WorldWideScience

Sample records for maximum pairwise lod

  1. The power and robustness of maximum LOD score statistics.

    Science.gov (United States)

    Yoo, Y J; Mendell, N R

    2008-07-01

    The maximum LOD score statistic is extremely powerful for gene mapping when calculated using the correct genetic parameter value. When the mode of genetic transmission is unknown, the maximum of the LOD scores obtained using several genetic parameter values is reported. This latter statistic requires higher critical value than the maximum LOD score statistic calculated from a single genetic parameter value. In this paper, we compare the power of maximum LOD scores based on three fixed sets of genetic parameter values with the power of the LOD score obtained after maximizing over the entire range of genetic parameter values. We simulate family data under nine generating models. For generating models with non-zero phenocopy rates, LOD scores maximized over the entire range of genetic parameters yielded greater power than maximum LOD scores for fixed sets of parameter values with zero phenocopy rates. No maximum LOD score was consistently more powerful than the others for generating models with a zero phenocopy rate. The power loss of the LOD score maximized over the entire range of genetic parameters, relative to the maximum LOD score calculated using the correct genetic parameter value, appeared to be robust to the generating models.

  2. Percentiles of the null distribution of 2 maximum lod score tests.

    Science.gov (United States)

    Ulgen, Ayse; Yoo, Yun Joo; Gordon, Derek; Finch, Stephen J; Mendell, Nancy R

    2004-01-01

    We here consider the null distribution of the maximum lod score (LOD-M) obtained upon maximizing over transmission model parameters (penetrance values, dominance, and allele frequency) as well as the recombination fraction. Also considered is the lod score maximized over a fixed choice of genetic model parameters and recombination-fraction values set prior to the analysis (MMLS) as proposed by Hodge et al. The objective is to fit parametric distributions to MMLS and LOD-M. Our results are based on 3,600 simulations of samples of n = 100 nuclear families ascertained for having one affected member and at least one other sibling available for linkage analysis. Each null distribution is approximately a mixture p(2)(0) + (1 - p)(2)(v). The values of MMLS appear to fit the mixture 0.20(2)(0) + 0.80chi(2)(1.6). The mixture distribution 0.13(2)(0) + 0.87chi(2)(2.8). appears to describe the null distribution of LOD-M. From these results we derive a simple method for obtaining critical values of LOD-M and MMLS. Copyright 2004 S. Karger AG, Basel

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

    Directory of Open Access Journals (Sweden)

    Manuel Gil

    2014-09-01

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

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

    Science.gov (United States)

    Gil, Manuel

    2014-01-01

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

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

    Science.gov (United States)

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

    2017-10-01

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

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

    Directory of Open Access Journals (Sweden)

    Richard R Stein

    2015-07-01

    Full Text Available 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.

  7. Analysis of Pairwise Interactions in a Maximum Likelihood Sense to Identify Leaders in a Group

    Directory of Open Access Journals (Sweden)

    Violet Mwaffo

    2017-07-01

    Full Text Available Collective motion in animal groups manifests itself in the form of highly coordinated maneuvers determined by local interactions among individuals. A particularly critical question in understanding the mechanisms behind such interactions is to detect and classify leader–follower relationships within the group. In the technical literature of coupled dynamical systems, several methods have been proposed to reconstruct interaction networks, including linear correlation analysis, transfer entropy, and event synchronization. While these analyses have been helpful in reconstructing network models from neuroscience to public health, rules on the most appropriate method to use for a specific dataset are lacking. Here, we demonstrate the possibility of detecting leaders in a group from raw positional data in a model-free approach that combines multiple methods in a maximum likelihood sense. We test our framework on synthetic data of groups of self-propelled Vicsek particles, where a single agent acts as a leader and both the size of the interaction region and the level of inherent noise are systematically varied. To assess the feasibility of detecting leaders in real-world applications, we study a synthetic dataset of fish shoaling, generated by using a recent data-driven model for social behavior, and an experimental dataset of pharmacologically treated zebrafish. Not only does our approach offer a robust strategy to detect leaders in synthetic data but it also allows for exploring the role of psychoactive compounds on leader–follower relationships.

  8. The lod score method.

    Science.gov (United States)

    Rice, J P; Saccone, N L; Corbett, J

    2001-01-01

    The lod score method originated in a seminal article by Newton Morton in 1955. The method is broadly concerned with issues of power and the posterior probability of linkage, ensuring that a reported linkage has a high probability of being a true linkage. In addition, the method is sequential, so that pedigrees or lod curves may be combined from published reports to pool data for analysis. This approach has been remarkably successful for 50 years in identifying disease genes for Mendelian disorders. After discussing these issues, we consider the situation for complex disorders, where the maximum lod score (MLS) statistic shares some of the advantages of the traditional lod score approach but is limited by unknown power and the lack of sharing of the primary data needed to optimally combine analytic results. We may still learn from the lod score method as we explore new methods in molecular biology and genetic analysis to utilize the complete human DNA sequence and the cataloging of all human genes.

  9. Two-locus maximum lod score analysis of a multifactorial trait: joint consideration of IDDM2 and IDDM4 with IDDM1 in type 1 diabetes.

    Science.gov (United States)

    Cordell, H J; Todd, J A; Bennett, S T; Kawaguchi, Y; Farrall, M

    1995-10-01

    To investigate the genetic component of multifactorial diseases such as type 1 (insulin-dependent) diabetes mellitus (IDDM), models involving the joint action of several disease loci are important. These models can give increased power to detect an effect and a greater understanding of etiological mechanisms. Here, we present an extension of the maximum lod score method of N. Risch, which allows the simultaneous detection and modeling of two unlinked disease loci. Genetic constraints on the identical-by-descent sharing probabilities, analogous to the "triangle" restrictions in the single-locus method, are derived, and the size and power of the test statistics are investigated. The method is applied to affected-sib-pair data, and the joint effects of IDDM1 (HLA) and IDDM2 (the INS VNTR) and of IDDM1 and IDDM4 (FGF3-linked) are assessed with relation to the development of IDDM. In the presence of genetic heterogeneity, there is seen to be a significant advantage in analyzing more than one locus simultaneously. Analysis of these families indicates that the effects at IDDM1 and IDDM2 are well described by a multiplicative genetic model, while those at IDDM1 and IDDM4 follow a heterogeneity model.

  10. Two-locus maximum lod score analysis of a multifactorial trait: Joint consideration of IDDM2 and IDDM4 with IDDMI in type 1 diabetes

    Energy Technology Data Exchange (ETDEWEB)

    Cordell, H.J.; Todd, J.A.; Bennett, S.T. [Univ. of Oxford (United Kingdom)] [and others

    1995-10-01

    To investigate the genetic component of multifactorial diseases such as type 1 (insulin-dependent) diabetes mellitus (IDDM), models involving the joint action of several disease loci are important. These models can give increased power to detect an effect and a greater understanding of etiological mechanisms. Here, we present an extension of the maximum lod score method of N. Risch, which allows the simultaneous detection and modeling of two unlinked disease loci. Genetic constraints on the identical-by-descent sharing probabilities, analogous to the {open_quotes}triangle{close_quotes} restrictions in the single-locus method, are derived, and the size and power of the test statistics are investigated. The method is applied to affected-sib-pair data, and the joint effects of IDDM1 (HLA) and IDDM2 (the INS VNTR) and of IDDM1 and IDDM4 (FGF3-linked) are assessed with relation to the development of IDDM. In the presence of genetic heterogeneity, there is seen to be a significant advantage in analyzing more than one locus simultaneously. Analysis of these families indicates that the effects at IDDM1 and IDDM2 are well described by a multiplicative genetic model, while those at IDDM1 and IDDM4 follow a heterogeneity model. 17 refs., 9 tabs.

  11. Automatic LOD selection

    OpenAIRE

    Forsman, Isabelle

    2017-01-01

    In this paper a method to automatically generate transition distances for LOD, improving image stability and performance is presented. Three different methods were tested all measuring the change between two level of details using the spatial frequency. The methods were implemented as an optional pre-processing step in order to determine the transition distances from multiple view directions. During run-time both view direction based selection and the furthest distance for each direction was ...

  12. Pairwise Choice Markov Chains

    OpenAIRE

    Ragain, Stephen; Ugander, Johan

    2016-01-01

    As datasets capturing human choices grow in richness and scale---particularly in online domains---there is an increasing need for choice models that escape traditional choice-theoretic axioms such as regularity, stochastic transitivity, and Luce's choice axiom. In this work we introduce the Pairwise Choice Markov Chain (PCMC) model of discrete choice, an inferentially tractable model that does not assume any of the above axioms while still satisfying the foundational axiom of uniform expansio...

  13. LOD estimation from DORIS observations

    Science.gov (United States)

    Stepanek, Petr; Filler, Vratislav; Buday, Michal; Hugentobler, Urs

    2016-04-01

    The difference between astronomically determined duration of the day and 86400 seconds is called length of day (LOD). The LOD could be also understood as the daily rate of the difference between the Universal Time UT1, based on the Earth rotation, and the International Atomic Time TAI. The LOD is estimated using various Satellite Geodesy techniques as GNSS and SLR, while absolute UT1-TAI difference is precisely determined by VLBI. Contrary to other IERS techniques, the LOD estimation using DORIS (Doppler Orbitography and Radiopositioning Integrated by satellite) measurement did not achieve a geodetic accuracy in the past, reaching the precision at the level of several ms per day. However, recent experiments performed by IDS (International DORIS Service) analysis centre at Geodetic Observatory Pecny show a possibility to reach accuracy around 0.1 ms per day, when not adjusting the cross-track harmonics in the Satellite orbit model. The paper presents the long term LOD series determined from the DORIS solutions. The series are compared with C04 as the reference. Results are discussed in the context of accuracy achieved with GNSS and SLR. Besides the multi-satellite DORIS solutions, also the LOD series from the individual DORIS satellite solutions are analysed.

  14. Pairwise harmonics for shape analysis

    KAUST Repository

    Zheng, Youyi

    2013-07-01

    This paper introduces a simple yet effective shape analysis mechanism for geometry processing. Unlike traditional shape analysis techniques which compute descriptors per surface point up to certain neighborhoods, we introduce a shape analysis framework in which the descriptors are based on pairs of surface points. Such a pairwise analysis approach leads to a new class of shape descriptors that are more global, discriminative, and can effectively capture the variations in the underlying geometry. Specifically, we introduce new shape descriptors based on the isocurves of harmonic functions whose global maximum and minimum occur at the point pair. We show that these shape descriptors can infer shape structures and consistently lead to simpler and more efficient algorithms than the state-of-the-art methods for three applications: intrinsic reflectional symmetry axis computation, matching shape extremities, and simultaneous surface segmentation and skeletonization. © 2012 IEEE.

  15. Lod score curves for phase-unknown matings.

    Science.gov (United States)

    Hulbert-Shearon, T; Boehnke, M; Lange, K

    1996-01-01

    For a phase-unknown nuclear family, we show that the likelihood and lod score are unimodal, and we describe conditions under which the maximum occurs at recombination fraction theta = 0, theta = 1/2, and 0 < theta < 1/2. These simply stated necessary and sufficient conditions seem to have escaped the notice of previous statistical geneticists.

  16. Meteorological interpretation of transient LOD changes

    Science.gov (United States)

    Masaki, Y.

    2008-04-01

    The Earth’s spin rate is mainly changed by zonal winds. For example, seasonal changes in global atmospheric circulation and episodic changes accompanied with El Nĩ os are clearly detected n in the Length-of-day (LOD). Sub-global to regional meteorological phenomena can also change the wind field, however, their effects on the LOD are uncertain because such LOD signals are expected to be subtle and transient. In our previous study (Masaki, 2006), we introduced atmospheric pressure gradients in the upper atmosphere in order to obtain a rough picture of the meteorological features that can change the LOD. In this presentation, we compare one-year LOD data with meteorological elements (winds, temperature, pressure, etc.) and make an attempt to link transient LOD changes with sub-global meteorological phenomena.

  17. Pragmatic Use of LOD - a Modular Approach

    DEFF Research Database (Denmark)

    Treldal, Niels; Vestergaard, Flemming; Karlshøj, Jan

    and reliability of deliveries along with use-case-specific information requirements provides a pragmatic approach for a LOD concept. The proposed solution combines LOD requirement definitions with Information Delivery Manual-based use case requirements to match the specific needs identified for a LOD framework......The concept of Level of Development (LOD) is a simple approach to specifying the requirements for the content of object-oriented models in a Building Information Modelling process. The concept has been implemented in many national and organization-specific variations and, in recent years, several...

  18. Pareto optimal pairwise sequence alignment.

    Science.gov (United States)

    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.

  19. LOD-a-lot : A queryable dump of the LOD cloud

    NARCIS (Netherlands)

    Fernández, Javier D.; Beek, Wouter; Martínez-Prieto, Miguel A.; Arias, Mario

    2017-01-01

    LOD-a-lot democratizes access to the Linked Open Data (LOD) Cloud by serving more than 28 billion unique triples from 650, K datasets over a single self-indexed file. This corpus can be queried online with a sustainable Linked Data Fragments interface, or downloaded and consumed locally: LOD-a-lot

  20. Posterior probability of linkage and maximal lod score.

    Science.gov (United States)

    Génin, E; Martinez, M; Clerget-Darpoux, F

    1995-01-01

    To detect linkage between a trait and a marker, Morton (1955) proposed to calculate the lod score z(theta 1) at a given value theta 1 of the recombination fraction. If z(theta 1) reaches +3 then linkage is concluded. However, in practice, lod scores are calculated for different values of the recombination fraction between 0 and 0.5 and the test is based on the maximum value of the lod score Zmax. The impact of this deviation of the test on the probability that in fact linkage does not exist, when linkage was concluded, is documented here. This posterior probability of no linkage can be derived by using Bayes' theorem. It is less than 5% when the lod score at a predetermined theta 1 is used for the test. But, for a Zmax of +3, we showed that it can reach 16.4%. Thus, considering a composite alternative hypothesis instead of a single one decreases the reliability of the test. The reliability decreases rapidly when Zmax is less than +3. Given a Zmax of +2.5, there is a 33% chance that linkage does not exist. Moreover, the posterior probability depends not only on the value of Zmax but also jointly on the family structures and on the genetic model. For a given Zmax, the chance that linkage exists may then vary.

  1. Comparison of empirical strategies to maximize GENEHUNTER lod scores.

    Science.gov (United States)

    Chen, C H; Finch, S J; Mendell, N R; Gordon, D

    1999-01-01

    We compare four strategies for finding the settings of genetic parameters that maximize the lod scores reported in GENEHUNTER 1.2. The four strategies are iterated complete factorial designs, iterated orthogonal Latin hypercubes, evolutionary operation, and numerical optimization. The genetic parameters that are set are the phenocopy rate, penetrance, and disease allele frequency; both recessive and dominant models are considered. We selected the optimization of a recessive model on the Collaborative Study on the Genetics of Alcoholism (COGA) data of chromosome 1 for complete analysis. Convergence to a setting producing a local maximum required the evaluation of over 100 settings (for a time budget of 800 minutes on a Pentium II 300 MHz PC). Two notable local maxima were detected, suggesting the need for a more extensive search before claiming that a global maximum had been found. The orthogonal Latin hypercube design was the best strategy for finding areas that produced high lod scores with small numbers of evaluations. Numerical optimization starting from a region producing high lod scores was the strategy that found the highest maximum observed.

  2. The power to detect linkage in complex disease by means of simple LOD-score analyses.

    Science.gov (United States)

    Greenberg, D A; Abreu, P; Hodge, S E

    1998-09-01

    Maximum-likelihood analysis (via LOD score) provides the most powerful method for finding linkage when the mode of inheritance (MOI) is known. However, because one must assume an MOI, the application of LOD-score analysis to complex disease has been questioned. Although it is known that one can legitimately maximize the maximum LOD score with respect to genetic parameters, this approach raises three concerns: (1) multiple testing, (2) effect on power to detect linkage, and (3) adequacy of the approximate MOI for the true MOI. We evaluated the power of LOD scores to detect linkage when the true MOI was complex but a LOD score analysis assumed simple models. We simulated data from 14 different genetic models, including dominant and recessive at high (80%) and low (20%) penetrances, intermediate models, and several additive two-locus models. We calculated LOD scores by assuming two simple models, dominant and recessive, each with 50% penetrance, then took the higher of the two LOD scores as the raw test statistic and corrected for multiple tests. We call this test statistic "MMLS-C." We found that the ELODs for MMLS-C are >=80% of the ELOD under the true model when the ELOD for the true model is >=3. Similarly, the power to reach a given LOD score was usually >=80% that of the true model, when the power under the true model was >=60%. These results underscore that a critical factor in LOD-score analysis is the MOI at the linked locus, not that of the disease or trait per se. Thus, a limited set of simple genetic models in LOD-score analysis can work well in testing for linkage.

  3. Sensitivity of lod scores to changes in diagnostic status.

    Science.gov (United States)

    Hodge, S E; Greenberg, D A

    1992-05-01

    This paper investigates effects on lod scores when one individual in a data set changes diagnostic or recombinant status. First we examine the situation in which a single offspring in a nuclear family changes status. The nuclear-family situation, in addition to being of interest in its own right, also has general theoretical importance, since nuclear families are "transparent"; that is, one can track genetic events more precisely in nuclear families than in complex pedigrees. We demonstrate that in nuclear families log10 [(1-theta)/theta] gives an upper limit on the impact that a single offspring's change in status can have on the lod score at that recombination fraction (theta). These limits hold for a fully penetrant dominant condition and fully informative marker, in either phase-known or phase-unknown matings. Moreover, log10 [(1-theta)/theta] (where theta denotes the value of theta at which Zmax occurs) gives an upper limit on the impact of a single offspring's status change on the maximum lod score (Zmax). In extended pedigrees, in contrast to nuclear families, no comparable limit can be set on the impact of a single individual on the lod score. Complex pedigrees are subject to both stabilizing and destabilizing influences, and these are described. Finally, we describe a "sensitivity analysis," in which, after all linkage analysis is completed, every informative individual in the data set is changed, one at a time, to see the effect which each separate change has on the lod scores. The procedure includes identifying "critical individuals," i.e., those who would have the greatest impact on the lod scores, should their diagnostic status in fact change. To illustrate use of the sensitivity analysis, we apply it to the large bipolar pedigree reported by Egeland et al. and Kelsoe et al. We show that the changes in lod scores observed there, on the order of 1.1-1.2 per person, are not unusual. We recommend that investigators include a sensitivity analysis as a

  4. Systematic effects in LOD from SLR observations

    Science.gov (United States)

    Bloßfeld, Mathis; Gerstl, Michael; Hugentobler, Urs; Angermann, Detlef; Müller, Horst

    2014-09-01

    Beside the estimation of station coordinates and the Earth’s gravity field, laser ranging observations to near-Earth satellites can be used to determine the rotation of the Earth. One parameter of this rotation is ΔLOD (excess Length Of Day) which describes the excess revolution time of the Earth w.r.t. 86,400 s. Due to correlations among the different parameter groups, it is difficult to obtain reliable estimates for all parameters. In the official ΔLOD products of the International Earth Rotation and Reference Systems Service (IERS), the ΔLOD information determined from laser ranging observations is excluded from the processing. In this paper, we study the existing correlations between ΔLOD, the orbital node Ω, the even zonal gravity field coefficients, cross-track empirical accelerations and relativistic accelerations caused by the Lense-Thirring and deSitter effect in detail using first order Gaussian perturbation equations. We found discrepancies due to different a priories by using different gravity field models of up to 1.0 ms for polar orbits at an altitude of 500 km and up to 40.0 ms, if the gravity field coefficients are estimated using only observations to LAGEOS 1. If observations to LAGEOS 2 are included, reliable ΔLOD estimates can be achieved. Nevertheless, an impact of the a priori gravity field even on the multi-satellite ΔLOD estimates can be clearly identified. Furthermore, we investigate the effect of empirical cross-track accelerations and the effect of relativistic accelerations of near-Earth satellites on ΔLOD. A total effect of 0.0088 ms is caused by not modeled Lense-Thirring and deSitter terms. The partial derivatives of these accelerations w.r.t. the position and velocity of the satellite cause very small variations (0.1 μs) on ΔLOD.

  5. Theory of pairwise lesion interaction

    International Nuclear Information System (INIS)

    Harder, Dietrich; Virsik-Peuckert, Patricia; Bartels, Ernst

    1992-01-01

    A comparison between repair time constants measured both at the molecular and cellular levels has shown that the DNA double strand break is the molecular change of key importance in the causation of cellular effects such as chromosome aberrations and cell inactivation. Cell fusion experiments provided the evidence that it needs the pairwise interaction between two double strand breaks - or more exactly between the two ''repair sites'' arising from them in the course of enzymatic repair - to provide the faulty chromatin crosslink which leads to cytogenetic and cytolethal effects. These modern experiments have confirmed the classical assumption of pairwise lesion interaction (PLI) on which the models of Lea and Neary were based. It seems worthwhile to continue and complete the mathematical treatment of their proposed mechanism in order to show in quantitative terms that the well-known fractionation, protraction and linear energy transfer (LET) irradiation effects are consequences of or can at least be partly attributed to PLI. Arithmetic treatment of PLI - a second order reaction - has also the advantage of providing a prerequisite for further investigations into the stages of development of misrepair products such as chromatin crosslinks. It has been possible to formulate a completely arithmetic theory of PLI by consequently applying three biophysically permitted approximations - pure first order lesion repair kinetics, dose-independent repair time constants and low yield of the ionization/lesion conversion. The mathematical approach will be summarized here, including several formulae not elaborated at the time of previous publications. We will also study an application which sheds light on the chain of events involved in PLI. (author)

  6. Lod scores for gene mapping in the presence of marker map uncertainty.

    Science.gov (United States)

    Stringham, H M; Boehnke, M

    2001-07-01

    Multipoint lod scores are typically calculated for a grid of locus positions, moving the putative disease locus across a fixed map of genetic markers. Changing the order of a set of markers and/or the distances between the markers can make a substantial difference in the resulting lod score curve and the location and height of its maximum. The typical approach of using the best maximum likelihood marker map is not easily justified if other marker orders are nearly as likely and give substantially different lod score curves. To deal with this problem, we propose three weighted multipoint lod score statistics that make use of information from all plausible marker orders. In each of these statistics, the information conditional on a particular marker order is included in a weighted sum, with weight equal to the posterior probability of that order. We evaluate the type 1 error rate and power of these three statistics on the basis of results from simulated data, and compare these results to those obtained using the best maximum likelihood map and the map with the true marker order. We find that the lod score based on a weighted sum of maximum likelihoods improves on using only the best maximum likelihood map, having a type 1 error rate and power closest to that of using the true marker order in the simulation scenarios we considered. Copyright 2001 Wiley-Liss, Inc.

  7. R-LODs: fast LOD-based ray tracing of massive models

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Sung-Eui; Lauterbach, Christian; Manocha, Dinesh

    2006-08-25

    We present a novel LOD (level-of-detail) algorithm to accelerate ray tracing of massive models. Our approach computes drastic simplifications of the model and the LODs are well integrated with the kd-tree data structure. We introduce a simple and efficient LOD metric to bound the error for primary and secondary rays. The LOD representation has small runtime overhead and our algorithm can be combined with ray coherence techniques and cache-coherent layouts to improve the performance. In practice, the use of LODs can alleviate aliasing artifacts and improve memory coherence. We implement our algorithm on both 32bit and 64bit machines and able to achieve up to 2.20 times improvement in frame rate of rendering models consisting of tens or hundreds of millions of triangles with little loss in image quality.

  8. Frank: The LOD cloud at your fingertips?

    NARCIS (Netherlands)

    Beek, Wouter; Rietveld, Laurens

    2015-01-01

    Large-scale, algorithmic access to LOD Cloud data has been hampered by the absence of queryable endpoints for many datasets, a plethora of serialization formats, and an abundance of idiosyncrasies such as syntax errors. As of late, very large-scale — hundreds of thousands of document, tens of

  9. Frank : The LOD cloud at your fingertips?

    NARCIS (Netherlands)

    Beek, Wouter; Rietveld, Laurens

    2015-01-01

    Large-scale, algorithmic access to LOD Cloud data has been hampered by the absence of queryable endpoints for many datasets, a plethora of serialization formats, and an abundance of idiosyncrasies such as syntax errors. As of late, very large-scale - hundreds of thousands of document, tens of

  10. LOD lab : Scalable linked data processing

    NARCIS (Netherlands)

    Beek, Wouter; Rietveld, Laurens; Ilievski, F.; Schlobach, Stefan

    2017-01-01

    With tens if not hundreds of billions of logical statements, the Linked Open Data (LOD) is one of the biggest knowledge bases ever built. As such it is a gigantic source of information for applications in various domains, but also given its size an ideal test-bed for knowledge representation and

  11. LOD 1 VS. LOD 2 - Preliminary Investigations Into Differences in Mobile Rendering Performance

    Science.gov (United States)

    Ellul, C.; Altenbuchner, J.

    2013-09-01

    The increasing availability, size and detail of 3D City Model datasets has led to a challenge when rendering such data on mobile devices. Understanding the limitations to the usability of such models on these devices is particularly important given the broadening range of applications - such as pollution or noise modelling, tourism, planning, solar potential - for which these datasets and resulting visualisations can be utilized. Much 3D City Model data is created by extrusion of 2D topographic datasets, resulting in what is known as Level of Detail (LoD) 1 buildings - with flat roofs. However, in the UK the National Mapping Agency (the Ordnance Survey, OS) is now releasing test datasets to Level of Detail (LoD) 2 - i.e. including roof structures. These datasets are designed to integrate with the LoD 1 datasets provided by the OS, and provide additional detail in particular on larger buildings and in town centres. The availability of such integrated datasets at two different Levels of Detail permits investigation into the impact of the additional roof structures (and hence the display of a more realistic 3D City Model) on rendering performance on a mobile device. This paper describes preliminary work carried out to investigate this issue, for the test area of the city of Sheffield (in the UK Midlands). The data is stored in a 3D spatial database as triangles and then extracted and served as a web-based data stream which is queried by an App developed on the mobile device (using the Android environment, Java and OpenGL for graphics). Initial tests have been carried out on two dataset sizes, for the city centre and a larger area, rendering the data onto a tablet to compare results. Results of 52 seconds for rendering LoD 1 data, and 72 seconds for LoD 1 mixed with LoD 2 data, show that the impact of LoD 2 is significant.

  12. Doctoral Program Selection Using Pairwise Comparisons.

    Science.gov (United States)

    Tadisina, Suresh K.; Bhasin, Vijay

    1989-01-01

    The application of a pairwise comparison methodology (Saaty's Analytic Hierarchy Process) to the doctoral program selection process is illustrated. A hierarchy for structuring and facilitating the doctoral program selection decision is described. (Author/MLW)

  13. Statistical physics of pairwise probability models

    Directory of Open Access Journals (Sweden)

    Yasser Roudi

    2009-11-01

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

  14. Extension of the lod score: the mod score.

    Science.gov (United States)

    Clerget-Darpoux, F

    2001-01-01

    In 1955 Morton proposed the lod score method both for testing linkage between loci and for estimating the recombination fraction between them. If a disease is controlled by a gene at one of these loci, the lod score computation requires the prior specification of an underlying model that assigns the probabilities of genotypes from the observed phenotypes. To address the case of linkage studies for diseases with unknown mode of inheritance, we suggested (Clerget-Darpoux et al., 1986) extending the lod score function to a so-called mod score function. In this function, the variables are both the recombination fraction and the disease model parameters. Maximizing the mod score function over all these parameters amounts to maximizing the probability of marker data conditional on the disease status. Under the absence of linkage, the mod score conforms to a chi-square distribution, with extra degrees of freedom in comparison to the lod score function (MacLean et al., 1993). The mod score is asymptotically maximum for the true disease model (Clerget-Darpoux and Bonaïti-Pellié, 1992; Hodge and Elston, 1994). Consequently, the power to detect linkage through mod score will be highest when the space of models where the maximization is performed includes the true model. On the other hand, one must avoid overparametrization of the model space. For example, when the approach is applied to affected sibpairs, only two constrained disease model parameters should be used (Knapp et al., 1994) for the mod score maximization. It is also important to emphasize the existence of a strong correlation between the disease gene location and the disease model. Consequently, there is poor resolution of the location of the susceptibility locus when the disease model at this locus is unknown. Of course, this is true regardless of the statistics used. The mod score may also be applied in a candidate gene strategy to model the potential effect of this gene in the disease. Since, however, it

  15. Metabolic network prediction through pairwise rational kernels.

    Science.gov (United States)

    Roche-Lima, Abiel; Domaratzki, Michael; Fristensky, Brian

    2014-09-26

    Metabolic networks are represented by the set of metabolic pathways. Metabolic pathways are a series of biochemical reactions, in which the product (output) from one reaction serves as the substrate (input) to another reaction. Many pathways remain incompletely characterized. One of the major challenges of computational biology is to obtain better models of metabolic pathways. Existing models are dependent on the annotation of the genes. This propagates error accumulation when the pathways are predicted by incorrectly annotated genes. Pairwise classification methods are supervised learning methods used to classify new pair of entities. Some of these classification methods, e.g., Pairwise Support Vector Machines (SVMs), use pairwise kernels. Pairwise kernels describe similarity measures between two pairs of entities. Using pairwise kernels to handle sequence data requires long processing times and large storage. Rational kernels are kernels based on weighted finite-state transducers that represent similarity measures between sequences or automata. They have been effectively used in problems that handle large amount of sequence information such as protein essentiality, natural language processing and machine translations. We create a new family of pairwise kernels using weighted finite-state transducers (called Pairwise Rational Kernel (PRK)) to predict metabolic pathways from a variety of biological data. PRKs take advantage of the simpler representations and faster algorithms of transducers. Because raw sequence data can be used, the predictor model avoids the errors introduced by incorrect gene annotations. We then developed several experiments with PRKs and Pairwise SVM to validate our methods using the metabolic network of Saccharomyces cerevisiae. As a result, when PRKs are used, our method executes faster in comparison with other pairwise kernels. Also, when we use PRKs combined with other simple kernels that include evolutionary information, the accuracy

  16. Medium- and Long-term Prediction of LOD Change by the Leap-step Autoregressive Model

    Science.gov (United States)

    Wang, Qijie

    2015-08-01

    The accuracy of medium- and long-term prediction of length of day (LOD) change base on combined least-square and autoregressive (LS+AR) deteriorates gradually. Leap-step autoregressive (LSAR) model can significantly reduce the edge effect of the observation sequence. Especially, LSAR model greatly improves the resolution of signals’ low-frequency components. Therefore, it can improve the efficiency of prediction. In this work, LSAR is used to forecast the LOD change. The LOD series from EOP 08 C04 provided by IERS is modeled by both the LSAR and AR models. The results of the two models are analyzed and compared. When the prediction length is between 10-30 days, the accuracy improvement is less than 10%. When the prediction length amounts to above 30 day, the accuracy improved obviously, with the maximum being around 19%. The results show that the LSAR model has higher prediction accuracy and stability in medium- and long-term prediction.

  17. Preference Learning and Ranking by Pairwise Comparison

    Science.gov (United States)

    Fürnkranz, Johannes; Hüllermeier, Eyke

    This chapter provides an overview of recent work on preference learning and ranking via pairwise classification. The learning by pairwise comparison (LPC) paradigm is the natural machine learning counterpart to the relational approach to preference modeling and decision making. From a machine learning point of view, LPC is especially appealing as it decomposes a possibly complex prediction problem into a certain number of learning problems of the simplest type, namely binary classification. We explain how to approach different preference learning problems, such as label and instance ranking, within the framework of LPC. We primarily focus on methodological aspects, but also address theoretical questions as well as algorithmic and complexity issues.

  18. Statistical physics of pairwise probability models

    DEFF Research Database (Denmark)

    Roudi, Yasser; Aurell, Erik; Hertz, John

    2009-01-01

    (dansk abstrakt findes ikke) Statistical models for describing the probability distribution over the states of biological systems are commonly used for dimensional reduction. Among these models, pairwise models are very attractive in part because they can be fit using a reasonable amount of  data......: knowledge of the means and correlations between pairs of elements in the system is sufficient. Not surprisingly, then, using pairwise models for studying neural data has been the focus of many studies in recent years. In this paper, we describe how tools from statistical physics can be employed for studying...

  19. Unjamming in models with analytic pairwise potentials

    NARCIS (Netherlands)

    Kooij, S.; Lerner, E.

    Canonical models for studying the unjamming scenario in systems of soft repulsive particles assume pairwise potentials with a sharp cutoff in the interaction range. The sharp cutoff renders the potential nonanalytic but makes it possible to describe many properties of the solid in terms of the

  20. A decomposition of pairwise continuity via ideals

    Directory of Open Access Journals (Sweden)

    Mahes Wari

    2016-02-01

    Full Text Available In this paper, we introduce and study the notions of (i, j - regular - ℐ -closed sets, (i, j - Aℐ -sets, (i, j - ℐ -locally closed sets, p- Aℐ -continuous functions and p- ℐ -LC-continuous functions in ideal bitopological spaces and investigate some of their properties. Also, a new decomposition of pairwise continuity is obtained using these sets.

  1. PAIRWISE BLENDING OF HIGH LEVEL WASTE

    International Nuclear Information System (INIS)

    CERTA, P.J.

    2006-01-01

    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

  2. Pairwise conjoint analysis of activity engagement choice

    NARCIS (Netherlands)

    Wang, Donggen; Oppewal, H.; Timmermans, H.J.P.

    2000-01-01

    Information overload is a well-known problem of conjoint choice models when respondents have to evaluate a large number of attributes and/or attribute levels. In this paper we develop an alternative conjoint modelling approach, called pairwise conjoint analysis. It differs from conventional conjoint

  3. Supplier Evaluation Process by Pairwise Comparisons

    Directory of Open Access Journals (Sweden)

    Arkadiusz Kawa

    2015-01-01

    Full Text Available We propose to assess suppliers by using consistency-driven pairwise comparisons for tangible and intangible criteria. The tangible criteria are simpler to compare (e.g., the price of a service is lower than that of another service with identical characteristics. Intangible criteria are more difficult to assess. The proposed model combines assessments of both types of criteria. The main contribution of this paper is the presentation of an extension framework for the selection of suppliers in a procurement process. The final weights are computed from relative pairwise comparisons. For the needs of the paper, surveys were conducted among Polish managers dealing with cooperation with suppliers in their enterprises. The Polish practice and restricted bidding are discussed, too.

  4. Meta-data for a lot of LOD

    NARCIS (Netherlands)

    Rietveld, Laurens; Beek, Wouter; Hoekstra, Rinke; Schlobach, Stefan

    2017-01-01

    This paper introduces the LOD Laundromat meta-dataset, a continuously updated RDF meta-dataset that describes the documents crawled, cleaned and (re)published by the LOD Laundromat. This meta-dataset of over 110 million triples contains structural information for more than 650,000 documents (and

  5. The dynamic system corresponding to LOD and AAM.

    Science.gov (United States)

    Liu, Shida; Liu, Shikuo; Chen, Jiong

    2000-02-01

    Using wavelet transform, the authors can reconstruct the 1-D map of a multifractal object. The wavelet transform of LOD and AAM shows that at 20 years scale, annual scale and 2 - 3 years scale, the jump points of LOD and AAM accord with each other very well, and their reconstructing 1-D mapping dynamic system are also very similar.

  6. Selecting numerical scales for pairwise comparisons

    International Nuclear Information System (INIS)

    Elliott, Michael A.

    2010-01-01

    It is often desirable in decision analysis problems to elicit from an individual the rankings of a population of attributes according to the individual's preference and to understand the degree to which each attribute is preferred to the others. A common method for obtaining this information involves the use of pairwise comparisons, which allows an analyst to convert subjective expressions of preference between two attributes into numerical values indicating preferences across the entire population of attributes. Key to the use of pairwise comparisons is the underlying numerical scale that is used to convert subjective linguistic expressions of preference into numerical values. This scale represents the psychological manner in which individuals perceive increments of preference among abstract attributes and it has important implications about the distribution and consistency of an individual's preferences. Three popular scale types, the traditional integer scales, balanced scales and power scales are examined. Results of a study of 64 individuals responding to a hypothetical decision problem show that none of these scales can accurately capture the preferences of all individuals. A study of three individuals working on an actual engineering decision problem involving the design of a decay heat removal system for a nuclear fission reactor show that the choice of scale can affect the preferred decision. It is concluded that applications of pairwise comparisons would benefit from permitting participants to choose the scale that best models their own particular way of thinking about the relative preference of attributes.

  7. Application of LOD Technology in German Libraries and Archives

    Directory of Open Access Journals (Sweden)

    Dong Jie

    2017-12-01

    Full Text Available [Purpose/significance] Linked Open Data (LOD has been widely used in large industries, as well as non-profit organizations and government organizations. Libraries and archives are ones of the early adopters of LOD technology. Libraries and archives promote the development of LOD. Germany is one of the developed countries in the libraries and archives industry, and there are many successful cases about the application of LOD in the libraries and archives. [Method/process] This paper analyzed the successful application of LOD technology in German libraries and archives by using the methods of document investigation, network survey and content analysis. [Result/conclusion] These cases reveal in the traditional field of computer science the relationship among research topics related to libraries and archives such as artificial intelligence, database and knowledge discovery. Summing up the characteristics and experience of German practice can provide more reference value for the development of relevant practice in China.

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

    Science.gov (United States)

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

    2016-03-01

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

  9. Unjamming in models with analytic pairwise potentials

    Science.gov (United States)

    Kooij, Stefan; Lerner, Edan

    2017-06-01

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

  10. Pairwise Trajectory Management (PTM): Concept Overview

    Science.gov (United States)

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

    2017-01-01

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

  11. Effect of misspecification of gene frequency on the two-point LOD score.

    Science.gov (United States)

    Pal, D K; Durner, M; Greenberg, D A

    2001-11-01

    In this study, we used computer simulation of simple and complex models to ask: (1) What is the penalty in evidence for linkage when the assumed gene frequency is far from the true gene frequency? (2) If the assumed model for gene frequency and inheritance are misspecified in the analysis, can this lead to a higher maximum LOD score than that obtained under the true parameters? Linkage data simulated under simple dominant, recessive, dominant and recessive with reduced penetrance, and additive models, were analysed assuming a single locus with both the correct and incorrect dominance model and assuming a range of different gene frequencies. We found that misspecifying the analysis gene frequency led to little penalty in maximum LOD score in all models examined, especially if the assumed gene frequency was lower than the generating one. Analysing linkage data assuming a gene frequency of the order of 0.01 for a dominant gene, and 0.1 for a recessive gene, appears to be a reasonable tactic in the majority of realistic situations because underestimating the gene frequency, even when the true gene frequency is high, leads to little penalty in the LOD score.

  12. GOOF: OCTOPUS error messages, ORDER, ORDERLIB, FLOE, CHAT, and LOD

    Energy Technology Data Exchange (ETDEWEB)

    Whitten, G.

    1977-07-10

    This is a compilation of the error messages returned by five parts of the Livermore timesharing system: the ORDER batch-processor, the ORDERLIB subroutine library, the FLOE operating system, the CHAT compiler, and the LOD loader.

  13. Direct power comparisons between simple LOD scores and NPL scores for linkage analysis in complex diseases.

    Science.gov (United States)

    Abreu, P C; Greenberg, D A; Hodge, S E

    1999-09-01

    Several methods have been proposed for linkage analysis of complex traits with unknown mode of inheritance. These methods include the LOD score maximized over disease models (MMLS) and the "nonparametric" linkage (NPL) statistic. In previous work, we evaluated the increase of type I error when maximizing over two or more genetic models, and we compared the power of MMLS to detect linkage, in a number of complex modes of inheritance, with analysis assuming the true model. In the present study, we compare MMLS and NPL directly. We simulated 100 data sets with 20 families each, using 26 generating models: (1) 4 intermediate models (penetrance of heterozygote between that of the two homozygotes); (2) 6 two-locus additive models; and (3) 16 two-locus heterogeneity models (admixture alpha = 1.0,.7,.5, and.3; alpha = 1.0 replicates simple Mendelian models). For LOD scores, we assumed dominant and recessive inheritance with 50% penetrance. We took the higher of the two maximum LOD scores and subtracted 0.3 to correct for multiple tests (MMLS-C). We compared expected maximum LOD scores and power, using MMLS-C and NPL as well as the true model. Since NPL uses only the affected family members, we also performed an affecteds-only analysis using MMLS-C. The MMLS-C was both uniformly more powerful than NPL for most cases we examined, except when linkage information was low, and close to the results for the true model under locus heterogeneity. We still found better power for the MMLS-C compared with NPL in affecteds-only analysis. The results show that use of two simple modes of inheritance at a fixed penetrance can have more power than NPL when the trait mode of inheritance is complex and when there is heterogeneity in the data set.

  14. Nonparametric predictive pairwise comparison with competing risks

    International Nuclear Information System (INIS)

    Coolen-Maturi, Tahani

    2014-01-01

    In reliability, failure data often correspond to competing risks, where several failure modes can cause a unit to fail. This paper presents nonparametric predictive inference (NPI) for pairwise comparison with competing risks data, assuming that the failure modes are independent. These failure modes could be the same or different among the two groups, and these can be both observed and unobserved failure modes. NPI is a statistical approach based on few assumptions, with inferences strongly based on data and with uncertainty quantified via lower and upper probabilities. The focus is on the lower and upper probabilities for the event that the lifetime of a future unit from one group, say Y, is greater than the lifetime of a future unit from the second group, say X. The paper also shows how the two groups can be compared based on particular failure mode(s), and the comparison of the two groups when some of the competing risks are combined is discussed

  15. Locating one pairwise interaction: Three recursive constructions

    Directory of Open Access Journals (Sweden)

    Charles J. Colbourn

    2016-09-01

    Full Text Available In a complex component-based system, choices (levels for components (factors may interact tocause faults in the system behaviour. When faults may be caused by interactions among few factorsat specific levels, covering arrays provide a combinatorial test suite for discovering the presence offaults. While well studied, covering arrays do not enable one to determine the specific levels of factorscausing the faults; locating arrays ensure that the results from test suite execution suffice to determinethe precise levels and factors causing faults, when the number of such causes is small. Constructionsfor locating arrays are at present limited to heuristic computational methods and quite specific directconstructions. In this paper three recursive constructions are developed for locating arrays to locateone pairwise interaction causing a fault.

  16. Enhanced LOD Concepts for Virtual 3d City Models

    Science.gov (United States)

    Benner, J.; Geiger, A.; Gröger, G.; Häfele, K.-H.; Löwner, M.-O.

    2013-09-01

    Virtual 3D city models contain digital three dimensional representations of city objects like buildings, streets or technical infrastructure. Because size and complexity of these models continuously grow, a Level of Detail (LoD) concept effectively supporting the partitioning of a complete model into alternative models of different complexity and providing metadata, addressing informational content, complexity and quality of each alternative model is indispensable. After a short overview on various LoD concepts, this paper discusses the existing LoD concept of the CityGML standard for 3D city models and identifies a number of deficits. Based on this analysis, an alternative concept is developed and illustrated with several examples. It differentiates between first, a Geometric Level of Detail (GLoD) and a Semantic Level of Detail (SLoD), and second between the interior building and its exterior shell. Finally, a possible implementation of the new concept is demonstrated by means of an UML model.

  17. Major strengths and weaknesses of the lod score method.

    Science.gov (United States)

    Ott, J

    2001-01-01

    Strengths and weaknesses of the lod score method for human genetic linkage analysis are discussed. The main weakness is its requirement for the specification of a detailed inheritance model for the trait. Various strengths are identified. For example, the lod score (likelihood) method has optimality properties when the trait to be studied is known to follow a Mendelian mode of inheritance. The ELOD is a useful measure for information content of the data. The lod score method can emulate various "nonparametric" methods, and this emulation is equivalent to the nonparametric methods. Finally, the possibility of building errors into the analysis will prove to be essential for the large amount of linkage and disequilibrium data expected in the near future.

  18. Statistical pairwise interaction model of stock market

    Science.gov (United States)

    Bury, Thomas

    2013-03-01

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

  19. Predicting community composition from pairwise interactions

    Science.gov (United States)

    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.

  20. El Nino, La Nina and VLBI Measured LOD

    Science.gov (United States)

    Clark, Thomas A.; Gipson, J. M.; Ma, C.

    1998-01-01

    VLBI is one of the most important techniques for measuring Earth orientation parameters (EOP), and is unique in its ability to make high accuracy measurements of UT1, and its time derivative, which is related to changes in the length of day, conventionally called LOD. These measurements of EOP give constraints on geophysical models of the solid-Earth, atmosphere and oceans. Changes in EOP are due either to external torques from gravitational forces, or to the exchange of angular momentum between the Earth, atmosphere and oceans. The effect of the external torques is strictly harmonic and nature, and is therefore easy to remove. We analyze an LOD time series derived from VLBI measurements with the goal of comparing this to predictions from AAM, and various ENSO indices. Previous work by ourselves and other investigators demonstrated a high degree of coherence between atmospheric angular momentum (AAM) and EOP. We continue to see this. As the angular momentum of the atmosphere increases, the rate of rotation of the Earth decreases, and vice versa. The signature of the ENSO is particularly strong. At the peak of the 1982-83 El Nino increased LOD by almost 1 ms. This was subsequently followed by a reduction in LOD of 0.75 ms. At its peak, in February of 1998, the 1997-98 El Nino increased LOD by 0.8 msec. As predicted at the 1998 Spring AGU, this has been followed by an abrupt decrease in LOD which is currently -0.4 ms. At this time (August, 1998) the current ENSO continues to develop in new and unexpected ways. We plan to update our analysis with all data available prior to the Fall AGU.

  1. Secular change of LOD caused by core evolution

    Science.gov (United States)

    Denis, C.; Rybicki, K. R.; Varga, P.

    2003-04-01

    Fossils and tidal deposits suggest that, on the average, the Earth's despinning rate had been five times less in the Proterozoic than in the Phanerozoic. This difference is probably due, for the major part, to the existence of a Proterozoic supercontinent. Nevertheless, core formation and core evolution should have compensated to some extent the effect of tidal friction, by diminishing the Earth's inertia moment. We have investigated quantitatively this contribution of the evolving core to the change of LOD. For the present epoch, we find that the solidification of the inner core causes a relative secular decrease of LOD of approximately 3 μs per century, whereas the macrodiffusion of iron oxides and sulfides from the D" into the outer core across the CMB (inasfar as Majewski's theory holds) leads to a relative secular decrease of LOD by about 15 μs per century. On the other hand, the theory of slow core formation developped by Runcorn in the early 1960s as a by-product of his theory of mantle-wide convection, leads to a relative secular decrease of LOD during most of the Proterozoic of about 0.25 ms per century. Although core formation is now widely assumed to have been a thermal run-away process that occurred shortly after the Earth itself had formed, Runcorn's theory of the growing core would nicely explain the observed palaeo-LOD curve. In any case, formation of the core implies, all in all, a relative decrease of LOD of typically 3 hours.

  2. Distribution of lod scores in oligogenic linkage analysis.

    Science.gov (United States)

    Williams, J T; North, K E; Martin, L J; Comuzzie, A G; Göring, H H; Blangero, J

    2001-01-01

    In variance component oligogenic linkage analysis it can happen that the residual additive genetic variance bounds to zero when estimating the effect of the ith quantitative trait locus. Using quantitative trait Q1 from the Genetic Analysis Workshop 12 simulated general population data, we compare the observed lod scores from oligogenic linkage analysis with the empirical lod score distribution under a null model of no linkage. We find that zero residual additive genetic variance in the null model alters the usual distribution of the likelihood-ratio statistic.

  3. Serial evaluation of the MODS, SOFA and LOD scores to predict ICU mortality in mixed critically ill patients.

    Science.gov (United States)

    Khwannimit, Bodin

    2008-09-01

    To perform a serial assessment and compare ability in predicting the intensive care unit (ICU) mortality of the multiple organ dysfunction score (MODS), sequential organ failure assessment (SOFA) and logistic organ dysfunction (LOD) score. The data were collected prospectively on consecutive ICU admissions over a 24-month period at a tertiary referral university hospital. The MODS, SOFA, and LOD scores were calculated on initial and repeated every 24 hrs. Two thousand fifty four patients were enrolled in the present study. The maximum and delta-scores of all the organ dysfunction scores correlated with ICU mortality. The maximum score of all models had better ability for predicting ICU mortality than initial or delta score. The areas under the receiver operating characteristic curve (AUC) for maximum scores was 0.892 for the MODS, 0.907 for the SOFA, and 0.92for the LOD. No statistical difference existed between all maximum scores and Acute Physiology and Chronic Health Evaluation II (APACHE II) score. Serial assessment of organ dysfunction during the ICU stay is reliable with ICU mortality. The maximum scores is the best discrimination comparable with APACHE II score in predicting ICU mortality.

  4. Linkage of familial Alzheimer disease to chromosome 14 in two large early-onset pedigrees: effects of marker allele frequencies on lod scores.

    Science.gov (United States)

    Nechiporuk, A; Fain, P; Kort, E; Nee, L E; Frommelt, E; Polinsky, R J; Korenberg, J R; Pulst, S M

    1993-05-01

    Alzheimer disease (AD) is a devastating neurodegenerative disease leading to global dementia. In addition to sporadic forms of AD, familial forms (FAD) have been recognized. Mutations in the amyloid precursor protein (APP) gene on chromosome (CHR) 21 have been shown to cause early-onset AD in a small number of pedigrees. Recently, linkage to markers on CHR 14 has been established in several early-onset FAD pedigrees. We now report lod scores for CHR 14 markers in two large early-onset FAD pedigrees. Pairwise linkage analysis suggested that in these pedigrees the mutation is tightly linked to the loci D14S43 and D14S53. However, assumptions regarding marker allele frequencies had a major and often unpredictable effect on calculated lod scores. Therefore, caution needs to be exercised when single pedigrees are analyzed with marker allele frequencies determined from the literature or from a pool of spouses.

  5. A scalable pairwise class interaction framework for multidimensional classification

    DEFF Research Database (Denmark)

    Arias, Jacinto; Gámez, Jose A.; Nielsen, Thomas Dyhre

    2016-01-01

    We present a general framework for multidimensional classification that cap- tures the pairwise interactions between class variables. The pairwise class inter- actions are encoded using a collection of base classifiers (Phase 1), for which the class predictions are combined in a Markov random fie...

  6. Effect of heterogeneity and assumed mode of inheritance on lod scores.

    Science.gov (United States)

    Durner, M; Greenberg, D A

    1992-02-01

    Heterogeneity is a major factor in many common, complex diseases and can confound linkage analysis. Using computer-simulated heterogeneous data we tested what effect unlinked families have on a linkage analysis when heterogeneity is not taken into account. We created 60 data sets of 40 nuclear families each with different proportions of linked and unlinked families and with different modes of inheritance. The ascertainment probability was 0.05, the disease had a penetrance of 0.6, and the recombination fraction for the linked families was zero. For the analysis we used a variety of assumed modes of inheritance and penetrances. Under these conditions we looked at the effect of the unlinked families on the lod score, the evaluation of the mode of inheritance, and the estimate of penetrance and of the recombination fraction in the linked families. 1. When the analysis was done under the correct mode of inheritance for the linked families, we found that the mode of inheritance of the unlinked families had minimal influence on the highest maximum lod score (MMLS) (i.e., we maximized the maximum lod score with respect to penetrance). Adding sporadic families decreased the MMLS less than adding recessive or dominant unlinked families. 2. The mixtures of dominant linked families with unlinked families always led to a higher MMLS when analyzed under the correct (dominant) mode of inheritance than when analyzed under the incorrect mode of inheritance. In the mixtures with recessive linked families, assuming the correct mode of inheritance generally led to a higher MMLS, but we observed broad variation.(ABSTRACT TRUNCATED AT 250 WORDS)

  7. SVM-dependent pairwise HMM: an application to protein pairwise alignments.

    Science.gov (United States)

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

    2017-12-15

    Methods able to provide reliable protein alignments are crucial for many bioinformatics applications. In the last years many different algorithms have been developed and various kinds of information, from sequence conservation to secondary structure, have been used to improve the alignment performances. This is especially relevant for proteins with highly divergent sequences. However, recent works suggest that different features may have different importance in diverse protein classes and it would be an advantage to have more customizable approaches, capable to deal with different alignment definitions. Here we present Rigapollo, a highly flexible pairwise alignment method based on a pairwise HMM-SVM that can use any type of information to build alignments. Rigapollo lets the user decide the optimal features to align their protein class of interest. It outperforms current state of the art methods on two well-known benchmark datasets when aligning highly divergent sequences. A Python implementation of the algorithm is available at http://ibsquare.be/rigapollo. wim.vranken@vub.be. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  8. Pseudoautosomal region in schizophrenia: linkage analysis of seven loci by sib-pair and lod-score methods.

    Science.gov (United States)

    d'Amato, T; Waksman, G; Martinez, M; Laurent, C; Gorwood, P; Campion, D; Jay, M; Petit, C; Savoye, C; Bastard, C

    1994-05-01

    In a previous study, we reported a nonrandom segregation between schizophrenia and the pseudoautosomal locus DXYS14 in a sample of 33 sibships. That study has been extended by the addition of 16 new sibships from 16 different families. Data from six other loci of the pseudoautosomal region and of the immediately adjacent part of the X specific region have also been analyzed. Two methods of linkage analysis were used: the affected sibling pair (ASP) method and the lod-score method. Lod-score analyses were performed on the basis of three different models--A, B, and C--all shown to be consistent with the epidemiological data on schizophrenia. No clear evidence for linkage was obtained with any of these models. However, whatever the genetic model and the disease classification, maximum lod scores were positive with most of the markers, with the highest scores generally being obtained for the DXYS14 locus. When the ASP method was used, the earlier finding of nonrandom segregation between schizophrenia and the DXYS14 locus was still supported in this larger data set, at an increased level of statistical significance. Findings of ASP analyses were not significant for the other loci. Thus, findings obtained from analyses using the ASP method, but not the lod-score method, were consistent with the pseudoautosomal hypothesis for schizophrenia.

  9. Pseudo inputs for pairwise learning with Gaussian processes

    DEFF Research Database (Denmark)

    Nielsen, Jens Brehm; Jensen, Bjørn Sand; Larsen, Jan

    2012-01-01

    We consider learning and prediction of pairwise comparisons between instances. The problem is motivated from a perceptual view point, where pairwise comparisons serve as an effective and extensively used paradigm. A state-of-the-art method for modeling pairwise data in high dimensional domains...... is based on a classical pairwise probit likelihood imposed with a Gaussian process prior. While extremely flexible, this non-parametric method struggles with an inconvenient O(n3) scaling in terms of the n input instances which limits the method only to smaller problems. To overcome this, we derive...... to other similar approximations that have been applied in standard Gaussian process regression and classification problems such as FI(T)C and PI(T)C....

  10. Robust LOD scores for variance component-based linkage analysis.

    Science.gov (United States)

    Blangero, J; Williams, J T; Almasy, L

    2000-01-01

    The variance component method is now widely used for linkage analysis of quantitative traits. Although this approach offers many advantages, the importance of the underlying assumption of multivariate normality of the trait distribution within pedigrees has not been studied extensively. Simulation studies have shown that traits with leptokurtic distributions yield linkage test statistics that exhibit excessive Type I error when analyzed naively. We derive analytical formulae relating the deviation from the expected asymptotic distribution of the lod score to the kurtosis and total heritability of the quantitative trait. A simple correction constant yields a robust lod score for any deviation from normality and for any pedigree structure, and effectively eliminates the problem of inflated Type I error due to misspecification of the underlying probability model in variance component-based linkage analysis.

  11. LOD wars: The affected-sib-pair paradigm strikes back!

    Energy Technology Data Exchange (ETDEWEB)

    Farrall, M. [Wellcome Trust Centre for Human Genetics, Oxford (United Kingdom)

    1997-03-01

    In a recent letter, Greenberg et al. aired their concerns that the affected-sib-pair (ASP) approach was becoming excessively popular, owing to misconceptions and ignorance of the properties and limitations of both the ASP and the classic LOD-score approaches. As an enthusiast of using the ASP approach to map susceptibility genes for multifactorial traits, I would like to contribute a few comments and explanatory notes in defense of the ASP paradigm. 18 refs.

  12. Quadtree of TIN: a new algorithm of dynamic LOD

    Science.gov (United States)

    Zhang, Junfeng; Fei, Lifan; Chen, Zhen

    2009-10-01

    Currently, Real-time visualization of large-scale digital elevation model mainly employs the regular structure of GRID based on quadtree and triangle simplification methods based on irregular triangulated network (TIN). TIN is a refined means to express the terrain surface in the computer science, compared with GRID. However, the data structure of TIN model is complex, and is difficult to realize view-dependence representation of level of detail (LOD) quickly. GRID is a simple method to realize the LOD of terrain, but contains more triangle count. A new algorithm, which takes full advantage of the two methods' merit, is presented in this paper. This algorithm combines TIN with quadtree structure to realize the view-dependence LOD controlling over the irregular sampling point sets, and holds the details through the distance of viewpoint and the geometric error of terrain. Experiments indicate that this approach can generate an efficient quadtree triangulation hierarchy over any irregular sampling point sets and achieve dynamic and visual multi-resolution performance of large-scale terrain at real-time.

  13. Minimum and Maximum Entropy Distributions for Binary Systems with Known Means and Pairwise Correlations

    Science.gov (United States)

    2017-08-21

    number of neurons. Time is discretized and we assume any neuron can spike no more than once in a time bin. We have ν ≤ µ because ν is the probability of a...Comput. Appl. Math . 2000, 121, 331–354. 27. Shalizi, C.; Crutchfield, J. Computational mechanics: Pattern and prediction, structure and simplicity. J...Minimization of a Linearly Constrained Function by Partition of Feasible Domain. Math . Oper. Res. 1983, 8, 215–230. Entropy 2017, 19, 427 33 of 33 54. Candes, E

  14. LOD Laundromat : Why the Semantic Web needs centralization (even if we don't like it)

    NARCIS (Netherlands)

    Beek, Wouter; Rietveld, Laurens; Schlobach, Stefan; van Harmelen, Frank

    2016-01-01

    LOD Laundromat poses a centralized solution for today's Semantic Web problems. This approach adheres more closely to the original vision of a Web of Data, providing uniform access to a large and ever-increasing subcollection of the LOD Cloud.

  15. The research of selection model based on LOD in multi-scale display of electronic map

    Science.gov (United States)

    Zhang, Jinming; You, Xiong; Liu, Yingzhen

    2008-10-01

    This paper proposes a selection model based on LOD to aid the display of electronic map. The ratio of display scale to map scale is regarded as a LOD operator. The categorization rule, classification rule, elementary rule and spatial geometry character rule of LOD operator setting are also concluded.

  16. LOD map--A visual interface for navigating multiresolution volume visualization.

    Science.gov (United States)

    Wang, Chaoli; Shen, Han-Wei

    2006-01-01

    In multiresolution volume visualization, a visual representation of level-of-detail (LOD) quality is important for us to examine, compare, and validate different LOD selection algorithms. While traditional methods rely on ultimate images for quality measurement, we introduce the LOD map--an alternative representation of LOD quality and a visual interface for navigating multiresolution data exploration. Our measure for LOD quality is based on the formulation of entropy from information theory. The measure takes into account the distortion and contribution of multiresolution data blocks. A LOD map is generated through the mapping of key LOD ingredients to a treemap representation. The ordered treemap layout is used for relative stable update of the LOD map when the view or LOD changes. This visual interface not only indicates the quality of LODs in an intuitive way, but also provides immediate suggestions for possible LOD improvement through visually-striking features. It also allows us to compare different views and perform rendering budget control. A set of interactive techniques is proposed to make the LOD adjustment a simple and easy task. We demonstrate the effectiveness and efficiency of our approach on large scientific and medical data sets.

  17. Pairwise Constraint-Guided Sparse Learning for Feature Selection.

    Science.gov (United States)

    Liu, Mingxia; Zhang, Daoqiang

    2016-01-01

    Feature selection aims to identify the most informative features for a compact and accurate data representation. As typical supervised feature selection methods, Lasso and its variants using L1-norm-based regularization terms have received much attention in recent studies, most of which use class labels as supervised information. Besides class labels, there are other types of supervised information, e.g., pairwise constraints that specify whether a pair of data samples belong to the same class (must-link constraint) or different classes (cannot-link constraint). However, most of existing L1-norm-based sparse learning methods do not take advantage of the pairwise constraints that provide us weak and more general supervised information. For addressing that problem, we propose a pairwise constraint-guided sparse (CGS) learning method for feature selection, where the must-link and the cannot-link constraints are used as discriminative regularization terms that directly concentrate on the local discriminative structure of data. Furthermore, we develop two variants of CGS, including: 1) semi-supervised CGS that utilizes labeled data, pairwise constraints, and unlabeled data and 2) ensemble CGS that uses the ensemble of pairwise constraint sets. We conduct a series of experiments on a number of data sets from University of California-Irvine machine learning repository, a gene expression data set, two real-world neuroimaging-based classification tasks, and two large-scale attribute classification tasks. Experimental results demonstrate the efficacy of our proposed methods, compared with several established feature selection methods.

  18. Quantification of type I error probabilities for heterogeneity LOD scores.

    Science.gov (United States)

    Abreu, Paula C; Hodge, Susan E; Greenberg, David A

    2002-02-01

    Locus heterogeneity is a major confounding factor in linkage analysis. When no prior knowledge of linkage exists, and one aims to detect linkage and heterogeneity simultaneously, classical distribution theory of log-likelihood ratios does not hold. Despite some theoretical work on this problem, no generally accepted practical guidelines exist. Nor has anyone rigorously examined the combined effect of testing for linkage and heterogeneity and simultaneously maximizing over two genetic models (dominant, recessive). The effect of linkage phase represents another uninvestigated issue. Using computer simulation, we investigated type I error (P value) of the "admixture" heterogeneity LOD (HLOD) score, i.e., the LOD score maximized over both recombination fraction theta and admixture parameter alpha and we compared this with the P values when one maximizes only with respect to theta (i.e., the standard LOD score). We generated datasets of phase-known and -unknown nuclear families, sizes k = 2, 4, and 6 children, under fully penetrant autosomal dominant inheritance. We analyzed these datasets (1) assuming a single genetic model, and maximizing the HLOD over theta and alpha; and (2) maximizing the HLOD additionally over two dominance models (dominant vs. recessive), then subtracting a 0.3 correction. For both (1) and (2), P values increased with family size k; rose less for phase-unknown families than for phase-known ones, with the former approaching the latter as k increased; and did not exceed the one-sided mixture distribution xi = (1/2) chi1(2) + (1/2) chi2(2). Thus, maximizing the HLOD over theta and alpha appears to add considerably less than an additional degree of freedom to the associated chi1(2) distribution. We conclude with practical guidelines for linkage investigators. Copyright 2002 Wiley-Liss, Inc.

  19. The Partition of Multi-Resolution LOD Based on Qtm

    Science.gov (United States)

    Hou, M.-L.; Xing, H.-Q.; Zhao, X.-S.; Chen, J.

    2011-08-01

    The partition hierarch of Quaternary Triangular Mesh (QTM) determine the accuracy of spatial analysis and application based on QTM. In order to resolve the problem that the partition hierarch of QTM is limited by the level of the computer hardware, the new method that Multi- Resolution LOD (Level of Details) based on QTM will be discussed in this paper. This method can make the resolution of the cells varying with the viewpoint position by partitioning the cells of QTM, selecting the particular area according to the viewpoint; dealing with the cracks caused by different subdivisions, it satisfies the request of unlimited partition in part.

  20. THE PARTITION OF MULTI-RESOLUTION LOD BASED ON QTM

    Directory of Open Access Journals (Sweden)

    M.-L. Hou

    2012-08-01

    Full Text Available The partition hierarch of Quaternary Triangular Mesh (QTM determine the accuracy of spatial analysis and application based on QTM. In order to resolve the problem that the partition hierarch of QTM is limited by the level of the computer hardware, the new method that Multi- Resolution LOD (Level of Details based on QTM will be discussed in this paper. This method can make the resolution of the cells varying with the viewpoint position by partitioning the cells of QTM, selecting the particular area according to the viewpoint; dealing with the cracks caused by different subdivisions, it satisfies the request of unlimited partition in part.

  1. Allele-sharing models: LOD scores and accurate linkage tests.

    Science.gov (United States)

    Kong, A; Cox, N J

    1997-11-01

    Starting with a test statistic for linkage analysis based on allele sharing, we propose an associated one-parameter model. Under general missing-data patterns, this model allows exact calculation of likelihood ratios and LOD scores and has been implemented by a simple modification of existing software. Most important, accurate linkage tests can be performed. Using an example, we show that some previously suggested approaches to handling less than perfectly informative data can be unacceptably conservative. Situations in which this model may not perform well are discussed, and an alternative model that requires additional computations is suggested.

  2. LOD First Estimates In 7406 SLR San Juan Argentina Station

    Science.gov (United States)

    Pacheco, A.; Podestá, R.; Yin, Z.; Adarvez, S.; Liu, W.; Zhao, L.; Alvis Rojas, H.; Actis, E.; Quinteros, J.; Alacoria, J.

    2015-10-01

    In this paper we show results derived from satellite observations at the San Juan SLR station of Felix Aguilar Astronomical Observatory (OAFA). The Satellite Laser Ranging (SLR) telescope was installed in early 2006, in accordance with an international cooperation agreement between the San Juan National University (UNSJ) and the Chinese Academy of Sciences (CAS). The SLR has been in successful operation since 2011 using NAOC SLR software for the data processing. This program was designed to calculate satellite orbits and station coordinates, however it was used in this work for the determination of LOD (Length Of Day) time series and Earth Rotation speed.

  3. Towards an Editable, Versionized LOD Service for Library Data

    Directory of Open Access Journals (Sweden)

    Felix Ostrowski

    2013-02-01

    Full Text Available The Northrhine-Westphalian Library Service Center (hbz launched its LOD service lobid.org in August 2010 and has since then continuously been improving the underlying conversion processes, data models and software. The present paper first explains the background and motivation for developing lobid.org . It then describes the underlying software framework Phresnel which is written in PHP and which provides presentation and editing capabilities of RDF data based on the Fresnel Display Vocabulary for RDF. The paper gives an overview of the current state of the Phresnel development and discusses the technical challenges encountered. Finally, possible prospects for further developing Phresnel are outlined.

  4. Distribution of model-based multipoint heterogeneity lod scores.

    Science.gov (United States)

    Xing, Chao; Morris, Nathan; Xing, Guan

    2010-12-01

    The distribution of two-point heterogeneity lod scores (HLOD) has been intensively investigated because the conventional χ(2) approximation to the likelihood ratio test is not directly applicable. However, there was no study investigating th e distribution of the multipoint HLOD despite its wide application. Here we want to point out that, compared with the two-point HLOD, the multipoint HLOD essentially tests for homogeneity given linkage and follows a relatively simple limiting distribution ½χ²₀+ ½χ²₁, which can be obtained by established statistical theory. We further examine the theoretical result by simulation studies. © 2010 Wiley-Liss, Inc.

  5. Automatic Camera Calibration Using Multiple Sets of Pairwise Correspondences.

    Science.gov (United States)

    Vasconcelos, Francisco; Barreto, Joao P; Boyer, Edmond

    2018-04-01

    We propose a new method to add an uncalibrated node into a network of calibrated cameras using only pairwise point correspondences. While previous methods perform this task using triple correspondences, these are often difficult to establish when there is limited overlap between different views. In such challenging cases we must rely on pairwise correspondences and our solution becomes more advantageous. Our method includes an 11-point minimal solution for the intrinsic and extrinsic calibration of a camera from pairwise correspondences with other two calibrated cameras, and a new inlier selection framework that extends the traditional RANSAC family of algorithms to sampling across multiple datasets. Our method is validated on different application scenarios where a lack of triple correspondences might occur: addition of a new node to a camera network; calibration and motion estimation of a moving camera inside a camera network; and addition of views with limited overlap to a Structure-from-Motion model.

  6. A predictive model of music preference using pairwise comparisons

    DEFF Research Database (Denmark)

    Jensen, Bjørn Sand; Gallego, Javier Saez; Larsen, Jan

    2012-01-01

    Music recommendation is an important aspect of many streaming services and multi-media systems, however, it is typically based on so-called collaborative filtering methods. In this paper we consider the recommendation task from a personal viewpoint and examine to which degree music preference can...... be elicited and predicted using simple and robust queries such as pairwise comparisons. We propose to model - and in turn predict - the pairwise music preference using a very flexible model based on Gaussian Process priors for which we describe the required inference. We further propose a specific covariance...

  7. Dynamics of pairwise motions in the Cosmic Web

    Science.gov (United States)

    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. Determinants of sovereign debt yield spreads under EMU: Pairwise approach

    NARCIS (Netherlands)

    Fazlioglu, S.

    2013-01-01

    This study aims at providing an empirical analysis of long-term determinants of sovereign debt yield spreads under European EMU (Economic and Monetary Union) through pairwise approach within panel framework. Panel gravity models are increasingly used in the cross-market correlation literature while

  9. Modeling Expressed Emotions in Music using Pairwise Comparisons

    DEFF Research Database (Denmark)

    Madsen, Jens; Nielsen, Jens Brehm; Jensen, Bjørn Sand

    2012-01-01

    We introduce a two-alternative forced-choice experimental paradigm to quantify expressed emotions in music using the two wellknown arousal and valence (AV) dimensions. In order to produce AV scores from the pairwise comparisons and to visualize the locations of excerpts in the AV space, we...

  10. Weighted combination of LOD values oa splitted into frequency windows

    Science.gov (United States)

    Fernandez, L. I.; Gambis, D.; Arias, E. F.

    In this analysis a one-day combined time series of LOD(length-of-day) estimates is presented. We use individual data series derived by 7 GPS and 3 SLR analysis centers, which routinely contribute to the IERS database over a recent 27-month period (Jul 1996 - Oct 1998). The result is compared to the multi-technique combined series C04 produced by the Central Bureau of the IERS that is commonly used as a reference for the study of the phenomena of Earth rotation variations. The Frequency Windows Combined Series procedure brings out a time series, which is close to C04 but shows an amplitude difference that might explain the evident periodic behavior present in the differences of these two combined series. This method could be useful to generate a new time series to be used as a reference in the high frequency variations of the Earth rotation studies.

  11. Pairwise structure alignment specifically tuned for surface pockets and interaction interfaces

    KAUST Repository

    Cui, Xuefeng

    2015-09-09

    (PROSTA) family of pairwise structure alignment methods [1, 2] that address the fragmentation issue of pockets and interfaces, and automatically align interfaces between any types of biological complexes. Our PROSTA structure alignment methods have two critical advantages comparing to existing structure alignment methods. First, our methods are completely sequence order independent, which is critical to the success of pairwise pocket and interface structure alignments. This is achieved by introducing contact groups that are not limited to backbone fragments, and by employing a maximum weighted bipartite matching solver from the beginning of the alignment process. In addition, our methods incorporate similarities of sequentially and structurally remote residues that potentially model the topology of the global structure. Comparing to existing methods that focus on local structure or whole sequence similarities, topological similarities are more reliable to find near-optimal structure alignments in the initial alignment state. As a result, a significant number of similar pockets and interfaces are newly discovered, and literatures also support that similar functions are shared between biological complexes in our cases studies. The PROSTA web-server and source codes are publicly available at "http://www.cbrc.kaust.edu.sa/prosta/".

  12. TLS for generating multi-LOD of 3D building model

    International Nuclear Information System (INIS)

    Akmalia, R; Setan, H; Majid, Z; Suwardhi, D; Chong, A

    2014-01-01

    The popularity of Terrestrial Laser Scanners (TLS) to capture three dimensional (3D) objects has been used widely for various applications. Development in 3D models has also led people to visualize the environment in 3D. Visualization of objects in a city environment in 3D can be useful for many applications. However, different applications require different kind of 3D models. Since a building is an important object, CityGML has defined a standard for 3D building models at four different levels of detail (LOD). In this research, the advantages of TLS for capturing buildings and the modelling process of the point cloud can be explored. TLS will be used to capture all the building details to generate multi-LOD. This task, in previous works, involves usually the integration of several sensors. However, in this research, point cloud from TLS will be processed to generate the LOD3 model. LOD2 and LOD1 will then be generalized from the resulting LOD3 model. Result from this research is a guiding process to generate the multi-LOD of 3D building starting from LOD3 using TLS. Lastly, the visualization for multi-LOD model will also be shown

  13. An Application to the Prediction of LOD Change Based on General Regression Neural Network

    Science.gov (United States)

    Zhang, X. H.; Wang, Q. J.; Zhu, J. J.; Zhang, H.

    2011-07-01

    Traditional prediction of the LOD (length of day) change was based on linear models, such as the least square model and the autoregressive technique, etc. Due to the complex non-linear features of the LOD variation, the performances of the linear model predictors are not fully satisfactory. This paper applies a non-linear neural network - general regression neural network (GRNN) model to forecast the LOD change, and the results are analyzed and compared with those obtained with the back propagation neural network and other models. The comparison shows that the performance of the GRNN model in the prediction of the LOD change is efficient and feasible.

  14. TLS for generating multi-LOD of 3D building model

    Science.gov (United States)

    Akmalia, R.; Setan, H.; Majid, Z.; Suwardhi, D.; Chong, A.

    2014-02-01

    The popularity of Terrestrial Laser Scanners (TLS) to capture three dimensional (3D) objects has been used widely for various applications. Development in 3D models has also led people to visualize the environment in 3D. Visualization of objects in a city environment in 3D can be useful for many applications. However, different applications require different kind of 3D models. Since a building is an important object, CityGML has defined a standard for 3D building models at four different levels of detail (LOD). In this research, the advantages of TLS for capturing buildings and the modelling process of the point cloud can be explored. TLS will be used to capture all the building details to generate multi-LOD. This task, in previous works, involves usually the integration of several sensors. However, in this research, point cloud from TLS will be processed to generate the LOD3 model. LOD2 and LOD1 will then be generalized from the resulting LOD3 model. Result from this research is a guiding process to generate the multi-LOD of 3D building starting from LOD3 using TLS. Lastly, the visualization for multi-LOD model will also be shown.

  15. Dynamics of pairwise entanglement between two Tavis-Cummings atoms

    International Nuclear Information System (INIS)

    Guo Jinliang; Song Heshan

    2008-01-01

    We investigate the time evolution of pairwise entanglement between two Tavis-Cummings atoms for various entangled initial states, including pure and mixed states. We find that the phenomenon of entanglement sudden death behaviors is distinct in the evolution of entanglement for different initial states. What deserves mentioning here is that the initial portion of the excited state in the initial state is responsible for the sudden death of entanglement, and the degree of this effect also depends on the initial states

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

    Science.gov (United States)

    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.

  17. Implementace algoritmu LoD terénu

    OpenAIRE

    Radil, Přemek

    2012-01-01

    Tato práce pojednává o implementaci algoritmu pro LoD vizualizaci terénu Seamless Patches for GPU-Based Terrain Rendering jako rozšíření knihovny Coin3D. Prezentuje postupy, za pomoci kterých tento algoritmus zobrazuje rozsáhlé terénní datasety. Celý terén je složen z plátů, které jsou uloženy v hierarchické struktuře. Hierarchie plátů je pak za běhu programu procházena jsou z ní generovány aktivní pláty na základě pozice pozorovatele. Každý plát se skládá z předem definovaných dlaždic a spoj...

  18. Proposal for a new LOD and multi-representation concept for CityGML

    NARCIS (Netherlands)

    Löwner, Marc-O; Gröger, Gerhard; Benner, Joachim; Biljecki, F.; Nagel, Claus; Dimopoulou, E.; van Oosterom, P.

    2016-01-01

    The Open Geospatial Consortium (OGC) CityGML standard offers a Level of Detail (LoD) concept that enables the representation of CityGML features from a very detailed to a less detailed description. Due to a rising application variety, the current LoD concept seems to be too inflexible. Here, we

  19. An LOD with improved breakdown voltage in full-frame CCD devices

    Science.gov (United States)

    Banghart, Edmund K.; Stevens, Eric G.; Doan, Hung Q.; Shepherd, John P.; Meisenzahl, Eric J.

    2005-02-01

    In full-frame image sensors, lateral overflow drain (LOD) structures are typically formed along the vertical CCD shift registers to provide a means for preventing charge blooming in the imager pixels. In a conventional LOD structure, the n-type LOD implant is made through the thin gate dielectric stack in the device active area and adjacent to the thick field oxidation that isolates the vertical CCD columns of the imager. In this paper, a novel LOD structure is described in which the n-type LOD impurities are placed directly under the field oxidation and are, therefore, electrically isolated from the gate electrodes. By reducing the electrical fields that cause breakdown at the silicon surface, this new structure permits a larger amount of n-type impurities to be implanted for the purpose of increasing the LOD conductivity. As a consequence of the improved conductance, the LOD width can be significantly reduced, enabling the design of higher resolution imaging arrays without sacrificing charge capacity in the pixels. Numerical simulations with MEDICI of the LOD leakage current are presented that identify the breakdown mechanism, while three-dimensional solutions to Poisson's equation are used to determine the charge capacity as a function of pixel dimension.

  20. Are LOD and LOQ Reliable Parameters for Sensitivity Evaluation of Spectroscopic Methods?

    Science.gov (United States)

    Ershadi, Saba; Shayanfar, Ali

    2018-03-22

    The limit of detection (LOD) and the limit of quantification (LOQ) are common parameters to assess the sensitivity of analytical methods. In this study, the LOD and LOQ of previously reported terbium sensitized analysis methods were calculated by different methods, and the results were compared with sensitivity parameters [lower limit of quantification (LLOQ)] of U.S. Food and Drug Administration guidelines. The details of the calibration curve and standard deviation of blank samples of three different terbium-sensitized luminescence methods for the quantification of mycophenolic acid, enrofloxacin, and silibinin were used for the calculation of LOD and LOQ. A comparison of LOD and LOQ values calculated by various methods and LLOQ shows a considerable difference. The significant difference of the calculated LOD and LOQ with various methods and LLOQ should be considered in the sensitivity evaluation of spectroscopic methods.

  1. One-Step Leapfrog LOD-BOR-FDTD Algorithm with CPML Implementation

    Directory of Open Access Journals (Sweden)

    Yi-Gang Wang

    2016-01-01

    Full Text Available An unconditionally stable one-step leapfrog locally one-dimensional finite-difference time-domain (LOD-FDTD algorithm towards body of revolution (BOR is presented. The equations of the proposed algorithm are obtained by the algebraic manipulation of those used in the conventional LOD-BOR-FDTD algorithm. The equations for z-direction electric and magnetic fields in the proposed algorithm should be treated specially. The new algorithm obtains a higher computational efficiency while preserving the properties of the conventional LOD-BOR-FDTD algorithm. Moreover, the convolutional perfectly matched layer (CPML is introduced into the one-step leapfrog LOD-BOR-FDTD algorithm. The equation of the one-step leapfrog CPML is concise. Numerical results show that its reflection error is small. It can be concluded that the similar CPML scheme can also be easily applied to the one-step leapfrog LOD-FDTD algorithm in the Cartesian coordinate system.

  2. Influence of LOD variations on seismic energy release

    Science.gov (United States)

    Riguzzi, F.; Krumm, F.; Wang, K.; Kiszely, M.; Varga, P.

    2009-04-01

    Tidal friction causes significant time variations of geodynamical parameters, among them geometrical flattening. The axial despinning of the Earth due to tidal friction through the change of flattening generates incremental meridional and azimuthal stresses. The stress pattern in an incompressible elastic upper mantle and crust is symmetric to the equator and has its inflection points at the critical latitude close to ±45°. Consequently the distribution of seismic energy released by strong, shallow focus earthquakes should have also sharp maxima at this latitude. To investigate the influence of length of day (LOD) variations on earthquake activity an earthquake catalogue of strongest seismic events (M>7.0) was completed for the period 1900-2007. It is shown with the use of this catalogue that for the studied time-interval the catalogue is complete and consists of the seismic events responsible for more than 90% of released seismic energy. Study of the catalogue for earthquakes M>7.0 shows that the seismic energy discharged by the strongest seismic events has significant maxima at ±45°, what renders probably that the seismic activity of our planet is influenced by an external component, i.e. by the tidal friction, which acts through the variation of the hydrostatic figure of the Earth caused by it. Distribution along the latitude of earthquake numbers and energies was investigated also for the case of global linear tectonic structures, such as mid ocean ridges and subduction zones. It can be shown that the number of the shallow focus shocks has a repartition along the latitude similar to the distribution of the linear tectonic structures. This means that the position of foci of seismic events is mainly controlled by the tectonic activity.

  3. Pairwise Trajectory Management (PTM): Concept Description and Documentation

    Science.gov (United States)

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

    2018-01-01

    Pairwise Trajectory Management (PTM) is an Interval Management (IM) concept that utilizes airborne and ground-based capabilities to enable the implementation of airborne pairwise spacing capabilities in oceanic regions. The goal of PTM is to use airborne surveillance and tools to manage an "at or greater than" inter-aircraft spacing. Due to the accuracy of Automatic Dependent Surveillance-Broadcast (ADS-B) information and the use of airborne spacing guidance, the minimum PTM spacing distance will be less than distances a controller can support with current automation systems that support oceanic operations. Ground tools assist the controller in evaluating the traffic picture and determining appropriate PTM clearances to be issued. Avionics systems provide guidance information that allows the flight crew to conform to the PTM clearance issued by the controller. The combination of a reduced minimum distance and airborne spacing management will increase the capacity and efficiency of aircraft operations at a given altitude or volume of airspace. This document provides an overview of the proposed application, a description of several key scenarios, a high level discussion of expected air and ground equipment and procedure changes, a description of a NASA human-machine interface (HMI) prototype for the flight crew that would support PTM operations, and initial benefits analysis results. Additionally, included as appendices, are the following documents: the PTM Operational Services and Environment Definition (OSED) document and a companion "Future Considerations for the Pairwise Trajectory Management (PTM) Concept: Potential Future Updates for the PTM OSED" paper, a detailed description of the PTM algorithm and PTM Limit Mach rules, initial PTM safety requirements and safety assessment documents, a detailed description of the design, development, and initial evaluations of the proposed flight crew HMI, an overview of the methodology and results of PTM pilot training

  4. Revision of Begomovirus taxonomy based on pairwise sequence comparisons

    KAUST Repository

    Brown, Judith K.

    2015-04-18

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

  5. Revision of Begomovirus taxonomy based on pairwise sequence comparisons

    KAUST Repository

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

    2015-01-01

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

  6. Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%

    DEFF Research Database (Denmark)

    Havgaard, Jakob Hull; Lyngsø, Rune B.; Stormo, Gary D.

    2005-01-01

    detect two genes with low sequence similarity, where the genes are part of a larger genomic region. Results: Here we present such an approach for pairwise local alignment which is based on FILDALIGN and the Sankoff algorithm for simultaneous structural alignment of multiple sequences. We include...... the ability to conduct mutual scans of two sequences of arbitrary length while searching for common local structural motifs of some maximum length. This drastically reduces the complexity of the algorithm. The scoring scheme includes structural parameters corresponding to those available for free energy....... The structure prediction performance for a family is typically around 0.7 using Matthews correlation coefficient. In case (2), the algorithm is successful at locating RNA families with an average sensitivity of 0.8 and a positive predictive value of 0.9 using a BLAST-like hit selection scheme. Availability...

  7. Tidal influence through LOD variations on the temporal distribution of earthquake occurrences

    Science.gov (United States)

    Varga, P.; Gambis, D.; Bizouard, Ch.; Bus, Z.; Kiszely, M.

    2006-10-01

    Stresses generated by the body tides are very small at the depth of crustal earth- quakes (~10^2 N/m2). The maximum value of the lunisolar stress within the depth range of earthquakes is 10^3 N/m2 (at depth of about 600 km). Surface loads, due to oceanic tides, in coastal areas are ~ 104 N/m2. These influences are however too small to affect the outbreak time of seismic events. Authors show the effect on time distribution of seismic activity due to ΔLOD generated by zonal tides for the case of Mf, Mm, Ssa and Sa tidal constituents can be much more effective to trigger earthquakes. According to this approach we show that the tides are not directly triggering the seismic events but through the generated length of day variations. That is the reason why in case of zonal tides a correlation of the lunisolar effect and seismic activity exists, what is not the case for the tesseral and sectorial tides.

  8. The score statistic of the LD-lod analysis: detecting linkage adaptive to linkage disequilibrium.

    Science.gov (United States)

    Huang, J; Jiang, Y

    2001-01-01

    We study the properties of a modified lod score method for testing linkage that incorporates linkage disequilibrium (LD-lod). By examination of its score statistic, we show that the LD-lod score method adaptively combines two sources of information: (a) the IBD sharing score which is informative for linkage regardless of the existence of LD and (b) the contrast between allele-specific IBD sharing scores which is informative for linkage only in the presence of LD. We also consider the connection between the LD-lod score method and the transmission-disequilibrium test (TDT) for triad data and the mean test for affected sib pair (ASP) data. We show that, for triad data, the recessive LD-lod test is asymptotically equivalent to the TDT; and for ASP data, it is an adaptive combination of the TDT and the ASP mean test. We demonstrate that the LD-lod score method has relatively good statistical efficiency in comparison with the ASP mean test and the TDT for a broad range of LD and the genetic models considered in this report. Therefore, the LD-lod score method is an interesting approach for detecting linkage when the extent of LD is unknown, such as in a genome-wide screen with a dense set of genetic markers. Copyright 2001 S. Karger AG, Basel

  9. Extension of Pairwise Broadcast Clock Synchronization for Multicluster Sensor Networks

    Directory of Open Access Journals (Sweden)

    Bruce W. Suter

    2008-01-01

    Full Text Available Time synchronization is crucial for wireless sensor networks (WSNs in performing a number of fundamental operations such as data coordination, power management, security, and localization. The Pairwise Broadcast Synchronization (PBS protocol was recently proposed to minimize the number of timing messages required for global network synchronization, which enables the design of highly energy-efficient WSNs. However, PBS requires all nodes in the network to lie within the communication ranges of two leader nodes, a condition which might not be available in some applications. This paper proposes an extension of PBS to the more general class of sensor networks. Based on the hierarchical structure of the network, an energy-efficient pair selection algorithm is proposed to select the best pairwise synchronization sequence to reduce the overall energy consumption. It is shown that in a multicluster networking environment, PBS requires a far less number of timing messages than other well-known synchronization protocols and incurs no loss in synchronization accuracy. Moreover, the proposed scheme presents significant energy savings for densely deployed WSNs.

  10. Using lod scores to detect sex differences in male-female recombination fractions.

    Science.gov (United States)

    Feenstra, B; Greenberg, D A; Hodge, S E

    2004-01-01

    Human recombination fraction (RF) can differ between males and females, but investigators do not always know which disease genes are located in genomic areas of large RF sex differences. Knowledge of RF sex differences contributes to our understanding of basic biology and can increase the power of a linkage study, improve gene localization, and provide clues to possible imprinting. One way to detect these differences is to use lod scores. In this study we focused on detecting RF sex differences and answered the following questions, in both phase-known and phase-unknown matings: (1) How large a sample size is needed to detect a RF sex difference? (2) What are "optimal" proportions of paternally vs. maternally informative matings? (3) Does ascertaining nonoptimal proportions of paternally or maternally informative matings lead to ascertainment bias? Our results were as follows: (1) We calculated expected lod scores (ELODs) under two different conditions: "unconstrained," allowing sex-specific RF parameters (theta(female), theta(male)); and "constrained," requiring theta(female) = theta(male). We then examined the DeltaELOD (identical with difference between maximized constrained and unconstrained ELODs) and calculated minimum sample sizes required to achieve statistically significant DeltaELODs. For large RF sex differences, samples as small as 10 to 20 fully informative matings can achieve statistical significance. We give general sample size guidelines for detecting RF differences in informative phase-known and phase-unknown matings. (2) We defined p as the proportion of paternally informative matings in the dataset; and the optimal proportion p(circ) as that value of p that maximizes DeltaELOD. We determined that, surprisingly, p(circ) does not necessarily equal (1/2), although it does fall between approximately 0.4 and 0.6 in most situations. (3) We showed that if p in a sample deviates from its optimal value, no bias is introduced (asymptotically) to the maximum

  11. Cycles, scaling and crossover phenomenon in length of the day (LOD) time series

    Science.gov (United States)

    Telesca, Luciano

    2007-06-01

    The dynamics of the temporal fluctuations of the length of the day (LOD) time series from January 1, 1962 to November 2, 2006 were investigated. The power spectrum of the whole time series has revealed annual, semi-annual, decadal and daily oscillatory behaviors, correlated with oceanic-atmospheric processes and interactions. The scaling behavior was analyzed by using the detrended fluctuation analysis (DFA), which has revealed two different scaling regimes, separated by a crossover timescale at approximately 23 days. Flicker-noise process can describe the dynamics of the LOD time regime involving intermediate and long timescales, while Brownian dynamics characterizes the LOD time series for small timescales.

  12. Forecasting irregular variations of UT1-UTC and LOD data caused by ENSO

    Science.gov (United States)

    Niedzielski, T.; Kosek, W.

    2008-04-01

    The research focuses on prediction of LOD and UT1-UTC time series up to one-year in the future with the particular emphasis on the prediction improvement during El Nĩ o or La Nĩ a n n events. The polynomial-harmonic least-squares model is applied to fit the deterministic function to LOD data. The stochastic residuals computed as the difference between LOD data and the polynomial- harmonic model reveal the extreme values driven by El Nĩ o or La Nĩ a. These peaks are modeled by the n n stochastic bivariate autoregressive prediction. This approach focuses on the auto- and cross-correlations between LOD and the axial component of the atmospheric angular momentum. This technique allows one to derive more accurate predictions than purely univariate forecasts, particularly during El Nĩ o/La n Nĩ a events. n

  13. PROPOSAL FOR A NEW LOD AND MULTI-REPRESENTATION CONCEPT FOR CITYGML

    Directory of Open Access Journals (Sweden)

    M.-O. Löwner

    2016-10-01

    Full Text Available The Open Geospatial Consortium (OGC CityGML standard offers a Level of Detail (LoD concept that enables the representation of CityGML features from a very detailed to a less detailed description. Due to a rising application variety, the current LoD concept seems to be too inflexible. Here, we present a multi representation concept (MRC that enables a user-defined definition of LoDs. Because CityGML is an international standard, official profiles of the MRC are proposed. However, encoding of the defined profiles reveals many problems including mapping the conceptual model to the normative encoding, missing technologies and so on. Therefore, we propose to use the MRC as a meta model for the further definition of an LoD concept for CityGML 3.0.

  14. Application of General Regression Neural Network to the Prediction of LOD Change

    Science.gov (United States)

    Zhang, Xiao-Hong; Wang, Qi-Jie; Zhu, Jian-Jun; Zhang, Hao

    2012-01-01

    Traditional methods for predicting the change in length of day (LOD change) are mainly based on some linear models, such as the least square model and autoregression model, etc. However, the LOD change comprises complicated non-linear factors and the prediction effect of the linear models is always not so ideal. Thus, a kind of non-linear neural network — general regression neural network (GRNN) model is tried to make the prediction of the LOD change and the result is compared with the predicted results obtained by taking advantage of the BP (back propagation) neural network model and other models. The comparison result shows that the application of the GRNN to the prediction of the LOD change is highly effective and feasible.

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

    Directory of Open Access Journals (Sweden)

    Jane Louie Fresco Zamora

    2015-01-01

    Full Text Available 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.

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

    Science.gov (United States)

    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. Pairwise comparisons and visual perceptions of equal area polygons.

    Science.gov (United States)

    Adamic, P; Babiy, V; Janicki, R; Kakiashvili, T; Koczkodaj, W W; Tadeusiewicz, R

    2009-02-01

    The number of studies related to visual perception has been plentiful in recent years. Participants rated the areas of five randomly generated shapes of equal area, using a reference unit area that was displayed together with the shapes. Respondents were 179 university students from Canada and Poland. The average error estimated by respondents using the unit square was 25.75%. The error was substantially decreased to 5.51% when the shapes were compared to one another in pairs. This gain of 20.24% for this two-dimensional experiment was substantially better than the 11.78% gain reported in the previous one-dimensional experiments. This is the first statistically sound two-dimensional experiment demonstrating that pairwise comparisons improve accuracy.

  18. The Use of Daily Geodetic UT1 and LOD Data in the Optimal Estimation of UT1 and LOD With the JPL Kalman Earth Orientation Filter

    Science.gov (United States)

    Freedman, A. P.; Steppe, J. A.

    1995-01-01

    The Jet Propulsion Laboratory Kalman Earth Orientation Filter (KEOF) uses several of the Earth rotation data sets available to generate optimally interpolated UT1 and LOD series to support spacecraft navigation. This paper compares use of various data sets within KEOF.

  19. Convergent cross-mapping and pairwise asymmetric inference.

    Science.gov (United States)

    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.

  20. Identifying the Academic Rising Stars via Pairwise Citation Increment Ranking

    KAUST Repository

    Zhang, Chuxu

    2017-08-02

    Predicting the fast-rising young researchers (the Academic Rising Stars) in the future provides useful guidance to the research community, e.g., offering competitive candidates to university for young faculty hiring as they are expected to have success academic careers. In this work, given a set of young researchers who have published the first first-author paper recently, we solve the problem of how to effectively predict the top k% researchers who achieve the highest citation increment in Δt years. We explore a series of factors that can drive an author to be fast-rising and design a novel pairwise citation increment ranking (PCIR) method that leverages those factors to predict the academic rising stars. Experimental results on the large ArnetMiner dataset with over 1.7 million authors demonstrate the effectiveness of PCIR. Specifically, it outperforms all given benchmark methods, with over 8% average improvement. Further analysis demonstrates that temporal features are the best indicators for rising stars prediction, while venue features are less relevant.

  1. The variants of an LOD of a 3D building model and their influence on spatial analyses

    Science.gov (United States)

    Biljecki, Filip; Ledoux, Hugo; Stoter, Jantien; Vosselman, George

    2016-06-01

    The level of detail (LOD) of a 3D city model indicates the model's grade and usability. However, there exist multiple valid variants of each LOD. As a consequence, the LOD concept is inconclusive as an instruction for the acquisition of 3D city models. For instance, the top surface of an LOD1 block model may be modelled at the eaves of a building or at its ridge height. Such variants, which we term geometric references, are often overlooked and are usually not documented in the metadata. Furthermore, the influence of a particular geometric reference on the performance of a spatial analysis is not known. In response to this research gap, we investigate a variety of LOD1 and LOD2 geometric references that are commonly employed, and perform numerical experiments to investigate their relative difference when used as input for different spatial analyses. We consider three use cases (estimation of the area of the building envelope, building volume, and shadows cast by buildings), and compute the deviations in a Monte Carlo simulation. The experiments, carried out with procedurally generated models, indicate that two 3D models representing the same building at the same LOD, but modelled according to different geometric references, may yield substantially different results when used in a spatial analysis. The outcome of our experiments also suggests that the geometric reference may have a bigger influence than the LOD, since an LOD1 with a specific geometric reference may yield a more accurate result than when using LOD2 models.

  2. The Role of Middlemen inEfficient and Strongly Pairwise Stable Networks

    NARCIS (Netherlands)

    Gilles, R.P.; Chakrabarti, S.; Sarangi, S.; Badasyan, N.

    2004-01-01

    We examine the strong pairwise stability concept in network formation theory under collective network benefits.Strong pairwise stability considers a pair of players to add a link through mutual consent while permitting them to unilaterally delete any subset of links under their control.We examine

  3. Linked open data creating knowledge out of interlinked data : results of the LOD2 project

    CERN Document Server

    Bryl, Volha; Tramp, Sebastian

    2014-01-01

    Linked Open Data (LOD) is a pragmatic approach for realizing the Semantic Web vision of making the Web a global, distributed, semantics-based information system. This book presents an overview on the results of the research project “LOD2 -- Creating Knowledge out of Interlinked Data”. LOD2 is a large-scale integrating project co-funded by the European Commission within the FP7 Information and Communication Technologies Work Program. Commencing in September 2010, this 4-year project comprised leading Linked Open Data research groups, companies, and service providers from across 11 European countries and South Korea. The aim of this project was to advance the state-of-the-art in research and development in four key areas relevant for Linked Data, namely 1. RDF data management; 2. the extraction, creation, and enrichment of structured RDF data; 3. the interlinking and fusion of Linked Data from different sources and 4. the authoring, exploration and visualization of Linked Data.

  4. A quantitative trait locus mixture model that avoids spurious LOD score peaks.

    Science.gov (United States)

    Feenstra, Bjarke; Skovgaard, Ib M

    2004-06-01

    In standard interval mapping of quantitative trait loci (QTL), the QTL effect is described by a normal mixture model. At any given location in the genome, the evidence of a putative QTL is measured by the likelihood ratio of the mixture model compared to a single normal distribution (the LOD score). This approach can occasionally produce spurious LOD score peaks in regions of low genotype information (e.g., widely spaced markers), especially if the phenotype distribution deviates markedly from a normal distribution. Such peaks are not indicative of a QTL effect; rather, they are caused by the fact that a mixture of normals always produces a better fit than a single normal distribution. In this study, a mixture model for QTL mapping that avoids the problems of such spurious LOD score peaks is presented.

  5. Medium- and Long-term Prediction of LOD Change with the Leap-step Autoregressive Model

    Science.gov (United States)

    Liu, Q. B.; Wang, Q. J.; Lei, M. F.

    2015-09-01

    It is known that the accuracies of medium- and long-term prediction of changes of length of day (LOD) based on the combined least-square and autoregressive (LS+AR) decrease gradually. The leap-step autoregressive (LSAR) model is more accurate and stable in medium- and long-term prediction, therefore it is used to forecast the LOD changes in this work. Then the LOD series from EOP 08 C04 provided by IERS (International Earth Rotation and Reference Systems Service) is used to compare the effectiveness of the LSAR and traditional AR methods. The predicted series resulted from the two models show that the prediction accuracy with the LSAR model is better than that from AR model in medium- and long-term prediction.

  6. Grip-Pattern Verification for Smart Gun Based on Maximum-Pairwise Comparison and Mean-Template Comparison

    NARCIS (Netherlands)

    Shang, X.; Veldhuis, Raymond N.J.

    2008-01-01

    In our biometric verification system of a smart gun, the rightful user of a gun is authenticated by grip-pattern recognition. In this work verification will be done using two types of comparison methods, respectively. One is mean-template comparison, where the matching score between a test image and

  7. Using lod-score differences to determine mode of inheritance: a simple, robust method even in the presence of heterogeneity and reduced penetrance.

    Science.gov (United States)

    Greenberg, D A; Berger, B

    1994-10-01

    Determining the mode of inheritance is often difficult under the best of circumstances, but when segregation analysis is used, the problems of ambiguous ascertainment procedures, reduced penetrance, heterogeneity, and misdiagnosis make mode-of-inheritance determinations even more unreliable. The mode of inheritance can also be determined using a linkage-based method (maximized maximum lod score or mod score) and association-based methods, which can overcome many of these problems. In this work, we determined how much information is necessary to reliably determine the mode of inheritance from linkage data when heterogeneity and reduced penetrance are present in the data set. We generated data sets under both dominant and recessive inheritance with reduced penetrance and with varying fractions of linked and unlinked families. We then analyzed those data sets, assuming reduced penetrance, both dominant and recessive inheritance, and no heterogeneity. We investigated the reliability of two methods for determining the mode of inheritance from the linkage data. The first method examined the difference (delta) between the maximum lod scores calculated under the two mode-of-inheritance assumptions. We found that if delta was > 1.5, then the higher of the two maximum lod scores reflected the correct mode of inheritance with high reliability and that a delta of 2.5 appeared to practically guarantee a correct mode-of-inheritance inference. Furthermore, this reliability appeared to be virtually independent of alpha, the fraction of linked families in the data set, although the reliability decreased slightly as alpha fell below .50.(ABSTRACT TRUNCATED AT 250 WORDS)

  8. Using lod-score differences to determine mode of inheritance: A simple, robust method even in the presence of heterogeneity and reduced penetrance

    Energy Technology Data Exchange (ETDEWEB)

    Greenberg, D.A.; Berger, B. [Mount Sinai Medical Center, New York, NY (United States)

    1994-10-01

    Determining the mode of inheritance is often difficult under the best of circumstances, but when segregation analysis is used, the problems of ambiguous ascertainment procedures, reduced penetrance, heterogeneity, and misdiagnosis make mode-of-inheritance determinations even more unreliable. The mode of inheritance can also be determined using a linkage-based method and association-based methods, which can overcome many of these problems. In this work, we determined how much information is necessary to reliably determine the mode of inheritance from linkage data when heterogeneity and reduced penetrance are present in the data set. We generated data sets under both dominant and recessive inheritance with reduced penetrance and with varying fractions of linked and unlinked families. We then analyzed those data sets, assuming reduced penetrance, both dominant and recessive inheritance, and no heterogeneity. We investigated the reliability of two methods for determining the mode of inheritance from the linkage data. The first method examined the difference ({Delta}) between the maximum lod scores calculated under the two mode-of-inheritance assumptions. We found that if {Delta} was >1.5, then the higher of the two maximum lod scores reflected the correct mode of inheritance with high reliability and that a {Delta} of 2.5 appeared to practically guarantee a correct mode-of-inheritance inference. Furthermore, this reliability appeared to be virtually independent of {alpha}, the fraction of linked families in the data set. The second method we tested was based on choosing the higher of the two maximum lod scores calculated under the different mode-of-inheritance assumptions. This method became unreliable as {alpha} decreased. These results suggest that the mode of inheritance can be inferred from linkage data with high reliability, even in the presence of heterogeneity and reduced penetrance. 12 refs., 3 figs., 2 tabs.

  9. Screening synteny blocks in pairwise genome comparisons through integer programming.

    Science.gov (United States)

    Tang, Haibao; Lyons, Eric; Pedersen, Brent; Schnable, James C; Paterson, Andrew H; Freeling, Michael

    2011-04-18

    It is difficult to accurately interpret chromosomal correspondences such as true orthology and paralogy due to significant divergence of genomes from a common ancestor. Analyses are particularly problematic among lineages that have repeatedly experienced whole genome duplication (WGD) events. To compare multiple "subgenomes" derived from genome duplications, we need to relax the traditional requirements of "one-to-one" syntenic matchings of genomic regions in order to reflect "one-to-many" or more generally "many-to-many" matchings. However this relaxation may result in the identification of synteny blocks that are derived from ancient shared WGDs that are not of interest. For many downstream analyses, we need to eliminate weak, low scoring alignments from pairwise genome comparisons. Our goal is to objectively select subset of synteny blocks whose total scores are maximized while respecting the duplication history of the genomes in comparison. We call this "quota-based" screening of synteny blocks in order to appropriately fill a quota of syntenic relationships within one genome or between two genomes having WGD events. We have formulated the synteny block screening as an optimization problem known as "Binary Integer Programming" (BIP), which is solved using existing linear programming solvers. The computer program QUOTA-ALIGN performs this task by creating a clear objective function that maximizes the compatible set of synteny blocks under given constraints on overlaps and depths (corresponding to the duplication history in respective genomes). Such a procedure is useful for any pairwise synteny alignments, but is most useful in lineages affected by multiple WGDs, like plants or fish lineages. For example, there should be a 1:2 ploidy relationship between genome A and B if genome B had an independent WGD subsequent to the divergence of the two genomes. We show through simulations and real examples using plant genomes in the rosid superorder that the quota

  10. BETASCAN: probable beta-amyloids identified by pairwise probabilistic analysis.

    Directory of Open Access Journals (Sweden)

    Allen W Bryan

    2009-03-01

    Full Text Available Amyloids and prion proteins are clinically and biologically important beta-structures, whose supersecondary structures are difficult to determine by standard experimental or computational means. In addition, significant conformational heterogeneity is known or suspected to exist in many amyloid fibrils. Recent work has indicated the utility of pairwise probabilistic statistics in beta-structure prediction. We develop here a new strategy for beta-structure prediction, emphasizing the determination of beta-strands and pairs of beta-strands as fundamental units of beta-structure. Our program, BETASCAN, calculates likelihood scores for potential beta-strands and strand-pairs based on correlations observed in parallel beta-sheets. The program then determines the strands and pairs with the greatest local likelihood for all of the sequence's potential beta-structures. BETASCAN suggests multiple alternate folding patterns and assigns relative a priori probabilities based solely on amino acid sequence, probability tables, and pre-chosen parameters. The algorithm compares favorably with the results of previous algorithms (BETAPRO, PASTA, SALSA, TANGO, and Zyggregator in beta-structure prediction and amyloid propensity prediction. Accurate prediction is demonstrated for experimentally determined amyloid beta-structures, for a set of known beta-aggregates, and for the parallel beta-strands of beta-helices, amyloid-like globular proteins. BETASCAN is able both to detect beta-strands with higher sensitivity and to detect the edges of beta-strands in a richly beta-like sequence. For two proteins (Abeta and Het-s, there exist multiple sets of experimental data implying contradictory structures; BETASCAN is able to detect each competing structure as a potential structure variant. The ability to correlate multiple alternate beta-structures to experiment opens the possibility of computational investigation of prion strains and structural heterogeneity of amyloid

  11. GraphAlignment: Bayesian pairwise alignment of biological networks

    Directory of Open Access Journals (Sweden)

    Kolář Michal

    2012-11-01

    Full Text Available Abstract Background With increased experimental availability and accuracy of bio-molecular networks, tools for their comparative and evolutionary analysis are needed. A key component for such studies is the alignment of networks. Results We introduce the Bioconductor package GraphAlignment for pairwise alignment of bio-molecular networks. The alignment incorporates information both from network vertices and network edges and is based on an explicit evolutionary model, allowing inference of all scoring parameters directly from empirical data. We compare the performance of our algorithm to an alternative algorithm, Græmlin 2.0. On simulated data, GraphAlignment outperforms Græmlin 2.0 in several benchmarks except for computational complexity. When there is little or no noise in the data, GraphAlignment is slower than Græmlin 2.0. It is faster than Græmlin 2.0 when processing noisy data containing spurious vertex associations. Its typical case complexity grows approximately as O(N2.6. On empirical bacterial protein-protein interaction networks (PIN and gene co-expression networks, GraphAlignment outperforms Græmlin 2.0 with respect to coverage and specificity, albeit by a small margin. On large eukaryotic PIN, Græmlin 2.0 outperforms GraphAlignment. Conclusions The GraphAlignment algorithm is robust to spurious vertex associations, correctly resolves paralogs, and shows very good performance in identification of homologous vertices defined by high vertex and/or interaction similarity. The simplicity and generality of GraphAlignment edge scoring makes the algorithm an appropriate choice for global alignment of networks.

  12. Secular changes of LOD associated with a growth of the inner core

    Science.gov (United States)

    Denis, C.; Rybicki, K. R.; Varga, P.

    2006-05-01

    From recent estimates of the age of the inner core based on the theory of thermal evolution of the core, we estimate that nowadays the growth of the inner core may perhaps contribute to the observed overall secular increase of LOD caused mainly by tidal friction (i.e., 1.72 ms per century) by a relative decrease of 2 to 7 μs per century. Another, albeit much less plausible, hypothesis is that crystallization of the inner core does not produce any change of LOD, but makes the inner core rotate differentially with respect to the outer core and mantle.

  13. Application of LOD technology to the economic residence GIS for industry and commerce administration

    Science.gov (United States)

    Song, Yongjun; Feng, Xuezhi; Zhao, Shuhe; Yin, Haiwei; Li, Yulin; Cui, Hongxia; Zhang, Hui; Zhong, Quanbao

    2007-06-01

    The LOD technology has an impact upon the multi-scale representation of spatial database. This paper takes advantage of LOD technology to express the multi-scale geographical data, and establish the exchange of multi-scale electronic map, further attain the goal that the details of geographic features such as point, line and polygon can be displayed more and more clearly with the display scale being enlarged to be convenient for the personnel of all offices of industry and commerce administration to label the locations of the corporations or enterprises.

  14. Status and Prospects for Combined GPS LOD and VLBI UT1 Measurements

    Science.gov (United States)

    Senior, K.; Kouba, J.; Ray, J.

    2010-01-01

    A Kalman filter was developed to combine VLBI estimates of UT1-TAI with biased length of day (LOD) estimates from GPS. The VLBI results are the analyses of the NASA Goddard Space Flight Center group from 24-hr multi-station observing sessions several times per week and the nearly daily 1-hr single-baseline sessions. Daily GPS LOD estimates from the International GNSS Service (IGS) are combined with the VLBI UT1-TAI by modeling the natural excitation of LOD as the integral of a white noise process (i.e., as a random walk) and the UT1 variations as the integration of LOD, similar to the method described by Morabito et al. (1988). To account for GPS technique errors, which express themselves mostly as temporally correlated biases in the LOD measurements, a Gauss-Markov model has been added to assimilate the IGS data, together with a fortnightly sinusoidal term to capture errors in the IGS treatments of tidal effects. Evaluated against independent atmospheric and oceanic axial angular momentum (AAM + OAM) excitations and compared to other UT1/LOD combinations, ours performs best overall in terms of lowest RMS residual and highest correlation with (AAM + OAM) over sliding intervals down to 3 d. The IERS 05C04 and Bulletin A combinations show strong high-frequency smoothing and other problems. Until modified, the JPL SPACE series suffered in the high frequencies from not including any GPS-based LODs. We find, surprisingly, that further improvements are possible in the Kalman filter combination by selective rejection of some VLBI data. The best combined results are obtained by excluding all the 1-hr single-baseline UT1 data as well as those 24-hr UT1 measurements with formal errors greater than 5 μs (about 18% of the multi-baseline sessions). A rescaling of the VLBI formal errors, rather than rejection, was not an effective strategy. These results suggest that the UT1 errors of the 1-hr and weaker 24-hr VLBI sessions are non-Gaussian and more heterogeneous than expected

  15. constNJ: an algorithm to reconstruct sets of phylogenetic trees satisfying pairwise topological constraints.

    Science.gov (United States)

    Matsen, Frederick A

    2010-06-01

    This article introduces constNJ (constrained neighbor-joining), an algorithm for phylogenetic reconstruction of sets of trees with constrained pairwise rooted subtree-prune-regraft (rSPR) distance. We are motivated by the problem of constructing sets of trees that must fit into a recombination, hybridization, or similar network. Rather than first finding a set of trees that are optimal according to a phylogenetic criterion (e.g., likelihood or parsimony) and then attempting to fit them into a network, constNJ estimates the trees while enforcing specified rSPR distance constraints. The primary input for constNJ is a collection of distance matrices derived from sequence blocks which are assumed to have evolved in a tree-like manner, such as blocks of an alignment which do not contain any recombination breakpoints. The other input is a set of rSPR constraint inequalities for any set of pairs of trees. constNJ is consistent and a strict generalization of the neighbor-joining algorithm; it uses the new notion of maximum agreement partitions (MAPs) to assure that the resulting trees satisfy the given rSPR distance constraints.

  16. Easy calculations of lod scores and genetic risks on small computers.

    Science.gov (United States)

    Lathrop, G M; Lalouel, J M

    1984-01-01

    A computer program that calculates lod scores and genetic risks for a wide variety of both qualitative and quantitative genetic traits is discussed. An illustration is given of the joint use of a genetic marker, affection status, and quantitative information in counseling situations regarding Duchenne muscular dystrophy. PMID:6585139

  17. Aspects Of 40- to 50-Day Oscillations In LOD And AAM

    Science.gov (United States)

    Dickey, Jean O.; Marcus, Steven L.; Ghil, Michael

    1992-01-01

    Report presents study of fluctuations in rotation of Earth, focusing on irregular intraseasonal oscillations in length of day (LOD) and atmospheric angular momentum (AAM) with periods varying from 40 to 50 days. Study draws upon and extends results of prior research.

  18. Exploring the Processes of Generating LOD (0-2) Citygml Models in Greater Municipality of Istanbul

    Science.gov (United States)

    Buyuksalih, I.; Isikdag, U.; Zlatanova, S.

    2013-08-01

    3D models of cities, visualised and exploded in 3D virtual environments have been available for several years. Currently a large number of impressive realistic 3D models have been regularly presented at scientific, professional and commercial events. One of the most promising developments is OGC standard CityGML. CityGML is object-oriented model that support 3D geometry and thematic semantics, attributes and relationships, and offers advanced options for realistic visualization. One of the very attractive characteristics of the model is the support of 5 levels of detail (LOD), starting from 2.5D less accurate model (LOD0) and ending with very detail indoor model (LOD4). Different local government offices and municipalities have different needs when utilizing the CityGML models, and the process of model generation depends on local and domain specific needs. Although the processes (i.e. the tasks and activities) for generating the models differs depending on its utilization purpose, there are also some common tasks (i.e. common denominator processes) in the model generation of City GML models. This paper focuses on defining the common tasks in generation of LOD (0-2) City GML models and representing them in a formal way with process modeling diagrams.

  19. LOD-A-lot : A single-file enabler for data science

    NARCIS (Netherlands)

    Beek, Wouter; Ferńandez, Javier D.; Verborgh, Ruben

    2017-01-01

    Many data scientists make use of Linked Open Data (LOD) as a huge interconnected knowledge base represented in RDF. However, the distributed nature of the information and the lack of a scalable approach to manage and consume such Big Semantic Data makes it difficult and expensive to conduct

  20. Pharmacological treatments in asthma-affected horses: A pair-wise and network meta-analysis.

    Science.gov (United States)

    Calzetta, L; Roncada, P; di Cave, D; Bonizzi, L; Urbani, A; Pistocchini, E; Rogliani, P; Matera, M G

    2017-11-01

    Equine asthma is a disease characterised by reversible airflow obstruction, bronchial hyper-responsiveness and airway inflammation following exposure of susceptible horses to specific airborne agents. Although clinical remission can be achieved in a low-airborne dust environment, repeated exacerbations may lead to irreversible airway remodelling. The available data on the pharmacotherapy of equine asthma result from several small studies, and no head-to-head clinical trials have been conducted among the available medications. To assess the impact of the pharmacological interventions in equine asthma and compare the effect of different classes of drugs on lung function. Pair-wise and network meta-analysis. Literature searches for clinical trials on the pharmacotherapy of equine asthma were performed. The risk of publication bias was assessed by funnel plots and Egger's test. Changes in maximum transpulmonary or pleural pressure, pulmonary resistance and dynamic lung compliance vs. control were analysed via random-effects models and Bayesian networks. The results obtained from 319 equine asthma-affected horses were extracted from 32 studies. Bronchodilators, corticosteroids and chromones improved maximum transpulmonary or pleural pressure (range: -8.0 to -21.4 cmH 2 O; Ptherapies. Long-term treatments were more effective than short-term treatments. Weak publication bias was detected. This study demonstrates that long-term treatments with inhaled corticosteroids and long-acting β 2 -AR agonists may represent the first choice for treating equine asthma. Further high quality clinical trials are needed to clarify whether inhaled bronchodilators should be preferred to inhaled corticosteroids or vice versa, and to investigate the potential superiority of combination therapy in equine asthma. © 2017 EVJ Ltd.

  1. LOD BIM Element specification for Railway Turnout Systems Risk Mitigation using the Information Delivery Manual

    Science.gov (United States)

    Gigante-Barrera, Ángel; Dindar, Serdar; Kaewunruen, Sakdirat; Ruikar, Darshan

    2017-10-01

    Railway turnouts are complex systems designed using complex geometries and grades which makes them difficult to be managed in terms of risk prevention. This feature poses a substantial peril to rail users as it is considered a cause of derailment. In addition, derailment deals to financial losses due to operational downtimes and monetary compensations in case of death or injure. These are fundamental drivers to consider mitigating risks arising from poor risk management during design. Prevention through design (PtD) is a process that introduces tacit knowledge from industry professionals during the design process. There is evidence that Building Information Modelling (BIM) can help to mitigate risk since the inception of the project. BIM is considered an Information System (IS) were tacit knowledge can be stored and retrieved from a digital database making easy to take promptly decisions as information is ready to be analysed. BIM at the model element level entails working with 3D elements and embedded data, therefore adding a layer of complexity to the management of information along the different stages of the project and across different disciplines. In order to overcome this problem, the industry has created a framework for model progression specification named Level of Development (LOD). The paper presents an IDM based framework for design risk mitigation through code validation using the LOD. This effort resulted on risk datasets which describe graphically and non-graphically a rail turnout as the model progresses. Thus, permitting its inclusion within risk information systems. The assignment of an LOD construct to a set of data, requires specialised management and process related expertise. Furthermore, the selection of a set of LOD constructs requires a purpose based analysis. Therefore, a framework for LOD constructs implementation within the IDM for code checking is required for the industry to progress in this particular field.

  2. Comparison of multipoint linkage analyses for quantitative traits in the CEPH data: parametric LOD scores, variance components LOD scores, and Bayes factors.

    Science.gov (United States)

    Sung, Yun Ju; Di, Yanming; Fu, Audrey Q; Rothstein, Joseph H; Sieh, Weiva; Tong, Liping; Thompson, Elizabeth A; Wijsman, Ellen M

    2007-01-01

    We performed multipoint linkage analyses with multiple programs and models for several gene expression traits in the Centre d'Etude du Polymorphisme Humain families. All analyses provided consistent results for both peak location and shape. Variance-components (VC) analysis gave wider peaks and Bayes factors gave fewer peaks. Among programs from the MORGAN package, lm_multiple performed better than lm_markers, resulting in less Markov-chain Monte Carlo (MCMC) variability between runs, and the program lm_twoqtl provided higher LOD scores by also including either a polygenic component or an additional quantitative trait locus.

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

    OpenAIRE

    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-...

  4. LOD +: Augmenting LOD with Skeletons

    OpenAIRE

    Lange , Benoit; Rodriguez , Nancy

    2010-01-01

    International audience; Until now computer graphic researchers have tried to solve visualization problems introduced by the size of meshes. Modern tools produce large models and hardware is not able to render them in full resolution. For example, the digital Michelangelo project extracted a model with more than one billion polygons. One can notice hardware has become more and more powerful but meshes have also become more and more complex. To solve this issue, people have worked on many solut...

  5. Strategy for determination of LOD and LOQ values--some basic aspects.

    Science.gov (United States)

    Uhrovčík, Jozef

    2014-02-01

    The paper is devoted to the evaluation of limit of detection (LOD) and limit of quantification (LOQ) values in concentration domain by using 4 different approaches; namely 3σ and 10σ approaches, ULA2 approach, PBA approach and MDL approach. Brief theoretical analyses of all above mentioned approaches are given together with directions for their practical use. Calculations and correct calibration design are exemplified by using of electrothermal atomic absorption spectrometry for determination of lead in drinking water sample. These validation parameters reached 1.6 μg L(-1) (LOD) and 5.4 μg L(-1) (LOQ) by using 3σ and 10σ approaches. For obtaining relevant values of analyte concentration the influence of calibration design and measurement methodology were examined. The most preferred technique has proven to be a method of preconcentration of the analyte on the surface of the graphite cuvette (boost cycle). © 2013 Elsevier B.V. All rights reserved.

  6. Smoothing of the bivariate LOD score for non-normal quantitative traits.

    Science.gov (United States)

    Buil, Alfonso; Dyer, Thomas D; Almasy, Laura; Blangero, John

    2005-12-30

    Variance component analysis provides an efficient method for performing linkage analysis for quantitative traits. However, type I error of variance components-based likelihood ratio testing may be affected when phenotypic data are non-normally distributed (especially with high values of kurtosis). This results in inflated LOD scores when the normality assumption does not hold. Even though different solutions have been proposed to deal with this problem with univariate phenotypes, little work has been done in the multivariate case. We present an empirical approach to adjust the inflated LOD scores obtained from a bivariate phenotype that violates the assumption of normality. Using the Collaborative Study on the Genetics of Alcoholism data available for the Genetic Analysis Workshop 14, we show how bivariate linkage analysis with leptokurtotic traits gives an inflated type I error. We perform a novel correction that achieves acceptable levels of type I error.

  7. Estimation of the POD function and the LOD of a qualitative microbiological measurement method.

    Science.gov (United States)

    Wilrich, Cordula; Wilrich, Peter-Theodor

    2009-01-01

    Qualitative microbiological measurement methods in which the measurement results are either 0 (microorganism not detected) or 1 (microorganism detected) are discussed. The performance of such a measurement method is described by its probability of detection as a function of the contamination (CFU/g or CFU/mL) of the test material, or by the LOD(p), i.e., the contamination that is detected (measurement result 1) with a specified probability p. A complementary log-log model was used to statistically estimate these performance characteristics. An intralaboratory experiment for the detection of Listeria monocytogenes in various food matrixes illustrates the method. The estimate of LOD50% is compared with the Spearman-Kaerber method.

  8. Conclusion of LOD-score analysis for family data generated under two-locus models.

    Science.gov (United States)

    Dizier, M H; Babron, M C; Clerget-Darpoux, F

    1996-06-01

    The power to detect linkage by the LOD-score method is investigated here for diseases that depend on the effects of two genes. The classical strategy is, first, to detect a major-gene (MG) effect by segregation analysis and, second, to seek for linkage with genetic markers by the LOD-score method using the MG parameters. We already showed that segregation analysis can lead to evidence for a MG effect for many two-locus models, with the estimates of the MG parameters being very different from those of the two genes involved in the disease. We show here that use of these MG parameter estimates in the LOD-score analysis may lead to a failure to detect linkage for some two-locus models. For these models, use of the sib-pair method gives a non-negligible increase of power to detect linkage. The linkage-homogeneity test among subsamples differing for the familial disease distribution provides evidence of parameter misspecification, when the MG parameters are used. Moreover, for most of the models, use of the MG parameters in LOD-score analysis leads to a large bias in estimation of the recombination fraction and sometimes also to a rejection of linkage for the true recombination fraction. A final important point is that a strong evidence of an MG effect, obtained by segregation analysis, does not necessarily imply that linkage will be detected for at least one of the two genes, even with the true parameters and with a close informative marker.

  9. Conclusions of LOD-score analysis for family data generated under two-locus models

    Energy Technology Data Exchange (ETDEWEB)

    Dizier, M.H.; Babron, M.C.; Clergt-Darpoux, F. [Unite de Recherches d`Epidemiologie Genetique, Paris (France)

    1996-06-01

    The power to detect linkage by the LOD-score method is investigated here for diseases that depend on the effects of two genes. The classical strategy is, first, to detect a major-gene (MG) effect by segregation analysis and, second, to seek for linkage with genetic markers by the LOD-score method using the MG parameters. We already showed that segregation analysis can lead to evidence for a MG effect for many two-locus models, with the estimates of the MG parameters being very different from those of the two genes involved in the disease. We show here that use of these MG parameter estimates in the LOD-score analysis may lead to a failure to detect linkage for some two-locus models. For these models, use of the sib-pair method gives a non-negligible increase of power to detect linkage. The linkage-homogeneity test among subsamples differing for the familial disease distribution provides evidence of parameter misspecification, when the MG parameters are used. Moreover, for most of the models, use of the MG parameters in LOD-score analysis leads to a large bias in estimation of the recombination fraction and sometimes also to a rejection of linkage for the true recombination fraction. A final important point is that a strong evidence of an MG effect, obtained by segregation analysis, does not necessarily imply that linkage will be detected for at least one of the two genes, even with the true parameters and with a close informative marker. 17 refs., 3 tabs.

  10. Efficient Simplification Methods for Generating High Quality LODs of 3D Meshes

    Institute of Scientific and Technical Information of China (English)

    Muhammad Hussain

    2009-01-01

    Two simplification algorithms are proposed for automatic decimation of polygonal models, and for generating their LODs. Each algorithm orders vertices according to their priority values and then removes them iteratively. For setting the priority value of each vertex, exploiting normal field of its one-ring neighborhood, we introduce a new measure of geometric fidelity that reflects well the local geometric features of the vertex. After a vertex is selected, using other measures of geometric distortion that are based on normal field deviation and distance measure, it is decided which of the edges incident on the vertex is to be collapsed for removing it. The collapsed edge is substituted with a new vertex whose position is found by minimizing the local quadric error measure. A comparison with the state-of-the-art algorithms reveals that the proposed algorithms are simple to implement, are computationally more efficient, generate LODs with better quality, and preserve salient features even after drastic simplification. The methods are useful for applications such as 3D computer games, virtual reality, where focus is on fast running time, reduced memory overhead, and high quality LODs.

  11. Multilocus lod scores in large pedigrees: combination of exact and approximate calculations.

    Science.gov (United States)

    Tong, Liping; Thompson, Elizabeth

    2008-01-01

    To detect the positions of disease loci, lod scores are calculated at multiple chromosomal positions given trait and marker data on members of pedigrees. Exact lod score calculations are often impossible when the size of the pedigree and the number of markers are both large. In this case, a Markov Chain Monte Carlo (MCMC) approach provides an approximation. However, to provide accurate results, mixing performance is always a key issue in these MCMC methods. In this paper, we propose two methods to improve MCMC sampling and hence obtain more accurate lod score estimates in shorter computation time. The first improvement generalizes the block-Gibbs meiosis (M) sampler to multiple meiosis (MM) sampler in which multiple meioses are updated jointly, across all loci. The second one divides the computations on a large pedigree into several parts by conditioning on the haplotypes of some 'key' individuals. We perform exact calculations for the descendant parts where more data are often available, and combine this information with sampling of the hidden variables in the ancestral parts. Our approaches are expected to be most useful for data on a large pedigree with a lot of missing data. (c) 2007 S. Karger AG, Basel

  12. Improvement of LOD in Fluorescence Detection with Spectrally Nonuniform Background by Optimization of Emission Filtering.

    Science.gov (United States)

    Galievsky, Victor A; Stasheuski, Alexander S; Krylov, Sergey N

    2017-10-17

    The limit-of-detection (LOD) in analytical instruments with fluorescence detection can be improved by reducing noise of optical background. Efficiently reducing optical background noise in systems with spectrally nonuniform background requires complex optimization of an emission filter-the main element of spectral filtration. Here, we introduce a filter-optimization method, which utilizes an expression for the signal-to-noise ratio (SNR) as a function of (i) all noise components (dark, shot, and flicker), (ii) emission spectrum of the analyte, (iii) emission spectrum of the optical background, and (iv) transmittance spectrum of the emission filter. In essence, the noise components and the emission spectra are determined experimentally and substituted into the expression. This leaves a single variable-the transmittance spectrum of the filter-which is optimized numerically by maximizing SNR. Maximizing SNR provides an accurate way of filter optimization, while a previously used approach based on maximizing a signal-to-background ratio (SBR) is the approximation that can lead to much poorer LOD specifically in detection of fluorescently labeled biomolecules. The proposed filter-optimization method will be an indispensable tool for developing new and improving existing fluorescence-detection systems aiming at ultimately low LOD.

  13. A Microfluidic Lab-on-a-Disc (LOD for Antioxidant Activities of Plant Extracts

    Directory of Open Access Journals (Sweden)

    Nurhaslina Abd Rahman

    2018-03-01

    Full Text Available Antioxidants are an important substance that can fight the deterioration of free radicals and can easily oxidize when exposed to light. There are many methods to measure the antioxidant activity in a biological sample, for example 2,2-diphenyl-1-picrylhydrazyl (DPPH antioxidant activity test, which is one of the simplest methods used. Despite its simplicity, the organic solvent that has been used to dilute DPPH is easily evaporated and degraded with respect to light exposure and time. Thus, it needs to be used at the earliest convenient time prior to the experiment. To overcome this issue, a rapid and close system for antioxidant activity is required. In this paper, we introduced the Lab-on-a-Disc (LoD method that integrates the DPPH antioxidant activity test on a microfluidic compact disc (CD. We used ascorbic acid, quercetin, Areca catechu, Polygonum minus, and Syzygium polyanthum plant extracts to compare the results of our proposed LoD method with the conventional method. Contrasted to the arduous laborious conventional method, our proposed method offer rapid analysis and simple determination of antioxidant. This proposed LoD method for antioxidant activity in plants would be a platform for the further development of antioxidant assay.

  14. Fault feature analysis of cracked gear based on LOD and analytical-FE method

    Science.gov (United States)

    Wu, Jiateng; Yang, Yu; Yang, Xingkai; Cheng, Junsheng

    2018-01-01

    At present, there are two main ideas for gear fault diagnosis. One is the model-based gear dynamic analysis; the other is signal-based gear vibration diagnosis. In this paper, a method for fault feature analysis of gear crack is presented, which combines the advantages of dynamic modeling and signal processing. Firstly, a new time-frequency analysis method called local oscillatory-characteristic decomposition (LOD) is proposed, which has the attractive feature of extracting fault characteristic efficiently and accurately. Secondly, an analytical-finite element (analytical-FE) method which is called assist-stress intensity factor (assist-SIF) gear contact model, is put forward to calculate the time-varying mesh stiffness (TVMS) under different crack states. Based on the dynamic model of the gear system with 6 degrees of freedom, the dynamic simulation response was obtained for different tooth crack depths. For the dynamic model, the corresponding relation between the characteristic parameters and the degree of the tooth crack is established under a specific condition. On the basis of the methods mentioned above, a novel gear tooth root crack diagnosis method which combines the LOD with the analytical-FE is proposed. Furthermore, empirical mode decomposition (EMD) and ensemble empirical mode decomposition (EEMD) are contrasted with the LOD by gear crack fault vibration signals. The analysis results indicate that the proposed method performs effectively and feasibility for the tooth crack stiffness calculation and the gear tooth crack fault diagnosis.

  15. LOD score exclusion analyses for candidate QTLs using random population samples.

    Science.gov (United States)

    Deng, Hong-Wen

    2003-11-01

    While extensive analyses have been conducted to test for, no formal analyses have been conducted to test against, the importance of candidate genes as putative QTLs using random population samples. Previously, we developed an LOD score exclusion mapping approach for candidate genes for complex diseases. Here, we extend this LOD score approach for exclusion analyses of candidate genes for quantitative traits. Under this approach, specific genetic effects (as reflected by heritability) and inheritance models at candidate QTLs can be analyzed and if an LOD score is < or = -2.0, the locus can be excluded from having a heritability larger than that specified. Simulations show that this approach has high power to exclude a candidate gene from having moderate genetic effects if it is not a QTL and is robust to population admixture. Our exclusion analysis complements association analysis for candidate genes as putative QTLs in random population samples. The approach is applied to test the importance of Vitamin D receptor (VDR) gene as a potential QTL underlying the variation of bone mass, an important determinant of osteoporosis.

  16. LOD-based clustering techniques for efficient large-scale terrain storage and visualization

    Science.gov (United States)

    Bao, Xiaohong; Pajarola, Renato

    2003-05-01

    Large multi-resolution terrain data sets are usually stored out-of-core. To visualize terrain data at interactive frame rates, the data needs to be organized on disk, loaded into main memory part by part, then rendered efficiently. Many main-memory algorithms have been proposed for efficient vertex selection and mesh construction. Organization of terrain data on disk is quite difficult because the error, the triangulation dependency and the spatial location of each vertex all need to be considered. Previous terrain clustering algorithms did not consider the per-vertex approximation error of individual terrain data sets. Therefore, the vertex sequences on disk are exactly the same for any terrain. In this paper, we propose a novel clustering algorithm which introduces the level-of-detail (LOD) information to terrain data organization to map multi-resolution terrain data to external memory. In our approach the LOD parameters of the terrain elevation points are reflected during clustering. The experiments show that dynamic loading and paging of terrain data at varying LOD is very efficient and minimizes page faults. Additionally, the preprocessing of this algorithm is very fast and works from out-of-core.

  17. Effects of lodoxamide (LOD), disodium cromoglycate (DSCG) and N-acetyl-aspartyl-glutamate sodium salt (NAAGA) on ocular active anaphylaxis.

    Science.gov (United States)

    Goldschmidt, P; Luyckx, J

    1996-04-01

    LOD, DSCG and NAAGA eye-drops were evaluated on experimentally-induced ocular active anaphylaxis in guinea pigs. Twelve animals per group were sensitized with egg albumin i.p. and challenged on the surface of the eye 14 days later. Two days before challenge, animals were treated with LOD, DSCG or NAAGA 4 times a day. Permeability indexes were calculated after intracardiac injection of Evans Blue. No effect on ocular active anaphylaxis was found with LOD nor with DSCG. NAAGA was able to significantly reduce blood-eye permeability indexes.

  18. Approximate maximum parsimony and ancestral maximum likelihood.

    Science.gov (United States)

    Alon, Noga; Chor, Benny; Pardi, Fabio; Rapoport, Anat

    2010-01-01

    We explore the maximum parsimony (MP) and ancestral maximum likelihood (AML) criteria in phylogenetic tree reconstruction. Both problems are NP-hard, so we seek approximate solutions. We formulate the two problems as Steiner tree problems under appropriate distances. The gist of our approach is the succinct characterization of Steiner trees for a small number of leaves for the two distances. This enables the use of known Steiner tree approximation algorithms. The approach leads to a 16/9 approximation ratio for AML and asymptotically to a 1.55 approximation ratio for MP.

  19. Maximum permissible dose

    International Nuclear Information System (INIS)

    Anon.

    1979-01-01

    This chapter presents a historic overview of the establishment of radiation guidelines by various national and international agencies. The use of maximum permissible dose and maximum permissible body burden limits to derive working standards is discussed

  20. Pairwise Comparison and Distance Measure of Hesitant Fuzzy Linguistic Term Sets

    Directory of Open Access Journals (Sweden)

    Han-Chen Huang

    2014-01-01

    Full Text Available A hesitant fuzzy linguistic term set (HFLTS, allowing experts using several possible linguistic terms to assess a qualitative linguistic variable, is very useful to express people’s hesitancy in practical decision-making problems. Up to now, a little research has been done on the comparison and distance measure of HFLTSs. In this paper, we present a comparison method for HFLTSs based on pairwise comparisons of each linguistic term in the two HFLTSs. Then, a distance measure method based on the pairwise comparison matrix of HFLTSs is proposed, and we prove that this distance is equal to the distance of the average values of HFLTSs, which makes the distance measure much more simple. Finally, the pairwise comparison and distance measure methods are utilized to develop two multicriteria decision-making approaches under hesitant fuzzy linguistic environments. The results analysis shows that our methods in this paper are more reasonable.

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

    Science.gov (United States)

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

    2015-08-01

    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. 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. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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

    Science.gov (United States)

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

    2005-07-01

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

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

    Directory of Open Access Journals (Sweden)

    Brejnev Muhizi Muhire

    Full Text Available 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.

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

    Science.gov (United States)

    Rajagopal, Prabha; Ravana, Sri Devi

    2017-01-01

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

  5. Image ranking in video sequences using pairwise image comparisons and temporal smoothing

    CSIR Research Space (South Africa)

    Burke, Michael

    2016-12-01

    Full Text Available The ability to predict the importance of an image is highly desirable in computer vision. This work introduces an image ranking scheme suitable for use in video or image sequences. Pairwise image comparisons are used to determine image ‘interest...

  6. Exact p-values for pairwise comparison of Friedman rank sums, with application to comparing classifiers

    NARCIS (Netherlands)

    Eisinga, R.N.; Heskes, T.M.; Pelzer, B.J.; Grotenhuis, H.F. te

    2017-01-01

    Background: The Friedman rank sum test is a widely-used nonparametric method in computational biology. In addition to examining the overall null hypothesis of no significant difference among any of the rank sums, it is typically of interest to conduct pairwise comparison tests. Current approaches to

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

    KAUST Repository

    Varsani, Arvind

    2014-01-25

    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). © 2014 Springer-Verlag Wien.

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

    KAUST Repository

    Varsani, Arvind; Martin, Darren Patrick; Navas-Castillo, Jesú s; Moriones, Enrique; Herná ndez-Zepeda, Cecilia; Idris, Ali; Murilo Zerbini, F.; Brown, Judith K.

    2014-01-01

    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). © 2014 Springer-Verlag Wien.

  9. A gradient approximation for calculating Debye temperatures from pairwise interatomic potentials

    International Nuclear Information System (INIS)

    Jackson, D.P.

    1975-09-01

    A simple gradient approximation is given for calculating the effective Debye temperature of a cubic crystal from central pairwise interatomic potentials. For examples of the Morse potential applied to cubic metals the results are in generally good agreement with experiment. (author)

  10. A Comparative Study of Pairwise Learning Methods Based on Kernel Ridge Regression.

    Science.gov (United States)

    Stock, Michiel; Pahikkala, Tapio; Airola, Antti; De Baets, Bernard; Waegeman, Willem

    2018-06-12

    Many machine learning problems can be formulated as predicting labels for a pair of objects. Problems of that kind are often referred to as pairwise learning, dyadic prediction, or network inference problems. During the past decade, kernel methods have played a dominant role in pairwise learning. They still obtain a state-of-the-art predictive performance, but a theoretical analysis of their behavior has been underexplored in the machine learning literature. In this work we review and unify kernel-based algorithms that are commonly used in different pairwise learning settings, ranging from matrix filtering to zero-shot learning. To this end, we focus on closed-form efficient instantiations of Kronecker kernel ridge regression. We show that independent task kernel ridge regression, two-step kernel ridge regression, and a linear matrix filter arise naturally as a special case of Kronecker kernel ridge regression, implying that all these methods implicitly minimize a squared loss. In addition, we analyze universality, consistency, and spectral filtering properties. Our theoretical results provide valuable insights into assessing the advantages and limitations of existing pairwise learning methods.

  11. On the calculation of x-ray scattering signals from pairwise radial distribution functions

    DEFF Research Database (Denmark)

    Dohn, Asmus Ougaard; Biasin, Elisa; Haldrup, Kristoffer

    2015-01-01

    We derive a formulation for evaluating (time-resolved) x-ray scattering signals of solvated chemical systems, based on pairwise radial distribution functions, with the aim of this formulation to accompany molecular dynamics simulations. The derivation is described in detail to eliminate any possi...

  12. ANIMATION STRATEGIES FOR SMOOTH TRANSFORMATIONS BETWEEN DISCRETE LODS OF 3D BUILDING MODELS

    Directory of Open Access Journals (Sweden)

    M. Kada

    2016-06-01

    Full Text Available The cartographic 3D visualization of urban areas has experienced tremendous progress over the last years. An increasing number of applications operate interactively in real-time and thus require advanced techniques to improve the quality and time response of dynamic scenes. The main focus of this article concentrates on the discussion of strategies for smooth transformation between two discrete levels of detail (LOD of 3D building models that are represented as restricted triangle meshes. Because the operation order determines the geometrical and topological properties of the transformation process as well as its visual perception by a human viewer, three different strategies are proposed and subsequently analyzed. The simplest one orders transformation operations by the length of the edges to be collapsed, while the other two strategies introduce a general transformation direction in the form of a moving plane. This plane either pushes the nodes that need to be removed, e.g. during the transformation of a detailed LOD model to a coarser one, towards the main building body, or triggers the edge collapse operations used as transformation paths for the cartographic generalization.

  13. Animation Strategies for Smooth Transformations Between Discrete Lods of 3d Building Models

    Science.gov (United States)

    Kada, Martin; Wichmann, Andreas; Filippovska, Yevgeniya; Hermes, Tobias

    2016-06-01

    The cartographic 3D visualization of urban areas has experienced tremendous progress over the last years. An increasing number of applications operate interactively in real-time and thus require advanced techniques to improve the quality and time response of dynamic scenes. The main focus of this article concentrates on the discussion of strategies for smooth transformation between two discrete levels of detail (LOD) of 3D building models that are represented as restricted triangle meshes. Because the operation order determines the geometrical and topological properties of the transformation process as well as its visual perception by a human viewer, three different strategies are proposed and subsequently analyzed. The simplest one orders transformation operations by the length of the edges to be collapsed, while the other two strategies introduce a general transformation direction in the form of a moving plane. This plane either pushes the nodes that need to be removed, e.g. during the transformation of a detailed LOD model to a coarser one, towards the main building body, or triggers the edge collapse operations used as transformation paths for the cartographic generalization.

  14. A comparison of LOD and UT1-UTC forecasts by different combined prediction techniques

    Science.gov (United States)

    Kosek, W.; Kalarus, M.; Johnson, T. J.; Wooden, W. H.; McCarthy, D. D.; Popiński, W.

    Stochastic prediction techniques including autocovariance, autoregressive, autoregressive moving average, and neural networks were applied to the UT1-UTC and Length of Day (LOD) International Earth Rotation and Reference Systems Servive (IERS) EOPC04 time series to evaluate the capabilities of each method. All known effects such as leap seconds and solid Earth zonal tides were first removed from the observed values of UT1-UTC and LOD. Two combination procedures were applied to predict the resulting LODR time series: 1) the combination of the least-squares (LS) extrapolation with a stochastic predition method, and 2) the combination of the discrete wavelet transform (DWT) filtering and a stochastic prediction method. The results of the combination of the LS extrapolation with different stochastic prediction techniques were compared with the results of the UT1-UTC prediction method currently used by the IERS Rapid Service/Prediction Centre (RS/PC). It was found that the prediction accuracy depends on the starting prediction epochs, and for the combined forecast methods, the mean prediction errors for 1 to about 70 days in the future are of the same order as those of the method used by the IERS RS/PC.

  15. Hereditary spastic paraplegia: LOD-score considerations for confirmation of linkage in a heterogeneous trait

    Energy Technology Data Exchange (ETDEWEB)

    Dube, M.P.; Kibar, Z.; Rouleau, G.A. [McGill Univ., Quebec (Canada)] [and others

    1997-03-01

    Hereditary spastic paraplegia (HSP) is a degenerative disorder of the motor system, defined by progressive weakness and spasticity of the lower limbs. HSP may be inherited as an autosomal dominant (AD), autosomal recessive, or an X-linked trait. AD HSP is genetically heterogeneous, and three loci have been identified so far: SPG3 maps to chromosome 14q, SPG4 to 2p, and SPG4a to 15q. We have undertaken linkage analysis with 21 uncomplicated AD families to the three AD HSP loci. We report significant linkage for three of our families to the SPG4 locus and exclude several families by multipoint linkage. We used linkage information from several different research teams to evaluate the statistical probability of linkage to the SPG4 locus for uncomplicated AD HSP families and established the critical LOD-score value necessary for confirmation of linkage to the SPG4 locus from Bayesian statistics. In addition, we calculated the empirical P-values for the LOD scores obtained with all families with computer simulation methods. Power to detect significant linkage, as well as type I error probabilities, were evaluated. This combined analytical approach permitted conclusive linkage analyses on small to medium-size families, under the restrictions of genetic heterogeneity. 19 refs., 1 fig., 1 tab.

  16. Highly sensitive lactate biosensor by engineering chitosan/PVI-Os/CNT/LOD network nanocomposite.

    Science.gov (United States)

    Cui, Xiaoqiang; Li, Chang Ming; Zang, Jianfeng; Yu, Shucong

    2007-06-15

    A novel chitosan/PVI-Os(polyvinylimidazole-Os)/CNT(carbon nanotube)/LOD (lactate oxidase) network nanocomposite was constructed on gold electrode for detection of lactate. The composite was nanoengineered by selected matched material components and optimized composition ratio to produce a superior lactate sensor. Positively charged chitosan and PVI-Os were used as the matrix and the mediator to immobilize the negatively charged LOD and to enhance the electron transfer, respectively. CNTs were introduced as the essential component in the composite for the network nanostructure. FESEM (field emission scan electron microscopy) and electrochemical characterization demonstrated that CNT behaved as a cross-linker to network PVI and chitosan due to its nanoscaled and negative charged nature. This significantly improved the conductivity, stability and electroactivity for detection of lactate. The standard deviation of the sensor without CNT in the composite was greatly reduced from 19.6 to 4.9% by addition of CNTs. With optimized conditions the sensitivity and detection limit of the lactate sensor was 19.7 microA mM(-1)cm(-2) and 5 microM, respectively. The sensitivity was remarkably improved in comparison to the newly reported values of 0.15-3.85 microA mM(-1)cm(-2). This novel nanoengineering approach for selecting matched components to form a network nanostructure could be extended to other enzyme biosensors, and to have broad potential applications in diagnostics, life science and food analysis.

  17. Hereditary spastic paraplegia: LOD-score considerations for confirmation of linkage in a heterogeneous trait.

    Science.gov (United States)

    Dubé, M P; Mlodzienski, M A; Kibar, Z; Farlow, M R; Ebers, G; Harper, P; Kolodny, E H; Rouleau, G A; Figlewicz, D A

    1997-03-01

    Hereditary spastic paraplegia (HSP) is a degenerative disorder of the motor system, defined by progressive weakness and spasticity of the lower limbs. HSP may be inherited as an autosomal dominant (AD), autosomal recessive, or an X-linked trait. AD HSP is genetically heterogeneous, and three loci have been identified so far: SPG3 maps to chromosome 14q, SPG4 to 2p, and SPG4a to 15q. We have undertaken linkage analysis with 21 uncomplicated AD families to the three AD HSP loci. We report significant linkage for three of our families to the SPG4 locus and exclude several families by multipoint linkage. We used linkage information from several different research teams to evaluate the statistical probability of linkage to the SPG4 locus for uncomplicated AD HSP families and established the critical LOD-score value necessary for confirmation of linkage to the SPG4 locus from Bayesian statistics. In addition, we calculated the empirical P-values for the LOD scores obtained with all families with computer simulation methods. Power to detect significant linkage, as well as type I error probabilities, were evaluated. This combined analytical approach permitted conclusive linkage analyses on small to medium-size families, under the restrictions of genetic heterogeneity.

  18. CA-LOD: Collision Avoidance Level of Detail for Scalable, Controllable Crowds

    Science.gov (United States)

    Paris, Sébastien; Gerdelan, Anton; O'Sullivan, Carol

    The new wave of computer-driven entertainment technology throws audiences and game players into massive virtual worlds where entire cities are rendered in real time. Computer animated characters run through inner-city streets teeming with pedestrians, all fully rendered with 3D graphics, animations, particle effects and linked to 3D sound effects to produce more realistic and immersive computer-hosted entertainment experiences than ever before. Computing all of this detail at once is enormously computationally expensive, and game designers as a rule, have sacrificed the behavioural realism in favour of better graphics. In this paper we propose a new Collision Avoidance Level of Detail (CA-LOD) algorithm that allows games to support huge crowds in real time with the appearance of more intelligent behaviour. We propose two collision avoidance models used for two different CA-LODs: a fuzzy steering focusing on the performances, and a geometric steering to obtain the best realism. Mixing these approaches allows to obtain thousands of autonomous characters in real time, resulting in a scalable but still controllable crowd.

  19. Replication of linkage to quantitative trait loci: variation in location and magnitude of the lod score.

    Science.gov (United States)

    Hsueh, W C; Göring, H H; Blangero, J; Mitchell, B D

    2001-01-01

    Replication of linkage signals from independent samples is considered an important step toward verifying the significance of linkage signals in studies of complex traits. The purpose of this empirical investigation was to examine the variability in the precision of localizing a quantitative trait locus (QTL) by analyzing multiple replicates of a simulated data set with the use of variance components-based methods. Specifically, we evaluated across replicates the variation in both the magnitude and the location of the peak lod scores. We analyzed QTLs whose effects accounted for 10-37% of the phenotypic variance in the quantitative traits. Our analyses revealed that the precision of QTL localization was directly related to the magnitude of the QTL effect. For a QTL with effect accounting for > 20% of total phenotypic variation, > 90% of the linkage peaks fall within 10 cM from the true gene location. We found no evidence that, for a given magnitude of the lod score, the presence of interaction influenced the precision of QTL localization.

  20. LOD score exclusion analyses for candidate genes using random population samples.

    Science.gov (United States)

    Deng, H W; Li, J; Recker, R R

    2001-05-01

    While extensive analyses have been conducted to test for, no formal analyses have been conducted to test against, the importance of candidate genes with random population samples. We develop a LOD score approach for exclusion analyses of candidate genes with random population samples. Under this approach, specific genetic effects and inheritance models at candidate genes can be analysed and if a LOD score is < or = - 2.0, the locus can be excluded from having an effect larger than that specified. Computer simulations show that, with sample sizes often employed in association studies, this approach has high power to exclude a gene from having moderate genetic effects. In contrast to regular association analyses, population admixture will not affect the robustness of our analyses; in fact, it renders our analyses more conservative and thus any significant exclusion result is robust. Our exclusion analysis complements association analysis for candidate genes in random population samples and is parallel to the exclusion mapping analyses that may be conducted in linkage analyses with pedigrees or relative pairs. The usefulness of the approach is demonstrated by an application to test the importance of vitamin D receptor and estrogen receptor genes underlying the differential risk to osteoporotic fractures.

  1. A maximum likelihood framework for protein design

    Directory of Open Access Journals (Sweden)

    Philippe Hervé

    2006-06-01

    Full Text Available Abstract Background The aim of protein design is to predict amino-acid sequences compatible with a given target structure. Traditionally envisioned as a purely thermodynamic question, this problem can also be understood in a wider context, where additional constraints are captured by learning the sequence patterns displayed by natural proteins of known conformation. In this latter perspective, however, we still need a theoretical formalization of the question, leading to general and efficient learning methods, and allowing for the selection of fast and accurate objective functions quantifying sequence/structure compatibility. Results We propose a formulation of the protein design problem in terms of model-based statistical inference. Our framework uses the maximum likelihood principle to optimize the unknown parameters of a statistical potential, which we call an inverse potential to contrast with classical potentials used for structure prediction. We propose an implementation based on Markov chain Monte Carlo, in which the likelihood is maximized by gradient descent and is numerically estimated by thermodynamic integration. The fit of the models is evaluated by cross-validation. We apply this to a simple pairwise contact potential, supplemented with a solvent-accessibility term, and show that the resulting models have a better predictive power than currently available pairwise potentials. Furthermore, the model comparison method presented here allows one to measure the relative contribution of each component of the potential, and to choose the optimal number of accessibility classes, which turns out to be much higher than classically considered. Conclusion Altogether, this reformulation makes it possible to test a wide diversity of models, using different forms of potentials, or accounting for other factors than just the constraint of thermodynamic stability. Ultimately, such model-based statistical analyses may help to understand the forces

  2. Maximum Acceleration Recording Circuit

    Science.gov (United States)

    Bozeman, Richard J., Jr.

    1995-01-01

    Coarsely digitized maximum levels recorded in blown fuses. Circuit feeds power to accelerometer and makes nonvolatile record of maximum level to which output of accelerometer rises during measurement interval. In comparison with inertia-type single-preset-trip-point mechanical maximum-acceleration-recording devices, circuit weighs less, occupies less space, and records accelerations within narrower bands of uncertainty. In comparison with prior electronic data-acquisition systems designed for same purpose, circuit simpler, less bulky, consumes less power, costs and analysis of data recorded in magnetic or electronic memory devices. Circuit used, for example, to record accelerations to which commodities subjected during transportation on trucks.

  3. Automated Reconstruction of Building LoDs from Airborne LiDAR Point Clouds Using an Improved Morphological Scale Space

    Directory of Open Access Journals (Sweden)

    Bisheng Yang

    2016-12-01

    Full Text Available Reconstructing building models at different levels of detail (LoDs from airborne laser scanning point clouds is urgently needed for wide application as this method can balance between the user’s requirements and economic costs. The previous methods reconstruct building LoDs from the finest 3D building models rather than from point clouds, resulting in heavy costs and inflexible adaptivity. The scale space is a sound theory for multi-scale representation of an object from a coarser level to a finer level. Therefore, this paper proposes a novel method to reconstruct buildings at different LoDs from airborne Light Detection and Ranging (LiDAR point clouds based on an improved morphological scale space. The proposed method first extracts building candidate regions following the separation of ground and non-ground points. For each building candidate region, the proposed method generates a scale space by iteratively using the improved morphological reconstruction with the increase of scale, and constructs the corresponding topological relationship graphs (TRGs across scales. Secondly, the proposed method robustly extracts building points by using features based on the TRG. Finally, the proposed method reconstructs each building at different LoDs according to the TRG. The experiments demonstrate that the proposed method robustly extracts the buildings with details (e.g., door eaves and roof furniture and illustrate good performance in distinguishing buildings from vegetation or other objects, while automatically reconstructing building LoDs from the finest building points.

  4. Classification between normal and tumor tissues based on the pair-wise gene expression ratio

    International Nuclear Information System (INIS)

    Yap, YeeLeng; Zhang, XueWu; Ling, MT; Wang, XiangHong; Wong, YC; Danchin, Antoine

    2004-01-01

    Precise classification of cancer types is critically important for early cancer diagnosis and treatment. Numerous efforts have been made to use gene expression profiles to improve precision of tumor classification. However, reliable cancer-related signals are generally lacking. Using recent datasets on colon and prostate cancer, a data transformation procedure from single gene expression to pair-wise gene expression ratio is proposed. Making use of the internal consistency of each expression profiling dataset this transformation improves the signal to noise ratio of the dataset and uncovers new relevant cancer-related signals (features). The efficiency in using the transformed dataset to perform normal/tumor classification was investigated using feature partitioning with informative features (gene annotation) as discriminating axes (single gene expression or pair-wise gene expression ratio). Classification results were compared to the original datasets for up to 10-feature model classifiers. 82 and 262 genes that have high correlation to tissue phenotype were selected from the colon and prostate datasets respectively. Remarkably, data transformation of the highly noisy expression data successfully led to lower the coefficient of variation (CV) for the within-class samples as well as improved the correlation with tissue phenotypes. The transformed dataset exhibited lower CV when compared to that of single gene expression. In the colon cancer set, the minimum CV decreased from 45.3% to 16.5%. In prostate cancer, comparable CV was achieved with and without transformation. This improvement in CV, coupled with the improved correlation between the pair-wise gene expression ratio and tissue phenotypes, yielded higher classification efficiency, especially with the colon dataset – from 87.1% to 93.5%. Over 90% of the top ten discriminating axes in both datasets showed significant improvement after data transformation. The high classification efficiency achieved suggested

  5. Maximum Quantum Entropy Method

    OpenAIRE

    Sim, Jae-Hoon; Han, Myung Joon

    2018-01-01

    Maximum entropy method for analytic continuation is extended by introducing quantum relative entropy. This new method is formulated in terms of matrix-valued functions and therefore invariant under arbitrary unitary transformation of input matrix. As a result, the continuation of off-diagonal elements becomes straightforward. Without introducing any further ambiguity, the Bayesian probabilistic interpretation is maintained just as in the conventional maximum entropy method. The applications o...

  6. Maximum power demand cost

    International Nuclear Information System (INIS)

    Biondi, L.

    1998-01-01

    The charging for a service is a supplier's remuneration for the expenses incurred in providing it. There are currently two charges for electricity: consumption and maximum demand. While no problem arises about the former, the issue is more complicated for the latter and the analysis in this article tends to show that the annual charge for maximum demand arbitrarily discriminates among consumer groups, to the disadvantage of some [it

  7. Another procedure for the preliminary ordering of loci based on two point lod scores.

    Science.gov (United States)

    Curtis, D

    1994-01-01

    Because of the difficulty of performing full likelihood analysis over multiple loci and the large numbers of possible orders, a number of methods have been proposed for quickly evaluating orders and, to a lesser extent, for generating good orders. A new method is proposed which uses a function which is moderately laborious to compute, the sum of lod scores between all pairs of loci. This function can be smoothly minimized by initially allowing the loci to be placed anywhere in space, and only subsequently constraining them to lie along a one-dimensional map. Application of this approach to sample data suggests that it has promise and might usefully be combined with other methods when loci need to be ordered.

  8. Singularity Processing Method of Microstrip Line Edge Based on LOD-FDTD

    Directory of Open Access Journals (Sweden)

    Lei Li

    2014-01-01

    Full Text Available In order to improve the performance of the accuracy and efficiency for analyzing the microstrip structure, a singularity processing method is proposed theoretically and experimentally based on the fundamental locally one-dimensional finite difference time domain (LOD-FDTD with second-order temporal accuracy (denoted as FLOD2-FDTD. The proposed method can highly improve the performance of the FLOD2-FDTD even when the conductor is embedded into more than half of the cell by the coordinate transformation. The experimental results showed that the proposed method can achieve higher accuracy when the time step size is less than or equal to 5 times of that the Courant-Friedrich-Levy (CFL condition allowed. In comparison with the previously reported methods, the proposed method for calculating electromagnetic field near microstrip line edge not only improves the efficiency, but also can provide a higher accuracy.

  9. D-dimer as marker for microcirculatory failure: correlation with LOD and APACHE II scores.

    Science.gov (United States)

    Angstwurm, Matthias W A; Reininger, Armin J; Spannagl, Michael

    2004-01-01

    The relevance of plasma d-dimer levels as marker for morbidity and organ dysfunction in severely ill patients is largely unknown. In a prospective study we determined d-dimer plasma levels of 800 unselected patients at admission to our intensive care unit. In 91% of the patients' samples d-dimer levels were elevated, in some patients up to several hundredfold as compared to normal values. The highest mean d-dimer values were present in the patient group with thromboembolic diseases, and particularly in non-survivors of pulmonary embolism. In patients with circulatory impairment (r=0.794) and in patients with infections (r=0.487) a statistically significant correlation was present between d-dimer levels and the APACHE II score (P<0.001). The logistic organ dysfunction score (LOD, P<0.001) correlated with d-dimer levels only in patients with circulatory impairment (r=0.474). On the contrary, patients without circulatory impairment demonstrated no correlation of d-dimer levels to the APACHE II or LOD score. Taking all patients together, no correlations of d-dimer levels with single organ failure or with indicators of infection could be detected. In conclusion, d-dimer plasma levels strongly correlated with the severity of the disease and organ dysfunction in patients with circulatory impairment or infections suggesting that elevated d-dimer levels may reflect the extent of microcirculatory failure. Thus, a therapeutic strategy to improve the microcirculation in such patients may be monitored using d-dimer plasma levels.

  10. Validation of the LOD score compared with APACHE II score in prediction of the hospital outcome in critically ill patients.

    Science.gov (United States)

    Khwannimit, Bodin

    2008-01-01

    The Logistic Organ Dysfunction score (LOD) is an organ dysfunction score that can predict hospital mortality. The aim of this study was to validate the performance of the LOD score compared with the Acute Physiology and Chronic Health Evaluation II (APACHE II) score in a mixed intensive care unit (ICU) at a tertiary referral university hospital in Thailand. The data were collected prospectively on consecutive ICU admissions over a 24 month period from July1, 2004 until June 30, 2006. Discrimination was evaluated by the area under the receiver operating characteristic curve (AUROC). The calibration was assessed by the Hosmer-Lemeshow goodness-of-fit H statistic. The overall fit of the model was evaluated by the Brier's score. Overall, 1,429 patients were enrolled during the study period. The mortality in the ICU was 20.9% and in the hospital was 27.9%. The median ICU and hospital lengths of stay were 3 and 18 days, respectively, for all patients. Both models showed excellent discrimination. The AUROC for the LOD and APACHE II were 0.860 [95% confidence interval (CI) = 0.838-0.882] and 0.898 (95% Cl = 0.879-0.917), respectively. The LOD score had perfect calibration with the Hosmer-Lemeshow goodness-of-fit H chi-2 = 10 (p = 0.44). However, the APACHE II had poor calibration with the Hosmer-Lemeshow goodness-of-fit H chi-2 = 75.69 (p < 0.001). Brier's score showed the overall fit for both models were 0.123 (95%Cl = 0.107-0.141) and 0.114 (0.098-0.132) for the LOD and APACHE II, respectively. Thus, the LOD score was found to be accurate for predicting hospital mortality for general critically ill patients in Thailand.

  11. GENERATION OF MULTI-LOD 3D CITY MODELS IN CITYGML WITH THE PROCEDURAL MODELLING ENGINE RANDOM3DCITY

    Directory of Open Access Journals (Sweden)

    F. Biljecki

    2016-09-01

    Full Text Available The production and dissemination of semantic 3D city models is rapidly increasing benefiting a growing number of use cases. However, their availability in multiple LODs and in the CityGML format is still problematic in practice. This hinders applications and experiments where multi-LOD datasets are required as input, for instance, to determine the performance of different LODs in a spatial analysis. An alternative approach to obtain 3D city models is to generate them with procedural modelling, which is – as we discuss in this paper – well suited as a method to source multi-LOD datasets useful for a number of applications. However, procedural modelling has not yet been employed for this purpose. Therefore, we have developed RANDOM3DCITY, an experimental procedural modelling engine for generating synthetic datasets of buildings and other urban features. The engine is designed to produce models in CityGML and does so in multiple LODs. Besides the generation of multiple geometric LODs, we implement the realisation of multiple levels of spatiosemantic coherence, geometric reference variants, and indoor representations. As a result of their permutations, each building can be generated in 392 different CityGML representations, an unprecedented number of modelling variants of the same feature. The datasets produced by RANDOM3DCITY are suited for several applications, as we show in this paper with documented uses. The developed engine is available under an open-source licence at Github at http://github.com/tudelft3d/Random3Dcity.

  12. Scalable Bayesian nonparametric measures for exploring pairwise dependence via Dirichlet Process Mixtures.

    Science.gov (United States)

    Filippi, Sarah; Holmes, Chris C; Nieto-Barajas, Luis E

    2016-11-16

    In this article we propose novel Bayesian nonparametric methods using Dirichlet Process Mixture (DPM) models for detecting pairwise dependence between random variables while accounting for uncertainty in the form of the underlying distributions. A key criteria is that the procedures should scale to large data sets. In this regard we find that the formal calculation of the Bayes factor for a dependent-vs.-independent DPM joint probability measure is not feasible computationally. To address this we present Bayesian diagnostic measures for characterising evidence against a "null model" of pairwise independence. In simulation studies, as well as for a real data analysis, we show that our approach provides a useful tool for the exploratory nonparametric Bayesian analysis of large multivariate data sets.

  13. Pairwise correlations via quantum discord and its geometric measure in a four-qubit spin chain

    Directory of Open Access Journals (Sweden)

    Abdel-Baset A. Mohamed

    2013-04-01

    Full Text Available The dynamic of pairwise correlations, including quantum entanglement (QE and discord (QD with geometric measure of quantum discord (GMQD, are shown in the four-qubit Heisenberg XX spin chain. The results show that the effect of the entanglement degree of the initial state on the pairwise correlations is stronger for alternate qubits than it is for nearest-neighbor qubits. This parameter results in sudden death for QE, but it cannot do so for QD and GMQD. With different values for this entanglement parameter of the initial state, QD and GMQD differ and are sensitive for any change in this parameter. It is found that GMQD is more robust than both QD and QE to describe correlations with nonzero values, which offers a valuable resource for quantum computation.

  14. A Relative-Localization Algorithm Using Incomplete Pairwise Distance Measurements for Underwater Applications

    Directory of Open Access Journals (Sweden)

    Kae Y. Foo

    2010-01-01

    Full Text Available The task of localizing underwater assets involves the relative localization of each unit using only pairwise distance measurements, usually obtained from time-of-arrival or time-delay-of-arrival measurements. In the fluctuating underwater environment, a complete set of pair-wise distance measurements can often be difficult to acquire, thus hindering a straightforward closed-form solution in deriving the assets' relative coordinates. An iterative multidimensional scaling approach is presented based upon a weighted-majorization algorithm that tolerates missing or inaccurate distance measurements. Substantial modifications are proposed to optimize the algorithm, while the effects of refractive propagation paths are considered. A parametric study of the algorithm based upon simulation results is shown. An acoustic field-trial was then carried out, presenting field measurements to highlight the practical implementation of this algorithm.

  15. A pragmatic pairwise group-decision method for selection of sites for nuclear power plants

    International Nuclear Information System (INIS)

    Kutbi, I.I.

    1987-01-01

    A pragmatic pairwise group-decision approach is applied to compare two regions in order to select the more suitable one for construction of nulcear power plants in the Kingdom of Saudi Arabia. The selection methodology is based on pairwise comparison by forced choice. The method facilitates rating of the regions or sites using simple calculations. Two regions, one close to Dhahran on the Arabian Gulf and another close to Jeddah on the Red Sea, are evaluated. No specific site in either region is considered at this stage. The comparison is based on a set of selection criteria which include (i) topography, (ii) geology, (iii) seismology, (iv) meteorology, (v) oceanography, (vi) hydrology and (vii) proximetry to oil and gas fields. The comparison shows that the Jeddah region is more suitable than the Dhahran region. (orig.)

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

    International Nuclear Information System (INIS)

    Daoud, M.; Ahl Laamara, R.

    2012-01-01

    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. -- Highlights: ► Pairwise quantum correlations multipartite coherent states. ► Explicit expression of geometric quantum discord. ► Entanglement sudden death and quantum discord robustness. ► Generalized coherent states interpolating between Werner and Greenberger–Horne–Zeilinger states

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

    Energy Technology Data Exchange (ETDEWEB)

    Daoud, M., E-mail: m_daoud@hotmail.com [Department of Physics, Faculty of Sciences, University Ibnou Zohr, Agadir (Morocco); Ahl Laamara, R., E-mail: ahllaamara@gmail.com [LPHE-Modeling and Simulation, Faculty of Sciences, University Mohammed V, Rabat (Morocco); Centre of Physics and Mathematics, CPM, CNESTEN, Rabat (Morocco)

    2012-07-16

    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. -- Highlights: ► Pairwise quantum correlations multipartite coherent states. ► Explicit expression of geometric quantum discord. ► Entanglement sudden death and quantum discord robustness. ► Generalized coherent states interpolating between Werner and Greenberger–Horne–Zeilinger states.

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

    Science.gov (United States)

    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. Criteria for the singularity of a pairwise l1-distance matrix and their generalizations

    International Nuclear Information System (INIS)

    D'yakonov, Alexander G

    2012-01-01

    We study the singularity problem for the pairwise distance matrix of a system of points, as well as generalizations of this problem that are connected with applications to interpolation theory and with an algebraic approach to recognition problems. We obtain necessary and sufficient conditions on a system under which the dimension of the range space of polynomials of bounded degree over the columns of the distance matrix is less than the number of points in the system.

  20. Criteria for the singularity of a pairwise l{sub 1}-distance matrix and their generalizations

    Energy Technology Data Exchange (ETDEWEB)

    D' yakonov, Alexander G [M. V. Lomonosov Moscow State University, Faculty of Computational Mathematics and Cybernetics, Moscow (Russian Federation)

    2012-06-30

    We study the singularity problem for the pairwise distance matrix of a system of points, as well as generalizations of this problem that are connected with applications to interpolation theory and with an algebraic approach to recognition problems. We obtain necessary and sufficient conditions on a system under which the dimension of the range space of polynomials of bounded degree over the columns of the distance matrix is less than the number of points in the system.

  1. Improving prediction of heterodimeric protein complexes using combination with pairwise kernel.

    Science.gov (United States)

    Ruan, Peiying; Hayashida, Morihiro; Akutsu, Tatsuya; Vert, Jean-Philippe

    2018-02-19

    Since many proteins become functional only after they interact with their partner proteins and form protein complexes, it is essential to identify the sets of proteins that form complexes. Therefore, several computational methods have been proposed to predict complexes from the topology and structure of experimental protein-protein interaction (PPI) network. These methods work well to predict complexes involving at least three proteins, but generally fail at identifying complexes involving only two different proteins, called heterodimeric complexes or heterodimers. There is however an urgent need for efficient methods to predict heterodimers, since the majority of known protein complexes are precisely heterodimers. In this paper, we use three promising kernel functions, Min kernel and two pairwise kernels, which are Metric Learning Pairwise Kernel (MLPK) and Tensor Product Pairwise Kernel (TPPK). We also consider the normalization forms of Min kernel. Then, we combine Min kernel or its normalization form and one of the pairwise kernels by plugging. We applied kernels based on PPI, domain, phylogenetic profile, and subcellular localization properties to predicting heterodimers. Then, we evaluate our method by employing C-Support Vector Classification (C-SVC), carrying out 10-fold cross-validation, and calculating the average F-measures. The results suggest that the combination of normalized-Min-kernel and MLPK leads to the best F-measure and improved the performance of our previous work, which had been the best existing method so far. We propose new methods to predict heterodimers, using a machine learning-based approach. We train a support vector machine (SVM) to discriminate interacting vs non-interacting protein pairs, based on informations extracted from PPI, domain, phylogenetic profiles and subcellular localization. We evaluate in detail new kernel functions to encode these data, and report prediction performance that outperforms the state-of-the-art.

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

    OpenAIRE

    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 i...

  3. Linkage analysis in nuclear families. 2: Relationship between affected sib-pair tests and lod score analysis.

    Science.gov (United States)

    Knapp, M; Seuchter, S A; Baur, M P

    1994-01-01

    It is believed that the main advantage of affected sib-pair tests is that their application requires no information about the underlying genetic mechanism of the disease. However, here it is proved that the mean test, which can be considered the most prominent of the affected sib-pair tests, is equivalent to lod score analysis for an assumed recessive mode of inheritance, irrespective of the true mode of the disease. Further relationships of certain sib-pair tests and lod score analysis under specific assumed genetic modes are investigated.

  4. Simultaneous-Fault Diagnosis of Gas Turbine Generator Systems Using a Pairwise-Coupled Probabilistic Classifier

    Directory of Open Access Journals (Sweden)

    Zhixin Yang

    2013-01-01

    Full Text Available A reliable fault diagnostic system for gas turbine generator system (GTGS, which is complicated and inherent with many types of component faults, is essential to avoid the interruption of electricity supply. However, the GTGS diagnosis faces challenges in terms of the existence of simultaneous-fault diagnosis and high cost in acquiring the exponentially increased simultaneous-fault vibration signals for constructing the diagnostic system. This research proposes a new diagnostic framework combining feature extraction, pairwise-coupled probabilistic classifier, and decision threshold optimization. The feature extraction module adopts wavelet packet transform and time-domain statistical features to extract vibration signal features. Kernel principal component analysis is then applied to further reduce the redundant features. The features of single faults in a simultaneous-fault pattern are extracted and then detected using a probabilistic classifier, namely, pairwise-coupled relevance vector machine, which is trained with single-fault patterns only. Therefore, the training dataset of simultaneous-fault patterns is unnecessary. To optimize the decision threshold, this research proposes to use grid search method which can ensure a global solution as compared with traditional computational intelligence techniques. Experimental results show that the proposed framework performs well for both single-fault and simultaneous-fault diagnosis and is superior to the frameworks without feature extraction and pairwise coupling.

  5. SFESA: a web server for pairwise alignment refinement by secondary structure shifts.

    Science.gov (United States)

    Tong, Jing; Pei, Jimin; Grishin, Nick V

    2015-09-03

    Protein sequence alignment is essential for a variety of tasks such as homology modeling and active site prediction. Alignment errors remain the main cause of low-quality structure models. A bioinformatics tool to refine alignments is needed to make protein alignments more accurate. We developed the SFESA web server to refine pairwise protein sequence alignments. Compared to the previous version of SFESA, which required a set of 3D coordinates for a protein, the new server will search a sequence database for the closest homolog with an available 3D structure to be used as a template. For each alignment block defined by secondary structure elements in the template, SFESA evaluates alignment variants generated by local shifts and selects the best-scoring alignment variant. A scoring function that combines the sequence score of profile-profile comparison and the structure score of template-derived contact energy is used for evaluation of alignments. PROMALS pairwise alignments refined by SFESA are more accurate than those produced by current advanced alignment methods such as HHpred and CNFpred. In addition, SFESA also improves alignments generated by other software. SFESA is a web-based tool for alignment refinement, designed for researchers to compute, refine, and evaluate pairwise alignments with a combined sequence and structure scoring of alignment blocks. To our knowledge, the SFESA web server is the only tool that refines alignments by evaluating local shifts of secondary structure elements. The SFESA web server is available at http://prodata.swmed.edu/sfesa.

  6. Maximum likely scale estimation

    DEFF Research Database (Denmark)

    Loog, Marco; Pedersen, Kim Steenstrup; Markussen, Bo

    2005-01-01

    A maximum likelihood local scale estimation principle is presented. An actual implementation of the estimation principle uses second order moments of multiple measurements at a fixed location in the image. These measurements consist of Gaussian derivatives possibly taken at several scales and/or ...

  7. Robust Maximum Association Estimators

    NARCIS (Netherlands)

    A. Alfons (Andreas); C. Croux (Christophe); P. Filzmoser (Peter)

    2017-01-01

    textabstractThe maximum association between two multivariate variables X and Y is defined as the maximal value that a bivariate association measure between one-dimensional projections αX and αY can attain. Taking the Pearson correlation as projection index results in the first canonical correlation

  8. LOD-climate Links: how the 2015-2016 El Niño Lengthened the Day by 0.8 ms, and Possible Rotational Forcing of Multidecadal Temperature Changes

    Science.gov (United States)

    Lambert, S. B.; de Viron, O.; Marcus, S.

    2016-12-01

    El Niño events are generally accompanied by significant changes in the Earth's length-of-day (LOD) that can be explained by two approaches. Considering the angular momentum conservation of the system composed by the solid Earth and the atmosphere, ENSO events are accompanied by a strengthening of the subtropical jet streams, and, therefore, a decrease of the Earth's rotation rate. Using the torque approach, the low pressure field of the Eastern Pacific, which is close to high mountain ranges along the Western American coasts, creates a negative torque of the atmosphere on the solid Earth which tends to slow down the Earth's rotation. The large 1983 event was associated with a lengthening of the day of about 1 ms. During the 2015-2016 winter season, a major ENSO event occurred, classified as very strong by meteorological agencies. This central Pacific event, for which the Nino 3.4 index is as high as in 1983, was also concurrent with positive phases of PDO, NAO, and AAO. It coincided with an excursion of the LOD as large as 0.8 ms over a few weeks reaching its maximum around 2016 New Year. We evaluate the mountain and friction torques responsible for the Earth's rotation variations during the winter season and compare to the mean situations and to previous strong ENSO events of 1983 and 1998. Especially, we noticed that the contribution from American mountain ranges is close to the value of 1983. The weaker LOD excursion comes from an inexistent torque over the Himalayas, a weaker contribution from Europe, and a noticeable positive contribution from Antarctica. On longer time scales, core-generated ms-scale LOD excursions are found to precede NH surface and global SST fluctuations by nearly a decade; although the cause of this apparent rotational effect is not known, reported correlations of LOD and tidal-orbital forcing with surface and submarine volcanic activity offer prospects to explain these observations in a core-to-climate chain of causality.

  9. Maximum power point tracking

    International Nuclear Information System (INIS)

    Enslin, J.H.R.

    1990-01-01

    A well engineered renewable remote energy system, utilizing the principal of Maximum Power Point Tracking can be m ore cost effective, has a higher reliability and can improve the quality of life in remote areas. This paper reports that a high-efficient power electronic converter, for converting the output voltage of a solar panel, or wind generator, to the required DC battery bus voltage has been realized. The converter is controlled to track the maximum power point of the input source under varying input and output parameters. Maximum power point tracking for relative small systems is achieved by maximization of the output current in a battery charging regulator, using an optimized hill-climbing, inexpensive microprocessor based algorithm. Through practical field measurements it is shown that a minimum input source saving of 15% on 3-5 kWh/day systems can easily be achieved. A total cost saving of at least 10-15% on the capital cost of these systems are achievable for relative small rating Remote Area Power Supply systems. The advantages at larger temperature variations and larger power rated systems are much higher. Other advantages include optimal sizing and system monitor and control

  10. Prediction of UT1-UTC, LOD and AAM χ3 by combination of least-squares and multivariate stochastic methods

    Science.gov (United States)

    Niedzielski, Tomasz; Kosek, Wiesław

    2008-02-01

    This article presents the application of a multivariate prediction technique for predicting universal time (UT1-UTC), length of day (LOD) and the axial component of atmospheric angular momentum (AAM χ 3). The multivariate predictions of LOD and UT1-UTC are generated by means of the combination of (1) least-squares (LS) extrapolation of models for annual, semiannual, 18.6-year, 9.3-year oscillations and for the linear trend, and (2) multivariate autoregressive (MAR) stochastic prediction of LS residuals (LS + MAR). The MAR technique enables the use of the AAM χ 3 time-series as the explanatory variable for the computation of LOD or UT1-UTC predictions. In order to evaluate the performance of this approach, two other prediction schemes are also applied: (1) LS extrapolation, (2) combination of LS extrapolation and univariate autoregressive (AR) prediction of LS residuals (LS + AR). The multivariate predictions of AAM χ 3 data, however, are computed as a combination of the extrapolation of the LS model for annual and semiannual oscillations and the LS + MAR. The AAM χ 3 predictions are also compared with LS extrapolation and LS + AR prediction. It is shown that the predictions of LOD and UT1-UTC based on LS + MAR taking into account the axial component of AAM are more accurate than the predictions of LOD and UT1-UTC based on LS extrapolation or on LS + AR. In particular, the UT1-UTC predictions based on LS + MAR during El Niño/La Niña events exhibit considerably smaller prediction errors than those calculated by means of LS or LS + AR. The AAM χ 3 time-series is predicted using LS + MAR with higher accuracy than applying LS extrapolation itself in the case of medium-term predictions (up to 100 days in the future). However, the predictions of AAM χ 3 reveal the best accuracy for LS + AR.

  11. Visualizing whole-brain DTI tractography with GPU-based Tuboids and LoD management.

    Science.gov (United States)

    Petrovic, Vid; Fallon, James; Kuester, Falko

    2007-01-01

    Diffusion Tensor Imaging (DTI) of the human brain, coupled with tractography techniques, enable the extraction of large-collections of three-dimensional tract pathways per subject. These pathways and pathway bundles represent the connectivity between different brain regions and are critical for the understanding of brain related diseases. A flexible and efficient GPU-based rendering technique for DTI tractography data is presented that addresses common performance bottlenecks and image-quality issues, allowing interactive render rates to be achieved on commodity hardware. An occlusion query-based pathway LoD management system for streamlines/streamtubes/tuboids is introduced that optimizes input geometry, vertex processing, and fragment processing loads, and helps reduce overdraw. The tuboid, a fully-shaded streamtube impostor constructed entirely on the GPU from streamline vertices, is also introduced. Unlike full streamtubes and other impostor constructs, tuboids require little to no preprocessing or extra space over the original streamline data. The supported fragment processing levels of detail range from texture-based draft shading to full raycast normal computation, Phong shading, environment mapping, and curvature-correct text labeling. The presented text labeling technique for tuboids provides adaptive, aesthetically pleasing labels that appear attached to the surface of the tubes. Furthermore, an occlusion query aggregating and scheduling scheme for tuboids is described that reduces the query overhead. Results for a tractography dataset are presented, and demonstrate that LoD-managed tuboids offer benefits over traditional streamtubes both in performance and appearance.

  12. The pairwise disconnectivity index as a new metric for the topological analysis of regulatory networks

    Directory of Open Access Journals (Sweden)

    Wingender Edgar

    2008-05-01

    Full Text Available Abstract Background Currently, there is a gap between purely theoretical studies of the topology of large bioregulatory networks and the practical traditions and interests of experimentalists. While the theoretical approaches emphasize the global characterization of regulatory systems, the practical approaches focus on the role of distinct molecules and genes in regulation. To bridge the gap between these opposite approaches, one needs to combine 'general' with 'particular' properties and translate abstract topological features of large systems into testable functional characteristics of individual components. Here, we propose a new topological parameter – the pairwise disconnectivity index of a network's element – that is capable of such bridging. Results The pairwise disconnectivity index quantifies how crucial an individual element is for sustaining the communication ability between connected pairs of vertices in a network that is displayed as a directed graph. Such an element might be a vertex (i.e., molecules, genes, an edge (i.e., reactions, interactions, as well as a group of vertices and/or edges. The index can be viewed as a measure of topological redundancy of regulatory paths which connect different parts of a given network and as a measure of sensitivity (robustness of this network to the presence (absence of each individual element. Accordingly, we introduce the notion of a path-degree of a vertex in terms of its corresponding incoming, outgoing and mediated paths, respectively. The pairwise disconnectivity index has been applied to the analysis of several regulatory networks from various organisms. The importance of an individual vertex or edge for the coherence of the network is determined by the particular position of the given element in the whole network. Conclusion Our approach enables to evaluate the effect of removing each element (i.e., vertex, edge, or their combinations from a network. The greatest potential value of

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

    Science.gov (United States)

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

    2017-01-01

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

  14. Effect of pairwise additivity on finite-temperature behavior of classical ideal gas

    Science.gov (United States)

    Shekaari, Ashkan; Jafari, Mahmoud

    2018-05-01

    Finite-temperature molecular dynamics simulations have been applied to inquire into the effect of pairwise additivity on the behavior of classical ideal gas within the temperature range of T = 250-4000 K via applying a variety of pair potentials and then examining the temperature dependence of a number of thermodynamical properties. Examining the compressibility factor reveals the most deviation from ideal-gas behavior for the Lennard-Jones system mainly due to the presence of both the attractive and repulsive terms. The systems with either attractive or repulsive intermolecular potentials are found to present no resemblance to real gases, but the most similarity to the ideal one as temperature rises.

  15. Structural profiles of human miRNA families from pairwise clustering

    DEFF Research Database (Denmark)

    Kaczkowski, Bogumil; Þórarinsson, Elfar; Reiche, Kristin

    2009-01-01

    secondary structure already predicted, little is known about the patterns of structural conservation among pre-miRNAs. We address this issue by clustering the human pre-miRNA sequences based on pairwise, sequence and secondary structure alignment using FOLDALIGN, followed by global multiple alignment...... of obtained clusters by WAR. As a result, the common secondary structure was successfully determined for four FOLDALIGN clusters: the RF00027 structural family of the Rfam database and three clusters with previously undescribed consensus structures. Availability: http://genome.ku.dk/resources/mirclust...

  16. The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search

    DEFF Research Database (Denmark)

    Havgaard, Jakob Hull; Lyngsø, Rune B.; Gorodkin, Jan

    2005-01-01

    FOLDALIGN is a Sankoff-based algorithm for making structural alignments of RNA sequences. Here, we present a web server for making pairwise alignments between two RNA sequences, using the recently updated version of FOLDALIGN. The server can be used to scan two sequences for a common structural RNA...... motif of limited size, or the entire sequences can be aligned locally or globally. The web server offers a graphical interface, which makes it simple to make alignments and manually browse the results. the web server can be accessed at http://foldalign.kvl.dk...

  17. Computing the Skewness of the Phylogenetic Mean Pairwise Distance in Linear Time

    DEFF Research Database (Denmark)

    Tsirogiannis, Constantinos; Sandel, Brody Steven

    2014-01-01

    The phylogenetic Mean Pairwise Distance (MPD) is one of the most popular measures for computing the phylogenetic distance between a given group of species. More specifically, for a phylogenetic tree and for a set of species R represented by a subset of the leaf nodes of , the MPD of R is equal...... to the average cost of all possible simple paths in that connect pairs of nodes in R. Among other phylogenetic measures, the MPD is used as a tool for deciding if the species of a given group R are closely related. To do this, it is important to compute not only the value of the MPD for this group but also...

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

    Science.gov (United States)

    Chartrand, Ryan; Ballard, Kathryn

    2017-01-01

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

  19. Atomic pairwise distribution function analysis of the amorphous phase prepared by different manufacturing routes

    DEFF Research Database (Denmark)

    Boetker, Johan P.; Koradia, Vishal; Rades, Thomas

    2012-01-01

    was subjected to quench cooling thereby creating an amorphous form of the drug from both starting materials. The milled and quench cooled samples were, together with the crystalline starting materials, analyzed with X-ray powder diffraction (XRPD), Raman spectroscopy and atomic pair-wise distribution function...... (PDF) analysis of the XRPD pattern. When compared to XRPD and Raman spectroscopy, the PDF analysis was superior in displaying the difference between the amorphous samples prepared by milling and quench cooling approaches of the two starting materials....

  20. Maximum entropy methods

    International Nuclear Information System (INIS)

    Ponman, T.J.

    1984-01-01

    For some years now two different expressions have been in use for maximum entropy image restoration and there has been some controversy over which one is appropriate for a given problem. Here two further entropies are presented and it is argued that there is no single correct algorithm. The properties of the four different methods are compared using simple 1D simulations with a view to showing how they can be used together to gain as much information as possible about the original object. (orig.)

  1. The last glacial maximum

    Science.gov (United States)

    Clark, P.U.; Dyke, A.S.; Shakun, J.D.; Carlson, A.E.; Clark, J.; Wohlfarth, B.; Mitrovica, J.X.; Hostetler, S.W.; McCabe, A.M.

    2009-01-01

    We used 5704 14C, 10Be, and 3He ages that span the interval from 10,000 to 50,000 years ago (10 to 50 ka) to constrain the timing of the Last Glacial Maximum (LGM) in terms of global ice-sheet and mountain-glacier extent. Growth of the ice sheets to their maximum positions occurred between 33.0 and 26.5 ka in response to climate forcing from decreases in northern summer insolation, tropical Pacific sea surface temperatures, and atmospheric CO2. Nearly all ice sheets were at their LGM positions from 26.5 ka to 19 to 20 ka, corresponding to minima in these forcings. The onset of Northern Hemisphere deglaciation 19 to 20 ka was induced by an increase in northern summer insolation, providing the source for an abrupt rise in sea level. The onset of deglaciation of the West Antarctic Ice Sheet occurred between 14 and 15 ka, consistent with evidence that this was the primary source for an abrupt rise in sea level ???14.5 ka.

  2. Interannual variations in length-of-day (LOD) as a tool to assess climate variability and climate change

    Science.gov (United States)

    Lehmann, E.

    2016-12-01

    On interannual time scales the atmosphere affects significantly fluctuations in the geodetic quantity of length-of-day (LOD). This effect is directly proportional to perturbations in the relative angular momentum of the atmosphere (AAM) computed from zonal winds. During El Niño events tropospheric westerlies increase due to elevated sea surface temperatures (SST) in the Pacific inducing peak anomalies in relative AAM and correspondingly, in LOD. However, El Niño events affect LOD variations differently strong and the causes of this varying effect are yet not clear. Here, we investigate the LOD-El Niño relationship in the 20th and 21st century (1982-2100) whether the quantity of LOD can be used as a geophysical tool to assess variability and change in a future climate. In our analysis we applied a windowed discrete Fourier transform on all de-seasonalized data to remove climatic signals outside of the El Niño frequency band. LOD (data: IERS) was related in space and time to relative AAM and SSTs (data: ERA-40 reanalysis, IPCC ECHAM05-OM1 20C, A1B). Results from mapped Pearson correlation coefficients and time frequency behavior analysis identified a teleconnection pattern that we term the EN≥65%-index. The EN≥65%-index prescribes a significant change in variation in length-of-day of +65% and more related to (1) SST anomalies of >2° in the Pacific Niño region (160°E-80°W, 5°S-5°N), (2) corresponding stratospheric warming anomalies of the quasi-biennial oscillation (QBO), and (3) strong westerly winds in the lower equatorial stratosphere. In our analysis we show that the coupled atmosphere-ocean conditions prescribed in the EN≥65%-index apply to the extreme El Niño events of 19982/83 and 1997/98, and to 75% of all El Niño events in the last third of the 21st century. At that period of time the EN≥65%-index describes a projected altered base state of the equatorial Pacific that shows almost continuous El Niño conditions under climate warming.

  3. Maximum Entropy Fundamentals

    Directory of Open Access Journals (Sweden)

    F. Topsøe

    2001-09-01

    Full Text Available Abstract: In its modern formulation, the Maximum Entropy Principle was promoted by E.T. Jaynes, starting in the mid-fifties. The principle dictates that one should look for a distribution, consistent with available information, which maximizes the entropy. However, this principle focuses only on distributions and it appears advantageous to bring information theoretical thinking more prominently into play by also focusing on the "observer" and on coding. This view was brought forward by the second named author in the late seventies and is the view we will follow-up on here. It leads to the consideration of a certain game, the Code Length Game and, via standard game theoretical thinking, to a principle of Game Theoretical Equilibrium. This principle is more basic than the Maximum Entropy Principle in the sense that the search for one type of optimal strategies in the Code Length Game translates directly into the search for distributions with maximum entropy. In the present paper we offer a self-contained and comprehensive treatment of fundamentals of both principles mentioned, based on a study of the Code Length Game. Though new concepts and results are presented, the reading should be instructional and accessible to a rather wide audience, at least if certain mathematical details are left aside at a rst reading. The most frequently studied instance of entropy maximization pertains to the Mean Energy Model which involves a moment constraint related to a given function, here taken to represent "energy". This type of application is very well known from the literature with hundreds of applications pertaining to several different elds and will also here serve as important illustration of the theory. But our approach reaches further, especially regarding the study of continuity properties of the entropy function, and this leads to new results which allow a discussion of models with so-called entropy loss. These results have tempted us to speculate over

  4. Exact method for the simulation of Coulombic systems by spherically truncated, pairwise r-1 summation

    International Nuclear Information System (INIS)

    Wolf, D.; Keblinski, P.; Phillpot, S.R.; Eggebrecht, J.

    1999-01-01

    Based on a recent result showing that the net Coulomb potential in condensed ionic systems is rather short ranged, an exact and physically transparent method permitting the evaluation of the Coulomb potential by direct summation over the r -1 Coulomb pair potential is presented. The key observation is that the problems encountered in determining the Coulomb energy by pairwise, spherically truncated r -1 summation are a direct consequence of the fact that the system summed over is practically never neutral. A simple method is developed that achieves charge neutralization wherever the r -1 pair potential is truncated. This enables the extraction of the Coulomb energy, forces, and stresses from a spherically truncated, usually charged environment in a manner that is independent of the grouping of the pair terms. The close connection of our approach with the Ewald method is demonstrated and exploited, providing an efficient method for the simulation of even highly disordered ionic systems by direct, pairwise r -1 summation with spherical truncation at rather short range, i.e., a method which fully exploits the short-ranged nature of the interactions in ionic systems. The method is validated by simulations of crystals, liquids, and interfacial systems, such as free surfaces and grain boundaries. copyright 1999 American Institute of Physics

  5. GapMis: a tool for pairwise sequence alignment with a single gap.

    Science.gov (United States)

    Flouri, Tomás; Frousios, Kimon; Iliopoulos, Costas S; Park, Kunsoo; Pissis, Solon P; Tischler, German

    2013-08-01

    Pairwise sequence alignment has received a new motivation due to the advent of recent patents in next-generation sequencing technologies, particularly so for the application of re-sequencing---the assembly of a genome directed by a reference sequence. After the fast alignment between a factor of the reference sequence and a high-quality fragment of a short read by a short-read alignment programme, an important problem is to find the alignment between a relatively short succeeding factor of the reference sequence and the remaining low-quality part of the read allowing a number of mismatches and the insertion of a single gap in the alignment. We present GapMis, a tool for pairwise sequence alignment with a single gap. It is based on a simple algorithm, which computes a different version of the traditional dynamic programming matrix. The presented experimental results demonstrate that GapMis is more suitable and efficient than most popular tools for this task.

  6. Pairwise registration of TLS point clouds using covariance descriptors and a non-cooperative game

    Science.gov (United States)

    Zai, Dawei; Li, Jonathan; Guo, Yulan; Cheng, Ming; Huang, Pengdi; Cao, Xiaofei; Wang, Cheng

    2017-12-01

    It is challenging to automatically register TLS point clouds with noise, outliers and varying overlap. In this paper, we propose a new method for pairwise registration of TLS point clouds. We first generate covariance matrix descriptors with an adaptive neighborhood size from point clouds to find candidate correspondences, we then construct a non-cooperative game to isolate mutual compatible correspondences, which are considered as true positives. The method was tested on three models acquired by two different TLS systems. Experimental results demonstrate that our proposed adaptive covariance (ACOV) descriptor is invariant to rigid transformation and robust to noise and varying resolutions. The average registration errors achieved on three models are 0.46 cm, 0.32 cm and 1.73 cm, respectively. The computational times cost on these models are about 288 s, 184 s and 903 s, respectively. Besides, our registration framework using ACOV descriptors and a game theoretic method is superior to the state-of-the-art methods in terms of both registration error and computational time. The experiment on a large outdoor scene further demonstrates the feasibility and effectiveness of our proposed pairwise registration framework.

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

    International Nuclear Information System (INIS)

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

    2016-01-01

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

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

    Science.gov (United States)

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

    2012-04-01

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

  9. Extraction of tacit knowledge from large ADME data sets via pairwise analysis.

    Science.gov (United States)

    Keefer, Christopher E; Chang, George; Kauffman, Gregory W

    2011-06-15

    Pharmaceutical companies routinely collect data across multiple projects for common ADME endpoints. Although at the time of collection the data is intended for use in decision making within a specific project, knowledge can be gained by data mining the entire cross-project data set for patterns of structure-activity relationships (SAR) that may be applied to any project. One such data mining method is pairwise analysis. This method has the advantage of being able to identify small structural changes that lead to significant changes in activity. In this paper, we describe the process for full pairwise analysis of our high-throughput ADME assays routinely used for compound discovery efforts at Pfizer (microsomal clearance, passive membrane permeability, P-gp efflux, and lipophilicity). We also describe multiple strategies for the application of these transforms in a prospective manner during compound design. Finally, a detailed analysis of the activity patterns in pairs of compounds that share the same molecular transformation reveals multiple types of transforms from an SAR perspective. These include bioisosteres, additives, multiplicatives, and a type we call switches as they act to either turn on or turn off an activity. Copyright © 2011 Elsevier Ltd. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    Woosang Lim

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

  11. TopFed: TCGA tailored federated query processing and linking to LOD.

    Science.gov (United States)

    Saleem, Muhammad; Padmanabhuni, Shanmukha S; Ngomo, Axel-Cyrille Ngonga; Iqbal, Aftab; Almeida, Jonas S; Decker, Stefan; Deus, Helena F

    2014-01-01

    The Cancer Genome Atlas (TCGA) is a multidisciplinary, multi-institutional effort to catalogue genetic mutations responsible for cancer using genome analysis techniques. One of the aims of this project is to create a comprehensive and open repository of cancer related molecular analysis, to be exploited by bioinformaticians towards advancing cancer knowledge. However, devising bioinformatics applications to analyse such large dataset is still challenging, as it often requires downloading large archives and parsing the relevant text files. Therefore, it is making it difficult to enable virtual data integration in order to collect the critical co-variates necessary for analysis. We address these issues by transforming the TCGA data into the Semantic Web standard Resource Description Format (RDF), link it to relevant datasets in the Linked Open Data (LOD) cloud and further propose an efficient data distribution strategy to host the resulting 20.4 billion triples data via several SPARQL endpoints. Having the TCGA data distributed across multiple SPARQL endpoints, we enable biomedical scientists to query and retrieve information from these SPARQL endpoints by proposing a TCGA tailored federated SPARQL query processing engine named TopFed. We compare TopFed with a well established federation engine FedX in terms of source selection and query execution time by using 10 different federated SPARQL queries with varying requirements. Our evaluation results show that TopFed selects on average less than half of the sources (with 100% recall) with query execution time equal to one third to that of FedX. With TopFed, we aim to offer biomedical scientists a single-point-of-access through which distributed TCGA data can be accessed in unison. We believe the proposed system can greatly help researchers in the biomedical domain to carry out their research effectively with TCGA as the amount and diversity of data exceeds the ability of local resources to handle its retrieval and

  12. 3D BUILDING MODELING IN LOD2 USING THE CITYGML STANDARD

    Directory of Open Access Journals (Sweden)

    D. Preka

    2016-10-01

    Full Text Available Over the last decade, scientific research has been increasingly focused on the third dimension in all fields and especially in sciences related to geographic information, the visualization of natural phenomena and the visualization of the complex urban reality. The field of 3D visualization has achieved rapid development and dynamic progress, especially in urban applications, while the technical restrictions on the use of 3D information tend to subside due to advancements in technology. A variety of 3D modeling techniques and standards has already been developed, as they gain more traction in a wide range of applications. Such a modern standard is the CityGML, which is open and allows for sharing and exchanging of 3D city models. Within the scope of this study, key issues for the 3D modeling of spatial objects and cities are considered and specifically the key elements and abilities of CityGML standard, which is used in order to produce a 3D model of 14 buildings that constitute a block at the municipality of Kaisariani, Athens, in Level of Detail 2 (LoD2, as well as the corresponding relational database. The proposed tool is based upon the 3DCityDB package in tandem with a geospatial database (PostgreSQL w/ PostGIS 2.0 extension. The latter allows for execution of complex queries regarding the spatial distribution of data. The system is implemented in order to facilitate a real-life scenario in a suburb of Athens.

  13. Probable maximum flood control

    International Nuclear Information System (INIS)

    DeGabriele, C.E.; Wu, C.L.

    1991-11-01

    This study proposes preliminary design concepts to protect the waste-handling facilities and all shaft and ramp entries to the underground from the probable maximum flood (PMF) in the current design configuration for the proposed Nevada Nuclear Waste Storage Investigation (NNWSI) repository protection provisions were furnished by the United States Bureau of Reclamation (USSR) or developed from USSR data. Proposed flood protection provisions include site grading, drainage channels, and diversion dikes. Figures are provided to show these proposed flood protection provisions at each area investigated. These areas are the central surface facilities (including the waste-handling building and waste treatment building), tuff ramp portal, waste ramp portal, men-and-materials shaft, emplacement exhaust shaft, and exploratory shafts facility

  14. Introduction to maximum entropy

    International Nuclear Information System (INIS)

    Sivia, D.S.

    1988-01-01

    The maximum entropy (MaxEnt) principle has been successfully used in image reconstruction in a wide variety of fields. We review the need for such methods in data analysis and show, by use of a very simple example, why MaxEnt is to be preferred over other regularizing functions. This leads to a more general interpretation of the MaxEnt method, and its use is illustrated with several different examples. Practical difficulties with non-linear problems still remain, this being highlighted by the notorious phase problem in crystallography. We conclude with an example from neutron scattering, using data from a filter difference spectrometer to contrast MaxEnt with a conventional deconvolution. 12 refs., 8 figs., 1 tab

  15. Solar maximum observatory

    International Nuclear Information System (INIS)

    Rust, D.M.

    1984-01-01

    The successful retrieval and repair of the Solar Maximum Mission (SMM) satellite by Shuttle astronauts in April 1984 permitted continuance of solar flare observations that began in 1980. The SMM carries a soft X ray polychromator, gamma ray, UV and hard X ray imaging spectrometers, a coronagraph/polarimeter and particle counters. The data gathered thus far indicated that electrical potentials of 25 MeV develop in flares within 2 sec of onset. X ray data show that flares are composed of compressed magnetic loops that have come too close together. Other data have been taken on mass ejection, impacts of electron beams and conduction fronts with the chromosphere and changes in the solar radiant flux due to sunspots. 13 references

  16. Introduction to maximum entropy

    International Nuclear Information System (INIS)

    Sivia, D.S.

    1989-01-01

    The maximum entropy (MaxEnt) principle has been successfully used in image reconstruction in a wide variety of fields. The author reviews the need for such methods in data analysis and shows, by use of a very simple example, why MaxEnt is to be preferred over other regularizing functions. This leads to a more general interpretation of the MaxEnt method, and its use is illustrated with several different examples. Practical difficulties with non-linear problems still remain, this being highlighted by the notorious phase problem in crystallography. He concludes with an example from neutron scattering, using data from a filter difference spectrometer to contrast MaxEnt with a conventional deconvolution. 12 refs., 8 figs., 1 tab

  17. Functional Maximum Autocorrelation Factors

    DEFF Research Database (Denmark)

    Larsen, Rasmus; Nielsen, Allan Aasbjerg

    2005-01-01

    MAF outperforms the functional PCA in concentrating the interesting' spectra/shape variation in one end of the eigenvalue spectrum and allows for easier interpretation of effects. Conclusions. Functional MAF analysis is a useful methods for extracting low dimensional models of temporally or spatially......Purpose. We aim at data where samples of an underlying function are observed in a spatial or temporal layout. Examples of underlying functions are reflectance spectra and biological shapes. We apply functional models based on smoothing splines and generalize the functional PCA in......\\verb+~+\\$\\backslash\\$cite{ramsay97} to functional maximum autocorrelation factors (MAF)\\verb+~+\\$\\backslash\\$cite{switzer85,larsen2001d}. We apply the method to biological shapes as well as reflectance spectra. {\\$\\backslash\\$bf Methods}. MAF seeks linear combination of the original variables that maximize autocorrelation between...

  18. Regularized maximum correntropy machine

    KAUST Repository

    Wang, Jim Jing-Yan; Wang, Yunji; Jing, Bing-Yi; Gao, Xin

    2015-01-01

    In this paper we investigate the usage of regularized correntropy framework for learning of classifiers from noisy labels. The class label predictors learned by minimizing transitional loss functions are sensitive to the noisy and outlying labels of training samples, because the transitional loss functions are equally applied to all the samples. To solve this problem, we propose to learn the class label predictors by maximizing the correntropy between the predicted labels and the true labels of the training samples, under the regularized Maximum Correntropy Criteria (MCC) framework. Moreover, we regularize the predictor parameter to control the complexity of the predictor. The learning problem is formulated by an objective function considering the parameter regularization and MCC simultaneously. By optimizing the objective function alternately, we develop a novel predictor learning algorithm. The experiments on two challenging pattern classification tasks show that it significantly outperforms the machines with transitional loss functions.

  19. Regularized maximum correntropy machine

    KAUST Repository

    Wang, Jim Jing-Yan

    2015-02-12

    In this paper we investigate the usage of regularized correntropy framework for learning of classifiers from noisy labels. The class label predictors learned by minimizing transitional loss functions are sensitive to the noisy and outlying labels of training samples, because the transitional loss functions are equally applied to all the samples. To solve this problem, we propose to learn the class label predictors by maximizing the correntropy between the predicted labels and the true labels of the training samples, under the regularized Maximum Correntropy Criteria (MCC) framework. Moreover, we regularize the predictor parameter to control the complexity of the predictor. The learning problem is formulated by an objective function considering the parameter regularization and MCC simultaneously. By optimizing the objective function alternately, we develop a novel predictor learning algorithm. The experiments on two challenging pattern classification tasks show that it significantly outperforms the machines with transitional loss functions.

  20. Office microlaparoscopic ovarian drilling (OMLOD) versus conventional laparoscopic ovarian drilling (LOD) for women with polycystic ovary syndrome.

    Science.gov (United States)

    Salah, Imaduldin M

    2013-02-01

    This was a prospective controlled study to compare the beneficial effects of office microlaparoscopic ovarian drilling (OMLOD) under augmented local anesthesia, as a new modality treatment option, compared to those following ovarian drilling with the conventional traditional 10-mm laparoscope (laparoscopic ovarian drilling, LOD) under general anesthesia. The study included 60 anovulatory women with polycystic ovary syndrome (PCOS) who underwent OMLOD (study group) and 60 anovulatory PCOS women, in whom conventional LOD using 10-mm laparoscope under general anesthesia was performed (comparison group). Transvaginal ultrasound scan and blood sampling to measure the serum concentrations of LH, FSH, testosterone and androstenedione were performed before and after the procedure. Intraoperative and postoperative pain scores in candidate women were evaluated during the office microlaparoscopic procedure, in addition to the number of candidates who needed extra analgesia. Women undergoing OMLOD showed good intraoperative and postoperative pain scores. The number of patients discharged within 2 h after the office procedure was significantly higher, without the need for postoperative analgesia in most patients. The LH:FSH ratio, mean serum concentrations of LH and testosterone and free androgen index decreased significantly after both OMLOD and LOD. The mean ovarian volume decreased significantly (P < 0.05) a year after both OMLOD and LOD. There were no significant differences in those results after both procedures. Intra- and postoperatively augmented local anesthesia allows outpatient bilateral ovarian drilling by microlaparoscopy without general anesthesia. The high pregnancy rate, the simplicity of the method and the faster discharge time offer a new option for patients with PCOS who are resistant to clomiphene citrate. Moreover, ovarian drilling could be performed simultaneously during the routine diagnostic microlaparoscopy and integrated into the fertility workup of

  1. Solar maximum mission

    International Nuclear Information System (INIS)

    Ryan, J.

    1981-01-01

    By understanding the sun, astrophysicists hope to expand this knowledge to understanding other stars. To study the sun, NASA launched a satellite on February 14, 1980. The project is named the Solar Maximum Mission (SMM). The satellite conducted detailed observations of the sun in collaboration with other satellites and ground-based optical and radio observations until its failure 10 months into the mission. The main objective of the SMM was to investigate one aspect of solar activity: solar flares. A brief description of the flare mechanism is given. The SMM satellite was valuable in providing information on where and how a solar flare occurs. A sequence of photographs of a solar flare taken from SMM satellite shows how a solar flare develops in a particular layer of the solar atmosphere. Two flares especially suitable for detailed observations by a joint effort occurred on April 30 and May 21 of 1980. These flares and observations of the flares are discussed. Also discussed are significant discoveries made by individual experiments

  2. Change detection on LOD 2 building models with very high resolution spaceborne stereo imagery

    Science.gov (United States)

    Qin, Rongjun

    2014-10-01

    Due to the fast development of the urban environment, the need for efficient maintenance and updating of 3D building models is ever increasing. Change detection is an essential step to spot the changed area for data (map/3D models) updating and urban monitoring. Traditional methods based on 2D images are no longer suitable for change detection in building scale, owing to the increased spectral variability of the building roofs and larger perspective distortion of the very high resolution (VHR) imagery. Change detection in 3D is increasingly being investigated using airborne laser scanning data or matched Digital Surface Models (DSM), but rare study has been conducted regarding to change detection on 3D city models with VHR images, which is more informative but meanwhile more complicated. This is due to the fact that the 3D models are abstracted geometric representation of the urban reality, while the VHR images record everything. In this paper, a novel method is proposed to detect changes directly on LOD (Level of Detail) 2 building models with VHR spaceborne stereo images from a different date, with particular focus on addressing the special characteristics of the 3D models. In the first step, the 3D building models are projected onto a raster grid, encoded with building object, terrain object, and planar faces. The DSM is extracted from the stereo imagery by hierarchical semi-global matching (SGM). In the second step, a multi-channel change indicator is extracted between the 3D models and stereo images, considering the inherent geometric consistency (IGC), height difference, and texture similarity for each planar face. Each channel of the indicator is then clustered with the Self-organizing Map (SOM), with "change", "non-change" and "uncertain change" status labeled through a voting strategy. The "uncertain changes" are then determined with a Markov Random Field (MRF) analysis considering the geometric relationship between faces. In the third step, buildings are

  3. Wavelet analysis of interannual LOD, AAM, and ENSO: 1997-98 El Niño and 1998-99 La Niña signals

    Science.gov (United States)

    Zhou, Y. H.; Zheng, D. W.; Liao, X. H.

    2001-05-01

    On the basis of the data series of the length of day (LOD), the atmospheric angular momentum (AAM) and the Southern Oscillation Index (SOI) for January 1970-June 1999, the relationship among Interannual LOD, AAM, and the EL Niño/Southern Oscillation (ENSO) is analyzed by the wavelet transform method. The results suggest that they have similar time-varying spectral structures. The signals of 1997-98 El Niño and 1998-99 La Niña events can be detected from the LOD or AAM data.

  4. A general transformation to canonical form for potentials in pairwise interatomic interactions.

    Science.gov (United States)

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

    2015-06-14

    A generalized formulation of explicit force-based transformations is introduced to investigate the concept of a canonical potential in both fundamental chemical and intermolecular bonding. Different classes of representative ground electronic state pairwise interatomic interactions are referenced to a chosen canonical potential illustrating application of such transformations. Specifically, accurately determined potentials of the diatomic molecules H2, H2(+), HF, LiH, argon dimer, and one-dimensional dissociative coordinates in Ar-HBr, OC-HF, and OC-Cl2 are investigated throughout their bound potentials. Advantages of the current formulation for accurately evaluating equilibrium dissociation energies and a fundamentally different unified perspective on nature of intermolecular interactions will be emphasized. In particular, this canonical approach has significance to previous assertions that there is no very fundamental distinction between van der Waals bonding and covalent bonding or for that matter hydrogen and halogen bonds.

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

    Science.gov (United States)

    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.

  6. Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix

    DEFF Research Database (Denmark)

    Havgaard, Jakob Hull; Torarinsson, Elfar; Gorodkin, Jan

    2007-01-01

    and backtracked in a normal fashion. Finally, the FOLDALIGN algorithm has also been updated with a better memory implementation and an improved energy model. With these improvements in the algorithm, the FOLDALIGN software package provides the molecular biologist with an efficient and user-friendly tool...... the advantage of providing the constraints dynamically. This has been included in a new implementation of the FOLDALIGN algorithm for pairwise local or global structural alignment of RNA sequences. It is shown that time and memory requirements are dramatically lowered while overall performance is maintained....... Furthermore, a new divide and conquer method is introduced to limit the memory requirement during global alignment and backtrack of local alignment. All branch points in the computed RNA structure are found and used to divide the structure into smaller unbranched segments. Each segment is then realigned...

  7. Linear VSS and Distributed Commitments Based on Secret Sharing and Pairwise Checks

    DEFF Research Database (Denmark)

    Fehr, Serge; Maurer, Ueli M.

    2002-01-01

    . VSS and DC are main building blocks for unconditional secure multi-party computation protocols. This general approach covers all known linear VSS and DC schemes. The main theorem states that the security of a scheme is equivalent to a pure linear-algebra condition on the linear mappings (e.......g. described as matrices and vectors) describing the scheme. The security of all known schemes follows as corollaries whose proofs are pure linear-algebra arguments, in contrast to some hybrid arguments used in the literature. Our approach is demonstrated for the CDM DC scheme, which we generalize to be secure......We present a general treatment of all non-cryptographic (i.e., information-theoretically secure) linear veriable-secret-sharing (VSS) and distributed-commitment (DC) schemes, based on an underlying secret sharing scheme, pairwise checks between players, complaints, and accusations of the dealer...

  8. The pairwise phase consistency in cortical network and its relationship with neuronal activation

    Directory of Open Access Journals (Sweden)

    Wang Daming

    2017-01-01

    Full Text Available Gamma-band neuronal oscillation and synchronization with the range of 30-90 Hz are ubiquitous phenomenon across numerous brain areas and various species, and correlated with plenty of cognitive functions. The phase of the oscillation, as one aspect of CTC (Communication through Coherence hypothesis, underlies various functions for feature coding, memory processing and behaviour performing. The PPC (Pairwise Phase Consistency, an improved coherence measure, statistically quantifies the strength of phase synchronization. In order to evaluate the PPC and its relationships with input stimulus, neuronal activation and firing rate, a simplified spiking neuronal network is constructed to simulate orientation columns in primary visual cortex. If the input orientation stimulus is preferred for a certain orientation column, neurons within this corresponding column will obtain higher firing rate and stronger neuronal activation, which consequently engender higher PPC values, with higher PPC corresponding to higher firing rate. In addition, we investigate the PPC in time resolved analysis with a sliding window.

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

    Science.gov (United States)

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

    2016-08-01

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

  10. Estimators of the Relations of Equivalence, Tolerance and Preference Based on Pairwise Comparisons with Random Errors

    Directory of Open Access Journals (Sweden)

    Leszek Klukowski

    2012-01-01

    Full Text Available This paper presents a review of results of the author in the area of estimation of the relations of equivalence, tolerance and preference within a finite set based on multiple, independent (in a stochastic way pairwise comparisons with random errors, in binary and multivalent forms. These estimators require weaker assumptions than those used in the literature on the subject. Estimates of the relations are obtained based on solutions to problems from discrete optimization. They allow application of both types of comparisons - binary and multivalent (this fact relates to the tolerance and preference relations. The estimates can be verified in a statistical way; in particular, it is possible to verify the type of the relation. The estimates have been applied by the author to problems regarding forecasting, financial engineering and bio-cybernetics. (original abstract

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

    Science.gov (United States)

    Newberg, Lee A

    2008-08-15

    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. Here we present an optimal checkpointing strategy, and demonstrate its utility with pairwise local sequence alignment of sequences of length 10,000. Sample C++-code for optimal backtrace is available in the Supplementary Materials. Supplementary data is available at Bioinformatics online.

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

    Science.gov (United States)

    Pickering, William; Lim, Chjan

    2017-07-01

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

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

    Science.gov (United States)

    Daily, Jeff

    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. A faster intra-sequence local pairwise alignment implementation is described and benchmarked, including new global and semi-global variants. Using a 375 residue query sequence a speed of 136 billion cell updates per second (GCUPS) was achieved on a dual Intel Xeon E5-2670 24-core processor system, the highest reported for an implementation based on Farrar's 'striped' approach. Rognes's SWIPE optimal database search application is still generally the fastest available at 1.2 to at best 2.4 times faster than Parasail for sequences shorter than 500 amino acids. However, Parasail was faster for longer sequences. For global alignments, Parasail's prefix scan implementation is generally the fastest, faster even than Farrar's 'striped' approach, however the opal library is faster for single-threaded applications. 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. Applications that require optimal alignment scores could benefit from the improved performance. For the first time, SIMD global, semi-global, and local alignments are available in a stand-alone C library.

  14. PairWise Neighbours database: overlaps and spacers among prokaryote genomes

    Directory of Open Access Journals (Sweden)

    Garcia-Vallvé Santiago

    2009-06-01

    Full Text Available Abstract Background Although prokaryotes live in a variety of habitats and possess different metabolic and genomic complexity, they have several genomic architectural features in common. The overlapping genes are a common feature of the prokaryote genomes. The overlapping lengths tend to be short because as the overlaps become longer they have more risk of deleterious mutations. The spacers between genes tend to be short too because of the tendency to reduce the non coding DNA among prokaryotes. However they must be long enough to maintain essential regulatory signals such as the Shine-Dalgarno (SD sequence, which is responsible of an efficient translation. Description PairWise Neighbours is an interactive and intuitive database used for retrieving information about the spacers and overlapping genes among bacterial and archaeal genomes. It contains 1,956,294 gene pairs from 678 fully sequenced prokaryote genomes and is freely available at the URL http://genomes.urv.cat/pwneigh. This database provides information about the overlaps and their conservation across species. Furthermore, it allows the wide analysis of the intergenic regions providing useful information such as the location and strength of the SD sequence. Conclusion There are experiments and bioinformatic analysis that rely on correct annotations of the initiation site. Therefore, a database that studies the overlaps and spacers among prokaryotes appears to be desirable. PairWise Neighbours database permits the reliability analysis of the overlapping structures and the study of the SD presence and location among the adjacent genes, which may help to check the annotation of the initiation sites.

  15. Improving pairwise comparison of protein sequences with domain co-occurrence

    Science.gov (United States)

    Gascuel, Olivier

    2018-01-01

    Comparing and aligning protein sequences is an essential task in bioinformatics. More specifically, local alignment tools like BLAST are widely used for identifying conserved protein sub-sequences, which likely correspond to protein domains or functional motifs. However, to limit the number of false positives, these tools are used with stringent sequence-similarity thresholds and hence can miss several hits, especially for species that are phylogenetically distant from reference organisms. A solution to this problem is then to integrate additional contextual information to the procedure. Here, we propose to use domain co-occurrence to increase the sensitivity of pairwise sequence comparisons. Domain co-occurrence is a strong feature of proteins, since most protein domains tend to appear with a limited number of other domains on the same protein. We propose a method to take this information into account in a typical BLAST analysis and to construct new domain families on the basis of these results. We used Plasmodium falciparum as a case study to evaluate our method. The experimental findings showed an increase of 14% of the number of significant BLAST hits and an increase of 25% of the proteome area that can be covered with a domain. Our method identified 2240 new domains for which, in most cases, no model of the Pfam database could be linked. Moreover, our study of the quality of the new domains in terms of alignment and physicochemical properties show that they are close to that of standard Pfam domains. Source code of the proposed approach and supplementary data are available at: https://gite.lirmm.fr/menichelli/pairwise-comparison-with-cooccurrence PMID:29293498

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

    Directory of Open Access Journals (Sweden)

    Jian-Bin Liu

    2013-03-01

    Full Text Available 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.

  17. Modulation of the SSTA decadal variation on ENSO events and relationships of SSTA With LOD,SOI, etc

    Science.gov (United States)

    Liao, D. C.; Zhou, Y. H.; Liao, X. H.

    2007-01-01

    Interannual and decadal components of the length of day (LOD), Southern Oscillation Index (SOI) and Sea Surface Temperature anomaly (SSTA) in Nino regions are extracted by band-pass filtering, and used for research of the modulation of the SSTA on the ENSO events. Results show that besides the interannual components, the decadal components in SSTA have strong impacts on monitoring and representing of the ENSO events. When the ENSO events are strong, the modulation of the decadal components of the SSTA tends to prolong the life-time of the events and enlarge the extreme anomalies of the SST, while the ENSO events, which are so weak that they can not be detected by the interannual components of the SSTA, can also be detected with the help of the modulation of the SSTA decadal components. The study further draws attention to the relationships of the SSTA interannual and decadal components with those of LOD, SOI, both of the sea level pressure anomalies (SLPA) and the trade wind anomalies (TWA) in tropic Pacific, and also with those of the axial components of the atmospheric angular momentum (AAM) and oceanic angular momentum (OAM). Results of the squared coherence and coherent phases among them reveal close connections with the SSTA and almost all of the parameters mentioned above on the interannual time scales, while on the decadal time scale significant connections are among the SSTA and SOI, SLPA, TWA, ?3w and ?3w+v as well, and slight weaker connections between the SSTA and LOD, ?3pib and ?3bp

  18. Visualizing dynamic geosciences phenomena using an octree-based view-dependent LOD strategy within virtual globes

    Science.gov (United States)

    Li, Jing; Wu, Huayi; Yang, Chaowei; Wong, David W.; Xie, Jibo

    2011-09-01

    Geoscientists build dynamic models to simulate various natural phenomena for a better understanding of our planet. Interactive visualizations of these geoscience models and their outputs through virtual globes on the Internet can help the public understand the dynamic phenomena related to the Earth more intuitively. However, challenges arise when the volume of four-dimensional data (4D), 3D in space plus time, is huge for rendering. Datasets loaded from geographically distributed data servers require synchronization between ingesting and rendering data. Also the visualization capability of display clients varies significantly in such an online visualization environment; some may not have high-end graphic cards. To enhance the efficiency of visualizing dynamic volumetric data in virtual globes, this paper proposes a systematic framework, in which an octree-based multiresolution data structure is implemented to organize time series 3D geospatial data to be used in virtual globe environments. This framework includes a view-dependent continuous level of detail (LOD) strategy formulated as a synchronized part of the virtual globe rendering process. Through the octree-based data retrieval process, the LOD strategy enables the rendering of the 4D simulation at a consistent and acceptable frame rate. To demonstrate the capabilities of this framework, data of a simulated dust storm event are rendered in World Wind, an open source virtual globe. The rendering performances with and without the octree-based LOD strategy are compared. The experimental results show that using the proposed data structure and processing strategy significantly enhances the visualization performance when rendering dynamic geospatial phenomena in virtual globes.

  19. Gene ontology analysis of pairwise genetic associations in two genome-wide studies of sporadic ALS

    Directory of Open Access Journals (Sweden)

    Kim Nora

    2012-07-01

    Full Text Available Abstract Background It is increasingly clear that common human diseases have a complex genetic architecture characterized by both additive and nonadditive genetic effects. The goal of the present study was to determine whether patterns of both additive and nonadditive genetic associations aggregate in specific functional groups as defined by the Gene Ontology (GO. Results We first estimated all pairwise additive and nonadditive genetic effects using the multifactor dimensionality reduction (MDR method that makes few assumptions about the underlying genetic model. Statistical significance was evaluated using permutation testing in two genome-wide association studies of ALS. The detection data consisted of 276 subjects with ALS and 271 healthy controls while the replication data consisted of 221 subjects with ALS and 211 healthy controls. Both studies included genotypes from approximately 550,000 single-nucleotide polymorphisms (SNPs. Each SNP was mapped to a gene if it was within 500 kb of the start or end. Each SNP was assigned a p-value based on its strongest joint effect with the other SNPs. We then used the Exploratory Visual Analysis (EVA method and software to assign a p-value to each gene based on the overabundance of significant SNPs at the α = 0.05 level in the gene. We also used EVA to assign p-values to each GO group based on the overabundance of significant genes at the α = 0.05 level. A GO category was determined to replicate if that category was significant at the α = 0.05 level in both studies. We found two GO categories that replicated in both studies. The first, ‘Regulation of Cellular Component Organization and Biogenesis’, a GO Biological Process, had p-values of 0.010 and 0.014 in the detection and replication studies, respectively. The second, ‘Actin Cytoskeleton’, a GO Cellular Component, had p-values of 0.040 and 0.046 in the detection and replication studies, respectively. Conclusions Pathway

  20. Classification of forest-based ecotourism areas in Pocahontas County of West Virginia using GIS and pairwise comparison method

    Science.gov (United States)

    Ishwar Dhami; Jinyang. Deng

    2012-01-01

    Many previous studies have examined ecotourism primarily from the perspective of tourists while largely ignoring ecotourism destinations. This study used geographical information system (GIS) and pairwise comparison to identify forest-based ecotourism areas in Pocahontas County, West Virginia. The study adopted the criteria and scores developed by Boyd and Butler (1994...

  1. Pair-Wise Trajectory Management-Oceanic (PTM-O) . [Concept of Operations—Version 3.9

    Science.gov (United States)

    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.

  2. The structure of pairwise correlation in mouse primary visual cortex reveals functional organization in the absence of an orientation map.

    Science.gov (United States)

    Denman, Daniel J; Contreras, Diego

    2014-10-01

    Neural responses to sensory stimuli are not independent. Pairwise correlation can reduce coding efficiency, occur independent of stimulus representation, or serve as an additional channel of information, depending on the timescale of correlation and the method of decoding. Any role for correlation depends on its magnitude and structure. In sensory areas with maps, like the orientation map in primary visual cortex (V1), correlation is strongly related to the underlying functional architecture, but it is unclear whether this correlation structure is an essential feature of the system or arises from the arrangement of cells in the map. We assessed the relationship between functional architecture and pairwise correlation by measuring both synchrony and correlated spike count variability in mouse V1, which lacks an orientation map. We observed significant pairwise synchrony, which was organized by distance and relative orientation preference between cells. We also observed nonzero correlated variability in both the anesthetized (0.16) and awake states (0.18). Our results indicate that the structure of pairwise correlation is maintained in the absence of an underlying anatomical organization and may be an organizing principle of the mammalian visual system preserved by nonrandom connectivity within local networks. © The Author 2013. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  3. Theory of pairwise coupling embedded in more general local dispersion relations

    International Nuclear Information System (INIS)

    Fuchs, V.; Bers, A.; Harten, L.

    1985-01-01

    Earlier work on the mode conversion theory by Fuchs, Ko, and Bers is detailed and expanded upon, and its relation to energy conservation is discussed. Given a local dispersion relation, D(ω; k, z) = 0, describing stable waves excited at an externally imposed frequency ω, a pairwise mode-coupling event embedded therein is extracted by expanding D(k, z) around a contour k = k/sub c/(z) given by partialD/partialk = 0. The branch points of D(k, z) = 0 are the turning points of a second-order differential-equation representation. In obtaining the fraction of mode-converted energy, the connection formula and conservation of energy must be used together. Also, proper attention must be given to distinguish cases for which the coupling disappears or persists upon confluence of the branches, a property which is shown to depend on the forward (v/sub g/v/sub ph/>0) or backward (v/sub g/v/sub ph/<0) nature of the waves. Examples occurring in ion-cyclotron and lower-hybrid heating are presented, illustrating the use of the theory

  4. ProteinWorldDB: querying radical pairwise alignments among protein sets from complete genomes.

    Science.gov (United States)

    Otto, Thomas Dan; Catanho, Marcos; Tristão, Cristian; Bezerra, Márcia; Fernandes, Renan Mathias; Elias, Guilherme Steinberger; Scaglia, Alexandre Capeletto; Bovermann, Bill; Berstis, Viktors; Lifschitz, Sergio; de Miranda, Antonio Basílio; Degrave, Wim

    2010-03-01

    Many analyses in modern biological research are based on comparisons between biological sequences, resulting in functional, evolutionary and structural inferences. When large numbers of sequences are compared, heuristics are often used resulting in a certain lack of accuracy. In order to improve and validate results of such comparisons, we have performed radical all-against-all comparisons of 4 million protein sequences belonging to the RefSeq database, using an implementation of the Smith-Waterman algorithm. This extremely intensive computational approach was made possible with the help of World Community Grid, through the Genome Comparison Project. The resulting database, ProteinWorldDB, which contains coordinates of pairwise protein alignments and their respective scores, is now made available. Users can download, compare and analyze the results, filtered by genomes, protein functions or clusters. ProteinWorldDB is integrated with annotations derived from Swiss-Prot, Pfam, KEGG, NCBI Taxonomy database and gene ontology. The database is a unique and valuable asset, representing a major effort to create a reliable and consistent dataset of cross-comparisons of the whole protein content encoded in hundreds of completely sequenced genomes using a rigorous dynamic programming approach. The database can be accessed through http://proteinworlddb.org

  5. pyRMSD: a Python package for efficient pairwise RMSD matrix calculation and handling.

    Science.gov (United States)

    Gil, Víctor A; Guallar, Víctor

    2013-09-15

    We introduce pyRMSD, an open source standalone Python package that aims at offering an integrative and efficient way of performing Root Mean Square Deviation (RMSD)-related calculations of large sets of structures. It is specially tuned to do fast collective RMSD calculations, as pairwise RMSD matrices, implementing up to three well-known superposition algorithms. pyRMSD provides its own symmetric distance matrix class that, besides the fact that it can be used as a regular matrix, helps to save memory and increases memory access speed. This last feature can dramatically improve the overall performance of any Python algorithm using it. In addition, its extensibility, testing suites and documentation make it a good choice to those in need of a workbench for developing or testing new algorithms. The source code (under MIT license), installer, test suites and benchmarks can be found at https://pele.bsc.es/ under the tools section. victor.guallar@bsc.es Supplementary data are available at Bioinformatics online.

  6. A pairwise residue contact area-based mean force potential for discrimination of native protein structure

    Directory of Open Access Journals (Sweden)

    Pezeshk Hamid

    2010-01-01

    Full Text Available Abstract Background Considering energy function to detect a correct protein fold from incorrect ones is very important for protein structure prediction and protein folding. Knowledge-based mean force potentials are certainly the most popular type of interaction function for protein threading. They are derived from statistical analyses of interacting groups in experimentally determined protein structures. These potentials are developed at the atom or the amino acid level. Based on orientation dependent contact area, a new type of knowledge-based mean force potential has been developed. Results We developed a new approach to calculate a knowledge-based potential of mean-force, using pairwise residue contact area. To test the performance of our approach, we performed it on several decoy sets to measure its ability to discriminate native structure from decoys. This potential has been able to distinguish native structures from the decoys in the most cases. Further, the calculated Z-scores were quite high for all protein datasets. Conclusions This knowledge-based potential of mean force can be used in protein structure prediction, fold recognition, comparative modelling and molecular recognition. The program is available at http://www.bioinf.cs.ipm.ac.ir/softwares/surfield

  7. Optimal Inconsistency Repairing of Pairwise Comparison Matrices Using Integrated Linear Programming and Eigenvector Methods

    Directory of Open Access Journals (Sweden)

    Haiqing Zhang

    2014-01-01

    Full Text Available Satisfying consistency requirements of pairwise comparison matrix (PCM is a critical step in decision making methodologies. An algorithm has been proposed to find a new modified consistent PCM in which it can replace the original inconsistent PCM in analytic hierarchy process (AHP or in fuzzy AHP. This paper defines the modified consistent PCM by the original inconsistent PCM and an adjustable consistent PCM combined. The algorithm adopts a segment tree to gradually approach the greatest lower bound of the distance with the original PCM to obtain the middle value of an adjustable PCM. It also proposes a theorem to obtain the lower value and the upper value of an adjustable PCM based on two constraints. The experiments for crisp elements show that the proposed approach can preserve more of the original information than previous works of the same consistent value. The convergence rate of our algorithm is significantly faster than previous works with respect to different parameters. The experiments for fuzzy elements show that our method could obtain suitable modified fuzzy PCMs.

  8. High Performance Biological Pairwise Sequence Alignment: FPGA versus GPU versus Cell BE versus GPP

    Directory of Open Access Journals (Sweden)

    Khaled Benkrid

    2012-01-01

    Full Text Available This paper explores the pros and cons of reconfigurable computing in the form of FPGAs for high performance efficient computing. In particular, the paper presents the results of a comparative study between three different acceleration technologies, namely, Field Programmable Gate Arrays (FPGAs, Graphics Processor Units (GPUs, and IBM’s Cell Broadband Engine (Cell BE, in the design and implementation of the widely-used Smith-Waterman pairwise sequence alignment algorithm, with general purpose processors as a base reference implementation. Comparison criteria include speed, energy consumption, and purchase and development costs. The study shows that FPGAs largely outperform all other implementation platforms on performance per watt criterion and perform better than all other platforms on performance per dollar criterion, although by a much smaller margin. Cell BE and GPU come second and third, respectively, on both performance per watt and performance per dollar criteria. In general, in order to outperform other technologies on performance per dollar criterion (using currently available hardware and development tools, FPGAs need to achieve at least two orders of magnitude speed-up compared to general-purpose processors and one order of magnitude speed-up compared to domain-specific technologies such as GPUs.

  9. Evaluation of advanced multiplex short tandem repeat systems in pairwise kinship analysis.

    Science.gov (United States)

    Tamura, Tomonori; Osawa, Motoki; Ochiai, Eriko; Suzuki, Takanori; Nakamura, Takashi

    2015-09-01

    The AmpFLSTR Identifiler Kit, comprising 15 autosomal short tandem repeat (STR) loci, is commonly employed in forensic practice for calculating match probabilities and parentage testing. The conventional system exhibits insufficient estimation for kinship analysis such as sibship testing because of shortness of examined loci. This study evaluated the power of the PowerPlex Fusion System, GlobalFiler Kit, and PowerPlex 21 System, which comprise more than 20 autosomal STR loci, to estimate pairwise blood relatedness (i.e., parent-child, full siblings, second-degree relatives, and first cousins). The genotypes of all 24 STR loci in 10,000 putative pedigrees were constructed by simulation. The likelihood ratio for each locus was calculated from joint probabilities for relatives and non-relatives. The combined likelihood ratio was calculated according to the product rule. The addition of STR loci improved separation between relatives and non-relatives. However, these systems were less effectively extended to the inference for first cousins. In conclusion, these advanced systems will be useful in forensic personal identification, especially in the evaluation of full siblings and second-degree relatives. Moreover, the additional loci may give rise to two major issues of more frequent mutational events and several pairs of linked loci on the same chromosome. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    Kaufmann Michael

    2004-09-01

    Full Text Available Abstract 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.

  11. The Dynamics of Multiple Pair-Wise Collisions in a Chain for Designing Optimal Shock Amplifiers

    Directory of Open Access Journals (Sweden)

    Bryan Rodgers

    2009-01-01

    Full Text Available The major focus of this work is to examine the dynamics of velocity amplification through pair-wise collisions between multiple masses in a chain, in order to develop useful machines. For instance low-cost machines based on this principle could be used for detailed, very-high acceleration shock-testing of MEMS devices. A theoretical basis for determining the number and mass of intermediate stages in such a velocity amplifier, based on simple rigid body mechanics, is proposed. The influence of mass ratios and the coefficient of restitution on the optimisation of the system is identified and investigated. In particular, two cases are examined: in the first, the velocity of the final mass in the chain (that would have the object under test mounted on it is maximised by defining the ratio of adjacent masses according to a power law relationship; in the second, the energy transfer efficiency of the system is maximised by choosing the mass ratios such that all masses except the final mass come to rest following impact. Comparisons are drawn between both cases and the results are used in proposing design guidelines for optimal shock amplifiers. It is shown that for most practical systems, a shock amplifier with mass ratios based on a power law relationship is optimal and can easily yield velocity amplifications of a factor 5–8 times. A prototype shock testing machine that was made using above principles is briefly introduced.

  12. Visualization of pairwise and multilocus linkage disequilibrium structure using latent forests.

    Directory of Open Access Journals (Sweden)

    Raphaël Mourad

    Full Text Available Linkage disequilibrium study represents a major issue in statistical genetics as it plays a fundamental role in gene mapping and helps us to learn more about human history. The linkage disequilibrium complex structure makes its exploratory data analysis essential yet challenging. Visualization methods, such as the triangular heat map implemented in Haploview, provide simple and useful tools to help understand complex genetic patterns, but remain insufficient to fully describe them. Probabilistic graphical models have been widely recognized as a powerful formalism allowing a concise and accurate modeling of dependences between variables. In this paper, we propose a method for short-range, long-range and chromosome-wide linkage disequilibrium visualization using forests of hierarchical latent class models. Thanks to its hierarchical nature, our method is shown to provide a compact view of both pairwise and multilocus linkage disequilibrium spatial structures for the geneticist. Besides, a multilocus linkage disequilibrium measure has been designed to evaluate linkage disequilibrium in hierarchy clusters. To learn the proposed model, a new scalable algorithm is presented. It constrains the dependence scope, relying on physical positions, and is able to deal with more than one hundred thousand single nucleotide polymorphisms. The proposed algorithm is fast and does not require phase genotypic data.

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

    Science.gov (United States)

    Chartrand, Ryan; Ballard, Kathryn

    2016-01-01

    Pairwise Trajectory Management (PTM) is a concept that utilizes airborne and ground-based capabilities to enable airborne spacing operations in oceanic regions. The goal of PTM is to use enhanced surveillance, along with airborne tools, to manage the spacing between aircraft. Due to the enhanced airborne surveillance of Automatic Dependent Surveillance-Broadcast (ADS-B) information and reduced communication, the PTM minimum spacing distance will be less than distances currently required of an air traffic controller. Reduced minimum distance will increase the capacity of aircraft operations at a given altitude or volume of airspace, thereby increasing time on desired trajectory and overall flight efficiency. PTM is designed to allow a flight crew to resolve a specific traffic conflict (or conflicts), identified by the air traffic controller, while maintaining the flight crew's desired altitude. The air traffic controller issues a PTM clearance to a flight crew authorized to conduct PTM operations in order to resolve a conflict for the pair (or pairs) of aircraft (i.e., the PTM aircraft and a designated target aircraft). This clearance requires the flight crew of the PTM aircraft to use their ADS-B-enabled onboard equipment to manage their spacing relative to the designated target aircraft to ensure spacing distances that are no closer than the PTM minimum distance. When the air traffic controller determines that PTM is no longer required, the controller issues a clearance to cancel the PTM operation.

  14. Prediction of microsleeps using pairwise joint entropy and mutual information between EEG channels.

    Science.gov (United States)

    Baseer, Abdul; Weddell, Stephen J; Jones, Richard D

    2017-07-01

    Microsleeps are involuntary and brief instances of complete loss of responsiveness, typically of 0.5-15 s duration. They adversely affect performance in extended attention-driven jobs and can be fatal. Our aim was to predict microsleeps from 16 channel EEG signals. Two information theoretic concepts - pairwise joint entropy and mutual information - were independently used to continuously extract features from EEG signals. k-nearest neighbor (kNN) with k = 3 was used to calculate both joint entropy and mutual information. Highly correlated features were discarded and the rest were ranked using Fisher score followed by an average of 3-fold cross-validation area under the curve of the receiver operating characteristic (AUC ROC ). Leave-one-out method (LOOM) was performed to test the performance of microsleep prediction system on independent data. The best prediction for 0.25 s ahead was AUCROC, sensitivity, precision, geometric mean (GM), and φ of 0.93, 0.68, 0.33, 0.75, and 0.38 respectively with joint entropy using single linear discriminant analysis (LDA) classifier.

  15. The quantitative LOD score: test statistic and sample size for exclusion and linkage of quantitative traits in human sibships.

    Science.gov (United States)

    Page, G P; Amos, C I; Boerwinkle, E

    1998-04-01

    We present a test statistic, the quantitative LOD (QLOD) score, for the testing of both linkage and exclusion of quantitative-trait loci in randomly selected human sibships. As with the traditional LOD score, the boundary values of 3, for linkage, and -2, for exclusion, can be used for the QLOD score. We investigated the sample sizes required for inferring exclusion and linkage, for various combinations of linked genetic variance, total heritability, recombination distance, and sibship size, using fixed-size sampling. The sample sizes required for both linkage and exclusion were not qualitatively different and depended on the percentage of variance being linked or excluded and on the total genetic variance. Information regarding linkage and exclusion in sibships larger than size 2 increased as approximately all possible pairs n(n-1)/2 up to sibships of size 6. Increasing the recombination (theta) distance between the marker and the trait loci reduced empirically the power for both linkage and exclusion, as a function of approximately (1-2theta)4.

  16. Credal Networks under Maximum Entropy

    OpenAIRE

    Lukasiewicz, Thomas

    2013-01-01

    We apply the principle of maximum entropy to select a unique joint probability distribution from the set of all joint probability distributions specified by a credal network. In detail, we start by showing that the unique joint distribution of a Bayesian tree coincides with the maximum entropy model of its conditional distributions. This result, however, does not hold anymore for general Bayesian networks. We thus present a new kind of maximum entropy models, which are computed sequentially. ...

  17. LOD lab: Experiments at LOD scale

    NARCIS (Netherlands)

    Rietveld, Laurens; Beek, Wouter; Schlobach, Stefan

    2015-01-01

    Contemporary Semantic Web research is in the business of optimizing algorithms for only a handful of datasets such as DBpedia, BSBM, DBLP and only a few more. This means that current practice does not generally take the true variety of Linked Data into account. With hundreds of thousands of datasets

  18. Pairwise structure alignment specifically tuned for surface pockets and interaction interfaces

    KAUST Repository

    Cui, Xuefeng; Naveed, Hammad; Gao, Xin

    2015-01-01

    that are not limited to backbone fragments, and by employing a maximum weighted bipartite matching solver from the beginning of the alignment process. In addition, our methods incorporate similarities of sequentially and structurally remote residues that potentially

  19. Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix.

    Directory of Open Access Journals (Sweden)

    Jakob H Havgaard

    2007-10-01

    Full Text Available It has become clear that noncoding RNAs (ncRNA play important roles in cells, and emerging studies indicate that there might be a large number of unknown ncRNAs in mammalian genomes. There exist computational methods that can be used to search for ncRNAs by comparing sequences from different genomes. One main problem with these methods is their computational complexity, and heuristics are therefore employed. Two heuristics are currently very popular: pre-folding and pre-aligning. However, these heuristics are not ideal, as pre-aligning is dependent on sequence similarity that may not be present and pre-folding ignores the comparative information. Here, pruning of the dynamical programming matrix is presented as an alternative novel heuristic constraint. All subalignments that do not exceed a length-dependent minimum score are discarded as the matrix is filled out, thus giving the advantage of providing the constraints dynamically. This has been included in a new implementation of the FOLDALIGN algorithm for pairwise local or global structural alignment of RNA sequences. It is shown that time and memory requirements are dramatically lowered while overall performance is maintained. Furthermore, a new divide and conquer method is introduced to limit the memory requirement during global alignment and backtrack of local alignment. All branch points in the computed RNA structure are found and used to divide the structure into smaller unbranched segments. Each segment is then realigned and backtracked in a normal fashion. Finally, the FOLDALIGN algorithm has also been updated with a better memory implementation and an improved energy model. With these improvements in the algorithm, the FOLDALIGN software package provides the molecular biologist with an efficient and user-friendly tool for searching for new ncRNAs. The software package is available for download at http://foldalign.ku.dk.

  20. Further investigations of the W-test for pairwise epistasis testing [version 1; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Richard Howey

    2017-07-01

    Full Text Available Background: In a recent paper, a novel W-test for pairwise epistasis testing was proposed that appeared, in computer simulations, to have higher power than competing alternatives. Application to genome-wide bipolar data detected significant epistasis between SNPs in genes of relevant biological function. Network analysis indicated that the implicated genes formed two separate interaction networks, each containing genes highly related to autism and neurodegenerative disorders. Methods: Here we investigate further the properties and performance of the W-test via theoretical evaluation, computer simulations and application to real data. Results: We demonstrate that, for common variants, the W-test is closely related to several existing tests of association allowing for interaction, including logistic regression on 8 degrees of freedom, although logistic regression can show inflated type I error for low minor allele frequencies,  whereas the W-test shows good/conservative type I error control. Although in some situations the W-test can show higher power, logistic regression is not limited to tests on 8 degrees of freedom but can instead be taylored to impose greater structure on the assumed alternative hypothesis, offering a power advantage when the imposed structure matches the true structure. Conclusions: The W-test is a potentially useful method for testing for association - without necessarily implying interaction - between genetic variants disease, particularly when one or more of the genetic variants are rare. For common variants, the advantages of the W-test are less clear, and, indeed, there are situations where existing methods perform better. In our investigations, we further uncover a number of problems with the practical implementation and application of the W-test (to bipolar disorder previously described, apparently due to inadequate use of standard data quality-control procedures. This observation leads us to urge caution in

  1. Heisenberg coupling constant predicted for molecular magnets with pairwise spin-contamination correction

    Energy Technology Data Exchange (ETDEWEB)

    Masunov, Artëm E., E-mail: amasunov@ucf.edu [NanoScience Technology Center, Department of Chemistry, and Department of Physics, University of Central Florida, Orlando, FL 32826 (United States); Photochemistry Center RAS, ul. Novatorov 7a, Moscow 119421 (Russian Federation); Gangopadhyay, Shruba [Department of Physics, University of California, Davis, CA 95616 (United States); IBM Almaden Research Center, 650 Harry Road, San Jose, CA 95120 (United States)

    2015-12-15

    New method to eliminate the spin-contamination in broken symmetry density functional theory (BS DFT) calculations is introduced. Unlike conventional spin-purification correction, this method is based on canonical Natural Orbitals (NO) for each high/low spin coupled electron pair. We derive an expression to extract the energy of the pure singlet state given in terms of energy of BS DFT solution, the occupation number of the bonding NO, and the energy of the higher spin state built on these bonding and antibonding NOs (not self-consistent Kohn–Sham orbitals of the high spin state). Compared to the other spin-contamination correction schemes, spin-correction is applied to each correlated electron pair individually. We investigate two binuclear Mn(IV) molecular magnets using this pairwise correction. While one of the molecules is described by magnetic orbitals strongly localized on the metal centers, and spin gap is accurately predicted by Noodleman and Yamaguchi schemes, for the other one the gap is predicted poorly by these schemes due to strong delocalization of the magnetic orbitals onto the ligands. We show our new correction to yield more accurate results in both cases. - Highlights: • Magnetic orbitails obtained for high and low spin states are not related. • Spin-purification correction becomes inaccurate for delocalized magnetic orbitals. • We use the natural orbitals of the broken symmetry state to build high spin state. • This new correction is made separately for each electron pair. • Our spin-purification correction is more accurate for delocalised magnetic orbitals.

  2. A discrete model of Ostwald ripening based on multiple pairwise interactions

    Science.gov (United States)

    Di Nunzio, Paolo Emilio

    2018-06-01

    A discrete multi-particle model of Ostwald ripening based on direct pairwise interactions is developed for particles with incoherent interfaces as an alternative to the classical LSW mean field theory. The rate of matter exchange depends on the average surface-to-surface interparticle distance, a characteristic feature of the system which naturally incorporates the effect of volume fraction of second phase. The multi-particle diffusion is described through the definition of an interaction volume containing all the particles involved in the exchange of solute. At small volume fractions this is proportional to the size of the central particle, at higher volume fractions it gradually reduces as a consequence of diffusion screening described on a geometrical basis. The topological noise present in real systems is also included. For volume fractions below about 0.1 the model predicts broad and right-skewed stationary size distributions resembling a lognormal function. Above this value, a transition to sharper, more symmetrical but still right-skewed shapes occurs. An excellent agreement with experiments is obtained for 3D particle size distributions of solid-solid and solid-liquid systems with volume fraction 0.07, 0.30, 0.52 and 0.74. The kinetic constant of the model depends on the cube root of volume fraction up to about 0.1, then increases rapidly with an upward concavity. It is in good agreement with the available literature data on solid-liquid mixtures in the volume fraction range from 0.20 to about 0.75.

  3. Pairwise additivity in the nuclear magnetic resonance interactions of atomic xenon.

    Science.gov (United States)

    Hanni, Matti; Lantto, Perttu; Vaara, Juha

    2009-04-14

    Nuclear magnetic resonance (NMR) of atomic (129/131)Xe is used as a versatile probe of the structure and dynamics of various host materials, due to the sensitivity of the Xe NMR parameters to intermolecular interactions. The principles governing this sensitivity can be investigated using the prototypic system of interacting Xe atoms. In the pairwise additive approximation (PAA), the binary NMR chemical shift, nuclear quadrupole coupling (NQC), and spin-rotation (SR) curves for the xenon dimer are utilized for fast and efficient evaluation of the corresponding NMR tensors in small xenon clusters Xe(n) (n = 2-12). If accurate, the preparametrized PAA enables the analysis of the NMR properties of xenon clusters, condensed xenon phases, and xenon gas without having to resort to electronic structure calculations of instantaneous configurations for n > 2. The binary parameters for Xe(2) at different internuclear distances were obtained at the nonrelativistic Hartree-Fock level of theory. Quantum-chemical (QC) calculations at the corresponding level were used to obtain the NMR parameters of the Xe(n) (n = 2-12) clusters at the equilibrium geometries. Comparison of PAA and QC data indicates that the direct use of the binary property curves of Xe(2) can be expected to be well-suited for the analysis of Xe NMR in the gaseous phase dominated by binary collisions. For use in condensed phases where many-body effects should be considered, effective binary property functions were fitted using the principal components of QC tensors from Xe(n) clusters. Particularly, the chemical shift in Xe(n) is strikingly well-described by the effective PAA. The coordination number Z of the Xe site is found to be the most important factor determining the chemical shift, with the largest shifts being found for high-symmetry sites with the largest Z. This is rationalized in terms of the density of virtual electronic states available for response to magnetic perturbations.

  4. The Little Ice Age was 1.0-1.5 °C cooler than current warm period according to LOD and NAO

    Science.gov (United States)

    Mazzarella, Adriano; Scafetta, Nicola

    2018-02-01

    We study the yearly values of the length of day (LOD, 1623-2016) and its link to the zonal index (ZI, 1873-2003), the Northern Atlantic oscillation index (NAO, 1659-2000) and the global sea surface temperature (SST, 1850-2016). LOD is herein assumed to be mostly the result of the overall circulations occurring within the ocean-atmospheric system. We find that LOD is negatively correlated with the global SST and with both the integral function of ZI and NAO, which are labeled as IZI and INAO. A first result is that LOD must be driven by a climatic change induced by an external (e.g. solar/astronomical) forcing since internal variability alone would have likely induced a positive correlation among the same variables because of the conservation of the Earth's angular momentum. A second result is that the high correlation among the variables implies that the LOD and INAO records can be adopted as global proxies to reconstruct past climate change. Tentative global SST reconstructions since the seventeenth century suggest that around 1700, that is during the coolest period of the Little Ice Age (LIA), SST could have been about 1.0-1.5 °C cooler than the 1950-1980 period. This estimated LIA cooling is greater than what some multiproxy global climate reconstructions suggested, but it is in good agreement with other more recent climate reconstructions including those based on borehole temperature data.

  5. How fast can we learn maximum entropy models of neural populations?

    Energy Technology Data Exchange (ETDEWEB)

    Ganmor, Elad; Schneidman, Elad [Department of Neuroscience, Weizmann Institute of Science, Rehovot 76100 (Israel); Segev, Ronen, E-mail: elad.ganmor@weizmann.ac.i, E-mail: elad.schneidman@weizmann.ac.i [Department of Life Sciences and Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer-Sheva 84105 (Israel)

    2009-12-01

    Most of our knowledge about how the brain encodes information comes from recordings of single neurons. However, computations in the brain are carried out by large groups of neurons. Modelling the joint activity of many interacting elements is computationally hard because of the large number of possible activity patterns and limited experimental data. Recently it was shown in several different neural systems that maximum entropy pairwise models, which rely only on firing rates and pairwise correlations of neurons, are excellent models for the distribution of activity patterns of neural populations, and in particular, their responses to natural stimuli. Using simultaneous recordings of large groups of neurons in the vertebrate retina responding to naturalistic stimuli, we show here that the relevant statistics required for finding the pairwise model can be accurately estimated within seconds. Furthermore, while higher order statistics may, in theory, improve model accuracy, they are, in practice, harmful for times of up to 20 minutes due to sampling noise. Finally, we demonstrate that trading accuracy for entropy may actually improve model performance when data is limited, and suggest an optimization method that automatically adjusts model constraints in order to achieve good performance.

  6. How fast can we learn maximum entropy models of neural populations?

    International Nuclear Information System (INIS)

    Ganmor, Elad; Schneidman, Elad; Segev, Ronen

    2009-01-01

    Most of our knowledge about how the brain encodes information comes from recordings of single neurons. However, computations in the brain are carried out by large groups of neurons. Modelling the joint activity of many interacting elements is computationally hard because of the large number of possible activity patterns and limited experimental data. Recently it was shown in several different neural systems that maximum entropy pairwise models, which rely only on firing rates and pairwise correlations of neurons, are excellent models for the distribution of activity patterns of neural populations, and in particular, their responses to natural stimuli. Using simultaneous recordings of large groups of neurons in the vertebrate retina responding to naturalistic stimuli, we show here that the relevant statistics required for finding the pairwise model can be accurately estimated within seconds. Furthermore, while higher order statistics may, in theory, improve model accuracy, they are, in practice, harmful for times of up to 20 minutes due to sampling noise. Finally, we demonstrate that trading accuracy for entropy may actually improve model performance when data is limited, and suggest an optimization method that automatically adjusts model constraints in order to achieve good performance.

  7. Assessing the effect of the relative atmospheric angular momentum (AAM) on length-of-day (LOD) variations under climate warming

    Science.gov (United States)

    Lehmann, E.; Hansen, F.; Ulbrich, U.; Nevir, P.; Leckebusch, G. C.

    2009-04-01

    While most studies on model-projected future climate warming discuss climatological quantities, this study investigates the response of the relative atmospheric angular momentum (AAM) to climate warming for the 21th century and discusses its possible effects on future length-of-day variations. Following the derivation of the dynamic relation between atmosphere and solid earth by Barnes et al. (Proc. Roy. Soc., 1985) this study relates the axial atmospheric excitation function X3 to changes in length-of-day that are proportional to variations in zonal winds. On interannual time scales changes in the relative AAM (ERA40 reanalyses) are well correlated with observed length-of-day (LOD, IERS EOP CO4) variability (r=0.75). The El Niño-Southern Oscillation (ENSO) is a prominent coupled ocean-atmosphere phenomenon to cause global climate variability on interannual time scales. Correspondingly, changes in observed LOD relate to ENSO due to observed strong wind anomalies. This study investigates the varying effect of AAM anomalies on observed LOD by relating AAM to variations to ENSO teleconnections (sea surface temperatures, SSTs) and the Pacific North America (PNA) oscillation for the 20th and 21st century. The differently strong effect of strong El Niño events (explained variance 71%-98%) on present time (1962-2000) observed LOD-AAM relation can be associated to variations in location and strength of jet streams in the upper troposphere. Correspondingly, the relation between AAM and SSTs in the NIÑO 3.4 region also varies between explained variances of 15% to 73%. Recent coupled ocean-atmosphere projections on future climate warming suggest changes in frequency and amplitude of ENSO events. Since changes in the relative AAM indicate shifts in large-scale atmospheric circulation patterns due to climate change, AAM - ENSO relations are assessed in coupled atmosphere-ocean (ECHAM5-OM1) climate warming projections (A1B) for the 21st century. A strong rise (+31%) in

  8. Historical demography of common carp estimated from individuals collected from various parts of the world using the pairwise sequentially markovian coalescent approach.

    Science.gov (United States)

    Yuan, Zihao; Huang, Wei; Liu, Shikai; Xu, Peng; Dunham, Rex; Liu, Zhanjiang

    2018-04-01

    The inference of historical demography of a species is helpful for understanding species' differentiation and its population dynamics. However, such inference has been previously difficult due to the lack of proper analytical methods and availability of genetic data. A recently developed method called Pairwise Sequentially Markovian Coalescent (PSMC) offers the capability for estimation of the trajectories of historical populations over considerable time periods using genomic sequences. In this study, we applied this approach to infer the historical demography of the common carp using samples collected from Europe, Asia and the Americas. Comparison between Asian and European common carp populations showed that the last glacial period starting 100 ka BP likely caused a significant decline in population size of the wild common carp in Europe, while it did not have much of an impact on its counterparts in Asia. This was probably caused by differences in glacial activities in East Asia and Europe, and suggesting a separation of the European and Asian clades before the last glacial maximum. The North American clade which is an invasive population shared a similar demographic history as those from Europe, consistent with the idea that the North American common carp probably had European ancestral origins. Our analysis represents the first reconstruction of the historical population demography of the common carp, which is important to elucidate the separation of European and Asian common carp clades during the Quaternary glaciation, as well as the dispersal of common carp across the world.

  9. Pair-Wise and Many-Body Dispersive Interactions Coupled to an Optimally Tuned Range-Separated Hybrid Functional.

    Science.gov (United States)

    Agrawal, Piyush; Tkatchenko, Alexandre; Kronik, Leeor

    2013-08-13

    We propose a nonempirical, pair-wise or many-body dispersion-corrected, optimally tuned range-separated hybrid functional. This functional retains the advantages of the optimal-tuning approach in the prediction of the electronic structure. At the same time, it gains accuracy in the prediction of binding energies for dispersively bound systems, as demonstrated on the S22 and S66 benchmark sets of weakly bound dimers.

  10. Combinación de Valores de Longitud del Día (LOD) según ventanas de frecuencia

    Science.gov (United States)

    Fernández, L. I.; Arias, E. F.; Gambis, D.

    El concepto de solución combinada se sustenta en el hecho de que las diferentes series temporales de datos derivadas a partir de distintas técnicas de la Geodesia Espacial son muy disimiles entre si. Las principales diferencias, fácilmente detectables, entre las distintas series son: diferente intervalo de muestreo, extensión temporal y calidad. Los datos cubren un período reciente de 27 meses (julio 96-oct. 98). Se utilizaron estimaciones de la longitud del día (LOD) originadas en 10 centros operativos del IERS (International Earth Rotation Service) a partir de las técnicas GPS (Global Positioning System) y SLR (Satellite Laser Ranging). La serie temporal combinada así obtenida se comparó con la solución EOP (Parámetros de la Orientación Terrestre) combinada multi-técnica derivada por el IERS (C04). El comportamiento del ruido en LOD para todas las técnicas mostró ser dependiente de la frecuencia (Vondrak, 1998). Por esto, las series dato se dividieron en ventanas de frecuencia, luego de haberles removido bies y tendencias. Luego, se asignaron diferentes factores de peso a cada ventana discriminando por técnicas. Finalmente estas soluciones parcialmente combinadas se mezclaron para obtener la solución combinada final. Sabemos que la mejor solución combinada tendrá una precisión menor que la precisión de las series temporales de datos que la originaron. Aun así, la importancia de una serie combinada confiable de EOP, esto es, de una precisión aceptable y libre de sistematismos evidentes, radica en la necesidad de una base de datos EOP de referencia para el estudio de fenómenos geofísicos que motivan variaciones en la rotación terrestre.

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

    Energy Technology Data Exchange (ETDEWEB)

    Bernardis, F. De; Vavagiakis, E.M.; Niemack, M.D.; Gallardo, P.A. [Department of Physics, Cornell University, Ithaca, NY 14853 (United States); Aiola, S. [Department of Physics and Astronomy, University of Pittsburgh, and Pittsburgh Particle Physics, Astrophysics, and Cosmology Center, 3941 O' Hara Street, Pittsburgh, PA 15260 (United States); Battaglia, N. [Department of Astrophysical Sciences, Peyton Hall, Princeton University, Princeton, NJ 08544 (United States); Beall, J.; Becker, D.T.; Cho, H.; Fox, A. [National Institute of Standards and Technology, Boulder, CO 80305 (United States); Bond, J.R. [CITA, University of Toronto, 60 St. George St., Toronto, ON M5S 3H8 (Canada); Calabrese, E.; Dunkley, J. [Sub-Department of Astrophysics, University of Oxford, Keble Road, Oxford, OX1 3RH (United Kingdom); Coughlin, K.; Datta, R. [Department of Physics, University of Michigan Ann Arbor, MI 48109 (United States); Devlin, M. [Department of Physics and Astronomy, University of Pennsylvania, 209 South 33rd Street, Philadelphia, PA 19104 (United States); Dunner, R. [Instituto de Astrofísica and Centro de Astro-Ingeniería, Facultad de Física, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, 7820436 Macul, Santiago (Chile); Ferraro, S. [Miller Institute for Basic Research in Science, University of California, Berkeley, CA 94720 (United States); Halpern, M. [University of British Columbia, Department of Physics and Astronomy, 6224 Agricultural Road, Vancouver BC V6T 1Z1 (Canada); Hand, N., E-mail: fdeberna@gmail.com [Astronomy Department, University of California, Berkeley, CA 94720 (United States); and others

    2017-03-01

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

  12. Probing dark energy models with extreme pairwise velocities of galaxy clusters from the DEUS-FUR simulations

    Science.gov (United States)

    Bouillot, Vincent R.; Alimi, Jean-Michel; Corasaniti, Pier-Stefano; Rasera, Yann

    2015-06-01

    Observations of colliding galaxy clusters with high relative velocity probe the tail of the halo pairwise velocity distribution with the potential of providing a powerful test of cosmology. As an example it has been argued that the discovery of the Bullet Cluster challenges standard Λ cold dark matter (ΛCDM) model predictions. Halo catalogues from N-body simulations have been used to estimate the probability of Bullet-like clusters. However, due to simulation volume effects previous studies had to rely on a Gaussian extrapolation of the pairwise velocity distribution to high velocities. Here, we perform a detail analysis using the halo catalogues from the Dark Energy Universe Simulation Full Universe Runs (DEUS-FUR), which enables us to resolve the high-velocity tail of the distribution and study its dependence on the halo mass definition, redshift and cosmology. Building upon these results, we estimate the probability of Bullet-like systems in the framework of Extreme Value Statistics. We show that the tail of extreme pairwise velocities significantly deviates from that of a Gaussian, moreover it carries an imprint of the underlying cosmology. We find the Bullet Cluster probability to be two orders of magnitude larger than previous estimates, thus easing the tension with the ΛCDM model. Finally, the comparison of the inferred probabilities for the different DEUS-FUR cosmologies suggests that observations of extreme interacting clusters can provide constraints on dark energy models complementary to standard cosmological tests.

  13. Using Parameters of Dynamic Pulse Function for 3d Modeling in LOD3 Based on Random Textures

    Science.gov (United States)

    Alizadehashrafi, B.

    2015-12-01

    The pulse function (PF) is a technique based on procedural preprocessing system to generate a computerized virtual photo of the façade with in a fixed size square(Alizadehashrafi et al., 2009, Musliman et al., 2010). Dynamic Pulse Function (DPF) is an enhanced version of PF which can create the final photo, proportional to real geometry. This can avoid distortion while projecting the computerized photo on the generated 3D model(Alizadehashrafi and Rahman, 2013). The challenging issue that might be handled for having 3D model in LoD3 rather than LOD2, is the final aim that have been achieved in this paper. In the technique based DPF the geometries of the windows and doors are saved in an XML file schema which does not have any connections with the 3D model in LoD2 and CityGML format. In this research the parameters of Dynamic Pulse Functions are utilized via Ruby programming language in SketchUp Trimble to generate (exact position and deepness) the windows and doors automatically in LoD3 based on the same concept of DPF. The advantage of this technique is automatic generation of huge number of similar geometries e.g. windows by utilizing parameters of DPF along with defining entities and window layers. In case of converting the SKP file to CityGML via FME software or CityGML plugins the 3D model contains the semantic database about the entities and window layers which can connect the CityGML to MySQL(Alizadehashrafi and Baig, 2014). The concept behind DPF, is to use logical operations to project the texture on the background image which is dynamically proportional to real geometry. The process of projection is based on two vertical and horizontal dynamic pulses starting from upper-left corner of the background wall in down and right directions respectively based on image coordinate system. The logical one/zero on the intersections of two vertical and horizontal dynamic pulses projects/does not project the texture on the background image. It is possible to define

  14. High-throughput detection of prostate cancer in histological sections using probabilistic pairwise Markov models.

    Science.gov (United States)

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

    2010-08-01

    In this paper we present a high-throughput system for detecting regions of carcinoma of the prostate (CaP) in HSs from radical prostatectomies (RPs) using probabilistic pairwise Markov models (PPMMs), a novel type of Markov random field (MRF). At diagnostic resolution a digitized HS can contain 80Kx70K pixels - far too many for current automated Gleason grading algorithms to process. However, grading can be separated into two distinct steps: (1) detecting cancerous regions and (2) then grading these regions. The detection step does not require diagnostic resolution and can be performed much more quickly. Thus, we introduce a CaP detection system capable of analyzing an entire digitized whole-mount HS (2x1.75cm(2)) in under three minutes (on a desktop computer) while achieving a CaP detection sensitivity and specificity of 0.87 and 0.90, respectively. We obtain this high-throughput by tailoring the system to analyze the HSs at low resolution (8microm per pixel). This motivates the following algorithm: (Step 1) glands are segmented, (Step 2) the segmented glands are classified as malignant or benign, and (Step 3) the malignant glands are consolidated into continuous regions. The classification of individual glands leverages two features: gland size and the tendency for proximate glands to share the same class. The latter feature describes a spatial dependency which we model using a Markov prior. Typically, Markov priors are expressed as the product of potential functions. Unfortunately, potential functions are mathematical abstractions, and constructing priors through their selection becomes an ad hoc procedure, resulting in simplistic models such as the Potts. Addressing this problem, we introduce PPMMs which formulate priors in terms of probability density functions, allowing the creation of more sophisticated models. To demonstrate the efficacy of our CaP detection system and assess the advantages of using a PPMM prior instead of the Potts, we alternately

  15. Pairwise protein expression classifier for candidate biomarker discovery for early detection of human disease prognosis

    Directory of Open Access Journals (Sweden)

    Kaur Parminder

    2012-08-01

    spectrometry data from “bottom up” proteomics methods, functionally related proteins/peptide pairs exhibiting co-ordinated changes expression profile are discovered, which represent a signature for patients progressing to various disease conditions. The method has been tested against clinical data from patients progressing to idiopthatic pneumonia syndrome (IPS following a bone marrow transplant. The data indicates that patients with improper regulation in the concentration of specific acute phase response proteins at the time of bone marrow transplant are highly likely to develop IPS within few weeks. The results lead to a specific set of protein pairs that can be efficiently verified by investigating the pairwise abundance change in independent cohorts using ELISA or targeted mass spectrometry techniques. This generalized classifier can be extended to other clinical problems in a variety of contexts.

  16. Stimulus-dependent maximum entropy models of neural population codes.

    Directory of Open Access Journals (Sweden)

    Einat Granot-Atedgi

    Full Text Available Neural populations encode information about their stimulus in a collective fashion, by joint activity patterns of spiking and silence. A full account of this mapping from stimulus to neural activity is given by the conditional probability distribution over neural codewords given the sensory input. For large populations, direct sampling of these distributions is impossible, and so we must rely on constructing appropriate models. We show here that in a population of 100 retinal ganglion cells in the salamander retina responding to temporal white-noise stimuli, dependencies between cells play an important encoding role. We introduce the stimulus-dependent maximum entropy (SDME model-a minimal extension of the canonical linear-nonlinear model of a single neuron, to a pairwise-coupled neural population. We find that the SDME model gives a more accurate account of single cell responses and in particular significantly outperforms uncoupled models in reproducing the distributions of population codewords emitted in response to a stimulus. We show how the SDME model, in conjunction with static maximum entropy models of population vocabulary, can be used to estimate information-theoretic quantities like average surprise and information transmission in a neural population.

  17. Determination of Oversulphated Chondroitin Sulphate and Dermatan Sulphate in unfractionated heparin by (1)H-NMR - Collaborative study for quantification and analytical determination of LoD.

    Science.gov (United States)

    McEwen, I; Mulloy, B; Hellwig, E; Kozerski, L; Beyer, T; Holzgrabe, U; Wanko, R; Spieser, J-M; Rodomonte, A

    2008-12-01

    Oversulphated Chondroitin Sulphate (OSCS) and Dermatan Sulphate (DS) in unfractionated heparins can be identified by nuclear magnetic resonance spectrometry (NMR). The limit of detection (LoD) of OSCS is 0.1% relative to the heparin content. This LoD is obtained at a signal-to-noise ratio (S/N) of 2000:1 of the heparin methyl signal. Quantification is best obtained by comparing peak heights of the OSCS and heparin methyl signals. Reproducibility of less than 10% relative standard deviation (RSD) has been obtained. The accuracy of quantification was good.

  18. Geophysical excitation of LOD/UT1 estimated from the output of the global circulation models of the atmosphere - ERA-40 reanalysis and of the ocean - OMCT

    Science.gov (United States)

    Korbacz, A.; Brzeziński, A.; Thomas, M.

    2008-04-01

    We use new estimates of the global atmospheric and oceanic angular momenta (AAM, OAM) to study the influence on LOD/UT1. The AAM series was calculated from the output fields of the atmospheric general circulation model ERA-40 reanalysis. The OAM series is an outcome of global ocean model OMCT simulation driven by global fields of the atmospheric parameters from the ERA- 40 reanalysis. The excitation data cover the period between 1963 and 2001. Our calculations concern atmospheric and oceanic effects in LOD/UT1 over the periods between 20 days and decades. Results are compared to those derived from the alternative AAM/OAM data sets.

  19. Finanční analýza sportovního střediska Loděnice Trója UK FTVS

    OpenAIRE

    Ocman, Josef

    2010-01-01

    Title: The financial analysis of sport centre Loděnice Troja FTVS UK Annotation: The main goal of the project is to detect prosperity and utilization of sport centre Loděnice Troja FTVS UK on base of evaluation of economy of the departments and his subdepartments. The goal is achived by an analyse of accouting data and with help of metod of financial analysis. . The project was firmed up on base of order of management FTVS UK. Keywords: Financial analysis, municipal firm, ratio, calculation 3

  20. Living network meta-analysis compared with pairwise meta-analysis in comparative effectiveness research: empirical study.

    Science.gov (United States)

    Nikolakopoulou, Adriani; Mavridis, Dimitris; Furukawa, Toshi A; Cipriani, Andrea; Tricco, Andrea C; Straus, Sharon E; Siontis, George C M; Egger, Matthias; Salanti, Georgia

    2018-02-28

    To examine whether the continuous updating of networks of prospectively planned randomised controlled trials (RCTs) ("living" network meta-analysis) provides strong evidence against the null hypothesis in comparative effectiveness of medical interventions earlier than the updating of conventional, pairwise meta-analysis. Empirical study of the accumulating evidence about the comparative effectiveness of clinical interventions. Database of network meta-analyses of RCTs identified through searches of Medline, Embase, and the Cochrane Database of Systematic Reviews until 14 April 2015. Network meta-analyses published after January 2012 that compared at least five treatments and included at least 20 RCTs. Clinical experts were asked to identify in each network the treatment comparison of greatest clinical interest. Comparisons were excluded for which direct and indirect evidence disagreed, based on side, or node, splitting test (Pmeta-analyses were performed for each selected comparison. Monitoring boundaries of statistical significance were constructed and the evidence against the null hypothesis was considered to be strong when the monitoring boundaries were crossed. A significance level was defined as α=5%, power of 90% (β=10%), and an anticipated treatment effect to detect equal to the final estimate from the network meta-analysis. The frequency and time to strong evidence was compared against the null hypothesis between pairwise and network meta-analyses. 49 comparisons of interest from 44 networks were included; most (n=39, 80%) were between active drugs, mainly from the specialties of cardiology, endocrinology, psychiatry, and rheumatology. 29 comparisons were informed by both direct and indirect evidence (59%), 13 by indirect evidence (27%), and 7 by direct evidence (14%). Both network and pairwise meta-analysis provided strong evidence against the null hypothesis for seven comparisons, but for an additional 10 comparisons only network meta-analysis provided

  1. Living network meta-analysis compared with pairwise meta-analysis in comparative effectiveness research: empirical study

    Science.gov (United States)

    Nikolakopoulou, Adriani; Mavridis, Dimitris; Furukawa, Toshi A; Cipriani, Andrea; Tricco, Andrea C; Straus, Sharon E; Siontis, George C M; Egger, Matthias

    2018-01-01

    Abstract Objective To examine whether the continuous updating of networks of prospectively planned randomised controlled trials (RCTs) (“living” network meta-analysis) provides strong evidence against the null hypothesis in comparative effectiveness of medical interventions earlier than the updating of conventional, pairwise meta-analysis. Design Empirical study of the accumulating evidence about the comparative effectiveness of clinical interventions. Data sources Database of network meta-analyses of RCTs identified through searches of Medline, Embase, and the Cochrane Database of Systematic Reviews until 14 April 2015. Eligibility criteria for study selection Network meta-analyses published after January 2012 that compared at least five treatments and included at least 20 RCTs. Clinical experts were asked to identify in each network the treatment comparison of greatest clinical interest. Comparisons were excluded for which direct and indirect evidence disagreed, based on side, or node, splitting test (Pmeta-analysis. The frequency and time to strong evidence was compared against the null hypothesis between pairwise and network meta-analyses. Results 49 comparisons of interest from 44 networks were included; most (n=39, 80%) were between active drugs, mainly from the specialties of cardiology, endocrinology, psychiatry, and rheumatology. 29 comparisons were informed by both direct and indirect evidence (59%), 13 by indirect evidence (27%), and 7 by direct evidence (14%). Both network and pairwise meta-analysis provided strong evidence against the null hypothesis for seven comparisons, but for an additional 10 comparisons only network meta-analysis provided strong evidence against the null hypothesis (P=0.002). The median time to strong evidence against the null hypothesis was 19 years with living network meta-analysis and 23 years with living pairwise meta-analysis (hazard ratio 2.78, 95% confidence interval 1.00 to 7.72, P=0.05). Studies directly comparing

  2. Maximum Entropy in Drug Discovery

    Directory of Open Access Journals (Sweden)

    Chih-Yuan Tseng

    2014-07-01

    Full Text Available Drug discovery applies multidisciplinary approaches either experimentally, computationally or both ways to identify lead compounds to treat various diseases. While conventional approaches have yielded many US Food and Drug Administration (FDA-approved drugs, researchers continue investigating and designing better approaches to increase the success rate in the discovery process. In this article, we provide an overview of the current strategies and point out where and how the method of maximum entropy has been introduced in this area. The maximum entropy principle has its root in thermodynamics, yet since Jaynes’ pioneering work in the 1950s, the maximum entropy principle has not only been used as a physics law, but also as a reasoning tool that allows us to process information in hand with the least bias. Its applicability in various disciplines has been abundantly demonstrated. We give several examples of applications of maximum entropy in different stages of drug discovery. Finally, we discuss a promising new direction in drug discovery that is likely to hinge on the ways of utilizing maximum entropy.

  3. Maximum stellar iron core mass

    Indian Academy of Sciences (India)

    60, No. 3. — journal of. March 2003 physics pp. 415–422. Maximum stellar iron core mass. F W GIACOBBE. Chicago Research Center/American Air Liquide ... iron core compression due to the weight of non-ferrous matter overlying the iron cores within large .... thermal equilibrium velocities will tend to be non-relativistic.

  4. Maximum entropy beam diagnostic tomography

    International Nuclear Information System (INIS)

    Mottershead, C.T.

    1985-01-01

    This paper reviews the formalism of maximum entropy beam diagnostic tomography as applied to the Fusion Materials Irradiation Test (FMIT) prototype accelerator. The same formalism has also been used with streak camera data to produce an ultrahigh speed movie of the beam profile of the Experimental Test Accelerator (ETA) at Livermore. 11 refs., 4 figs

  5. Maximum entropy beam diagnostic tomography

    International Nuclear Information System (INIS)

    Mottershead, C.T.

    1985-01-01

    This paper reviews the formalism of maximum entropy beam diagnostic tomography as applied to the Fusion Materials Irradiation Test (FMIT) prototype accelerator. The same formalism has also been used with streak camera data to produce an ultrahigh speed movie of the beam profile of the Experimental Test Accelerator (ETA) at Livermore

  6. A portable storage maximum thermometer

    International Nuclear Information System (INIS)

    Fayart, Gerard.

    1976-01-01

    A clinical thermometer storing the voltage corresponding to the maximum temperature in an analog memory is described. End of the measurement is shown by a lamp switch out. The measurement time is shortened by means of a low thermal inertia platinum probe. This portable thermometer is fitted with cell test and calibration system [fr

  7. Neutron spectra unfolding with maximum entropy and maximum likelihood

    International Nuclear Information System (INIS)

    Itoh, Shikoh; Tsunoda, Toshiharu

    1989-01-01

    A new unfolding theory has been established on the basis of the maximum entropy principle and the maximum likelihood method. This theory correctly embodies the Poisson statistics of neutron detection, and always brings a positive solution over the whole energy range. Moreover, the theory unifies both problems of overdetermined and of underdetermined. For the latter, the ambiguity in assigning a prior probability, i.e. the initial guess in the Bayesian sense, has become extinct by virtue of the principle. An approximate expression of the covariance matrix for the resultant spectra is also presented. An efficient algorithm to solve the nonlinear system, which appears in the present study, has been established. Results of computer simulation showed the effectiveness of the present theory. (author)

  8. Accuracy of a composite score using daily SAPS II and LOD scores for predicting hospital mortality in ICU patients hospitalized for more than 72 h.

    Science.gov (United States)

    Timsit, J F; Fosse, J P; Troché, G; De Lassence, A; Alberti, C; Garrouste-Orgeas, M; Azoulay, E; Chevret, S; Moine, P; Cohen, Y

    2001-06-01

    In most databases used to build general severity scores the median duration of intensive care unit (ICU) stay is less than 3 days. Consequently, these scores are not the most appropriate tools for measuring prognosis in studies dealing with ICU patients hospitalized for more than 72 h. To develop a new prognostic model based on a general severity score (SAPS II), an organ dysfunction score (LOD) and evolution of both scores during the first 3 days of ICU stay. Prospective multicenter study. Twenty-eight intensive care units (ICUs) in France. A training data-set was created with four ICUs during an 18-month period (893 patients). Seventy percent of the patients were medical (628) aged 66 years. The median SAPS II was 38. The ICU and hospital mortality rates were 22.7% and 30%, respectively. Forty-seven percent (420 patients) were transferred from hospital wards. In this population, the calibration (Hosmer-Lemeshow chi-square: 37.4, P = 0.001) and the discrimination [area under the ROC curves: 0.744 (95 % CI: 0.714-0.773)] of the original SAPS II were relatively poor. A validation data set was created with a random panel of 24 French ICUs during March 1999 (312 patients). The LOD and SAPS II scores were calculated during the first (SAPS1, LOD1), second (SAPS2, LOD2), and third (SAPS3, LOD3) calendar days. The LOD and SAPS scores alterations were assigned the value "1" when scores increased with time and "0" otherwise. A multivariable logistic regression model was used to select variables measured during the first three calendar days, and independently associated with death. Selected variables were: SAPS II at admission [OR: 1.04 (95 % CI: 1.027-1.053) per point], LOD [OR: 1.16 (95 % CI: 1.085-1.253) per point], transfer from ward [OR: 1.74 (95 % CI: 1.25-2.42)], as well as SAPS3-SAPS2 alterations [OR: 1.516 (95 % CI: 1.04-2.22)], and LOD3-LOD2 alterations [OR: 2.00 (95 % CI: 1.29-3.11)]. The final model has good calibration and discrimination properties in the

  9. A configuration space of homologous proteins conserving mutual information and allowing a phylogeny inference based on pair-wise Z-score probabilities

    OpenAIRE

    Maréchal Eric; Ortet Philippe; Roy Sylvaine; Bastien Olivier

    2005-01-01

    Abstract Background Popular methods to reconstruct molecular phylogenies are based on multiple sequence alignments, in which addition or removal of data may change the resulting tree topology. We have sought a representation of homologous proteins that would conserve the information of pair-wise sequence alignments, respect probabilistic properties of Z-scores (Monte Carlo methods applied to pair-wise comparisons) and be the basis for a novel method of consistent and stable phylogenetic recon...

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

    Science.gov (United States)

    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.

  11. An efficient genetic algorithm for structural RNA pairwise alignment and its application to non-coding RNA discovery in yeast

    Directory of Open Access Journals (Sweden)

    Taneda Akito

    2008-12-01

    Full Text Available Abstract Background Aligning RNA sequences with low sequence identity has been a challenging problem since such a computation essentially needs an algorithm with high complexities for taking structural conservation into account. Although many sophisticated algorithms for the purpose have been proposed to date, further improvement in efficiency is necessary to accelerate its large-scale applications including non-coding RNA (ncRNA discovery. Results We developed a new genetic algorithm, Cofolga2, for simultaneously computing pairwise RNA sequence alignment and consensus folding, and benchmarked it using BRAliBase 2.1. The benchmark results showed that our new algorithm is accurate and efficient in both time and memory usage. Then, combining with the originally trained SVM, we applied the new algorithm to novel ncRNA discovery where we compared S. cerevisiae genome with six related genomes in a pairwise manner. By focusing our search to the relatively short regions (50 bp to 2,000 bp sandwiched by conserved sequences, we successfully predict 714 intergenic and 1,311 sense or antisense ncRNA candidates, which were found in the pairwise alignments with stable consensus secondary structure and low sequence identity (≤ 50%. By comparing with the previous predictions, we found that > 92% of the candidates is novel candidates. The estimated rate of false positives in the predicted candidates is 51%. Twenty-five percent of the intergenic candidates has supports for expression in cell, i.e. their genomic positions overlap those of the experimentally determined transcripts in literature. By manual inspection of the results, moreover, we obtained four multiple alignments with low sequence identity which reveal consensus structures shared by three species/sequences. Conclusion The present method gives an efficient tool complementary to sequence-alignment-based ncRNA finders.

  12. Establishing an Appropriate Level of Detail (LoD) for a Building Information Model (BIM) - West Block, Parliament Hill, Ottawa, Canada

    Science.gov (United States)

    Fai, S.; Rafeiro, J.

    2014-05-01

    In 2011, Public Works and Government Services Canada (PWGSC) embarked on a comprehensive rehabilitation of the historically significant West Block of Canada's Parliament Hill. With over 17 thousand square meters of floor space, the West Block is one of the largest projects of its kind in the world. As part of the rehabilitation, PWGSC is working with the Carleton Immersive Media Studio (CIMS) to develop a building information model (BIM) that can serve as maintenance and life-cycle management tool once construction is completed. The scale and complexity of the model have presented many challenges. One of these challenges is determining appropriate levels of detail (LoD). While still a matter of debate in the development of international BIM standards, LoD is further complicated in the context of heritage buildings because we must reconcile the LoD of the BIM with that used in the documentation process (terrestrial laser scan and photogrammetric survey data). In this paper, we will discuss our work to date on establishing appropriate LoD within the West Block BIM that will best serve the end use. To facilitate this, we have developed a single parametric model for gothic pointed arches that can be used for over seventy-five unique window types present in the West Block. Using the AEC (CAN) BIM as a reference, we have developed a workflow to test each of these window types at three distinct levels of detail. We have found that the parametric Gothic arch significantly reduces the amount of time necessary to develop scenarios to test appropriate LoD.

  13. Clustering patterns of LOD scores for asthma-related phenotypes revealed by a genome-wide screen in 295 French EGEA families.

    Science.gov (United States)

    Bouzigon, Emmanuelle; Dizier, Marie-Hélène; Krähenbühl, Christine; Lemainque, Arnaud; Annesi-Maesano, Isabella; Betard, Christine; Bousquet, Jean; Charpin, Denis; Gormand, Frédéric; Guilloud-Bataille, Michel; Just, Jocelyne; Le Moual, Nicole; Maccario, Jean; Matran, Régis; Neukirch, Françoise; Oryszczyn, Marie-Pierre; Paty, Evelyne; Pin, Isabelle; Rosenberg-Bourgin, Myriam; Vervloet, Daniel; Kauffmann, Francine; Lathrop, Mark; Demenais, Florence

    2004-12-15

    A genome-wide scan for asthma phenotypes was conducted in the whole sample of 295 EGEA families selected through at least one asthmatic subject. In addition to asthma, seven phenotypes involved in the main asthma physiopathological pathways were considered: SPT (positive skin prick test response to at least one of 11 allergens), SPTQ score being the number of positive skin test responses to 11 allergens, Phadiatop (positive specific IgE response to a mixture of allergens), total IgE levels, eosinophils, bronchial responsiveness (BR) to methacholine challenge and %predicted FEV(1). Four regions showed evidence for linkage (PLOD scores. This analysis revealed clustering of LODs for asthma, SPT and Phadiatop on one axis and clustering of LODs for %FEV(1), BR and SPTQ on the other, while LODs for IgE and eosinophils appeared to be independent from all other LODs. These results provide new insights into the potential sharing of genetic determinants by asthma-related phenotypes.

  14. 75 FR 53730 - Culturally Significant Object Imported for Exhibition Determinations: “The Roman Mosaic from Lod...

    Science.gov (United States)

    2010-09-01

    ...Notice is hereby given of the following determinations: Pursuant to the authority vested in me by the Act of October 19, 1965 (79 Stat. 985; 22 U.S.C. 2459), Executive Order 12047 of March 27, 1978, the Foreign Affairs Reform and Restructuring Act of 1998 (112 Stat. 2681, et seq.; 22 U.S.C. 6501 note, et seq.), Delegation of Authority No. 234 of October 1, 1999, and Delegation of Authority No. 236-3 of August 28, 2000, I hereby determine that the object to be included in the exhibition ``The Roman Mosaic from Lod, Israel,'' imported from abroad for temporary exhibition within the United States, is of cultural significance. The object is imported pursuant to a loan agreement with the foreign owner or custodian. I also determine that the exhibition or display of the exhibit object at the Metropolitan Museum of Art, New York, New York, from on or about September 28, 2010, until on or about April 3, 2011, the Legion of Honor Museum, San Francisco, California, from on or about April 23, 2011, until on or about July 24, 2011, and at possible additional exhibitions or venues yet to be determined, is in the national interest. I have ordered that Public Notice of these Determinations be published in the Federal Register.

  15. On Maximum Entropy and Inference

    Directory of Open Access Journals (Sweden)

    Luigi Gresele

    2017-11-01

    Full Text Available Maximum entropy is a powerful concept that entails a sharp separation between relevant and irrelevant variables. It is typically invoked in inference, once an assumption is made on what the relevant variables are, in order to estimate a model from data, that affords predictions on all other (dependent variables. Conversely, maximum entropy can be invoked to retrieve the relevant variables (sufficient statistics directly from the data, once a model is identified by Bayesian model selection. We explore this approach in the case of spin models with interactions of arbitrary order, and we discuss how relevant interactions can be inferred. In this perspective, the dimensionality of the inference problem is not set by the number of parameters in the model, but by the frequency distribution of the data. We illustrate the method showing its ability to recover the correct model in a few prototype cases and discuss its application on a real dataset.

  16. Maximum Water Hammer Sensitivity Analysis

    OpenAIRE

    Jalil Emadi; Abbas Solemani

    2011-01-01

    Pressure waves and Water Hammer occur in a pumping system when valves are closed or opened suddenly or in the case of sudden failure of pumps. Determination of maximum water hammer is considered one of the most important technical and economical items of which engineers and designers of pumping stations and conveyance pipelines should take care. Hammer Software is a recent application used to simulate water hammer. The present study focuses on determining significance of ...

  17. Maximum Gene-Support Tree

    Directory of Open Access Journals (Sweden)

    Yunfeng Shan

    2008-01-01

    Full Text Available Genomes and genes diversify during evolution; however, it is unclear to what extent genes still retain the relationship among species. Model species for molecular phylogenetic studies include yeasts and viruses whose genomes were sequenced as well as plants that have the fossil-supported true phylogenetic trees available. In this study, we generated single gene trees of seven yeast species as well as single gene trees of nine baculovirus species using all the orthologous genes among the species compared. Homologous genes among seven known plants were used for validation of the finding. Four algorithms—maximum parsimony (MP, minimum evolution (ME, maximum likelihood (ML, and neighbor-joining (NJ—were used. Trees were reconstructed before and after weighting the DNA and protein sequence lengths among genes. Rarely a gene can always generate the “true tree” by all the four algorithms. However, the most frequent gene tree, termed “maximum gene-support tree” (MGS tree, or WMGS tree for the weighted one, in yeasts, baculoviruses, or plants was consistently found to be the “true tree” among the species. The results provide insights into the overall degree of divergence of orthologous genes of the genomes analyzed and suggest the following: 1 The true tree relationship among the species studied is still maintained by the largest group of orthologous genes; 2 There are usually more orthologous genes with higher similarities between genetically closer species than between genetically more distant ones; and 3 The maximum gene-support tree reflects the phylogenetic relationship among species in comparison.

  18. LCLS Maximum Credible Beam Power

    International Nuclear Information System (INIS)

    Clendenin, J.

    2005-01-01

    The maximum credible beam power is defined as the highest credible average beam power that the accelerator can deliver to the point in question, given the laws of physics, the beam line design, and assuming all protection devices have failed. For a new accelerator project, the official maximum credible beam power is determined by project staff in consultation with the Radiation Physics Department, after examining the arguments and evidence presented by the appropriate accelerator physicist(s) and beam line engineers. The definitive parameter becomes part of the project's safety envelope. This technical note will first review the studies that were done for the Gun Test Facility (GTF) at SSRL, where a photoinjector similar to the one proposed for the LCLS is being tested. In Section 3 the maximum charge out of the gun for a single rf pulse is calculated. In Section 4, PARMELA simulations are used to track the beam from the gun to the end of the photoinjector. Finally in Section 5 the beam through the matching section and injected into Linac-1 is discussed

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  20. Generic maximum likely scale selection

    DEFF Research Database (Denmark)

    Pedersen, Kim Steenstrup; Loog, Marco; Markussen, Bo

    2007-01-01

    in this work is on applying this selection principle under a Brownian image model. This image model provides a simple scale invariant prior for natural images and we provide illustrative examples of the behavior of our scale estimation on such images. In these illustrative examples, estimation is based......The fundamental problem of local scale selection is addressed by means of a novel principle, which is based on maximum likelihood estimation. The principle is generally applicable to a broad variety of image models and descriptors, and provides a generic scale estimation methodology. The focus...

  1. Extreme Maximum Land Surface Temperatures.

    Science.gov (United States)

    Garratt, J. R.

    1992-09-01

    There are numerous reports in the literature of observations of land surface temperatures. Some of these, almost all made in situ, reveal maximum values in the 50°-70°C range, with a few, made in desert regions, near 80°C. Consideration of a simplified form of the surface energy balance equation, utilizing likely upper values of absorbed shortwave flux (1000 W m2) and screen air temperature (55°C), that surface temperatures in the vicinity of 90°-100°C may occur for dry, darkish soils of low thermal conductivity (0.1-0.2 W m1 K1). Numerical simulations confirm this and suggest that temperature gradients in the first few centimeters of soil may reach 0.5°-1°C mm1 under these extreme conditions. The study bears upon the intrinsic interest of identifying extreme maximum temperatures and yields interesting information regarding the comfort zone of animals (including man).

  2. Analysis of pairwise correlations in multi-parametric PET/MR data for biological tumor characterization and treatment individualization strategies

    Energy Technology Data Exchange (ETDEWEB)

    Leibfarth, Sara; Moennich, David; Thorwarth, Daniela [University Hospital Tuebingen, Section for Biomedical Physics, Department of Radiation Oncology, Tuebingen (Germany); Simoncic, Urban [University Hospital Tuebingen, Section for Biomedical Physics, Department of Radiation Oncology, Tuebingen (Germany); University of Ljubljana, Faculty of Mathematics and Physics, Ljubljana (Slovenia); Jozef Stefan Institute, Ljubljana (Slovenia); Welz, Stefan; Zips, Daniel [University Hospital Tuebingen, Department of Radiation Oncology, Tuebingen (Germany); Schmidt, Holger; Schwenzer, Nina [University Hospital Tuebingen, Department of Diagnostic and Interventional Radiology, Tuebingen (Germany)

    2016-07-15

    The aim of this pilot study was to explore simultaneous functional PET/MR for biological characterization of tumors and potential future treatment adaptations. To investigate the extent of complementarity between different PET/MR-based functional datasets, a pairwise correlation analysis was performed. Functional datasets of N=15 head and neck (HN) cancer patients were evaluated. For patients of group A (N=7), combined PET/MR datasets including FDG-PET and ADC maps were available. Patients of group B (N=8) had FMISO-PET, DCE-MRI and ADC maps from combined PET/MRI, an additional dynamic FMISO-PET/CT acquired directly after FMISO tracer injection as well as an FDG-PET/CT acquired a few days earlier. From DCE-MR, parameter maps K{sup trans}, v{sub e} and v{sub p} were obtained with the extended Tofts model. Moreover, parameter maps of mean DCE enhancement, ΔS{sub DCE}, and mean FMISO signal 0-4 min p.i., anti A{sub FMISO}, were derived. Pairwise correlations were quantified using the Spearman correlation coefficient (r) on both a voxel and a regional level within the gross tumor volume. Between some pairs of functional imaging modalities moderate correlations were observed with respect to the median over all patient datasets, whereas distinct correlations were only present on an individual basis. Highest inter-modality median correlations on the voxel level were obtained for FDG/FMISO (r = 0.56), FDG/ anti A{sub FMISO} (r = 0.55), anti A{sub FMISO}/ΔS{sub DCE} (r = 0.46), and FDG/ADC (r = -0.39). Correlations on the regional level showed comparable results. The results of this study suggest that the examined functional datasets provide complementary information. However, only pairwise correlations were examined, and correlations could still exist between combinations of three or more datasets. These results might contribute to the future design of individually adapted treatment approaches based on multiparametric functional imaging.

  3. Comparison of sensitivity to artificial spectral errors and multivariate LOD in NIR spectroscopy - Determining the performance of miniaturizations on melamine in milk powder.

    Science.gov (United States)

    Henn, Raphael; Kirchler, Christian G; Grossgut, Maria-Elisabeth; Huck, Christian W

    2017-05-01

    This study compared three commercially available spectrometers - whereas two of them were miniaturized - in terms of prediction ability of melamine in milk powder (infant formula). Therefore all spectra were split into calibration- and validation-set using Kennard Stone and Duplex algorithm in comparison. For each instrument the three best performing PLSR models were constructed using SNV and Savitzky Golay derivatives. The best RMSEP values were 0.28g/100g, 0.33g/100g and 0.27g/100g for the NIRFlex N-500, the microPHAZIR and the microNIR2200 respectively. Furthermore the multivariate LOD interval [LOD min , LOD max ] was calculated for all the PLSR models unveiling significant differences among the spectrometers showing values of 0.20g/100g - 0.27g/100g, 0.28g/100g - 0.54g/100g and 0.44g/100g - 1.01g/100g for the NIRFlex N-500, the microPHAZIR and the microNIR2200 respectively. To assess the robustness of all models, artificial introduction of white noise, baseline shift, multiplicative effect, spectral shrink and stretch, stray light and spectral shift were applied. Monitoring the RMSEP as function of the perturbation gave indication of robustness of the models and helped to compare the performances of the spectrometers. Not taking the additional information from the LOD calculations into account one could falsely assume that all the spectrometers perform equally well which is not the case when the multivariate evaluation and robustness data were considered. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. System for memorizing maximum values

    Science.gov (United States)

    Bozeman, Richard J., Jr.

    1992-08-01

    The invention discloses a system capable of memorizing maximum sensed values. The system includes conditioning circuitry which receives the analog output signal from a sensor transducer. The conditioning circuitry rectifies and filters the analog signal and provides an input signal to a digital driver, which may be either linear or logarithmic. The driver converts the analog signal to discrete digital values, which in turn triggers an output signal on one of a plurality of driver output lines n. The particular output lines selected is dependent on the converted digital value. A microfuse memory device connects across the driver output lines, with n segments. Each segment is associated with one driver output line, and includes a microfuse that is blown when a signal appears on the associated driver output line.

  5. Remarks on the maximum luminosity

    Science.gov (United States)

    Cardoso, Vitor; Ikeda, Taishi; Moore, Christopher J.; Yoo, Chul-Moon

    2018-04-01

    The quest for fundamental limitations on physical processes is old and venerable. Here, we investigate the maximum possible power, or luminosity, that any event can produce. We show, via full nonlinear simulations of Einstein's equations, that there exist initial conditions which give rise to arbitrarily large luminosities. However, the requirement that there is no past horizon in the spacetime seems to limit the luminosity to below the Planck value, LP=c5/G . Numerical relativity simulations of critical collapse yield the largest luminosities observed to date, ≈ 0.2 LP . We also present an analytic solution to the Einstein equations which seems to give an unboundedly large luminosity; this will guide future numerical efforts to investigate super-Planckian luminosities.

  6. Maximum mutual information regularized classification

    KAUST Repository

    Wang, Jim Jing-Yan

    2014-09-07

    In this paper, a novel pattern classification approach is proposed by regularizing the classifier learning to maximize mutual information between the classification response and the true class label. We argue that, with the learned classifier, the uncertainty of the true class label of a data sample should be reduced by knowing its classification response as much as possible. The reduced uncertainty is measured by the mutual information between the classification response and the true class label. To this end, when learning a linear classifier, we propose to maximize the mutual information between classification responses and true class labels of training samples, besides minimizing the classification error and reducing the classifier complexity. An objective function is constructed by modeling mutual information with entropy estimation, and it is optimized by a gradient descend method in an iterative algorithm. Experiments on two real world pattern classification problems show the significant improvements achieved by maximum mutual information regularization.

  7. Scintillation counter, maximum gamma aspect

    International Nuclear Information System (INIS)

    Thumim, A.D.

    1975-01-01

    A scintillation counter, particularly for counting gamma ray photons, includes a massive lead radiation shield surrounding a sample-receiving zone. The shield is disassembleable into a plurality of segments to allow facile installation and removal of a photomultiplier tube assembly, the segments being so constructed as to prevent straight-line access of external radiation through the shield into radiation-responsive areas. Provisions are made for accurately aligning the photomultiplier tube with respect to one or more sample-transmitting bores extending through the shield to the sample receiving zone. A sample elevator, used in transporting samples into the zone, is designed to provide a maximum gamma-receiving aspect to maximize the gamma detecting efficiency. (U.S.)

  8. Maximum mutual information regularized classification

    KAUST Repository

    Wang, Jim Jing-Yan; Wang, Yi; Zhao, Shiguang; Gao, Xin

    2014-01-01

    In this paper, a novel pattern classification approach is proposed by regularizing the classifier learning to maximize mutual information between the classification response and the true class label. We argue that, with the learned classifier, the uncertainty of the true class label of a data sample should be reduced by knowing its classification response as much as possible. The reduced uncertainty is measured by the mutual information between the classification response and the true class label. To this end, when learning a linear classifier, we propose to maximize the mutual information between classification responses and true class labels of training samples, besides minimizing the classification error and reducing the classifier complexity. An objective function is constructed by modeling mutual information with entropy estimation, and it is optimized by a gradient descend method in an iterative algorithm. Experiments on two real world pattern classification problems show the significant improvements achieved by maximum mutual information regularization.

  9. Socio-economic scenario development for the assessment of climate change impacts on agricultural land use: a pairwise comparison approach

    DEFF Research Database (Denmark)

    Abildtrup, Jens; Audsley, E.; Fekete-Farkas, M.

    2006-01-01

    Assessment of the vulnerability of agriculture to climate change is strongly dependent on concurrent changes in socio-economic development pathways. This paper presents an integrated approach to the construction of socio-economic scenarios required for the analysis of climate change impacts...... on European agricultural land use. The scenarios are interpreted from the storylines described in the intergovernmental panel on climate change (IPCC) special report on emission scenarios (SRES), which ensures internal consistency between the evolution of socio-economics and climate change. A stepwise...... downscaling procedure based on expert-judgement and pairwise comparison is presented to obtain quantitative socio-economic parameters, e.g. prices and productivity estimates that are input to the ACCELERATES integrated land use model. In the first step, the global driving forces are identified and quantified...

  10. Dynamical pairwise entanglement and two-point correlations in the three-ligand spin-star structure

    Science.gov (United States)

    Motamedifar, M.

    2017-10-01

    We consider the three-ligand spin-star structure through homogeneous Heisenberg interactions (XXX-3LSSS) in the framework of dynamical pairwise entanglement. It is shown that the time evolution of the central qubit ;one-particle; state (COPS) brings about the generation of quantum W states at periodical time instants. On the contrary, W states cannot be generated from the time evolution of a ligand ;one-particle; state (LOPS). We also investigate the dynamical behavior of two-point quantum correlations as well as the expectation values of the different spin-components for each element in the XXX-3LSSS. It is found that when a W state is generated, the same value of the concurrence between any two arbitrary qubits arises from the xx and yy two-point quantum correlations. On the opposite, zz quantum correlation between any two qubits vanishes at these time instants.

  11. Pairwise NMR experiments for the determination of protein backbone dihedral angle Φ based on cross-correlated spin relaxation

    International Nuclear Information System (INIS)

    Takahashi, Hideo; Shimada, Ichio

    2007-01-01

    Novel cross-correlated spin relaxation (CCR) experiments are described, which measure pairwise CCR rates for obtaining peptide dihedral angles Φ. The experiments utilize intra-HNCA type coherence transfer to refocus 2-bond J NCα coupling evolution and generate the N (i)-C α (i) or C'(i-1)-C α (i) multiple quantum coherences which are required for measuring the desired CCR rates. The contribution from other coherences is also discussed and an appropriate setting of the evolution delays is presented. These CCR experiments were applied to 15 N- and 13 C-labeled human ubiquitin. The relevant CCR rates showed a high degree of correlation with the Φ angles observed in the X-ray structure. By utilizing these CCR experiments in combination with those previously established for obtaining dihedral angle Ψ, we can determine high resolution structures of peptides that bind weakly to large target molecules

  12. Assessment of crystalline disorder in cryo-milled samples of indomethacin using atomic pair-wise distribution functions

    DEFF Research Database (Denmark)

    Bøtker, Johan P; Karmwar, Pranav; Strachan, Clare J

    2011-01-01

    to analyse the cryo-milled samples. The high similarity between the ¿-indomethacin cryogenic ball milled samples and the crude ¿-indomethacin indicated that milled samples retained residual order of the ¿-form. The PDF analysis encompassed the capability of achieving a correlation with the physical......The aim of this study was to investigate the usefulness of the atomic pair-wise distribution function (PDF) to detect the extension of disorder/amorphousness induced into a crystalline drug using a cryo-milling technique, and to determine the optimal milling times to achieve amorphisation. The PDF...... properties determined from DSC, ss-NMR and stability experiments. Multivariate data analysis (MVDA) was used to visualize the differences in the PDF and XRPD data. The MVDA approach revealed that PDF is more efficient in assessing the introduced degree of disorder in ¿-indomethacin after cryo-milling than...

  13. Plant lock and ant key: pairwise coevolution of an exclusion filter in an ant-plant mutualism.

    Science.gov (United States)

    Brouat, C; Garcia, N; Andary, C; McKey, D

    2001-10-22

    Although observations suggest pairwise coevolution in specific ant-plant symbioses, coevolutionary processes have rarely been demonstrated. We report on, what is to the authors' knowledge, the strongest evidence yet for reciprocal adaptation of morphological characters in a species-specific ant-plant mutualism. The plant character is the prostoma, which is a small unlignified organ at the apex of the domatia in which symbiotic ants excavate an entrance hole. Each myrmecophyte in the genus Leonardoxa has evolved a prostoma with a different shape. By performing precise measurements on the prostomata of three related myrmecophytes, on their specific associated ants and on the entrance holes excavated by symbiotic ants at the prostomata, we showed that correspondence of the plant and ant traits forms a morphological and behavioural filter. We have strong evidence for coevolution between the dimensions and shape of the symbiotic ants and the prostoma in one of the three ant-Leonardoxa associations.

  14. Galaxy and Mass Assembly (GAMA): small-scale anisotropic galaxy clustering and the pairwise velocity dispersion of galaxies

    Science.gov (United States)

    Loveday, J.; Christodoulou, L.; Norberg, P.; Peacock, J. A.; Baldry, I. K.; Bland-Hawthorn, J.; Brown, M. J. I.; Colless, M.; Driver, S. P.; Holwerda, B. W.; Hopkins, A. M.; Kafle, P. R.; Liske, J.; Lopez-Sanchez, A. R.; Taylor, E. N.

    2018-03-01

    The galaxy pairwise velocity dispersion (PVD) can provide important tests of non-standard gravity and galaxy formation models. We describe measurements of the 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 PVD to smaller scales (r⊥ = 0.01 h - 1 Mpc) than previous work. The measured PVD at projected separations r⊥ ≲ 1 h - 1 Mpc increases near monotonically with increasing luminosity from σ12 ≈ 200 km s - 1 at Mr = -17 mag to σ12 ≈ 600 km s - 1 at Mr ≈ -22 mag. Analysis of the Gonzalez-Perez et al. (2014) GALFORM semi-analytic model yields no such trend of PVD with luminosity: the model overpredicts the PVD for faint galaxies. This is most likely a result of the model placing too many low-luminosity galaxies in massive haloes.

  15. AllerHunter: a SVM-pairwise system for assessment of allergenicity and allergic cross-reactivity in proteins.

    Directory of Open Access Journals (Sweden)

    Hon Cheng Muh

    Full Text Available Allergy is a major health problem in industrialized countries. The number of transgenic food crops is growing rapidly creating the need for allergenicity assessment before they are introduced into human food chain. While existing bioinformatic methods have achieved good accuracies for highly conserved sequences, the discrimination of allergens and non-allergens from allergen-like non-allergen sequences remains difficult. We describe AllerHunter, a web-based computational system for the assessment of potential allergenicity and allergic cross-reactivity in proteins. It combines an iterative pairwise sequence similarity encoding scheme with SVM as the discriminating engine. The pairwise vectorization framework allows the system to model essential features in allergens that are involved in cross-reactivity, but not limited to distinct sets of physicochemical properties. The system was rigorously trained and tested using 1,356 known allergen and 13,449 putative non-allergen sequences. Extensive testing was performed for validation of the prediction models. The system is effective for distinguishing allergens and non-allergens from allergen-like non-allergen sequences. Testing results showed that AllerHunter, with a sensitivity of 83.4% and specificity of 96.4% (accuracy = 95.3%, area under the receiver operating characteristic curve AROC = 0.928+/-0.004 and Matthew's correlation coefficient MCC = 0.738, performs significantly better than a number of existing methods using an independent dataset of 1443 protein sequences. AllerHunter is available at (http://tiger.dbs.nus.edu.sg/AllerHunter.

  16. Surface feeding and aggressive behaviour of diploid and triploid brown trout Salmo trutta during allopatric pair-wise matchings.

    Science.gov (United States)

    Preston, A C; Taylor, J F; Adams, C E; Migaud, H

    2014-09-01

    Diploid and triploid brown trout Salmo trutta were acclimated for 6 weeks on two feeding regimes (floating and sinking). Thereafter, aggression and surface feeding response were compared between pairs of all diploid, all triploid and diploid and triploid S. trutta in an experimental stream. In each pair-wise matching, fish of similar size were placed in allopatry and rank was determined by the total number of aggressive interactions recorded. Dominant individuals initiated more aggression than subordinates, spent more time defending a territory and positioned themselves closer to the surface food source (Gammarus pulex), whereas subordinates occupied the peripheries. In cross ploidy trials, diploid S. trutta were more aggressive than triploid, and dominated their sibling when placed in pair-wise matchings. Surface feeding, however, did not differ statistically between ploidy irrespective of feeding regime. Triploids adopted a sneak feeding strategy while diploids expended more time defending a territory. In addition, we also tested whether triploids exhibit a similar social dominance to diploids when placed in allopatry. Although aggression was lower in triploid pairs than in the diploid and triploid pairs, a dominance hierarchy was also observed between individuals of the same ploidy. Dominant triploid fish were more aggressive and consumed more feed items than subordinate individuals. Subordinate fish displayed a darker colour index than dominant fish suggesting increased stress levels. Dominant triploid fish, however, appeared to be more tolerant of subordinate individuals and did not display the same degree of invasive aggression as seen in the diploid and diploid or diploid and triploid matchings. These novel findings suggest that sterile triploid S. trutta feed similarly but are less aggressive than diploid trout. Future studies should determine the habitat choice of triploid S. trutta after release and the interaction between wild fish and triploids during

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

    Science.gov (United States)

    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

  18. Maximum entropy and Bayesian methods

    International Nuclear Information System (INIS)

    Smith, C.R.; Erickson, G.J.; Neudorfer, P.O.

    1992-01-01

    Bayesian probability theory and Maximum Entropy methods are at the core of a new view of scientific inference. These 'new' ideas, along with the revolution in computational methods afforded by modern computers allow astronomers, electrical engineers, image processors of any type, NMR chemists and physicists, and anyone at all who has to deal with incomplete and noisy data, to take advantage of methods that, in the past, have been applied only in some areas of theoretical physics. The title workshops have been the focus of a group of researchers from many different fields, and this diversity is evident in this book. There are tutorial and theoretical papers, and applications in a very wide variety of fields. Almost any instance of dealing with incomplete and noisy data can be usefully treated by these methods, and many areas of theoretical research are being enhanced by the thoughtful application of Bayes' theorem. Contributions contained in this volume present a state-of-the-art overview that will be influential and useful for many years to come

  19. Maximum entropy principal for transportation

    International Nuclear Information System (INIS)

    Bilich, F.; Da Silva, R.

    2008-01-01

    In this work we deal with modeling of the transportation phenomenon for use in the transportation planning process and policy-impact studies. The model developed is based on the dependence concept, i.e., the notion that the probability of a trip starting at origin i is dependent on the probability of a trip ending at destination j given that the factors (such as travel time, cost, etc.) which affect travel between origin i and destination j assume some specific values. The derivation of the solution of the model employs the maximum entropy principle combining a priori multinomial distribution with a trip utility concept. This model is utilized to forecast trip distributions under a variety of policy changes and scenarios. The dependence coefficients are obtained from a regression equation where the functional form is derived based on conditional probability and perception of factors from experimental psychology. The dependence coefficients encode all the information that was previously encoded in the form of constraints. In addition, the dependence coefficients encode information that cannot be expressed in the form of constraints for practical reasons, namely, computational tractability. The equivalence between the standard formulation (i.e., objective function with constraints) and the dependence formulation (i.e., without constraints) is demonstrated. The parameters of the dependence-based trip-distribution model are estimated, and the model is also validated using commercial air travel data in the U.S. In addition, policy impact analyses (such as allowance of supersonic flights inside the U.S. and user surcharge at noise-impacted airports) on air travel are performed.

  20. Last Glacial Maximum Salinity Reconstruction

    Science.gov (United States)

    Homola, K.; Spivack, A. J.

    2016-12-01

    It has been previously demonstrated that salinity can be reconstructed from sediment porewater. The goal of our study is to reconstruct high precision salinity during the Last Glacial Maximum (LGM). Salinity is usually determined at high precision via conductivity, which requires a larger volume of water than can be extracted from a sediment core, or via chloride titration, which yields lower than ideal precision. It has been demonstrated for water column samples that high precision density measurements can be used to determine salinity at the precision of a conductivity measurement using the equation of state of seawater. However, water column seawater has a relatively constant composition, in contrast to porewater, where variations from standard seawater composition occur. These deviations, which affect the equation of state, must be corrected for through precise measurements of each ion's concentration and knowledge of apparent partial molar density in seawater. We have developed a density-based method for determining porewater salinity that requires only 5 mL of sample, achieving density precisions of 10-6 g/mL. We have applied this method to porewater samples extracted from long cores collected along a N-S transect across the western North Atlantic (R/V Knorr cruise KN223). Density was determined to a precision of 2.3x10-6 g/mL, which translates to salinity uncertainty of 0.002 gms/kg if the effect of differences in composition is well constrained. Concentrations of anions (Cl-, and SO4-2) and cations (Na+, Mg+, Ca+2, and K+) were measured. To correct salinities at the precision required to unravel LGM Meridional Overturning Circulation, our ion precisions must be better than 0.1% for SO4-/Cl- and Mg+/Na+, and 0.4% for Ca+/Na+, and K+/Na+. Alkalinity, pH and Dissolved Inorganic Carbon of the porewater were determined to precisions better than 4% when ratioed to Cl-, and used to calculate HCO3-, and CO3-2. Apparent partial molar densities in seawater were

  1. Maximum Parsimony on Phylogenetic networks

    Science.gov (United States)

    2012-01-01

    Background Phylogenetic networks are generalizations of phylogenetic trees, that are used to model evolutionary events in various contexts. Several different methods and criteria have been introduced for reconstructing phylogenetic trees. Maximum Parsimony is a character-based approach that infers a phylogenetic tree by minimizing the total number of evolutionary steps required to explain a given set of data assigned on the leaves. Exact solutions for optimizing parsimony scores on phylogenetic trees have been introduced in the past. Results In this paper, we define the parsimony score on networks as the sum of the substitution costs along all the edges of the network; and show that certain well-known algorithms that calculate the optimum parsimony score on trees, such as Sankoff and Fitch algorithms extend naturally for networks, barring conflicting assignments at the reticulate vertices. We provide heuristics for finding the optimum parsimony scores on networks. Our algorithms can be applied for any cost matrix that may contain unequal substitution costs of transforming between different characters along different edges of the network. We analyzed this for experimental data on 10 leaves or fewer with at most 2 reticulations and found that for almost all networks, the bounds returned by the heuristics matched with the exhaustively determined optimum parsimony scores. Conclusion The parsimony score we define here does not directly reflect the cost of the best tree in the network that displays the evolution of the character. However, when searching for the most parsimonious network that describes a collection of characters, it becomes necessary to add additional cost considerations to prefer simpler structures, such as trees over networks. The parsimony score on a network that we describe here takes into account the substitution costs along the additional edges incident on each reticulate vertex, in addition to the substitution costs along the other edges which are

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

    International Nuclear Information System (INIS)

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

    2013-01-01

    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

  3. Evolution of biological sequences implies an extreme value distribution of type I for both global and local pairwise alignment scores.

    Science.gov (United States)

    Bastien, Olivier; Maréchal, Eric

    2008-08-07

    Confidence in pairwise alignments of biological sequences, obtained by various methods such as Blast or Smith-Waterman, is critical for automatic analyses of genomic data. Two statistical models have been proposed. In the asymptotic limit of long sequences, the Karlin-Altschul model is based on the computation of a P-value, assuming that the number of high scoring matching regions above a threshold is Poisson distributed. Alternatively, the Lipman-Pearson model is based on the computation of a Z-value from a random score distribution obtained by a Monte-Carlo simulation. Z-values allow the deduction of an upper bound of the P-value (1/Z-value2) following the TULIP theorem. Simulations of Z-value distribution is known to fit with a Gumbel law. This remarkable property was not demonstrated and had no obvious biological support. We built a model of evolution of sequences based on aging, as meant in Reliability Theory, using the fact that the amount of information shared between an initial sequence and the sequences in its lineage (i.e., mutual information in Information Theory) is a decreasing function of time. This quantity is simply measured by a sequence alignment score. In systems aging, the failure rate is related to the systems longevity. The system can be a machine with structured components, or a living entity or population. "Reliability" refers to the ability to operate properly according to a standard. Here, the "reliability" of a sequence refers to the ability to conserve a sufficient functional level at the folded and maturated protein level (positive selection pressure). Homologous sequences were considered as systems 1) having a high redundancy of information reflected by the magnitude of their alignment scores, 2) which components are the amino acids that can independently be damaged by random DNA mutations. From these assumptions, we deduced that information shared at each amino acid position evolved with a constant rate, corresponding to the

  4. Evolution of biological sequences implies an extreme value distribution of type I for both global and local pairwise alignment scores

    Directory of Open Access Journals (Sweden)

    Maréchal Eric

    2008-08-01

    Full Text Available Abstract Background Confidence in pairwise alignments of biological sequences, obtained by various methods such as Blast or Smith-Waterman, is critical for automatic analyses of genomic data. Two statistical models have been proposed. In the asymptotic limit of long sequences, the Karlin-Altschul model is based on the computation of a P-value, assuming that the number of high scoring matching regions above a threshold is Poisson distributed. Alternatively, the Lipman-Pearson model is based on the computation of a Z-value from a random score distribution obtained by a Monte-Carlo simulation. Z-values allow the deduction of an upper bound of the P-value (1/Z-value2 following the TULIP theorem. Simulations of Z-value distribution is known to fit with a Gumbel law. This remarkable property was not demonstrated and had no obvious biological support. Results We built a model of evolution of sequences based on aging, as meant in Reliability Theory, using the fact that the amount of information shared between an initial sequence and the sequences in its lineage (i.e., mutual information in Information Theory is a decreasing function of time. This quantity is simply measured by a sequence alignment score. In systems aging, the failure rate is related to the systems longevity. The system can be a machine with structured components, or a living entity or population. "Reliability" refers to the ability to operate properly according to a standard. Here, the "reliability" of a sequence refers to the ability to conserve a sufficient functional level at the folded and maturated protein level (positive selection pressure. Homologous sequences were considered as systems 1 having a high redundancy of information reflected by the magnitude of their alignment scores, 2 which components are the amino acids that can independently be damaged by random DNA mutations. From these assumptions, we deduced that information shared at each amino acid position evolved with a

  5. Two-dimensional maximum entropy image restoration

    International Nuclear Information System (INIS)

    Brolley, J.E.; Lazarus, R.B.; Suydam, B.R.; Trussell, H.J.

    1977-07-01

    An optical check problem was constructed to test P LOG P maximum entropy restoration of an extremely distorted image. Useful recovery of the original image was obtained. Comparison with maximum a posteriori restoration is made. 7 figures

  6. Optimal definition of inter-residual contact in globular proteins based on pairwise interaction energy calculations, its robustness, and applications.

    Science.gov (United States)

    Fačkovec, Boris; Vondrášek, Jiří

    2012-10-25

    Although a contact is an essential measurement for the topology as well as strength of non-covalent interactions in biomolecules and their complexes, there is no general agreement in the definition of this feature. Most of the definitions work with simple geometric criteria which do not fully reflect the energy content or ability of the biomolecular building blocks to arrange their environment. We offer a reasonable solution to this problem by distinguishing between "productive" and "non-productive" contacts based on their interaction energy strength and properties. We have proposed a method which converts the protein topology into a contact map that represents interactions with statistically significant high interaction energies. We do not prove that these contacts are exclusively stabilizing, but they represent a gateway to thermodynamically important rather than geometry-based contacts. The process is based on protein fragmentation and calculation of interaction energies using the OPLS force field and relies on pairwise additivity of amino acid interactions. Our approach integrates the treatment of different types of interactions, avoiding the problems resulting from different contributions to the overall stability and the different effect of the environment. The first applications on a set of homologous proteins have shown the usefulness of this classification for a sound estimate of protein stability.

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    Xin Yi Ng

    2015-01-01

    Full Text Available 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.

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

    Science.gov (United States)

    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.

  10. Randomized Approaches for Nearest Neighbor Search in Metric Space When Computing the Pairwise Distance Is Extremely Expensive

    Science.gov (United States)

    Wang, Lusheng; Yang, Yong; Lin, Guohui

    Finding the closest object for a query in a database is a classical problem in computer science. For some modern biological applications, computing the similarity between two objects might be very time consuming. For example, it takes a long time to compute the edit distance between two whole chromosomes and the alignment cost of two 3D protein structures. In this paper, we study the nearest neighbor search problem in metric space, where the pair-wise distance between two objects in the database is known and we want to minimize the number of distances computed on-line between the query and objects in the database in order to find the closest object. We have designed two randomized approaches for indexing metric space databases, where objects are purely described by their distances with each other. Analysis and experiments show that our approaches only need to compute O(logn) objects in order to find the closest object, where n is the total number of objects in the database.

  11. Pairwise Sequence Alignment Library

    Energy Technology Data Exchange (ETDEWEB)

    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.

  12. Receiver function estimated by maximum entropy deconvolution

    Institute of Scientific and Technical Information of China (English)

    吴庆举; 田小波; 张乃铃; 李卫平; 曾融生

    2003-01-01

    Maximum entropy deconvolution is presented to estimate receiver function, with the maximum entropy as the rule to determine auto-correlation and cross-correlation functions. The Toeplitz equation and Levinson algorithm are used to calculate the iterative formula of error-predicting filter, and receiver function is then estimated. During extrapolation, reflective coefficient is always less than 1, which keeps maximum entropy deconvolution stable. The maximum entropy of the data outside window increases the resolution of receiver function. Both synthetic and real seismograms show that maximum entropy deconvolution is an effective method to measure receiver function in time-domain.

  13. Maximum Power from a Solar Panel

    Directory of Open Access Journals (Sweden)

    Michael Miller

    2010-01-01

    Full Text Available Solar energy has become a promising alternative to conventional fossil fuel sources. Solar panels are used to collect solar radiation and convert it into electricity. One of the techniques used to maximize the effectiveness of this energy alternative is to maximize the power output of the solar collector. In this project the maximum power is calculated by determining the voltage and the current of maximum power. These quantities are determined by finding the maximum value for the equation for power using differentiation. After the maximum values are found for each time of day, each individual quantity, voltage of maximum power, current of maximum power, and maximum power is plotted as a function of the time of day.

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

    Science.gov (United States)

    Bianchi, Davide; Chiesa, Matteo; Guzzo, Luigi

    2015-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Lara-Castells, María Pilar de, E-mail: Pilar.deLara.Castells@csic.es [Instituto de Física Fundamental (CSIC), Serrano 123, E-28006 Madrid (Spain); Fernández-Perea, Ricardo [Instituto de Estructura de la Materia (CSIC), Serrano 123, E-28006 Madrid (Spain); Madzharova, Fani; Voloshina, Elena, E-mail: elena.voloshina@hu-berlin.de [Humboldt-Universität zu Berlin, Institut für Chemie, Unter den Linden 6, 10099 Berlin (Germany)

    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.

  16. Acupuncture-Related Techniques for Psoriasis: A Systematic Review with Pairwise and Network Meta-Analyses of Randomized Controlled Trials.

    Science.gov (United States)

    Yeh, Mei-Ling; Ko, Shu-Hua; Wang, Mei-Hua; Chi, Ching-Chi; Chung, Yu-Chu

    2017-12-01

    There has be a large body of evidence on the pharmacological treatments for psoriasis, but whether nonpharmacological interventions are effective in managing psoriasis remains largely unclear. This systematic review conducted pairwise and network meta-analyses to determine the effects of acupuncture-related techniques on acupoint stimulation for the treatment of psoriasis and to determine the order of effectiveness of these remedies. This study searched the following databases from inception to March 15, 2016: Medline, PubMed, Cochrane Central Register of Controlled Trials, EBSCO (including Academic Search Premier, American Doctoral Dissertations, and CINAHL), Airiti Library, and China National Knowledge Infrastructure. Randomized controlled trials (RCTs) on the effects of acupuncture-related techniques on acupoint stimulation as intervention for psoriasis were independently reviewed by two researchers. A total of 13 RCTs with 1,060 participants were included. The methodological quality of included studies was not rigorous. Acupoint stimulation, compared with nonacupoint stimulation, had a significant treatment for psoriasis. However, the most common adverse events were thirst and dry mouth. Subgroup analysis was further done to confirm that the short-term treatment effect was superior to that of the long-term effect in treating psoriasis. Network meta-analysis identified acupressure or acupoint catgut embedding, compared with medication, and had a significant effect for improving psoriasis. It was noted that acupressure was the most effective treatment. Acupuncture-related techniques could be considered as an alternative or adjuvant therapy for psoriasis in short term, especially of acupressure and acupoint catgut embedding. This study recommends further well-designed, methodologically rigorous, and more head-to-head randomized trials to explore the effects of acupuncture-related techniques for treating psoriasis.

  17. The effect of fiscal incentives on market penetration of electric vehicles: A pairwise comparison of total cost of ownership

    International Nuclear Information System (INIS)

    Lévay, Petra Zsuzsa; Drossinos, Yannis; Thiel, Christian

    2017-01-01

    An important barrier to electric vehicle (EV) sales is their high purchase price compared to internal combustion engine (ICE) vehicles. We conducted total cost of ownership (TCO) calculations to study how costs and sales of EVs relate to each other and to examine the role of fiscal incentives in reducing TCO and increasing EV sales. We composed EV-ICE vehicle pairs that allowed cross-segment and cross-country comparison in eight European countries. Actual car prices were used to calculate the incentives for each model in each country. We found a negative TCO-sales relationship that differs across car segments. Compared to their ICE vehicle pair, big EVs have lower TCO, higher sales, and seem to be less price responsive than small EVs. Three country groups can be distinguished according to the level of fiscal incentives and their impact on TCO and EV sales. In Norway, incentives led to the lowest TCO for the EVs. In the Netherlands, France, and UK the TCO of EVs is close to the TCO of the ICE pairs. In the other countries the TCO of EVs exceeds that of the ICE vehicles. We found that exemptions from flat taxes favour big EVs, while lump-sum subsidies favour small EVs. - Highlights: • Pairwise comparison of EV and ICE vehicle TCO and sales in eight European countries. • In NO, EV TCO is lower than ICE TCO; in NL, FR, and UK, EV TCO is slightly higher. • Compared to ICE vehicles, big EVs have lower TCO and higher sales than small EVs. • Exemptions from flat taxes favour big EVs, lump-sum subsidies favour small EVs. • Most popular EV models: Tesla Model S, Nissan Leaf, Mitsubishi Outlander PHEV.

  18. Maximum permissible voltage of YBCO coated conductors

    Energy Technology Data Exchange (ETDEWEB)

    Wen, J.; Lin, B.; Sheng, J.; Xu, J.; Jin, Z. [Department of Electrical Engineering, Shanghai Jiao Tong University, Shanghai (China); Hong, Z., E-mail: zhiyong.hong@sjtu.edu.cn [Department of Electrical Engineering, Shanghai Jiao Tong University, Shanghai (China); Wang, D.; Zhou, H.; Shen, X.; Shen, C. [Qingpu Power Supply Company, State Grid Shanghai Municipal Electric Power Company, Shanghai (China)

    2014-06-15

    Highlights: • We examine three kinds of tapes’ maximum permissible voltage. • We examine the relationship between quenching duration and maximum permissible voltage. • Continuous I{sub c} degradations under repetitive quenching where tapes reaching maximum permissible voltage. • The relationship between maximum permissible voltage and resistance, temperature. - Abstract: Superconducting fault current limiter (SFCL) could reduce short circuit currents in electrical power system. One of the most important thing in developing SFCL is to find out the maximum permissible voltage of each limiting element. The maximum permissible voltage is defined as the maximum voltage per unit length at which the YBCO coated conductors (CC) do not suffer from critical current (I{sub c}) degradation or burnout. In this research, the time of quenching process is changed and voltage is raised until the I{sub c} degradation or burnout happens. YBCO coated conductors test in the experiment are from American superconductor (AMSC) and Shanghai Jiao Tong University (SJTU). Along with the quenching duration increasing, the maximum permissible voltage of CC decreases. When quenching duration is 100 ms, the maximum permissible of SJTU CC, 12 mm AMSC CC and 4 mm AMSC CC are 0.72 V/cm, 0.52 V/cm and 1.2 V/cm respectively. Based on the results of samples, the whole length of CCs used in the design of a SFCL can be determined.

  19. A configuration space of homologous proteins conserving mutual information and allowing a phylogeny inference based on pair-wise Z-score probabilities.

    Science.gov (United States)

    Bastien, Olivier; Ortet, Philippe; Roy, Sylvaine; Maréchal, Eric

    2005-03-10

    Popular methods to reconstruct molecular phylogenies are based on multiple sequence alignments, in which addition or removal of data may change the resulting tree topology. We have sought a representation of homologous proteins that would conserve the information of pair-wise sequence alignments, respect probabilistic properties of Z-scores (Monte Carlo methods applied to pair-wise comparisons) and be the basis for a novel method of consistent and stable phylogenetic reconstruction. We have built up a spatial representation of protein sequences using concepts from particle physics (configuration space) and respecting a frame of constraints deduced from pair-wise alignment score properties in information theory. The obtained configuration space of homologous proteins (CSHP) allows the representation of real and shuffled sequences, and thereupon an expression of the TULIP theorem for Z-score probabilities. Based on the CSHP, we propose a phylogeny reconstruction using Z-scores. Deduced trees, called TULIP trees, are consistent with multiple-alignment based trees. Furthermore, the TULIP tree reconstruction method provides a solution for some previously reported incongruent results, such as the apicomplexan enolase phylogeny. The CSHP is a unified model that conserves mutual information between proteins in the way physical models conserve energy. Applications include the reconstruction of evolutionary consistent and robust trees, the topology of which is based on a spatial representation that is not reordered after addition or removal of sequences. The CSHP and its assigned phylogenetic topology, provide a powerful and easily updated representation for massive pair-wise genome comparisons based on Z-score computations.

  20. A configuration space of homologous proteins conserving mutual information and allowing a phylogeny inference based on pair-wise Z-score probabilities

    Directory of Open Access Journals (Sweden)

    Maréchal Eric

    2005-03-01

    Full Text Available Abstract Background Popular methods to reconstruct molecular phylogenies are based on multiple sequence alignments, in which addition or removal of data may change the resulting tree topology. We have sought a representation of homologous proteins that would conserve the information of pair-wise sequence alignments, respect probabilistic properties of Z-scores (Monte Carlo methods applied to pair-wise comparisons and be the basis for a novel method of consistent and stable phylogenetic reconstruction. Results We have built up a spatial representation of protein sequences using concepts from particle physics (configuration space and respecting a frame of constraints deduced from pair-wise alignment score properties in information theory. The obtained configuration space of homologous proteins (CSHP allows the representation of real and shuffled sequences, and thereupon an expression of the TULIP theorem for Z-score probabilities. Based on the CSHP, we propose a phylogeny reconstruction using Z-scores. Deduced trees, called TULIP trees, are consistent with multiple-alignment based trees. Furthermore, the TULIP tree reconstruction method provides a solution for some previously reported incongruent results, such as the apicomplexan enolase phylogeny. Conclusion The CSHP is a unified model that conserves mutual information between proteins in the way physical models conserve energy. Applications include the reconstruction of evolutionary consistent and robust trees, the topology of which is based on a spatial representation that is not reordered after addition or removal of sequences. The CSHP and its assigned phylogenetic topology, provide a powerful and easily updated representation for massive pair-wise genome comparisons based on Z-score computations.

  1. Ensemble survival tree models to reveal pairwise interactions of variables with time-to-events outcomes in low-dimensional setting

    Science.gov (United States)

    Dazard, Jean-Eudes; Ishwaran, Hemant; Mehlotra, Rajeev; Weinberg, Aaron; Zimmerman, Peter

    2018-01-01

    Unraveling interactions among variables such as genetic, clinical, demographic and environmental factors is essential to understand the development of common and complex diseases. To increase the power to detect such variables interactions associated with clinical time-to-events outcomes, we borrowed established concepts from random survival forest (RSF) models. We introduce a novel RSF-based pairwise interaction estimator and derive a randomization method with bootstrap confidence intervals for inferring interaction significance. Using various linear and nonlinear time-to-events survival models in simulation studies, we first show the efficiency of our approach: true pairwise interaction-effects between variables are uncovered, while they may not be accompanied with their corresponding main-effects, and may not be detected by standard semi-parametric regression modeling and test statistics used in survival analysis. Moreover, using a RSF-based cross-validation scheme for generating prediction estimators, we show that informative predictors may be inferred. We applied our approach to an HIV cohort study recording key host gene polymorphisms and their association with HIV change of tropism or AIDS progression. Altogether, this shows how linear or nonlinear pairwise statistical interactions of variables may be efficiently detected with a predictive value in observational studies with time-to-event outcomes. PMID:29453930

  2. Revealing the Maximum Strength in Nanotwinned Copper

    DEFF Research Database (Denmark)

    Lu, L.; Chen, X.; Huang, Xiaoxu

    2009-01-01

    boundary–related processes. We investigated the maximum strength of nanotwinned copper samples with different twin thicknesses. We found that the strength increases with decreasing twin thickness, reaching a maximum at 15 nanometers, followed by a softening at smaller values that is accompanied by enhanced...

  3. Modelling maximum canopy conductance and transpiration in ...

    African Journals Online (AJOL)

    There is much current interest in predicting the maximum amount of water that can be transpired by Eucalyptus trees. It is possible that industrial waste water may be applied as irrigation water to eucalypts and it is important to predict the maximum transpiration rates of these plantations in an attempt to dispose of this ...

  4. Comparison of sputum collection methods for tuberculosis diagnosis: a systematic review and pairwise and network meta-analysis.

    Science.gov (United States)

    Datta, Sumona; Shah, Lena; Gilman, Robert H; Evans, Carlton A

    2017-08-01

    The performance of laboratory tests to diagnose pulmonary tuberculosis is dependent on the quality of the sputum sample tested. The relative merits of sputum collection methods to improve tuberculosis diagnosis are poorly characterised. We therefore aimed to investigate the effects of sputum collection methods on tuberculosis diagnosis. We did a systematic review and meta-analysis to investigate whether non-invasive sputum collection methods in people aged at least 12 years improve the diagnostic performance of laboratory testing for pulmonary tuberculosis. We searched PubMed, Google Scholar, ProQuest, Web of Science, CINAHL, and Embase up to April 14, 2017, to identify relevant experimental, case-control, or cohort studies. We analysed data by pairwise meta-analyses with a random-effects model and by network meta-analysis. All diagnostic performance data were calculated at the sputum-sample level, except where authors only reported data at the individual patient-level. Heterogeneity was assessed, with potential causes identified by logistic meta-regression. We identified 23 eligible studies published between 1959 and 2017, involving 8967 participants who provided 19 252 sputum samples. Brief, on-demand spot sputum collection was the main reference standard. Pooled sputum collection increased tuberculosis diagnosis by microscopy (odds ratio [OR] 1·6, 95% CI 1·3-1·9, pmeta-analysis confirmed these findings, and revealed that both pooled and instructed spot sputum collections were similarly effective techniques for increasing the diagnostic performance of microscopy. Tuberculosis diagnoses were substantially increased by either pooled collection or by providing instruction on how to produce a sputum sample taken at any time of the day. Both interventions had a similar effect to that reported for the introduction of new, expensive laboratory tests, and therefore warrant further exploration in the drive to end the global tuberculosis epidemic. Wellcome Trust

  5. Pairwise and higher-order correlations among drug-resistance mutations in HIV-1 subtype B protease

    Directory of Open Access Journals (Sweden)

    Morozov Alexandre V

    2009-08-01

    individually smaller but may have a collective effect. Together they lead to correlations which could have an important impact on the dynamics of the evolution of cross-resistance, by allowing the virus to pass through otherwise unlikely mutational states. These findings also indicate that pairwise and possibly higher-order effects should be included in the models of protein evolution, instead of assuming that all residues mutate independently of one another.

  6. MXLKID: a maximum likelihood parameter identifier

    International Nuclear Information System (INIS)

    Gavel, D.T.

    1980-07-01

    MXLKID (MaXimum LiKelihood IDentifier) is a computer program designed to identify unknown parameters in a nonlinear dynamic system. Using noisy measurement data from the system, the maximum likelihood identifier computes a likelihood function (LF). Identification of system parameters is accomplished by maximizing the LF with respect to the parameters. The main body of this report briefly summarizes the maximum likelihood technique and gives instructions and examples for running the MXLKID program. MXLKID is implemented LRLTRAN on the CDC7600 computer at LLNL. A detailed mathematical description of the algorithm is given in the appendices. 24 figures, 6 tables

  7. Maximum neutron flux in thermal reactors

    International Nuclear Information System (INIS)

    Strugar, P.V.

    1968-12-01

    Direct approach to the problem is to calculate spatial distribution of fuel concentration if the reactor core directly using the condition of maximum neutron flux and comply with thermal limitations. This paper proved that the problem can be solved by applying the variational calculus, i.e. by using the maximum principle of Pontryagin. Mathematical model of reactor core is based on the two-group neutron diffusion theory with some simplifications which make it appropriate from maximum principle point of view. Here applied theory of maximum principle are suitable for application. The solution of optimum distribution of fuel concentration in the reactor core is obtained in explicit analytical form. The reactor critical dimensions are roots of a system of nonlinear equations and verification of optimum conditions can be done only for specific examples

  8. Maximum allowable load on wheeled mobile manipulators

    International Nuclear Information System (INIS)

    Habibnejad Korayem, M.; Ghariblu, H.

    2003-01-01

    This paper develops a computational technique for finding the maximum allowable load of mobile manipulator during a given trajectory. The maximum allowable loads which can be achieved by a mobile manipulator during a given trajectory are limited by the number of factors; probably the dynamic properties of mobile base and mounted manipulator, their actuator limitations and additional constraints applied to resolving the redundancy are the most important factors. To resolve extra D.O.F introduced by the base mobility, additional constraint functions are proposed directly in the task space of mobile manipulator. Finally, in two numerical examples involving a two-link planar manipulator mounted on a differentially driven mobile base, application of the method to determining maximum allowable load is verified. The simulation results demonstrates the maximum allowable load on a desired trajectory has not a unique value and directly depends on the additional constraint functions which applies to resolve the motion redundancy

  9. Maximum phytoplankton concentrations in the sea

    DEFF Research Database (Denmark)

    Jackson, G.A.; Kiørboe, Thomas

    2008-01-01

    A simplification of plankton dynamics using coagulation theory provides predictions of the maximum algal concentration sustainable in aquatic systems. These predictions have previously been tested successfully against results from iron fertilization experiments. We extend the test to data collect...

  10. Maximum-Likelihood Detection Of Noncoherent CPM

    Science.gov (United States)

    Divsalar, Dariush; Simon, Marvin K.

    1993-01-01

    Simplified detectors proposed for use in maximum-likelihood-sequence detection of symbols in alphabet of size M transmitted by uncoded, full-response continuous phase modulation over radio channel with additive white Gaussian noise. Structures of receivers derived from particular interpretation of maximum-likelihood metrics. Receivers include front ends, structures of which depends only on M, analogous to those in receivers of coherent CPM. Parts of receivers following front ends have structures, complexity of which would depend on N.

  11. Maximum gravitational redshift of white dwarfs

    International Nuclear Information System (INIS)

    Shapiro, S.L.; Teukolsky, S.A.

    1976-01-01

    The stability of uniformly rotating, cold white dwarfs is examined in the framework of the Parametrized Post-Newtonian (PPN) formalism of Will and Nordtvedt. The maximum central density and gravitational redshift of a white dwarf are determined as functions of five of the nine PPN parameters (γ, β, zeta 2 , zeta 3 , and zeta 4 ), the total angular momentum J, and the composition of the star. General relativity predicts that the maximum redshifts is 571 km s -1 for nonrotating carbon and helium dwarfs, but is lower for stars composed of heavier nuclei. Uniform rotation can increase the maximum redshift to 647 km s -1 for carbon stars (the neutronization limit) and to 893 km s -1 for helium stars (the uniform rotation limit). The redshift distribution of a larger sample of white dwarfs may help determine the composition of their cores

  12. A new method of linkage analysis using LOD scores for quantitative traits supports linkage of monoamine oxidase activity to D17S250 in the Collaborative Study on the Genetics of Alcoholism pedigrees.

    Science.gov (United States)

    Curtis, David; Knight, Jo; Sham, Pak C

    2005-09-01

    Although LOD score methods have been applied to diseases with complex modes of inheritance, linkage analysis of quantitative traits has tended to rely on non-parametric methods based on regression or variance components analysis. Here, we describe a new method for LOD score analysis of quantitative traits which does not require specification of a mode of inheritance. The technique is derived from the MFLINK method for dichotomous traits. A range of plausible transmission models is constructed, constrained to yield the correct population mean and variance for the trait but differing with respect to the contribution to the variance due to the locus under consideration. Maximized LOD scores under homogeneity and admixture are calculated, as is a model-free LOD score which compares the maximized likelihoods under admixture assuming linkage and no linkage. These LOD scores have known asymptotic distributions and hence can be used to provide a statistical test for linkage. The method has been implemented in a program called QMFLINK. It was applied to data sets simulated using a variety of transmission models and to a measure of monoamine oxidase activity in 105 pedigrees from the Collaborative Study on the Genetics of Alcoholism. With the simulated data, the results showed that the new method could detect linkage well if the true allele frequency for the trait was close to that specified. However, it performed poorly on models in which the true allele frequency was much rarer. For the Collaborative Study on the Genetics of Alcoholism data set only a modest overlap was observed between the results obtained from the new method and those obtained when the same data were analysed previously using regression and variance components analysis. Of interest is that D17S250 produced a maximized LOD score under homogeneity and admixture of 2.6 but did not indicate linkage using the previous methods. However, this region did produce evidence for linkage in a separate data set

  13. Maximum entropy analysis of EGRET data

    DEFF Research Database (Denmark)

    Pohl, M.; Strong, A.W.

    1997-01-01

    EGRET data are usually analysed on the basis of the Maximum-Likelihood method \\cite{ma96} in a search for point sources in excess to a model for the background radiation (e.g. \\cite{hu97}). This method depends strongly on the quality of the background model, and thus may have high systematic unce...... uncertainties in region of strong and uncertain background like the Galactic Center region. Here we show images of such regions obtained by the quantified Maximum-Entropy method. We also discuss a possible further use of MEM in the analysis of problematic regions of the sky....

  14. The Maximum Resource Bin Packing Problem

    DEFF Research Database (Denmark)

    Boyar, J.; Epstein, L.; Favrholdt, L.M.

    2006-01-01

    Usually, for bin packing problems, we try to minimize the number of bins used or in the case of the dual bin packing problem, maximize the number or total size of accepted items. This paper presents results for the opposite problems, where we would like to maximize the number of bins used...... algorithms, First-Fit-Increasing and First-Fit-Decreasing for the maximum resource variant of classical bin packing. For the on-line variant, we define maximum resource variants of classical and dual bin packing. For dual bin packing, no on-line algorithm is competitive. For classical bin packing, we find...

  15. Shower maximum detector for SDC calorimetry

    International Nuclear Information System (INIS)

    Ernwein, J.

    1994-01-01

    A prototype for the SDC end-cap (EM) calorimeter complete with a pre-shower and a shower maximum detector was tested in beams of electrons and Π's at CERN by an SDC subsystem group. The prototype was manufactured from scintillator tiles and strips read out with 1 mm diameter wave-length shifting fibers. The design and construction of the shower maximum detector is described, and results of laboratory tests on light yield and performance of the scintillator-fiber system are given. Preliminary results on energy and position measurements with the shower max detector in the test beam are shown. (authors). 4 refs., 5 figs

  16. Topics in Bayesian statistics and maximum entropy

    International Nuclear Information System (INIS)

    Mutihac, R.; Cicuttin, A.; Cerdeira, A.; Stanciulescu, C.

    1998-12-01

    Notions of Bayesian decision theory and maximum entropy methods are reviewed with particular emphasis on probabilistic inference and Bayesian modeling. The axiomatic approach is considered as the best justification of Bayesian analysis and maximum entropy principle applied in natural sciences. Particular emphasis is put on solving the inverse problem in digital image restoration and Bayesian modeling of neural networks. Further topics addressed briefly include language modeling, neutron scattering, multiuser detection and channel equalization in digital communications, genetic information, and Bayesian court decision-making. (author)

  17. Density estimation by maximum quantum entropy

    International Nuclear Information System (INIS)

    Silver, R.N.; Wallstrom, T.; Martz, H.F.

    1993-01-01

    A new Bayesian method for non-parametric density estimation is proposed, based on a mathematical analogy to quantum statistical physics. The mathematical procedure is related to maximum entropy methods for inverse problems and image reconstruction. The information divergence enforces global smoothing toward default models, convexity, positivity, extensivity and normalization. The novel feature is the replacement of classical entropy by quantum entropy, so that local smoothing is enforced by constraints on differential operators. The linear response of the estimate is proportional to the covariance. The hyperparameters are estimated by type-II maximum likelihood (evidence). The method is demonstrated on textbook data sets

  18. 3D Space Shift from CityGML LoD3-Based Multiple Building Elements to a 3D Volumetric Object

    Directory of Open Access Journals (Sweden)

    Shen Ying

    2017-01-01

    Full Text Available In contrast with photorealistic visualizations, urban landscape applications, and building information system (BIM, 3D volumetric presentations highlight specific calculations and applications of 3D building elements for 3D city planning and 3D cadastres. Knowing the precise volumetric quantities and the 3D boundary locations of 3D building spaces is a vital index which must remain constant during data processing because the values are related to space occupation, tenure, taxes, and valuation. To meet these requirements, this paper presents a five-step algorithm for performing a 3D building space shift. This algorithm is used to convert multiple building elements into a single 3D volumetric building object while maintaining the precise volume of the 3D space and without changing the 3D locations or displacing the building boundaries. As examples, this study used input data and building elements based on City Geography Markup Language (CityGML LoD3 models. This paper presents a method for 3D urban space and 3D property management with the goal of constructing a 3D volumetric object for an integral building using CityGML objects, by fusing the geometries of various building elements. The resulting objects possess true 3D geometry that can be represented by solid geometry and saved to a CityGML file for effective use in 3D urban planning and 3D cadastres.

  19. +2.71 LOD score at zero recombination is not sufficient for establishing linkage between X-linked mental retardation and X-chromosome markers

    Energy Technology Data Exchange (ETDEWEB)

    Robledo, R.; Melis, P.; Siniscalco, M. [and others

    1996-07-12

    Nonspecific X-linked mental retardation (MRX) is the denomination attributed to the familial type of mental retardation compatible with X-linked inheritance but lacking specific phenotypic manifestations. It is thus to be expected that families falling under such broad definition are genetically heterogeneous in the sense that they may be due to different types of mutations occurring, most probably, at distinct X-chromosome loci. To facilitate a genetic classification of these conditions, the Nomenclature Committee of the Eleventh Human Gene Mapping Workshop proposed to assign a unique MRX-serial number to each family where evidence of linkage with one or more X-chromosome markers had been established with a LOD score of at least +2 at zero recombination. This letter is meant to emphasize the inadequacy of this criterion for a large pedigree where the segregation of the disease has been evaluated against the haplotype constitution of the entire X-chromosome carrying the mutation in question. 12 refs., 2 figs., 1 tab.

  20. Nonsymmetric entropy and maximum nonsymmetric entropy principle

    International Nuclear Information System (INIS)

    Liu Chengshi

    2009-01-01

    Under the frame of a statistical model, the concept of nonsymmetric entropy which generalizes the concepts of Boltzmann's entropy and Shannon's entropy, is defined. Maximum nonsymmetric entropy principle is proved. Some important distribution laws such as power law, can be derived from this principle naturally. Especially, nonsymmetric entropy is more convenient than other entropy such as Tsallis's entropy in deriving power laws.

  1. Maximum speed of dewetting on a fiber

    NARCIS (Netherlands)

    Chan, Tak Shing; Gueudre, Thomas; Snoeijer, Jacobus Hendrikus

    2011-01-01

    A solid object can be coated by a nonwetting liquid since a receding contact line cannot exceed a critical speed. We theoretically investigate this forced wetting transition for axisymmetric menisci on fibers of varying radii. First, we use a matched asymptotic expansion and derive the maximum speed

  2. Maximum potential preventive effect of hip protectors

    NARCIS (Netherlands)

    van Schoor, N.M.; Smit, J.H.; Bouter, L.M.; Veenings, B.; Asma, G.B.; Lips, P.T.A.M.

    2007-01-01

    OBJECTIVES: To estimate the maximum potential preventive effect of hip protectors in older persons living in the community or homes for the elderly. DESIGN: Observational cohort study. SETTING: Emergency departments in the Netherlands. PARTICIPANTS: Hip fracture patients aged 70 and older who

  3. Maximum gain of Yagi-Uda arrays

    DEFF Research Database (Denmark)

    Bojsen, J.H.; Schjær-Jacobsen, Hans; Nilsson, E.

    1971-01-01

    Numerical optimisation techniques have been used to find the maximum gain of some specific parasitic arrays. The gain of an array of infinitely thin, equispaced dipoles loaded with arbitrary reactances has been optimised. The results show that standard travelling-wave design methods are not optimum....... Yagi–Uda arrays with equal and unequal spacing have also been optimised with experimental verification....

  4. correlation between maximum dry density and cohesion

    African Journals Online (AJOL)

    HOD

    represents maximum dry density, signifies plastic limit and is liquid limit. Researchers [6, 7] estimate compaction parameters. Aside from the correlation existing between compaction parameters and other physical quantities there are some other correlations that have been investigated by other researchers. The well-known.

  5. Weak scale from the maximum entropy principle

    Science.gov (United States)

    Hamada, Yuta; Kawai, Hikaru; Kawana, Kiyoharu

    2015-03-01

    The theory of the multiverse and wormholes suggests that the parameters of the Standard Model (SM) are fixed in such a way that the radiation of the S3 universe at the final stage S_rad becomes maximum, which we call the maximum entropy principle. Although it is difficult to confirm this principle generally, for a few parameters of the SM, we can check whether S_rad actually becomes maximum at the observed values. In this paper, we regard S_rad at the final stage as a function of the weak scale (the Higgs expectation value) vh, and show that it becomes maximum around vh = {{O}} (300 GeV) when the dimensionless couplings in the SM, i.e., the Higgs self-coupling, the gauge couplings, and the Yukawa couplings are fixed. Roughly speaking, we find that the weak scale is given by vh ˜ T_{BBN}2 / (M_{pl}ye5), where ye is the Yukawa coupling of electron, T_BBN is the temperature at which the Big Bang nucleosynthesis starts, and M_pl is the Planck mass.

  6. The maximum-entropy method in superspace

    Czech Academy of Sciences Publication Activity Database

    van Smaalen, S.; Palatinus, Lukáš; Schneider, M.

    2003-01-01

    Roč. 59, - (2003), s. 459-469 ISSN 0108-7673 Grant - others:DFG(DE) XX Institutional research plan: CEZ:AV0Z1010914 Keywords : maximum-entropy method, * aperiodic crystals * electron density Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.558, year: 2003

  7. Achieving maximum sustainable yield in mixed fisheries

    NARCIS (Netherlands)

    Ulrich, Clara; Vermard, Youen; Dolder, Paul J.; Brunel, Thomas; Jardim, Ernesto; Holmes, Steven J.; Kempf, Alexander; Mortensen, Lars O.; Poos, Jan Jaap; Rindorf, Anna

    2017-01-01

    Achieving single species maximum sustainable yield (MSY) in complex and dynamic fisheries targeting multiple species (mixed fisheries) is challenging because achieving the objective for one species may mean missing the objective for another. The North Sea mixed fisheries are a representative example

  8. 5 CFR 534.203 - Maximum stipends.

    Science.gov (United States)

    2010-01-01

    ... maximum stipend established under this section. (e) A trainee at a non-Federal hospital, clinic, or medical or dental laboratory who is assigned to a Federal hospital, clinic, or medical or dental... Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS PAY UNDER OTHER SYSTEMS Student...

  9. Minimal length, Friedmann equations and maximum density

    Energy Technology Data Exchange (ETDEWEB)

    Awad, Adel [Center for Theoretical Physics, British University of Egypt,Sherouk City 11837, P.O. Box 43 (Egypt); Department of Physics, Faculty of Science, Ain Shams University,Cairo, 11566 (Egypt); Ali, Ahmed Farag [Centre for Fundamental Physics, Zewail City of Science and Technology,Sheikh Zayed, 12588, Giza (Egypt); Department of Physics, Faculty of Science, Benha University,Benha, 13518 (Egypt)

    2014-06-16

    Inspired by Jacobson’s thermodynamic approach, Cai et al. have shown the emergence of Friedmann equations from the first law of thermodynamics. We extend Akbar-Cai derivation http://dx.doi.org/10.1103/PhysRevD.75.084003 of Friedmann equations to accommodate a general entropy-area law. Studying the resulted Friedmann equations using a specific entropy-area law, which is motivated by the generalized uncertainty principle (GUP), reveals the existence of a maximum energy density closed to Planck density. Allowing for a general continuous pressure p(ρ,a) leads to bounded curvature invariants and a general nonsingular evolution. In this case, the maximum energy density is reached in a finite time and there is no cosmological evolution beyond this point which leaves the big bang singularity inaccessible from a spacetime prospective. The existence of maximum energy density and a general nonsingular evolution is independent of the equation of state and the spacial curvature k. As an example we study the evolution of the equation of state p=ωρ through its phase-space diagram to show the existence of a maximum energy which is reachable in a finite time.

  10. Improved scFv Anti-HIV-1 p17 Binding Affinity Guided from the Theoretical Calculation of Pairwise Decomposition Energies and Computational Alanine Scanning

    Directory of Open Access Journals (Sweden)

    Panthip Tue-ngeun

    2013-01-01

    Full Text Available Computational approaches have been used to evaluate and define important residues for protein-protein interactions, especially antigen-antibody complexes. In our previous study, pairwise decomposition of residue interaction energies of single chain Fv with HIV-1 p17 epitope variants has indicated the key specific residues in the complementary determining regions (CDRs of scFv anti-p17. In this present investigation in order to determine whether a specific side chain group of residue in CDRs plays an important role in bioactivity, computational alanine scanning has been applied. Molecular dynamics simulations were done with several complexes of original scFv anti-p17 and scFv anti-p17mutants with HIV-1 p17 epitope variants with a production run up to 10 ns. With the combination of pairwise decomposition residue interaction and alanine scanning calculations, the point mutation has been initially selected at the position MET100 to improve the residue binding affinity. The calculated docking interaction energy between a single mutation from methionine to either arginine or glycine has shown the improved binding affinity, contributed from the electrostatic interaction with the negative favorably interaction energy, compared to the wild type. Theoretical calculations agreed well with the results from the peptide ELISA results.

  11. Leaf habit does not determine the investment in both physical and chemical defences and pair-wise correlations between these defensive traits.

    Science.gov (United States)

    Moreira, X; Pearse, I S

    2017-05-01

    Plant life-history strategies associated with resource acquisition and economics (e.g. leaf habit) are thought to be fundamental determinants of the traits and mechanisms that drive herbivore pressure, resource allocation to plant defensive traits, and the simultaneous expression (positive correlations) or trade-offs (negative correlations) between these defensive traits. In particular, it is expected that evergreen species - which usually grow slower and support constant herbivore pressure in comparison with deciduous species - will exhibit higher levels of both physical and chemical defences and a higher predisposition to the simultaneous expression of physical and chemical defensive traits. Here, by using a dataset which included 56 oak species (Quercus genus), we investigated whether leaf habit of plant species governs the investment in both physical and chemical defences and pair-wise correlations between these defensive traits. Our results showed that leaf habit does not determine the production of most leaf physical and chemical defences. Although evergreen oak species had higher levels of leaf toughness and specific leaf mass (physical defences) than deciduous oak species, both traits are essentially prerequisites for evergreenness. Similarly, our results also showed that leaf habit does not determine pair-wise correlations between defensive traits because most physical and chemical defensive traits were simultaneously expressed in both evergreen and deciduous oak species. Our findings indicate that leaf habit does not substantially contribute to oak species differences in plant defence investment. © 2017 German Botanical Society and The Royal Botanical Society of the Netherlands.

  12. Analyse av LOD-tiltak

    OpenAIRE

    Kunduraci, Meltem

    2016-01-01

    Endrede klimatiske forhold og større urbanisering medfører økte oversvømmelsesskader i urbane områder. Ekstreme nedbørhendelser opptrer oftere og kraftigere. Utbygging med tette flater hindrer infiltrasjon til grunnen. Den naturlige utjevningen av overvann reduseres. Dette resulterer i økende belastninger på det eksisterende avløpssystemet. Kapasiteten på avløpsnettet er mange steder overbelastet og er ikke i stand til å håndtere overvannsmengder under styrtregn. Lokal overvannsdisponering el...

  13. Maximum concentrations at work and maximum biologically tolerable concentration for working materials 1991

    International Nuclear Information System (INIS)

    1991-01-01

    The meaning of the term 'maximum concentration at work' in regard of various pollutants is discussed. Specifically, a number of dusts and smokes are dealt with. The valuation criteria for maximum biologically tolerable concentrations for working materials are indicated. The working materials in question are corcinogeneous substances or substances liable to cause allergies or mutate the genome. (VT) [de

  14. 75 FR 43840 - Inflation Adjustment of the Ordinary Maximum and Aggravated Maximum Civil Monetary Penalties for...

    Science.gov (United States)

    2010-07-27

    ...-17530; Notice No. 2] RIN 2130-ZA03 Inflation Adjustment of the Ordinary Maximum and Aggravated Maximum... remains at $250. These adjustments are required by the Federal Civil Penalties Inflation Adjustment Act [email protected] . SUPPLEMENTARY INFORMATION: The Federal Civil Penalties Inflation Adjustment Act of 1990...

  15. Zipf's law, power laws and maximum entropy

    International Nuclear Information System (INIS)

    Visser, Matt

    2013-01-01

    Zipf's law, and power laws in general, have attracted and continue to attract considerable attention in a wide variety of disciplines—from astronomy to demographics to software structure to economics to linguistics to zoology, and even warfare. A recent model of random group formation (RGF) attempts a general explanation of such phenomena based on Jaynes' notion of maximum entropy applied to a particular choice of cost function. In the present paper I argue that the specific cost function used in the RGF model is in fact unnecessarily complicated, and that power laws can be obtained in a much simpler way by applying maximum entropy ideas directly to the Shannon entropy subject only to a single constraint: that the average of the logarithm of the observable quantity is specified. (paper)

  16. Maximum-entropy description of animal movement.

    Science.gov (United States)

    Fleming, Chris H; Subaşı, Yiğit; Calabrese, Justin M

    2015-03-01

    We introduce a class of maximum-entropy states that naturally includes within it all of the major continuous-time stochastic processes that have been applied to animal movement, including Brownian motion, Ornstein-Uhlenbeck motion, integrated Ornstein-Uhlenbeck motion, a recently discovered hybrid of the previous models, and a new model that describes central-place foraging. We are also able to predict a further hierarchy of new models that will emerge as data quality improves to better resolve the underlying continuity of animal movement. Finally, we also show that Langevin equations must obey a fluctuation-dissipation theorem to generate processes that fall from this class of maximum-entropy distributions when the constraints are purely kinematic.

  17. Pareto versus lognormal: a maximum entropy test.

    Science.gov (United States)

    Bee, Marco; Riccaboni, Massimo; Schiavo, Stefano

    2011-08-01

    It is commonly found that distributions that seem to be lognormal over a broad range change to a power-law (Pareto) distribution for the last few percentiles. The distributions of many physical, natural, and social events (earthquake size, species abundance, income and wealth, as well as file, city, and firm sizes) display this structure. We present a test for the occurrence of power-law tails in statistical distributions based on maximum entropy. This methodology allows one to identify the true data-generating processes even in the case when it is neither lognormal nor Pareto. The maximum entropy approach is then compared with other widely used methods and applied to different levels of aggregation of complex systems. Our results provide support for the theory that distributions with lognormal body and Pareto tail can be generated as mixtures of lognormally distributed units.

  18. Maximum likelihood estimation for integrated diffusion processes

    DEFF Research Database (Denmark)

    Baltazar-Larios, Fernando; Sørensen, Michael

    We propose a method for obtaining maximum likelihood estimates of parameters in diffusion models when the data is a discrete time sample of the integral of the process, while no direct observations of the process itself are available. The data are, moreover, assumed to be contaminated...... EM-algorithm to obtain maximum likelihood estimates of the parameters in the diffusion model. As part of the algorithm, we use a recent simple method for approximate simulation of diffusion bridges. In simulation studies for the Ornstein-Uhlenbeck process and the CIR process the proposed method works...... by measurement errors. Integrated volatility is an example of this type of observations. Another example is ice-core data on oxygen isotopes used to investigate paleo-temperatures. The data can be viewed as incomplete observations of a model with a tractable likelihood function. Therefore we propose a simulated...

  19. A Maximum Radius for Habitable Planets.

    Science.gov (United States)

    Alibert, Yann

    2015-09-01

    We compute the maximum radius a planet can have in order to fulfill two constraints that are likely necessary conditions for habitability: 1- surface temperature and pressure compatible with the existence of liquid water, and 2- no ice layer at the bottom of a putative global ocean, that would prevent the operation of the geologic carbon cycle to operate. We demonstrate that, above a given radius, these two constraints cannot be met: in the Super-Earth mass range (1-12 Mearth), the overall maximum that a planet can have varies between 1.8 and 2.3 Rearth. This radius is reduced when considering planets with higher Fe/Si ratios, and taking into account irradiation effects on the structure of the gas envelope.

  20. Maximum parsimony on subsets of taxa.

    Science.gov (United States)

    Fischer, Mareike; Thatte, Bhalchandra D

    2009-09-21

    In this paper we investigate mathematical questions concerning the reliability (reconstruction accuracy) of Fitch's maximum parsimony algorithm for reconstructing the ancestral state given a phylogenetic tree and a character. In particular, we consider the question whether the maximum parsimony method applied to a subset of taxa can reconstruct the ancestral state of the root more accurately than when applied to all taxa, and we give an example showing that this indeed is possible. A surprising feature of our example is that ignoring a taxon closer to the root improves the reliability of the method. On the other hand, in the case of the two-state symmetric substitution model, we answer affirmatively a conjecture of Li, Steel and Zhang which states that under a molecular clock the probability that the state at a single taxon is a correct guess of the ancestral state is a lower bound on the reconstruction accuracy of Fitch's method applied to all taxa.

  1. Maximum entropy analysis of liquid diffraction data

    International Nuclear Information System (INIS)

    Root, J.H.; Egelstaff, P.A.; Nickel, B.G.

    1986-01-01

    A maximum entropy method for reducing truncation effects in the inverse Fourier transform of structure factor, S(q), to pair correlation function, g(r), is described. The advantages and limitations of the method are explored with the PY hard sphere structure factor as model input data. An example using real data on liquid chlorine, is then presented. It is seen that spurious structure is greatly reduced in comparison to traditional Fourier transform methods. (author)

  2. A Maximum Resonant Set of Polyomino Graphs

    Directory of Open Access Journals (Sweden)

    Zhang Heping

    2016-05-01

    Full Text Available A polyomino graph P is a connected finite subgraph of the infinite plane grid such that each finite face is surrounded by a regular square of side length one and each edge belongs to at least one square. A dimer covering of P corresponds to a perfect matching. Different dimer coverings can interact via an alternating cycle (or square with respect to them. A set of disjoint squares of P is a resonant set if P has a perfect matching M so that each one of those squares is M-alternating. In this paper, we show that if K is a maximum resonant set of P, then P − K has a unique perfect matching. We further prove that the maximum forcing number of a polyomino graph is equal to the cardinality of a maximum resonant set. This confirms a conjecture of Xu et al. [26]. We also show that if K is a maximal alternating set of P, then P − K has a unique perfect matching.

  3. Automatic maximum entropy spectral reconstruction in NMR

    International Nuclear Information System (INIS)

    Mobli, Mehdi; Maciejewski, Mark W.; Gryk, Michael R.; Hoch, Jeffrey C.

    2007-01-01

    Developments in superconducting magnets, cryogenic probes, isotope labeling strategies, and sophisticated pulse sequences together have enabled the application, in principle, of high-resolution NMR spectroscopy to biomolecular systems approaching 1 megadalton. In practice, however, conventional approaches to NMR that utilize the fast Fourier transform, which require data collected at uniform time intervals, result in prohibitively lengthy data collection times in order to achieve the full resolution afforded by high field magnets. A variety of approaches that involve nonuniform sampling have been proposed, each utilizing a non-Fourier method of spectrum analysis. A very general non-Fourier method that is capable of utilizing data collected using any of the proposed nonuniform sampling strategies is maximum entropy reconstruction. A limiting factor in the adoption of maximum entropy reconstruction in NMR has been the need to specify non-intuitive parameters. Here we describe a fully automated system for maximum entropy reconstruction that requires no user-specified parameters. A web-accessible script generator provides the user interface to the system

  4. maximum neutron flux at thermal nuclear reactors

    International Nuclear Information System (INIS)

    Strugar, P.

    1968-10-01

    Since actual research reactors are technically complicated and expensive facilities it is important to achieve savings by appropriate reactor lattice configurations. There is a number of papers, and practical examples of reactors with central reflector, dealing with spatial distribution of fuel elements which would result in higher neutron flux. Common disadvantage of all the solutions is that the choice of best solution is done starting from the anticipated spatial distributions of fuel elements. The weakness of these approaches is lack of defined optimization criteria. Direct approach is defined as follows: determine the spatial distribution of fuel concentration starting from the condition of maximum neutron flux by fulfilling the thermal constraints. Thus the problem of determining the maximum neutron flux is solving a variational problem which is beyond the possibilities of classical variational calculation. This variational problem has been successfully solved by applying the maximum principle of Pontrjagin. Optimum distribution of fuel concentration was obtained in explicit analytical form. Thus, spatial distribution of the neutron flux and critical dimensions of quite complex reactor system are calculated in a relatively simple way. In addition to the fact that the results are innovative this approach is interesting because of the optimization procedure itself [sr

  5. Design of chemical space networks using a Tanimoto similarity variant based upon maximum common substructures.

    Science.gov (United States)

    Zhang, Bijun; Vogt, Martin; Maggiora, Gerald M; Bajorath, Jürgen

    2015-10-01

    Chemical space networks (CSNs) have recently been introduced as an alternative to other coordinate-free and coordinate-based chemical space representations. In CSNs, nodes represent compounds and edges pairwise similarity relationships. In addition, nodes are annotated with compound property information such as biological activity. CSNs have been applied to view biologically relevant chemical space in comparison to random chemical space samples and found to display well-resolved topologies at low edge density levels. The way in which molecular similarity relationships are assessed is an important determinant of CSN topology. Previous CSN versions were based on numerical similarity functions or the assessment of substructure-based similarity. Herein, we report a new CSN design that is based upon combined numerical and substructure similarity evaluation. This has been facilitated by calculating numerical similarity values on the basis of maximum common substructures (MCSs) of compounds, leading to the introduction of MCS-based CSNs (MCS-CSNs). This CSN design combines advantages of continuous numerical similarity functions with a robust and chemically intuitive substructure-based assessment. Compared to earlier version of CSNs, MCS-CSNs are characterized by a further improved organization of local compound communities as exemplified by the delineation of drug-like subspaces in regions of biologically relevant chemical space.

  6. A pairwise unit-root-test based approach to investigating convergence of household debts in South Africa and the United States

    Directory of Open Access Journals (Sweden)

    Ntebogang Dinah Moroke

    2015-05-01

    Full Text Available The purpose of this paper was to test convergence of household debts in the United States and South Africa taking a pairwise unit root tests based approaches into account. Substantial number of studies dealt with convergence of several macroeconomic variables but to my knowledge no study considered this subject with respect to household debts of the identified countries. Quarterly data on household debts consisting of 88 observations in the South Africa and United States spanning the period 1990 to 2013 was collected from the South African and St. Louis Federal Reserve Banks. Focused on the absolute value of household debts, this study proved that South Africa is far from catching-up with the United States in terms of overcoming household debts for the selected period. The findings of this study can be used by relevant authorities to help improve ways and means of dealing with household debts South Africa

  7. A spreadsheet template compatible with Microsoft Excel and iWork Numbers that returns the simultaneous confidence intervals for all pairwise differences between multiple sample means.

    Science.gov (United States)

    Brown, Angus M

    2010-04-01

    The objective of the method described in this paper is to develop a spreadsheet template for the purpose of comparing multiple sample means. An initial analysis of variance (ANOVA) test on the data returns F--the test statistic. If F is larger than the critical F value drawn from the F distribution at the appropriate degrees of freedom, convention dictates rejection of the null hypothesis and allows subsequent multiple comparison testing to determine where the inequalities between the sample means lie. A variety of multiple comparison methods are described that return the 95% confidence intervals for differences between means using an inclusive pairwise comparison of the sample means. 2009 Elsevier Ireland Ltd. All rights reserved.

  8. Maximum entropy decomposition of quadrupole mass spectra

    International Nuclear Information System (INIS)

    Toussaint, U. von; Dose, V.; Golan, A.

    2004-01-01

    We present an information-theoretic method called generalized maximum entropy (GME) for decomposing mass spectra of gas mixtures from noisy measurements. In this GME approach to the noisy, underdetermined inverse problem, the joint entropies of concentration, cracking, and noise probabilities are maximized subject to the measured data. This provides a robust estimation for the unknown cracking patterns and the concentrations of the contributing molecules. The method is applied to mass spectroscopic data of hydrocarbons, and the estimates are compared with those received from a Bayesian approach. We show that the GME method is efficient and is computationally fast

  9. Maximum power operation of interacting molecular motors

    DEFF Research Database (Denmark)

    Golubeva, Natalia; Imparato, Alberto

    2013-01-01

    , as compared to the non-interacting system, in a wide range of biologically compatible scenarios. We furthermore consider the case where the motor-motor interaction directly affects the internal chemical cycle and investigate the effect on the system dynamics and thermodynamics.......We study the mechanical and thermodynamic properties of different traffic models for kinesin which are relevant in biological and experimental contexts. We find that motor-motor interactions play a fundamental role by enhancing the thermodynamic efficiency at maximum power of the motors...

  10. Maximum entropy method in momentum density reconstruction

    International Nuclear Information System (INIS)

    Dobrzynski, L.; Holas, A.

    1997-01-01

    The Maximum Entropy Method (MEM) is applied to the reconstruction of the 3-dimensional electron momentum density distributions observed through the set of Compton profiles measured along various crystallographic directions. It is shown that the reconstruction of electron momentum density may be reliably carried out with the aid of simple iterative algorithm suggested originally by Collins. A number of distributions has been simulated in order to check the performance of MEM. It is shown that MEM can be recommended as a model-free approach. (author). 13 refs, 1 fig

  11. On the maximum drawdown during speculative bubbles

    Science.gov (United States)

    Rotundo, Giulia; Navarra, Mauro

    2007-08-01

    A taxonomy of large financial crashes proposed in the literature locates the burst of speculative bubbles due to endogenous causes in the framework of extreme stock market crashes, defined as falls of market prices that are outlier with respect to the bulk of drawdown price movement distribution. This paper goes on deeper in the analysis providing a further characterization of the rising part of such selected bubbles through the examination of drawdown and maximum drawdown movement of indices prices. The analysis of drawdown duration is also performed and it is the core of the risk measure estimated here.

  12. Multi-Channel Maximum Likelihood Pitch Estimation

    DEFF Research Database (Denmark)

    Christensen, Mads Græsbøll

    2012-01-01

    In this paper, a method for multi-channel pitch estimation is proposed. The method is a maximum likelihood estimator and is based on a parametric model where the signals in the various channels share the same fundamental frequency but can have different amplitudes, phases, and noise characteristics....... This essentially means that the model allows for different conditions in the various channels, like different signal-to-noise ratios, microphone characteristics and reverberation. Moreover, the method does not assume that a certain array structure is used but rather relies on a more general model and is hence...

  13. Conductivity maximum in a charged colloidal suspension

    Energy Technology Data Exchange (ETDEWEB)

    Bastea, S

    2009-01-27

    Molecular dynamics simulations of a charged colloidal suspension in the salt-free regime show that the system exhibits an electrical conductivity maximum as a function of colloid charge. We attribute this behavior to two main competing effects: colloid effective charge saturation due to counterion 'condensation' and diffusion slowdown due to the relaxation effect. In agreement with previous observations, we also find that the effective transported charge is larger than the one determined by the Stern layer and suggest that it corresponds to the boundary fluid layer at the surface of the colloidal particles.

  14. Dynamical maximum entropy approach to flocking.

    Science.gov (United States)

    Cavagna, Andrea; Giardina, Irene; Ginelli, Francesco; Mora, Thierry; Piovani, Duccio; Tavarone, Raffaele; Walczak, Aleksandra M

    2014-04-01

    We derive a new method to infer from data the out-of-equilibrium alignment dynamics of collectively moving animal groups, by considering the maximum entropy model distribution consistent with temporal and spatial correlations of flight direction. When bird neighborhoods evolve rapidly, this dynamical inference correctly learns the parameters of the model, while a static one relying only on the spatial correlations fails. When neighbors change slowly and the detailed balance is satisfied, we recover the static procedure. We demonstrate the validity of the method on simulated data. The approach is applicable to other systems of active matter.

  15. Maximum Temperature Detection System for Integrated Circuits

    Science.gov (United States)

    Frankiewicz, Maciej; Kos, Andrzej

    2015-03-01

    The paper describes structure and measurement results of the system detecting present maximum temperature on the surface of an integrated circuit. The system consists of the set of proportional to absolute temperature sensors, temperature processing path and a digital part designed in VHDL. Analogue parts of the circuit where designed with full-custom technique. The system is a part of temperature-controlled oscillator circuit - a power management system based on dynamic frequency scaling method. The oscillator cooperates with microprocessor dedicated for thermal experiments. The whole system is implemented in UMC CMOS 0.18 μm (1.8 V) technology.

  16. Maximum entropy PDF projection: A review

    Science.gov (United States)

    Baggenstoss, Paul M.

    2017-06-01

    We review maximum entropy (MaxEnt) PDF projection, a method with wide potential applications in statistical inference. The method constructs a sampling distribution for a high-dimensional vector x based on knowing the sampling distribution p(z) of a lower-dimensional feature z = T (x). Under mild conditions, the distribution p(x) having highest possible entropy among all distributions consistent with p(z) may be readily found. Furthermore, the MaxEnt p(x) may be sampled, making the approach useful in Monte Carlo methods. We review the theorem and present a case study in model order selection and classification for handwritten character recognition.

  17. Multiperiod Maximum Loss is time unit invariant.

    Science.gov (United States)

    Kovacevic, Raimund M; Breuer, Thomas

    2016-01-01

    Time unit invariance is introduced as an additional requirement for multiperiod risk measures: for a constant portfolio under an i.i.d. risk factor process, the multiperiod risk should equal the one period risk of the aggregated loss, for an appropriate choice of parameters and independent of the portfolio and its distribution. Multiperiod Maximum Loss over a sequence of Kullback-Leibler balls is time unit invariant. This is also the case for the entropic risk measure. On the other hand, multiperiod Value at Risk and multiperiod Expected Shortfall are not time unit invariant.

  18. Maximum a posteriori decoder for digital communications

    Science.gov (United States)

    Altes, Richard A. (Inventor)

    1997-01-01

    A system and method for decoding by identification of the most likely phase coded signal corresponding to received data. The present invention has particular application to communication with signals that experience spurious random phase perturbations. The generalized estimator-correlator uses a maximum a posteriori (MAP) estimator to generate phase estimates for correlation with incoming data samples and for correlation with mean phases indicative of unique hypothesized signals. The result is a MAP likelihood statistic for each hypothesized transmission, wherein the highest value statistic identifies the transmitted signal.

  19. Improved Maximum Parsimony Models for Phylogenetic Networks.

    Science.gov (United States)

    Van Iersel, Leo; Jones, Mark; Scornavacca, Celine

    2018-05-01

    Phylogenetic networks are well suited to represent evolutionary histories comprising reticulate evolution. Several methods aiming at reconstructing explicit phylogenetic networks have been developed in the last two decades. In this article, we propose a new definition of maximum parsimony for phylogenetic networks that permits to model biological scenarios that cannot be modeled by the definitions currently present in the literature (namely, the "hardwired" and "softwired" parsimony). Building on this new definition, we provide several algorithmic results that lay the foundations for new parsimony-based methods for phylogenetic network reconstruction.

  20. Ancestral sequence reconstruction with Maximum Parsimony

    OpenAIRE

    Herbst, Lina; Fischer, Mareike

    2017-01-01

    One of the main aims in phylogenetics is the estimation of ancestral sequences based on present-day data like, for instance, DNA alignments. One way to estimate the data of the last common ancestor of a given set of species is to first reconstruct a phylogenetic tree with some tree inference method and then to use some method of ancestral state inference based on that tree. One of the best-known methods both for tree inference as well as for ancestral sequence inference is Maximum Parsimony (...

  1. Enthalpic pairwise self-association of L-carnitine in aqueous solutions of some alkali halides at T = 298.15 K

    International Nuclear Information System (INIS)

    Wang, Hua-Qin; Cheng, Wei-Na; Zhu, Li-Yuan; Hu, Xin-Gen

    2016-01-01

    Highlights: • Dilution enthalpies of L-carnitine in aqueous alkali halide solutions by ITC. • The second virial coefficients of enthalpy (h_2) have been calculated. • The values of h_2 increase with increasing molalities of aqueous salt solutions. • The signs of h_2 turn from negative in pure water to positive in salt solutions. • The trends is ascribed to the salt effects on pairwise self-associations. - Abstract: Knowledge of the influence of ions of various nature on intermolecular hydrophilic and hydrophobic interactions in solutions is required in many research fields. In this paper, dilution enthalpies of zwitterion L-carnitine in aqueous NaCl, KCl and NaBr solutions of various molalities (b = 0 to 3.0 mol · kg"−"1) have been determined respectively at T = (298.15 ± 0.01) K and p = (0.100 ± 0.005) MPa by isothermal titration calorimetry (ITC). In light of the MacMillan–Mayer theory, the 2nd virial enthalpic coefficients (h_2) have been calculated. The h_2 coefficients increase gradually with increasing molality (b) of the three aqueous alkali halides solutions, from small negative values in pure water to relatively larger positive values in solution. The trends of h_2 coefficients are ascribed to the salt effects on the balance between hydrophilic and hydrophobic interactions in pairwise self-associations. It is considered that the size of cations and anions exert influences on h_2 coefficients through their surface charge densities and hydration (or dehydration) abilities.

  2. Fast-GPU-PCC: A GPU-Based Technique to Compute Pairwise Pearson's Correlation Coefficients for Time Series Data-fMRI Study.

    Science.gov (United States)

    Eslami, Taban; Saeed, Fahad

    2018-04-20

    Functional magnetic resonance imaging (fMRI) is a non-invasive brain imaging technique, which has been regularly used for studying brain’s functional activities in the past few years. A very well-used measure for capturing functional associations in brain is Pearson’s correlation coefficient. Pearson’s correlation is widely used for constructing functional network and studying dynamic functional connectivity of the brain. These are useful measures for understanding the effects of brain disorders on connectivities among brain regions. The fMRI scanners produce huge number of voxels and using traditional central processing unit (CPU)-based techniques for computing pairwise correlations is very time consuming especially when large number of subjects are being studied. In this paper, we propose a graphics processing unit (GPU)-based algorithm called Fast-GPU-PCC for computing pairwise Pearson’s correlation coefficient. Based on the symmetric property of Pearson’s correlation, this approach returns N ( N − 1 ) / 2 correlation coefficients located at strictly upper triangle part of the correlation matrix. Storing correlations in a one-dimensional array with the order as proposed in this paper is useful for further usage. Our experiments on real and synthetic fMRI data for different number of voxels and varying length of time series show that the proposed approach outperformed state of the art GPU-based techniques as well as the sequential CPU-based versions. We show that Fast-GPU-PCC runs 62 times faster than CPU-based version and about 2 to 3 times faster than two other state of the art GPU-based methods.

  3. Objective Bayesianism and the Maximum Entropy Principle

    Directory of Open Access Journals (Sweden)

    Jon Williamson

    2013-09-01

    Full Text Available Objective Bayesian epistemology invokes three norms: the strengths of our beliefs should be probabilities; they should be calibrated to our evidence of physical probabilities; and they should otherwise equivocate sufficiently between the basic propositions that we can express. The three norms are sometimes explicated by appealing to the maximum entropy principle, which says that a belief function should be a probability function, from all those that are calibrated to evidence, that has maximum entropy. However, the three norms of objective Bayesianism are usually justified in different ways. In this paper, we show that the three norms can all be subsumed under a single justification in terms of minimising worst-case expected loss. This, in turn, is equivalent to maximising a generalised notion of entropy. We suggest that requiring language invariance, in addition to minimising worst-case expected loss, motivates maximisation of standard entropy as opposed to maximisation of other instances of generalised entropy. Our argument also provides a qualified justification for updating degrees of belief by Bayesian conditionalisation. However, conditional probabilities play a less central part in the objective Bayesian account than they do under the subjective view of Bayesianism, leading to a reduced role for Bayes’ Theorem.

  4. Efficient heuristics for maximum common substructure search.

    Science.gov (United States)

    Englert, Péter; Kovács, Péter

    2015-05-26

    Maximum common substructure search is a computationally hard optimization problem with diverse applications in the field of cheminformatics, including similarity search, lead optimization, molecule alignment, and clustering. Most of these applications have strict constraints on running time, so heuristic methods are often preferred. However, the development of an algorithm that is both fast enough and accurate enough for most practical purposes is still a challenge. Moreover, in some applications, the quality of a common substructure depends not only on its size but also on various topological features of the one-to-one atom correspondence it defines. Two state-of-the-art heuristic algorithms for finding maximum common substructures have been implemented at ChemAxon Ltd., and effective heuristics have been developed to improve both their efficiency and the relevance of the atom mappings they provide. The implementations have been thoroughly evaluated and compared with existing solutions (KCOMBU and Indigo). The heuristics have been found to greatly improve the performance and applicability of the algorithms. The purpose of this paper is to introduce the applied methods and present the experimental results.

  5. Hydraulic Limits on Maximum Plant Transpiration

    Science.gov (United States)

    Manzoni, S.; Vico, G.; Katul, G. G.; Palmroth, S.; Jackson, R. B.; Porporato, A. M.

    2011-12-01

    Photosynthesis occurs at the expense of water losses through transpiration. As a consequence of this basic carbon-water interaction at the leaf level, plant growth and ecosystem carbon exchanges are tightly coupled to transpiration. In this contribution, the hydraulic constraints that limit transpiration rates under well-watered conditions are examined across plant functional types and climates. The potential water flow through plants is proportional to both xylem hydraulic conductivity (which depends on plant carbon economy) and the difference in water potential between the soil and the atmosphere (the driving force that pulls water from the soil). Differently from previous works, we study how this potential flux changes with the amplitude of the driving force (i.e., we focus on xylem properties and not on stomatal regulation). Xylem hydraulic conductivity decreases as the driving force increases due to cavitation of the tissues. As a result of this negative feedback, more negative leaf (and xylem) water potentials would provide a stronger driving force for water transport, while at the same time limiting xylem hydraulic conductivity due to cavitation. Here, the leaf water potential value that allows an optimum balance between driving force and xylem conductivity is quantified, thus defining the maximum transpiration rate that can be sustained by the soil-to-leaf hydraulic system. To apply the proposed framework at the global scale, a novel database of xylem conductivity and cavitation vulnerability across plant types and biomes is developed. Conductivity and water potential at 50% cavitation are shown to be complementary (in particular between angiosperms and conifers), suggesting a tradeoff between transport efficiency and hydraulic safety. Plants from warmer and drier biomes tend to achieve larger maximum transpiration than plants growing in environments with lower atmospheric water demand. The predicted maximum transpiration and the corresponding leaf water

  6. Analogue of Pontryagin's maximum principle for multiple integrals minimization problems

    OpenAIRE

    Mikhail, Zelikin

    2016-01-01

    The theorem like Pontryagin's maximum principle for multiple integrals is proved. Unlike the usual maximum principle, the maximum should be taken not over all matrices, but only on matrices of rank one. Examples are given.

  7. Lake Basin Fetch and Maximum Length/Width

    Data.gov (United States)

    Minnesota Department of Natural Resources — Linear features representing the Fetch, Maximum Length and Maximum Width of a lake basin. Fetch, maximum length and average width are calcuated from the lake polygon...

  8. Maximum Likelihood Reconstruction for Magnetic Resonance Fingerprinting.

    Science.gov (United States)

    Zhao, Bo; Setsompop, Kawin; Ye, Huihui; Cauley, Stephen F; Wald, Lawrence L

    2016-08-01

    This paper introduces a statistical estimation framework for magnetic resonance (MR) fingerprinting, a recently proposed quantitative imaging paradigm. Within this framework, we present a maximum likelihood (ML) formalism to estimate multiple MR tissue parameter maps directly from highly undersampled, noisy k-space data. A novel algorithm, based on variable splitting, the alternating direction method of multipliers, and the variable projection method, is developed to solve the resulting optimization problem. Representative results from both simulations and in vivo experiments demonstrate that the proposed approach yields significantly improved accuracy in parameter estimation, compared to the conventional MR fingerprinting reconstruction. Moreover, the proposed framework provides new theoretical insights into the conventional approach. We show analytically that the conventional approach is an approximation to the ML reconstruction; more precisely, it is exactly equivalent to the first iteration of the proposed algorithm for the ML reconstruction, provided that a gridding reconstruction is used as an initialization.

  9. Maximum Profit Configurations of Commercial Engines

    Directory of Open Access Journals (Sweden)

    Yiran Chen

    2011-06-01

    Full Text Available An investigation of commercial engines with finite capacity low- and high-price economic subsystems and a generalized commodity transfer law [n ∝ Δ (P m] in commodity flow processes, in which effects of the price elasticities of supply and demand are introduced, is presented in this paper. Optimal cycle configurations of commercial engines for maximum profit are obtained by applying optimal control theory. In some special cases, the eventual state—market equilibrium—is solely determined by the initial conditions and the inherent characteristics of two subsystems; while the different ways of transfer affect the model in respects of the specific forms of the paths of prices and the instantaneous commodity flow, i.e., the optimal configuration.

  10. The worst case complexity of maximum parsimony.

    Science.gov (United States)

    Carmel, Amir; Musa-Lempel, Noa; Tsur, Dekel; Ziv-Ukelson, Michal

    2014-11-01

    One of the core classical problems in computational biology is that of constructing the most parsimonious phylogenetic tree interpreting an input set of sequences from the genomes of evolutionarily related organisms. We reexamine the classical maximum parsimony (MP) optimization problem for the general (asymmetric) scoring matrix case, where rooted phylogenies are implied, and analyze the worst case bounds of three approaches to MP: The approach of Cavalli-Sforza and Edwards, the approach of Hendy and Penny, and a new agglomerative, "bottom-up" approach we present in this article. We show that the second and third approaches are faster than the first one by a factor of Θ(√n) and Θ(n), respectively, where n is the number of species.

  11. Modelling maximum likelihood estimation of availability

    International Nuclear Information System (INIS)

    Waller, R.A.; Tietjen, G.L.; Rock, G.W.

    1975-01-01

    Suppose the performance of a nuclear powered electrical generating power plant is continuously monitored to record the sequence of failure and repairs during sustained operation. The purpose of this study is to assess one method of estimating the performance of the power plant when the measure of performance is availability. That is, we determine the probability that the plant is operational at time t. To study the availability of a power plant, we first assume statistical models for the variables, X and Y, which denote the time-to-failure and the time-to-repair variables, respectively. Once those statistical models are specified, the availability, A(t), can be expressed as a function of some or all of their parameters. Usually those parameters are unknown in practice and so A(t) is unknown. This paper discusses the maximum likelihood estimator of A(t) when the time-to-failure model for X is an exponential density with parameter, lambda, and the time-to-repair model for Y is an exponential density with parameter, theta. Under the assumption of exponential models for X and Y, it follows that the instantaneous availability at time t is A(t)=lambda/(lambda+theta)+theta/(lambda+theta)exp[-[(1/lambda)+(1/theta)]t] with t>0. Also, the steady-state availability is A(infinity)=lambda/(lambda+theta). We use the observations from n failure-repair cycles of the power plant, say X 1 , X 2 , ..., Xsub(n), Y 1 , Y 2 , ..., Ysub(n) to present the maximum likelihood estimators of A(t) and A(infinity). The exact sampling distributions for those estimators and some statistical properties are discussed before a simulation model is used to determine 95% simulation intervals for A(t). The methodology is applied to two examples which approximate the operating history of two nuclear power plants. (author)

  12. A maximum power point tracking for photovoltaic-SPE system using a maximum current controller

    Energy Technology Data Exchange (ETDEWEB)

    Muhida, Riza [Osaka Univ., Dept. of Physical Science, Toyonaka, Osaka (Japan); Osaka Univ., Dept. of Electrical Engineering, Suita, Osaka (Japan); Park, Minwon; Dakkak, Mohammed; Matsuura, Kenji [Osaka Univ., Dept. of Electrical Engineering, Suita, Osaka (Japan); Tsuyoshi, Akira; Michira, Masakazu [Kobe City College of Technology, Nishi-ku, Kobe (Japan)

    2003-02-01

    Processes to produce hydrogen from solar photovoltaic (PV)-powered water electrolysis using solid polymer electrolysis (SPE) are reported. An alternative control of maximum power point tracking (MPPT) in the PV-SPE system based on the maximum current searching methods has been designed and implemented. Based on the characteristics of voltage-current and theoretical analysis of SPE, it can be shown that the tracking of the maximum current output of DC-DC converter in SPE side will track the MPPT of photovoltaic panel simultaneously. This method uses a proportional integrator controller to control the duty factor of DC-DC converter with pulse-width modulator (PWM). The MPPT performance and hydrogen production performance of this method have been evaluated and discussed based on the results of the experiment. (Author)

  13. Maximum mass of magnetic white dwarfs

    International Nuclear Information System (INIS)

    Paret, Daryel Manreza; Horvath, Jorge Ernesto; Martínez, Aurora Perez

    2015-01-01

    We revisit the problem of the maximum masses of magnetized white dwarfs (WDs). The impact of a strong magnetic field on the structure equations is addressed. The pressures become anisotropic due to the presence of the magnetic field and split into parallel and perpendicular components. We first construct stable solutions of the Tolman-Oppenheimer-Volkoff equations for parallel pressures and find that physical solutions vanish for the perpendicular pressure when B ≳ 10 13 G. This fact establishes an upper bound for a magnetic field and the stability of the configurations in the (quasi) spherical approximation. Our findings also indicate that it is not possible to obtain stable magnetized WDs with super-Chandrasekhar masses because the values of the magnetic field needed for them are higher than this bound. To proceed into the anisotropic regime, we can apply results for structure equations appropriate for a cylindrical metric with anisotropic pressures that were derived in our previous work. From the solutions of the structure equations in cylindrical symmetry we have confirmed the same bound for B ∼ 10 13 G, since beyond this value no physical solutions are possible. Our tentative conclusion is that massive WDs with masses well beyond the Chandrasekhar limit do not constitute stable solutions and should not exist. (paper)

  14. TRENDS IN ESTIMATED MIXING DEPTH DAILY MAXIMUMS

    Energy Technology Data Exchange (ETDEWEB)

    Buckley, R; Amy DuPont, A; Robert Kurzeja, R; Matt Parker, M

    2007-11-12

    Mixing depth is an important quantity in the determination of air pollution concentrations. Fireweather forecasts depend strongly on estimates of the mixing depth as a means of determining the altitude and dilution (ventilation rates) of smoke plumes. The Savannah River United States Forest Service (USFS) routinely conducts prescribed fires at the Savannah River Site (SRS), a heavily wooded Department of Energy (DOE) facility located in southwest South Carolina. For many years, the Savannah River National Laboratory (SRNL) has provided forecasts of weather conditions in support of the fire program, including an estimated mixing depth using potential temperature and turbulence change with height at a given location. This paper examines trends in the average estimated mixing depth daily maximum at the SRS over an extended period of time (4.75 years) derived from numerical atmospheric simulations using two versions of the Regional Atmospheric Modeling System (RAMS). This allows for differences to be seen between the model versions, as well as trends on a multi-year time frame. In addition, comparisons of predicted mixing depth for individual days in which special balloon soundings were released are also discussed.

  15. Mammographic image restoration using maximum entropy deconvolution

    International Nuclear Information System (INIS)

    Jannetta, A; Jackson, J C; Kotre, C J; Birch, I P; Robson, K J; Padgett, R

    2004-01-01

    An image restoration approach based on a Bayesian maximum entropy method (MEM) has been applied to a radiological image deconvolution problem, that of reduction of geometric blurring in magnification mammography. The aim of the work is to demonstrate an improvement in image spatial resolution in realistic noisy radiological images with no associated penalty in terms of reduction in the signal-to-noise ratio perceived by the observer. Images of the TORMAM mammographic image quality phantom were recorded using the standard magnification settings of 1.8 magnification/fine focus and also at 1.8 magnification/broad focus and 3.0 magnification/fine focus; the latter two arrangements would normally give rise to unacceptable geometric blurring. Measured point-spread functions were used in conjunction with the MEM image processing to de-blur these images. The results are presented as comparative images of phantom test features and as observer scores for the raw and processed images. Visualization of high resolution features and the total image scores for the test phantom were improved by the application of the MEM processing. It is argued that this successful demonstration of image de-blurring in noisy radiological images offers the possibility of weakening the link between focal spot size and geometric blurring in radiology, thus opening up new approaches to system optimization

  16. Maximum Margin Clustering of Hyperspectral Data

    Science.gov (United States)

    Niazmardi, S.; Safari, A.; Homayouni, S.

    2013-09-01

    In recent decades, large margin methods such as Support Vector Machines (SVMs) are supposed to be the state-of-the-art of supervised learning methods for classification of hyperspectral data. However, the results of these algorithms mainly depend on the quality and quantity of available training data. To tackle down the problems associated with the training data, the researcher put effort into extending the capability of large margin algorithms for unsupervised learning. One of the recent proposed algorithms is Maximum Margin Clustering (MMC). The MMC is an unsupervised SVMs algorithm that simultaneously estimates both the labels and the hyperplane parameters. Nevertheless, the optimization of the MMC algorithm is a non-convex problem. Most of the existing MMC methods rely on the reformulating and the relaxing of the non-convex optimization problem as semi-definite programs (SDP), which are computationally very expensive and only can handle small data sets. Moreover, most of these algorithms are two-class classification, which cannot be used for classification of remotely sensed data. In this paper, a new MMC algorithm is used that solve the original non-convex problem using Alternative Optimization method. This algorithm is also extended for multi-class classification and its performance is evaluated. The results of the proposed algorithm show that the algorithm has acceptable results for hyperspectral data clustering.

  17. Paving the road to maximum productivity.

    Science.gov (United States)

    Holland, C

    1998-01-01

    "Job security" is an oxymoron in today's environment of downsizing, mergers, and acquisitions. Workers find themselves living by new rules in the workplace that they may not understand. How do we cope? It is the leader's charge to take advantage of this chaos and create conditions under which his or her people can understand the need for change and come together with a shared purpose to effect that change. The clinical laboratory at Arkansas Children's Hospital has taken advantage of this chaos to down-size and to redesign how the work gets done to pave the road to maximum productivity. After initial hourly cutbacks, the workers accepted the cold, hard fact that they would never get their old world back. They set goals to proactively shape their new world through reorganizing, flexing staff with workload, creating a rapid response laboratory, exploiting information technology, and outsourcing. Today the laboratory is a lean, productive machine that accepts change as a way of life. We have learned to adapt, trust, and support each other as we have journeyed together over the rough roads. We are looking forward to paving a new fork in the road to the future.

  18. Maximum power flux of auroral kilometric radiation

    International Nuclear Information System (INIS)

    Benson, R.F.; Fainberg, J.

    1991-01-01

    The maximum auroral kilometric radiation (AKR) power flux observed by distant satellites has been increased by more than a factor of 10 from previously reported values. This increase has been achieved by a new data selection criterion and a new analysis of antenna spin modulated signals received by the radio astronomy instrument on ISEE 3. The method relies on selecting AKR events containing signals in the highest-frequency channel (1980, kHz), followed by a careful analysis that effectively increased the instrumental dynamic range by more than 20 dB by making use of the spacecraft antenna gain diagram during a spacecraft rotation. This analysis has allowed the separation of real signals from those created in the receiver by overloading. Many signals having the appearance of AKR harmonic signals were shown to be of spurious origin. During one event, however, real second harmonic AKR signals were detected even though the spacecraft was at a great distance (17 R E ) from Earth. During another event, when the spacecraft was at the orbital distance of the Moon and on the morning side of Earth, the power flux of fundamental AKR was greater than 3 x 10 -13 W m -2 Hz -1 at 360 kHz normalized to a radial distance r of 25 R E assuming the power falls off as r -2 . A comparison of these intense signal levels with the most intense source region values (obtained by ISIS 1 and Viking) suggests that multiple sources were observed by ISEE 3

  19. Maximum likelihood window for time delay estimation

    International Nuclear Information System (INIS)

    Lee, Young Sup; Yoon, Dong Jin; Kim, Chi Yup

    2004-01-01

    Time delay estimation for the detection of leak location in underground pipelines is critically important. Because the exact leak location depends upon the precision of the time delay between sensor signals due to leak noise and the speed of elastic waves, the research on the estimation of time delay has been one of the key issues in leak lovating with the time arrival difference method. In this study, an optimal Maximum Likelihood window is considered to obtain a better estimation of the time delay. This method has been proved in experiments, which can provide much clearer and more precise peaks in cross-correlation functions of leak signals. The leak location error has been less than 1 % of the distance between sensors, for example the error was not greater than 3 m for 300 m long underground pipelines. Apart from the experiment, an intensive theoretical analysis in terms of signal processing has been described. The improved leak locating with the suggested method is due to the windowing effect in frequency domain, which offers a weighting in significant frequencies.

  20. Ancestral Sequence Reconstruction with Maximum Parsimony.

    Science.gov (United States)

    Herbst, Lina; Fischer, Mareike

    2017-12-01

    One of the main aims in phylogenetics is the estimation of ancestral sequences based on present-day data like, for instance, DNA alignments. One way to estimate the data of the last common ancestor of a given set of species is to first reconstruct a phylogenetic tree with some tree inference method and then to use some method of ancestral state inference based on that tree. One of the best-known methods both for tree inference and for ancestral sequence inference is Maximum Parsimony (MP). In this manuscript, we focus on this method and on ancestral state inference for fully bifurcating trees. In particular, we investigate a conjecture published by Charleston and Steel in 1995 concerning the number of species which need to have a particular state, say a, at a particular site in order for MP to unambiguously return a as an estimate for the state of the last common ancestor. We prove the conjecture for all even numbers of character states, which is the most relevant case in biology. We also show that the conjecture does not hold in general for odd numbers of character states, but also present some positive results for this case.

  1. 49 CFR 230.24 - Maximum allowable stress.

    Science.gov (United States)

    2010-10-01

    ... 49 Transportation 4 2010-10-01 2010-10-01 false Maximum allowable stress. 230.24 Section 230.24... Allowable Stress § 230.24 Maximum allowable stress. (a) Maximum allowable stress value. The maximum allowable stress value on any component of a steam locomotive boiler shall not exceed 1/4 of the ultimate...

  2. 20 CFR 226.52 - Total annuity subject to maximum.

    Science.gov (United States)

    2010-04-01

    ... 20 Employees' Benefits 1 2010-04-01 2010-04-01 false Total annuity subject to maximum. 226.52... COMPUTING EMPLOYEE, SPOUSE, AND DIVORCED SPOUSE ANNUITIES Railroad Retirement Family Maximum § 226.52 Total annuity subject to maximum. The total annuity amount which is compared to the maximum monthly amount to...

  3. Half-width at half-maximum, full-width at half-maximum analysis

    Indian Academy of Sciences (India)

    addition to the well-defined parameter full-width at half-maximum (FWHM). The distribution of ... optical side-lobes in the diffraction pattern resulting in steep central maxima [6], reduc- tion of effects of ... and broad central peak. The idea of.

  4. Cosmic shear measurement with maximum likelihood and maximum a posteriori inference

    Science.gov (United States)

    Hall, Alex; Taylor, Andy

    2017-06-01

    We investigate the problem of noise bias in maximum likelihood and maximum a posteriori estimators for cosmic shear. We derive the leading and next-to-leading order biases and compute them in the context of galaxy ellipticity measurements, extending previous work on maximum likelihood inference for weak lensing. We show that a large part of the bias on these point estimators can be removed using information already contained in the likelihood when a galaxy model is specified, without the need for external calibration. We test these bias-corrected estimators on simulated galaxy images similar to those expected from planned space-based weak lensing surveys, with promising results. We find that the introduction of an intrinsic shape prior can help with mitigation of noise bias, such that the maximum a posteriori estimate can be made less biased than the maximum likelihood estimate. Second-order terms offer a check on the convergence of the estimators, but are largely subdominant. We show how biases propagate to shear estimates, demonstrating in our simple set-up that shear biases can be reduced by orders of magnitude and potentially to within the requirements of planned space-based surveys at mild signal-to-noise ratio. We find that second-order terms can exhibit significant cancellations at low signal-to-noise ratio when Gaussian noise is assumed, which has implications for inferring the performance of shear-measurement algorithms from simplified simulations. We discuss the viability of our point estimators as tools for lensing inference, arguing that they allow for the robust measurement of ellipticity and shear.

  5. Maximum entropy production rate in quantum thermodynamics

    Energy Technology Data Exchange (ETDEWEB)

    Beretta, Gian Paolo, E-mail: beretta@ing.unibs.i [Universita di Brescia, via Branze 38, 25123 Brescia (Italy)

    2010-06-01

    In the framework of the recent quest for well-behaved nonlinear extensions of the traditional Schroedinger-von Neumann unitary dynamics that could provide fundamental explanations of recent experimental evidence of loss of quantum coherence at the microscopic level, a recent paper [Gheorghiu-Svirschevski 2001 Phys. Rev. A 63 054102] reproposes the nonlinear equation of motion proposed by the present author [see Beretta G P 1987 Found. Phys. 17 365 and references therein] for quantum (thermo)dynamics of a single isolated indivisible constituent system, such as a single particle, qubit, qudit, spin or atomic system, or a Bose-Einstein or Fermi-Dirac field. As already proved, such nonlinear dynamics entails a fundamental unifying microscopic proof and extension of Onsager's reciprocity and Callen's fluctuation-dissipation relations to all nonequilibrium states, close and far from thermodynamic equilibrium. In this paper we propose a brief but self-contained review of the main results already proved, including the explicit geometrical construction of the equation of motion from the steepest-entropy-ascent ansatz and its exact mathematical and conceptual equivalence with the maximal-entropy-generation variational-principle formulation presented in Gheorghiu-Svirschevski S 2001 Phys. Rev. A 63 022105. Moreover, we show how it can be extended to the case of a composite system to obtain the general form of the equation of motion, consistent with the demanding requirements of strong separability and of compatibility with general thermodynamics principles. The irreversible term in the equation of motion describes the spontaneous attraction of the state operator in the direction of steepest entropy ascent, thus implementing the maximum entropy production principle in quantum theory. The time rate at which the path of steepest entropy ascent is followed has so far been left unspecified. As a step towards the identification of such rate, here we propose a possible

  6. Determination of the maximum-depth to potential field sources by a maximum structural index method

    Science.gov (United States)

    Fedi, M.; Florio, G.

    2013-01-01

    A simple and fast determination of the limiting depth to the sources may represent a significant help to the data interpretation. To this end we explore the possibility of determining those source parameters shared by all the classes of models fitting the data. One approach is to determine the maximum depth-to-source compatible with the measured data, by using for example the well-known Bott-Smith rules. These rules involve only the knowledge of the field and its horizontal gradient maxima, and are independent from the density contrast. Thanks to the direct relationship between structural index and depth to sources we work out a simple and fast strategy to obtain the maximum depth by using the semi-automated methods, such as Euler deconvolution or depth-from-extreme-points method (DEXP). The proposed method consists in estimating the maximum depth as the one obtained for the highest allowable value of the structural index (Nmax). Nmax may be easily determined, since it depends only on the dimensionality of the problem (2D/3D) and on the nature of the analyzed field (e.g., gravity field or magnetic field). We tested our approach on synthetic models against the results obtained by the classical Bott-Smith formulas and the results are in fact very similar, confirming the validity of this method. However, while Bott-Smith formulas are restricted to the gravity field only, our method is applicable also to the magnetic field and to any derivative of the gravity and magnetic field. Our method yields a useful criterion to assess the source model based on the (∂f/∂x)max/fmax ratio. The usefulness of the method in real cases is demonstrated for a salt wall in the Mississippi basin, where the estimation of the maximum depth agrees with the seismic information.

  7. Pairwise harmonics for shape analysis

    KAUST Repository

    Zheng, Youyi; Tai, Chiewlan; Zhang, Eugene; Xu, Pengfei

    2013-01-01

    efficient algorithms than the state-of-the-art methods for three applications: intrinsic reflectional symmetry axis computation, matching shape extremities, and simultaneous surface segmentation and skeletonization. © 2012 IEEE.

  8. Weighted Maximum-Clique Transversal Sets of Graphs

    OpenAIRE

    Chuan-Min Lee

    2011-01-01

    A maximum-clique transversal set of a graph G is a subset of vertices intersecting all maximum cliques of G. The maximum-clique transversal set problem is to find a maximum-clique transversal set of G of minimum cardinality. Motivated by the placement of transmitters for cellular telephones, Chang, Kloks, and Lee introduced the concept of maximum-clique transversal sets on graphs in 2001. In this paper, we study the weighted version of the maximum-clique transversal set problem for split grap...

  9. Pattern formation, logistics, and maximum path probability

    Science.gov (United States)

    Kirkaldy, J. S.

    1985-05-01

    The concept of pattern formation, which to current researchers is a synonym for self-organization, carries the connotation of deductive logic together with the process of spontaneous inference. Defining a pattern as an equivalence relation on a set of thermodynamic objects, we establish that a large class of irreversible pattern-forming systems, evolving along idealized quasisteady paths, approaches the stable steady state as a mapping upon the formal deductive imperatives of a propositional function calculus. In the preamble the classical reversible thermodynamics of composite systems is analyzed as an externally manipulated system of space partitioning and classification based on ideal enclosures and diaphragms. The diaphragms have discrete classification capabilities which are designated in relation to conserved quantities by descriptors such as impervious, diathermal, and adiabatic. Differentiability in the continuum thermodynamic calculus is invoked as equivalent to analyticity and consistency in the underlying class or sentential calculus. The seat of inference, however, rests with the thermodynamicist. In the transition to an irreversible pattern-forming system the defined nature of the composite reservoirs remains, but a given diaphragm is replaced by a pattern-forming system which by its nature is a spontaneously evolving volume partitioner and classifier of invariants. The seat of volition or inference for the classification system is thus transferred from the experimenter or theoretician to the diaphragm, and with it the full deductive facility. The equivalence relations or partitions associated with the emerging patterns may thus be associated with theorems of the natural pattern-forming calculus. The entropy function, together with its derivatives, is the vehicle which relates the logistics of reservoirs and diaphragms to the analog logistics of the continuum. Maximum path probability or second-order differentiability of the entropy in isolation are

  10. Accurate modeling and maximum power point detection of ...

    African Journals Online (AJOL)

    Accurate modeling and maximum power point detection of photovoltaic ... Determination of MPP enables the PV system to deliver maximum available power. ..... adaptive artificial neural network: Proposition for a new sizing procedure.

  11. Maximum power per VA control of vector controlled interior ...

    Indian Academy of Sciences (India)

    Thakur Sumeet Singh

    2018-04-11

    Apr 11, 2018 ... Department of Electrical Engineering, Indian Institute of Technology Delhi, New ... The MPVA operation allows maximum-utilization of the drive-system. ... Permanent magnet motor; unity power factor; maximum VA utilization; ...

  12. Electron density distribution in Si and Ge using multipole, maximum ...

    Indian Academy of Sciences (India)

    Si and Ge has been studied using multipole, maximum entropy method (MEM) and ... and electron density distribution using the currently available versatile ..... data should be subjected to maximum possible utility for the characterization of.

  13. Investigation of the range of validity of the pairwise summation method applied to the calculation of the surface roughness correction to the van der Waals force

    Science.gov (United States)

    Gusso, André; Burnham, Nancy A.

    2016-09-01

    It has long been recognized that stochastic surface roughness can considerably change the van der Waals (vdW) force between interacting surfaces and particles. However, few analytical expressions for the vdW force between rough surfaces have been presented in the literature. Because they have been derived using perturbative methods or the proximity force approximation the expressions are valid when the roughness correction is small and for a limited range of roughness parameters and surface separation. In this work, a nonperturbative approach, the effective density method (EDM) is proposed to circumvent some of these limitations. The method simplifies the calculations of the roughness correction based on pairwise summation (PWS), and allows us to derive simple expressions for the vdW force and energy between two semispaces covered with stochastic rough surfaces. Because the range of applicability of PWS and, therefore, of our results, are not known a priori, we compare the predictions based on the EDM with those based on the multilayer effective medium model, whose range of validity can be defined more properly and which is valid when the roughness correction is comparatively large. We conclude that the PWS can be used for roughness characterized by a correlation length of the order of its rms amplitude, when this amplitude is of the order of or smaller than a few nanometers, and only for typically insulating materials such as silicon dioxide, silicon nitride, diamond, and certain glasses, polymers and ceramics. The results are relevant for the correct modeling of systems where the vdW force can play a significant role such as micro and nanodevices, for the calculation of the tip-sample force in atomic force microscopy, and in problems involving adhesion.

  14. SubVis: an interactive R package for exploring the effects of multiple substitution matrices on pairwise sequence alignment

    Directory of Open Access Journals (Sweden)

    Scott Barlowe

    2017-06-01

    Full Text Available Understanding how proteins mutate is critical to solving a host of biological problems. Mutations occur when an amino acid is substituted for another in a protein sequence. The set of likelihoods for amino acid substitutions is stored in a matrix and input to alignment algorithms. The quality of the resulting alignment is used to assess the similarity of two or more sequences and can vary according to assumptions modeled by the substitution matrix. Substitution strategies with minor parameter variations are often grouped together in families. For example, the BLOSUM and PAM matrix families are commonly used because they provide a standard, predefined way of modeling substitutions. However, researchers often do not know if a given matrix family or any individual matrix within a family is the most suitable. Furthermore, predefined matrix families may inaccurately reflect a particular hypothesis that a researcher wishes to model or otherwise result in unsatisfactory alignments. In these cases, the ability to compare the effects of one or more custom matrices may be needed. This laborious process is often performed manually because the ability to simultaneously load multiple matrices and then compare their effects on alignments is not readily available in current software tools. This paper presents SubVis, an interactive R package for loading and applying multiple substitution matrices to pairwise alignments. Users can simultaneously explore alignments resulting from multiple predefined and custom substitution matrices. SubVis utilizes several of the alignment functions found in R, a common language among protein scientists. Functions are tied together with the Shiny platform which allows the modification of input parameters. Information regarding alignment quality and individual amino acid substitutions is displayed with the JavaScript language which provides interactive visualizations for revealing both high-level and low-level alignment

  15. Enhancing pairwise state-transition weights: A new weighting scheme in simulated tempering that can minimize transition time between a pair of conformational states

    Science.gov (United States)

    Qiao, Qin; Zhang, Hou-Dao; Huang, Xuhui

    2016-04-01

    Simulated tempering (ST) is a widely used enhancing sampling method for Molecular Dynamics simulations. As one expanded ensemble method, ST is a combination of canonical ensembles at different temperatures and the acceptance probability of cross-temperature transitions is determined by both the temperature difference and the weights of each temperature. One popular way to obtain the weights is to adopt the free energy of each canonical ensemble, which achieves uniform sampling among temperature space. However, this uniform distribution in temperature space may not be optimal since high temperatures do not always speed up the conformational transitions of interest, as anti-Arrhenius kinetics are prevalent in protein and RNA folding. Here, we propose a new method: Enhancing Pairwise State-transition Weights (EPSW), to obtain the optimal weights by minimizing the round-trip time for transitions among different metastable states at the temperature of interest in ST. The novelty of the EPSW algorithm lies in explicitly considering the kinetics of conformation transitions when optimizing the weights of different temperatures. We further demonstrate the power of EPSW in three different systems: a simple two-temperature model, a two-dimensional model for protein folding with anti-Arrhenius kinetics, and the alanine dipeptide. The results from these three systems showed that the new algorithm can substantially accelerate the transitions between conformational states of interest in the ST expanded ensemble and further facilitate the convergence of thermodynamics compared to the widely used free energy weights. We anticipate that this algorithm is particularly useful for studying functional conformational changes of biological systems where the initial and final states are often known from structural biology experiments.

  16. Enhancing pairwise state-transition weights: A new weighting scheme in simulated tempering that can minimize transition time between a pair of conformational states

    International Nuclear Information System (INIS)

    Qiao, Qin; Zhang, Hou-Dao; Huang, Xuhui

    2016-01-01

    Simulated tempering (ST) is a widely used enhancing sampling method for Molecular Dynamics simulations. As one expanded ensemble method, ST is a combination of canonical ensembles at different temperatures and the acceptance probability of cross-temperature transitions is determined by both the temperature difference and the weights of each temperature. One popular way to obtain the weights is to adopt the free energy of each canonical ensemble, which achieves uniform sampling among temperature space. However, this uniform distribution in temperature space may not be optimal since high temperatures do not always speed up the conformational transitions of interest, as anti-Arrhenius kinetics are prevalent in protein and RNA folding. Here, we propose a new method: Enhancing Pairwise State-transition Weights (EPSW), to obtain the optimal weights by minimizing the round-trip time for transitions among different metastable states at the temperature of interest in ST. The novelty of the EPSW algorithm lies in explicitly considering the kinetics of conformation transitions when optimizing the weights of different temperatures. We further demonstrate the power of EPSW in three different systems: a simple two-temperature model, a two-dimensional model for protein folding with anti-Arrhenius kinetics, and the alanine dipeptide. The results from these three systems showed that the new algorithm can substantially accelerate the transitions between conformational states of interest in the ST expanded ensemble and further facilitate the convergence of thermodynamics compared to the widely used free energy weights. We anticipate that this algorithm is particularly useful for studying functional conformational changes of biological systems where the initial and final states are often known from structural biology experiments.

  17. ChIP-PIT: Enhancing the Analysis of ChIP-Seq Data Using Convex-Relaxed Pair-Wise Interaction Tensor Decomposition.

    Science.gov (United States)

    Zhu, Lin; Guo, Wei-Li; Deng, Su-Ping; Huang, De-Shuang

    2016-01-01

    In recent years, thanks to the efforts of individual scientists and research consortiums, a huge amount of chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) experimental data have been accumulated. Instead of investigating them independently, several recent studies have convincingly demonstrated that a wealth of scientific insights can be gained by integrative analysis of these ChIP-seq data. However, when used for the purpose of integrative analysis, a serious drawback of current ChIP-seq technique is that it is still expensive and time-consuming to generate ChIP-seq datasets of high standard. Most researchers are therefore unable to obtain complete ChIP-seq data for several TFs in a wide variety of cell lines, which considerably limits the understanding of transcriptional regulation pattern. In this paper, we propose a novel method called ChIP-PIT to overcome the aforementioned limitation. In ChIP-PIT, ChIP-seq data corresponding to a diverse collection of cell types, TFs and genes are fused together using the three-mode pair-wise interaction tensor (PIT) model, and the prediction of unperformed ChIP-seq experimental results is formulated as a tensor completion problem. Computationally, we propose efficient first-order method based on extensions of coordinate descent method to learn the optimal solution of ChIP-PIT, which makes it particularly suitable for the analysis of massive scale ChIP-seq data. Experimental evaluation the ENCODE data illustrate the usefulness of the proposed model.

  18. Enhancing pairwise state-transition weights: A new weighting scheme in simulated tempering that can minimize transition time between a pair of conformational states

    Energy Technology Data Exchange (ETDEWEB)

    Qiao, Qin, E-mail: qqiao@ust.hk; Zhang, Hou-Dao [Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon (Hong Kong); Huang, Xuhui, E-mail: xuhuihuang@ust.hk [Department of Chemistry, Division of Biomedical Engineering, Center of Systems Biology and Human Health, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon (Hong Kong); The HKUST Shenzhen Research Institute, Shenzhen (China)

    2016-04-21

    Simulated tempering (ST) is a widely used enhancing sampling method for Molecular Dynamics simulations. As one expanded ensemble method, ST is a combination of canonical ensembles at different temperatures and the acceptance probability of cross-temperature transitions is determined by both the temperature difference and the weights of each temperature. One popular way to obtain the weights is to adopt the free energy of each canonical ensemble, which achieves uniform sampling among temperature space. However, this uniform distribution in temperature space may not be optimal since high temperatures do not always speed up the conformational transitions of interest, as anti-Arrhenius kinetics are prevalent in protein and RNA folding. Here, we propose a new method: Enhancing Pairwise State-transition Weights (EPSW), to obtain the optimal weights by minimizing the round-trip time for transitions among different metastable states at the temperature of interest in ST. The novelty of the EPSW algorithm lies in explicitly considering the kinetics of conformation transitions when optimizing the weights of different temperatures. We further demonstrate the power of EPSW in three different systems: a simple two-temperature model, a two-dimensional model for protein folding with anti-Arrhenius kinetics, and the alanine dipeptide. The results from these three systems showed that the new algorithm can substantially accelerate the transitions between conformational states of interest in the ST expanded ensemble and further facilitate the convergence of thermodynamics compared to the widely used free energy weights. We anticipate that this algorithm is particularly useful for studying functional conformational changes of biological systems where the initial and final states are often known from structural biology experiments.

  19. 40 CFR 141.13 - Maximum contaminant levels for turbidity.

    Science.gov (United States)

    2010-07-01

    ... turbidity. 141.13 Section 141.13 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER... Maximum contaminant levels for turbidity. The maximum contaminant levels for turbidity are applicable to... part. The maximum contaminant levels for turbidity in drinking water, measured at a representative...

  20. Maximum Power Training and Plyometrics for Cross-Country Running.

    Science.gov (United States)

    Ebben, William P.

    2001-01-01

    Provides a rationale for maximum power training and plyometrics as conditioning strategies for cross-country runners, examining: an evaluation of training methods (strength training and maximum power training and plyometrics); biomechanic and velocity specificity (role in preventing injury); and practical application of maximum power training and…

  1. 13 CFR 107.840 - Maximum term of Financing.

    Science.gov (United States)

    2010-01-01

    ... 13 Business Credit and Assistance 1 2010-01-01 2010-01-01 false Maximum term of Financing. 107.840... COMPANIES Financing of Small Businesses by Licensees Structuring Licensee's Financing of An Eligible Small Business: Terms and Conditions of Financing § 107.840 Maximum term of Financing. The maximum term of any...

  2. 7 CFR 3565.210 - Maximum interest rate.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 15 2010-01-01 2010-01-01 false Maximum interest rate. 3565.210 Section 3565.210... AGRICULTURE GUARANTEED RURAL RENTAL HOUSING PROGRAM Loan Requirements § 3565.210 Maximum interest rate. The interest rate for a guaranteed loan must not exceed the maximum allowable rate specified by the Agency in...

  3. Characterizing graphs of maximum matching width at most 2

    DEFF Research Database (Denmark)

    Jeong, Jisu; Ok, Seongmin; Suh, Geewon

    2017-01-01

    The maximum matching width is a width-parameter that is de ned on a branch-decomposition over the vertex set of a graph. The size of a maximum matching in the bipartite graph is used as a cut-function. In this paper, we characterize the graphs of maximum matching width at most 2 using the minor o...

  4. Dāvida Lodža „Mazā pasaule” un „Paradīzes jaunumi” kā piedzīvojumu romāni

    OpenAIRE

    Kaušakīte, Inessa

    2007-01-01

    Maģistra darbā „Deivida Lodža „Mazā pasaule” un „Paradīzes Jaunumi” kā piedzīvojumu romāni” mērķis ir pievērst uzmanību piedzīvojuma žanra dažādām īpatnībām mūsdienu angļu romānista darbos. Darbs arī atklāj postmodernā piedzīvojumu romāna varoņa rakstura īpatnības. Pirmā nodaļa izceļ klasiskā 16. gadsimta spāņu literatūras piedzīvojumu romāna svarīgākās īpatnības. Šī nodaļa pēta apstākļus, kas palīdzējuši žanra attīstībai Anglijā. Otrā nodaļa pievērš uzmanību Deivida Lodža liktenim, kas kā...

  5. Assessment of average of normals (AON) procedure for outlier-free datasets including qualitative values below limit of detection (LoD): an application within tumor markers such as CA 15-3, CA 125, and CA 19-9.

    Science.gov (United States)

    Usta, Murat; Aral, Hale; Mete Çilingirtürk, Ahmet; Kural, Alev; Topaç, Ibrahim; Semerci, Tuna; Hicri Köseoğlu, Mehmet

    2016-11-01

    Average of normals (AON) is a quality control procedure that is sensitive only to systematic errors that can occur in an analytical process in which patient test results are used. The aim of this study was to develop an alternative model in order to apply the AON quality control procedure to datasets that include qualitative values below limit of detection (LoD). The reported patient test results for tumor markers, such as CA 15-3, CA 125, and CA 19-9, analyzed by two instruments, were retrieved from the information system over a period of 5 months, using the calibrator and control materials with the same lot numbers. The median as a measure of central tendency and the median absolute deviation (MAD) as a measure of dispersion were used for the complementary model of AON quality control procedure. The u bias values, which were determined for the bias component of the measurement uncertainty, were partially linked to the percentages of the daily median values of the test results that fall within the control limits. The results for these tumor markers, in which lower limits of reference intervals are not medically important for clinical diagnosis and management, showed that the AON quality control procedure, using the MAD around the median, can be applied for datasets including qualitative values below LoD.

  6. 40 CFR 1042.140 - Maximum engine power, displacement, power density, and maximum in-use engine speed.

    Science.gov (United States)

    2010-07-01

    ... cylinders having an internal diameter of 13.0 cm and a 15.5 cm stroke length, the rounded displacement would... 40 Protection of Environment 32 2010-07-01 2010-07-01 false Maximum engine power, displacement... Maximum engine power, displacement, power density, and maximum in-use engine speed. This section describes...

  7. The maximum entropy production and maximum Shannon information entropy in enzyme kinetics

    Science.gov (United States)

    Dobovišek, Andrej; Markovič, Rene; Brumen, Milan; Fajmut, Aleš

    2018-04-01

    We demonstrate that the maximum entropy production principle (MEPP) serves as a physical selection principle for the description of the most probable non-equilibrium steady states in simple enzymatic reactions. A theoretical approach is developed, which enables maximization of the density of entropy production with respect to the enzyme rate constants for the enzyme reaction in a steady state. Mass and Gibbs free energy conservations are considered as optimization constraints. In such a way computed optimal enzyme rate constants in a steady state yield also the most uniform probability distribution of the enzyme states. This accounts for the maximal Shannon information entropy. By means of the stability analysis it is also demonstrated that maximal density of entropy production in that enzyme reaction requires flexible enzyme structure, which enables rapid transitions between different enzyme states. These results are supported by an example, in which density of entropy production and Shannon information entropy are numerically maximized for the enzyme Glucose Isomerase.

  8. Solar Maximum Mission Experiment - Ultraviolet Spectroscopy and Polarimetry on the Solar Maximum Mission

    Science.gov (United States)

    Tandberg-Hanssen, E.; Cheng, C. C.; Woodgate, B. E.; Brandt, J. C.; Chapman, R. D.; Athay, R. G.; Beckers, J. M.; Bruner, E. C.; Gurman, J. B.; Hyder, C. L.

    1981-01-01

    The Ultraviolet Spectrometer and Polarimeter on the Solar Maximum Mission spacecraft is described. It is pointed out that the instrument, which operates in the wavelength range 1150-3600 A, has a spatial resolution of 2-3 arcsec and a spectral resolution of 0.02 A FWHM in second order. A Gregorian telescope, with a focal length of 1.8 m, feeds a 1 m Ebert-Fastie spectrometer. A polarimeter comprising rotating Mg F2 waveplates can be inserted behind the spectrometer entrance slit; it permits all four Stokes parameters to be determined. Among the observing modes are rasters, spectral scans, velocity measurements, and polarimetry. Examples of initial observations made since launch are presented.

  9. Constructing disease-specific gene networks using pair-wise relevance metric: Application to colon cancer identifies interleukin 8, desmin and enolase 1 as the central elements

    Directory of Open Access Journals (Sweden)

    Jiang Wei

    2008-08-01

    Full Text Available Abstract Background With the advance of large-scale omics technologies, it is now feasible to reversely engineer the underlying genetic networks that describe the complex interplays of molecular elements that lead to complex diseases. Current networking approaches are mainly focusing on building genetic networks at large without probing the interaction mechanisms specific to a physiological or disease condition. The aim of this study was thus to develop such a novel networking approach based on the relevance concept, which is ideal to reveal integrative effects of multiple genes in the underlying genetic circuit for complex diseases. Results The approach started with identification of multiple disease pathways, called a gene forest, in which the genes extracted from the decision forest constructed by supervised learning of the genome-wide transcriptional profiles for patients and normal samples. Based on the newly identified disease mechanisms, a novel pair-wise relevance metric, adjusted frequency value, was used to define the degree of genetic relationship between two molecular determinants. We applied the proposed method to analyze a publicly available microarray dataset for colon cancer. The results demonstrated that the colon cancer-specific gene network captured the most important genetic interactions in several cellular processes, such as proliferation, apoptosis, differentiation, mitogenesis and immunity, which are known to be pivotal for tumourigenesis. Further analysis of the topological architecture of the network identified three known hub cancer genes [interleukin 8 (IL8 (p ≈ 0, desmin (DES (p = 2.71 × 10-6 and enolase 1 (ENO1 (p = 4.19 × 10-5], while two novel hub genes [RNA binding motif protein 9 (RBM9 (p = 1.50 × 10-4 and ribosomal protein L30 (RPL30 (p = 1.50 × 10-4] may define new central elements in the gene network specific to colon cancer. Gene Ontology (GO based analysis of the colon cancer-specific gene network and

  10. Constructing disease-specific gene networks using pair-wise relevance metric: application to colon cancer identifies interleukin 8, desmin and enolase 1 as the central elements.

    Science.gov (United States)

    Jiang, Wei; Li, Xia; Rao, Shaoqi; Wang, Lihong; Du, Lei; Li, Chuanxing; Wu, Chao; Wang, Hongzhi; Wang, Yadong; Yang, Baofeng

    2008-08-10

    With the advance of large-scale omics technologies, it is now feasible to reversely engineer the underlying genetic networks that describe the complex interplays of molecular elements that lead to complex diseases. Current networking approaches are mainly focusing on building genetic networks at large without probing the interaction mechanisms specific to a physiological or disease condition. The aim of this study was thus to develop such a novel networking approach based on the relevance concept, which is ideal to reveal integrative effects of multiple genes in the underlying genetic circuit for complex diseases. The approach started with identification of multiple disease pathways, called a gene forest, in which the genes extracted from the decision forest constructed by supervised learning of the genome-wide transcriptional profiles for patients and normal samples. Based on the newly identified disease mechanisms, a novel pair-wise relevance metric, adjusted frequency value, was used to define the degree of genetic relationship between two molecular determinants. We applied the proposed method to analyze a publicly available microarray dataset for colon cancer. The results demonstrated that the colon cancer-specific gene network captured the most important genetic interactions in several cellular processes, such as proliferation, apoptosis, differentiation, mitogenesis and immunity, which are known to be pivotal for tumourigenesis. Further analysis of the topological architecture of the network identified three known hub cancer genes [interleukin 8 (IL8) (p approximately 0), desmin (DES) (p = 2.71 x 10(-6)) and enolase 1 (ENO1) (p = 4.19 x 10(-5))], while two novel hub genes [RNA binding motif protein 9 (RBM9) (p = 1.50 x 10(-4)) and ribosomal protein L30 (RPL30) (p = 1.50 x 10(-4))] may define new central elements in the gene network specific to colon cancer. Gene Ontology (GO) based analysis of the colon cancer-specific gene network and the sub-network that

  11. Benefits of the maximum tolerated dose (MTD) and maximum tolerated concentration (MTC) concept in aquatic toxicology

    International Nuclear Information System (INIS)

    Hutchinson, Thomas H.; Boegi, Christian; Winter, Matthew J.; Owens, J. Willie

    2009-01-01

    There is increasing recognition of the need to identify specific sublethal effects of chemicals, such as reproductive toxicity, and specific modes of actions of the chemicals, such as interference with the endocrine system. To achieve these aims requires criteria which provide a basis to interpret study findings so as to separate these specific toxicities and modes of action from not only acute lethality per se but also from severe inanition and malaise that non-specifically compromise reproductive capacity and the response of endocrine endpoints. Mammalian toxicologists have recognized that very high dose levels are sometimes required to elicit both specific adverse effects and present the potential of non-specific 'systemic toxicity'. Mammalian toxicologists have developed the concept of a maximum tolerated dose (MTD) beyond which a specific toxicity or action cannot be attributed to a test substance due to the compromised state of the organism. Ecotoxicologists are now confronted by a similar challenge and must develop an analogous concept of a MTD and the respective criteria. As examples of this conundrum, we note recent developments in efforts to validate protocols for fish reproductive toxicity and endocrine screens (e.g. some chemicals originally selected as 'negatives' elicited decreases in fecundity or changes in endpoints intended to be biomarkers for endocrine modes of action). Unless analogous criteria can be developed, the potentially confounding effects of systemic toxicity may then undermine the reliable assessment of specific reproductive effects or biomarkers such as vitellogenin or spiggin. The same issue confronts other areas of aquatic toxicology (e.g., genotoxicity) and the use of aquatic animals for preclinical assessments of drugs (e.g., use of zebrafish for drug safety assessment). We propose that there are benefits to adopting the concept of an MTD for toxicology and pharmacology studies using fish and other aquatic organisms and the

  12. Microprocessor Controlled Maximum Power Point Tracker for Photovoltaic Application

    International Nuclear Information System (INIS)

    Jiya, J. D.; Tahirou, G.

    2002-01-01

    This paper presents a microprocessor controlled maximum power point tracker for photovoltaic module. Input current and voltage are measured and multiplied within the microprocessor, which contains an algorithm to seek the maximum power point. The duly cycle of the DC-DC converter, at which the maximum power occurs is obtained, noted and adjusted. The microprocessor constantly seeks for improvement of obtained power by varying the duty cycle

  13. MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

    Science.gov (United States)

    Tamura, Koichiro; Peterson, Daniel; Peterson, Nicholas; Stecher, Glen; Nei, Masatoshi; Kumar, Sudhir

    2011-01-01

    Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version 5 (MEGA5), which is a user-friendly software for mining online databases, building sequence alignments and phylogenetic trees, and using methods of evolutionary bioinformatics in basic biology, biomedicine, and evolution. The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models (nucleotide or amino acid), inferring ancestral states and sequences (along with probabilities), and estimating evolutionary rates site-by-site. In computer simulation analyses, ML tree inference algorithms in MEGA5 compared favorably with other software packages in terms of computational efficiency and the accuracy of the estimates of phylogenetic trees, substitution parameters, and rate variation among sites. The MEGA user interface has now been enhanced to be activity driven to make it easier for the use of both beginners and experienced scientists. This version of MEGA is intended for the Windows platform, and it has been configured for effective use on Mac OS X and Linux desktops. It is available free of charge from http://www.megasoftware.net. PMID:21546353

  14. 49 CFR 195.406 - Maximum operating pressure.

    Science.gov (United States)

    2010-10-01

    ... 49 Transportation 3 2010-10-01 2010-10-01 false Maximum operating pressure. 195.406 Section 195.406 Transportation Other Regulations Relating to Transportation (Continued) PIPELINE AND HAZARDOUS... HAZARDOUS LIQUIDS BY PIPELINE Operation and Maintenance § 195.406 Maximum operating pressure. (a) Except for...

  15. 78 FR 49370 - Inflation Adjustment of Maximum Forfeiture Penalties

    Science.gov (United States)

    2013-08-14

    ... ``civil monetary penalties provided by law'' at least once every four years. DATES: Effective September 13... increases the maximum civil monetary forfeiture penalties available to the Commission under its rules... maximum civil penalties established in that section to account for inflation since the last adjustment to...

  16. 22 CFR 201.67 - Maximum freight charges.

    Science.gov (United States)

    2010-04-01

    ..., commodity rate classification, quantity, vessel flag category (U.S.-or foreign-flag), choice of ports, and... the United States. (2) Maximum charter rates. (i) USAID will not finance ocean freight under any... owner(s). (4) Maximum liner rates. USAID will not finance ocean freight for a cargo liner shipment at a...

  17. Maximum penetration level of distributed generation without violating voltage limits

    NARCIS (Netherlands)

    Morren, J.; Haan, de S.W.H.

    2009-01-01

    Connection of Distributed Generation (DG) units to a distribution network will result in a local voltage increase. As there will be a maximum on the allowable voltage increase, this will limit the maximum allowable penetration level of DG. By reactive power compensation (by the DG unit itself) a

  18. Particle Swarm Optimization Based of the Maximum Photovoltaic ...

    African Journals Online (AJOL)

    Photovoltaic electricity is seen as an important source of renewable energy. The photovoltaic array is an unstable source of power since the peak power point depends on the temperature and the irradiation level. A maximum peak power point tracking is then necessary for maximum efficiency. In this work, a Particle Swarm ...

  19. Maximum-entropy clustering algorithm and its global convergence analysis

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Constructing a batch of differentiable entropy functions touniformly approximate an objective function by means of the maximum-entropy principle, a new clustering algorithm, called maximum-entropy clustering algorithm, is proposed based on optimization theory. This algorithm is a soft generalization of the hard C-means algorithm and possesses global convergence. Its relations with other clustering algorithms are discussed.

  20. Application of maximum entropy to neutron tunneling spectroscopy

    International Nuclear Information System (INIS)

    Mukhopadhyay, R.; Silver, R.N.

    1990-01-01

    We demonstrate the maximum entropy method for the deconvolution of high resolution tunneling data acquired with a quasielastic spectrometer. Given a precise characterization of the instrument resolution function, a maximum entropy analysis of lutidine data obtained with the IRIS spectrometer at ISIS results in an effective factor of three improvement in resolution. 7 refs., 4 figs

  1. The regulation of starch accumulation in Panicum maximum Jacq ...

    African Journals Online (AJOL)

    ... decrease the starch level. These observations are discussed in relation to the photosynthetic characteristics of P. maximum. Keywords: accumulation; botany; carbon assimilation; co2 fixation; growth conditions; mesophyll; metabolites; nitrogen; nitrogen levels; nitrogen supply; panicum maximum; plant physiology; starch; ...

  2. 32 CFR 842.35 - Depreciation and maximum allowances.

    Science.gov (United States)

    2010-07-01

    ... 32 National Defense 6 2010-07-01 2010-07-01 false Depreciation and maximum allowances. 842.35... LITIGATION ADMINISTRATIVE CLAIMS Personnel Claims (31 U.S.C. 3701, 3721) § 842.35 Depreciation and maximum allowances. The military services have jointly established the “Allowance List-Depreciation Guide” to...

  3. The maximum significant wave height in the Southern North Sea

    NARCIS (Netherlands)

    Bouws, E.; Tolman, H.L.; Holthuijsen, L.H.; Eldeberky, Y.; Booij, N.; Ferier, P.

    1995-01-01

    The maximum possible wave conditions along the Dutch coast, which seem to be dominated by the limited water depth, have been estimated in the present study with numerical simulations. Discussions with meteorologists suggest that the maximum possible sustained wind speed in North Sea conditions is

  4. PTree: pattern-based, stochastic search for maximum parsimony phylogenies

    OpenAIRE

    Gregor, Ivan; Steinbr?ck, Lars; McHardy, Alice C.

    2013-01-01

    Phylogenetic reconstruction is vital to analyzing the evolutionary relationship of genes within and across populations of different species. Nowadays, with next generation sequencing technologies producing sets comprising thousands of sequences, robust identification of the tree topology, which is optimal according to standard criteria such as maximum parsimony, maximum likelihood or posterior probability, with phylogenetic inference methods is a computationally very demanding task. Here, we ...

  5. 5 CFR 838.711 - Maximum former spouse survivor annuity.

    Science.gov (United States)

    2010-01-01

    ... 5 Administrative Personnel 2 2010-01-01 2010-01-01 false Maximum former spouse survivor annuity... Orders Awarding Former Spouse Survivor Annuities Limitations on Survivor Annuities § 838.711 Maximum former spouse survivor annuity. (a) Under CSRS, payments under a court order may not exceed the amount...

  6. Maximum physical capacity testing in cancer patients undergoing chemotherapy

    DEFF Research Database (Denmark)

    Knutsen, L.; Quist, M; Midtgaard, J

    2006-01-01

    BACKGROUND: Over the past few years there has been a growing interest in the field of physical exercise in rehabilitation of cancer patients, leading to requirements for objective maximum physical capacity measurement (maximum oxygen uptake (VO(2max)) and one-repetition maximum (1RM)) to determin...... early in the treatment process. However, the patients were self-referred and thus highly motivated and as such are not necessarily representative of the whole population of cancer patients treated with chemotherapy....... in performing maximum physical capacity tests as these motivated them through self-perceived competitiveness and set a standard that served to encourage peak performance. CONCLUSION: The positive attitudes in this sample towards maximum physical capacity open the possibility of introducing physical testing...

  7. Maximum Principles for Discrete and Semidiscrete Reaction-Diffusion Equation

    Directory of Open Access Journals (Sweden)

    Petr Stehlík

    2015-01-01

    Full Text Available We study reaction-diffusion equations with a general reaction function f on one-dimensional lattices with continuous or discrete time ux′  (or  Δtux=k(ux-1-2ux+ux+1+f(ux, x∈Z. We prove weak and strong maximum and minimum principles for corresponding initial-boundary value problems. Whereas the maximum principles in the semidiscrete case (continuous time exhibit similar features to those of fully continuous reaction-diffusion model, in the discrete case the weak maximum principle holds for a smaller class of functions and the strong maximum principle is valid in a weaker sense. We describe in detail how the validity of maximum principles depends on the nonlinearity and the time step. We illustrate our results on the Nagumo equation with the bistable nonlinearity.

  8. 78 FR 9845 - Minimum and Ordinary Maximum and Aggravated Maximum Civil Monetary Penalties for a Violation of...

    Science.gov (United States)

    2013-02-12

    ... maximum penalty amount of $75,000 for each violation, except that if the violation results in death... the maximum civil penalty for a violation is $175,000 if the violation results in death, serious... Penalties for a Violation of the Hazardous Materials Transportation Laws or Regulations, Orders, Special...

  9. A Simulated Annealing Algorithm for Maximum Common Edge Subgraph Detection in Biological Networks

    DEFF Research Database (Denmark)

    Larsen, Simon; Alkærsig, Frederik G.; Ditzel, Henrik

    2016-01-01

    Network alignment is a challenging computational problem that identifies node or edge mappings between two or more networks, with the aim to unravel common patterns among them. Pairwise network alignment is already intractable, making multiple network comparison even more difficult. Here, we intr...

  10. Parameters determining maximum wind velocity in a tropical cyclone

    International Nuclear Information System (INIS)

    Choudhury, A.M.

    1984-09-01

    The spiral structure of a tropical cyclone was earlier explained by a tangential velocity distribution which varies inversely as the distance from the cyclone centre outside the circle of maximum wind speed. The case has been extended in the present paper by adding a radial velocity. It has been found that a suitable combination of radial and tangential velocities can account for the spiral structure of a cyclone. This enables parametrization of the cyclone. Finally a formula has been derived relating maximum velocity in a tropical cyclone with angular momentum, radius of maximum wind speed and the spiral angle. The shapes of the spirals have been computed for various spiral angles. (author)

  11. Enthalpic discrimination of homochiral pairwise interactions: Enantiomers of proline and hydroxyproline in (dimethyl formamide (DMF) + H2O) and (dimethylsulfoxide (DMSO) + H2O) mixtures at 298.15 K

    International Nuclear Information System (INIS)

    Hu, Xin-Gen; Liu, Jia-Min; Guo, Zheng; Liang, Hong-Yu; Jia, Zhao-Peng; Cheng, Wei-Na; Guo, Ai-Di; Zhang, He-Juan

    2013-01-01

    Highlights: • The h xx values of each α-amino acids decrease gradually with the mass fractions of cosolvents. • The absolute values of h xx of L-enantiomers are larger than D-enantiomers in the range w COS = 0 to 0.30. • The h xx values of the two proline enantiomers are all positive at each composition of mixed solvents. • When a hydrophilic hydroxyl group is introduced into proline enantiomers, the values of h xx become negative. -- Abstract: Dilution enthalpies of two pairs of α-amino acid enantiomers, namely L-proline vsD-proline, and L-hydroxyproline vsD-hydroxyproline, in water-rich regions of dimethyl formamide (DMF) + H 2 O and dimethylsulfoxide (DMSO) + H 2 O mixtures (mass fractions of cosolvents w COS = 0 to 0.30) have been determined respectively at 298.15 K by isothermal titration calorimetry (ITC). The successive values of dilution enthalpy obtained in a single run of ITC determination were used to calculate homochiral enthalpic pairwise interaction coefficients (h xx ) at the corresponding composition of mixed solvents according to the McMillan–Mayer’ statistical thermodynamic approach. The sign and magnitude of h xx were interpreted in terms of solute–solute interactions mediated by solvent and cosolvent molecules, and preferential configurations of homochiral pairwise interactions (L–L or D–D pairs) in aqueous solutions. The variations of h xx with w COS were considered to be dependent greatly on the competition equilibrium between hydrophobic and hydrophilic interactions, as well as the structural alteration of water caused by the two highly polar aprotic cosolvents (DMF and DMSO). Especially, it was found that when one of the two kinds of interactions (hydrophobic or hydrophilic interactions) preponderates over the other in solutions, enthalpic effect of homochiral pairwise interactions is always remarkable, and is characterized by a large absolute value of h xx , positive or negative, which corresponds respectively to the

  12. Environmental Monitoring, Water Quality - Total Maximum Daily Load (TMDL)

    Data.gov (United States)

    NSGIC Education | GIS Inventory — The Clean Water Act Section 303(d) establishes the Total Maximum Daily Load (TMDL) program. The purpose of the TMDL program is to identify sources of pollution and...

  13. Probabilistic maximum-value wind prediction for offshore environments

    DEFF Research Database (Denmark)

    Staid, Andrea; Pinson, Pierre; Guikema, Seth D.

    2015-01-01

    statistical models to predict the full distribution of the maximum-value wind speeds in a 3 h interval. We take a detailed look at the performance of linear models, generalized additive models and multivariate adaptive regression splines models using meteorological covariates such as gust speed, wind speed......, convective available potential energy, Charnock, mean sea-level pressure and temperature, as given by the European Center for Medium-Range Weather Forecasts forecasts. The models are trained to predict the mean value of maximum wind speed, and the residuals from training the models are used to develop...... the full probabilistic distribution of maximum wind speed. Knowledge of the maximum wind speed for an offshore location within a given period can inform decision-making regarding turbine operations, planned maintenance operations and power grid scheduling in order to improve safety and reliability...

  14. Combining Experiments and Simulations Using the Maximum Entropy Principle

    DEFF Research Database (Denmark)

    Boomsma, Wouter; Ferkinghoff-Borg, Jesper; Lindorff-Larsen, Kresten

    2014-01-01

    are not in quantitative agreement with experimental data. The principle of maximum entropy is a general procedure for constructing probability distributions in the light of new data, making it a natural tool in cases when an initial model provides results that are at odds with experiments. The number of maximum entropy...... in the context of a simple example, after which we proceed with a real-world application in the field of molecular simulations, where the maximum entropy procedure has recently provided new insight. Given the limited accuracy of force fields, macromolecular simulations sometimes produce results....... Three very recent papers have explored this problem using the maximum entropy approach, providing both new theoretical and practical insights to the problem. We highlight each of these contributions in turn and conclude with a discussion on remaining challenges....

  15. Parametric optimization of thermoelectric elements footprint for maximum power generation

    DEFF Research Database (Denmark)

    Rezania, A.; Rosendahl, Lasse; Yin, Hao

    2014-01-01

    The development studies in thermoelectric generator (TEG) systems are mostly disconnected to parametric optimization of the module components. In this study, optimum footprint ratio of n- and p-type thermoelectric (TE) elements is explored to achieve maximum power generation, maximum cost......-performance, and variation of efficiency in the uni-couple over a wide range of the heat transfer coefficient on the cold junction. The three-dimensional (3D) governing equations of the thermoelectricity and the heat transfer are solved using the finite element method (FEM) for temperature dependent properties of TE...... materials. The results, which are in good agreement with the previous computational studies, show that the maximum power generation and the maximum cost-performance in the module occur at An/Ap

  16. Ethylene Production Maximum Achievable Control Technology (MACT) Compliance Manual

    Science.gov (United States)

    This July 2006 document is intended to help owners and operators of ethylene processes understand and comply with EPA's maximum achievable control technology standards promulgated on July 12, 2002, as amended on April 13, 2005 and April 20, 2006.

  17. ORIGINAL ARTICLES Surgical practice in a maximum security prison

    African Journals Online (AJOL)

    Prison Clinic, Mangaung Maximum Security Prison, Bloemfontein. F Kleinhans, BA (Cur) .... HIV positivity rate and the use of the rectum to store foreign objects. ... fruit in sunlight. Other positive health-promoting factors may also play a role,.

  18. A technique for estimating maximum harvesting effort in a stochastic ...

    Indian Academy of Sciences (India)

    Unknown

    Estimation of maximum harvesting effort has a great impact on the ... fluctuating environment has been developed in a two-species competitive system, which shows that under realistic .... The existence and local stability properties of the equi-.

  19. Water Quality Assessment and Total Maximum Daily Loads Information (ATTAINS)

    Data.gov (United States)

    U.S. Environmental Protection Agency — The Water Quality Assessment TMDL Tracking And Implementation System (ATTAINS) stores and tracks state water quality assessment decisions, Total Maximum Daily Loads...

  20. Post optimization paradigm in maximum 3-satisfiability logic programming

    Science.gov (United States)

    Mansor, Mohd. Asyraf; Sathasivam, Saratha; Kasihmuddin, Mohd Shareduwan Mohd

    2017-08-01

    Maximum 3-Satisfiability (MAX-3SAT) is a counterpart of the Boolean satisfiability problem that can be treated as a constraint optimization problem. It deals with a conundrum of searching the maximum number of satisfied clauses in a particular 3-SAT formula. This paper presents the implementation of enhanced Hopfield network in hastening the Maximum 3-Satisfiability (MAX-3SAT) logic programming. Four post optimization techniques are investigated, including the Elliot symmetric activation function, Gaussian activation function, Wavelet activation function and Hyperbolic tangent activation function. The performances of these post optimization techniques in accelerating MAX-3SAT logic programming will be discussed in terms of the ratio of maximum satisfied clauses, Hamming distance and the computation time. Dev-C++ was used as the platform for training, testing and validating our proposed techniques. The results depict the Hyperbolic tangent activation function and Elliot symmetric activation function can be used in doing MAX-3SAT logic programming.