-like proteins. We propose that the IRBIT domain serves as an anchor for targeting AHCY-like proteins towards cytoplasmic targets. This leads to regulation of (i) intracellular Ca2+ via the inositol 1,4,5-trisphosphate receptor (IP3R), (ii) intracellular pH via the Na+/HCO3 - cotransporters (NBCs); whereas inactivation of the IRBIT domain induces (iii) nuclear translocation and regulation of AHCY activity. Dysfunction of AHCY-like proteins will disturb these three important functions, with various biological implications.

  16. Does aquaculture add resilience to the global food system?

    PubMed

    Troell, Max; Naylor, Rosamond L; Metian, Marc; Beveridge, Malcolm; Tyedmers, Peter H; Folke, Carl; Arrow, Kenneth J; Barrett, Scott; Crépin, Anne-Sophie; Ehrlich, Paul R; Gren, Asa; Kautsky, Nils; Levin, Simon A; Nyborg, Karine; Österblom, Henrik; Polasky, Stephen; Scheffer, Marten; Walker, Brian H; Xepapadeas, Tasos; de Zeeuw, Aart

    2014-09-16

    Aquaculture is the fastest growing food sector and continues to expand alongside terrestrial crop and livestock production. Using portfolio theory as a conceptual framework, we explore how current interconnections between the aquaculture, crop, livestock, and fisheries sectors act as an impediment to, or an opportunity for, enhanced resilience in the global food system given increased resource scarcity and climate change. Aquaculture can potentially enhance resilience through improved resource use efficiencies and increased diversification of farmed species, locales of production, and feeding strategies. However, aquaculture's reliance on terrestrial crops and wild fish for feeds, its dependence on freshwater and land for culture sites, and its broad array of environmental impacts diminishes its ability to add resilience. Feeds for livestock and farmed fish that are fed rely largely on the same crops, although the fraction destined for aquaculture is presently small (∼4%). As demand for high-value fed aquaculture products grows, competition for these crops will also rise, as will the demand for wild fish as feed inputs. Many of these crops and forage fish are also consumed directly by humans and provide essential nutrition for low-income households. Their rising use in aquafeeds has the potential to increase price levels and volatility, worsening food insecurity among the most vulnerable populations. Although the diversification of global food production systems that includes aquaculture offers promise for enhanced resilience, such promise will not be realized if government policies fail to provide adequate incentives for resource efficiency, equity, and environmental protection.

  17. Nonlinear effects in the correlation of tracks and covariance propagation

    NASA Astrophysics Data System (ADS)

    Sabol, C.; Hill, K.; Alfriend, K.; Sukut, T.

    2013-03-01

    Even though there are methods for the nonlinear propagation of the covariance the propagation of the covariance in current operational programs is based on the state transition matrix of the 1st variational equations, thus it is a linear propagation. If the measurement errors are zero mean Gaussian, the orbit errors, statistically represented by the covariance, are Gaussian. When the orbit errors become too large they are no longer Gaussian and not represented by the covariance. One use of the covariance is the association of uncorrelated tracks (UCTs). A UCT is an object tracked by a space surveillance system that does not correlate to another object in the space object data base. For an object to be entered into the data base three or more tracks must be correlated. Associating UCTs is a major challenge for a space surveillance system since every object entered into the space object catalog begins as a UCT. It has been proved that if the orbit errors are Gaussian, the error ellipsoid represented by the covariance is the optimum association volume. When the time between tracks becomes large, hours or even days, the orbit errors can become large and are no longer Gaussian, and this has a negative effect on the association of UCTs. This paper further investigates the nonlinear effects on the accuracy of the covariance for use in correlation. The use of the best coordinate system and the unscented Kalman Filter (UKF) for providing a more accurate covariance are investigated along with assessing how these approaches would result in the ability to correlate tracks that are further separated in time.

  18. Multilevel summation methods for efficient evaluation of long-range pairwise interactions in atomistic and coarse-grained molecular simulation.

    SciTech Connect

    Bond, Stephen D.

    2014-01-01

    The availability of efficient algorithms for long-range pairwise interactions is central to the success of numerous applications, ranging in scale from atomic-level modeling of materials to astrophysics. This report focuses on the implementation and analysis of the multilevel summation method for approximating long-range pairwise interactions. The computational cost of the multilevel summation method is proportional to the number of particles, N, which is an improvement over FFTbased methods whos cost is asymptotically proportional to N logN. In addition to approximating electrostatic forces, the multilevel summation method can be use to efficiently approximate convolutions with long-range kernels. As an application, we apply the multilevel summation method to a discretized integral equation formulation of the regularized generalized Poisson equation. Numerical results are presented using an implementation of the multilevel summation method in the LAMMPS software package. Preliminary results show that the computational cost of the method scales as expected, but there is still a need for further optimization.

  19. Label-free quantitative phosphoproteomics with novel pairwise abundance normalization reveals synergistic RAS and CIP2A signaling.

    PubMed

    Kauko, Otto; Laajala, Teemu Daniel; Jumppanen, Mikael; Hintsanen, Petteri; Suni, Veronika; Haapaniemi, Pekka; Corthals, Garry; Aittokallio, Tero; Westermarck, Jukka; Imanishi, Susumu Y

    2015-08-17

    Hyperactivated RAS drives progression of many human malignancies. However, oncogenic activity of RAS is dependent on simultaneous inactivation of protein phosphatase 2A (PP2A) activity. Although PP2A is known to regulate some of the RAS effector pathways, it has not been systematically assessed how these proteins functionally interact. Here we have analyzed phosphoproteomes regulated by either RAS or PP2A, by phosphopeptide enrichment followed by mass-spectrometry-based label-free quantification. To allow data normalization in situations where depletion of RAS or PP2A inhibitor CIP2A causes a large uni-directional change in the phosphopeptide abundance, we developed a novel normalization strategy, named pairwise normalization. This normalization is based on adjusting phosphopeptide abundances measured before and after the enrichment. The superior performance of the pairwise normalization was verified by various independent methods. Additionally, we demonstrate how the selected normalization method influences the downstream analyses and interpretation of pathway activities. Consequently, bioinformatics analysis of RAS and CIP2A regulated phosphoproteomes revealed a significant overlap in their functional pathways. This is most likely biologically meaningful as we observed a synergistic survival effect between CIP2A and RAS expression as well as KRAS activating mutations in TCGA pan-cancer data set, and synergistic relationship between CIP2A and KRAS depletion in colony growth assays.

  20. Pairwise decomposition of residue interaction energies using semiempirical quantum mechanical methods in studies of protein-ligand interaction.

    PubMed

    Raha, Kaushik; van der Vaart, Arjan J; Riley, Kevin E; Peters, Martin B; Westerhoff, Lance M; Kim, Hwanho; Merz, Kenneth M

    2005-05-11

    Pairwise decomposition of the interaction energy between molecules is shown to be a powerful tool that can increase our understanding of macromolecular recognition processes. Herein we calculate the pairwise decomposition of the interaction energy between the protein human carbonic anhydrase II (HCAII) and the fluorine-substituted ligand N-(4-sulfamylbenzoyl)benzylamine (SBB) using semiempirical quantum mechanics based methods. We dissect the interaction between the ligand and the protein by dividing the ligand and the protein into subsystems to understand the structure-activity relationships as a result of fluorine substitution. In particular, the off-diagonal elements of the Fock matrix that is composed of the interaction between the ionic core and the valence electrons and the exchange energy between the subsystems or atoms of interest is examined in detail. Our analysis reveals that the fluorine-substituted benzylamine group of SBB does not directly affect the binding energy. Rather, we find that the strength of the interaction between Thr199 of HCAII and the sulfamylbenzoyl group of SBB affects the binding affinity between the protein and the ligand. These observations underline the importance of the sulfonamide group in binding affinity as shown by previous experiments (Maren, T. H.; Wiley: C. E. J. Med. Chem. 1968, 11, 228-232). Moreover, our calculations qualitatively agree with the structural aspects of these protein-ligand complexes as determined by X-ray crystallography.

  1. Bayesian latent structure models with space-time-dependent covariates.

    PubMed

    Cai, Bo; Lawson, Andrew B; Hossain, Md Monir; Choi, Jungsoon

    2012-04-01

    Spatial-temporal data requires flexible regression models which can model the dependence of responses on space- and time-dependent covariates. In this paper, we describe a semiparametric space-time model from a Bayesian perspective. Nonlinear time dependence of covariates and the interactions among the covariates are constructed by local linear and piecewise linear models, allowing for more flexible orientation and position of the covariate plane by using time-varying basis functions. Space-varying covariate linkage coefficients are also incorporated to allow for the variation of space structures across the geographical location. The formulation accommodates uncertainty in the number and locations of the piecewise basis functions to characterize the global effects, spatially structured and unstructured random effects in relation to covariates. The proposed approach relies on variable selection-type mixture priors for uncertainty in the number and locations of basis functions and in the space-varying linkage coefficients. A simulation example is presented to evaluate the performance of the proposed approach with the competing models. A real data example is used for illustration.

  2. Gaussian covariance matrices for anisotropic galaxy clustering measurements

    NASA Astrophysics Data System (ADS)

    Grieb, Jan Niklas; Sánchez, Ariel G.; Salazar-Albornoz, Salvador; Dalla Vecchia, Claudio

    2016-04-01

    Measurements of the redshift-space galaxy clustering have been a prolific source of cosmological information in recent years. Accurate covariance estimates are an essential step for the validation of galaxy clustering models of the redshift-space two-point statistics. Usually, only a limited set of accurate N-body simulations is available. Thus, assessing the data covariance is not possible or only leads to a noisy estimate. Further, relying on simulated realizations of the survey data means that tests of the cosmology dependence of the covariance are expensive. With these points in mind, this work presents a simple theoretical model for the linear covariance of anisotropic galaxy clustering observations with synthetic catalogues. Considering the Legendre moments (`multipoles') of the two-point statistics and projections into wide bins of the line-of-sight parameter (`clustering wedges'), we describe the modelling of the covariance for these anisotropic clustering measurements for galaxy samples with a trivial geometry in the case of a Gaussian approximation of the clustering likelihood. As main result of this paper, we give the explicit formulae for Fourier and configuration space covariance matrices. To validate our model, we create synthetic halo occupation distribution galaxy catalogues by populating the haloes of an ensemble of large-volume N-body simulations. Using linear and non-linear input power spectra, we find very good agreement between the model predictions and the measurements on the synthetic catalogues in the quasi-linear regime.

  3. [Clinical research XIX. From clinical judgment to analysis of covariance].

    PubMed

    Pérez-Rodríguez, Marcela; Palacios-Cruz, Lino; Moreno, Jorge; Rivas-Ruiz, Rodolfo; Talavera, Juan O

    2014-01-01

    The analysis of covariance (ANCOVA) is based on the general linear models. This technique involves a regression model, often multiple, in which the outcome is presented as a continuous variable, the independent variables are qualitative or are introduced into the model as dummy or dichotomous variables, and factors for which adjustment is required (covariates) can be in any measurement level (i.e. nominal, ordinal or continuous). The maneuvers can be entered into the model as 1) fixed effects, or 2) random effects. The difference between fixed effects and random effects depends on the type of information we want from the analysis of the effects. ANCOVA effect separates the independent variables from the effect of co-variables, i.e., corrects the dependent variable eliminating the influence of covariates, given that these variables change in conjunction with maneuvers or treatments, affecting the outcome variable. ANCOVA should be done only if it meets three assumptions: 1) the relationship between the covariate and the outcome is linear, 2) there is homogeneity of slopes, and 3) the covariate and the independent variable are independent from each other.

  4. Summary of the Workshop on Neutron Cross Section Covariances

    SciTech Connect

    Smith, Donald L.

    2008-12-15

    A Workshop on Neutron Cross Section Covariances was held from June 24-27, 2008, in Port Jefferson, New York. This Workshop was organized by the National Nuclear Data Center, Brookhaven National Laboratory, to provide a forum for reporting on the status of the growing field of neutron cross section covariances for applications and for discussing future directions of the work in this field. The Workshop focused on the following four major topical areas: covariance methodology, recent covariance evaluations, covariance applications, and user perspectives. Attention was given to the entire spectrum of neutron cross section covariance concerns ranging from light nuclei to the actinides, and from the thermal energy region to 20 MeV. The papers presented at this conference explored topics ranging from fundamental nuclear physics concerns to very specific applications in advanced reactor design and nuclear criticality safety. This paper provides a summary of this workshop. Brief comments on the highlights of each Workshop contribution are provided. In addition, a perspective on the achievements and shortcomings of the Workshop as well as on the future direction of research in this field is offered.

  5. A three domain covariance framework for EEG/MEG data.

    PubMed

    Roś, Beata P; Bijma, Fetsje; de Gunst, Mathisca C M; de Munck, Jan C

    2015-10-01

    In this paper we introduce a covariance framework for the analysis of single subject EEG and MEG data that takes into account observed temporal stationarity on small time scales and trial-to-trial variations. We formulate a model for the covariance matrix, which is a Kronecker product of three components that correspond to space, time and epochs/trials, and consider maximum likelihood estimation of the unknown parameter values. An iterative algorithm that finds approximations of the maximum likelihood estimates is proposed. Our covariance model is applicable in a variety of cases where spontaneous EEG or MEG acts as source of noise and realistic noise covariance estimates are needed, such as in evoked activity studies, or where the properties of spontaneous EEG or MEG are themselves the topic of interest, like in combined EEG-fMRI experiments in which the correlation between EEG and fMRI signals is investigated. We use a simulation study to assess the performance of the estimator and investigate the influence of different assumptions about the covariance factors on the estimated covariance matrix and on its components. We apply our method to real EEG and MEG data sets.

  6. Covariance fitting of highly-correlated data in lattice QCD

    NASA Astrophysics Data System (ADS)

    Yoon, Boram; Jang, Yong-Chull; Jung, Chulwoo; Lee, Weonjong

    2013-07-01

    We address a frequently-asked question on the covariance fitting of highly-correlated data such as our B K data based on the SU(2) staggered chiral perturbation theory. Basically, the essence of the problem is that we do not have a fitting function accurate enough to fit extremely precise data. When eigenvalues of the covariance matrix are small, even a tiny error in the fitting function yields a large chi-square value and spoils the fitting procedure. We have applied a number of prescriptions available in the market, such as the cut-off method, modified covariance matrix method, and Bayesian method. We also propose a brand new method, the eigenmode shift (ES) method, which allows a full covariance fitting without modifying the covariance matrix at all. We provide a pedagogical example of data analysis in which the cut-off method manifestly fails in fitting, but the rest work well. In our case of the B K fitting, the diagonal approximation, the cut-off method, the ES method, and the Bayesian method work reasonably well in an engineering sense. However, interpreting the meaning of χ 2 is easier in the case of the ES method and the Bayesian method in a theoretical sense aesthetically. Hence, the ES method can be a useful alternative optional tool to check the systematic error caused by the covariance fitting procedure.

  7. Large Covariance Estimation by Thresholding Principal Orthogonal Complements

    PubMed Central

    Fan, Jianqing; Liao, Yuan; Mincheva, Martina

    2012-01-01

    This paper deals with the estimation of a high-dimensional covariance with a conditional sparsity structure and fast-diverging eigenvalues. By assuming sparse error covariance matrix in an approximate factor model, we allow for the presence of some cross-sectional correlation even after taking out common but unobservable factors. We introduce the Principal Orthogonal complEment Thresholding (POET) method to explore such an approximate factor structure with sparsity. The POET estimator includes the sample covariance matrix, the factor-based covariance matrix (Fan, Fan, and Lv, 2008), the thresholding estimator (Bickel and Levina, 2008) and the adaptive thresholding estimator (Cai and Liu, 2011) as specific examples. We provide mathematical insights when the factor analysis is approximately the same as the principal component analysis for high-dimensional data. The rates of convergence of the sparse residual covariance matrix and the conditional sparse covariance matrix are studied under various norms. It is shown that the impact of estimating the unknown factors vanishes as the dimensionality increases. The uniform rates of convergence for the unobserved factors and their factor loadings are derived. The asymptotic results are also verified by extensive simulation studies. Finally, a real data application on portfolio allocation is presented. PMID:24348088

  8. The Performance Analysis Based on SAR Sample Covariance Matrix

    PubMed Central

    Erten, Esra

    2012-01-01

    Multi-channel systems appear in several fields of application in science. In the Synthetic Aperture Radar (SAR) context, multi-channel systems may refer to different domains, as multi-polarization, multi-interferometric or multi-temporal data, or even a combination of them. Due to the inherent speckle phenomenon present in SAR images, the statistical description of the data is almost mandatory for its utilization. The complex images acquired over natural media present in general zero-mean circular Gaussian characteristics. In this case, second order statistics as the multi-channel covariance matrix fully describe the data. For practical situations however, the covariance matrix has to be estimated using a limited number of samples, and this sample covariance matrix follow the complex Wishart distribution. In this context, the eigendecomposition of the multi-channel covariance matrix has been shown in different areas of high relevance regarding the physical properties of the imaged scene. Specifically, the maximum eigenvalue of the covariance matrix has been frequently used in different applications as target or change detection, estimation of the dominant scattering mechanism in polarimetric data, moving target indication, etc. In this paper, the statistical behavior of the maximum eigenvalue derived from the eigendecomposition of the sample multi-channel covariance matrix in terms of multi-channel SAR images is simplified for SAR community. Validation is performed against simulated data and examples of estimation and detection problems using the analytical expressions are as well given. PMID:22736976

  9. Conservative Extensions of Linkage Disequilibrium Measures from Pairwise to Multi-loci and Algorithms for Optimal Tagging SNP Selection

    NASA Astrophysics Data System (ADS)

    Tarpine, Ryan; Lam, Fumei; Istrail, Sorin

    We present results on two classes of problems. The first result addresses the long standing open problem of finding unifying principles for Linkage Disequilibrium (LD) measures in population genetics (Lewontin 1964 [10], Hedrick 1987 [8], Devlin and Risch 1995 [5]). Two desirable properties have been proposed in the extensive literature on this topic and the mutual consistency between these properties has remained at the heart of statistical and algorithmic difficulties with haplotype and genome-wide association study analysis. The first axiom is (1) The ability to extend LD measures to multiple loci as a conservative extension of pairwise LD. All widely used LD measures are pairwise measures. Despite significant attempts, it is not clear how to naturally extend these measures to multiple loci, leading to a "curse of the pairwise". The second axiom is (2) The Interpretability of Intermediate Values. In this paper, we resolve this mutual consistency problem by introducing a new LD measure, directed informativeness overrightarrow{I} (the directed graph theoretic counterpart of the informativeness measure introduced by Halldorsson et al. [6]) and show that it satisfies both of the above axioms. We also show the maximum informative subset of tagging SNPs based on overrightarrow{I} can be computed exactly in polynomial time for realistic genome-wide data. Furthermore, we present polynomial time algorithms for optimal genome-wide tagging SNPs selection for a number of commonly used LD measures, under the bounded neighborhood assumption for linked pairs of SNPs. One problem in the area is the search for a quality measure for tagging SNPs selection that unifies the LD-based methods such as LD-select (implemented in Tagger, de Bakker et al. 2005 [4], Carlson et al. 2004 [3]) and the information-theoretic ones such as informativeness. We show that the objective function of the LD-select algorithm is the Minimal Dominating Set (MDS) on r 2-SNP graphs and show that we can

  10. Embedding objects during 3D printing to add new functionalities.

    PubMed

    Yuen, Po Ki

    2016-07-01

    A novel method for integrating and embedding objects to add new functionalities during 3D printing based on fused deposition modeling (FDM) (also known as fused filament fabrication or molten polymer deposition) is presented. Unlike typical 3D printing, FDM-based 3D printing could allow objects to be integrated and embedded during 3D printing and the FDM-based 3D printed devices do not typically require any post-processing and finishing. Thus, various fluidic devices with integrated glass cover slips or polystyrene films with and without an embedded porous membrane, and optical devices with embedded Corning(®) Fibrance™ Light-Diffusing Fiber were 3D printed to demonstrate the versatility of the FDM-based 3D printing and embedding method. Fluid perfusion flow experiments with a blue colored food dye solution were used to visually confirm fluid flow and/or fluid perfusion through the embedded porous membrane in the 3D printed fluidic devices. Similar to typical 3D printed devices, FDM-based 3D printed devices are translucent at best unless post-polishing is performed and optical transparency is highly desirable in any fluidic devices; integrated glass cover slips or polystyrene films would provide a perfect optical transparent window for observation and visualization. In addition, they also provide a compatible flat smooth surface for biological or biomolecular applications. The 3D printed fluidic devices with an embedded porous membrane are applicable to biological or chemical applications such as continuous perfusion cell culture or biocatalytic synthesis but without the need for any post-device assembly and finishing. The 3D printed devices with embedded Corning(®) Fibrance™ Light-Diffusing Fiber would have applications in display, illumination, or optical applications. Furthermore, the FDM-based 3D printing and embedding method could also be utilized to print casting molds with an integrated glass bottom for polydimethylsiloxane (PDMS) device replication

  11. Embedding objects during 3D printing to add new functionalities.

    PubMed

    Yuen, Po Ki

    2016-07-01

    A novel method for integrating and embedding objects to add new functionalities during 3D printing based on fused deposition modeling (FDM) (also known as fused filament fabrication or molten polymer deposition) is presented. Unlike typical 3D printing, FDM-based 3D printing could allow objects to be integrated and embedded during 3D printing and the FDM-based 3D printed devices do not typically require any post-processing and finishing. Thus, various fluidic devices with integrated glass cover slips or polystyrene films with and without an embedded porous membrane, and optical devices with embedded Corning(®) Fibrance™ Light-Diffusing Fiber were 3D printed to demonstrate the versatility of the FDM-based 3D printing and embedding method. Fluid perfusion flow experiments with a blue colored food dye solution were used to visually confirm fluid flow and/or fluid perfusion through the embedded porous membrane in the 3D printed fluidic devices. Similar to typical 3D printed devices, FDM-based 3D printed devices are translucent at best unless post-polishing is performed and optical transparency is highly desirable in any fluidic devices; integrated glass cover slips or polystyrene films would provide a perfect optical transparent window for observation and visualization. In addition, they also provide a compatible flat smooth surface for biological or biomolecular applications. The 3D printed fluidic devices with an embedded porous membrane are applicable to biological or chemical applications such as continuous perfusion cell culture or biocatalytic synthesis but without the need for any post-device assembly and finishing. The 3D printed devices with embedded Corning(®) Fibrance™ Light-Diffusing Fiber would have applications in display, illumination, or optical applications. Furthermore, the FDM-based 3D printing and embedding method could also be utilized to print casting molds with an integrated glass bottom for polydimethylsiloxane (PDMS) device replication

  12. An Empirical State Error Covariance Matrix for Batch State Estimation

    NASA Technical Reports Server (NTRS)

    Frisbee, Joseph H., Jr.

    2011-01-01

    State estimation techniques serve effectively to provide mean state estimates. However, the state error covariance matrices provided as part of these techniques suffer from some degree of lack of confidence in their ability to adequately describe the uncertainty in the estimated states. A specific problem with the traditional form of state error covariance matrices is that they represent only a mapping of the assumed observation error characteristics into the state space. Any errors that arise from other sources (environment modeling, precision, etc.) are not directly represented in a traditional, theoretical state error covariance matrix. Consider that an actual observation contains only measurement error and that an estimated observation contains all other errors, known and unknown. It then follows that a measurement residual (the difference between expected and observed measurements) contains all errors for that measurement. Therefore, a direct and appropriate inclusion of the actual measurement residuals in the state error covariance matrix will result in an empirical state error covariance matrix. This empirical state error covariance matrix will fully account for the error in the state estimate. By way of a literal reinterpretation of the equations involved in the weighted least squares estimation algorithm, it is possible to arrive at an appropriate, and formally correct, empirical state error covariance matrix. The first specific step of the method is to use the average form of the weighted measurement residual variance performance index rather than its usual total weighted residual form. Next it is helpful to interpret the solution to the normal equations as the average of a collection of sample vectors drawn from a hypothetical parent population. From here, using a standard statistical analysis approach, it directly follows as to how to determine the standard empirical state error covariance matrix. This matrix will contain the total uncertainty in the

  13. Newton law in covariant unimodular F(R) gravity

    NASA Astrophysics Data System (ADS)

    Nojiri, S.; Odintsov, S. D.; Oikonomou, V. K.

    2016-09-01

    We investigate the Newton law in the unimodular F(R) gravity. In the standard F(R) gravity, due to the extra scalar mode, there often appear the large corrections to the Newton law and such models are excluded by the experiments and/or the observations. In the unimodular F(R) gravity, however, the extra scalar mode become not to be dynamical due to the unimodular constraint and there is not any correction to the Newton law. Even in the unimodular Einstein gravity, the Newton law is reproduced but the mechanism is a little bit different from that in the unimodular F(R) gravity. We also investigate the unimodular F(R) gravity in the covariant formulation. In the covariant formulation, we include the three-form field. We show that the three-form field could not have any unwanted property, like ghost nor correction to the Newton law. In the covariant formulation, however, the above extra scalar mode becomes dynamical and could give a correction to the Newton law. We also show that there are no difference in the Friedmann-Robertson-Walker (FRW) dynamics in the non-covariant and covariant formulation.

  14. Neutron Cross Section Covariances: Recent Workshop and Advanced Reactor Systems

    NASA Astrophysics Data System (ADS)

    Oblozinsky, Pavel

    2008-10-01

    The recent Workshop on Neutron Cross Section Covariances, organized by BNL and attended by more than 50 scientists, responded to demands of many user groups, including advanced reactor systems, for uncertainty and correlation information. These demands can be explained by considerable progress in advanced neutronics simulation that probe covariances and their impact on design and operational margins of nuclear systems. The Workshop addressed evaluation methodology, recent evaluations as well as user's perspective, marking era of revival of covariance development that started some two years ago. We illustrate urgent demand for covariances in the case of advanced reactor systems, including fast actinide burner under GNEP, new generation of power reactors, Gen-IV, and reactors under AFCI. A common feature of many of these systems is presence of large amount of minor actinides and fission products that require improved nuclear data. Advanced simulation codes rely on quality input, to be obtained by adjusting the data library, such as the new ENDF/B-VII.0, by considering integral experiments as currently pursued by GNEP. To this end the nuclear data community is developing covariances for formidable amount of 112 materials (isotopes).

  15. Shrinkage Estimation of Varying Covariate Effects Based On Quantile Regression

    PubMed Central

    Peng, Limin; Xu, Jinfeng; Kutner, Nancy

    2013-01-01

    Varying covariate effects often manifest meaningful heterogeneity in covariate-response associations. In this paper, we adopt a quantile regression model that assumes linearity at a continuous range of quantile levels as a tool to explore such data dynamics. The consideration of potential non-constancy of covariate effects necessitates a new perspective for variable selection, which, under the assumed quantile regression model, is to retain variables that have effects on all quantiles of interest as well as those that influence only part of quantiles considered. Current work on l1-penalized quantile regression either does not concern varying covariate effects or may not produce consistent variable selection in the presence of covariates with partial effects, a practical scenario of interest. In this work, we propose a shrinkage approach by adopting a novel uniform adaptive LASSO penalty. The new approach enjoys easy implementation without requiring smoothing. Moreover, it can consistently identify the true model (uniformly across quantiles) and achieve the oracle estimation efficiency. We further extend the proposed shrinkage method to the case where responses are subject to random right censoring. Numerical studies confirm the theoretical results and support the utility of our proposals. PMID:25332515

  16. Covariant Lyapunov vectors of chaotic Rayleigh-Bénard convection.

    PubMed

    Xu, M; Paul, M R

    2016-06-01

    We explore numerically the high-dimensional spatiotemporal chaos of Rayleigh-Bénard convection using covariant Lyapunov vectors. We integrate the three-dimensional and time-dependent Boussinesq equations for a convection layer in a shallow square box geometry with an aspect ratio of 16 for very long times and for a range of Rayleigh numbers. We simultaneously integrate many copies of the tangent space equations in order to compute the covariant Lyapunov vectors. The dynamics explored has fractal dimensions of 20≲D_{λ}≲50, and we compute on the order of 150 covariant Lyapunov vectors. We use the covariant Lyapunov vectors to quantify the degree of hyperbolicity of the dynamics and the degree of Oseledets splitting and to explore the temporal and spatial dynamics of the Lyapunov vectors. Our results indicate that the chaotic dynamics of Rayleigh-Bénard convection is nonhyperbolic for all of the Rayleigh numbers we have explored. Our results yield that the entire spectrum of covariant Lyapunov vectors that we have computed are tangled as indicated by near tangencies with neighboring vectors. A closer look at the spatiotemporal features of the Lyapunov vectors suggests contributions from structures at two different length scales with differing amounts of localization. PMID:27415256

  17. Covariant Lyapunov vectors of chaotic Rayleigh-Bénard convection

    NASA Astrophysics Data System (ADS)

    Xu, M.; Paul, M. R.

    2016-06-01

    We explore numerically the high-dimensional spatiotemporal chaos of Rayleigh-Bénard convection using covariant Lyapunov vectors. We integrate the three-dimensional and time-dependent Boussinesq equations for a convection layer in a shallow square box geometry with an aspect ratio of 16 for very long times and for a range of Rayleigh numbers. We simultaneously integrate many copies of the tangent space equations in order to compute the covariant Lyapunov vectors. The dynamics explored has fractal dimensions of 20 ≲Dλ≲50 , and we compute on the order of 150 covariant Lyapunov vectors. We use the covariant Lyapunov vectors to quantify the degree of hyperbolicity of the dynamics and the degree of Oseledets splitting and to explore the temporal and spatial dynamics of the Lyapunov vectors. Our results indicate that the chaotic dynamics of Rayleigh-Bénard convection is nonhyperbolic for all of the Rayleigh numbers we have explored. Our results yield that the entire spectrum of covariant Lyapunov vectors that we have computed are tangled as indicated by near tangencies with neighboring vectors. A closer look at the spatiotemporal features of the Lyapunov vectors suggests contributions from structures at two different length scales with differing amounts of localization.

  18. Improving the modelling of redshift-space distortions - II. A pairwise velocity model covering large and small scales

    NASA Astrophysics Data System (ADS)

    Bianchi, Davide; Percival, Will J.; Bel, Julien

    2016-09-01

    We develop a model for the redshift-space correlation function, valid for both dark matter particles and halos on scales >5 h-1Mpc. In its simplest formulation, the model requires the knowledge of the first three moments of the line-of-sight pairwise velocity distribution plus two well-defined dimensionless parameters. The model is obtained by extending the Gaussian-Gaussianity prescription for the velocity distribution, developed in a previous paper, to a more general concept allowing for local skewness, which is required to match simulations. We compare the model with the well known Gaussian streaming model and the more recent Edgeworth streaming model. Using N-body simulations as a reference, we show that our model gives a precise description of the redshift-space clustering over a wider range of scales. We do not discuss the theoretical prescription for the evaluation of the velocity moments, leaving this topic to further investigation.

  19. Evaluation of intra- and interspecific divergence of satellite DNA sequences by nucleotide frequency calculation and pairwise sequence comparison

    PubMed Central

    2003-01-01

    Satellite DNA sequences are known to be highly variable and to have been subjected to concerted evolution that homogenizes member sequences within species. We have analyzed the mode of evolution of satellite DNA sequences in four fishes from the genus Diplodus by calculating the nucleotide frequency of the sequence array and the phylogenetic distances between member sequences. Calculation of nucleotide frequency and pairwise sequence comparison enabled us to characterize the divergence among member sequences in this satellite DNA family. The results suggest that the evolutionary rate of satellite DNA in D. bellottii is about two-fold greater than the average of the other three fishes, and that the sequence homogenization event occurred in D. puntazzo more recently than in the others. The procedures described here are effective to characterize mode of evolution of satellite DNA. PMID:12734555

  20. Evaluation of intra- and interspecific divergence of satellite DNA sequences by nucleotide frequency calculation and pairwise sequence comparison.

    PubMed

    Kato, Mikio

    2003-01-01

    Satellite DNA sequences are known to be highly variable and to have been subjected to concerted evolution that homogenizes member sequences within species. We have analyzed the mode of evolution of satellite DNA sequences in four fishes from the genus Diplodus by calculating the nucleotide frequency of the sequence array and the phylogenetic distances between member sequences. Calculation of nucleotide frequency and pairwise sequence comparison enabled us to characterize the divergence among member sequences in this satellite DNA family. The results suggest that the evolutionary rate of satellite DNA in D. bellottii is about two-fold greater than the average of the other three fishes, and that the sequence homogenization event occurred in D. puntazzo more recently than in the others. The procedures described here are effective to characterize mode of evolution of satellite DNA. PMID:12734555

  1. PhyPA: Phylogenetic method with pairwise sequence alignment outperforms likelihood methods in phylogenetics involving highly diverged sequences.

    PubMed

    Xia, Xuhua

    2016-09-01

    While pairwise sequence alignment (PSA) by dynamic programming is guaranteed to generate one of the optimal alignments, multiple sequence alignment (MSA) of highly divergent sequences often results in poorly aligned sequences, plaguing all subsequent phylogenetic analysis. One way to avoid this problem is to use only PSA to reconstruct phylogenetic trees, which can only be done with distance-based methods. I compared the accuracy of this new computational approach (named PhyPA for phylogenetics by pairwise alignment) against the maximum likelihood method using MSA (the ML+MSA approach), based on nucleotide, amino acid and codon sequences simulated with different topologies and tree lengths. I present a surprising discovery that the fast PhyPA method consistently outperforms the slow ML+MSA approach for highly diverged sequences even when all optimization options were turned on for the ML+MSA approach. Only when sequences are not highly diverged (i.e., when a reliable MSA can be obtained) does the ML+MSA approach outperforms PhyPA. The true topologies are always recovered by ML with the true alignment from the simulation. However, with MSA derived from alignment programs such as MAFFT or MUSCLE, the recovered topology consistently has higher likelihood than that for the true topology. Thus, the failure to recover the true topology by the ML+MSA is not because of insufficient search of tree space, but by the distortion of phylogenetic signal by MSA methods. I have implemented in DAMBE PhyPA and two approaches making use of multi-gene data sets to derive phylogenetic support for subtrees equivalent to resampling techniques such as bootstrapping and jackknifing.

  2. PhyPA: Phylogenetic method with pairwise sequence alignment outperforms likelihood methods in phylogenetics involving highly diverged sequences.

    PubMed

    Xia, Xuhua

    2016-09-01

    While pairwise sequence alignment (PSA) by dynamic programming is guaranteed to generate one of the optimal alignments, multiple sequence alignment (MSA) of highly divergent sequences often results in poorly aligned sequences, plaguing all subsequent phylogenetic analysis. One way to avoid this problem is to use only PSA to reconstruct phylogenetic trees, which can only be done with distance-based methods. I compared the accuracy of this new computational approach (named PhyPA for phylogenetics by pairwise alignment) against the maximum likelihood method using MSA (the ML+MSA approach), based on nucleotide, amino acid and codon sequences simulated with different topologies and tree lengths. I present a surprising discovery that the fast PhyPA method consistently outperforms the slow ML+MSA approach for highly diverged sequences even when all optimization options were turned on for the ML+MSA approach. Only when sequences are not highly diverged (i.e., when a reliable MSA can be obtained) does the ML+MSA approach outperforms PhyPA. The true topologies are always recovered by ML with the true alignment from the simulation. However, with MSA derived from alignment programs such as MAFFT or MUSCLE, the recovered topology consistently has higher likelihood than that for the true topology. Thus, the failure to recover the true topology by the ML+MSA is not because of insufficient search of tree space, but by the distortion of phylogenetic signal by MSA methods. I have implemented in DAMBE PhyPA and two approaches making use of multi-gene data sets to derive phylogenetic support for subtrees equivalent to resampling techniques such as bootstrapping and jackknifing. PMID:27377322

  3. Synchronization of pairwise-coupled, identical, relaxation oscillators based on metal-insulator phase transition devices: A model study

    NASA Astrophysics Data System (ADS)

    Parihar, Abhinav; Shukla, Nikhil; Datta, Suman; Raychowdhury, Arijit

    2015-02-01

    Computing with networks of synchronous oscillators has attracted wide-spread attention as novel materials and device topologies have enabled realization of compact, scalable and low-power coupled oscillatory systems. Of particular interest are compact and low-power relaxation oscillators that have been recently demonstrated using MIT (metal-insulator-transition) devices using properties of correlated oxides. Further the computational capability of pairwise coupled relaxation oscillators has also been shown to outperform traditional Boolean digital logic circuits. This paper presents an analysis of the dynamics and synchronization of a system of two such identical coupled relaxation oscillators implemented with MIT devices. We focus on two implementations of the oscillator: (a) a D-D configuration where complementary MIT devices (D) are connected in series to provide oscillations and (b) a D-R configuration where it is composed of a resistor (R) in series with a voltage-triggered state changing MIT device (D). The MIT device acts like a hysteresis resistor with different resistances in the two different states. The synchronization dynamics of such a system has been analyzed with purely charge based coupling using a resistive (RC) and a capacitive (CC) element in parallel. It is shown that in a D-D configuration symmetric, identical and capacitively coupled relaxation oscillator system synchronizes to an anti-phase locking state, whereas when coupled resistively the system locks in phase. Further, we demonstrate that for certain range of values of RC and CC, a bistable system is possible which can have potential applications in associative computing. In D-R configuration, we demonstrate the existence of rich dynamics including non-monotonic flows and complex phase relationship governed by the ratios of the coupling impedance. Finally, the developed theoretical formulations have been shown to explain experimentally measured waveforms of such pairwise coupled

  4. Pair-wise automatic registration of three-dimensional laser scanning data from historical building by created two-dimensional images

    NASA Astrophysics Data System (ADS)

    Altuntas, Cihan

    2014-05-01

    Registration of a point cloud is a great challenge in the process of laser scanning data. So far, many registration methods have been introduced by range data, integrated camera image, and a combination of them. Moreover, the automatic registration of three-dimensional point clouds is an important research topic in both geomatics and computer sciences. In this study, keypoint-based registration of point clouds was introduced. Intensity images were created from the laser scanning data, and then a pair-wise automatic registration was performed with the keypoints extracted from the intensity images by a scale invariant feature transform (SIFT) and affine SIFT (ASIFT). The results were compared with the iterative closest point, which has high accuracy and is the extensively adopted method for the pair-wise registration. Consequently, SIFT and ASIFT keypoints which were extracted from intensity images can be exploited to pair-wise automatic registration of the point clouds.

  5. FPGA-based Hyperspectral Covariance Coprocessor for Size, Weight, and Power Constrained Platforms

    NASA Astrophysics Data System (ADS)

    Kusinsky, David Alan

    , respectively. The coprocessor requires 45% less energy during processing. This research shows that FPGA-based acceleration of HSI data covariance computations is promising from a size, weight, and power perspective. Significant unused FPGA resources in the coprocessor's FPGA can be used to add additional HSI data processing operations and direct HSI camera interfacing in the future.

  6. Testing power-law cross-correlations: rescaled covariance test

    NASA Astrophysics Data System (ADS)

    Kristoufek, Ladislav

    2013-10-01

    We introduce a new test for detection of power-law cross-correlations among a pair of time series - the rescaled covariance test. The test is based on a power-law divergence of the covariance of the partial sums of the long-range cross-correlated processes. Utilizing a heteroskedasticity and auto-correlation robust estimator of the long-term covariance, we develop a test with desirable statistical properties which is well able to distinguish between short- and long-range cross-correlations. Such test should be used as a starting point in the analysis of long-range cross-correlations prior to an estimation of bivariate long-term memory parameters. As an application, we show that the relationship between volatility and traded volume, and volatility and returns in the financial markets can be labeled as the power-law cross-correlated one.

  7. Data Covariances from R-Matrix Analyses of Light Nuclei

    SciTech Connect

    Hale, G.M. Paris, M.W.

    2015-01-15

    After first reviewing the parametric description of light-element reactions in multichannel systems using R-matrix theory and features of the general LANL R-matrix analysis code EDA, we describe how its chi-square minimization procedure gives parameter covariances. This information is used, together with analytically calculated sensitivity derivatives, to obtain cross section covariances for all reactions included in the analysis by first-order error propagation. Examples are given of the covariances obtained for systems with few resonances ({sup 5}He) and with many resonances ({sup 13}C ). We discuss the prevalent problem of this method leading to cross section uncertainty estimates that are unreasonably small for large data sets. The answer to this problem appears to be using parameter confidence intervals in place of standard errors.

  8. Adaptive Covariance Inflation in a Multi-Resolution Assimilation Scheme

    NASA Astrophysics Data System (ADS)

    Hickmann, K. S.; Godinez, H. C.

    2015-12-01

    When forecasts are performed using modern data assimilation methods observation and model error can be scaledependent. During data assimilation the blending of error across scales can result in model divergence since largeerrors at one scale can be propagated across scales during the analysis step. Wavelet based multi-resolution analysiscan be used to separate scales in model and observations during the application of an ensemble Kalman filter. However,this separation is done at the cost of implementing an ensemble Kalman filter at each scale. This presents problemswhen tuning the covariance inflation parameter at each scale. We present a method to adaptively tune a scale dependentcovariance inflation vector based on balancing the covariance of the innovation and the covariance of observations ofthe ensemble. Our methods are demonstrated on a one dimensional Kuramoto-Sivashinsky (K-S) model known todemonstrate non-linear interactions between scales.

  9. Realistic Covariance Prediction for the Earth Science Constellation

    NASA Technical Reports Server (NTRS)

    Duncan, Matthew; Long, Anne

    2006-01-01

    Routine satellite operations for the Earth Science Constellation (ESC) include collision risk assessment between members of the constellation and other orbiting space objects. One component of the risk assessment process is computing the collision probability between two space objects. The collision probability is computed using Monte Carlo techniques as well as by numerically integrating relative state probability density functions. Each algorithm takes as inputs state vector and state vector uncertainty information for both objects. The state vector uncertainty information is expressed in terms of a covariance matrix. The collision probability computation is only as good as the inputs. Therefore, to obtain a collision calculation that is a useful decision-making metric, realistic covariance matrices must be used as inputs to the calculation. This paper describes the process used by the NASA/Goddard Space Flight Center's Earth Science Mission Operations Project to generate realistic covariance predictions for three of the Earth Science Constellation satellites: Aqua, Aura and Terra.

  10. Realistic Covariance Prediction For the Earth Science Constellations

    NASA Technical Reports Server (NTRS)

    Duncan, Matthew; Long, Anne

    2006-01-01

    Routine satellite operations for the Earth Science Constellations (ESC) include collision risk assessment between members of the constellations and other orbiting space objects. One component of the risk assessment process is computing the collision probability between two space objects. The collision probability is computed via Monte Carlo techniques as well as numerically integrating relative probability density functions. Each algorithm takes as inputs state vector and state vector uncertainty information for both objects. The state vector uncertainty information is expressed in terms of a covariance matrix. The collision probability computation is only as good as the inputs. Therefore, to obtain a collision calculation that is a useful decision-making metric, realistic covariance matrices must be used as inputs to the calculation. This paper describes the process used by NASA Goddard's Earth Science Mission Operations Project to generate realistic covariance predictions for three of the ESC satellites: Aqua, Aura, and Terra

  11. Evaluation of Covariances for Actinides and Light Elements at LANL

    SciTech Connect

    Kawano, T. Talou, P.; Young, P.G.; Hale, G.; Chadwick, M.B.; Little, R.C.

    2008-12-15

    Los Alamos evaluates covariances for the evaluated nuclear data library (ENDF), mainly for actinides above the resonance region and for light elements in the entire energy range. We also develop techniques to evaluate the covariance data, like Bayesian and least-squares fitting methods, which are important to explore the uncertainty information on different types of physical quantities such as elastic scattering angular distribution, or prompt neutron fission spectra. This paper summarizes our current activities of the covariance evaluation work at LANL, including the actinide and light element data mainly for criticality safety studies and transmutation technology. The Bayesian method based on the Kalman filter technique, which combines uncertainties in the theoretical model and experimental data, is discussed.

  12. Experience in using the covariances of some ENDF/B-V dosimetry cross sections: proposed improvements and addition of cross-reaction covariances

    SciTech Connect

    Fu, C.Y.; Hetrick, D.M.

    1982-01-01

    Recent ratio data, with carefully evaluated covariances, were combined with eleven of the ENDF/B-V dosimetry cross sections using the generalized least-squares method. The purpose was to improve these evaluated cross sections and covariances, as well as to generate values for the cross-reaction covariances. The results represent improved cross sections as well as realistic and usable covariances. The latter are necessary for meaningful intergral-differential comparisons and for spectrum unfolding.

  13. Exploration of regularized covariance estimates with analytical shrinkage intensity for producing invertible covariance matrices in high dimensional hyperspectral data

    SciTech Connect

    Walsh, Stephen J.; Tardiff, Mark F.

    2007-10-01

    Removing background from hyperspectral scenes is a common step in the process of searching for materials of interest. Some approaches to background subtraction use spectral library data and require invertible covariance matrices for each member of the library. This is challenging because the covariance matrix can be calculated but standard methods for estimating the inverse requires that the data set for each library member have many more spectral measurements than spectral channels, which is rarely the case. An alternative approach is called shrinkage estimation. This method is investigated as an approach to providing an invertible covariance matrix estimate in the case where the number of spectral measurements is less than the number of spectral channels. The approach is an analytic method for arriving at a target matrix and the shrinkage parameter that modify the existing covariance matrix for the data to make it invertible. The theory is discussed to develop different estimates. The resulting estimates are computed and inspected on a set of hyperspectral data. This technique shows some promise for arriving at an invertible covariance estimate for small hyperspectral data sets.

  14. Abnormalities in structural covariance of cortical gyrification in schizophrenia.

    PubMed

    Palaniyappan, Lena; Park, Bert; Balain, Vijender; Dangi, Raj; Liddle, Peter

    2015-07-01

    The highly convoluted shape of the adult human brain results from several well-coordinated maturational events that start from embryonic development and extend through the adult life span. Disturbances in these maturational events can result in various neurological and psychiatric disorders, resulting in abnormal patterns of morphological relationship among cortical structures (structural covariance). Structural covariance can be studied using graph theory-based approaches that evaluate topological properties of brain networks. Covariance-based graph metrics allow cross-sectional study of coordinated maturational relationship among brain regions. Disrupted gyrification of focal brain regions is a consistent feature of schizophrenia. However, it is unclear if these localized disturbances result from a failure of coordinated development of brain regions in schizophrenia. We studied the structural covariance of gyrification in a sample of 41 patients with schizophrenia and 40 healthy controls by constructing gyrification-based networks using a 3-dimensional index. We found that several key regions including anterior insula and dorsolateral prefrontal cortex show increased segregation in schizophrenia, alongside reduced segregation in somato-sensory and occipital regions. Patients also showed a lack of prominence of the distributed covariance (hubness) of cingulate cortex. The abnormal segregated folding pattern in the right peri-sylvian regions (insula and fronto-temporal cortex) was associated with greater severity of illness. The study of structural covariance in cortical folding supports the presence of subtle deviation in the coordinated development of cortical convolutions in schizophrenia. The heterogeneity in the severity of schizophrenia could be explained in part by aberrant trajectories of neurodevelopment.

  15. Covariance Matrix Estimation for the Cryo-EM Heterogeneity Problem*

    PubMed Central

    Katsevich, E.; Katsevich, A.; Singer, A.

    2015-01-01

    In cryo-electron microscopy (cryo-EM), a microscope generates a top view of a sample of randomly oriented copies of a molecule. The problem of single particle reconstruction (SPR) from cryo-EM is to use the resulting set of noisy two-dimensional projection images taken at unknown directions to reconstruct the three-dimensional (3D) structure of the molecule. In some situations, the molecule under examination exhibits structural variability, which poses a fundamental challenge in SPR. The heterogeneity problem is the task of mapping the space of conformational states of a molecule. It has been previously suggested that the leading eigenvectors of the covariance matrix of the 3D molecules can be used to solve the heterogeneity problem. Estimating the covariance matrix is challenging, since only projections of the molecules are observed, but not the molecules themselves. In this paper, we formulate a general problem of covariance estimation from noisy projections of samples. This problem has intimate connections with matrix completion problems and high-dimensional principal component analysis. We propose an estimator and prove its consistency. When there are finitely many heterogeneity classes, the spectrum of the estimated covariance matrix reveals the number of classes. The estimator can be found as the solution to a certain linear system. In the cryo-EM case, the linear operator to be inverted, which we term the projection covariance transform, is an important object in covariance estimation for tomographic problems involving structural variation. Inverting it involves applying a filter akin to the ramp filter in tomography. We design a basis in which this linear operator is sparse and thus can be tractably inverted despite its large size. We demonstrate via numerical experiments on synthetic datasets the robustness of our algorithm to high levels of noise. PMID:25699132

  16. Neutron Cross Section Covariances for Structural Materials and Fission Products

    SciTech Connect

    Hoblit, S.; Hoblit,S.; Cho,Y.-S.; Herman,M.; Mattoon,C.M.; Mughabghab,S.F.; Oblozinsky,P.; Pigni,M.T.; Sonzogni,A.A.

    2011-12-01

    We describe neutron cross section covariances for 78 structural materials and fission products produced for the new US evaluated nuclear reaction library ENDF/B-VII.1. Neutron incident energies cover full range from 10{sup -5} eV to 20 MeV and covariances are primarily provided for capture, elastic and inelastic scattering as well as (n,2n). The list of materials follows priorities defined by the Advanced Fuel Cycle Initiative, the major application being data adjustment for advanced fast reactor systems. Thus, in addition to 28 structural materials and 49 fission products, the list includes also {sup 23}Na which is important fast reactor coolant. Due to extensive amount of materials, we adopted a variety of methodologies depending on the priority of a specific material. In the resolved resonance region we primarily used resonance parameter uncertainties given in Atlas of Neutron Resonances and either applied the kernel approximation to propagate these uncertainties into cross section uncertainties or resorted to simplified estimates based on integral quantities. For several priority materials we adopted MF32 covariances produced by SAMMY at ORNL, modified by us by adding MF33 covariances to account for systematic uncertainties. In the fast neutron region we resorted to three methods. The most sophisticated was EMPIRE-KALMAN method which combines experimental data from EXFOR library with nuclear reaction modeling and least-squares fitting. The two other methods used simplified estimates, either based on the propagation of nuclear reaction model parameter uncertainties or on a dispersion analysis of central cross section values in recent evaluated data files. All covariances were subject to quality assurance procedures adopted recently by CSEWG. In addition, tools were developed to allow inspection of processed covariances and computed integral quantities, and for comparing these values to data from the Atlas and the astrophysics database KADoNiS.

  17. Covariance and gauge invariance in relativistic theories of gravity

    NASA Astrophysics Data System (ADS)

    Papini, Giorgio

    2014-04-01

    Any metric theory of gravity whose interaction with quantum particles is described by a covariant wave equation is equivalent to a vector theory that satisfies Maxwell-type equations identically. This result does not depend on any particular set of field equations for the metric tensor, but only on covariance. It is derived in the linear case, but can be extended to any order of approximation in the metric deviation. In this formulation of the interaction of gravity with matter, angular momentum and momentum are conserved locally.

  18. Realization of the optimal phase-covariant quantum cloning machine

    SciTech Connect

    Sciarrino, Fabio; De Martini, Francesco

    2005-12-15

    In several quantum information (QI) phenomena of large technological importance the information is carried by the phase of the quantum superposition states, or qubits. The phase-covariant cloning machine (PQCM) addresses precisely the problem of optimally copying these qubits with the largest attainable 'fidelity'. We present a general scheme which realizes the 1{yields}3 phase covariant cloning process by a combination of three different QI processes: the universal cloning, the NOT gate, and the projection over the symmetric subspace of the output qubits. The experimental implementation of a PQCM for polarization encoded qubits, the first ever realized with photons, is reported.

  19. Realization of the optimal phase-covariant quantum cloning machine

    NASA Astrophysics Data System (ADS)

    Sciarrino, Fabio; de Martini, Francesco

    2005-12-01

    In several quantum information (QI) phenomena of large technological importance the information is carried by the phase of the quantum superposition states, or qubits. The phase-covariant cloning machine (PQCM) addresses precisely the problem of optimally copying these qubits with the largest attainable “fidelity.” We present a general scheme which realizes the 1→3 phase covariant cloning process by a combination of three different QI processes: the universal cloning, the NOT gate, and the projection over the symmetric subspace of the output qubits. The experimental implementation of a PQCM for polarization encoded qubits, the first ever realized with photons, is reported.

  20. Vector order parameter in general relativity: Covariant equations

    SciTech Connect

    Meierovich, Boris E.

    2010-07-15

    Phase transitions with spontaneous symmetry breaking and vector order parameter are considered in multidimensional theory of general relativity. Covariant equations, describing the gravitational properties of topological defects, are derived. The topological defects are classified in accordance with the symmetry of the covariant derivative of the vector order parameter. The abilities of the derived equations are demonstrated in application to the braneworld concept. New solutions of the Einstein equations with a transverse vector order parameter are presented. In the vicinity of phase transition, the solutions are found analytically.

  1. Analysis of Compressible Mixing Layers Using Dilatational Covariances Model

    NASA Technical Reports Server (NTRS)

    Thangam, S.; Zhou, Y.; Ristorcelli, J. R.

    1996-01-01

    Compressible mixing layers are analyzed using a dilatational covariances model based on a pseudo-sound constitutive relation. The calculations are used to evaluate the different physical phenomena affecting compressible mixing layers. The rate of growth of the mixing layer is retarded by both the compressible dissipation and the pressure-dilatational covariances. The pressure-dilatational, essentially a nonequilibrium effect, reduces the amount of excess production over dissipation available for the turbulence energy growth. The pseudo-sound model also includes a history dependent portion: this is also investigated. All constants in the model and used in these computations are predicted by the theory.

  2. Neutron Resonance Parameters and Covariance Matrix of 239Pu

    SciTech Connect

    Derrien, Herve; Leal, Luiz C; Larson, Nancy M

    2008-08-01

    In order to obtain the resonance parameters in a single energy range and the corresponding covariance matrix, a reevaluation of 239Pu was performed with the code SAMMY. The most recent experimental data were analyzed or reanalyzed in the energy range thermal to 2.5 keV. The normalization of the fission cross section data was reconsidered by taking into account the most recent measurements of Weston et al. and Wagemans et al. A full resonance parameter covariance matrix was generated. The method used to obtain realistic uncertainties on the average cross section calculated by SAMMY or other processing codes was examined.

  3. Quasilocal conserved charges in a covariant theory of gravity.

    PubMed

    Kim, Wontae; Kulkarni, Shailesh; Yi, Sang-Heon

    2013-08-23

    In any generally covariant theory of gravity, we show the relationship between the linearized asymptotically conserved current and its nonlinear completion through the identically conserved current. Our formulation for conserved charges is based on the Lagrangian description, and so completely covariant. By using this result, we give a prescription to define quasilocal conserved charges in any higher derivative gravity. As applications of our approach, we demonstrate the angular momentum invariance along the radial direction of black holes and reproduce more efficiently the linearized potential on the asymptotic anti-de Sitter space.

  4. An Empirical State Error Covariance Matrix Orbit Determination Example

    NASA Technical Reports Server (NTRS)

    Frisbee, Joseph H., Jr.

    2015-01-01

    State estimation techniques serve effectively to provide mean state estimates. However, the state error covariance matrices provided as part of these techniques suffer from some degree of lack of confidence in their ability to adequately describe the uncertainty in the estimated states. A specific problem with the traditional form of state error covariance matrices is that they represent only a mapping of the assumed observation error characteristics into the state space. Any errors that arise from other sources (environment modeling, precision, etc.) are not directly represented in a traditional, theoretical state error covariance matrix. First, consider that an actual observation contains only measurement error and that an estimated observation contains all other errors, known and unknown. Then it follows that a measurement residual (the difference between expected and observed measurements) contains all errors for that measurement. Therefore, a direct and appropriate inclusion of the actual measurement residuals in the state error covariance matrix of the estimate will result in an empirical state error covariance matrix. This empirical state error covariance matrix will fully include all of the errors in the state estimate. The empirical error covariance matrix is determined from a literal reinterpretation of the equations involved in the weighted least squares estimation algorithm. It is a formally correct, empirical state error covariance matrix obtained through use of the average form of the weighted measurement residual variance performance index rather than the usual total weighted residual form. Based on its formulation, this matrix will contain the total uncertainty in the state estimate, regardless as to the source of the uncertainty and whether the source is anticipated or not. It is expected that the empirical error covariance matrix will give a better, statistical representation of the state error in poorly modeled systems or when sensor performance

  5. 7 CFR 360.500 - Petitions to add a taxon to the noxious weed list.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 5 2014-01-01 2014-01-01 false Petitions to add a taxon to the noxious weed list. 360... PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE NOXIOUS WEED REGULATIONS § 360.500 Petitions to add a taxon to the noxious weed list. A person may petition the Administrator to have a...

  6. 7 CFR 360.500 - Petitions to add a taxon to the noxious weed list.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 5 2011-01-01 2011-01-01 false Petitions to add a taxon to the noxious weed list. 360... PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE NOXIOUS WEED REGULATIONS § 360.500 Petitions to add a taxon to the noxious weed list. A person may petition the Administrator to have a...

  7. 7 CFR 360.500 - Petitions to add a taxon to the noxious weed list.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 5 2012-01-01 2012-01-01 false Petitions to add a taxon to the noxious weed list. 360... PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE NOXIOUS WEED REGULATIONS § 360.500 Petitions to add a taxon to the noxious weed list. A person may petition the Administrator to have a...

  8. 7 CFR 360.500 - Petitions to add a taxon to the noxious weed list.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 5 2013-01-01 2013-01-01 false Petitions to add a taxon to the noxious weed list. 360... PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE NOXIOUS WEED REGULATIONS § 360.500 Petitions to add a taxon to the noxious weed list. A person may petition the Administrator to have a...

  9. 75 FR 73075 - Notice of Motion To Add Exhibit to Petition for Declaratory Order and Complaint

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-11-29

    ... Energy Regulatory Commission Notice of Motion To Add Exhibit to Petition for Declaratory Order and... of Pella, Iowa (Complainant) filed a motion to add a document as Exhibit P-28 to its July 2, 2010... wishing to become a party must file a notice of intervention or motion to intervene, as appropriate....

  10. Measuring Narcissism within Add Health: The Development and Validation of a New Scale

    ERIC Educational Resources Information Center

    Davis, Mark S.; Brunell, Amy B.

    2012-01-01

    This study reports the development of a measure of narcissism within the National Longitudinal Study of Adolescent Health (Add Health) data set. In Study 1, items were selected from Wave III to form the Add Health Narcissism Scale (AHNS). These were factor analyzed, yielding a single factor comprised of five subscales. We correlated the AHNS and…

  11. Prevalence of Aggression and Defiance in Children with ADD/ADHD Tendencies

    ERIC Educational Resources Information Center

    Hill, Janella

    2011-01-01

    Attention Deficit Disorder (ADD) and Attention Deficit Hyperactivity Disorder (ADHD) appear to have become more prevalent in the past few years. Many children who display ADD/ADHD tendencies also display behaviors which cause problems in a classroom setting. Considering the fact that these behaviors could be displayed by the student population as…

  12. Cognitive Control and Attentional Selection in Adolescents with ADHD versus ADD

    ERIC Educational Resources Information Center

    Carr, Laurie; Henderson, John; Nigg, Joel T.

    2010-01-01

    An important research question is whether Attention Deficit Hyperactivity Disorder (ADHD) is related to early- or late-stage attentional control mechanisms and whether this differentiates a nonhyperactive subtype (ADD). This question was addressed in a sample of 145 ADD/ADHD and typically developing comparison adolescents (aged 13-17). Attentional…

  13. Gauge covariant fermion propagator in quenched, chirally symmetric quantum electrodynamics

    SciTech Connect

    Roberts, C.D.; Dong, Z.; Munczek, H.J.

    1995-08-01

    The chirally symmetric solution of the massless, quenched, Dyson-Schwinger equation (DSE) for the fermion propagator in three- and four-dimensional quantum electrodynamics was obtained. The DSEs are a valuable nonperturbative tool for studying field theories. In recent years a good deal of progress was made in addressing the limitations of the DSE approach in the study of Abelian gauge theories. Key to this progress is an understanding of the role of the dressed fermion/gauge-boson vertex in ensuring gauge covariance and multiplicative renormalizability of the solution of the fermion DSE. The solutions we obtain are manifestly gauge covariant and a general gauge covariance constraint on the fermion/gauge-boson vertex is presented, which motivates a vertex Ansatz that, for the first time, both satisfies the Ward identity when the fermion self-mass is zero and ensures gauge covariance of the fermion propagator. This research facilitates gauge-invariant, nonperturbative studies of continuum quantum electrodynamics and has already been used by others in studies of the chiral phase transition.

  14. Alternative Test Criteria in Covariance Structure Analysis: A Unified Approach.

    ERIC Educational Resources Information Center

    Satorra, Albert

    1989-01-01

    Within covariance structural analysis, a unified approach to asymptotic theory of alternative test criteria for testing parametric restrictions is provided. More general statistics for addressing the case where the discrepancy function is not asymptotically optimal, and issues concerning power analysis and the asymptotic theory of testing-related…

  15. Altered Cerebral Blood Flow Covariance Network in Schizophrenia

    PubMed Central

    Liu, Feng; Zhuo, Chuanjun; Yu, Chunshui

    2016-01-01

    Many studies have shown abnormal cerebral blood flow (CBF) in schizophrenia; however, it remains unclear how topological properties of CBF network are altered in this disorder. Here, arterial spin labeling (ASL) MRI was employed to measure resting-state CBF in 96 schizophrenia patients and 91 healthy controls. CBF covariance network of each group was constructed by calculating across-subject CBF covariance between 90 brain regions. Graph theory was used to compare intergroup differences in global and nodal topological measures of the network. Both schizophrenia patients and healthy controls had small-world topology in CBF covariance networks, implying an optimal balance between functional segregation and integration. Compared with healthy controls, schizophrenia patients showed reduced small-worldness, normalized clustering coefficient and local efficiency of the network, suggesting a shift toward randomized network topology in schizophrenia. Furthermore, schizophrenia patients exhibited altered nodal centrality in the perceptual-, affective-, language-, and spatial-related regions, indicating functional disturbance of these systems in schizophrenia. This study demonstrated for the first time that schizophrenia patients have disrupted topological properties in CBF covariance network, which provides a new perspective (efficiency of blood flow distribution between brain regions) for understanding neural mechanisms of schizophrenia. PMID:27445677

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

    ERIC Educational Resources Information Center

    Woods, Rebecca J.; Wilcox, Teresa

    2010-01-01

    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…

  17. Eddy Covariance Measurements of the Sea-Spray Aerosol Flu

    NASA Astrophysics Data System (ADS)

    Brooks, I. M.; Norris, S. J.; Yelland, M. J.; Pascal, R. W.; Prytherch, J.

    2015-12-01

    Historically, almost all estimates of the sea-spray aerosol source flux have been inferred through various indirect methods. Direct estimates via eddy covariance have been attempted by only a handful of studies, most of which measured only the total number flux, or achieved rather coarse size segregation. Applying eddy covariance to the measurement of sea-spray fluxes is challenging: most instrumentation must be located in a laboratory space requiring long sample lines to an inlet collocated with a sonic anemometer; however, larger particles are easily lost to the walls of the sample line. Marine particle concentrations are generally low, requiring a high sample volume to achieve adequate statistics. The highly hygroscopic nature of sea salt means particles change size rapidly with fluctuations in relative humidity; this introduces an apparent bias in flux measurements if particles are sized at ambient humidity. The Compact Lightweight Aerosol Spectrometer Probe (CLASP) was developed specifically to make high rate measurements of aerosol size distributions for use in eddy covariance measurements, and the instrument and data processing and analysis techniques have been refined over the course of several projects. Here we will review some of the issues and limitations related to making eddy covariance measurements of the sea spray source flux over the open ocean, summarise some key results from the last decade, and present new results from a 3-year long ship-based measurement campaign as part of the WAGES project. Finally we will consider requirements for future progress.

  18. Covariance matrices for use in criticality safety predictability studies

    SciTech Connect

    Derrien, H.; Larson, N.M.; Leal, L.C.

    1997-09-01

    Criticality predictability applications require as input the best available information on fissile and other nuclides. In recent years important work has been performed in the analysis of neutron transmission and cross-section data for fissile nuclei in the resonance region by using the computer code SAMMY. The code uses Bayes method (a form of generalized least squares) for sequential analyses of several sets of experimental data. Values for Reich-Moore resonance parameters, their covariances, and the derivatives with respect to the adjusted parameters (data sensitivities) are obtained. In general, the parameter file contains several thousand values and the dimension of the covariance matrices is correspondingly large. These matrices are not reported in the current evaluated data files due to their large dimensions and to the inadequacy of the file formats. The present work has two goals: the first is to calculate the covariances of group-averaged cross sections from the covariance files generated by SAMMY, because these can be more readily utilized in criticality predictability calculations. The second goal is to propose a more practical interface between SAMMY and the evaluated files. Examples are given for {sup 235}U in the popular 199- and 238-group structures, using the latest ORNL evaluation of the {sup 235}U resonance parameters.

  19. Performance of Four Multivariate Tests under Variance-Covariance Heteroscedasticity.

    ERIC Educational Resources Information Center

    Tang, K. Linda; Algina, James

    1993-01-01

    Type I error rates of four multivariate tests (Pilai-Bartlett trace, Johansen's test, James' first-order test, and James' second-order test) were compared for heterogeneous covariance matrices in 360 simulated experiments. The superior performance of Johansen's test and James' second-order test is discussed. (SLD)

  20. Analyzing Multivariate Repeated Measures Designs When Covariance Matrices Are Heterogeneous.

    ERIC Educational Resources Information Center

    Lix, Lisa M.; And Others

    Methods for the analysis of within-subjects effects in multivariate groups by trials repeated measures designs are considered in the presence of heteroscedasticity of the group variance-covariance matrices and multivariate nonnormality. Under a doubly multivariate model approach to hypothesis testing, within-subjects main and interaction effect…

  1. Testing Repeated Measures Hypotheses When Covariance Matrices Are Heterogeneous.

    ERIC Educational Resources Information Center

    Keselman, H. J.; And Others

    1993-01-01

    This article shows how a multivariate approximate degrees of freedom procedure based on the Welch-James procedure as simplified by S. Johansen (1980) can be applied to the analysis of repeated measures designs without assuming covariance homogeneity. A Monte Carlo study illustrates the approach. (SLD)

  2. RNA search with decision trees and partial covariance models.

    PubMed

    Smith, Jennifer A

    2009-01-01

    The use of partial covariance models to search for RNA family members in genomic sequence databases is explored. The partial models are formed from contiguous subranges of the overall RNA family multiple alignment columns. A binary decision-tree framework is presented for choosing the order to apply the partial models and the score thresholds on which to make the decisions. The decision trees are chosen to minimize computation time subject to the constraint that all of the training sequences are passed to the full covariance model for final evaluation. Computational intelligence methods are suggested to select the decision tree since the tree can be quite complex and there is no obvious method to build the tree in these cases. Experimental results from seven RNA families shows execution times of 0.066-0.268 relative to using the full covariance model alone. Tests on the full sets of known sequences for each family show that at least 95 percent of these sequences are found for two families and 100 percent for five others. Since the full covariance model is run on all sequences accepted by the partial model decision tree, the false alarm rate is at least as low as that of the full model alone.

  3. Triangular covariance factorizations for. Ph.D. Thesis. - Calif. Univ.

    NASA Technical Reports Server (NTRS)

    Thornton, C. L.

    1976-01-01

    An improved computational form of the discrete Kalman filter is derived using an upper triangular factorization of the error covariance matrix. The covariance P is factored such that P = UDUT where U is unit upper triangular and D is diagonal. Recursions are developed for propagating the U-D covariance factors together with the corresponding state estimate. The resulting algorithm, referred to as the U-D filter, combines the superior numerical precision of square root filtering techniques with an efficiency comparable to that of Kalman's original formula. Moreover, this method is easily implemented and involves no more computer storage than the Kalman algorithm. These characteristics make the U-D method an attractive realtime filtering technique. A new covariance error analysis technique is obtained from an extension of the U-D filter equations. This evaluation method is flexible and efficient and may provide significantly improved numerical results. Cost comparisons show that for a large class of problems the U-D evaluation algorithm is noticeably less expensive than conventional error analysis methods.

  4. Effect on Prediction when Modeling Covariates in Bayesian Nonparametric Models.

    PubMed

    Cruz-Marcelo, Alejandro; Rosner, Gary L; Müller, Peter; Stewart, Clinton F

    2013-04-01

    In biomedical research, it is often of interest to characterize biologic processes giving rise to observations and to make predictions of future observations. Bayesian nonparametric methods provide a means for carrying out Bayesian inference making as few assumptions about restrictive parametric models as possible. There are several proposals in the literature for extending Bayesian nonparametric models to include dependence on covariates. Limited attention, however, has been directed to the following two aspects. In this article, we examine the effect on fitting and predictive performance of incorporating covariates in a class of Bayesian nonparametric models by one of two primary ways: either in the weights or in the locations of a discrete random probability measure. We show that different strategies for incorporating continuous covariates in Bayesian nonparametric models can result in big differences when used for prediction, even though they lead to otherwise similar posterior inferences. When one needs the predictive density, as in optimal design, and this density is a mixture, it is better to make the weights depend on the covariates. We demonstrate these points via a simulated data example and in an application in which one wants to determine the optimal dose of an anticancer drug used in pediatric oncology. PMID:23687472

  5. A Review of Nonparametric Alternatives to Analysis of Covariance.

    ERIC Educational Resources Information Center

    Olejnik, Stephen F.; Algina, James

    1985-01-01

    Five distribution-free alternatives to parametric analysis of covariance are presented and demonstrated: Quade's distribution-free test, Puri and Sen's solution, McSweeney and Porter's rank transformation, Burnett and Barr's rank difference scores, and Shirley's general linear model solution. The results of simulation studies regarding Type I…

  6. A Review of Nonparametric Alternatives to Analysis of Covariance.

    ERIC Educational Resources Information Center

    Olejnik, Stephen F.; Algina, James

    Five distribution-free alternatives to parametric analysis of covariance (ANCOVA) are presented and demonstrated using a specific data example. The procedures considered are those suggested by Quade (1967); Puri and Sen (1969); McSweeney and Porter (1971); Burnett and Barr (1978); and Shirley (1981). The results of simulation studies investigating…

  7. Proportional Hazards Model with Covariate Measurement Error and Instrumental Variables

    PubMed Central

    Song, Xiao; Wang, Ching-Yun

    2014-01-01

    In biomedical studies, covariates with measurement error may occur in survival data. Existing approaches mostly require certain replications on the error-contaminated covariates, which may not be available in the data. In this paper, we develop a simple nonparametric correction approach for estimation of the regression parameters in the proportional hazards model using a subset of the sample where instrumental variables are observed. The instrumental variables are related to the covariates through a general nonparametric model, and no distributional assumptions are placed on the error and the underlying true covariates. We further propose a novel generalized methods of moments nonparametric correction estimator to improve the efficiency over the simple correction approach. The efficiency gain can be substantial when the calibration subsample is small compared to the whole sample. The estimators are shown to be consistent and asymptotically normal. Performance of the estimators is evaluated via simulation studies and by an application to data from an HIV clinical trial. Estimation of the baseline hazard function is not addressed. PMID:25663724

  8. Block diagonal representations for covariance based anomalous change detectors

    SciTech Connect

    Matsekh, Anna; Theiler, James

    2009-01-01

    Change detection methods are of crucial importance in many remote sensing applications such as monitoring and surveillance, where the goal is to identify and separate changes of interest from pervasive changes inevitably present in images taken at different times and in different environmental and illumination conditions. Anomalous change detection (ACD) methods aim to identify rare, unusual, or anomalous changes among the changes of interest. Covariance-based ACD methods provide a powerful tool for detection of unusual changes in hyper-spectral images. In this paper we study the properties of the eigenvalue spectra of a family of ACD matrices in order to better understand the algebraic and numerical behavior of the covariance-based quadratic ACD methods. We propose to use singular vectors of covariance matrices of two hyper-spectral images in whitened coordinates for obtaining block-diagonal representations of the matrices of quadratic ACD methods. SVD transformation gives an equivalent representation of ACD matrices in compact block-diagonal form. In the paper we show that the eigenvalue spectrum of a block-diagonal ACD matrix can be identified analytically as a function of the singular value spectrum of the corresponding covariance matrix in whitened coordinates.

  9. Students' Notions regarding "Covariance" of a Physical Theory

    ERIC Educational Resources Information Center

    Bandyopadhyay, Atanu; Kumar, Arvind

    2010-01-01

    A physical theory is said to be covariant with respect to a certain class of transformations when its basic equations retain their "form" under those transformations. It is one of the basic notions encountered in physics, particularly in the domain of relativity. In this paper we study in some detail how students deal with this notion in different…

  10. On variance estimate for covariate adjustment by propensity score analysis.

    PubMed

    Zou, Baiming; Zou, Fei; Shuster, Jonathan J; Tighe, Patrick J; Koch, Gary G; Zhou, Haibo

    2016-09-10

    Propensity score (PS) methods have been used extensively to adjust for confounding factors in the statistical analysis of observational data in comparative effectiveness research. There are four major PS-based adjustment approaches: PS matching, PS stratification, covariate adjustment by PS, and PS-based inverse probability weighting. Though covariate adjustment by PS is one of the most frequently used PS-based methods in clinical research, the conventional variance estimation of the treatment effects estimate under covariate adjustment by PS is biased. As Stampf et al. have shown, this bias in variance estimation is likely to lead to invalid statistical inference and could result in erroneous public health conclusions (e.g., food and drug safety and adverse events surveillance). To address this issue, we propose a two-stage analytic procedure to develop a valid variance estimator for the covariate adjustment by PS analysis strategy. We also carry out a simple empirical bootstrap resampling scheme. Both proposed procedures are implemented in an R function for public use. Extensive simulation results demonstrate the bias in the conventional variance estimator and show that both proposed variance estimators offer valid estimates for the true variance, and they are robust to complex confounding structures. The proposed methods are illustrated for a post-surgery pain study. Copyright © 2016 John Wiley & Sons, Ltd. PMID:26999553

  11. Covariance Structure Models for Gene Expression Microarray Data

    ERIC Educational Resources Information Center

    Xie, Jun; Bentler, Peter M.

    2003-01-01

    Covariance structure models are applied to gene expression data using a factor model, a path model, and their combination. The factor model is based on a few factors that capture most of the expression information. A common factor of a group of genes may represent a common protein factor for the transcript of the co-expressed genes, and hence, it…

  12. Treatment decisions based on scalar and functional baseline covariates.

    PubMed

    Ciarleglio, Adam; Petkova, Eva; Ogden, R Todd; Tarpey, Thaddeus

    2015-12-01

    The amount and complexity of patient-level data being collected in randomized-controlled trials offer both opportunities and challenges for developing personalized rules for assigning treatment for a given disease or ailment. For example, trials examining treatments for major depressive disorder are not only collecting typical baseline data such as age, gender, or scores on various tests, but also data that measure the structure and function of the brain such as images from magnetic resonance imaging (MRI), functional MRI (fMRI), or electroencephalography (EEG). These latter types of data have an inherent structure and may be considered as functional data. We propose an approach that uses baseline covariates, both scalars and functions, to aid in the selection of an optimal treatment. In addition to providing information on which treatment should be selected for a new patient, the estimated regime has the potential to provide insight into the relationship between treatment response and the set of baseline covariates. Our approach can be viewed as an extension of "advantage learning" to include both scalar and functional covariates. We describe our method and how to implement it using existing software. Empirical performance of our method is evaluated with simulated data in a variety of settings and also applied to data arising from a study of patients with major depressive disorder from whom baseline scalar covariates as well as functional data from EEG are available.

  13. Altered Cerebral Blood Flow Covariance Network in Schizophrenia.

    PubMed

    Liu, Feng; Zhuo, Chuanjun; Yu, Chunshui

    2016-01-01

    Many studies have shown abnormal cerebral blood flow (CBF) in schizophrenia; however, it remains unclear how topological properties of CBF network are altered in this disorder. Here, arterial spin labeling (ASL) MRI was employed to measure resting-state CBF in 96 schizophrenia patients and 91 healthy controls. CBF covariance network of each group was constructed by calculating across-subject CBF covariance between 90 brain regions. Graph theory was used to compare intergroup differences in global and nodal topological measures of the network. Both schizophrenia patients and healthy controls had small-world topology in CBF covariance networks, implying an optimal balance between functional segregation and integration. Compared with healthy controls, schizophrenia patients showed reduced small-worldness, normalized clustering coefficient and local efficiency of the network, suggesting a shift toward randomized network topology in schizophrenia. Furthermore, schizophrenia patients exhibited altered nodal centrality in the perceptual-, affective-, language-, and spatial-related regions, indicating functional disturbance of these systems in schizophrenia. This study demonstrated for the first time that schizophrenia patients have disrupted topological properties in CBF covariance network, which provides a new perspective (efficiency of blood flow distribution between brain regions) for understanding neural mechanisms of schizophrenia. PMID:27445677

  14. Latent Variable Models of Genotype-Environment Covariance.

    ERIC Educational Resources Information Center

    Hershberger, Scott L.

    2003-01-01

    Results of a study involving 136 pairs of identical twins reared together, 175 pairs of fraternal twins reared together, 83 pairs of identical twins reared apart, and 182 pairs of fraternal twins reared apart suggest that genotype- environment covariance is important for the work environment and should be included as a parameter in behavior…

  15. Locally Dependent Linear Logistic Test Model with Person Covariates

    ERIC Educational Resources Information Center

    Ip, Edward H.; Smits, Dirk J. M.; De Boeck, Paul

    2009-01-01

    The article proposes a family of item-response models that allow the separate and independent specification of three orthogonal components: item attribute, person covariate, and local item dependence. Special interest lies in extending the linear logistic test model, which is commonly used to measure item attributes, to tests with embedded item…

  16. A new eddy-covariance method using empirical mode decomposition

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We introduce a new eddy-covariance method that uses a spectral decomposition algorithm called empirical mode decomposition. The technique is able to calculate contributions to near-surface fluxes from different periodic components. Unlike traditional Fourier methods, this method allows for non-ortho...

  17. An alternative covariance estimator to investigate genetic heterogeneity in populations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genomic predictions and GWAS have used mixed models for identification of associations and trait predictions. In both cases, the covariance between individuals for performance is estimated using molecular markers. Mixed model properties indicate that the use of the data for prediction is optimal if ...

  18. Altered Cerebral Blood Flow Covariance Network in Schizophrenia.

    PubMed

    Liu, Feng; Zhuo, Chuanjun; Yu, Chunshui

    2016-01-01

    Many studies have shown abnormal cerebral blood flow (CBF) in schizophrenia; however, it remains unclear how topological properties of CBF network are altered in this disorder. Here, arterial spin labeling (ASL) MRI was employed to measure resting-state CBF in 96 schizophrenia patients and 91 healthy controls. CBF covariance network of each group was constructed by calculating across-subject CBF covariance between 90 brain regions. Graph theory was used to compare intergroup differences in global and nodal topological measures of the network. Both schizophrenia patients and healthy controls had small-world topology in CBF covariance networks, implying an optimal balance between functional segregation and integration. Compared with healthy controls, schizophrenia patients showed reduced small-worldness, normalized clustering coefficient and local efficiency of the network, suggesting a shift toward randomized network topology in schizophrenia. Furthermore, schizophrenia patients exhibited altered nodal centrality in the perceptual-, affective-, language-, and spatial-related regions, indicating functional disturbance of these systems in schizophrenia. This study demonstrated for the first time that schizophrenia patients have disrupted topological properties in CBF covariance network, which provides a new perspective (efficiency of blood flow distribution between brain regions) for understanding neural mechanisms of schizophrenia.

  19. Flowing on Riemannian manifold: domain adaptation by shifting covariance.

    PubMed

    Cui, Zhen; Li, Wen; Xu, Dong; Shan, Shiguang; Chen, Xilin; Li, Xuelong

    2014-12-01

    Domain adaptation has shown promising results in computer vision applications. In this paper, we propose a new unsupervised domain adaptation method called domain adaptation by shifting covariance (DASC) for object recognition without requiring any labeled samples from the target domain. By characterizing samples from each domain as one covariance matrix, the source and target domain are represented into two distinct points residing on a Riemannian manifold. Along the geodesic constructed from the two points, we then interpolate some intermediate points (i.e., covariance matrices), which are used to bridge the two domains. By utilizing the principal components of each covariance matrix, samples from each domain are further projected into intermediate feature spaces, which finally leads to domain-invariant features after the concatenation of these features from intermediate points. In the multiple source domain adaptation task, we also need to effectively integrate different types of features between each pair of source and target domains. We additionally propose an SVM based method to simultaneously learn the optimal target classifier as well as the optimal weights for different source domains. Extensive experiments demonstrate the effectiveness of our method for both single source and multiple source domain adaptation tasks.

  20. Evolution of sexual dimorphism in phenotypic covariance structure in Phymata.

    PubMed

    Punzalan, David; Rowe, Locke

    2015-06-01

    Sexual dimorphism is a consequence of both sex-specific selection and potential constraints imposed by a shared genetic architecture underlying sexually homologous traits. However, genetic architecture is expected to evolve to mitigate these constraints, allowing the sexes to approach their respective optimal mean phenotype. In addition, sex-specific selection is expected to generate sexual dimorphism of trait covariance structure (e.g., the phenotypic covariance matrix, P), but previous empirical work has not fully addressed this prediction. We compared patterns of phenotypic divergence, for three traits in seven taxa in the insect genus Phymata (Reduviidae), to ask whether sexual dimorphism in P is common and whether its magnitude relates to the extent of sexual dimorphism in trait means. We found that sexual dimorphism in both mean and covariance structure was pervasive but also that the multivariate distance between sex-specific means was correlated with sex differences in the leading eigenvector of P, while accounting for uncertainty in phylogenetic relationships. Collectively, our findings suggest that sexual dimorphism in covariance structure may be a common but underappreciated feature of dioecious populations.

  1. Detection of fungal damaged popcorn using image property covariance features

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Covariance-matrix-based features were applied to the detection of popcorn infected by a fungus that cause a symptom called “blue-eye.” This infection of popcorn kernels causes economic losses because of their poor appearance and the frequently disagreeable flavor of the popped kernels. Images of ker...

  2. Scale covariant physics: a 'quantum deformation' of classical electrodynamics

    NASA Astrophysics Data System (ADS)

    Knoll, Yehonatan; Yavneh, Irad

    2010-02-01

    We present a deformation of classical electrodynamics, continuously depending on a 'quantum parameter', featuring manifest gauge, Poincaré and scale covariance. The theory, dubbed extended charge dynamics (ECD), associates a certain length scale with each charge which, due to scale covariance, is an attribute of a solution, not a parameter of the theory. When the EM field experienced by an ECD charge is slowly varying over that length scale, the dynamics of the charge reduces to classical dynamics, its emitted radiation reduces to the familiar Liénard-Wiechert potential and the above length scale is identified as the charge's Compton length. It is conjectured that quantum mechanics describes statistical aspects of ensembles of ECD solutions, much like classical thermodynamics describes statistical aspects of ensembles of classical solutions. A unique 'remote sensing' feature of ECD, supporting that conjecture, is presented, along with an explanation for the illusion of a photon within a classical treatment of the EM field. Finally, a novel conservation law associated with the scale covariance of ECD is derived, indicating that the scale of a solution may 'drift' with time at a constant rate, much like translation covariance implies a uniform drift of the (average) position.

  3. Phenotypic Covariation and Morphological Diversification in the Ruminant Skull.

    PubMed

    Haber, Annat

    2016-05-01

    Differences among clades in their diversification patterns result from a combination of extrinsic and intrinsic factors. In this study, I examined the role of intrinsic factors in the morphological diversification of ruminants, in general, and in the differences between bovids and cervids, in particular. Using skull morphology, which embodies many of the adaptations that distinguish bovids and cervids, I examined 132 of the 200 extant ruminant species. As a proxy for intrinsic constraints, I quantified different aspects of the phenotypic covariation structure within species and compared them with the among-species divergence patterns, using phylogenetic comparative methods. My results show that for most species, divergence is well aligned with their phenotypic covariance matrix and that those that are better aligned have diverged further away from their ancestor. Bovids have dispersed into a wider range of directions in morphospace than cervids, and their overall disparity is higher. This difference is best explained by the lower eccentricity of bovids' within-species covariance matrices. These results are consistent with the role of intrinsic constraints in determining amount, range, and direction of dispersion and demonstrate that intrinsic constraints can influence macroevolutionary patterns even as the covariance structure evolves. PMID:27104991

  4. FLUXPART: An FOSS solution for Eddy covariance flux partitioning

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We report on efforts to develop a FOSS solution for a particular geoscience application. Eddy covariance (EC) instruments are routinely used to measure field-scale evapotranspiration and CO2 fluxes. For many applications, it is desirable to partition the measured evapotranspiration flux into its c...

  5. Different Approaches to Covariate Inclusion in the Mixture Rasch Model

    ERIC Educational Resources Information Center

    Li, Tongyun; Jiao, Hong; Macready, George B.

    2016-01-01

    The present study investigates different approaches to adding covariates and the impact in fitting mixture item response theory models. Mixture item response theory models serve as an important methodology for tackling several psychometric issues in test development, including the detection of latent differential item functioning. A Monte Carlo…

  6. A covariant approach to the gravitational refractive index

    NASA Astrophysics Data System (ADS)

    Simaciu, I.; Ionescu-Pallas, N.

    A covariant formulation of the Maxwell's field equations in a gravitational field, based on the bimetric interpretation of general relativity Theory, is given. The purpose of the work is in adequate definition of the gravitational refractive index in agreement with both wave equations propagation and a relationship between refractive index and the Minkovskian tensor of gravitational permitivity.

  7. Manufacturing time operators: Covariance, selection criteria, and examples

    SciTech Connect

    Hegerfeldt, G. C.; Muga, J. G.; Munoz, J.

    2010-07-15

    We provide the most general forms of covariant and normalized time operators and their probability densities, with applications to quantum clocks, the time of arrival, and Lyapunov quantum operators. Examples are discussed of the profusion of possible operators and their physical meaning. Criteria to define unique, optimal operators for specific cases are given.

  8. The QCD evolution of TMD in the covariant approach

    NASA Astrophysics Data System (ADS)

    Efremov, A. V.; Teryaev, O. V.; Zavada, P.

    2016-02-01

    The procedure for calculation of the QCD evolution of transverse momentum dependent distributions within the covariant approach is suggested. The standard collinear QCD evolution together with the requirements of relativistic invariance and rotational symmetry of the nucleon in its rest frame represent the basic ingredients of our approach. The obtained results are compared with the predictions of some other approaches.

  9. Some asymptotic properties of kriging when the covariance function is misspecified

    SciTech Connect

    Stein, M.L.; Handcock, M.S.

    1989-02-01

    The impact of using an incorrect covariance function of kriging predictors is investigated. Results of Stein (1988) show that the impact on the kriging predictor from not using the correct covariance function is asymptotically negligible as the number of observations increases if the covariance function used is compatible with the actual covariance function on the region of interest R. The definition and some properties of compatibility of covariance functions are given. The compatibility of generalized covariances also is defined. Compatibility supports the intuitively sensible concept that usually only the behavior near the origin of the covariance function is critical for purposes of kriging. However, the commonly used spherical covariance function is an exception: observations at a distance near the range of a spherical covariance function can have a nonnegligible effect on kriging predictors for three-dimensional processes. Finally, a comparison is made with the perturbation approach of Diamond and Armstrong (1984) and some observations of Warnes (1986) are clarified.

  10. Radio Telescopes Will Add to Cassini-Huygens Discoveries

    NASA Astrophysics Data System (ADS)

    2004-12-01

    When the European Space Agency's Huygens spacecraft makes its plunge into the atmosphere of Saturn's moon Titan on January 14, radio telescopes of the National Science Foundation's National Radio Astronomy Observatory (NRAO) will help international teams of scientists extract the maximum possible amount of irreplaceable information from an experiment unique in human history. Huygens is the 700-pound probe that has accompanied the larger Cassini spacecraft on a mission to thoroughly explore Saturn, its rings and its numerous moons. The Green Bank Telescope The Robert C. Byrd Green Bank Telescope CREDIT: NRAO/AUI/NSF (Click on image for GBT gallery) The Robert C. Byrd Green Bank Telescope (GBT) in West Virginia and eight of the ten telescopes of the continent-wide Very Long Baseline Array (VLBA), located at Pie Town and Los Alamos, NM, Fort Davis, TX, North Liberty, IA, Kitt Peak, AZ, Brewster, WA, Owens Valley, CA, and Mauna Kea, HI, will directly receive the faint signal from Huygens during its descent. Along with other radio telescopes in Australia, Japan, and China, the NRAO facilities will add significantly to the information about Titan and its atmosphere that will be gained from the Huygens mission. A European-led team will use the radio telescopes to make extremely precise measurements of the probe's position during its descent, while a U.S.-led team will concentrate on gathering measurements of the probe's descent speed and the direction of its motion. The radio-telescope measurements will provide data vital to gaining a full understanding of the winds that Huygens encounters in Titan's atmosphere. Currently, scientists know little about Titan's winds. Data from the Voyager I spacecraft's 1980 flyby indicated that east-west winds may reach 225 mph or more. North-south winds and possible vertical winds, while probably much weaker, may still be significant. There are competing theoretical models of Titan's winds, and the overall picture is best summarized as

  11. Pairwise comparisons of ten porcine tissues identify differential transcriptional regulation at the gene, isoform, promoter and transcription start site level

    SciTech Connect

    Farajzadeh, Leila; Hornshøj, Henrik; Momeni, Jamal; Thomsen, Bo; Larsen, Knud; Hedegaard, Jakob; Bendixen, Christian; Madsen, Lone Bruhn

    2013-08-23

    Highlights: •Transcriptome sequencing yielded 223 mill porcine RNA-seq reads, and 59,000 transcribed locations. •Establishment of unique transcription profiles for ten porcine tissues including four brain tissues. •Comparison of transcription profiles at gene, isoform, promoter and transcription start site level. •Highlights a high level of regulation of neuro-related genes at both gene, isoform, and TSS level. •Our results emphasize the pig as a valuable animal model with respect to human biological issues. -- Abstract: The transcriptome is the absolute set of transcripts in a tissue or cell at the time of sampling. In this study RNA-Seq is employed to enable the differential analysis of the transcriptome profile for ten porcine tissues in order to evaluate differences between the tissues at the gene and isoform expression level, together with an analysis of variation in transcription start sites, promoter usage, and splicing. Totally, 223 million RNA fragments were sequenced leading to the identification of 59,930 transcribed gene locations and 290,936 transcript variants using Cufflinks with similarity to approximately 13,899 annotated human genes. Pairwise analysis of tissues for differential expression at the gene level showed that the smallest differences were between tissues originating from the porcine brain. Interestingly, the relative level of differential expression at the isoform level did generally not vary between tissue contrasts. Furthermore, analysis of differential promoter usage between tissues, revealed a proportionally higher variation between cerebellum (CBE) versus frontal cortex and cerebellum versus hypothalamus (HYP) than in the remaining comparisons. In addition, the comparison of differential transcription start sites showed that the number of these sites is generally increased in comparisons including hypothalamus in contrast to other pairwise assessments. A comprehensive analysis of one of the tissue contrasts, i

  12. Assessing spatial covariance among time series of abundance.

    PubMed

    Jorgensen, Jeffrey C; Ward, Eric J; Scheuerell, Mark D; Zabel, Richard W

    2016-04-01

    For species of conservation concern, an essential part of the recovery planning process is identifying discrete population units and their location with respect to one another. A common feature among geographically proximate populations is that the number of organisms tends to covary through time as a consequence of similar responses to exogenous influences. In turn, high covariation among populations can threaten the persistence of the larger metapopulation. Historically, explorations of the covariance in population size of species with many (>10) time series have been computationally difficult. Here, we illustrate how dynamic factor analysis (DFA) can be used to characterize diversity among time series of population abundances and the degree to which all populations can be represented by a few common signals. Our application focuses on anadromous Chinook salmon (Oncorhynchus tshawytscha), a species listed under the US Endangered Species Act, that is impacted by a variety of natural and anthropogenic factors. Specifically, we fit DFA models to 24 time series of population abundance and used model selection to identify the minimum number of latent variables that explained the most temporal variation after accounting for the effects of environmental covariates. We found support for grouping the time series according to 5 common latent variables. The top model included two covariates: the Pacific Decadal Oscillation in spring and summer. The assignment of populations to the latent variables matched the currently established population structure at a broad spatial scale. At a finer scale, there was more population grouping complexity. Some relatively distant populations were grouped together, and some relatively close populations - considered to be more aligned with each other - were more associated with populations further away. These coarse- and fine-grained examinations of spatial structure are important because they reveal different structural patterns not evident

  13. Assessing spatial covariance among time series of abundance.

    PubMed

    Jorgensen, Jeffrey C; Ward, Eric J; Scheuerell, Mark D; Zabel, Richard W

    2016-04-01

    For species of conservation concern, an essential part of the recovery planning process is identifying discrete population units and their location with respect to one another. A common feature among geographically proximate populations is that the number of organisms tends to covary through time as a consequence of similar responses to exogenous influences. In turn, high covariation among populations can threaten the persistence of the larger metapopulation. Historically, explorations of the covariance in population size of species with many (>10) time series have been computationally difficult. Here, we illustrate how dynamic factor analysis (DFA) can be used to characterize diversity among time series of population abundances and the degree to which all populations can be represented by a few common signals. Our application focuses on anadromous Chinook salmon (Oncorhynchus tshawytscha), a species listed under the US Endangered Species Act, that is impacted by a variety of natural and anthropogenic factors. Specifically, we fit DFA models to 24 time series of population abundance and used model selection to identify the minimum number of latent variables that explained the most temporal variation after accounting for the effects of environmental covariates. We found support for grouping the time series according to 5 common latent variables. The top model included two covariates: the Pacific Decadal Oscillation in spring and summer. The assignment of populations to the latent variables matched the currently established population structure at a broad spatial scale. At a finer scale, there was more population grouping complexity. Some relatively distant populations were grouped together, and some relatively close populations - considered to be more aligned with each other - were more associated with populations further away. These coarse- and fine-grained examinations of spatial structure are important because they reveal different structural patterns not evident

  14. Ensemble Kalman filter implementations based on shrinkage covariance matrix estimation

    NASA Astrophysics Data System (ADS)

    Nino-Ruiz, Elias D.; Sandu, Adrian

    2015-11-01

    This paper develops efficient ensemble Kalman filter (EnKF) implementations based on shrinkage covariance estimation. The forecast ensemble members at each step are used to estimate the background error covariance matrix via the Rao-Blackwell Ledoit and Wolf estimator, which has been specifically developed to approximate high-dimensional covariance matrices using a small number of samples. Two implementations are considered: in the EnKF full-space (EnKF-FS) approach, the assimilation process is performed in the model space, while the EnKF reduce-space (EnKF-RS) formulation performs the analysis in the subspace spanned by the ensemble members. In the context of EnKF-RS, additional samples are taken from the normal distribution described by the background ensemble mean and the estimated background covariance matrix, in order to increase the size of the ensemble and reduce the sampling error of the filter. This increase in the size of the ensemble is obtained without running the forward model. After the assimilation step, the additional samples are discarded and only the model-based ensemble members are propagated further. Methodologies to reduce the impact of spurious correlations and under-estimation of sample variances in the context of the EnKF-FS and EnKF-RS implementations are discussed. An adjoint-free four-dimensional extension of EnKF-RS is also discussed. Numerical experiments carried out with the Lorenz-96 model and a quasi-geostrophic model show that the use of shrinkage covariance matrix estimation can mitigate the impact of spurious correlations during the assimilation process.

  15. Prediction of Antimicrobial Peptides Based on Sequence Alignment and Support Vector Machine-Pairwise Algorithm Utilizing LZ-Complexity

    PubMed Central

    Shahrudin, Shahriza

    2015-01-01

    This study concerns an attempt to establish a new method for predicting antimicrobial peptides (AMPs) which are important to the immune system. Recently, researchers are interested in designing alternative drugs based on AMPs because they have found that a large number of bacterial strains have become resistant to available antibiotics. However, researchers have encountered obstacles in the AMPs designing process as experiments to extract AMPs from protein sequences are costly and require a long set-up time. Therefore, a computational tool for AMPs prediction is needed to resolve this problem. In this study, an integrated algorithm is newly introduced to predict AMPs by integrating sequence alignment and support vector machine- (SVM-) LZ complexity pairwise algorithm. It was observed that, when all sequences in the training set are used, the sensitivity of the proposed algorithm is 95.28% in jackknife test and 87.59% in independent test, while the sensitivity obtained for jackknife test and independent test is 88.74% and 78.70%, respectively, when only the sequences that has less than 70% similarity are used. Applying the proposed algorithm may allow researchers to effectively predict AMPs from unknown protein peptide sequences with higher sensitivity. PMID:25802839

  16. Simple pair-wise interactions for hybrid Monte Carlo-molecular dynamics simulations of titania/yttria-doped iron.

    PubMed

    Hammond, Karl D; Voigt, Hyon-Jee Lee; Marus, Lauren A; Juslin, Niklas; Wirth, Brian D

    2013-02-01

    We present pair-wise, charge-neutral model potentials for an iron-titanium-yttrium-oxygen system. These simple models are designed to provide a tractable method of simulating nanostructured ferritic alloys (NFAs) using off-lattice Monte Carlo and molecular dynamics techniques without deviating significantly from the formalism employed in existing Monte Carlo simulations. The model is fitted to diamagnetic density functional theory (DFT) calculations of the various species over a range of densities and concentrations. The resulting model potentials provide reasonable and in some cases even excellent mechanical and thermodynamic properties for the pure metals. The model replicates the qualitative trends in formation energy predicted by DFT, though the energies of formation do not agree as well for dilute systems as they do for more concentrated systems. We find that on-lattice models will consistently favor tetrahedral oxygen interstitial sites over octahedral interstitial sites, while relaxed systems typically favor octahedral sites. This emphasizes the need for the off-lattice simulations for which this potential was designed. PMID:23288578

  17. Evaluation of criteria for sustainability of community-based rural homestay programs via a modified pairwise comparison method

    NASA Astrophysics Data System (ADS)

    Ramli, Rohaini; Kasim, Maznah Mat; Ramli, Razamin; Kayat, Kalsom; Razak, Rafidah Abd

    2014-12-01

    Ministry of Tourism and Culture Malaysia has long introduced homestay programs across the country to enhance the quality of life of people, especially those living in rural areas. This type of program is classified as a community-based tourism (CBT) as it is expected to economically improve livelihood through cultural and community associated activities. It is the aspiration of the ministry to see that the income imbalance between people in the rural and urban areas is reduced, thus would contribute towards creating more developed states of Malaysia. Since 1970s, there are 154 homestay programs registered with the ministry. However, the performance and sustainability of the programs are still not satisfying. There are only a number of homestay programs that perform well and able to sustain. Thus, the aim of this paper is to identify relevant criteria contributing to the sustainability of a homestay program. The criteria are evaluated for their levels of importance via the use of a modified pairwise method and analyzed for other potentials. The findings will help the homestay operators to focus on the necessary criteria and thus, effectively perform as the CBT business initiative.

  18. The use of a modified pairwise comparison method in evaluating critical success factors for community-based rural homestay programmes

    NASA Astrophysics Data System (ADS)

    Daud, Shahidah Md; Ramli, Razamin; Kasim, Maznah Mat; Kayat, Kalsom; Razak, Rafidah Abd

    2014-12-01

    Tourism industry has become the highlighted sector which has amazingly increased the national income level. Despite the tourism industry being one of the highest income generating sectors, Homestay Programme as a Community-Based Tourism (CBT) product in Malaysia does not absorbed much of the incoming wealth. Homestay Programme refers to a programme in a community where a tourist stays together with a host family and experiences the everyday way of life of the family in both direct and indirect manner. There are over 100 Homestay Programme currently being registered with the Ministry of Culture and Tourism Malaysia which mostly are located in rural areas, but only a few excel and enjoying the fruit of the booming industry. Hence, this article seeks to identify the critical success factors for a Community-Based Rural Homestay Programme in Malaysia. A modified pairwise method is utilized to further evaluate the identified success factors in a more meaningful way. The findings will help Homestay Programme function as a community development tool that manages tourism resources. Thus, help the community in improving local economy and creating job opportunities.

  19. Mechanism of densification in silica glass under pressure as revealed by a bottom-up pairwise effective interaction model

    NASA Astrophysics Data System (ADS)

    Izvekov, Sergei; Rice, Betsy M.

    2012-04-01

    A new short-range pairwise numerical potential for silica is presented. The potential is derived from a single ab initio molecular dynamics (AIMD) simulation of molten silica using the force-matching method with the forces being represented numerically by piecewise functions (splines). The AIMD simulation is performed using the Born-Oppenheimer method with the generalized gradient approximation (BLYP) for the XC energy functional. The new effective potential includes a soft-repulsive shoulder to describe the interactions of oxygen ions at short separations. The new potential, despite being short-ranged and derived from single-phase data, exhibits a good transferability to silica crystalline polymorphs and amorphous silica. The importance of the O-O soft-repulsive shoulder interaction on glass densification under cold and shock compressions is assessed from MD simulations of silica glass under room and shock Hugoniot conditions, respectively. Results from these simulations indicate that the appearance of oxygen complexes (primarily pairs) interacting through soft-repulsive shoulder potential occurs at 8-10 GPa, and under cold compression conditions becomes notable at 40 GPa, essentially coinciding with the transition to a Si sixfold coordination state. An analysis of changes in system structure in compressed and shocked states reveals that the O ions interacting through the soft-repulsive shoulder potential in denser states of silica glass may create a mechanical multi-stability under elevated pressures and thus to contribute to the observed anomalous densification.

  20. The atom-surface interaction potential for He-NaCl: A model based on pairwise additivity

    NASA Astrophysics Data System (ADS)

    Hutson, Jeremy M.; Fowler, P. W.

    1986-08-01

    The recently developed semi-empirical model of Fowler and Hutson is applied to the He-NaCl atom-surface interaction potential. Ab initio self-consistent field calculations of the repulsive interactions between He atoms and in-crystal Cl - and Na + ions are performed. Dispersion coefficients involving in-crystal ions are also calculated. The atom-surface potential is constructed using a model based on pairwise additivity of atom-ion forces. With a small adjustment of the repulsive part, this potential gives good agreement with the experimental bound state energies obtained from selective adsorption resonances in low-energy atom scattering experiments. Close-coupling calculations of the resonant scattering are performed, and good agreement with the experimental peak positions and intensity patterns is obtained. It is concluded that there are no bound states deeper than those observed in the selective adsorption experiments, and that the well depth of the He-NaCl potential is 6.0 ± 0.2 meV.

  1. Effect of neural connectivity on autocovariance and cross covariance estimates

    PubMed Central

    Stecker, Mark M

    2007-01-01

    Background Measurements of auto and cross covariance functions are frequently used to investigate neural systems. In interpreting this data, it is commonly assumed that the largest contribution to the recordings comes from sources near the electrode. However, the potential recorded at an electrode represents the superimposition of the potentials generated by large numbers of active neural structures. This creates situations under which the measured auto and cross covariance functions are dominated by the activity in structures far from the electrode and in which the distance dependence of the cross-covariance function differs significantly from that describing the activity in the actual neural structures. Methods Direct application of electrostatics to calculate the theoretical auto and cross covariance functions that would be recorded from electrodes immersed in a large volume filled with active neural structures with specific statistical properties. Results It is demonstrated that the potentials recorded from a monopolar electrode surrounded by dipole sources in a uniform medium are predominantly due to activity in neural structures far from the electrode when neuronal correlations drop more slowly than 1/r3 or when the size of the neural system is much smaller than a known correlation distance. Recordings from quadrupolar sources are strongly dependent on distant neurons when correlations drop more slowly than 1/r or the size of the system is much smaller than the correlation distance. Differences between bipolar and monopolar recordings are discussed. It is also demonstrated that the cross covariance of the recorded in two spatially separated electrodes declines as a power-law function of the distance between them even when the electrical activity from different neuronal structures is uncorrelated. Conclusion When extracellular electrophysiologic recordings are made from systems containing large numbers of neural structures, it is important to interpret

  2. Construction and use of gene expression covariation matrix

    PubMed Central

    Hennetin, Jérôme; Pehkonen, Petri; Bellis, Michel

    2009-01-01

    Background One essential step in the massive analysis of transcriptomic profiles is the calculation of the correlation coefficient, a value used to select pairs of genes with similar or inverse transcriptional profiles across a large fraction of the biological conditions examined. Until now, the choice between the two available methods for calculating the coefficient has been dictated mainly by technological considerations. Specifically, in analyses based on double-channel techniques, researchers have been required to use covariation correlation, i.e. the correlation between gene expression changes measured between several pairs of biological conditions, expressed for example as fold-change. In contrast, in analyses of single-channel techniques scientists have been restricted to the use of coexpression correlation, i.e. correlation between gene expression levels. To our knowledge, nobody has ever examined the possible benefits of using covariation instead of coexpression in massive analyses of single channel microarray results. Results We describe here how single-channel techniques can be treated like double-channel techniques and used to generate both gene expression changes and covariation measures. We also present a new method that allows the calculation of both positive and negative correlation coefficients between genes. First, we perform systematic comparisons between two given biological conditions and classify, for each comparison, genes as increased (I), decreased (D), or not changed (N). As a result, the original series of n gene expression level measures assigned to each gene is replaced by an ordered string of n(n-1)/2 symbols, e.g. IDDNNIDID....DNNNNNNID, with the length of the string corresponding to the number of comparisons. In a second step, positive and negative covariation matrices (CVM) are constructed by calculating statistically significant positive or negative correlation scores for any pair of genes by comparing their strings of symbols

  3. Eddy Covariance Method: Overview of General Guidelines and Conventional Workflow

    NASA Astrophysics Data System (ADS)

    Burba, G. G.; Anderson, D. J.; Amen, J. L.

    2007-12-01

    Atmospheric flux measurements are widely used to estimate water, heat, carbon dioxide and trace gas exchange between the ecosystem and the atmosphere. The Eddy Covariance method is one of the most direct, defensible ways to measure and calculate turbulent fluxes within the atmospheric boundary layer. However, the method is mathematically complex, and requires significant care to set up and process data. These reasons may be why the method is currently used predominantly by micrometeorologists. Modern instruments and software can potentially expand the use of this method beyond micrometeorology and prove valuable for plant physiology, hydrology, biology, ecology, entomology, and other non-micrometeorological areas of research. The main challenge of the method for a non-expert is the complexity of system design, implementation, and processing of the large volume of data. In the past several years, efforts of the flux networks (e.g., FluxNet, Ameriflux, CarboEurope, Fluxnet-Canada, Asiaflux, etc.) have led to noticeable progress in unification of the terminology and general standardization of processing steps. The methodology itself, however, is difficult to unify, because various experimental sites and different purposes of studies dictate different treatments, and site-, measurement- and purpose-specific approaches. Here we present an overview of theory and typical workflow of the Eddy Covariance method in a format specifically designed to (i) familiarize a non-expert with general principles, requirements, applications, and processing steps of the conventional Eddy Covariance technique, (ii) to assist in further understanding the method through more advanced references such as textbooks, network guidelines and journal papers, (iii) to help technicians, students and new researchers in the field deployment of the Eddy Covariance method, and (iv) to assist in its use beyond micrometeorology. The overview is based, to a large degree, on the frequently asked questions

  4. Covariation of mutations: A computational approach for determination of function and structure from sequence

    SciTech Connect

    Haussler, D.; Hughey, R.; Karplus, K.; Cline, M.; Grate, L.; Kulp, D.; Sjolander, K.; Lapedes, A.S.

    1998-11-01

    The authors have developed and enhanced a set of tools for fold recognition with hidden Markov models (HMMs), and used these tools effectively in the CASP2 protein structure prediction contest [KKB+97]. HMMs have limitations, and one limitation is that they do not model the long-range pairwise interactions that define the shape of a protein. As such, the authors are working on modeling pairwise interactions to incorporate them into the HMM-based framework. Classical fold recognition methods are based on the premise of distinct pairwise preferences between two given amino acids. The authors have studied these preferences extensively and found that in the general case, this information is limited. Yet by modeling pairwise interactions in context of phylogenetic relationships and by modeling one specific type of contact, the contact between interacting beta strand residues, they have recovered significant information for prediction and analysis of protein structure.

  5. Pairwise Sequence Alignment Library

    SciTech Connect

    Jeff Daily, PNNL

    2015-05-20

    Vector extensions, such as SSE, have been part of the x86 CPU since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprint that features complex data dependencies. The trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. Therefore, a novel SIMD implementation of a parallel scan-based sequence alignment algorithm that can better exploit wider SIMD units was implemented as part of the Parallel Sequence Alignment Library (parasail). Parasail features: Reference implementations of all known vectorized sequence alignment approaches. Implementations of Smith Waterman (SW), semi-global (SG), and Needleman Wunsch (NW) sequence alignment algorithms. Implementations across all modern CPU instruction sets including AVX2 and KNC. Language interfaces for C/C++ and Python.

  6. Pairwise Sequence Alignment Library

    2015-05-20

    Vector extensions, such as SSE, have been part of the x86 CPU since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprintmore » that features complex data dependencies. The trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. Therefore, a novel SIMD implementation of a parallel scan-based sequence alignment algorithm that can better exploit wider SIMD units was implemented as part of the Parallel Sequence Alignment Library (parasail). Parasail features: Reference implementations of all known vectorized sequence alignment approaches. Implementations of Smith Waterman (SW), semi-global (SG), and Needleman Wunsch (NW) sequence alignment algorithms. Implementations across all modern CPU instruction sets including AVX2 and KNC. Language interfaces for C/C++ and Python.« less

  7. Covariances of evaluated nuclear data based upon uncertainty information of experimental data and nuclear models

    SciTech Connect

    Poenitz, W.P.; Peelle, R.W.

    1986-11-17

    A straightforward derivation is presented for the covariance matrix of evaluated cross sections based on the covariance matrix of the experimental data and propagation through nuclear model parameters. 10 refs.

  8. Markov modulated Poisson process models incorporating covariates for rainfall intensity.

    PubMed

    Thayakaran, R; Ramesh, N I

    2013-01-01

    Time series of rainfall bucket tip times at the Beaufort Park station, Bracknell, in the UK are modelled by a class of Markov modulated Poisson processes (MMPP) which may be thought of as a generalization of the Poisson process. Our main focus in this paper is to investigate the effects of including covariate information into the MMPP model framework on statistical properties. In particular, we look at three types of time-varying covariates namely temperature, sea level pressure, and relative humidity that are thought to be affecting the rainfall arrival process. Maximum likelihood estimation is used to obtain the parameter estimates, and likelihood ratio tests are employed in model comparison. Simulated data from the fitted model are used to make statistical inferences about the accumulated rainfall in the discrete time interval. Variability of the daily Poisson arrival rates is studied.

  9. From liquid structure to configurational entropy: introducing structural covariance

    NASA Astrophysics Data System (ADS)

    Ronceray, Pierre; Harrowell, Peter

    2016-08-01

    We connect the configurational entropy of a liquid to the geometrical properties of its local energy landscape, using a high-temperature expansion. It is proposed that correlations between local structures arises from their overlap and, being geometrical in nature, can be usefully determined using the inherent structures of high temperature liquids. We show quantitatively how the high-temperature covariance of these local structural fluctuations arising from their geometrical overlap, combined with their energetic stability, control the decrease of entropy with decreasing energy. We apply this formalism to a family of favoured local structure (FLS) lattice models with two low symmetry FLS’s which are found to either crystallize or form a glass on cooling. The covariance, crystal energy and estimated freezing temperature are tested as possible predictors of glass-forming ability in the model system.

  10. Covariance-based approaches to aeroacoustic noise source analysis.

    PubMed

    Du, Lin; Xu, Luzhou; Li, Jian; Guo, Bin; Stoica, Petre; Bahr, Chris; Cattafesta, Louis N

    2010-11-01

    In this paper, several covariance-based approaches are proposed for aeroacoustic noise source analysis under the assumptions of a single dominant source and all observers contaminated solely by uncorrelated noise. The Cramér-Rao Bounds (CRB) of the unbiased source power estimates are also derived. The proposed methods are evaluated using both simulated data as well as data acquired from an airfoil trailing edge noise experiment in an open-jet aeroacoustic facility. The numerical examples show that the covariance-based algorithms significantly outperform an existing least-squares approach and provide accurate power estimates even under low signal-to-noise ratio (SNR) conditions. Furthermore, the mean-squared-errors (MSEs) of the so-obtained estimates are close to the corresponding CRB especially for a large number of data samples. The experimental results show that the power estimates of the proposed approaches are consistent with one another as long as the core analysis assumptions are obeyed.

  11. An efficient algorithm for estimating noise covariances in distributed systems

    NASA Technical Reports Server (NTRS)

    Dee, D. P.; Cohn, S. E.; Ghil, M.; Dalcher, A.

    1985-01-01

    An efficient computational algorithm for estimating the noise covariance matrices of large linear discrete stochatic-dynamic systems is presented. Such systems arise typically by discretizing distributed-parameter systems, and their size renders computational efficiency a major consideration. The proposed adaptive filtering algorithm is based on the ideas of Belanger, and is algebraically equivalent to his algorithm. The earlier algorithm, however, has computational complexity proportional to p to the 6th, where p is the number of observations of the system state, while the new algorithm has complexity proportional to only p-cubed. Further, the formulation of noise covariance estimation as a secondary filter, analogous to state estimation as a primary filter, suggests several generalizations of the earlier algorithm. The performance of the proposed algorithm is demonstrated for a distributed system arising in numerical weather prediction.

  12. Scale-covariant theory of gravitation and astrophysical applications

    NASA Technical Reports Server (NTRS)

    Canuto, V.; Adams, P. J.; Hsieh, S.-H.; Tsiang, E.

    1977-01-01

    A scale-covariant theory of gravitation is presented which is characterized by a set of equations that are complete only after a choice of the scale function is made. Special attention is given to gauge conditions and units which allow gravitational phenomena to be described in atomic units. The generalized gravitational-field equations are derived by performing a direct scale transformation, by extending Riemannian geometry to Weyl geometry through the introduction of the notion of cotensors, and from a variation principle. Modified conservation laws are provided, a set of dynamical equations is obtained, and astrophysical consequences are considered. The theory is applied to examine certain homogeneous cosmological solutions, perihelion shifts, light deflections, secular variations of planetary orbital elements, stellar structure equations for a star in quasi-static equilibrium, and the past thermal history of earth. The possible relation of the scale-covariant theory to gauge field theories and their predictions of cosmological constants is discussed.

  13. κ-deformed covariant quantum phase spaces as Hopf algebroids

    NASA Astrophysics Data System (ADS)

    Lukierski, Jerzy; Škoda, Zoran; Woronowicz, Mariusz

    2015-11-01

    We consider the general D = 4 (10 + 10)-dimensional κ-deformed quantum phase space as given by Heisenberg double H of D = 4κ-deformed Poincaré-Hopf algebra H. The standard (4 + 4)-dimensional κ-deformed covariant quantum phase space spanned by κ-deformed Minkowski coordinates and commuting momenta generators (xˆμ ,pˆμ) is obtained as the subalgebra of H. We study further the property that Heisenberg double defines particular quantum spaces with Hopf algebroid structure. We calculate by using purely algebraic methods the explicit Hopf algebroid structure of standard κ-deformed quantum covariant phase space in Majid-Ruegg bicrossproduct basis. The coproducts for Hopf algebroids are not unique, determined modulo the coproduct gauge freedom. Finally we consider the interpretation of the algebraic description of quantum phase spaces as Hopf algebroids.

  14. A Causal, Covariant Theory of Dissipative Fluid Flow

    NASA Astrophysics Data System (ADS)

    Scofield, Dillon; Huq, Pablo

    2015-04-01

    The use of newtonian viscous dissipation theory in covariant fluid flow theories is known to lead to predictions that are inconsistent with the second law of thermodynamics and to predictions that are acausal. For instance, these problems effectively limit the covariant form of the Navier-Stokes theory (NST) to time-independent flow regimes. Thus the NST, the work horse of fluid dynamical theory, is limited in its ability to model time-dependent turbulent, stellar or thermonuclear flows. We show how such problems are avoided by a new geometrodynamical theory of fluids. This theory is based on a recent result of geometrodynamics showing current conservation implies gauge field creation, called the vortex field lemma and classification of flows by their Pfaff dimension. Experimental confirmation of the theory is reviewed.

  15. 77 FR 59610 - Flonicamid; Applications To Add New Food Uses on Previously Registered Pesticide Products

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-09-28

    ... applications to add new food uses on previously registered pesticide products containing the insecticide, flonicamide, pursuant to the provisions of section 3(c) of the Federal Insecticide, Fungicide, and Rodenticide... registered pesticide products containing the insecticide, flonicamid,...

  16. Mothers whose children have ADD/ADHD discuss their children's medication use: an investigation of blogs.

    PubMed

    Clarke, Juanne N; Lang, Laura

    2012-01-01

    This article presents the results of a frame and discourse analysis of Internet blog sites where parents (usually mothers) discuss their concerns about medication use by their children with attention deficit disorder or attention deficit hyperactivity disorder (ADD/ADHD). This is a particularly important topic in an era characterized by powerful circulating discourses around the contentious medicalization of, and prevalent pharmaceutical treatments for, ADD/ADHD, as well as the mother blame associated with having a child diagnosed with ADD/ADHD. The findings document that the mothers see ADD/ADHD as legitimate medical diagnoses and view themselves as caretakers of children with brain and neuro-chemical anomalies affecting the behavior of their children. They favor pharmaceutical use and describe themselves as experts in the difficult and complex issues related to pharmaceuticalized parenting. At the same time their adoption of medicalization is contingent as they express specific critiques of some doctors, some types of doctors, and critically evaluate science.

  17. Multilevel image recognition using discriminative patches and kernel covariance descriptor

    NASA Astrophysics Data System (ADS)

    Lu, Le; Yao, Jianhua; Turkbey, Evrim; Summers, Ronald M.

    2014-03-01

    Computer-aided diagnosis of medical images has emerged as an important tool to objectively improve the performance, accuracy and consistency for clinical workflow. To computerize the medical image diagnostic recognition problem, there are three fundamental problems: where to look (i.e., where is the region of interest from the whole image/volume), image feature description/encoding, and similarity metrics for classification or matching. In this paper, we exploit the motivation, implementation and performance evaluation of task-driven iterative, discriminative image patch mining; covariance matrix based descriptor via intensity, gradient and spatial layout; and log-Euclidean distance kernel for support vector machine, to address these three aspects respectively. To cope with often visually ambiguous image patterns for the region of interest in medical diagnosis, discovery of multilabel selective discriminative patches is desired. Covariance of several image statistics summarizes their second order interactions within an image patch and is proved as an effective image descriptor, with low dimensionality compared with joint statistics and fast computation regardless of the patch size. We extensively evaluate two extended Gaussian kernels using affine-invariant Riemannian metric or log-Euclidean metric with support vector machines (SVM), on two medical image classification problems of degenerative disc disease (DDD) detection on cortical shell unwrapped CT maps and colitis detection on CT key images. The proposed approach is validated with promising quantitative results on these challenging tasks. Our experimental findings and discussion also unveil some interesting insights on the covariance feature composition with or without spatial layout for classification and retrieval, and different kernel constructions for SVM. This will also shed some light on future work using covariance feature and kernel classification for medical image analysis.

  18. Covariance in models of loop quantum gravity: Gowdy systems

    NASA Astrophysics Data System (ADS)

    Bojowald, Martin; Brahma, Suddhasattwa

    2015-09-01

    Recent results in the construction of anomaly-free models of loop quantum gravity have shown obstacles when local physical degrees of freedom are present. Here, a set of no-go properties is derived in polarized Gowdy models, raising the question of whether these systems can be covariant beyond a background treatment. As a side product, it is shown that normal deformations in classical polarized Gowdy models can be Abelianized.

  19. OD Covariance in Conjunction Assessment: Introduction and Issues

    NASA Technical Reports Server (NTRS)

    Hejduk, M. D.; Duncan, M.

    2015-01-01

    Primary and secondary covariances combined and projected into conjunction plane (plane perpendicular to relative velocity vector at TCA) Primary placed on x-axis at (miss distance, 0) and represented by circle of radius equal to sum of both spacecraft circumscribing radiiZ-axis perpendicular to x-axis in conjunction plane Pc is portion of combined error ellipsoid that falls within the hard-body radius circle

  20. Increasing the Efficiency of Prevention Trials by Incorporating Baseline Covariates.

    PubMed

    Zhang, Min; Gilbert, Peter B

    2010-01-01

    Most randomized efficacy trials of interventions to prevent HIV or other infectious diseases have assessed intervention efficacy by a method that either does not incorporate baseline covariates, or that incorporates them in a non-robust or inefficient way. Yet, it has long been known that randomized treatment effects can be assessed with greater efficiency by incorporating baseline covariates that predict the response variable. Tsiatis et al. (2007) and Zhang et al. (2008) advocated a semiparametric efficient approach, based on the theory of Robins et al. (1994), for consistently estimating randomized treatment effects that optimally incorporates predictive baseline covariates, without any parametric assumptions. They stressed the objectivity of the approach, which is achieved by separating the modeling of baseline predictors from the estimation of the treatment effect. While their work adequately justifies implementation of the method for large Phase 3 trials (because its optimality is in terms of asymptotic properties), its performance for intermediate-sized screening Phase 2b efficacy trials, which are increasing in frequency, is unknown. Furthermore, the past work did not consider a right-censored time-to-event endpoint, which is the usual primary endpoint for a prevention trial. For Phase 2b HIV vaccine efficacy trials, we study finite-sample performance of Zhang et al.'s (2008) method for a dichotomous endpoint, and develop and study an adaptation of this method to a discrete right-censored time-to-event endpoint. We show that, given the predictive capacity of baseline covariates collected in real HIV prevention trials, the methods achieve 5-15% gains in efficiency compared to methods in current use. We apply the methods to the first HIV vaccine efficacy trial. This work supports implementation of the discrete failure time method for prevention trials. PMID:21152074

  1. Recent Use of Covariance Data for Criticality Safety Assessment

    NASA Astrophysics Data System (ADS)

    Rearden, B. T.; Mueller, D. E.

    2008-12-01

    The TSUNAMI codes of the Oak Ridge National Laboratory SCALE code system were applied to a burnup credit application to demonstrate the use of sensitivity and uncertainty analysis with recent cross section covariance data for criticality safety code and data validation. The use of sensitivity and uncertainty analysis provides for the assessment of a defensible computational bias, bias uncertainty, and gap analysis for a complex system that otherwise could be assessed only through the use of expert judgment and conservative assumptions.

  2. The fitting of radioactive decay data by covariance methods

    SciTech Connect

    Smith, D.L.; Osadebe, F.A.N.

    1994-04-01

    The fitting of radioactive decay data is examined when radiations from two or more processes are indistinguishable. The model is a nonlinear sum of exponentials which cannot be linearized by transformations. Simple and generalized least-squares procedures utilizing covariance matrices are applied. The validity of the midpoint approximation is demonstrated. Guidelines for acquiring adequate radioactive decay data are suggested. The relevance to activation cross section determination is discussed.

  3. Recent Use of Covariance Data for Criticality Safety Assessment

    SciTech Connect

    Rearden, Bradley T; Mueller, Don

    2008-01-01

    The TSUNAMI codes of the Oak Ridge National Laboratory SCALE code system were applied to a burnup credit application to demonstrate the use of sensitivity and uncertainty analysis with recent cross section covariance data for criticality safety code and data validation. The use of sensitivity and uncertainty analysis provides for the assessment of a defensible computational bias, bias uncertainty, and gap analysis for a complex system that otherwise could be assessed only through the use of expert judgment and conservative assumptions.

  4. Covariant diagonalization of the perfect fluid stress-energy tensor

    NASA Astrophysics Data System (ADS)

    Garat, Alcides

    2015-02-01

    We introduce new tetrads that manifestly and covariantly diagonalize the stress-energy tensor for a perfect fluid with vorticity at every spacetime point. This new tetrad can be applied to introduce simplification in the analysis of astrophysical relativistic problems where vorticity is present through the Carter-Lichnerowicz equation. We also discuss the origin of inertia in this special case from the standpoint of our new local tetrads.

  5. The Polarized TMDs in the covariant parton model approach

    SciTech Connect

    A.V. Efremov, P. Schweitzer, O.V. Teryaev, P. Zavada

    2011-05-01

    We derive relations between polarized transverse momentum dependent distribution functions (TMDs) and the usual parton distribution functions (PDFs) in the 3D covariant parton model, which follow from Lorentz invariance and the assumption of a rotationally symmetric distribution of parton momenta in the nucleon rest frame. Using the known PDF $g_{1}^{q}(x)$ as input we predict the $x$- and $\\mathbf{p}_{T}$-dependence of all polarized twist-2 naively time-reversal even (T-even) TMDs.

  6. Covariant Star Product for Exterior Differential Forms on Symplectic Manifolds

    SciTech Connect

    McCurdy, Shannon; Zumino, Bruno

    2010-02-10

    After a brief description of the Z-graded differential Poisson algebra, we introduce a covariant star product for exterior differential forms and give an explicit expression for it up to second order in the deformation parameter h, in the case of symplectic manifolds. The graded differential Poisson algebra endows the manifold with a connection, not necessarily torsion-free, and places upon the connection various constraints.

  7. Covariance Applications in Criticality Safety, Light Water Reactor Analysis, and Spent Fuel Characterization

    NASA Astrophysics Data System (ADS)

    Williams, M. L.; Wiarda, D.; Ilas, G.; Marshall, W. J.; Rearden, B. T.

    2015-01-01

    A new covariance data library based on ENDF/B-VII.1 was recently processed for the SCALE nuclear analysis code system. The multigroup covariance data are discussed here, along with testing and application results for critical benchmark experiments. The cross section covariance library, along with covariances for fission product yields and decay data, is used to compute uncertainties in the decay heat produced by a burned reactor fuel assembly.

  8. Covariance Applications in Criticality Safety, Light Water Reactor Analysis, and Spent Fuel Characterization

    DOE PAGES

    Williams, M. L.; Wiarda, D.; Ilas, G.; Marshall, W. J.; Rearden, B. T.

    2014-06-15

    Recently, we processed a new covariance data library based on ENDF/B-VII.1 for the SCALE nuclear analysis code system. The multigroup covariance data are discussed here, along with testing and application results for critical benchmark experiments. Moreover, the cross section covariance library, along with covariances for fission product yields and decay data, is used to compute uncertainties in the decay heat produced by a burned reactor fuel assembly.

  9. Covariance Applications in Criticality Safety, Light Water Reactor Analysis, and Spent Fuel Characterization

    SciTech Connect

    Williams, M.L. Wiarda, D.; Ilas, G.; Marshall, W.J.; Rearden, B.T.

    2015-01-15

    A new covariance data library based on ENDF/B-VII.1 was recently processed for the SCALE nuclear analysis code system. The multigroup covariance data are discussed here, along with testing and application results for critical benchmark experiments. The cross section covariance library, along with covariances for fission product yields and decay data, is used to compute uncertainties in the decay heat produced by a burned reactor fuel assembly.

  10. Defining habitat covariates in camera-trap based occupancy studies.

    PubMed

    Niedballa, Jürgen; Sollmann, Rahel; bin Mohamed, Azlan; Bender, Johannes; Wilting, Andreas

    2015-01-01

    In species-habitat association studies, both the type and spatial scale of habitat covariates need to match the ecology of the focal species. We assessed the potential of high-resolution satellite imagery for generating habitat covariates using camera-trapping data from Sabah, Malaysian Borneo, within an occupancy framework. We tested the predictive power of covariates generated from satellite imagery at different resolutions and extents (focal patch sizes, 10-500 m around sample points) on estimates of occupancy patterns of six small to medium sized mammal species/species groups. High-resolution land cover information had considerably more model support for small, patchily distributed habitat features, whereas it had no advantage for large, homogeneous habitat features. A comparison of different focal patch sizes including remote sensing data and an in-situ measure showed that patches with a 50-m radius had most support for the target species. Thus, high-resolution satellite imagery proved to be particularly useful in heterogeneous landscapes, and can be used as a surrogate for certain in-situ measures, reducing field effort in logistically challenging environments. Additionally, remote sensed data provide more flexibility in defining appropriate spatial scales, which we show to impact estimates of wildlife-habitat associations.

  11. Analysis of the Proportional Hazards Model with Sparse Longitudinal Covariates

    PubMed Central

    Cao, Hongyuan; Churpek, Mathew M.; Zeng, Donglin; Fine, Jason P.

    2014-01-01

    Regression analysis of censored failure observations via the proportional hazards model permits time-varying covariates which are observed at death times. In practice, such longitudinal covariates are typically sparse and only measured at infrequent and irregularly spaced follow-up times. Full likelihood analyses of joint models for longitudinal and survival data impose stringent modelling assumptions which are difficult to verify in practice and which are complicated both inferentially and computationally. In this article, a simple kernel weighted score function is proposed with minimal assumptions. Two scenarios are considered: half kernel estimation in which observation ceases at the time of the event and full kernel estimation for data where observation may continue after the event, as with recurrent events data. It is established that these estimators are consistent and asymptotically normal. However, they converge at rates which are slower than the parametric rates which may be achieved with fully observed covariates, with the full kernel method achieving an optimal convergence rate which is superior to that of the half kernel method. Simulation results demonstrate that the large sample approximations are adequate for practical use and may yield improved performance relative to last value carried forward approach and joint modelling method. The analysis of the data from a cardiac arrest study demonstrates the utility of the proposed methods. PMID:26576066

  12. Defining habitat covariates in camera-trap based occupancy studies

    PubMed Central

    Niedballa, Jürgen; Sollmann, Rahel; Mohamed, Azlan bin; Bender, Johannes; Wilting, Andreas

    2015-01-01

    In species-habitat association studies, both the type and spatial scale of habitat covariates need to match the ecology of the focal species. We assessed the potential of high-resolution satellite imagery for generating habitat covariates using camera-trapping data from Sabah, Malaysian Borneo, within an occupancy framework. We tested the predictive power of covariates generated from satellite imagery at different resolutions and extents (focal patch sizes, 10–500 m around sample points) on estimates of occupancy patterns of six small to medium sized mammal species/species groups. High-resolution land cover information had considerably more model support for small, patchily distributed habitat features, whereas it had no advantage for large, homogeneous habitat features. A comparison of different focal patch sizes including remote sensing data and an in-situ measure showed that patches with a 50-m radius had most support for the target species. Thus, high-resolution satellite imagery proved to be particularly useful in heterogeneous landscapes, and can be used as a surrogate for certain in-situ measures, reducing field effort in logistically challenging environments. Additionally, remote sensed data provide more flexibility in defining appropriate spatial scales, which we show to impact estimates of wildlife-habitat associations. PMID:26596779

  13. A model selection approach to analysis of variance and covariance.

    PubMed

    Alber, Susan A; Weiss, Robert E

    2009-06-15

    An alternative to analysis of variance is a model selection approach where every partition of the treatment means into clusters with equal value is treated as a separate model. The null hypothesis that all treatments are equal corresponds to the partition with all means in a single cluster. The alternative hypothesis correspond to the set of all other partitions of treatment means. A model selection approach can also be used for a treatment by covariate interaction, where the null hypothesis and each alternative correspond to a partition of treatments into clusters with equal covariate effects. We extend the partition-as-model approach to simultaneous inference for both treatment main effect and treatment interaction with a continuous covariate with separate partitions for the intercepts and treatment-specific slopes. The model space is the Cartesian product of the intercept partition and the slope partition, and we develop five joint priors for this model space. In four of these priors the intercept and slope partition are dependent. We advise on setting priors over models, and we use the model to analyze an orthodontic data set that compares the frictional resistance created by orthodontic fixtures.

  14. Generalized covariance analysis for partially autonomous deep space missions

    NASA Technical Reports Server (NTRS)

    Boone, Jack N.

    1991-01-01

    A new covariance analysis method is presented that is suitable for the evaluation of multiple impulsive controllers acting on some stochastic process x. The method accommodates batch and sequential estimators with equal ease and accounts for time-delay effects in a natural manner. The formalism is developed in terms of a generalized state vector that is formed from the system state vector x, augmented by various fixed epoch estimates, and a data vector formed from discrete time observations of the system. Recursions are developed for time transition, measurement incorporation, and impulsive control updating of the generalized covariance matrix. Means of limiting the dimensional growth of the generalized state vector via the processes of estimator epoch adjustment and measurement vector deflation are described and the application of numerically stable matrix factorization methods to the generalized covariance recursions is outlined. The method is applied to the Magellan spacecraft to demonstrate the capability of ground-based optimal estimation and control of gyro/star scanner misalignment.

  15. Spatial Covariance between Aesthetic Value & Other Ecosystem Services

    PubMed Central

    Casalegno, Stefano; Inger, Richard; DeSilvey, Caitlin; Gaston, Kevin J.

    2013-01-01

    Mapping the spatial distribution of ecosystem goods and services represents a burgeoning field of research, although how different services covary with one another remains poorly understood. This is particularly true for the covariation of supporting, provisioning and regulating services with cultural services (the non-material benefits people gain from nature). This is largely because of challenges associated with the spatially specific quantification of cultural ecosystem services. We propose an innovative approach for evaluating a cultural service, the perceived aesthetic value of ecosystems, by quantifying geo-tagged digital photographs uploaded to social media resources. Our analysis proceeds from the premise that images will be captured by greater numbers of people in areas that are more highly valued for their aesthetic attributes. This approach was applied in Cornwall, UK, to carry out a spatial analysis of the covariation between ecosystem services: soil carbon stocks, agricultural production, and aesthetic value. Our findings suggest that online geo-tagged images provide an effective metric for mapping a key component of cultural ecosystem services. They also highlight the non-stationarity in the spatial relationships between patterns of ecosystem services. PMID:23840853

  16. Visual saliency estimation by nonlinearly integrating features using region covariances.

    PubMed

    Erdem, Erkut; Erdem, Aykut

    2013-03-18

    To detect visually salient elements of complex natural scenes, computational bottom-up saliency models commonly examine several feature channels such as color and orientation in parallel. They compute a separate feature map for each channel and then linearly combine these maps to produce a master saliency map. However, only a few studies have investigated how different feature dimensions contribute to the overall visual saliency. We address this integration issue and propose to use covariance matrices of simple image features (known as region covariance descriptors in the computer vision community; Tuzel, Porikli, & Meer, 2006) as meta-features for saliency estimation. As low-dimensional representations of image patches, region covariances capture local image structures better than standard linear filters, but more importantly, they naturally provide nonlinear integration of different features by modeling their correlations. We also show that first-order statistics of features could be easily incorporated to the proposed approach to improve the performance. Our experimental evaluation on several benchmark data sets demonstrate that the proposed approach outperforms the state-of-art models on various tasks including prediction of human eye fixations, salient object detection, and image-retargeting.

  17. Bilinear covariants and spinor fields duality in quantum Clifford algebras

    SciTech Connect

    Abłamowicz, Rafał; Gonçalves, Icaro; Rocha, Roldão da

    2014-10-15

    Classification of quantum spinor fields according to quantum bilinear covariants is introduced in a context of quantum Clifford algebras on Minkowski spacetime. Once the bilinear covariants are expressed in terms of algebraic spinor fields, the duality between spinor and quantum spinor fields can be discussed. Thus, by endowing the underlying spacetime with an arbitrary bilinear form with an antisymmetric part in addition to a symmetric spacetime metric, quantum algebraic spinor fields and deformed bilinear covariants can be constructed. They are thus compared to the classical (non quantum) ones. Classes of quantum spinor fields classes are introduced and compared with Lounesto's spinor field classification. A physical interpretation of the deformed parts and the underlying Z-grading is proposed. The existence of an arbitrary bilinear form endowing the spacetime already has been explored in the literature in the context of quantum gravity [S. W. Hawking, “The unpredictability of quantum gravity,” Commun. Math. Phys. 87, 395 (1982)]. Here, it is shown further to play a prominent role in the structure of Dirac, Weyl, and Majorana spinor fields, besides the most general flagpoles and flag-dipoles. We introduce a new duality between the standard and the quantum spinor fields, by showing that when Clifford algebras over vector spaces endowed with an arbitrary bilinear form are taken into account, a mixture among the classes does occur. Consequently, novel features regarding the spinor fields can be derived.

  18. A role for α-adducin (ADD-1) in nematode and human memory

    PubMed Central

    Vukojevic, Vanja; Gschwind, Leo; Vogler, Christian; Demougin, Philippe; de Quervain, Dominique J-F; Papassotiropoulos, Andreas; Stetak, Attila

    2012-01-01

    Identifying molecular mechanisms that underlie learning and memory is one of the major challenges in neuroscience. Taken the advantages of the nematode Caenorhabditis elegans, we investigated α-adducin (add-1) in aversive olfactory associative learning and memory. Loss of add-1 function selectively impaired short- and long-term memory without causing acquisition, sensory, or motor deficits. We showed that α-adducin is required for consolidation of synaptic plasticity, for sustained synaptic increase of AMPA-type glutamate receptor (GLR-1) content and altered GLR-1 turnover dynamics. ADD-1, in a splice-form- and tissue-specific manner, controlled the storage of memories presumably through actin-capping activity. In support of the C. elegans results, genetic variability of the human ADD1 gene was significantly associated with episodic memory performance in healthy young subjects. Finally, human ADD1 expression in nematodes restored loss of C. elegans add-1 gene function. Taken together, our findings support a role for α-adducin in memory from nematodes to humans. Studying the molecular and genetic underpinnings of memory across distinct species may be helpful in the development of novel strategies to treat memory-related diseases. PMID:22307086

  19. Conditioning of the stationary kriging matrices for some well-known covariance models

    SciTech Connect

    Posa, D. )

    1989-10-01

    In this paper, the condition number of the stationary kriging matrix is studied for some well-known covariance models. Indeed, the robustness of the kriging weights is strongly affected by this measure. Such an analysis can justify the choice of a covariance function among other admissible models which could fit a given experimental covariance equally well.

  20. Bayesian Analysis of Structural Equation Models with Nonlinear Covariates and Latent Variables

    ERIC Educational Resources Information Center

    Song, Xin-Yuan; Lee, Sik-Yum

    2006-01-01

    In this article, we formulate a nonlinear structural equation model (SEM) that can accommodate covariates in the measurement equation and nonlinear terms of covariates and exogenous latent variables in the structural equation. The covariates can come from continuous or discrete distributions. A Bayesian approach is developed to analyze the…

  1. Sample Size for Confidence Interval of Covariate-Adjusted Mean Difference

    ERIC Educational Resources Information Center

    Liu, Xiaofeng Steven

    2010-01-01

    This article provides a way to determine adequate sample size for the confidence interval of covariate-adjusted mean difference in randomized experiments. The standard error of adjusted mean difference depends on covariate variance and balance, which are two unknown quantities at the stage of planning sample size. If covariate observations are…

  2. Post-Hartree-Fock studies of the He/Mg(0001) interaction: Anti-corrugation, screening, and pairwise additivity

    NASA Astrophysics Data System (ADS)

    de Lara-Castells, María Pilar; Fernández-Perea, Ricardo; Madzharova, Fani; Voloshina, Elena

    2016-06-01

    The adsorption of noble gases on metallic surfaces represents a paradigmatic case of van-der-Waals (vdW) interaction due to the role of screening effects on the corrugation of the interaction potential [J. L. F. Da Silva et al., Phys. Rev. Lett. 90, 066104 (2003)]. The extremely small adsorption energy of He atoms on the Mg(0001) surface (below 3 meV) and the delocalized nature and mobility of the surface electrons make the He/Mg(0001) system particularly challenging, even for state-of-the-art vdW-corrected density functional-based (vdW-DFT) approaches [M. P. de Lara-Castells et al., J. Chem. Phys. 143, 194701 (2015)]. In this work, we meet this challenge by applying two different procedures. First, the dispersion-corrected second-order Möller-Plesset perturbation theory (MP2C) approach is adopted, using bare metal clusters of increasing size. Second, the method of increments [H. Stoll, J. Chem. Phys. 97, 8449 (1992)] is applied at coupled cluster singles and doubles and perturbative triples level, using embedded cluster models of the metal surface. Both approaches provide clear evidences of the anti-corrugation of the interaction potential: the He atom prefers on-top sites, instead of the expected hollow sites. This is interpreted as a signature of the screening of the He atom by the metal for the on-top configuration. The strong screening in the metal is clearly reflected in the relative contribution of successively deeper surface layers to the main dispersion contribution. Aimed to assist future dynamical simulations, a pairwise potential model for the He/surface interaction as a sum of effective He-Mg pair potentials is also presented, as an improvement of the approximation using isolated He-Mg pairs.

  3. Post-Hartree-Fock studies of the He/Mg(0001) interaction: Anti-corrugation, screening, and pairwise additivity.

    PubMed

    de Lara-Castells, María Pilar; Fernández-Perea, Ricardo; Madzharova, Fani; Voloshina, Elena

    2016-06-28

    The adsorption of noble gases on metallic surfaces represents a paradigmatic case of van-der-Waals (vdW) interaction due to the role of screening effects on the corrugation of the interaction potential [J. L. F. Da Silva et al., Phys. Rev. Lett. 90, 066104 (2003)]. The extremely small adsorption energy of He atoms on the Mg(0001) surface (below 3 meV) and the delocalized nature and mobility of the surface electrons make the He/Mg(0001) system particularly challenging, even for state-of-the-art vdW-corrected density functional-based (vdW-DFT) approaches [M. P. de Lara-Castells et al., J. Chem. Phys. 143, 194701 (2015)]. In this work, we meet this challenge by applying two different procedures. First, the dispersion-corrected second-order Möller-Plesset perturbation theory (MP2C) approach is adopted, using bare metal clusters of increasing size. Second, the method of increments [H. Stoll, J. Chem. Phys. 97, 8449 (1992)] is applied at coupled cluster singles and doubles and perturbative triples level, using embedded cluster models of the metal surface. Both approaches provide clear evidences of the anti-corrugation of the interaction potential: the He atom prefers on-top sites, instead of the expected hollow sites. This is interpreted as a signature of the screening of the He atom by the metal for the on-top configuration. The strong screening in the metal is clearly reflected in the relative contribution of successively deeper surface layers to the main dispersion contribution. Aimed to assist future dynamical simulations, a pairwise potential model for the He/surface interaction as a sum of effective He-Mg pair potentials is also presented, as an improvement of the approximation using isolated He-Mg pairs. PMID:27369533

  4. Pairwise comparisons to reconstruct mean temperature in the Arctic Atlantic Region over the last 2,000 years

    NASA Astrophysics Data System (ADS)

    Hanhijärvi, Sami; Tingley, Martin P.; Korhola, Atte

    2013-10-01

    Existing multi-proxy climate reconstruction methods assume the suitably transformed proxy time series are linearly related to the target climate variable, which is likely a simplifying assumption for many proxy records. Furthermore, with a single exception, these methods face problems with varying temporal resolutions of the proxy data. Here we introduce a new reconstruction method that uses the ordering of all pairs of proxy observations within each record to arrive at a consensus time series that best agrees with all proxy records. The resulting unitless composite time series is subsequently calibrated to the instrumental record to provide an estimate of past climate. By considering only pairwise comparisons, this method, which we call PaiCo, facilitates the inclusion of records with differing temporal resolutions, and relaxes the assumption of linearity to the more general assumption of a monotonically increasing relationship between each proxy series and the target climate variable. We apply PaiCo to a newly assembled collection of high-quality proxy data to reconstruct the mean temperature of the Northernmost Atlantic region, which we call Arctic Atlantic, over the last 2,000 years. The Arctic Atlantic is a dynamically important region known to feature substantial temperature variability over recent millennia, and PaiCo allows for a more thorough investigation of the Arctic Atlantic regional climate as we include a diverse array of terrestrial and marine proxies with annual to multidecadal temporal resolutions. Comparisons of the PaiCo reconstruction to recent reconstructions covering larger areas indicate greater climatic variability in the Arctic Atlantic than for the Arctic as a whole. The Arctic Atlantic reconstruction features temperatures during the Roman Warm Period and Medieval Climate Anomaly that are comparable or even warmer than those of the twentieth century, and coldest temperatures in the middle of the nineteenth century, just prior to the onset

  5. Approximating large resonance parameter covariance matrices with group-wise covariance matrices for advanced nuclear fuel cycle applications

    SciTech Connect

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

    2008-01-01

    The large size of resonance parameter covariance matrices (RPCM) in the actinide region often renders them impractical for dissemination via ENDF. Therefore, a method of approximating the RPCM by a much smaller group-wise covariance matrix (GWCM) is described, implemented, and examined. In this work, 233U RPCM is used to generate GWCM's for the 44 group AMPX, 100 group GE, 171 group VITAMIN-C, and 240 group CSWEG. Each of these GWCM's is then used to compute group-wise uncertainties for the groups of the remaining group structures. The group-wise uncertainties thus obtained are compared with those obtained from a full RPCM, i.e. without the approximation. A systematic comparison of group-wise uncertainties based on GWCM's vs. RPCM, for a variety of group structures, will shed light on the validity of this approximation and may suggest which group structure(s) yield a GWCM that could be used in lieu of the RPCM.

  6. A hierarchical nest survival model integrating incomplete temporally varying covariates.

    PubMed

    Converse, Sarah J; Royle, J Andrew; Adler, Peter H; Urbanek, Richard P; Barzen, Jeb A

    2013-11-01

    Nest success is a critical determinant of the dynamics of avian populations, and nest survival modeling has played a key role in advancing avian ecology and management. Beginning with the development of daily nest survival models, and proceeding through subsequent extensions, the capacity for modeling the effects of hypothesized factors on nest survival has expanded greatly. We extend nest survival models further by introducing an approach to deal with incompletely observed, temporally varying covariates using a hierarchical model. Hierarchical modeling offers a way to separate process and observational components of demographic models to obtain estimates of the parameters of primary interest, and to evaluate structural effects of ecological and management interest. We built a hierarchical model for daily nest survival to analyze nest data from reintroduced whooping cranes (Grus americana) in the Eastern Migratory Population. This reintroduction effort has been beset by poor reproduction, apparently due primarily to nest abandonment by breeding birds. We used the model to assess support for the hypothesis that nest abandonment is caused by harassment from biting insects. We obtained indices of blood-feeding insect populations based on the spatially interpolated counts of insects captured in carbon dioxide traps. However, insect trapping was not conducted daily, and so we had incomplete information on a temporally variable covariate of interest. We therefore supplemented our nest survival model with a parallel model for estimating the values of the missing insect covariates. We used Bayesian model selection to identify the best predictors of daily nest survival. Our results suggest that the black fly Simulium annulus may be negatively affecting nest survival of reintroduced whooping cranes, with decreasing nest survival as abundance of S. annulus increases. The modeling framework we have developed will be applied in the future to a larger data set to evaluate the

  7. A hierarchical nest survival model integrating incomplete temporally varying covariates

    USGS Publications Warehouse

    Converse, Sarah J.; Royle, J. Andrew; Adler, Peter H.; Urbanek, Richard P.; Barzan, Jeb A.

    2013-01-01

    Nest success is a critical determinant of the dynamics of avian populations, and nest survival modeling has played a key role in advancing avian ecology and management. Beginning with the development of daily nest survival models, and proceeding through subsequent extensions, the capacity for modeling the effects of hypothesized factors on nest survival has expanded greatly. We extend nest survival models further by introducing an approach to deal with incompletely observed, temporally varying covariates using a hierarchical model. Hierarchical modeling offers a way to separate process and observational components of demographic models to obtain estimates of the parameters of primary interest, and to evaluate structural effects of ecological and management interest. We built a hierarchical model for daily nest survival to analyze nest data from reintroduced whooping cranes (Grus americana) in the Eastern Migratory Population. This reintroduction effort has been beset by poor reproduction, apparently due primarily to nest abandonment by breeding birds. We used the model to assess support for the hypothesis that nest abandonment is caused by harassment from biting insects. We obtained indices of blood-feeding insect populations based on the spatially interpolated counts of insects captured in carbon dioxide traps. However, insect trapping was not conducted daily, and so we had incomplete information on a temporally variable covariate of interest. We therefore supplemented our nest survival model with a parallel model for estimating the values of the missing insect covariates. We used Bayesian model selection to identify the best predictors of daily nest survival. Our results suggest that the black fly Simulium annulus may be negatively affecting nest survival of reintroduced whooping cranes, with decreasing nest survival as abundance of S. annulus increases. The modeling framework we have developed will be applied in the future to a larger data set to evaluate the

  8. A hierarchical nest survival model integrating incomplete temporally varying covariates.

    PubMed

    Converse, Sarah J; Royle, J Andrew; Adler, Peter H; Urbanek, Richard P; Barzen, Jeb A

    2013-11-01

    Nest success is a critical determinant of the dynamics of avian populations, and nest survival modeling has played a key role in advancing avian ecology and management. Beginning with the development of daily nest survival models, and proceeding through subsequent extensions, the capacity for modeling the effects of hypothesized factors on nest survival has expanded greatly. We extend nest survival models further by introducing an approach to deal with incompletely observed, temporally varying covariates using a hierarchical model. Hierarchical modeling offers a way to separate process and observational components of demographic models to obtain estimates of the parameters of primary interest, and to evaluate structural effects of ecological and management interest. We built a hierarchical model for daily nest survival to analyze nest data from reintroduced whooping cranes (Grus americana) in the Eastern Migratory Population. This reintroduction effort has been beset by poor reproduction, apparently due primarily to nest abandonment by breeding birds. We used the model to assess support for the hypothesis that nest abandonment is caused by harassment from biting insects. We obtained indices of blood-feeding insect populations based on the spatially interpolated counts of insects captured in carbon dioxide traps. However, insect trapping was not conducted daily, and so we had incomplete information on a temporally variable covariate of interest. We therefore supplemented our nest survival model with a parallel model for estimating the values of the missing insect covariates. We used Bayesian model selection to identify the best predictors of daily nest survival. Our results suggest that the black fly Simulium annulus may be negatively affecting nest survival of reintroduced whooping cranes, with decreasing nest survival as abundance of S. annulus increases. The modeling framework we have developed will be applied in the future to a larger data set to evaluate the

  9. 42 CFR 82.16 - How will NIOSH add to monitoring data to remedy limitations of individual monitoring and missed...

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 42 Public Health 1 2011-10-01 2011-10-01 false How will NIOSH add to monitoring data to remedy... PROGRAM ACT OF 2000 Dose Reconstruction Process § 82.16 How will NIOSH add to monitoring data to remedy... to add this to the total dose estimate. For monitoring periods where external dosimetry data...

  10. A covariance-adaptive approach for regularized inversion in linear models

    NASA Astrophysics Data System (ADS)

    Kotsakis, Christopher

    2007-11-01

    The optimal inversion of a linear model under the presence of additive random noise in the input data is a typical problem in many geodetic and geophysical applications. Various methods have been developed and applied for the solution of this problem, ranging from the classic principle of least-squares (LS) estimation to other more complex inversion techniques such as the Tikhonov-Philips regularization, truncated singular value decomposition, generalized ridge regression, numerical iterative methods (Landweber, conjugate gradient) and others. In this paper, a new type of optimal parameter estimator for the inversion of a linear model is presented. The proposed methodology is based on a linear transformation of the classic LS estimator and it satisfies two basic criteria. First, it provides a solution for the model parameters that is optimally fitted (in an average quadratic sense) to the classic LS parameter solution. Second, it complies with an external user-dependent constraint that specifies a priori the error covariance (CV) matrix of the estimated model parameters. The formulation of this constrained estimator offers a unified framework for the description of many regularization techniques that are systematically used in geodetic inverse problems, particularly for those methods that correspond to an eigenvalue filtering of the ill-conditioned normal matrix in the underlying linear model. Our study lies on the fact that it adds an alternative perspective on the statistical properties and the regularization mechanism of many inversion techniques commonly used in geodesy and geophysics, by interpreting them as a family of `CV-adaptive' parameter estimators that obey a common optimal criterion and differ only on the pre-selected form of their error CV matrix under a fixed model design.

  11. Controlling ecological bias in evidence synthesis of trials reporting on collapsed and overlapping covariate categories.

    PubMed

    Govan, L; Ades, A E; Weir, C J; Welton, N J; Langhorne, P

    2010-05-30

    Meta-analysis of randomized controlled trials based on aggregated data is vulnerable to ecological bias if trial results are pooled over covariates that influence the outcome variable, even when the covariate does not modify the treatment effect, or is not associated with the treatment. This paper shows how, when trial results are aggregated over different levels of covariates, the within-study covariate distribution, and the effects of both covariates and treatments can be simultaneously estimated, and ecological bias reduced. Bayesian Markov chain Monte Carlo methods are used. The method is applied to a mixed treatment comparison evidence synthesis of six alternative approaches to post-stroke inpatient care. Results are compared with a model using only the stratified covariate data available, where each stratum is treated as a separate trial, and a model using fully aggregated data, where no covariate data are used. PMID:20191599

  12. Real-Time Access to Meteosat Data Using the ADDE Server Technology

    NASA Astrophysics Data System (ADS)

    Koenig, M.; Gaertner, V. K.

    2006-05-01

    The McIDAS ADDE technology is used by EUMETSAT to provide access to real-time Meteosat-8 image data to globally foster training activities within and outside classroom courses. (McIDAS - Man computer Interactive Data Access System, ADDE - Abstract Data Distribution Environment). The advanced imaging capabilities of Meteosat-8 - a satellite of the Meteosat Second Generation series - provides full disk Earth coverage in 11 spectral channels every 15 minutes. A further 12th channel covers the land surfaces in a 1 km spatial resolution in a solar wavelength. Real-time operational services use the EUMETCast dissemination mechanism for timely access to the image data. EUMETCast covers the geographic area of Europe, Africa, South America and parts of North America and Asia. Details of the EUMETCast system are given in a separate presentation by Gaertner and Koenig in this conference. In addition to EUMETCast, however, for training purposes, access is also made available in near real-time on the basis of the ADDE technology. This is an internet based data access, i.e. it is globally available. ADDE offers the possibility to retrieve only the area of interest, e.g. a special geographic area and only selected channels. This implies that the actual data transfer is small so that the internet is used very efficiently. ADDE was developed as part of the McIDAS software, and is now also freely available in the OpenADDE package (http://www.ssec.wisc.edu/mcidas/software/openadde). Other than McIDAS itself, there is a variety of application packages that are ADDE enabled, as e.g. McIDAS-Lite, the Unidata Integrated Data Viewer, Hydra, IDL, or Matlab. These tools also offer further analysis concepts. Examples will be shown during the presentation. The user community of the ADDE access also needs to be licensed according to the EUMETSAT data policy. After the successful commissioning of Meteosat-9, the data of this satellite will of course be incorporated into the ADDE data provision.

  13. Pairwise velocities of dark matter haloes: a test for the Λ cold dark matter model using the bullet cluster

    NASA Astrophysics Data System (ADS)

    Thompson, Robert; Nagamine, Kentaro

    2012-02-01

    The existence of a bullet cluster (such as 1E 0657-56) poses a challenge to the concordance Λ cold dark matter (ΛCDM) model. Here we investigate the velocity distribution of dark matter (DM) halo pairs in large N-body simulations with differing box sizes (250 h-1 Mpc? Gpc) and resolutions. We examine various basic statistics such as the halo masses, pairwise halo velocities (v12), collisional angles and pair separation distances. We then compare our results to the initial conditions required to reproduce the observational properties of 1E 0657-56 in non-cosmological hydrodynamical simulations. We find that the high-velocity tail of the v12 distribution extends to greater velocities as we increase the simulation box size. We also find that the number of high v12 pairs increases as we increase the particle count and resolution with a fixed box size; however, this increase is mostly due to lower mass haloes which do not match the observed masses of 1E 0657-56. We find that the redshift evolution effect is not very strong for the v12 distribution function between z= 0.0 and z˜ 0.5. We identify some pairs whose v12 resemble the required initial conditions, however, even the best candidates have either wrong halo mass ratios or too large separations. Our simulations suggest that it is very difficult to produce such initial conditions at z= 0.0, 0.296 and 0.489 in comoving volumes as large as (2 h-1 Gpc)3. Based on the extrapolation of our cumulative v12 function, we find that one needs a simulation with a comoving box size of (4.48 h-1 Gpc)3 and 22403 DM particles in order to produce at least one pair of haloes that resembles the required v12 and observed masses of 1E 0657-56. From our simulated v12 probability distribution function, we find that the probability of finding a halo pair with v12≥ 3000 km s-1 and masses ? to be 2.76 × 10-8 at z= 0.489. We conclude that either 1E 0657-56 is incompatible with the concordance ΛCDM universe or the initial conditions

  14. Rigorous covariance propagation of geoid errors to geodetic MDT estimates

    NASA Astrophysics Data System (ADS)

    Pail, R.; Albertella, A.; Fecher, T.; Savcenko, R.

    2012-04-01

    The mean dynamic topography (MDT) is defined as the difference between the mean sea surface (MSS) derived from satellite altimetry, averaged over several years, and the static geoid. Assuming geostrophic conditions, from the MDT the ocean surface velocities as important component of global ocean circulation can be derived from it. Due to the availability of GOCE gravity field models, for the very first time MDT can now be derived solely from satellite observations (altimetry and gravity) down to spatial length-scales of 100 km and even below. Global gravity field models, parameterized in terms of spherical harmonic coefficients, are complemented by the full variance-covariance matrix (VCM). Therefore, for the geoid component a realistic statistical error estimate is available, while the error description of the altimetric component is still an open issue and is, if at all, attacked empirically. In this study we make the attempt to perform, based on the full gravity VCM, rigorous error propagation to derived geostrophic surface velocities, thus also considering all correlations. For the definition of the static geoid we use the third release of the time-wise GOCE model, as well as the satellite-only combination model GOCO03S. In detail, we will investigate the velocity errors resulting from the geoid component in dependence of the harmonic degree, and the impact of using/no using covariances on the MDT errors and its correlations. When deriving an MDT, it is spectrally filtered to a certain maximum degree, which is usually driven by the signal content of the geoid model, by applying isotropic or non-isotropic filters. Since this filtering is acting also on the geoid component, the consistent integration of this filter process into the covariance propagation shall be performed, and its impact shall be quantified. The study will be performed for MDT estimates in specific test areas of particular oceanographic interest.

  15. Energetic Consistency and Coupling of the Mean and Covariance Dynamics

    NASA Technical Reports Server (NTRS)

    Cohn, Stephen E.

    2008-01-01

    The dynamical state of the ocean and atmosphere is taken to be a large dimensional random vector in a range of large-scale computational applications, including data assimilation, ensemble prediction, sensitivity analysis, and predictability studies. In each of these applications, numerical evolution of the covariance matrix of the random state plays a central role, because this matrix is used to quantify uncertainty in the state of the dynamical system. Since atmospheric and ocean dynamics are nonlinear, there is no closed evolution equation for the covariance matrix, nor for the mean state. Therefore approximate evolution equations must be used. This article studies theoretical properties of the evolution equations for the mean state and covariance matrix that arise in the second-moment closure approximation (third- and higher-order moment discard). This approximation was introduced by EPSTEIN [1969] in an early effort to introduce a stochastic element into deterministic weather forecasting, and was studied further by FLEMING [1971a,b], EPSTEIN and PITCHER [1972], and PITCHER [1977], also in the context of atmospheric predictability. It has since fallen into disuse, with a simpler one being used in current large-scale applications. The theoretical results of this article make a case that this approximation should be reconsidered for use in large-scale applications, however, because the second moment closure equations possess a property of energetic consistency that the approximate equations now in common use do not possess. A number of properties of solutions of the second-moment closure equations that result from this energetic consistency will be established.

  16. Einstein's investigations of Galilean covariant electrodynamics prior to 1905

    NASA Astrophysics Data System (ADS)

    Norton, John D.

    2004-11-01

    Einstein learned from the magnet and conductor thought experiment how to use field transformation laws to extend the covariance of Maxwells electrodynamics. If he persisted in his use of this device, he would have found that the theory cleaves into two Galilean covariant parts, each with different field transformation laws. The tension between the two parts reflects a failure not mentioned by Einstein: that the relativity of motion manifested by observables in the magnet and conductor thought experiment does not extend to all observables in electrodynamics. An examination of Ritz's work shows that Einstein's early view could not have coincided with Ritz's on an emission theory of light, but only with that of a conveniently reconstructed Ritz. One Ritz-like emission theory, attributed by Pauli to Ritz, proves to be a natural extension of the Galilean covariant part of Maxwell's theory that happens also to accommodate the magnet and conductor thought experiment. Einstein's famous chasing a light beam thought experiment fails as an objection to an ether-based, electrodynamical theory of light. However it would allow Einstein to formulate his general objections to all emission theories of light in a very sharp form. Einstein found two well known experimental results of 18th and 19th century optics compelling (Fizeau's experiment, stellar aberration), while the accomplished Michelson-Morley experiment played no memorable role. I suggest they owe their importance to their providing a direct experimental grounding for Lorentz' local time, the precursor of Einstein's relativity of simultaneity, and doing it essentially independently of electrodynamical theory. I attribute Einstein's success to his determination to implement a principle of relativity in electrodynamics, but I urge that we not invest this stubbornness with any mystical prescience.

  17. a Reference for Our Covariant Hamiltonian Boundary Term

    NASA Astrophysics Data System (ADS)

    Nester, James M.; Chen, Chiang-Mei; Liu, Jian-Liang; Sun, Gang

    2015-01-01

    Our covariant Hamiltonian for dynamic geometry generates the evolution of a spatial region along a vector field. It includes a boundary term which determines both the value of the Hamiltonian and the boundary conditions. The value gives the quasi-local quantities: energy-momentum, angular-momentum/center-of-mass. The boundary term depends not only on the dynamical variables but also on their reference values, the latter determine the ground state (having vanishing quasi-local quantities). For our preferred boundary term for Einstein's GR we propose using 4D isometric matching and extremizing the energy to determine the "best matched" reference metric and connection values.

  18. Implementation of optimal phase-covariant cloning machines

    SciTech Connect

    Sciarrino, Fabio; De Martini, Francesco

    2007-07-15

    The optimal phase-covariant quantum cloning machine (PQCM) broadcasts the information associated to an input qubit into a multiqubit system, exploiting a partial a priori knowledge of the input state. This additional a priori information leads to a higher fidelity than for the universal cloning. The present article first analyzes different innovative schemes to implement the 1{yields}3 PQCM. The method is then generalized to any 1{yields}M machine for an odd value of M by a theoretical approach based on the general angular momentum formalism. Finally different experimental schemes based either on linear or nonlinear methods and valid for single photon polarization encoded qubits are discussed.

  19. Role of Experiment Covariance in Cross Section Adjustments

    SciTech Connect

    Giuseppe Palmiotti; M. Salvatores

    2014-06-01

    This paper is dedicated to the memory of R. D. McKnight, which gave a seminal contribution in establishing methodology and rigorous approach in the evaluation of the covariance of reactor physics integral experiments. His original assessment of the ZPPR experiment uncertainties and correlations has made nuclear data adjustments, based on these experiments, much more robust and reliable. In the present paper it has been shown with some numerical examples the actual impact on an adjustment of accounting for or neglecting such correlations.

  20. FBST for covariance structures of generalized Gompertz models

    NASA Astrophysics Data System (ADS)

    Maranhão, Viviane Teles de Lucca; Lauretto, Marcelo De Souza; Stern, Julio Michael

    2012-10-01

    The Gompertz distribution is commonly used in biology for modeling fatigue and mortality. This paper studies a class of models proposed by Adham and Walker, featuring a Gompertz type distribution where the dependence structure is modeled by a lognormal distribution, and develops a new multivariate formulation that facilitates several numerical and computational aspects. This paper also implements the FBST, the Full Bayesian Significance Test for pertinent sharp (precise) hypotheses on the lognormal covariance structure. The FBST's e-value, ev(H), gives the epistemic value of hypothesis, H, or the value of evidence in the observed in support of H.