WorldWideScience

Sample records for scale structure inference

  1. Inferring synaptic structure in presence of neural interaction time scales.

    Directory of Open Access Journals (Sweden)

    Cristiano Capone

    Full Text Available Biological networks display a variety of activity patterns reflecting a web of interactions that is complex both in space and time. Yet inference methods have mainly focused on reconstructing, from the network's activity, the spatial structure, by assuming equilibrium conditions or, more recently, a probabilistic dynamics with a single arbitrary time-step. Here we show that, under this latter assumption, the inference procedure fails to reconstruct the synaptic matrix of a network of integrate-and-fire neurons when the chosen time scale of interaction does not closely match the synaptic delay or when no single time scale for the interaction can be identified; such failure, moreover, exposes a distinctive bias of the inference method that can lead to infer as inhibitory the excitatory synapses with interaction time scales longer than the model's time-step. We therefore introduce a new two-step method, that first infers through cross-correlation profiles the delay-structure of the network and then reconstructs the synaptic matrix, and successfully test it on networks with different topologies and in different activity regimes. Although step one is able to accurately recover the delay-structure of the network, thus getting rid of any a priori guess about the time scales of the interaction, the inference method introduces nonetheless an arbitrary time scale, the time-bin dt used to binarize the spike trains. We therefore analytically and numerically study how the choice of dt affects the inference in our network model, finding that the relationship between the inferred couplings and the real synaptic efficacies, albeit being quadratic in both cases, depends critically on dt for the excitatory synapses only, whilst being basically independent of it for the inhibitory ones.

  2. Unifying Inference of Meso-Scale Structures in Networks.

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    Birkan Tunç

    Full Text Available Networks are among the most prevalent formal representations in scientific studies, employed to depict interactions between objects such as molecules, neuronal clusters, or social groups. Studies performed at meso-scale that involve grouping of objects based on their distinctive interaction patterns form one of the main lines of investigation in network science. In a social network, for instance, meso-scale structures can correspond to isolated social groupings or groups of individuals that serve as a communication core. Currently, the research on different meso-scale structures such as community and core-periphery structures has been conducted via independent approaches, which precludes the possibility of an algorithmic design that can handle multiple meso-scale structures and deciding which structure explains the observed data better. In this study, we propose a unified formulation for the algorithmic detection and analysis of different meso-scale structures. This facilitates the investigation of hybrid structures that capture the interplay between multiple meso-scale structures and statistical comparison of competing structures, all of which have been hitherto unavailable. We demonstrate the applicability of the methodology in analyzing the human brain network, by determining the dominant organizational structure (communities of the brain, as well as its auxiliary characteristics (core-periphery.

  3. Unifying Inference of Meso-Scale Structures in Networks.

    Science.gov (United States)

    Tunç, Birkan; Verma, Ragini

    2015-01-01

    Networks are among the most prevalent formal representations in scientific studies, employed to depict interactions between objects such as molecules, neuronal clusters, or social groups. Studies performed at meso-scale that involve grouping of objects based on their distinctive interaction patterns form one of the main lines of investigation in network science. In a social network, for instance, meso-scale structures can correspond to isolated social groupings or groups of individuals that serve as a communication core. Currently, the research on different meso-scale structures such as community and core-periphery structures has been conducted via independent approaches, which precludes the possibility of an algorithmic design that can handle multiple meso-scale structures and deciding which structure explains the observed data better. In this study, we propose a unified formulation for the algorithmic detection and analysis of different meso-scale structures. This facilitates the investigation of hybrid structures that capture the interplay between multiple meso-scale structures and statistical comparison of competing structures, all of which have been hitherto unavailable. We demonstrate the applicability of the methodology in analyzing the human brain network, by determining the dominant organizational structure (communities) of the brain, as well as its auxiliary characteristics (core-periphery).

  4. Probing the Small-scale Structure in Strongly Lensed Systems via Transdimensional Inference

    Science.gov (United States)

    Daylan, Tansu; Cyr-Racine, Francis-Yan; Diaz Rivero, Ana; Dvorkin, Cora; Finkbeiner, Douglas P.

    2018-02-01

    Strong lensing is a sensitive probe of the small-scale density fluctuations in the Universe. We implement a pipeline to model strongly lensed systems using probabilistic cataloging, which is a transdimensional, hierarchical, and Bayesian framework to sample from a metamodel (union of models with different dimensionality) consistent with observed photon count maps. Probabilistic cataloging allows one to robustly characterize modeling covariances within and across lens models with different numbers of subhalos. Unlike traditional cataloging of subhalos, it does not require model subhalos to improve the goodness of fit above the detection threshold. Instead, it allows the exploitation of all information contained in the photon count maps—for instance, when constraining the subhalo mass function. We further show that, by not including these small subhalos in the lens model, fixed-dimensional inference methods can significantly mismodel the data. Using a simulated Hubble Space Telescope data set, we show that the subhalo mass function can be probed even when many subhalos in the sample catalogs are individually below the detection threshold and would be absent in a traditional catalog. The implemented software, Probabilistic Cataloger (PCAT) is made publicly available at https://github.com/tdaylan/pcat.

  5. Small-scale structure of the geodynamo inferred from Ørsted and Magsat satellite data

    DEFF Research Database (Denmark)

    Hulot, G.; Eymin, C.; Langlais, B.

    2002-01-01

    The 'geodynamo' in the Earth's liquid outer core produces a magnetic field that dominates the large and medium length scales of the magnetic field observed at the Earth's surface(1,2). Here we use data from the currently operating Danish Oersted(3) satellite, and from the US Magsat(2) satellite...... that operated in 1979/80, to identify and interpret variations in the magnetic field over the past 20 years, down to length scales previously inaccessible. Projected down to the surface of the Earth's core, we found these variations to be small below the Pacific Ocean, and large at polar latitudes...... and in a region centred below southern Africa. The flow pattern at the surface of the core that we calculate to account for these changes is characterized by a westward flow concentrated in retrograde polar vortices and an asymmetric ring where prograde vortices are correlated with highs (and retrograde vortices...

  6. CONE: Community Oriented Network Estimation Is a Versatile Framework for Inferring Population Structure in Large-Scale Sequencing Data

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    Markku O. Kuismin

    2017-10-01

    Full Text Available Estimation of genetic population structure based on molecular markers is a common task in population genetics and ecology. We apply a generalized linear model with LASSO regularization to infer relationships between individuals and populations from molecular marker data. Specifically, we apply a neighborhood selection algorithm to infer population genetic structure and gene flow between populations. The resulting relationships are used to construct an individual-level population graph. Different network substructures known as communities are then dissociated from each other using a community detection algorithm. Inference of population structure using networks combines the good properties of: (i network theory (broad collection of tools, including aesthetically pleasing visualization, (ii principal component analysis (dimension reduction together with simple visual inspection, and (iii model-based methods (e.g., ancestry coefficient estimates. We have named our process CONE (for community oriented network estimation. CONE has fewer restrictions than conventional assignment methods in that properties such as the number of subpopulations need not be fixed before the analysis and the sample may include close relatives or involve uneven sampling. Applying CONE on simulated data sets resulted in more accurate estimates of the true number of subpopulations than model-based methods, and provided comparable ancestry coefficient estimates. Inference of empirical data sets of teosinte single nucleotide polymorphism, bacterial disease outbreak, and the human genome diversity panel illustrate that population structures estimated with CONE are consistent with the earlier findings

  7. CONE: Community Oriented Network Estimation Is a Versatile Framework for Inferring Population Structure in Large-Scale Sequencing Data.

    Science.gov (United States)

    Kuismin, Markku O; Ahlinder, Jon; Sillanpӓӓ, Mikko J

    2017-10-05

    Estimation of genetic population structure based on molecular markers is a common task in population genetics and ecology. We apply a generalized linear model with LASSO regularization to infer relationships between individuals and populations from molecular marker data. Specifically, we apply a neighborhood selection algorithm to infer population genetic structure and gene flow between populations. The resulting relationships are used to construct an individual-level population graph. Different network substructures known as communities are then dissociated from each other using a community detection algorithm. Inference of population structure using networks combines the good properties of: (i) network theory (broad collection of tools, including aesthetically pleasing visualization), (ii) principal component analysis (dimension reduction together with simple visual inspection), and (iii) model-based methods (e.g., ancestry coefficient estimates). We have named our process CONE (for community oriented network estimation). CONE has fewer restrictions than conventional assignment methods in that properties such as the number of subpopulations need not be fixed before the analysis and the sample may include close relatives or involve uneven sampling. Applying CONE on simulated data sets resulted in more accurate estimates of the true number of subpopulations than model-based methods, and provided comparable ancestry coefficient estimates. Inference of empirical data sets of teosinte single nucleotide polymorphism, bacterial disease outbreak, and the human genome diversity panel illustrate that population structures estimated with CONE are consistent with the earlier findings. Copyright © 2017 Kuismin et al.

  8. Inferring network structure from cascades

    Science.gov (United States)

    Ghonge, Sushrut; Vural, Dervis Can

    2017-07-01

    Many physical, biological, and social phenomena can be described by cascades taking place on a network. Often, the activity can be empirically observed, but not the underlying network of interactions. In this paper we offer three topological methods to infer the structure of any directed network given a set of cascade arrival times. Our formulas hold for a very general class of models where the activation probability of a node is a generic function of its degree and the number of its active neighbors. We report high success rates for synthetic and real networks, for several different cascade models.

  9. Quantifying the multi-scale performance of network inference algorithms.

    Science.gov (United States)

    Oates, Chris J; Amos, Richard; Spencer, Simon E F

    2014-10-01

    Graphical models are widely used to study complex multivariate biological systems. Network inference algorithms aim to reverse-engineer such models from noisy experimental data. It is common to assess such algorithms using techniques from classifier analysis. These metrics, based on ability to correctly infer individual edges, possess a number of appealing features including invariance to rank-preserving transformation. However, regulation in biological systems occurs on multiple scales and existing metrics do not take into account the correctness of higher-order network structure. In this paper novel performance scores are presented that share the appealing properties of existing scores, whilst capturing ability to uncover regulation on multiple scales. Theoretical results confirm that performance of a network inference algorithm depends crucially on the scale at which inferences are to be made; in particular strong local performance does not guarantee accurate reconstruction of higher-order topology. Applying these scores to a large corpus of data from the DREAM5 challenge, we undertake a data-driven assessment of estimator performance. We find that the "wisdom of crowds" network, that demonstrated superior local performance in the DREAM5 challenge, is also among the best performing methodologies for inference of regulation on multiple length scales.

  10. Nonparametric inference of network structure and dynamics

    Science.gov (United States)

    Peixoto, Tiago P.

    The network structure of complex systems determine their function and serve as evidence for the evolutionary mechanisms that lie behind them. Despite considerable effort in recent years, it remains an open challenge to formulate general descriptions of the large-scale structure of network systems, and how to reliably extract such information from data. Although many approaches have been proposed, few methods attempt to gauge the statistical significance of the uncovered structures, and hence the majority cannot reliably separate actual structure from stochastic fluctuations. Due to the sheer size and high-dimensionality of many networks, this represents a major limitation that prevents meaningful interpretations of the results obtained with such nonstatistical methods. In this talk, I will show how these issues can be tackled in a principled and efficient fashion by formulating appropriate generative models of network structure that can have their parameters inferred from data. By employing a Bayesian description of such models, the inference can be performed in a nonparametric fashion, that does not require any a priori knowledge or ad hoc assumptions about the data. I will show how this approach can be used to perform model comparison, and how hierarchical models yield the most appropriate trade-off between model complexity and quality of fit based on the statistical evidence present in the data. I will also show how this general approach can be elegantly extended to networks with edge attributes, that are embedded in latent spaces, and that change in time. The latter is obtained via a fully dynamic generative network model, based on arbitrary-order Markov chains, that can also be inferred in a nonparametric fashion. Throughout the talk I will illustrate the application of the methods with many empirical networks such as the internet at the autonomous systems level, the global airport network, the network of actors and films, social networks, citations among

  11. Efficient Exact Inference With Loss Augmented Objective in Structured Learning.

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    Bauer, Alexander; Nakajima, Shinichi; Muller, Klaus-Robert

    2016-08-19

    Structural support vector machine (SVM) is an elegant approach for building complex and accurate models with structured outputs. However, its applicability relies on the availability of efficient inference algorithms--the state-of-the-art training algorithms repeatedly perform inference to compute a subgradient or to find the most violating configuration. In this paper, we propose an exact inference algorithm for maximizing nondecomposable objectives due to special type of a high-order potential having a decomposable internal structure. As an important application, our method covers the loss augmented inference, which enables the slack and margin scaling formulations of structural SVM with a variety of dissimilarity measures, e.g., Hamming loss, precision and recall, Fβ-loss, intersection over union, and many other functions that can be efficiently computed from the contingency table. We demonstrate the advantages of our approach in natural language parsing and sequence segmentation applications.

  12. Inference problems in structural biology

    DEFF Research Database (Denmark)

    Olsson, Simon

    The structure and dynamics of biological molecules are essential for their function. Consequently, a wealth of experimental techniques have been developed to study these features. However, while experiments yield detailed information about geometrical features of molecules, this information is of...

  13. Scale dependent inference in landscape genetics

    Science.gov (United States)

    Samuel A. Cushman; Erin L. Landguth

    2010-01-01

    Ecological relationships between patterns and processes are highly scale dependent. This paper reports the first formal exploration of how changing scale of research away from the scale of the processes governing gene flow affects the results of landscape genetic analysis. We used an individual-based, spatially explicit simulation model to generate patterns of genetic...

  14. Inferring ontology graph structures using OWL reasoning

    KAUST Repository

    Rodriguez-Garcia, Miguel Angel

    2018-01-05

    Ontologies are representations of a conceptualization of a domain. Traditionally, ontologies in biology were represented as directed acyclic graphs (DAG) which represent the backbone taxonomy and additional relations between classes. These graphs are widely exploited for data analysis in the form of ontology enrichment or computation of semantic similarity. More recently, ontologies are developed in a formal language such as the Web Ontology Language (OWL) and consist of a set of axioms through which classes are defined or constrained. While the taxonomy of an ontology can be inferred directly from the axioms of an ontology as one of the standard OWL reasoning tasks, creating general graph structures from OWL ontologies that exploit the ontologies\\' semantic content remains a challenge.We developed a method to transform ontologies into graphs using an automated reasoner while taking into account all relations between classes. Searching for (existential) patterns in the deductive closure of ontologies, we can identify relations between classes that are implied but not asserted and generate graph structures that encode for a large part of the ontologies\\' semantic content. We demonstrate the advantages of our method by applying it to inference of protein-protein interactions through semantic similarity over the Gene Ontology and demonstrate that performance is increased when graph structures are inferred using deductive inference according to our method. Our software and experiment results are available at http://github.com/bio-ontology-research-group/Onto2Graph .Onto2Graph is a method to generate graph structures from OWL ontologies using automated reasoning. The resulting graphs can be used for improved ontology visualization and ontology-based data analysis.

  15. A Robust Method for Inferring Network Structures.

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    Yang, Yang; Luo, Tingjin; Li, Zhoujun; Zhang, Xiaoming; Yu, Philip S

    2017-07-12

    Inferring the network structure from limited observable data is significant in molecular biology, communication and many other areas. It is challenging, primarily because the observable data are sparse, finite and noisy. The development of machine learning and network structure study provides a great chance to solve the problem. In this paper, we propose an iterative smoothing algorithm with structure sparsity (ISSS) method. The elastic penalty in the model is introduced for the sparse solution, identifying group features and avoiding over-fitting, and the total variation (TV) penalty in the model can effectively utilize the structure information to identify the neighborhood of the vertices. Due to the non-smoothness of the elastic and structural TV penalties, an efficient algorithm with the Nesterov's smoothing optimization technique is proposed to solve the non-smooth problem. The experimental results on both synthetic and real-world networks show that the proposed model is robust against insufficient data and high noise. In addition, we investigate many factors that play important roles in identifying the performance of ISSS.

  16. Inferring cell-scale signalling networks via compressive sensing.

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    Lei Nie

    Full Text Available Signalling network inference is a central problem in system biology. Previous studies investigate this problem by independently inferring local signalling networks and then linking them together via crosstalk. Since a cellular signalling system is in fact indivisible, this reductionistic approach may have an impact on the accuracy of the inference results. Preferably, a cell-scale signalling network should be inferred as a whole. However, the holistic approach suffers from three practical issues: scalability, measurement and overfitting. Here we make this approach feasible based on two key observations: 1 variations of concentrations are sparse due to separations of timescales; 2 several species can be measured together using cross-reactivity. We propose a method, CCELL, for cell-scale signalling network inference from time series generated by immunoprecipitation using Bayesian compressive sensing. A set of benchmark networks with varying numbers of time-variant species is used to demonstrate the effectiveness of our method. Instead of exhaustively measuring all individual species, high accuracy is achieved from relatively few measurements.

  17. Genetic structure of earthworm populations at a regional scale: inferences from mitochondrial and microsatellite molecular markers in Aporrectodea icterica (Savigny 1826).

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    Torres-Leguizamon, Magally; Mathieu, Jérôme; Decaëns, Thibaud; Dupont, Lise

    2014-01-01

    Despite the fundamental role that soil invertebrates (e.g. earthworms) play in soil ecosystems, the magnitude of their spatial genetic variation is still largely unknown and only a few studies have investigated the population genetic structure of these organisms. Here, we investigated the genetic structure of seven populations of a common endogeic earthworm (Aporrectodea icterica) sampled in northern France to explore how historical species range changes, microevolutionary processes and human activities interact in shaping genetic variation at a regional scale. Because combining markers with distinct modes of inheritance can provide extra, complementary information on gene flow, we compared the patterns of genetic structure revealed using nuclear (7 microsatellite loci) and mitochondrial markers (COI). Both types of markers indicated low genetic polymorphism compared to other earthworm species, a result that can be attributed to ancient bottlenecks, for instance due to species isolation in southern refugia during the ice ages with subsequent expansion toward northern Europe. Historical events can also be responsible for the existence of two divergent, but randomly interbreeding mitochondrial lineages within all study populations. In addition, the comparison of observed heterozygosity among microsatellite loci and heterozygosity expected under mutation-drift equilibrium suggested a recent decrease in effective size in some populations that could be due to contemporary events such as habitat fragmentation. The absence of relationship between geographic and genetic distances estimated from microsatellite allele frequency data also suggested that dispersal is haphazard and that human activities favour passive dispersal among geographically distant populations.

  18. Genetic structure of earthworm populations at a regional scale: inferences from mitochondrial and microsatellite molecular markers in Aporrectodea icterica (Savigny 1826.

    Directory of Open Access Journals (Sweden)

    Magally Torres-Leguizamon

    Full Text Available Despite the fundamental role that soil invertebrates (e.g. earthworms play in soil ecosystems, the magnitude of their spatial genetic variation is still largely unknown and only a few studies have investigated the population genetic structure of these organisms. Here, we investigated the genetic structure of seven populations of a common endogeic earthworm (Aporrectodea icterica sampled in northern France to explore how historical species range changes, microevolutionary processes and human activities interact in shaping genetic variation at a regional scale. Because combining markers with distinct modes of inheritance can provide extra, complementary information on gene flow, we compared the patterns of genetic structure revealed using nuclear (7 microsatellite loci and mitochondrial markers (COI. Both types of markers indicated low genetic polymorphism compared to other earthworm species, a result that can be attributed to ancient bottlenecks, for instance due to species isolation in southern refugia during the ice ages with subsequent expansion toward northern Europe. Historical events can also be responsible for the existence of two divergent, but randomly interbreeding mitochondrial lineages within all study populations. In addition, the comparison of observed heterozygosity among microsatellite loci and heterozygosity expected under mutation-drift equilibrium suggested a recent decrease in effective size in some populations that could be due to contemporary events such as habitat fragmentation. The absence of relationship between geographic and genetic distances estimated from microsatellite allele frequency data also suggested that dispersal is haphazard and that human activities favour passive dispersal among geographically distant populations.

  19. Toward a "structural BLAST": using structural relationships to infer function.

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    Dey, Fabian; Cliff Zhang, Qiangfeng; Petrey, Donald; Honig, Barry

    2013-04-01

    We outline a set of strategies to infer protein function from structure. The overall approach depends on extensive use of homology modeling, the exploitation of a wide range of global and local geometric relationships between protein structures and the use of machine learning techniques. The combination of modeling with broad searches of protein structure space defines a "structural BLAST" approach to infer function with high genomic coverage. Applications are described to the prediction of protein-protein and protein-ligand interactions. In the context of protein-protein interactions, our structure-based prediction algorithm, PrePPI, has comparable accuracy to high-throughput experiments. An essential feature of PrePPI involves the use of Bayesian methods to combine structure-derived information with non-structural evidence (e.g. co-expression) to assign a likelihood for each predicted interaction. This, combined with a structural BLAST approach significantly expands the range of applications of protein structure in the annotation of protein function, including systems level biological applications where it has previously played little role. Copyright © 2013 The Protein Society.

  20. Genetic structure of earthworm populations at a regional scale: inferences from mitochondrial and microsatellite molecular markers in Aporrectodea icterica (Savigny 1826)

    National Research Council Canada - National Science Library

    Torres-Leguizamon, Magally; Mathieu, Jérôme; Decaëns, Thibaud; Dupont, Lise

    2014-01-01

    ... (Aporrectodea icterica) sampled in northern France to explore how historical species range changes, microevolutionary processes and human activities interact in shaping genetic variation at a regional scale...

  1. Genetic Structure of Earthworm Populations at a Regional Scale: Inferences from Mitochondrial and Microsatellite Molecular Markers in Aporrectodea icterica (Savigny 1826): e101597

    National Research Council Canada - National Science Library

    Magally Torres-Leguizamon; Jérôme Mathieu; Thibaud Decaëns; Lise Dupont

    2014-01-01

    ... (Aporrectodea icterica) sampled in northern France to explore how historical species range changes, microevolutionary processes and human activities interact in shaping genetic variation at a regional scale...

  2. Inferring epidemic contact structure from phylogenetic trees.

    Directory of Open Access Journals (Sweden)

    Gabriel E Leventhal

    Full Text Available Contact structure is believed to have a large impact on epidemic spreading and consequently using networks to model such contact structure continues to gain interest in epidemiology. However, detailed knowledge of the exact contact structure underlying real epidemics is limited. Here we address the question whether the structure of the contact network leaves a detectable genetic fingerprint in the pathogen population. To this end we compare phylogenies generated by disease outbreaks in simulated populations with different types of contact networks. We find that the shape of these phylogenies strongly depends on contact structure. In particular, measures of tree imbalance allow us to quantify to what extent the contact structure underlying an epidemic deviates from a null model contact network and illustrate this in the case of random mixing. Using a phylogeny from the Swiss HIV epidemic, we show that this epidemic has a significantly more unbalanced tree than would be expected from random mixing.

  3. Quantum inferring acausal structures and the Monty Hall problem

    Science.gov (United States)

    Kurzyk, Dariusz; Glos, Adam

    2016-12-01

    This paper presents a quantum version of the Monty Hall problem based upon the quantum inferring acausal structures, which can be identified with generalization of Bayesian networks. Considered structures are expressed in formalism of quantum information theory, where density operators are identified with quantum generalization of probability distributions. Conditional relations between quantum counterpart of random variables are described by quantum conditional operators. Presented quantum inferring structures are used to construct a model inspired by scenario of well-known Monty Hall game, where we show the differences between classical and quantum Bayesian reasoning.

  4. Accelerated probabilistic inference of RNA structure evolution

    Directory of Open Access Journals (Sweden)

    Holmes Ian

    2005-03-01

    Full Text Available Abstract Background Pairwise stochastic context-free grammars (Pair SCFGs are powerful tools for evolutionary analysis of RNA, including simultaneous RNA sequence alignment and secondary structure prediction, but the associated algorithms are intensive in both CPU and memory usage. The same problem is faced by other RNA alignment-and-folding algorithms based on Sankoff's 1985 algorithm. It is therefore desirable to constrain such algorithms, by pre-processing the sequences and using this first pass to limit the range of structures and/or alignments that can be considered. Results We demonstrate how flexible classes of constraint can be imposed, greatly reducing the computational costs while maintaining a high quality of structural homology prediction. Any score-attributed context-free grammar (e.g. energy-based scoring schemes, or conditionally normalized Pair SCFGs is amenable to this treatment. It is now possible to combine independent structural and alignment constraints of unprecedented general flexibility in Pair SCFG alignment algorithms. We outline several applications to the bioinformatics of RNA sequence and structure, including Waterman-Eggert N-best alignments and progressive multiple alignment. We evaluate the performance of the algorithm on test examples from the RFAM database. Conclusion A program, Stemloc, that implements these algorithms for efficient RNA sequence alignment and structure prediction is available under the GNU General Public License.

  5. Accelerated probabilistic inference of RNA structure evolution.

    Science.gov (United States)

    Holmes, Ian

    2005-03-24

    Pairwise stochastic context-free grammars (Pair SCFGs) are powerful tools for evolutionary analysis of RNA, including simultaneous RNA sequence alignment and secondary structure prediction, but the associated algorithms are intensive in both CPU and memory usage. The same problem is faced by other RNA alignment-and-folding algorithms based on Sankoff's 1985 algorithm. It is therefore desirable to constrain such algorithms, by pre-processing the sequences and using this first pass to limit the range of structures and/or alignments that can be considered. We demonstrate how flexible classes of constraint can be imposed, greatly reducing the computational costs while maintaining a high quality of structural homology prediction. Any score-attributed context-free grammar (e.g. energy-based scoring schemes, or conditionally normalized Pair SCFGs) is amenable to this treatment. It is now possible to combine independent structural and alignment constraints of unprecedented general flexibility in Pair SCFG alignment algorithms. We outline several applications to the bioinformatics of RNA sequence and structure, including Waterman-Eggert N-best alignments and progressive multiple alignment. We evaluate the performance of the algorithm on test examples from the RFAM database. A program, Stemloc, that implements these algorithms for efficient RNA sequence alignment and structure prediction is available under the GNU General Public License.

  6. Inference

    DEFF Research Database (Denmark)

    Møller, Jesper

    .1 with the title ‘Inference'.) This contribution concerns statistical inference for parametric models used in stochastic geometry and based on quick and simple simulation free procedures as well as more comprehensive methods using Markov chain Monte Carlo (MCMC) simulations. Due to space limitations the focus......(This text written by Jesper Møller, Aalborg University, is submitted for the collection ‘Stochastic Geometry: Highlights, Interactions and New Perspectives', edited by Wilfrid S. Kendall and Ilya Molchanov, to be published by ClarendonPress, Oxford, and planned to appear as Section 4...... is on spatial point processes....

  7. Inference

    DEFF Research Database (Denmark)

    Møller, Jesper

    2010-01-01

    Chapter 9: This contribution concerns statistical inference for parametric models used in stochastic geometry and based on quick and simple simulation free procedures as well as more comprehensive methods based on a maximum likelihood or Bayesian approach combined with markov chain Monte Carlo...... (MCMC) techniques. Due to space limitations the focus is on spatial point processes....

  8. Dependence and independence: Structure and inference.

    Science.gov (United States)

    Vexler, Albert; Chen, Xiwei; Hutson, Alan D

    2017-10-01

    Evaluations of relationships between pairs of variables, including testing for independence, are increasingly important. Erich Leo Lehmann noted that "the study of the power and efficiency of tests of independence is complicated by the difficulty of defining natural classes of alternatives to the hypothesis of independence." This paper presents a general review, discussion and comparison of classical and novel tests of independence. We investigate a broad spectrum of dependence structures with/without random effects, including those that are well addressed in both the applied and the theoretical scientific literatures as well as scenarios when the classical tests of independence may break down completely. Motivated by practical considerations, the impact of random effects in dependence structures are studied in the additive and multiplicative forms. A novel index of dependence is proposed based on the area under the Kendall plot. In conjunction with the scatterplot and the Kendall plot, the proposed method provides a comprehensive presentation of the data in terms of graphing and conceptualizing the dependence. We also present a graphical methodology based on heat maps to effectively compare the powers of various tests. Practical examples illustrate the use of various tests of independence and the graphical representations of dependence structures.

  9. Large-scale structure

    CERN Document Server

    White, S D M

    1993-01-01

    Abstract. Recent observational surveys have made substantial progress in quantifying the structure of the Universe on large scales. Galaxy density and galaxy velocity fields show deviations from the predictions of a homogeneous and isotropic world model on scales approaching one percent of the current hori— zon scale. A comparison of the amplitudes in density and in velocity provides the first direct dynamical evidence in favour of a high mean density similar to that required for closure. The fluctuations observed on these scales have the amplitude predicted by the standard Cold Dark Matter (CDM) model when this model is normalised to agree with the microwave background fluc- tuations measured on much larger scales by the COBE satellite. However, a CDM model with this amplitude appears inconsistent with observational data on smaller scales. In addition it predicts a scale dependence of fluctua— tion amplitude which disagrees with that observed for galaxies in the APM survey of two million faint galaxi...

  10. Large scale inference in the Infinite Relational Model: Gibbs sampling is not enough

    DEFF Research Database (Denmark)

    Albers, Kristoffer Jon; Moth, Andreas Leon Aagard; Mørup, Morten

    2013-01-01

    The stochastic block-model and its non-parametric extension, the Infinite Relational Model (IRM), have become key tools for discovering group-structure in complex networks. Identifying these groups is a combinatorial inference problem which is usually solved by Gibbs sampling. However, whether...... Gibbs sampling suffices and can be scaled to the modeling of large scale real world complex networks has not been examined sufficiently. In this paper we evaluate the performance and mixing ability of Gibbs sampling in the Infinite Relational Model (IRM) by implementing a high performance Gibbs sampler....... We find that Gibbs sampling can be computationally scaled to handle millions of nodes and billions of links. Investigating the behavior of the Gibbs sampler for different sizes of networks we find that the mixing ability decreases drastically with the network size, clearly indicating a need...

  11. Causal inference between bioavailability of heavy metals and environmental factors in a large-scale region.

    Science.gov (United States)

    Liu, Yuqiong; Du, Qingyun; Wang, Qi; Yu, Huanyun; Liu, Jianfeng; Tian, Yu; Chang, Chunying; Lei, Jing

    2017-07-01

    The causation between bioavailability of heavy metals and environmental factors are generally obtained from field experiments at local scales at present, and lack sufficient evidence from large scales. However, inferring causation between bioavailability of heavy metals and environmental factors across large-scale regions is challenging. Because the conventional correlation-based approaches used for causation assessments across large-scale regions, at the expense of actual causation, can result in spurious insights. In this study, a general approach framework, Intervention calculus when the directed acyclic graph (DAG) is absent (IDA) combined with the backdoor criterion (BC), was introduced to identify causation between the bioavailability of heavy metals and the potential environmental factors across large-scale regions. We take the Pearl River Delta (PRD) in China as a case study. The causal structures and effects were identified based on the concentrations of heavy metals (Zn, As, Cu, Hg, Pb, Cr, Ni and Cd) in soil (0-20 cm depth) and vegetable (lettuce) and 40 environmental factors (soil properties, extractable heavy metals and weathering indices) in 94 samples across the PRD. Results show that the bioavailability of heavy metals (Cd, Zn, Cr, Ni and As) was causally influenced by soil properties and soil weathering factors, whereas no causal factor impacted the bioavailability of Cu, Hg and Pb. No latent factor was found between the bioavailability of heavy metals and environmental factors. The causation between the bioavailability of heavy metals and environmental factors at field experiments is consistent with that on a large scale. The IDA combined with the BC provides a powerful tool to identify causation between the bioavailability of heavy metals and environmental factors across large-scale regions. Causal inference in a large system with the dynamic changes has great implications for system-based risk management. Copyright © 2017 Elsevier Ltd. All

  12. Statistical inference and visualization in scale-space for spatially dependent images

    KAUST Repository

    Vaughan, Amy

    2012-03-01

    SiZer (SIgnificant ZERo crossing of the derivatives) is a graphical scale-space visualization tool that allows for statistical inferences. In this paper we develop a spatial SiZer for finding significant features and conducting goodness-of-fit tests for spatially dependent images. The spatial SiZer utilizes a family of kernel estimates of the image and provides not only exploratory data analysis but also statistical inference with spatial correlation taken into account. It is also capable of comparing the observed image with a specific null model being tested by adjusting the statistical inference using an assumed covariance structure. Pixel locations having statistically significant differences between the image and a given null model are highlighted by arrows. The spatial SiZer is compared with the existing independent SiZer via the analysis of simulated data with and without signal on both planar and spherical domains. We apply the spatial SiZer method to the decadal temperature change over some regions of the Earth. © 2011 The Korean Statistical Society.

  13. Bayesian Inference for Structured Spike and Slab Priors

    DEFF Research Database (Denmark)

    Andersen, Michael Riis; Winther, Ole; Hansen, Lars Kai

    2014-01-01

    Sparse signal recovery addresses the problem of solving underdetermined linear inverse problems subject to a sparsity constraint. We propose a novel prior formulation, the structured spike and slab prior, which allows to incorporate a priori knowledge of the sparsity pattern by imposing a spatial...... Gaussian process on the spike and slab probabilities. Thus, prior information on the structure of the sparsity pattern can be encoded using generic covariance functions. Furthermore, we provide a Bayesian inference scheme for the proposed model based on the expectation propagation framework. Using...

  14. Large scale statistical inference of signaling pathways from RNAi and microarray data

    Directory of Open Access Journals (Sweden)

    Poustka Annemarie

    2007-10-01

    Full Text Available Abstract Background The advent of RNA interference techniques enables the selective silencing of biologically interesting genes in an efficient way. In combination with DNA microarray technology this enables researchers to gain insights into signaling pathways by observing downstream effects of individual knock-downs on gene expression. These secondary effects can be used to computationally reverse engineer features of the upstream signaling pathway. Results In this paper we address this challenging problem by extending previous work by Markowetz et al., who proposed a statistical framework to score networks hypotheses in a Bayesian manner. Our extensions go in three directions: First, we introduce a way to omit the data discretization step needed in the original framework via a calculation based on p-values instead. Second, we show how prior assumptions on the network structure can be incorporated into the scoring scheme using regularization techniques. Third and most important, we propose methods to scale up the original approach, which is limited to around 5 genes, to large scale networks. Conclusion Comparisons of these methods on artificial data are conducted. Our proposed module network is employed to infer the signaling network between 13 genes in the ER-α pathway in human MCF-7 breast cancer cells. Using a bootstrapping approach this reconstruction can be found with good statistical stability. The code for the module network inference method is available in the latest version of the R-package nem, which can be obtained from the Bioconductor homepage.

  15. Inference and Evolutionary Analysis of Genome-Scale Regulatory Networks in Large Phylogenies.

    Science.gov (United States)

    Koch, Christopher; Konieczka, Jay; Delorey, Toni; Lyons, Ana; Socha, Amanda; Davis, Kathleen; Knaack, Sara A; Thompson, Dawn; O'Shea, Erin K; Regev, Aviv; Roy, Sushmita

    2017-05-24

    Changes in transcriptional regulatory networks can significantly contribute to species evolution and adaptation. However, identification of genome-scale regulatory networks is an open challenge, especially in non-model organisms. Here, we introduce multi-species regulatory network learning (MRTLE), a computational approach that uses phylogenetic structure, sequence-specific motifs, and transcriptomic data, to infer the regulatory networks in different species. Using simulated data from known networks and transcriptomic data from six divergent yeasts, we demonstrate that MRTLE predicts networks with greater accuracy than existing methods because it incorporates phylogenetic information. We used MRTLE to infer the structure of the transcriptional networks that control the osmotic stress responses of divergent, non-model yeast species and then validated our predictions experimentally. Interrogating these networks reveals that gene duplication promotes network divergence across evolution. Taken together, our approach facilitates study of regulatory network evolutionary dynamics across multiple poorly studied species. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  16. Multi-scale marine biodiversity patterns inferred efficiently from habitat image processing.

    Science.gov (United States)

    Mellin, Camille; Parrott, Lael; Andréfouët, Serge; Bradshaw, Corey J A; MacNeil, M Aaron; Caley, M Julian

    2012-04-01

    Cost-effective proxies of biodiversity and species abundance, applicable across a range of spatial scales, are needed for setting conservation priorities and planning action. We outline a rapid, efficient, and low-cost measure of spectral signal from digital habitat images that, being an effective proxy for habitat complexity, correlates with species diversity and requires little image processing or interpretation. We validated this method for coral reefs of the Great Barrier Reef (GBR), Australia, across a range of spatial scales (1 m to 10 km), using digital photographs of benthic communities at the transect scale and high-resolution Landsat satellite images at the reef scale. We calculated an index of image-derived spatial heterogeneity, the mean information gain (MIG), for each scale and related it to univariate (species richness and total abundance summed across species) and multivariate (species abundance matrix) measures of fish community structure, using two techniques that account for the hierarchical structure of the data: hierarchical (mixed-effect) linear models and distance-based partial redundancy analysis. Over the length and breadth of the GBR, MIG alone explained up to 29% of deviance in fish species richness, 33% in total fish abundance, and 25% in fish community structure at multiple scales, thus demonstrating the possibility of easily and rapidly exploiting spatial information contained in digital images to complement existing methods for inferring diversity and abundance patterns among fish communities. Thus, the spectral signal of unprocessed remotely sensed images provides an efficient and low-cost way to optimize the design of surveys used in conservation planning. In data-sparse situations, this simple approach also offers a viable method for rapid assessment of potential local biodiversity, particularly where there is little local capacity in terms of skills or resources for mounting in-depth biodiversity surveys.

  17. Large-scale Inference Problems in Astronomy: Building a 3D Galactic Dust Map

    Science.gov (United States)

    Finkbeiner, Douglas

    2016-03-01

    The term ''Big Data'' has become trite, as modern technology has made data sets of terabytes or even petabytes easy to store. Such data sets provide a sandbox in which to develop new statistical inference techniques that can extract interesting results from increasingly rich (and large) databases. I will give an example from my work on mapping the interstellar dust of the Milky Way. 2D emission-based maps have been used for decades to estimate the reddening and emission from interstellar dust, with applications from CMB foregrounds to surveys of large-scale structure. For studies within the Milky Way, however, the third dimension is required. I will present our work on a 3D dust map based on Pan-STARRS1 and 2MASS over 3/4 of the sky (http://arxiv.org/abs/1507.01005), assess its usefulness relative to other dust maps, and discuss future work. Supported by the NSF.

  18. Demographic inferences from large-scale NGS data

    DEFF Research Database (Denmark)

    Pedersen, Casper-Emil Tingskov

    conservation concerns. Investigating the plains zebra, we disentangle the complex genetic structure across a large geographical area and further provide detailed insights into the past phylogeography of this species, including finding a likely plains zebra “cradle” from which all plains zebra populations arose...

  19. Inferring structural connectivity using Ising couplings in models of neuronal networks.

    Science.gov (United States)

    Kadirvelu, Balasundaram; Hayashi, Yoshikatsu; Nasuto, Slawomir J

    2017-08-15

    Functional connectivity metrics have been widely used to infer the underlying structural connectivity in neuronal networks. Maximum entropy based Ising models have been suggested to discount the effect of indirect interactions and give good results in inferring the true anatomical connections. However, no benchmarking is currently available to assess the performance of Ising couplings against other functional connectivity metrics in the microscopic scale of neuronal networks through a wide set of network conditions and network structures. In this paper, we study the performance of the Ising model couplings to infer the synaptic connectivity in in silico networks of neurons and compare its performance against partial and cross-correlations for different correlation levels, firing rates, network sizes, network densities, and topologies. Our results show that the relative performance amongst the three functional connectivity metrics depends primarily on the network correlation levels. Ising couplings detected the most structural links at very weak network correlation levels, and partial correlations outperformed Ising couplings and cross-correlations at strong correlation levels. The result was consistent across varying firing rates, network sizes, and topologies. The findings of this paper serve as a guide in choosing the right functional connectivity tool to reconstruct the structural connectivity.

  20. Inference for One-Way ANOVA with Equicorrelation Error Structure

    Directory of Open Access Journals (Sweden)

    Weiyan Mu

    2014-01-01

    Full Text Available We consider inferences in a one-way ANOVA model with equicorrelation error structures. Hypotheses of the equality of the means are discussed. A generalized F-test has been proposed by in the literature to compare the means of all populations. However, they did not discuss the performance of that test. We propose two methods, a generalized pivotal quantities-based method and a parametric bootstrap method, to test the hypotheses of equality of the means. We compare the empirical performance of the proposed tests with the generalized F-test. It can be seen from the simulation results that the generalized F-test does not perform well in terms of Type I error rate, and the proposed tests perform much better. We also provide corresponding simultaneous confidence intervals for all pair-wise differences of the means, whose coverage probabilities are close to the confidence level.

  1. Multi-agent based control of large-scale complex systems employing distributed dynamic inference engine

    Science.gov (United States)

    Zhang, Daili

    are made for critical agents and are organized into logical rings. This architecture maintains clear guidelines for complexity decomposition and also increases the robustness of the whole system. Multiple Sectioned Dynamic Bayesian Networks (MSDBNs) as a distributed dynamic probabilistic inference engine, can be embedded into the control architecture to handle uncertainties of general large-scale complex systems. MSDBNs decomposes a large knowledge-based system into many agents. Each agent holds its partial perspective of a large problem domain by representing its knowledge as a Dynamic Bayesian Network (DBN). Each agent accesses local evidence from its corresponding local sensors and communicates with other agents through finite message passing. If the distributed agents can be organized into a tree structure, satisfying the running intersection property and d-sep set requirements, globally consistent inferences are achievable in a distributed way. By using different frequencies for local DBN agent belief updating and global system belief updating, it balances the communication cost with the global consistency of inferences. In this dissertation, a fully factorized Boyen-Koller (BK) approximation algorithm is used for local DBN agent belief updating, and the static Junction Forest Linkage Tree (JFLT) algorithm is used for global system belief updating. MSDBNs assume a static structure and a stable communication network for the whole system. However, for a real system, sub-Bayesian networks as nodes could be lost, and the communication network could be shut down due to partial damage in the system. Therefore, on-line and automatic MSDBNs structure formation is necessary for making robust state estimations and increasing survivability of the whole system. A Distributed Spanning Tree Optimization (DSTO) algorithm, a Distributed D-Sep Set Satisfaction (DDSSS) algorithm, and a Distributed Running Intersection Satisfaction (DRIS) algorithm are proposed in this dissertation

  2. Inferring Selection Intensity and Allele Age from Multilocus Haplotype Structure

    Science.gov (United States)

    Chen, Hua; Slatkin, Montgomery

    2013-01-01

    It is a challenging task to infer selection intensity and allele age from population genetic data. Here we present a method that can efficiently estimate selection intensity and allele age from the multilocus haplotype structure in the vicinity of a segregating mutant under positive selection. We use a structured-coalescent approach to model the effect of directional selection on the gene genealogies of neutral markers linked to the selected mutant. The frequency trajectory of the selected allele follows the Wright-Fisher model. Given the position of the selected mutant, we propose a simplified multilocus haplotype model that can efficiently model the dynamics of the ancestral haplotypes under the joint influence of selection and recombination. This model approximates the ancestral genealogies of the sample, which reduces the number of states from an exponential function of the number of single-nucleotide polymorphism loci to a quadratic function. That allows parameter inference from data covering DNA regions as large as several hundred kilo-bases. Importance sampling algorithms are adopted to evaluate the probability of a sample by exploring the space of both allele frequency trajectories of the selected mutation and gene genealogies of the linked sites. We demonstrate by simulation that the method can accurately estimate selection intensity for moderate and strong positive selection. We apply the method to a data set of the G6PD gene in an African population and obtain an estimate of 0.0456 (95% confidence interval 0.0144−0.0769) for the selection intensity. The proposed method is novel in jointly modeling the multilocus haplotype pattern caused by recombination and mutation, allowing the analysis of haplotype data in recombining regions. Moreover, the method is applicable to data from populations under exponential growth and a variety of other demographic histories. PMID:23797107

  3. Extreme-Scale Bayesian Inference for Uncertainty Quantification of Complex Simulations

    Energy Technology Data Exchange (ETDEWEB)

    Biros, George [Univ. of Texas, Austin, TX (United States)

    2018-01-12

    Uncertainty quantification (UQ)—that is, quantifying uncertainties in complex mathematical models and their large-scale computational implementations—is widely viewed as one of the outstanding challenges facing the field of CS&E over the coming decade. The EUREKA project set to address the most difficult class of UQ problems: those for which both the underlying PDE model as well as the uncertain parameters are of extreme scale. In the project we worked on these extreme-scale challenges in the following four areas: 1. Scalable parallel algorithms for sampling and characterizing the posterior distribution that exploit the structure of the underlying PDEs and parameter-to-observable map. These include structure-exploiting versions of the randomized maximum likelihood method, which aims to overcome the intractability of employing conventional MCMC methods for solving extreme-scale Bayesian inversion problems by appealing to and adapting ideas from large-scale PDE-constrained optimization, which have been very successful at exploring high-dimensional spaces. 2. Scalable parallel algorithms for construction of prior and likelihood functions based on learning methods and non-parametric density estimation. Constructing problem-specific priors remains a critical challenge in Bayesian inference, and more so in high dimensions. Another challenge is construction of likelihood functions that capture unmodeled couplings between observations and parameters. We will create parallel algorithms for non-parametric density estimation using high dimensional N-body methods and combine them with supervised learning techniques for the construction of priors and likelihood functions. 3. Bayesian inadequacy models, which augment physics models with stochastic models that represent their imperfections. The success of the Bayesian inference framework depends on the ability to represent the uncertainty due to imperfections of the mathematical model of the phenomena of interest. This is a

  4. Structural Inference in the Art of Violin Making.

    Science.gov (United States)

    Morse-Fortier, Leonard Joseph

    The "secrets" of success of early Italian violins have long been sought. Among their many efforts to reproduce the results of Stradiveri, Guarneri, and Amati, luthiers have attempted to order and match natural resonant frequencies in the free violin plates. This tap-tone plate tuning technique is simply an eigenvalue extraction scheme. In the final stages of carving, the violin maker complements considerable intuitive knowledge of violin plate structure and of modal attributes with tap-tone frequency estimates to better understand plate structure and to inform decisions about plate carving and completeness. Examining the modal attributes of violin plates, this work develops and incorporates an impulse-response scheme for modal inference, measures resonant frequencies and modeshapes for a pair of violin plates, and presents modeshapes through a unique computer visualization scheme developed specifically for this purpose. The work explores, through simple examples questions of how plate modal attributes reflect underlying structure, and questions about the so -called evolution of modeshapes and frequencies through assembly of the violin. Separately, the work develops computer code for a carved, anisotropic, plate/shell finite element. Solutions are found to the static displacement and free-vibration eigenvalue problems for an orthotropic plate, and used to verify element accuracy. Finally, a violin back plate is modelled with full consideration of plate thickness and arching. Model estimates for modal attributes compare very well against experimentally acquired values. Finally, the modal synthesis technique is applied to predicting the modal attributes of the violin top plate with ribs attached from those of the top plate alone, and with an estimate of rib mass and stiffness. This last analysis serves to verify the modal synthesis method, and to quantify its limits of applicability in attempting to solve problems with severe structural modification. Conclusions

  5. Uncovering Scaling Laws to Infer Multi-drug Response of Resistant Microbes and Cancer Cells

    OpenAIRE

    Wood, Kevin B.; Wood, Kris C.; Nishida, Satoshi; Cluzel, Philippe

    2014-01-01

    Drug resistance in bacterial infections and cancers constitutes a major threat to human health. Treatments often include several interacting drugs, but even potent therapies can become ineffective in resistant mutants. Here, we simplify the picture of drug resistance by identifying scaling laws that unify the multidrug responses of drug-sensitive and -resistant cells. On the basis of these scaling relationships, we are able to infer the two-drug response of resistant mutants in previously uns...

  6. Fine-scale population dynamics in a marine fish species inferred from dynamic state-space models.

    Science.gov (United States)

    Rogers, Lauren A; Storvik, Geir O; Knutsen, Halvor; Olsen, Esben M; Stenseth, Nils C

    2017-07-01

    Identifying the spatial scale of population structuring is critical for the conservation of natural populations and for drawing accurate ecological inferences. However, population studies often use spatially aggregated data to draw inferences about population trends and drivers, potentially masking ecologically relevant population sub-structure and dynamics. The goals of this study were to investigate how population dynamics models with and without spatial structure affect inferences on population trends and the identification of intrinsic drivers of population dynamics (e.g. density dependence). Specifically, we developed dynamic, age-structured, state-space models to test different hypotheses regarding the spatial structure of a population complex of coastal Atlantic cod (Gadus morhua). Data were from a 93-year survey of juvenile (age 0 and 1) cod sampled along >200 km of the Norwegian Skagerrak coast. We compared two models: one which assumes all sampled cod belong to one larger population, and a second which assumes that each fjord contains a unique population with locally determined dynamics. Using the best supported model, we then reconstructed the historical spatial and temporal dynamics of Skagerrak coastal cod. Cross-validation showed that the spatially structured model with local dynamics had better predictive ability. Furthermore, posterior predictive checks showed that a model which assumes one homogeneous population failed to capture the spatial correlation pattern present in the survey data. The spatially structured model indicated that population trends differed markedly among fjords, as did estimates of population parameters including density-dependent survival. Recent biomass was estimated to be at a near-record low all along the coast, but the finer scale model indicated that the decline occurred at different times in different regions. Warm temperatures were associated with poor recruitment, but local changes in habitat and fishing pressure may

  7. Inferring infection hazard in wildlife populations by linking data across individual and population scales

    Science.gov (United States)

    Pepin, Kim M.; Kay, Shannon L.; Golas, Ben D.; Shriner, Susan A.; Gilbert, Amy T.; Miller, Ryan S.; Graham, Andrea L.; Riley, Steven; Cross, Paul C.; Samuel, Michael D.; Hooten, Mevin B.; Hoeting, Jennifer A.; Lloyd-Smith, James O.; Webb, Colleen T.; Buhnerkempe, Michael G.

    2017-01-01

    Our ability to infer unobservable disease-dynamic processes such as force of infection (infection hazard for susceptible hosts) has transformed our understanding of disease transmission mechanisms and capacity to predict disease dynamics. Conventional methods for inferring FOI estimate a time-averaged value and are based on population-level processes. Because many pathogens exhibit epidemic cycling and FOI is the result of processes acting across the scales of individuals and populations, a flexible framework that extends to epidemic dynamics and links within-host processes to FOI is needed. Specifically, within-host antibody kinetics in wildlife hosts can be short-lived and produce patterns that are repeatable across individuals, suggesting individual-level antibody concentrations could be used to infer time since infection and hence FOI. Using simulations and case studies (influenza A in lesser snow geese and Yersinia pestis in coyotes), we argue that with careful experimental and surveillance design, the population-level FOI signal can be recovered from individual-level antibody kinetics, despite substantial individual-level variation. In addition to improving inference, the cross-scale quantitative antibody approach we describe can reveal insights into drivers of individual-based variation in disease response, and the role of poorly understood processes such as secondary infections, in population-level dynamics of disease.

  8. Inferring causal phenotype networks using structural equation models

    Directory of Open Access Journals (Sweden)

    de los Campos Gustavo

    2011-02-01

    Full Text Available Abstract Phenotypic traits may exert causal effects between them. For example, on the one hand, high yield in dairy cows may increase the liability to certain diseases and, on the other hand, the incidence of a disease may affect yield negatively. Likewise, the transcriptome may be a function of the reproductive status in mammals and the latter may depend on other physiological variables. Knowledge of phenotype networks describing such interrelationships can be used to predict the behavior of complex systems, e.g. biological pathways underlying complex traits such as diseases, growth and reproduction. Structural Equation Models (SEM can be used to study recursive and simultaneous relationships among phenotypes in multivariate systems such as genetical genomics, system biology, and multiple trait models in quantitative genetics. Hence, SEM can produce an interpretation of relationships among traits which differs from that obtained with traditional multiple trait models, in which all relationships are represented by symmetric linear associations among random variables, such as covariances and correlations. In this review, we discuss the application of SEM and related techniques for the study of multiple phenotypes. Two basic scenarios are considered, one pertaining to genetical genomics studies, in which QTL or molecular marker information is used to facilitate causal inference, and another related to quantitative genetic analysis in livestock, in which only phenotypic and pedigree information is available. Advantages and limitations of SEM compared to traditional approaches commonly used for the analysis of multiple traits, as well as some indication of future research in this area are presented in a concluding section.

  9. A Replica Inference Approach to Unsupervised Multi-Scale Image Segmentation

    OpenAIRE

    Hu, Dandan; Ronhovde, Peter; Nussinov, Zohar

    2011-01-01

    We apply a replica inference based Potts model method to unsupervised image segmentation on multiple scales. This approach was inspired by the statistical mechanics problem of "community detection" and its phase diagram. Specifically, the problem is cast as identifying tightly bound clusters ("communities" or "solutes") against a background or "solvent". Within our multiresolution approach, we compute information theory based correlations among multiple solutions ("replicas") of the same grap...

  10. The feasibility of genome-scale biological network inference using Graphics Processing Units.

    Science.gov (United States)

    Thiagarajan, Raghuram; Alavi, Amir; Podichetty, Jagdeep T; Bazil, Jason N; Beard, Daniel A

    2017-01-01

    Systems research spanning fields from biology to finance involves the identification of models to represent the underpinnings of complex systems. Formal approaches for data-driven identification of network interactions include statistical inference-based approaches and methods to identify dynamical systems models that are capable of fitting multivariate data. Availability of large data sets and so-called 'big data' applications in biology present great opportunities as well as major challenges for systems identification/reverse engineering applications. For example, both inverse identification and forward simulations of genome-scale gene regulatory network models pose compute-intensive problems. This issue is addressed here by combining the processing power of Graphics Processing Units (GPUs) and a parallel reverse engineering algorithm for inference of regulatory networks. It is shown that, given an appropriate data set, information on genome-scale networks (systems of 1000 or more state variables) can be inferred using a reverse-engineering algorithm in a matter of days on a small-scale modern GPU cluster.

  11. A new asynchronous parallel algorithm for inferring large-scale gene regulatory networks.

    Directory of Open Access Journals (Sweden)

    Xiangyun Xiao

    Full Text Available The reconstruction of gene regulatory networks (GRNs from high-throughput experimental data has been considered one of the most important issues in systems biology research. With the development of high-throughput technology and the complexity of biological problems, we need to reconstruct GRNs that contain thousands of genes. However, when many existing algorithms are used to handle these large-scale problems, they will encounter two important issues: low accuracy and high computational cost. To overcome these difficulties, the main goal of this study is to design an effective parallel algorithm to infer large-scale GRNs based on high-performance parallel computing environments. In this study, we proposed a novel asynchronous parallel framework to improve the accuracy and lower the time complexity of large-scale GRN inference by combining splitting technology and ordinary differential equation (ODE-based optimization. The presented algorithm uses the sparsity and modularity of GRNs to split whole large-scale GRNs into many small-scale modular subnetworks. Through the ODE-based optimization of all subnetworks in parallel and their asynchronous communications, we can easily obtain the parameters of the whole network. To test the performance of the proposed approach, we used well-known benchmark datasets from Dialogue for Reverse Engineering Assessments and Methods challenge (DREAM, experimentally determined GRN of Escherichia coli and one published dataset that contains more than 10 thousand genes to compare the proposed approach with several popular algorithms on the same high-performance computing environments in terms of both accuracy and time complexity. The numerical results demonstrate that our parallel algorithm exhibits obvious superiority in inferring large-scale GRNs.

  12. Plant dispersal in the sub-Antarctic inferred from anisotropic genetic structure.

    Science.gov (United States)

    Born, Céline; Le Roux, Peter C; Spohr, Colin; McGeoch, Melodie A; Van Vuuren, Bettine Jansen

    2012-01-01

    Climatic conditions and landscape features often strongly affect species' local distribution patterns, dispersal, reproduction and survival and may therefore have considerable impacts on species' fine-scale spatial genetic structure (SGS). In this study, we demonstrate the efficacy of combining fine-scale SGS analyses with isotropic and anisotropic spatial autocorrelation techniques to infer the impact of wind patterns on plant dispersal processes. We genotyped 1304 Azorella selago (Apiaceae) specimens, a wind-pollinated and wind-dispersed plant, from four populations distributed across sub-Antarctic Marion Island. SGS was variable with Sp values ranging from 0.001 to 0.014, suggesting notable variability in dispersal distance and wind velocities between sites. Nonetheless, the data supported previous hypotheses of a strong NW-SE gradient in wind strength across the island. Anisotropic autocorrelation analyses further suggested that dispersal is strongly directional, but varying between sites depending on the local prevailing winds. Despite the high frequency of gale-force winds on Marion Island, gene dispersal distance estimates (σ) were surprisingly low (<10 m), most probably because of a low pollen dispersal efficiency. An SGS approach in association with isotropic and anisotropic analyses provides a powerful means to assess the relative influence of abiotic factors on dispersal and allow inferences that would not be possible without this combined approach. © 2011 Blackwell Publishing Ltd.

  13. Parallelization and High-Performance Computing Enables Automated Statistical Inference of Multi-scale Models.

    Science.gov (United States)

    Jagiella, Nick; Rickert, Dennis; Theis, Fabian J; Hasenauer, Jan

    2017-02-22

    Mechanistic understanding of multi-scale biological processes, such as cell proliferation in a changing biological tissue, is readily facilitated by computational models. While tools exist to construct and simulate multi-scale models, the statistical inference of the unknown model parameters remains an open problem. Here, we present and benchmark a parallel approximate Bayesian computation sequential Monte Carlo (pABC SMC) algorithm, tailored for high-performance computing clusters. pABC SMC is fully automated and returns reliable parameter estimates and confidence intervals. By running the pABC SMC algorithm for ∼10(6) hr, we parameterize multi-scale models that accurately describe quantitative growth curves and histological data obtained in vivo from individual tumor spheroid growth in media droplets. The models capture the hybrid deterministic-stochastic behaviors of 10(5)-10(6) of cells growing in a 3D dynamically changing nutrient environment. The pABC SMC algorithm reliably converges to a consistent set of parameters. Our study demonstrates a proof of principle for robust, data-driven modeling of multi-scale biological systems and the feasibility of multi-scale model parameterization through statistical inference. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  14. Boosting Bayesian parameter inference of nonlinear stochastic differential equation models by Hamiltonian scale separation.

    Science.gov (United States)

    Albert, Carlo; Ulzega, Simone; Stoop, Ruedi

    2016-04-01

    Parameter inference is a fundamental problem in data-driven modeling. Given observed data that is believed to be a realization of some parameterized model, the aim is to find parameter values that are able to explain the observed data. In many situations, the dominant sources of uncertainty must be included into the model for making reliable predictions. This naturally leads to stochastic models. Stochastic models render parameter inference much harder, as the aim then is to find a distribution of likely parameter values. In Bayesian statistics, which is a consistent framework for data-driven learning, this so-called posterior distribution can be used to make probabilistic predictions. We propose a novel, exact, and very efficient approach for generating posterior parameter distributions for stochastic differential equation models calibrated to measured time series. The algorithm is inspired by reinterpreting the posterior distribution as a statistical mechanics partition function of an object akin to a polymer, where the measurements are mapped on heavier beads compared to those of the simulated data. To arrive at distribution samples, we employ a Hamiltonian Monte Carlo approach combined with a multiple time-scale integration. A separation of time scales naturally arises if either the number of measurement points or the number of simulation points becomes large. Furthermore, at least for one-dimensional problems, we can decouple the harmonic modes between measurement points and solve the fastest part of their dynamics analytically. Our approach is applicable to a wide range of inference problems and is highly parallelizable.

  15. Structural Similitude and Scaling Laws

    Science.gov (United States)

    Simitses, George J.

    1998-01-01

    Aircraft and spacecraft comprise the class of aerospace structures that require efficiency and wisdom in design, sophistication and accuracy in analysis and numerous and careful experimental evaluations of components and prototype, in order to achieve the necessary system reliability, performance and safety. Preliminary and/or concept design entails the assemblage of system mission requirements, system expected performance and identification of components and their connections as well as of manufacturing and system assembly techniques. This is accomplished through experience based on previous similar designs, and through the possible use of models to simulate the entire system characteristics. Detail design is heavily dependent on information and concepts derived from the previous steps. This information identifies critical design areas which need sophisticated analyses, and design and redesign procedures to achieve the expected component performance. This step may require several independent analysis models, which, in many instances, require component testing. The last step in the design process, before going to production, is the verification of the design. This step necessitates the production of large components and prototypes in order to test component and system analytical predictions and verify strength and performance requirements under the worst loading conditions that the system is expected to encounter in service. Clearly then, full-scale testing is in many cases necessary and always very expensive. In the aircraft industry, in addition to full-scale tests, certification and safety necessitate large component static and dynamic testing. Such tests are extremely difficult, time consuming and definitely absolutely necessary. Clearly, one should not expect that prototype testing will be totally eliminated in the aircraft industry. It is hoped, though, that we can reduce full-scale testing to a minimum. Full-scale large component testing is necessary in

  16. Incorporating Spatial Structures in Ecological Inference: An Information Theory Approach

    Directory of Open Access Journals (Sweden)

    Rosa Bernardini Papalia

    2010-10-01

    Full Text Available This paper introduces an Information Theory-based method for modeling economic aggregates and estimating their sub-group (sub-area decomposition when no individual or sub-group data are available. This method offers a flexible framework for modeling the underlying variation in sub-group indicators, by addressing the spatial dependency problem. A basic ecological inference problem, which allows for spatial heterogeneity and dependence, is presented with the aim of first estimating the model at the aggregate level, and then of employing the estimated coefficients to obtain the sub-group level indicators.

  17. Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center.

    Science.gov (United States)

    Shin, Dong Hae; Hou, Jingtong; Chandonia, John-Marc; Das, Debanu; Choi, In-Geol; Kim, Rosalind; Kim, Sung-Hou

    2007-09-01

    Advances in sequence genomics have resulted in an accumulation of a huge number of protein sequences derived from genome sequences. However, the functions of a large portion of them cannot be inferred based on the current methods of sequence homology detection to proteins of known functions. Three-dimensional structure can have an important impact in providing inference of molecular function (physical and chemical function) of a protein of unknown function. Structural genomics centers worldwide have been determining many 3-D structures of the proteins of unknown functions, and possible molecular functions of them have been inferred based on their structures. Combined with bioinformatics and enzymatic assay tools, the successful acceleration of the process of protein structure determination through high throughput pipelines enables the rapid functional annotation of a large fraction of hypothetical proteins. We present a brief summary of the process we used at the Berkeley Structural Genomics Center to infer molecular functions of proteins of unknown function.

  18. Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Sung-Hou; Shin, Dong Hae; Hou, Jingtong; Chandonia, John-Marc; Das, Debanu; Choi, In-Geol; Kim, Rosalind; Kim, Sung-Hou

    2007-09-02

    Advances in sequence genomics have resulted in an accumulation of a huge number of protein sequences derived from genome sequences. However, the functions of a large portion of them cannot be inferred based on the current methods of sequence homology detection to proteins of known functions. Three-dimensional structure can have an important impact in providing inference of molecular function (physical and chemical function) of a protein of unknown function. Structural genomics centers worldwide have been determining many 3-D structures of the proteins of unknown functions, and possible molecular functions of them have been inferred based on their structures. Combined with bioinformatics and enzymatic assay tools, the successful acceleration of the process of protein structure determination through high throughput pipelines enables the rapid functional annotation of a large fraction of hypothetical proteins. We present a brief summary of the process we used at the Berkeley Structural Genomics Center to infer molecular functions of proteins of unknown function.

  19. Inference from the small scales of cosmic shear with current and future Dark Energy Survey data

    Science.gov (United States)

    MacCrann, N.; Aleksić, J.; Amara, A.; Bridle, S. L.; Bruderer, C.; Chang, C.; Dodelson, S.; Eifler, T. F.; Huff, E. M.; Huterer, D.; Kacprzak, T.; Refregier, A.; Suchyta, E.; Wechsler, R. H.; Zuntz, J.; Abbott, T. M. C.; Allam, S.; Annis, J.; Armstrong, R.; Benoit-Lévy, A.; Brooks, D.; Burke, D. L.; Carnero Rosell, A.; Carrasco Kind, M.; Carretero, J.; Castander, F. J.; Crocce, M.; Cunha, C. E.; da Costa, L. N.; Desai, S.; Diehl, H. T.; Dietrich, J. P.; Doel, P.; Evrard, A. E.; Flaugher, B.; Fosalba, P.; Gerdes, D. W.; Goldstein, D. A.; Gruen, D.; Gruendl, R. A.; Gutierrez, G.; Honscheid, K.; James, D. J.; Jarvis, M.; Krause, E.; Kuehn, K.; Kuropatkin, N.; Lima, M.; Marshall, J. L.; Melchior, P.; Menanteau, F.; Miquel, R.; Plazas, A. A.; Romer, A. K.; Rykoff, E. S.; Sanchez, E.; Scarpine, V.; Sevilla-Noarbe, I.; Sheldon, E.; Soares-Santos, M.; Swanson, M. E. C.; Tarle, G.; Thomas, D.; Vikram, V.; DES Collaboration

    2017-03-01

    Cosmic shear is sensitive to fluctuations in the cosmological matter density field, including on small physical scales, where matter clustering is affected by baryonic physics in galaxies and galaxy clusters, such as star formation, supernovae feedback, and active galactic nuclei feedback. While muddying any cosmological information that is contained in small-scale cosmic shear measurements, this does mean that cosmic shear has the potential to constrain baryonic physics and galaxy formation. We perform an analysis of the Dark Energy Survey (DES) Science Verification (SV) cosmic shear measurements, now extended to smaller scales, and using the Mead et al. (2015) halo model to account for baryonic feedback. While the SV data has limited statistical power, we demonstrate using a simulated likelihood analysis that the final DES data will have the statistical power to differentiate among baryonic feedback scenarios. We also explore some of the difficulties in interpreting the small scales in cosmic shear measurements, presenting estimates of the size of several other systematic effects that make inference from small scales difficult, including uncertainty in the modelling of intrinsic alignment on non-linear scales, 'lensing bias', and shape measurement selection effects. For the latter two, we make use of novel image simulations. While future cosmic shear data sets have the statistical power to constrain baryonic feedback scenarios, there are several systematic effects that require improved treatments, in order to make robust conclusions about baryonic feedback.

  20. Multi-scale inference of interaction rules in animal groups using Bayesian model selection.

    Directory of Open Access Journals (Sweden)

    Richard P Mann

    2012-01-01

    Full Text Available Inference of interaction rules of animals moving in groups usually relies on an analysis of large scale system behaviour. Models are tuned through repeated simulation until they match the observed behaviour. More recent work has used the fine scale motions of animals to validate and fit the rules of interaction of animals in groups. Here, we use a Bayesian methodology to compare a variety of models to the collective motion of glass prawns (Paratya australiensis. We show that these exhibit a stereotypical 'phase transition', whereby an increase in density leads to the onset of collective motion in one direction. We fit models to this data, which range from: a mean-field model where all prawns interact globally; to a spatial Markovian model where prawns are self-propelled particles influenced only by the current positions and directions of their neighbours; up to non-Markovian models where prawns have 'memory' of previous interactions, integrating their experiences over time when deciding to change behaviour. We show that the mean-field model fits the large scale behaviour of the system, but does not capture fine scale rules of interaction, which are primarily mediated by physical contact. Conversely, the Markovian self-propelled particle model captures the fine scale rules of interaction but fails to reproduce global dynamics. The most sophisticated model, the non-Markovian model, provides a good match to the data at both the fine scale and in terms of reproducing global dynamics. We conclude that prawns' movements are influenced by not just the current direction of nearby conspecifics, but also those encountered in the recent past. Given the simplicity of prawns as a study system our research suggests that self-propelled particle models of collective motion should, if they are to be realistic at multiple biological scales, include memory of previous interactions and other non-Markovian effects.

  1. Multi-scale inference of interaction rules in animal groups using Bayesian model selection.

    Science.gov (United States)

    Mann, Richard P; Perna, Andrea; Strömbom, Daniel; Garnett, Roman; Herbert-Read, James E; Sumpter, David J T; Ward, Ashley J W

    2012-01-01

    Inference of interaction rules of animals moving in groups usually relies on an analysis of large scale system behaviour. Models are tuned through repeated simulation until they match the observed behaviour. More recent work has used the fine scale motions of animals to validate and fit the rules of interaction of animals in groups. Here, we use a Bayesian methodology to compare a variety of models to the collective motion of glass prawns (Paratya australiensis). We show that these exhibit a stereotypical 'phase transition', whereby an increase in density leads to the onset of collective motion in one direction. We fit models to this data, which range from: a mean-field model where all prawns interact globally; to a spatial Markovian model where prawns are self-propelled particles influenced only by the current positions and directions of their neighbours; up to non-Markovian models where prawns have 'memory' of previous interactions, integrating their experiences over time when deciding to change behaviour. We show that the mean-field model fits the large scale behaviour of the system, but does not capture fine scale rules of interaction, which are primarily mediated by physical contact. Conversely, the Markovian self-propelled particle model captures the fine scale rules of interaction but fails to reproduce global dynamics. The most sophisticated model, the non-Markovian model, provides a good match to the data at both the fine scale and in terms of reproducing global dynamics. We conclude that prawns' movements are influenced by not just the current direction of nearby conspecifics, but also those encountered in the recent past. Given the simplicity of prawns as a study system our research suggests that self-propelled particle models of collective motion should, if they are to be realistic at multiple biological scales, include memory of previous interactions and other non-Markovian effects. © 2012 Mann et al.

  2. Uncovering Scaling Laws to Infer Multidrug Response of Resistant Microbes and Cancer Cells

    Directory of Open Access Journals (Sweden)

    Kevin B. Wood

    2014-03-01

    Full Text Available Drug resistance in bacterial infections and cancers constitutes a major threat to human health. Treatments often include several interacting drugs, but even potent therapies can become ineffective in resistant mutants. Here, we simplify the picture of drug resistance by identifying scaling laws that unify the multidrug responses of drug-sensitive and -resistant cells. On the basis of these scaling relationships, we are able to infer the two-drug response of resistant mutants in previously unsampled regions of dosage space in clinically relevant microbes such as E. coli, E. faecalis, S. aureus, and S. cerevisiae as well as human non-small-cell lung cancer, melanoma, and breast cancer stem cells. Importantly, we find that scaling relations also apply across evolutionarily close strains. Finally, scaling allows one to rapidly identify new drug combinations and predict potent dosage regimes for targeting resistant mutants without any prior mechanistic knowledge about the specific resistance mechanism.

  3. Uncovering scaling laws to infer multidrug response of resistant microbes and cancer cells.

    Science.gov (United States)

    Wood, Kevin B; Wood, Kris C; Nishida, Satoshi; Cluzel, Philippe

    2014-03-27

    Drug resistance in bacterial infections and cancers constitutes a major threat to human health. Treatments often include several interacting drugs, but even potent therapies can become ineffective in resistant mutants. Here, we simplify the picture of drug resistance by identifying scaling laws that unify the multidrug responses of drug-sensitive and -resistant cells. On the basis of these scaling relationships, we are able to infer the two-drug response of resistant mutants in previously unsampled regions of dosage space in clinically relevant microbes such as E. coli, E. faecalis, S. aureus, and S. cerevisiae as well as human non-small-cell lung cancer, melanoma, and breast cancer stem cells. Importantly, we find that scaling relations also apply across evolutionarily close strains. Finally, scaling allows one to rapidly identify new drug combinations and predict potent dosage regimes for targeting resistant mutants without any prior mechanistic knowledge about the specific resistance mechanism. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

  4. PASSML: combining evolutionary inference and protein secondary structure prediction.

    Science.gov (United States)

    Liò, P; Goldman, N; Thorne, J L; Jones3, D T

    1998-01-01

    Evolutionary models of amino acid sequences can be adapted to incorporate structure information; protein structure biologists can use phylogenetic relationships among species to improve prediction accuracy. Results : A computer program called PASSML ('Phylogeny and Secondary Structure using Maximum Likelihood') has been developed to implement an evolutionary model that combines protein secondary structure and amino acid replacement. The model is related to that of Dayhoff and co-workers, but we distinguish eight categories of structural environment: alpha helix, beta sheet, turn and coil, each further classified according to solvent accessibility, i.e. buried or exposed. The model of sequence evolution for each of the eight categories is a Markov process with discrete states in continuous time, and the organization of structure along protein sequences is described by a hidden Markov model. This paper describes the PASSML software and illustrates how it allows both the reconstruction of phylogenies and prediction of secondary structure from aligned amino acid sequences. PASSML 'ANSI C' source code and the example data sets described here are available at http://ng-dec1.gen.cam.ac.uk/hmm/Passml.html and 'downstream' Web pages. P.Lio@gen.cam.ac.uk

  5. Bayesian Hierarchical Scale Mixtures of Log-Normal Models for Inference in Reliability with Stochastic Constraint

    Directory of Open Access Journals (Sweden)

    Hea-Jung Kim

    2017-06-01

    Full Text Available This paper develops Bayesian inference in reliability of a class of scale mixtures of log-normal failure time (SMLNFT models with stochastic (or uncertain constraint in their reliability measures. The class is comprehensive and includes existing failure time (FT models (such as log-normal, log-Cauchy, and log-logistic FT models as well as new models that are robust in terms of heavy-tailed FT observations. Since classical frequency approaches to reliability analysis based on the SMLNFT model with stochastic constraint are intractable, the Bayesian method is pursued utilizing a Markov chain Monte Carlo (MCMC sampling based approach. This paper introduces a two-stage maximum entropy (MaxEnt prior, which elicits a priori uncertain constraint and develops Bayesian hierarchical SMLNFT model by using the prior. The paper also proposes an MCMC method for Bayesian inference in the SMLNFT model reliability and calls attention to properties of the MaxEnt prior that are useful for method development. Finally, two data sets are used to illustrate how the proposed methodology works.

  6. Bayesian inference of protein structure from chemical shift data

    DEFF Research Database (Denmark)

    Bratholm, Lars Andersen; Christensen, Anders Steen; Hamelryck, Thomas Wim

    2015-01-01

    Protein chemical shifts are routinely used to augment molecular mechanics force fields in protein structure simulations, with weights of the chemical shift restraints determined empirically. These weights, however, might not be an optimal descriptor of a given protein structure and predictive model...... Monte Carlo simulations of three small proteins (ENHD, Protein G and the SMN Tudor Domain) using the PROFASI force field and the chemical shift predictor CamShift. Using a clustering-criterion for identifying the best structure, together with the addition of a solvent exposure scoring term......, result in overall better convergence to the native fold, suggesting that both types of distribution might be useful in different aspects of the protein structure prediction....

  7. Adaptive Neuro-Fuzzy Inference System Models for Force Prediction of a Mechatronic Flexible Structure

    DEFF Research Database (Denmark)

    Achiche, S.; Shlechtingen, M.; Raison, M.

    2016-01-01

    This paper presents the results obtained from a research work investigating the performance of different Adaptive Neuro-Fuzzy Inference System (ANFIS) models developed to predict excitation forces on a dynamically loaded flexible structure. For this purpose, a flexible structure is equipped...

  8. Multi-scale inference of interaction rules in animal groups using Bayesian model selection.

    Directory of Open Access Journals (Sweden)

    Richard P Mann

    Full Text Available Inference of interaction rules of animals moving in groups usually relies on an analysis of large scale system behaviour. Models are tuned through repeated simulation until they match the observed behaviour. More recent work has used the fine scale motions of animals to validate and fit the rules of interaction of animals in groups. Here, we use a Bayesian methodology to compare a variety of models to the collective motion of glass prawns (Paratya australiensis. We show that these exhibit a stereotypical 'phase transition', whereby an increase in density leads to the onset of collective motion in one direction. We fit models to this data, which range from: a mean-field model where all prawns interact globally; to a spatial Markovian model where prawns are self-propelled particles influenced only by the current positions and directions of their neighbours; up to non-Markovian models where prawns have 'memory' of previous interactions, integrating their experiences over time when deciding to change behaviour. We show that the mean-field model fits the large scale behaviour of the system, but does not capture the observed locality of interactions. Traditional self-propelled particle models fail to capture the fine scale dynamics of the system. The most sophisticated model, the non-Markovian model, provides a good match to the data at both the fine scale and in terms of reproducing global dynamics, while maintaining a biologically plausible perceptual range. We conclude that prawns' movements are influenced by not just the current direction of nearby conspecifics, but also those encountered in the recent past. Given the simplicity of prawns as a study system our research suggests that self-propelled particle models of collective motion should, if they are to be realistic at multiple biological scales, include memory of previous interactions and other non-Markovian effects.

  9. Mind the scales: Harnessing spatial big data for infectious disease surveillance and inferences

    CERN Document Server

    Lee, Elizabeth C; Goldlust, Sandra; Kraemer, John D; Lawson, Andrew B; Bansal, Shweta

    2016-01-01

    Spatial big data have the "velocity," "volume," and "variety" of big data sources and additional geographic information about the record. Digital data sources, such as medical claims, mobile phone call data records, and geo-tagged tweets, have entered infectious disease epidemiology as novel sources of data to complement traditional infectious disease surveillance. In this work, we provide examples of how spatial big data have been used thus far in epidemiological analyses and describe opportunities for these sources to improve public health coordination and disease mitigation strategies. In addition, we consider the technical, practical, and ethical challenges with the use of spatial big data in infectious disease surveillance and inference. Finally, we discuss the implications of the rising use of spatial big data in epidemiology to health risk communications, across-scale public health coordination, and public health policy recommendation.

  10. Mind the Scales: Harnessing Spatial Big Data for Infectious Disease Surveillance and Inference.

    Science.gov (United States)

    Lee, Elizabeth C; Asher, Jason M; Goldlust, Sandra; Kraemer, John D; Lawson, Andrew B; Bansal, Shweta

    2016-12-01

    Spatial big data have the velocity, volume, and variety of big data sources and contain additional geographic information. Digital data sources, such as medical claims, mobile phone call data records, and geographically tagged tweets, have entered infectious diseases epidemiology as novel sources of data to complement traditional infectious disease surveillance. In this work, we provide examples of how spatial big data have been used thus far in epidemiological analyses and describe opportunities for these sources to improve disease-mitigation strategies and public health coordination. In addition, we consider the technical, practical, and ethical challenges with the use of spatial big data in infectious disease surveillance and inference. Finally, we discuss the implications of the rising use of spatial big data in epidemiology to health risk communication, and public health policy recommendations and coordination across scales. © The Author 2016. Published by Oxford University Press for the Infectious Diseases Society of America.

  11. Significant scales in community structure.

    Science.gov (United States)

    Traag, V A; Krings, G; Van Dooren, P

    2013-10-14

    Many complex networks show signs of modular structure, uncovered by community detection. Although many methods succeed in revealing various partitions, it remains difficult to detect at what scale some partition is significant. This problem shows foremost in multi-resolution methods. We here introduce an efficient method for scanning for resolutions in one such method. Additionally, we introduce the notion of "significance" of a partition, based on subgraph probabilities. Significance is independent of the exact method used, so could also be applied in other methods, and can be interpreted as the gain in encoding a graph by making use of a partition. Using significance, we can determine "good" resolution parameters, which we demonstrate on benchmark networks. Moreover, optimizing significance itself also shows excellent performance. We demonstrate our method on voting data from the European Parliament. Our analysis suggests the European Parliament has become increasingly ideologically divided and that nationality plays no role.

  12. Stock portfolio structure of individual investors infers future trading behavior.

    Science.gov (United States)

    Bohlin, Ludvig; Rosvall, Martin

    2014-01-01

    Although the understanding of and motivation behind individual trading behavior is an important puzzle in finance, little is known about the connection between an investor's portfolio structure and her trading behavior in practice. In this paper, we investigate the relation between what stocks investors hold, and what stocks they buy, and show that investors with similar portfolio structures to a great extent trade in a similar way. With data from the central register of shareholdings in Sweden, we model the market in a similarity network, by considering investors as nodes, connected with links representing portfolio similarity. From the network, we find investor groups that not only identify different investment strategies, but also represent individual investors trading in a similar way. These findings suggest that the stock portfolios of investors hold meaningful information, which could be used to earn a better understanding of stock market dynamics.

  13. Stock Portfolio Structure of Individual Investors Infers Future Trading Behavior

    Science.gov (United States)

    Bohlin, Ludvig; Rosvall, Martin

    2014-01-01

    Although the understanding of and motivation behind individual trading behavior is an important puzzle in finance, little is known about the connection between an investor's portfolio structure and her trading behavior in practice. In this paper, we investigate the relation between what stocks investors hold, and what stocks they buy, and show that investors with similar portfolio structures to a great extent trade in a similar way. With data from the central register of shareholdings in Sweden, we model the market in a similarity network, by considering investors as nodes, connected with links representing portfolio similarity. From the network, we find investor groups that not only identify different investment strategies, but also represent individual investors trading in a similar way. These findings suggest that the stock portfolios of investors hold meaningful information, which could be used to earn a better understanding of stock market dynamics. PMID:25068302

  14. Gravity inferred subsurface structure of Gadwal schist belt, Andhra ...

    Indian Academy of Sciences (India)

    The results indicate a synformal structure having a width of 1.8 km at the surface, tapering at a depth of about 2.6 km with a positive density contrast of 0.15 gm/cc with respect to the surrounding peninsular gneissic complex. 1. Introduction. Detailed geophysical appraisal of the northern schist belts of the Dharwar craton, (i.e. ...

  15. Color-Biased Dispersal Inferred by Fine-Scale Genetic Spatial Autocorrelation in a Color Polymorphic Salamander.

    Science.gov (United States)

    Grant, Alexa H; Liebgold, Eric B

    2017-07-01

    Behavioral traits can be influenced by predation rates of color morphs, potentially leading to reduced boldness or increased escape behaviors in one color morph. The red-backed salamander, Plethodon cinereus, is a small terrestrial salamander whose color morphs have different diets and select different microhabitats, but little is known about potential differences in dispersal behaviors. We used fine-scale genetic spatial autocorrelation to examine 122 P. cinereus in a color-polymorphic population at 10 microsatellite loci in order to generate estimates of spatial genetic structure for each color morph. Differences in spatial genetic structure have been used extensively to infer within-population sex-biased dispersal but have never been used to test for dispersal differences between other groups within populations such as color morphs. We found evidence for color-biased dispersal, but not sex-biased dispersal. Striped salamanders had significant positive genetic structure in the shortest distance classes indicating philopatry. In contrast, unstriped salamanders showed a lack of spatial genetic structure at shorter distances and higher than expected genetic similarity at further distances, as expected if they are dispersing from their natal site. These results show that genetic methods typically used for sex-biased dispersal can be used to investigate differences in dispersal between morphs that vary discretely in polymorphic populations, such as color morphs. © The American Genetic Association 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  16. Remote sensing of seasonal distribution of precipitable water vapor over the oceans and inference of boundary layer structure

    Science.gov (United States)

    Prabhakara, C.

    1979-01-01

    Over the ocean satellite infrared spectral measurements in the 18 micrometer water vapor band and the 11 micrometer window region were used to derive precipitable water vapor, w, in the atmosphere and the sea surface temperature, SST. Seasonal maps of w on the oceans derived from these data reveal the dynamical influence of the large scale atmospheric circulation. With the help of a model for the vertical distribution of water vapor, the configuration of the atmospheric boundary layer over the oceans can be inferred from w when the information of SST is combined. The gross seasonal mean structure of the boundary layer inferred in this fashion reveals the broad areas of the trade wind inversion and the convectively active areas such as the intertropical convergence zones.

  17. Sparse Bayesian Inference and the Temperature Structure of the Solar Corona

    Science.gov (United States)

    Warren, Harry P.; Byers, Jeff M.; Crump, Nicholas A.

    2017-02-01

    Measuring the temperature structure of the solar atmosphere is critical to understanding how it is heated to high temperatures. Unfortunately, the temperature of the upper atmosphere cannot be observed directly, but must be inferred from spectrally resolved observations of individual emission lines that span a wide range of temperatures. Such observations are “inverted” to determine the distribution of plasma temperatures along the line of sight. This inversion is ill posed and, in the absence of regularization, tends to produce wildly oscillatory solutions. We introduce the application of sparse Bayesian inference to the problem of inferring the temperature structure of the solar corona. Within a Bayesian framework a preference for solutions that utilize a minimum number of basis functions can be encoded into the prior and many ad hoc assumptions can be avoided. We demonstrate the efficacy of the Bayesian approach by considering a test library of 40 assumed temperature distributions.

  18. Unleashing the power of meta-threading for evolution/structure-based function inference of proteins

    Directory of Open Access Journals (Sweden)

    Michal eBrylinski

    2013-06-01

    Full Text Available Protein threading is widely used in the prediction of protein structure and the subsequent functional annotation. Most threading approaches employ similar criteria for the template identification for use in both protein structure and function modeling. Using structure similarity alone might result in a high false positive rate in protein function inference, which suggests that selecting functional templates should be subject to a different set of constraints. In this study, we extend the functionality of eThread, a recently developed approach to meta-threading, focusing on the optimal selection of functional templates. We optimized the selection of template proteins to cover a broad spectrum of protein molecular function: ligand, metal, inorganic cluster, protein and nucleic acid binding. In large-scale benchmarks, we demonstrate that the recognition rates in identifying templates that bind molecular partners in similar locations are very high, typically 70-80%, at the expense of a relatively low false positive rate. eThread also provides useful insights into the chemical properties of binding molecules and the structural features of binding. For instance, the sensitivity in recognizing similar protein-binding interfaces is 58% at only 18% false positive rate. Furthermore, in comparative analysis, we demonstrate that meta-threading supported by machine learning outperforms single-threading approaches in functional template selection. We show that meta-threading effectively detects many facets of protein molecular function, even in a low sequence identity regime. The enhanced version of eThread is freely available as a webserver and stand-alone software at www.brylinski.org/ethread.

  19. Using Vertical Structure to Infer the Total Mass Hidden in a Debris Disk

    Science.gov (United States)

    Daley, Cail; Hughes, A. Meredith; Carter, Evan; Flaherty, Kevin; Stafford Lambros, Zachary; Pan, Margaret; Schlichting, Hilke; Chiang, Eugene; Wilner, David; Dent, Bill; Carpenter, John; Andrews, Sean; MacGregor, Meredith Ann; Moor, Attila; Kospal, Agnes

    2018-01-01

    Disks of optically thin debris dust surround ≥ 20% of main sequence stars and mark the final stage of planetary system evolution. The features of debris disks encode dynamical interactions between the dust and any unseen planets embedded in the disk. The vertical distribution of the dust is particularly sensitive to the total mass of planetesimal bodies in the disk, and is therefore well suited for constraining the prevalence of otherwise unobservable Uranus and Neptune analogs. Inferences of mass from debris disk vertical structure have previously been applied to infrared and optical observations of several systems, but the smaller particles traced by short-wavelength observations are ‘puffed up’ by radiation pressure, yielding only upper limits on the total embedded mass. The large grains that dominate the emission at millimeter wavelengths are essentially impervious to the effects of stellar radiation, and therefore trace the underlying mass distribution more directly. Here we present 1.3mm dust continuum observations of the debris disk around the nearby M star AU Mic with the Atacama Large Millimeter/submillimeter Array (ALMA). The 3 au spatial resolution of the observations, combined with the favorable edge-on geometry of the system, allows us to measure the vertical structure of a debris disk at millimeter wavelengths for the first time. We analyze the data using a ray-tracing code that translates a 2-D density and temperature structure into a model sky image of the disk. This model image is then compared directly to the interferometric data in the visibility domain, and the model parameters are explored using a Markov Chain Monte Carlo routine. We measure a scale height-to-radius ratio of 0.03, which we then compare to a theoretical model of steady-state, size-dependent velocity distributions in the collisional cascade to infer a total mass within the disk of ∼ 1.7 Earth masses. These measurements rule out the presence of a gas giant or Neptune

  20. Earth's structure and evolution inferred from topography, gravity, and seismicity.

    Science.gov (United States)

    Watkinson, A. J.; Menard, J.; Patton, R. L.

    2016-12-01

    Earth's wavelength-dependent response to loading, reflected in observed topography, gravity, and seismicity, can be interpreted in terms of a stack of layers under the assumption of transverse isotropy. The theory of plate tectonics holds that the outermost layers of this stack are mobile, produced at oceanic ridges, and consumed at subduction zones. Their toroidal motions are generally consistent with those of several rigid bodies, except in the world's active mountain belts where strains are partitioned and preserved in tectonite fabrics. Even portions of the oceanic lithosphere exhibit non-rigid behavior. Earth's gravity-topography cross-spectrum exhibits notable variations in signal amplitude and character at spherical harmonic degrees l=13, 116, 416, and 1389. Corresponding Cartesian wavelengths are approximately equal to the respective thicknesses of Earth's mantle, continental mantle lithosphere, oceanic thermal lithosphere, and continental crust, all known from seismology. Regional variations in seismic moment release with depth, derived from the global Centroid Moment Tensor catalog, are also evident in the crust and mantle lithosphere. Combined, these observations provide powerful constraints for the structure and evolution of the crust, mantle lithosphere, and mantle as a whole. All that is required is a dynamically consistent mechanism relating wavelength to layer thickness and shear-strain localization. A statistically-invariant 'diharmonic' relation exhibiting these properties appears as the leading order approximation to toroidal motions on a self-gravitating body of differential grade-2 material. We use this relation, specifically its predictions of weakness and rigidity, and of folding and shear banding response as a function of wavelength-to-thickness ratio, to interpret Earth's gravity, topography, and seismicity in four-dimensions. We find the mantle lithosphere to be about 255-km thick beneath the Himalaya and the Andes, and the long

  1. Climate-induced changes in lake ecosystem structure inferred from coupled neo- and paleoecological approaches

    Science.gov (United States)

    Saros, Jasmine E.; Stone, Jeffery R.; Pederson, Gregory T.; Slemmons, Krista; Spanbauer, Trisha; Schliep, Anna; Cahl, Douglas; Williamson, Craig E.; Engstrom, Daniel R.

    2015-01-01

    Over the 20th century, surface water temperatures have increased in many lake ecosystems around the world, but long-term trends in the vertical thermal structure of lakes remain unclear, despite the strong control that thermal stratification exerts on the biological response of lakes to climate change. Here we used both neo- and paleoecological approaches to develop a fossil-based inference model for lake mixing depths and thereby refine understanding of lake thermal structure change. We focused on three common planktonic diatom taxa, the distributions of which previous research suggests might be affected by mixing depth. Comparative lake surveys and growth rate experiments revealed that these species respond to lake thermal structure when nitrogen is sufficient, with species optima ranging from shallower to deeper mixing depths. The diatom-based mixing depth model was applied to sedimentary diatom profiles extending back to 1750 AD in two lakes with moderate nitrate concentrations but differing climate settings. Thermal reconstructions were consistent with expected changes, with shallower mixing depths inferred for an alpine lake where treeline has advanced, and deeper mixing depths inferred for a boreal lake where wind strength has increased. The inference model developed here provides a new tool to expand and refine understanding of climate-induced changes in lake ecosystems.

  2. A symmetry-based method to infer structural brain networks from probabilistic tractography data

    Directory of Open Access Journals (Sweden)

    Kamal Shadi

    2016-11-01

    Full Text Available Recent progress in diffusion MRI and tractography algorithms as well as the launch of the Human Connectome Project (HCP have provided brain research with an abundance of structural connectivity data. In this work, we describe and evaluate a method that can infer the structural brain network that interconnects a given set of Regions of Interest (ROIs from probabilistic tractography data. The proposed method, referred to as Minimum Asymmetry Network Inference Algorithm (MANIA, does not determine the connectivity between two ROIs based on an arbitrary connectivity threshold. Instead, we exploit a basic limitation of the tractography process: the observed streamlines from a source to a target do not provide any information about the polarity of the underlying white matter, and so if there are some fibers connecting two voxels (or two ROIs X and Y, tractography should be able in principle to follow this connection in both directions, from X to Y and from Y to X. We leverage this limitation to formulate the network inference process as an optimization problem that minimizes the (appropriately normalized asymmetry of the observed network. We evaluate the proposed method using both the FiberCup dataset and based on a noise model that randomly corrupts the observed connectivity of synthetic networks. As a case-study, we apply MANIA on diffusion MRI data from 28 healthy subjects to infer the structural network between 18 corticolimbic ROIs that are associated with various neuropsychiatric conditions including depression, anxiety and addiction.

  3. ELISA: Structure-Function Inferences based on statistically significant and evolutionarily inspired observations

    Directory of Open Access Journals (Sweden)

    DeLisi Charles

    2003-09-01

    Full Text Available Abstract The problem of functional annotation based on homology modeling is primary to current bioinformatics research. Researchers have noted regularities in sequence, structure and even chromosome organization that allow valid functional cross-annotation. However, these methods provide a lot of false negatives due to limited specificity inherent in the system. We want to create an evolutionarily inspired organization of data that would approach the issue of structure-function correlation from a new, probabilistic perspective. Such organization has possible applications in phylogeny, modeling of functional evolution and structural determination. ELISA (Evolutionary Lineage Inferred from Structural Analysis, http://romi.bu.edu/elisa is an online database that combines functional annotation with structure and sequence homology modeling to place proteins into sequence-structure-function "neighborhoods". The atomic unit of the database is a set of sequences and structural templates that those sequences encode. A graph that is built from the structural comparison of these templates is called PDUG (protein domain universe graph. We introduce a method of functional inference through a probabilistic calculation done on an arbitrary set of PDUG nodes. Further, all PDUG structures are mapped onto all fully sequenced proteomes allowing an easy interface for evolutionary analysis and research into comparative proteomics. ELISA is the first database with applicability to evolutionary structural genomics explicitly in mind. Availability: The database is available at http://romi.bu.edu/elisa.

  4. Empirically determining the sample size for large-scale gene network inference algorithms.

    Science.gov (United States)

    Altay, G

    2012-04-01

    The performance of genome-wide gene regulatory network inference algorithms depends on the sample size. It is generally considered that the larger the sample size, the better the gene network inference performance. Nevertheless, there is not adequate information on determining the sample size for optimal performance. In this study, the author systematically demonstrates the effect of sample size on information-theory-based gene network inference algorithms with an ensemble approach. The empirical results showed that the inference performances of the considered algorithms tend to converge after a particular sample size region. As a specific example, the sample size region around ≃64 is sufficient to obtain the most of the inference performance with respect to precision using the representative algorithm C3NET on the synthetic steady-state data sets of Escherichia coli and also time-series data set of a homo sapiens subnetworks. The author verified the convergence result on a large, real data set of E. coli as well. The results give evidence to biologists to better design experiments to infer gene networks. Further, the effect of cutoff on inference performances over various sample sizes is considered. [Includes supplementary material].

  5. Cosmology from large-scale structure observations: a subjective review

    Science.gov (United States)

    Bilicki, Maciej; Hellwing, Wojciech A.

    2017-08-01

    In these lecture notes we give a brief overview of cosmological inference from the observed large-scale structure (LSS) of the Universe. After a general introduction, we briefly summarize the current status of the standard cosmological model, ΛCDM, and then discuss a few general puzzles related to this otherwise successful model. Next, after a concise presentation of LSS properties, we describe various observational cosmological probes, such as baryon acoustic oscillations, redshift space distortions and weak gravitational lensing. We also provide examples of how the rapidly developing technique of cross-correlations of cosmological datasets is applied. Finally, we briefly mention the promise brought to cosmology by gravitational wave detections.

  6. Jury-Contestant Bipartite Competition Network: Identifying Biased Scores and Their Impact on Network Structure Inference

    CERN Document Server

    Jeon, Gyuhyeon

    2016-01-01

    A common form of competition is one where judges grade contestants' performances which are then compiled to determine the final ranking of the contestants. Unlike in another common form of competition where two contestants play a head-to-head match to produce a winner as in football or basketball, the objectivity of judges are prone to be questioned, potentially undermining the public's trust in the fairness of the competition. In this work we show, by modeling the judge--contestant competition as a weighted bipartite network, how we can identify biased scores and measure their impact on our inference of the network structure. Analyzing the prestigious International Chopin Piano Competition of 2015 with a well-publicized scoring controversy as an example, we show that even a single statistically uncharacteristic score can be enough to gravely distort our inference of the community structure, demonstrating the importance of detecting and eliminating biases. In the process we also find that there does not exist...

  7. Inflation, large scale structure and particle physics

    Indian Academy of Sciences (India)

    We review experimental and theoretical developments in inflation and its application to structure formation, including the curvation idea. We then discuss a particle physics model of supersymmetric hybrid inflation at the intermediate scale in which the Higgs scalar field is responsible for large scale structure, show how such ...

  8. Oceanic Domains - Observed Relationship With Tomographic Features and Inferred Mantle Structure

    Science.gov (United States)

    Loubet, M.

    A persistent contradiction exists between the current views of mantle stratification derived from geochemistry and number of geophysical and simulations which sug- gest the existence of a significant material exchange throughout the entire mantle and favor mixing processes. In this presentation, we will show that the common interpre- tation of oceanic basalt heterogeneities can be contested and that a new interpretation of these heterogeneities can be done which leads to interesting relationships between geochemical and geophysical (tomographic) features. The new approach is based on (a) identification of mantle heterogeneities at the scale of oceanic domains recovering in some cases MORB and OIB basalt types and (b) use of incompatible element ratios in (Cx/Cz,Cy/Cz) representations as in particular the (Th/La,Nb/La) representation. This last representation is very interesting for identification of magmatic processes and for estimating magma sources compositions. Analysis of oceanic basalts compo- sitions based on a large set of literature data leads to identify 4 (eventually 5) large scale oceanic domains: Atlantic East Pacific (AEP), Indian ocean (IO), South Central Pacific (SCP), Kerguelen South Atlantic (KSA) (and eventually Hawaï (H)). The two first ones which include MORB sources extend at upper mantle levels. The good geo- graphical recovery of the SCP and KSA domains with tomographic features assigned to take place within the mantle at the D" level in the Central Pacific and South Africa (Masters et al., 2000) leads to interpret the basalts from the KSA and SCP domains as issued from D" layer source. Two different mantle structures (general ones before discussing more complex ones), both comprising a D" layer (composed of recycled oceanic crust enriched materials) at the CMB, can be inferred from these oceanic basalt source interpretations: (a) a layered mantle with an upper and a lower mantle with primitive mantle material composing a significant part of

  9. Topological Privacy: Lattice Structures and Information Bubbles for Inference and Obfuscation

    Science.gov (United States)

    2016-12-19

    NAME(S) AND ADDRESS(ES). Enter the name and address of the organization(s) financially responsible for and monitoring the work. 10. SPONSOR/MONITOR’S...release. Topological Privacy: Lattice Structures and Information Bubbles for Inference and Obfuscation Final Report to AFOSR Award FA9550-14-1-0012...44 10.7 Hidden Holes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45 10.8 Bubbles

  10. Final Report: Large-Scale Optimization for Bayesian Inference in Complex Systems

    Energy Technology Data Exchange (ETDEWEB)

    Ghattas, Omar [The University of Texas at Austin

    2013-10-15

    The SAGUARO (Scalable Algorithms for Groundwater Uncertainty Analysis and Robust Optimiza- tion) Project focuses on the development of scalable numerical algorithms for large-scale Bayesian inversion in complex systems that capitalize on advances in large-scale simulation-based optimiza- tion and inversion methods. Our research is directed in three complementary areas: efficient approximations of the Hessian operator, reductions in complexity of forward simulations via stochastic spectral approximations and model reduction, and employing large-scale optimization concepts to accelerate sampling. Our efforts are integrated in the context of a challenging testbed problem that considers subsurface reacting flow and transport. The MIT component of the SAGUARO Project addresses the intractability of conventional sampling methods for large-scale statistical inverse problems by devising reduced-order models that are faithful to the full-order model over a wide range of parameter values; sampling then employs the reduced model rather than the full model, resulting in very large computational savings. Results indicate little effect on the computed posterior distribution. On the other hand, in the Texas-Georgia Tech component of the project, we retain the full-order model, but exploit inverse problem structure (adjoint-based gradients and partial Hessian information of the parameter-to- observation map) to implicitly extract lower dimensional information on the posterior distribution; this greatly speeds up sampling methods, so that fewer sampling points are needed. We can think of these two approaches as "reduce then sample" and "sample then reduce." In fact, these two approaches are complementary, and can be used in conjunction with each other. Moreover, they both exploit deterministic inverse problem structure, in the form of adjoint-based gradient and Hessian information of the underlying parameter-to-observation map, to achieve their speedups.

  11. Inferring transcriptional compensation interactions in yeast via stepwise structure equation modeling

    Directory of Open Access Journals (Sweden)

    Wang Woei-Fuh

    2008-03-01

    Full Text Available Abstract Background With the abundant information produced by microarray technology, various approaches have been proposed to infer transcriptional regulatory networks. However, few approaches have studied subtle and indirect interaction such as genetic compensation, the existence of which is widely recognized although its mechanism has yet to be clarified. Furthermore, when inferring gene networks most models include only observed variables whereas latent factors, such as proteins and mRNA degradation that are not measured by microarrays, do participate in networks in reality. Results Motivated by inferring transcriptional compensation (TC interactions in yeast, a stepwise structural equation modeling algorithm (SSEM is developed. In addition to observed variables, SSEM also incorporates hidden variables to capture interactions (or regulations from latent factors. Simulated gene networks are used to determine with which of six possible model selection criteria (MSC SSEM works best. SSEM with Bayesian information criterion (BIC results in the highest true positive rates, the largest percentage of correctly predicted interactions from all existing interactions, and the highest true negative (non-existing interactions rates. Next, we apply SSEM using real microarray data to infer TC interactions among (1 small groups of genes that are synthetic sick or lethal (SSL to SGS1, and (2 a group of SSL pairs of 51 yeast genes involved in DNA synthesis and repair that are of interest. For (1, SSEM with BIC is shown to outperform three Bayesian network algorithms and a multivariate autoregressive model, checked against the results of qRT-PCR experiments. The predictions for (2 are shown to coincide with several known pathways of Sgs1 and its partners that are involved in DNA replication, recombination and repair. In addition, experimentally testable interactions of Rad27 are predicted. Conclusion SSEM is a useful tool for inferring genetic networks, and the

  12. Netter: re-ranking gene network inference predictions using structural network properties.

    Science.gov (United States)

    Ruyssinck, Joeri; Demeester, Piet; Dhaene, Tom; Saeys, Yvan

    2016-02-09

    Many algorithms have been developed to infer the topology of gene regulatory networks from gene expression data. These methods typically produce a ranking of links between genes with associated confidence scores, after which a certain threshold is chosen to produce the inferred topology. However, the structural properties of the predicted network do not resemble those typical for a gene regulatory network, as most algorithms only take into account connections found in the data and do not include known graph properties in their inference process. This lowers the prediction accuracy of these methods, limiting their usability in practice. We propose a post-processing algorithm which is applicable to any confidence ranking of regulatory interactions obtained from a network inference method which can use, inter alia, graphlets and several graph-invariant properties to re-rank the links into a more accurate prediction. To demonstrate the potential of our approach, we re-rank predictions of six different state-of-the-art algorithms using three simple network properties as optimization criteria and show that Netter can improve the predictions made on both artificially generated data as well as the DREAM4 and DREAM5 benchmarks. Additionally, the DREAM5 E.coli. community prediction inferred from real expression data is further improved. Furthermore, Netter compares favorably to other post-processing algorithms and is not restricted to correlation-like predictions. Lastly, we demonstrate that the performance increase is robust for a wide range of parameter settings. Netter is available at http://bioinformatics.intec.ugent.be. Network inference from high-throughput data is a long-standing challenge. In this work, we present Netter, which can further refine network predictions based on a set of user-defined graph properties. Netter is a flexible system which can be applied in unison with any method producing a ranking from omics data. It can be tailored to specific prior

  13. Response function of the large-scale structure of the universe to the small scale inhomogeneities

    Energy Technology Data Exchange (ETDEWEB)

    Nishimichi, Takahiro, E-mail: takahiro.nishimichi@ipmu.jp [Sorbonne Universités, UPMC Univ Paris 6 et CNRS, UMR 7095, Institut d' Astrophysique de Paris, 98 bis bd Arago, 75014 Paris (France); Kavli Institute for the Physics and Mathematics of the Universe (WPI), The University of Tokyo Institutes for Advanced Study, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8583 (Japan); CREST, JST, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012 (Japan); Bernardeau, Francis, E-mail: francis.bernardeau@iap.fr [Sorbonne Universités, UPMC Univ Paris 6 et CNRS, UMR 7095, Institut d' Astrophysique de Paris, 98 bis bd Arago, 75014 Paris (France); CEA, CNRS, UMR 3681, Institut de Physique Théorique, F-91191 Gif-sur-Yvette (France); Taruya, Atsushi, E-mail: ataruya@yukawa.kyoto-u.ac.jp [Yukawa Institute for Theoretical Physics, Kyoto University, Kyoto 606-8502 (Japan); Kavli Institute for the Physics and Mathematics of the Universe (WPI), The University of Tokyo Institutes for Advanced Study, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8583 (Japan)

    2016-11-10

    In order to infer the impact of the small-scale physics to the large-scale properties of the universe, we use a series of cosmological N-body simulations of self-gravitating matter inhomogeneities to measure, for the first time, the response function of such a system defined as a functional derivative of the nonlinear power spectrum with respect to its linear counterpart. Its measured shape and amplitude are found to be in good agreement with perturbation theory predictions except for the coupling from small to large-scale perturbations. The latter is found to be significantly damped, following a Lorentzian form. These results shed light on validity regime of perturbation theory calculations giving a useful guideline for regularization of small scale effects in analytical modeling. Most importantly our result indicates that the statistical properties of the large-scale structure of the universe are remarkably insensitive to the details of the small-scale physics, astrophysical or gravitational, paving the way for the derivation of robust estimates of theoretical uncertainties on the determination of cosmological parameters from large-scale survey observations.

  14. Computational applications of DNA structural scales

    DEFF Research Database (Denmark)

    Baldi, P.; Chauvin, Y.; Brunak, Søren

    1998-01-01

    that these scales provide an alternative or complementary compact representation of DNA sequences. As an example, we construct a strand-invariant representation of DNA sequences. The scales can also be used to analyze and discover new DNA structural patterns, especially in combination with hidden Markov models...

  15. Mediation analysis with intermediate confounding: structural equation modeling viewed through the causal inference lens.

    Science.gov (United States)

    De Stavola, Bianca L; Daniel, Rhian M; Ploubidis, George B; Micali, Nadia

    2015-01-01

    The study of mediation has a long tradition in the social sciences and a relatively more recent one in epidemiology. The first school is linked to path analysis and structural equation models (SEMs), while the second is related mostly to methods developed within the potential outcomes approach to causal inference. By giving model-free definitions of direct and indirect effects and clear assumptions for their identification, the latter school has formalized notions intuitively developed in the former and has greatly increased the flexibility of the models involved. However, through its predominant focus on nonparametric identification, the causal inference approach to effect decomposition via natural effects is limited to settings that exclude intermediate confounders. Such confounders are naturally dealt with (albeit with the caveats of informality and modeling inflexibility) in the SEM framework. Therefore, it seems pertinent to revisit SEMs with intermediate confounders, armed with the formal definitions and (parametric) identification assumptions from causal inference. Here we investigate: 1) how identification assumptions affect the specification of SEMs, 2) whether the more restrictive SEM assumptions can be relaxed, and 3) whether existing sensitivity analyses can be extended to this setting. Data from the Avon Longitudinal Study of Parents and Children (1990-2005) are used for illustration. © The Author 2014. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health.

  16. An improved algorithm for generalized community structure inference in complex networks

    Science.gov (United States)

    Qu, Yingfei; Shi, Weiren; Shi, Xin

    2017-07-01

    In recent years, the research of the community detection is not only on the structure that densely connected internally, but also on the structure of more patterns, such as heterogeneity, overlapping, core-periphery. In this paper, we build the network model based on the random graph models and propose an improved algorithm to infer the generalized community structures. We achieve it by introducing the generalized Bernstein polynomials and computing the latent parameters of vertices. The algorithm is tested both on the computer-generated benchmark networks and the real-world networks. Results show that the algorithm makes better performances on convergence speed and is able to discover the latent continuous structures in networks.

  17. Diagnostic SNPs for inferring population structure in American mink (Neovison vison) identified through RAD sequencing

    DEFF Research Database (Denmark)

    2015-01-01

    Data from: "Diagnostic SNPs for inferring population structure in American mink (Neovison vison) identified through RAD sequencing" in Genomic Resources Notes accepted 1 October 2014 to 30 November 2014....

  18. Inference of gene regulatory networks with sparse structural equation models exploiting genetic perturbations.

    Directory of Open Access Journals (Sweden)

    Xiaodong Cai

    Full Text Available Integrating genetic perturbations with gene expression data not only improves accuracy of regulatory network topology inference, but also enables learning of causal regulatory relations between genes. Although a number of methods have been developed to integrate both types of data, the desiderata of efficient and powerful algorithms still remains. In this paper, sparse structural equation models (SEMs are employed to integrate both gene expression data and cis-expression quantitative trait loci (cis-eQTL, for modeling gene regulatory networks in accordance with biological evidence about genes regulating or being regulated by a small number of genes. A systematic inference method named sparsity-aware maximum likelihood (SML is developed for SEM estimation. Using simulated directed acyclic or cyclic networks, the SML performance is compared with that of two state-of-the-art algorithms: the adaptive Lasso (AL based scheme, and the QTL-directed dependency graph (QDG method. Computer simulations demonstrate that the novel SML algorithm offers significantly better performance than the AL-based and QDG algorithms across all sample sizes from 100 to 1,000, in terms of detection power and false discovery rate, in all the cases tested that include acyclic or cyclic networks of 10, 30 and 300 genes. The SML method is further applied to infer a network of 39 human genes that are related to the immune function and are chosen to have a reliable eQTL per gene. The resulting network consists of 9 genes and 13 edges. Most of the edges represent interactions reasonably expected from experimental evidence, while the remaining may just indicate the emergence of new interactions. The sparse SEM and efficient SML algorithm provide an effective means of exploiting both gene expression and perturbation data to infer gene regulatory networks. An open-source computer program implementing the SML algorithm is freely available upon request.

  19. Predicting fracture in micron-scale polycrystalline silicon MEMS structures.

    Energy Technology Data Exchange (ETDEWEB)

    Hazra, Siddharth S. (Carnegie Mellon University, Pittsburgh, PA); de Boer, Maarten Pieter (Carnegie Mellon University, Pittsburgh, PA); Boyce, Brad Lee; Ohlhausen, James Anthony; Foulk, James W., III; Reedy, Earl David, Jr.

    2010-09-01

    Designing reliable MEMS structures presents numerous challenges. Polycrystalline silicon fractures in a brittle manner with considerable variability in measured strength. Furthermore, it is not clear how to use a measured tensile strength distribution to predict the strength of a complex MEMS structure. To address such issues, two recently developed high throughput MEMS tensile test techniques have been used to measure strength distribution tails. The measured tensile strength distributions enable the definition of a threshold strength as well as an inferred maximum flaw size. The nature of strength-controlling flaws has been identified and sources of the observed variation in strength investigated. A double edge-notched specimen geometry was also tested to study the effect of a severe, micron-scale stress concentration on the measured strength distribution. Strength-based, Weibull-based, and fracture mechanics-based failure analyses were performed and compared with the experimental results.

  20. Remote sensing of seasonal distribution of precipitable water vapor over the oceans and the inference of boundary-layer structure

    Science.gov (United States)

    Prabhakara, C.; Lo, R. C.; Nath, N. R.; Dalu, G.

    1979-01-01

    From the depth of the water vapor spectral lines in the 8-9 micron window region, measured by the Nimbus 4 Infrared Interferometer Spectrometer (IRIS) with a resolution of about 3/cm, the precipitable water vapor over the oceans is remotely sensed. In addition the IRIS spectral data in the 11-13 micron window region have been used to derive the sea surface temperature (SST). Seasonal maps of w on the oceans deduced from the spectral data reveal the dynamical influence of the large-scale atmospheric circulation. With the help of a model for the vertical distribution of water vapor, the configuration of the atmospheric boundary layer over the oceans can be inferred from these remotely sensed w and SST. The gross seasonal mean structure of the boundary layer inferred in this fashion reveals the broad areas of trade wind inversion and the convectively active areas such as the ITCZ. The derived information is in reasonable agreement with some observed climatological patterns over the oceans.

  1. Using AFLP markers and the Geneland program for the inference of population genetic structure

    DEFF Research Database (Denmark)

    Guillot, Gilles; Santos, Filipe

    2010-01-01

    The use of dominant markers such as amplified fragment length polymorphism (AFLP) for population genetics analyses is often impeded by the lack of appropriate computer programs and rarely motivated by objective considerations. The point of the present note is twofold: (i) we describe how...... the computer program Geneland designed to infer population structure has been adapted to deal with dominant markers; and (ii) we use Geneland for numerical comparison of dominant and codominant markers to perform clustering. AFLP markers lead to less accurate results than bi-allelic codominant markers...

  2. Inferring a district-based hierarchical structure of social contacts from census data.

    Science.gov (United States)

    Yu, Z; Liu, J; Zhu, X

    2015-01-01

    Researchers have recently paid attention to social contact patterns among individuals due to their useful applications in such areas as epidemic evaluation and control, public health decisions, chronic disease research and social network research. Although some studies have estimated social contact patterns from social networks and surveys, few have considered how to infer the hierarchical structure of social contacts directly from census data. In this paper, we focus on inferring an individual's social contact patterns from detailed census data, and generate various types of social contact patterns such as hierarchical-district-structure-based, cross-district and age-district-based patterns. We evaluate newly generated contact patterns derived from detailed 2011 Hong Kong census data by incorporating them into a model and simulation of the 2009 Hong Kong H1N1 epidemic. We then compare the newly generated social contact patterns with the mixing patterns that are often used in the literature, and draw the following conclusions. First, the generation of social contact patterns based on a hierarchical district structure allows for simulations at different district levels. Second, the newly generated social contact patterns reflect individuals social contacts. Third, the newly generated social contact patterns improve the accuracy of the SEIR-based epidemic model.

  3. Hebbian Wiring Plasticity Generates Efficient Network Structures for Robust Inference with Synaptic Weight Plasticity.

    Science.gov (United States)

    Hiratani, Naoki; Fukai, Tomoki

    2016-01-01

    In the adult mammalian cortex, a small fraction of spines are created and eliminated every day, and the resultant synaptic connection structure is highly nonrandom, even in local circuits. However, it remains unknown whether a particular synaptic connection structure is functionally advantageous in local circuits, and why creation and elimination of synaptic connections is necessary in addition to rich synaptic weight plasticity. To answer these questions, we studied an inference task model through theoretical and numerical analyses. We demonstrate that a robustly beneficial network structure naturally emerges by combining Hebbian-type synaptic weight plasticity and wiring plasticity. Especially in a sparsely connected network, wiring plasticity achieves reliable computation by enabling efficient information transmission. Furthermore, the proposed rule reproduces experimental observed correlation between spine dynamics and task performance.

  4. Permeability and hydraulic diffusivity of Waste Isolation Pilot Plant repository salt inferred from small-scale brine inflow experiments

    Energy Technology Data Exchange (ETDEWEB)

    McTigue, D.F.

    1993-06-01

    Brine seepage to 17 boreholes in salt at the Waste Isolation Pilot Plant (WIPP) facility horizon has been monitored for several years. A simple model for one-dimensional, radial, darcy flow due to relaxation of ambient pore-water pressure is applied to analyze the field data. Fits of the model response to the data yield estimates of two parameters that characterize the magnitude of the flow and the time scale over which it evolves. With further assumptions, these parameters are related to the permeability and the hydraulic diffusivity of the salt. For those data that are consistent with the model prediction, estimated permeabilities are typically 10{sup {minus}22} to 10{sup {minus}21} m{sup 2}. The relatively small range of inferred permeabilities reflects the observation that the measured seepage fluxes are fairly consistent from hole to hole, of the order of 10{sup {minus}10} m/s. Estimated diffusivities are typically 10{sup {minus}10} to 10{sup {minus}8} m{sup 2}/s. The greater scatter in inferred hydraulic diffusivities is due to the difficulty of matching the idealized model history to the observed evolution of the flows. The data obtained from several of the monitored holes are not consistent with the simple model adopted here; material properties could not be inferred in these cases.

  5. Large Scale Structure of the Universe

    Science.gov (United States)

    Kaplinghat, Manoj

    2011-03-01

    These notes are based on 4 lectures given at Theoretical Advanced Study Institute in 2009 on the large scale structure of the universe. They provide a pedagogical introduction to the temporal evolution of linear density perturbations in the universe and a discussion of how density perturbations on small scales depend on the particle properties of dark matter. The notes assume the reader is familiar with the concepts and mathematics required to describe isotropic and homogeneous cosmology.

  6. Inferring the structure of latent class models using a genetic algorithm.

    Science.gov (United States)

    van der Maas, Han L J; Raijmakers, Maartje E J; Visser, Ingmar

    2005-05-01

    Present optimization techniques in latent class analysis apply the expectation maximization algorithm or the Newton-Raphson algorithm for optimizing the parameter values of a prespecified model. These techniques can be used to find maximum likelihood estimates of the parameters, given the specified structure of the model, which is defined by the number of classes and, possibly, fixation and equality constraints. The model structure is usually chosen on theoretical grounds. A large variety of structurally different latent class models can be compared using goodness-of-fit indices of the chi-square family, Akaike's information criterion, the Bayesian information criterion, and various other statistics. However, finding the optimal structure for a given goodness-of-fit index often requires a lengthy search in which all kinds of model structures are tested. Moreover, solutions may depend on the choice of initial values for the parameters. This article presents a new method by which one can simultaneously infer the model structure from the data and optimize the parameter values. The method consists of a genetic algorithm in which any goodness-of-fit index can be used as a fitness criterion. In a number of test cases in which data sets from the literature were used, it is shown that this method provides models that fit equally well as or better than the models suggested in the original articles.

  7. Algorithms, data structures, and numerics for likelihood-based phylogenetic inference of huge trees

    Directory of Open Access Journals (Sweden)

    Izquierdo-Carrasco Fernando

    2011-12-01

    Full Text Available Abstract Background The rapid accumulation of molecular sequence data, driven by novel wet-lab sequencing technologies, poses new challenges for large-scale maximum likelihood-based phylogenetic analyses on trees with more than 30,000 taxa and several genes. The three main computational challenges are: numerical stability, the scalability of search algorithms, and the high memory requirements for computing the likelihood. Results We introduce methods for solving these three key problems and provide respective proof-of-concept implementations in RAxML. The mechanisms presented here are not RAxML-specific and can thus be applied to any likelihood-based (Bayesian or maximum likelihood tree inference program. We develop a new search strategy that can reduce the time required for tree inferences by more than 50% while yielding equally good trees (in the statistical sense for well-chosen starting trees. We present an adaptation of the Subtree Equality Vector technique for phylogenomic datasets with missing data (already available in RAxML v728 that can reduce execution times and memory requirements by up to 50%. Finally, we discuss issues pertaining to the numerical stability of the Γ model of rate heterogeneity on very large trees and argue in favor of rate heterogeneity models that use a single rate or rate category for each site to resolve these problems. Conclusions We address three major issues pertaining to large scale tree reconstruction under maximum likelihood and propose respective solutions. Respective proof-of-concept/production-level implementations of our ideas are made available as open-source code.

  8. Statistics of Caustics in Large-Scale Structure Formation

    Science.gov (United States)

    Feldbrugge, Job L.; Hidding, Johan; van de Weygaert, Rien

    2016-10-01

    The cosmic web is a complex spatial pattern of walls, filaments, cluster nodes and underdense void regions. It emerged through gravitational amplification from the Gaussian primordial density field. Here we infer analytical expressions for the spatial statistics of caustics in the evolving large-scale mass distribution. In our analysis, following the quasi-linear Zel'dovich formalism and confined to the 1D and 2D situation, we compute number density and correlation properties of caustics in cosmic density fields that evolve from Gaussian primordial conditions. The analysis can be straightforwardly extended to the 3D situation. We moreover, are currently extending the approach to the non-linear regime of structure formation by including higher order Lagrangian approximations and Lagrangian effective field theory.

  9. Large-scale film structures in space

    Science.gov (United States)

    Simon, Kirill

    Up-to-date space technology calls for not only taking account of, but also employment of, specific attributes of the outer space environment such as weightlessness, centrifugal forces, hard vacuum, powerful solar radiation. These specific characteristics of outer space allow the use of various structures in space whose development and operation is impossible and inexpedient on Earth. Currently, interest in large-scale space structures is growing; there are various projects on such multi-body space structures and experiments are being conducted for their development. Such designs are represented by spacecraft with solar sails, orbiting solar reflectors, solar energy concentrators, low frequency antennas and others. This paper examines a large-scale flexible space structure made from thin reflective film used as the working surface of the sunlight reflector or the sailcraft. Specifically, this paper deals with techniques of modeling large-scale space structure attitude motion, numerical calculation of vibrations which occur in the system after a spatial slew is performed, as well as optimal trajectory computations. Various methods of the film structure attitude control and stabilization, including optimal slewing programs, are discussed.

  10. Inferring the mesoscale structure of layered, edge-valued, and time-varying networks

    Science.gov (United States)

    Peixoto, Tiago P.

    2015-10-01

    Many network systems are composed of interdependent but distinct types of interactions, which cannot be fully understood in isolation. These different types of interactions are often represented as layers, attributes on the edges, or as a time dependence of the network structure. Although they are crucial for a more comprehensive scientific understanding, these representations offer substantial challenges. Namely, it is an open problem how to precisely characterize the large or mesoscale structure of network systems in relation to these additional aspects. Furthermore, the direct incorporation of these features invariably increases the effective dimension of the network description, and hence aggravates the problem of overfitting, i.e., the use of overly complex characterizations that mistake purely random fluctuations for actual structure. In this work, we propose a robust and principled method to tackle these problems, by constructing generative models of modular network structure, incorporating layered, attributed and time-varying properties, as well as a nonparametric Bayesian methodology to infer the parameters from data and select the most appropriate model according to statistical evidence. We show that the method is capable of revealing hidden structure in layered, edge-valued, and time-varying networks, and that the most appropriate level of granularity with respect to the additional dimensions can be reliably identified. We illustrate our approach on a variety of empirical systems, including a social network of physicians, the voting correlations of deputies in the Brazilian national congress, the global airport network, and a proximity network of high-school students.

  11. From Coexpression to Coregulation: An Approach to Inferring Transcriptional Regulation Among Gene Classes from Large-Scale Expression Data

    Science.gov (United States)

    Mjolsness, Eric; Castano, Rebecca; Mann, Tobias; Wold, Barbara

    2000-01-01

    We provide preliminary evidence that existing algorithms for inferring small-scale gene regulation networks from gene expression data can be adapted to large-scale gene expression data coming from hybridization microarrays. The essential steps are (I) clustering many genes by their expression time-course data into a minimal set of clusters of co-expressed genes, (2) theoretically modeling the various conditions under which the time-courses are measured using a continuous-time analog recurrent neural network for the cluster mean time-courses, (3) fitting such a regulatory model to the cluster mean time courses by simulated annealing with weight decay, and (4) analysing several such fits for commonalities in the circuit parameter sets including the connection matrices. This procedure can be used to assess the adequacy of existing and future gene expression time-course data sets for determining transcriptional regulatory relationships such as coregulation.

  12. Scalings of intermittent structures in magnetohydrodynamic turbulence

    CERN Document Server

    Zhdankin, Vladimir; Uzdensky, Dmitri A

    2016-01-01

    Turbulence is ubiquitous in plasmas, leading to rich dynamics characterized by irregularity, irreversibility, energy fluctuations across many scales, and energy transfer across many scales. Another fundamental and generic feature of turbulence, although sometimes overlooked, is the inhomogeneous dissipation of energy in space and in time. This is a consequence of intermittency, the scale-dependent inhomogeneity of dynamics caused by fluctuations in the turbulent cascade. Intermittency causes turbulent plasmas to self-organize into coherent dissipative structures, which may govern heating, diffusion, particle acceleration, and radiation emissions. In this paper, we present recent progress on understanding intermittency in incompressible magnetohydrodynamic turbulence with a strong guide field. We focus on the statistical analysis of intermittent dissipative structures, which occupy a small fraction of the volume but arguably account for the majority of energy dissipation. We show that, in our numerical simulat...

  13. structSSI: Simultaneous and Selective Inference for Grouped or Hierarchically Structured Data.

    Science.gov (United States)

    Sankaran, Kris; Holmes, Susan

    The package structSSI provides an accessible implementation of two recently developed simultaneous and selective inference techniques: the group Benjamini-Hochberg and hierarchical false discovery rate procedures. Unlike many multiple testing schemes, these methods specifically incorporate existing information about the grouped or hierarchical dependence between hypotheses under consideration while controlling the false discovery rate. Doing so increases statistical power and interpretability. Furthermore, these procedures provide novel approaches to the central problem of encoding complex dependency between hypotheses. We briefly describe the group Benjamini-Hochberg and hierarchical false discovery rate procedures and then illustrate them using two examples, one a measure of ecological microbial abundances and the other a global temperature time series. For both procedures, we detail the steps associated with the analysis of these particular data sets, including establishing the dependence structures, performing the test, and interpreting the results. These steps are encapsulated by functions, and we explain their applicability to general data sets.

  14. Free phase gas processes in a northern peatland inferred from autonomous field‐scale resistivity imaging

    National Research Council Canada - National Science Library

    Terry, Neil; Slater, Lee; Comas, Xavier; Reeve, Andrew S; Schäfer, Karina V. R; Yu, Zhongjie

    2016-01-01

    .... Electrical resistivity imaging (ERI) is capable of autonomously collecting three‐dimensional data on the centimeter to tens of meter scale and thus provides a unique opportunity to observe FPG dynamics in situ. We collected 127 3...

  15. Life-history traits of the Miocene Hipparion concudense (Spain inferred from bone histological structure.

    Directory of Open Access Journals (Sweden)

    Cayetana Martinez-Maza

    Full Text Available Histological analyses of fossil bones have provided clues on the growth patterns and life history traits of several extinct vertebrates that would be unavailable for classical morphological studies. We analyzed the bone histology of Hipparion to infer features of its life history traits and growth pattern. Microscope analysis of thin sections of a large sample of humeri, femora, tibiae and metapodials of Hipparion concudense from the upper Miocene site of Los Valles de Fuentidueña (Segovia, Spain has shown that the number of growth marks is similar among the different limb bones, suggesting that equivalent skeletochronological inferences for this Hipparion population might be achieved by means of any of the elements studied. Considering their abundance, we conducted a skeletechronological study based on the large sample of third metapodials from Los Valles de Fuentidueña together with another large sample from the Upper Miocene locality of Concud (Teruel, Spain. The data obtained enabled us to distinguish four age groups in both samples and to determine that Hipparion concudense tended to reach skeletal maturity during its third year of life. Integration of bone microstructure and skeletochronological data allowed us to identify ontogenetic changes in bone structure and growth rate and to distinguish three histologic ontogenetic stages corresponding to immature, subadult and adult individuals. Data on secondary osteon density revealed an increase in bone remodeling throughout the ontogenetic stages and a lesser degree thereof in the Concud population, which indicates different biomechanical stresses in the two populations, likely due to environmental differences. Several individuals showed atypical growth patterns in the Concud sample, which may also reflect environmental differences between the two localities. Finally, classification of the specimens' age within groups enabled us to characterize the age structure of both samples, which is

  16. Life-History Traits of the Miocene Hipparion concudense (Spain) Inferred from Bone Histological Structure

    Science.gov (United States)

    Martinez-Maza, Cayetana; Alberdi, Maria Teresa; Nieto-Diaz, Manuel; Prado, José Luis

    2014-01-01

    Histological analyses of fossil bones have provided clues on the growth patterns and life history traits of several extinct vertebrates that would be unavailable for classical morphological studies. We analyzed the bone histology of Hipparion to infer features of its life history traits and growth pattern. Microscope analysis of thin sections of a large sample of humeri, femora, tibiae and metapodials of Hipparion concudense from the upper Miocene site of Los Valles de Fuentidueña (Segovia, Spain) has shown that the number of growth marks is similar among the different limb bones, suggesting that equivalent skeletochronological inferences for this Hipparion population might be achieved by means of any of the elements studied. Considering their abundance, we conducted a skeletechronological study based on the large sample of third metapodials from Los Valles de Fuentidueña together with another large sample from the Upper Miocene locality of Concud (Teruel, Spain). The data obtained enabled us to distinguish four age groups in both samples and to determine that Hipparion concudense tended to reach skeletal maturity during its third year of life. Integration of bone microstructure and skeletochronological data allowed us to identify ontogenetic changes in bone structure and growth rate and to distinguish three histologic ontogenetic stages corresponding to immature, subadult and adult individuals. Data on secondary osteon density revealed an increase in bone remodeling throughout the ontogenetic stages and a lesser degree thereof in the Concud population, which indicates different biomechanical stresses in the two populations, likely due to environmental differences. Several individuals showed atypical growth patterns in the Concud sample, which may also reflect environmental differences between the two localities. Finally, classification of the specimens’ age within groups enabled us to characterize the age structure of both samples, which is typical of

  17. Inferring Passenger Denial Behavior of Taxi Drivers from Large-Scale Taxi Traces.

    Directory of Open Access Journals (Sweden)

    Sihai Zhang

    Full Text Available How to understand individual human actions is a fundamental question to modern science, which drives and incurs many social, technological, racial, religious and economic phenomena. Human dynamics tries to reveal the temporal pattern and internal mechanism of human actions in letter or electronic communications, from the perspective of continuous interactions among friends or acquaintances. For interactions between stranger to stranger, taxi industry provide fruitful phenomina and evidence to investigate the action decisions. In fact, one striking disturbing events commonly reported in taxi industry is passenger refusing or denial, whose reasons vary, including skin color, blind passenger, being a foreigner or too close destination, religion reasons and anti specific nationality, so that complaints about taxi passenger refusing have to be concerned and processed carefully by local governments. But more universal factors for this phenomena are of great significance, which might be fulfilled by big data research to obtain novel insights in this question. In this paper, we demonstrate the big data analytics application in revealing novel insights from massive taxi trace data, which, for the first time, validates the passengers denial in taxi industry and estimates the denial ratio in Beijing city. We first quantify the income differentiation facts among taxi drivers. Then we find out that choosing the drop-off places also contributes to the high income for taxi drivers, compared to the previous explanation of mobility intelligence. Moreover, we propose the pick-up, drop-off and grid diversity concepts and related diversity analysis suggest that, high income taxi drivers will deny passengers in some situations, so as to choose the passengers' destination they prefer. Finally we design an estimation method for denial ratio and infer that high income taxi drivers will deny passengers with 8.52% likelihood in Beijing. Our work exhibits the power of big

  18. Inferring single-cell behaviour from large-scale epithelial sheet migration patterns.

    Science.gov (United States)

    Lee, Rachel M; Yue, Haicen; Rappel, Wouter-Jan; Losert, Wolfgang

    2017-05-01

    Cell migration plays an important role in a wide variety of biological processes and can incorporate both individual cell motion and collective behaviour. The emergent properties of collective migration are receiving increasing attention as collective motion's role in diseases such as metastatic cancer becomes clear. Yet, how individual cell behaviour influences large-scale, multi-cell collective motion remains unclear. In this study, we provide insight into the mechanisms behind collective migration by studying cell migration in a spreading monolayer of epithelial MCF10A cells. We quantify migration using particle image velocimetry and find that cell groups have features of motion that span multiple length scales. Comparing our experimental results to a model of collective cell migration, we find that cell migration within the monolayer can be affected in qualitatively different ways by cell motion at the boundary, yet it is not necessary to introduce leader cells at the boundary or specify other large-scale features to recapitulate this large-scale phenotype in simulations. Instead, in our model, collective motion can be enhanced by increasing the overall activity of the cells or by giving the cells a stronger coupling between their motion and polarity. This suggests that investigating the activity and polarity persistence of individual cells will add insight into the collective migration phenotypes observed during development and disease. © 2017 The Author(s).

  19. Study of structural colour of Hebomoia glaucippe butterfly wing scales

    Science.gov (United States)

    Shur, V. Ya; Kuznetsov, D. K.; Pryakhina, V. I.; Kosobokov, M. S.; Zubarev, I. V.; Boymuradova, S. K.; Volchetskaya, K. V.

    2017-10-01

    Structural colours of Hebomoia glaucippe butterfly wing scales have been studied experimentally using high resolution scanning electron microscopy. Visualization of scales structures and computer simulation allowed distinguishing correlation between nanostructures on the scales and their colour.

  20. Structural response of reduced scale naval structures under impact tests

    Directory of Open Access Journals (Sweden)

    Calle M.A.G.

    2014-01-01

    Full Text Available Scaled models are important in naval engineering since actual ship size makes too expensive to test prototypes. However, the analysis of ship collision events employing naval structures in reduced scale is not an ordinary ship research area. The aim of this work is to create the basis for a posterior similarity study by analysing reduced scale ship structures submitted to impact loads. Two basic naval structures, commonly found in the construction of large ships, were considered for this study: a T cross-section beam submitted to a mid-span impact test and a double plate panel with inner cross reinforcement also submitted to a central impact load. These models were made in a reduced scale of 1:100. The experimental material characterization was also carried out in this work, including the evaluation of the stress strain curve under quasi static conditions, the strain rate sensitivity and the structural failure using three criteria developed particularly for numerical modelling of ship collision by other authors.

  1. Beyond co-localization: inferring spatial interactions between sub-cellular structures from microscopy images

    Directory of Open Access Journals (Sweden)

    Paul Grégory

    2010-07-01

    Full Text Available Abstract Background Sub-cellular structures interact in numerous direct and indirect ways in order to fulfill cellular functions. While direct molecular interactions crucially depend on spatial proximity, other interactions typically result in spatial correlations between the interacting structures. Such correlations are the target of microscopy-based co-localization analysis, which can provide hints of potential interactions. Two complementary approaches to co-localization analysis can be distinguished: intensity correlation methods capitalize on pattern discovery, whereas object-based methods emphasize detection power. Results We first reinvestigate the classical co-localization measure in the context of spatial point pattern analysis. This allows us to unravel the set of implicit assumptions inherent to this measure and to identify potential confounding factors commonly ignored. We generalize object-based co-localization analysis to a statistical framework involving spatial point processes. In this framework, interactions are understood as position co-dependencies in the observed localization patterns. The framework is based on a model of effective pairwise interaction potentials and the specification of a null hypothesis for the expected pattern in the absence of interaction. Inferred interaction potentials thus reflect all significant effects that are not explained by the null hypothesis. Our model enables the use of a wealth of well-known statistical methods for analyzing experimental data, as demonstrated on synthetic data and in a case study considering virus entry into live cells. We show that the classical co-localization measure typically under-exploits the information contained in our data. Conclusions We establish a connection between co-localization and spatial interaction of sub-cellular structures by formulating the object-based interaction analysis problem in a spatial statistics framework based on nearest-neighbor distance

  2. A model to infer the demographic structure evolution of endangered donkey populations.

    Science.gov (United States)

    Navas, F J; Jordana, J; León, J M; Barba, C; Delgado, J V

    2017-05-16

    Stemming from The Worldwide Donkey Breeds Project, an initiative aiming at connecting international researchers and entities working with the donkey species, molecularly tested pedigree analyses were carried out to study the genetic diversity, structure and historical evolution of the Andalusian donkey breed since the 1980s to infer a model to study the situation of international endangered donkey breeds under the remarkably frequent unknown genetical background status behind them. Demographic and genetic variability parameters were evaluated using ENDOG (v4.8). Pedigree completeness and generation length were quantified for the four gametic pathways. Despite mean inbreeding was low, highly inbred animals were present in the pedigree. Average coancestry, relatedness, and non-random mating degree trends were computed. The effective population size based on individual inbreeding rate was about half when based on individual coancestry rate. Nei's distances and equivalent subpopulations number indicated differentiated farms in a highly structured population. Although genetic diversity loss since the founder generations could be considered small, intraherd breeding policies and the excessive contribution of few ancestors to the gene pool could lead to narrower pedigree bottlenecks. Long average generation intervals could be considered when reducing inbreeding. Wright's fixation statistics indicated slight inbreeding between farms. Pedigree shallowness suggested applying new breeding strategies to reliably estimate descriptive parameters and control the negative effects of inbreeding, which could indeed, mean the key to preserve such valuable animal resources avoiding the extinction they potentially head towards, making the present model become an international referent when assessing endangered donkey populations.

  3. Upper trophic structure in the Atlantic Patagonian shelf break as inferred from stable isotope analysis

    Science.gov (United States)

    Zhu, Guoping; Zhang, Haiting; Yang, Yang; Wang, Shaoqin; Wei, Lian; Yang, Qingyuan

    2017-09-01

    The Patagonian Shelf is a very productive region with different ecosystem structures. A long history of fishing in the Southwestern Atlantic Ocean combined with a complex hydrographic structure, with a permanent front over the shelf-break and different coastal frontal regions, and a wide non-frontal area in between have made the food web in this area more complex and have resulted in changes to the spatial-temporal scale. Stable isotopes of carbon and nitrogen were used to determine the trophic structure of the Patagonian shelf break which was previously poorly understood. The results indicated that the average δ15N value of pelagic guild (Illex argentinus) was remarkable lower than those of the other guilds. The δ13C values of almost all species ranged from -17‰ to -18‰, but Stromateus brasiliensis had a significant lower δ13C value. Compared with the southern Patagonian shelf, short food chain length also occurred. The impact of complex oceanographic structures has resulted in food web structure change to the temporal-spatial scale on the Patagonian shelf. The Patagonian shelf break can be considered as a separated ecosystem structure with lower δ15N values.

  4. Tropical entrainment time scales inferred from stratospheric N2O and CH4 observations

    Science.gov (United States)

    Herman, R. L.; Scott, D. C.; Webster, C. R.; May, R. D.; Moyer, E. J.; Salawitch, R. J.; Yung, Y. L.; Toon, G. C.; Sen, B.; Margitan, J. J.; Rosenlof, K. H.; Michelsen, H. A.; Elkins, J. W.

    Simultaneous in situ measurements of N2O and CH4 were made with a tunable diode laser spectrometer (ALIAS II) aboard the Observations from the Middle Stratosphere (OMS) balloon platform from New Mexico, Alaska, and Brazil during 1996 and 1997. We find different compact relationships of CH4 with N2O in the tropics and extra-tropics because mixing is slow between these regions. Transport into the extra-tropics from the tropics or the polar vortex leads to deviations from the normal compact relationship. We use measured N2O and CH4 and a simple model to quantify entrainment of mid-latitude stratospheric air into the tropics. The entrainment time scale is estimated to be 16 (+17, -8) months for altitudes between 20 and 28 km. The fraction of tropical air entrained from the extra-tropical stratosphere is 50% (+18%, -30%) at 20 km, increasing to 78% (+11%, -19%) at 28 km.

  5. Crustal structure of the Dabie orogenic belt (eastern China) inferred from gravity and magnetic data

    Science.gov (United States)

    Yang, Yu-shan; Li, Yuan-yuan

    2018-01-01

    In order to better characterize the crustal structure of the Dabie orogen and its tectonic history, we present a crustal structure along a 500 km long profile across the Dabie orogenic belt using various data processing and interpretation of the gravity and magnetic data. Source depth estimations from the spectral analysis by continuous wavelet transform (CWT) provide better constraints for constructing the initial density model. The calculated gravity effects from the initial model show great discrepancy with the observed data, especially at the center of the profile. More practical factors are then incorporated into the gravity modeling. First, we add a high density body right beneath the high pressure metamorphic (HPM) and ultrahigh pressure metamorphic (UHPM) belt considering the exposed HPM and UHPM rocks in the mid of our profile. Then, the anomalous bodies A, B, and C inferred from the CWT-based spectral analysis results are fixed in the model geometry. In the final crustal density structure, two anomalous bodies B and C with high density and low magnetization could possibly be attributed to metasomatised mantle materials by SiO2-rich melt derived from the foundering subducted mafic lower crust. Under the extensional environment in the early Cretaceous, the upwelling metasomatised mantle was partially melted to produce the parental magma of the post-collisional mafic-ultramafic intrusive rocks. As for the low density body A with strong magnetization located in the lower crust right beneath the HP and UHP metamorphic belt, it is more likely to be composed of serpentinized mantle peridotite (SMP). This serpentinized mantle peridotite body (SMPB) represents the emplacement of mantle-derived peridotites in the crust, accompanying the exhumation of the UHP metamorphic rocks.

  6. Imaging meso-scale ionospheric structures

    Science.gov (United States)

    Burston, Robert

    2012-06-01

    The accuracy and capacity to resolve meso-scale structures of a four dimensional ionospheric imaging algorithm in the circumstance of data from dense networks of permanent GNSS ground receiver stations were investigated. Simulation studies were conducted in order to be able to assess the performance of the algorithm over the entire imaged region. The Multi-instrument Data Assimilation Software (MIDAS) algorithm was used for this purpose. Simulated input data in Receiver Independent Exchange Format (RINEX) were produced by calculating slant Total Electron Content (sTEC) values for satellite to receiver raypaths through an artificially generated ionosphere. Modeling these signals including Differential Code Biases (DCBs) and noise had negligible impact on the output from the imaging algorithm when compared with modeled signals that included neither. Comparing the output from MIDAS using a range of grid definitions show that finer grids have improved capacity to resolve meso-scale structures in the input model but over all are less accurate than coarser grids. The greatest errors occur in low-data regions of the grid and where structures in the input have the greatest gradients in vertical Total Electron Content (vTEC). A good compromise between the conflicting needs of resolution and accuracy is given by a grid defined with 2° × 2° latitude by longitude local horizontal grid divisions.

  7. INFERRING THE MAGNETOHYDRODYNAMIC STRUCTURE OF SOLAR FLARE SUPRA-ARCADE PLASMAS FROM A DATA-ASSIMILATED FIELD TRANSPORT MODEL

    Energy Technology Data Exchange (ETDEWEB)

    Scott, Roger B.; McKenzie, David E.; Longcope, Dana W. [Montana State University, P.O. Box 173840, Bozeman, MT 59717-3840 (United States)

    2016-03-01

    Supra-arcade fans are highly dynamic structures that form in the region above post-reconnection flare arcades. In these features the plasma density and temperature evolve on the scale of a few seconds, despite the much slower dynamics of the underlying arcade. Further, the motion of supra-arcade plasma plumes appears to be inconsistent with the low-beta conditions that are often assumed to exist in the solar corona. In order to understand the nature of these highly debated structures, it is, therefore, important to investigate the interplay of the magnetic field with the plasma. Here we present a technique for inferring the underlying magnetohydrodynamic processes that might lead to the types of motions seen in supra-arcade structures. Taking as a case study the 2011 October 22 event, we begin with extreme-ultraviolet observations and develop a time-dependent velocity field that is consistent with both continuity and local correlation tracking. We then assimilate this velocity field into a simplified magnetohydrodynamic simulation, which deals simultaneously with regions of high and low signal-to-noise ratio, thereby allowing the magnetic field to evolve self-consistently with the fluid. Ultimately, we extract the missing contributions from the momentum equation in order to estimate the relative strength of the various forcing terms. In this way we are able to make estimates of the plasma beta, as well as predict the spectral character and total power of Alfvén waves radiated from the supra-arcade region.

  8. Large scale structure statistics: Finite volume effects

    Science.gov (United States)

    Colombi, S.; Bouchet, F. R.; Schaeffer, R.

    1994-01-01

    We study finite volume effects on the count probability distribution function PN(l) and the averaged Q-body correlations Xi-barQ (2 less than or = Q less than or equal 5). These statistics are computed for cubic cells, of size l. We use as an example the case of the matter distribution of a cold dark matter (CDM) universe involving approximately 3 x 105 particles. The main effect of the finiteness of the sampled volume is to induce an abrupt cut-off on the function PN(l) at large N. This clear signature makes an analysis of the consequences easy, and one can envisage a correction procedure. As a matter of fact, we demonstrate how an unfair sample can strongly affect the estimates of the functions Xi-barQ for Q greater than or = 3 (and decrease the measured zero of the two-body correlation function). We propose a method to correct for this are fact, or at least to evaluate the corresponding errors. We show that the correlations are systematically underestimated by direct measurements. We find that, once corrected, the statistical properties of the CDM universe appear compatible with the scaling relation SQ identically equals Xi-bar2 exp Q-1 = constant with respect to scale, in the non-linear regime; it was not the case with direct measurments. However, we note a deviation from scaling at scales close to the correlation length. It is probably due to the transition between the highly non-linear regime and the weakly correlated regime, where the functions SQ also seem to present a plateau. We apply the same procedure to simulations with hot dark matter (HDM) and white noise initial conditions, with similar results. Our method thus provides the first accurate measurement of the normalized skewness, S3, and the normalized kurtosis, S4, for three typical models of large scale structure formation in an expanding universe.

  9. Incorrect likelihood methods were used to infer scaling laws of marine predator search behaviour.

    Science.gov (United States)

    Edwards, Andrew M; Freeman, Mervyn P; Breed, Greg A; Jonsen, Ian D

    2012-01-01

    Ecologists are collecting extensive data concerning movements of animals in marine ecosystems. Such data need to be analysed with valid statistical methods to yield meaningful conclusions. We demonstrate methodological issues in two recent studies that reached similar conclusions concerning movements of marine animals (Nature 451:1098; Science 332:1551). The first study analysed vertical movement data to conclude that diverse marine predators (Atlantic cod, basking sharks, bigeye tuna, leatherback turtles and Magellanic penguins) exhibited "Lévy-walk-like behaviour", close to a hypothesised optimal foraging strategy. By reproducing the original results for the bigeye tuna data, we show that the likelihood of tested models was calculated from residuals of regression fits (an incorrect method), rather than from the likelihood equations of the actual probability distributions being tested. This resulted in erroneous Akaike Information Criteria, and the testing of models that do not correspond to valid probability distributions. We demonstrate how this led to overwhelming support for a model that has no biological justification and that is statistically spurious because its probability density function goes negative. Re-analysis of the bigeye tuna data, using standard likelihood methods, overturns the original result and conclusion for that data set. The second study observed Lévy walk movement patterns by mussels. We demonstrate several issues concerning the likelihood calculations (including the aforementioned residuals issue). Re-analysis of the data rejects the original Lévy walk conclusion. We consequently question the claimed existence of scaling laws of the search behaviour of marine predators and mussels, since such conclusions were reached using incorrect methods. We discourage the suggested potential use of "Lévy-like walks" when modelling consequences of fishing and climate change, and caution that any resulting advice to managers of marine ecosystems

  10. Incorrect likelihood methods were used to infer scaling laws of marine predator search behaviour.

    Directory of Open Access Journals (Sweden)

    Andrew M Edwards

    Full Text Available BACKGROUND: Ecologists are collecting extensive data concerning movements of animals in marine ecosystems. Such data need to be analysed with valid statistical methods to yield meaningful conclusions. PRINCIPAL FINDINGS: We demonstrate methodological issues in two recent studies that reached similar conclusions concerning movements of marine animals (Nature 451:1098; Science 332:1551. The first study analysed vertical movement data to conclude that diverse marine predators (Atlantic cod, basking sharks, bigeye tuna, leatherback turtles and Magellanic penguins exhibited "Lévy-walk-like behaviour", close to a hypothesised optimal foraging strategy. By reproducing the original results for the bigeye tuna data, we show that the likelihood of tested models was calculated from residuals of regression fits (an incorrect method, rather than from the likelihood equations of the actual probability distributions being tested. This resulted in erroneous Akaike Information Criteria, and the testing of models that do not correspond to valid probability distributions. We demonstrate how this led to overwhelming support for a model that has no biological justification and that is statistically spurious because its probability density function goes negative. Re-analysis of the bigeye tuna data, using standard likelihood methods, overturns the original result and conclusion for that data set. The second study observed Lévy walk movement patterns by mussels. We demonstrate several issues concerning the likelihood calculations (including the aforementioned residuals issue. Re-analysis of the data rejects the original Lévy walk conclusion. CONCLUSIONS: We consequently question the claimed existence of scaling laws of the search behaviour of marine predators and mussels, since such conclusions were reached using incorrect methods. We discourage the suggested potential use of "Lévy-like walks" when modelling consequences of fishing and climate change, and caution

  11. Physical scale experiments on torrential filter structures

    Science.gov (United States)

    Chiari, Michael; Moser, Markus; Trojer, Martin; Hübl, Johannes

    2016-04-01

    In the framework of the INTERREG Project "SedAlp" physical scale model experiments are carried out in the hydraulic laboratory of the Institute of Mountain Risk Engineering at the University of Life Sciences in Vienna in order to optimize torrent protection structures. Two different types of check dams are investigated. A screen-dam with inclined vertical beams is compared with a beam-dam with horizontal beams. The experiments evaluate the variation of sediment transport of these structures including the influence of coarse woody debris. Therefore the distance between the steel elements can be adjusted to show their ability to filter sediment. The physical scale of the experiments is 1:30. All experimental runs are Froude scaled. Both dams are tested in elongated and pear-shaped sediment retention basins in order to investigate the shape effect of the deposition area. For a systematic comparison of the two check dams experiments with fluvial bedload transport are made. First a typical hydrograph for an extreme flood with unlimited sediment supply is modelled. A typical torrential sediment mixture with a wide grain-size distribution is fed by a conveyor belt according the transport capacity of the upstream reach. Then the deposition is scanned with a laser-scan device in order to analyse the deposition pattern and the deposited volume. Afterwards a flood with a lower reoccurrence period without sediment transport from upstream is modelled to investigate the ability of the protection structure for self-emptying. To investigate the influence of driftwood on the deposition behaviour experiments with logs are made. Different log diameters and lengths are added upstream the basin. The results show, that the deposition during the experiments was not controlled by sorting-effects at the location of the dam. The deposition always started from upstream, where the transport capacity was reduced due to the milder slope and the widening of the basin. No grain sorting effects

  12. Seismic cycle in the Nepal Himalaya inferred from instantaneous modelling across time scales

    Science.gov (United States)

    Dal Zilio, Luca; van Dinther, Ylona; Gerya, Taras

    2017-04-01

    The Himalayan mountain range has been the locus of some of the largest continental earthquakes, including the 2015 magnitude 7.8 Gorkha earthquake. This event ruptured a previously locked portion of the Main Himalayan Thrust (MHT) fault that has not slipped in a large event since 1833 (Mw 7.6). The earthquake sequence was well recorded by geodetic and seismic instruments, enhancing our understanding of earthquake physics and induced ground shaking. One of the main remaining questions—very relevant for the hundreds of millions of people living in the Ganges plains—is why did the Gorkha earthquake not rupture the frontal part of the MHT-fault? How likely is it to rupture in future earthquakes? And what does this tell us about its frictional properties? To explore these challenging questions we analyze the relation between interseismic periods and the kinematic rupture process of the MHT-fault in the Nepal Himalaya using a new 2D Instantaneous Seismo-Thermo-Mechanical (I-STM). This approach utilizes a visco-elasto-plastic rheology with slip rate-dependent friction to simulate spontaneous rapid slip events throughout the orogen. By employing geodetic data, combined with a geological and geophysical analysis, we design a high-resolution model (200 m) of the present-day lithospheric structure and geometry of the MHT beneath the Kathmandu area. Results show how large earthquakes nucleate on the lower edge of the locked portion, grow and terminate on the MHT-fault in relation to the long-term interseismic period. In agreement with observed geodetic data, our numerical experiments suggest that interseismic convergence across the Himalaya is mostly accommodated by MHT—no relevant slip on smaller faults is required. Fault slip during coseismic MHT events causes up to 1-2 m of uplift in the Kathmandu basin and the surrounding Lesser Himalaya, whereas a large region of the higher Himalaya subside by about 1 m. After partial ruptures of the MHT we observe upward transfer

  13. Seeing Scale: Richard Dunn’s Structuralism

    Directory of Open Access Journals (Sweden)

    Keith Broadfoot

    2012-11-01

    Full Text Available Writing on the occasion of a retrospective of Richard Dunn’s work, Terence Maloon argued that ‘structuralism had an important bearing on virtually all of Richard Dunn’s mature works’, with ‘his modular, “crossed” formats’ being the most obvious manifestation of this. In this article I wish to reconsider this relation, withdrawing from a broad consideration of the framework of structuralism to focus on some of the quite particular ideas that Lacan proposed in response to structuralism. Beginning from a pivotal painting in the 1960s that developed out of Dunn’s experience of viewing the work of Barnett Newman, I wish to suggest a relation between the ongoing exploration of the thematic of scale in Dunn’s work and the idea of the symbolic that Lacan derives from structuralist thought. This relation, I argue, opens up a different way of understanding the art historical transition from Minimalism to Conceptual art.

  14. Fire structures pine serotiny at different scales.

    Science.gov (United States)

    Hernández-Serrano, Ana; Verdú, Miguel; González-Martínez, Santiago C; Pausas, Juli G

    2013-12-01

    Serotiny (delayed seed release with the consequent accumulation of a canopy seedbank) confers fitness benefits in environments with crown-fire regimes. Thus, we predicted that serotiny level should be higher in populations recurrently subjected to crown-fires than in populations where crown-fires are rare. In addition, under a high frequency of fires, space and resources are recurrently available, permitting recruitment around each mother to follow the seed rain shadow. Thus, we also predicted spatial aggregation of serotiny within populations. We compared serotiny, considering both the proportion and the age of serotinous cones, in populations living in contrasting fire regimes for two iconic Mediterranean pine species (Pinus halepensis, P. pinaster). We framed our results by quantitatively comparing the strength of the fire-serotiny relationship with previous studies worldwide. For the two species, populations living under high crown-fire recurrence regimes had a higher serotiny level than those populations where the recurrence of crown-fires was low. For P. halepensis (the species with higher serotiny), populations in high fire recurrence regimes had higher fine-scale spatial aggregation of serotiny than those inhabiting low fire recurrence systems. The strength of the observed fire-serotiny relationship in P. halepensis is among the highest in published literature. Fire regime shapes serotiny level among populations, and in populations with high serotiny, recurrent fires maintain a significant spatial structure for this trait. Consequently, fire has long-term evolutionary implications at different scales, emphasizing its prominent role in shaping the ecology of pines.

  15. Responses in large-scale structure

    Science.gov (United States)

    Barreira, Alexandre; Schmidt, Fabian

    2017-06-01

    We introduce a rigorous definition of general power-spectrum responses as resummed vertices with two hard and n soft momenta in cosmological perturbation theory. These responses measure the impact of long-wavelength perturbations on the local small-scale power spectrum. The kinematic structure of the responses (i.e., their angular dependence) can be decomposed unambiguously through a ``bias'' expansion of the local power spectrum, with a fixed number of physical response coefficients, which are only a function of the hard wavenumber k. Further, the responses up to n-th order completely describe the (n+2)-point function in the squeezed limit, i.e. with two hard and n soft modes, which one can use to derive the response coefficients. This generalizes previous results, which relate the angle-averaged squeezed limit to isotropic response coefficients. We derive the complete expression of first- and second-order responses at leading order in perturbation theory, and present extrapolations to nonlinear scales based on simulation measurements of the isotropic response coefficients. As an application, we use these results to predict the non-Gaussian part of the angle-averaged matter power spectrum covariance CovNGl=0(k1,k2), in the limit where one of the modes, say k2, is much smaller than the other. Without any free parameters, our model results are in very good agreement with simulations for k2 lesssim 0.06 h Mpc-1, and for any k1 gtrsim 2k2. The well-defined kinematic structure of the power spectrum response also permits a quick evaluation of the angular dependence of the covariance matrix. While we focus on the matter density field, the formalism presented here can be generalized to generic tracers such as galaxies.

  16. Eight challenges in phylodynamic inference

    Directory of Open Access Journals (Sweden)

    Simon D.W. Frost

    2015-03-01

    Full Text Available The field of phylodynamics, which attempts to enhance our understanding of infectious disease dynamics using pathogen phylogenies, has made great strides in the past decade. Basic epidemiological and evolutionary models are now well characterized with inferential frameworks in place. However, significant challenges remain in extending phylodynamic inference to more complex systems. These challenges include accounting for evolutionary complexities such as changing mutation rates, selection, reassortment, and recombination, as well as epidemiological complexities such as stochastic population dynamics, host population structure, and different patterns at the within-host and between-host scales. An additional challenge exists in making efficient inferences from an ever increasing corpus of sequence data.

  17. Correlations between scale structure and pigmentation in butterfly wings.

    Science.gov (United States)

    Janssen, J M; Monteiro, A; Brakefield, P M

    2001-01-01

    We examined the correlation between color and structure of wing scales in the nymphalid butterflies Bicyclus anynana and Heliconius melpomene. All scales in B. anynana are rather similar in comparison to the clear structural differences of differently pigmented scales in H. melpomene. Where scale structural differences in H. melpomene are qualitative, they seem to be quantitative in B. anynana. There is a "gradient" in the density of some structural elements, the cross ribs, in the scales of B. anynana: black, gold, and brown scales show progressively lower cross rib density within an individual. There is, however, high individual variation in the absolute cross rib densities (i.e., scales with a particular color and cross rib density in one individual may have a different color but similar density in another individual). By ectopically inducing color pattern during early pupal development, we examined whether a scale's color and its microstructure could be uncoupled. The effect of these manipulations appears to be different in B. anynana and H. melpomene. In Bicyclus, "black" scales induced by wing damage at an ectopic location normally containing brown scales acquire both an intermediate structure and color between that of brown and normal black scales. In Heliconius, however, intermediate colors or scale structure were never observed, and scales with an altered color (due to damage) always have the same structure as normal scales with that color. The results are discussed on the basis of gene expression patterns, variability in rates of scale development and pigment, and scale sclerotization pathways.

  18. The confounding effect of population structure on bayesian skyline plot inferences of demographic history

    DEFF Research Database (Denmark)

    Heller, Rasmus; Chikhi, Lounes; Siegismund, Hans

    2013-01-01

    Many coalescent-based methods aiming to infer the demographic history of populations assume a single, isolated and panmictic population (i.e. a Wright-Fisher model). While this assumption may be reasonable under many conditions, several recent studies have shown that the results can be misleading...

  19. Structure Discovery in Large Semantic Graphs Using Extant Ontological Scaling and Descriptive Statistics

    Energy Technology Data Exchange (ETDEWEB)

    al-Saffar, Sinan; Joslyn, Cliff A.; Chappell, Alan R.

    2011-07-18

    As semantic datasets grow to be very large and divergent, there is a need to identify and exploit their inherent semantic structure for discovery and optimization. Towards that end, we present here a novel methodology to identify the semantic structures inherent in an arbitrary semantic graph dataset. We first present the concept of an extant ontology as a statistical description of the semantic relations present amongst the typed entities modeled in the graph. This serves as a model of the underlying semantic structure to aid in discovery and visualization. We then describe a method of ontological scaling in which the ontology is employed as a hierarchical scaling filter to infer different resolution levels at which the graph structures are to be viewed or analyzed. We illustrate these methods on three large and publicly available semantic datasets containing more than one billion edges each. Keywords-Semantic Web; Visualization; Ontology; Multi-resolution Data Mining;

  20. FACTOR STRUCTURE OF MF SCALES AND ITEMS.

    Science.gov (United States)

    LUNNEBORG, CLIFFORD E.; LUNNEBORG, PATRICIA W.

    FACTOR ANALYSES WERE PERFORMED UPON FOUR MASCULINITY-FEMINITY (MF) SCALES AND UPON THE 136-ITEMS COMPRISING THESE SCALES. RESULTS OF THE FIRST ANALYSIS ILLUSTRATED THE DIFFICULTY OF INTERPRETING FACTORS BASED ON HETEROGENEOUS SCALES. THE ITEM FACTORING REVEALED THE MULTIDIMENSIONALITY OF MF. CERTAIN ITEM FACTORS WERE UNCORRELATED WITH SEX STATUS…

  1. Quantifying the scale- and process- dependent reorganization of landscape under climatic change: inferences from an experimental landscape

    Science.gov (United States)

    Singh, A.; Tejedor, A.; Grimaud, J. L.; Zaliapin, I. V.; Foufoula-Georgiou, E.

    2016-12-01

    Knowledge of the dynamics of evolving landscapes in terms of their geomorphic and topologic re-organization in response to changing climatic or tectonic forcing is of scientific and practical interest. Although several studies have addressed the large-scale response (e.g., change in mean relief), studies on the smaller-scale drainage pattern re-organization and quantification of landscape vulnerability to the timing, magnitude, and frequency of changing forcing are lacking. The reason is the absence of data for such an analysis. To that goal, a series of controlled laboratory experiments were conducted at the St. Anthony Falls laboratory of the University of Minnesota to study the effect of changing precipitation patterns on landscape evolution at the short and long-time scales. High resolution digital elevation (DEM) both in space and time were measured for a range of rainfall patterns and uplift rates. Results from our study show a distinct signature of the precipitation increase on the probabilistic and geometrical structure of landscape features, evident in widening and deepening of channels and valleys, change in drainage patterns within sub-basins and change in the space-time structure of erosional and depositional events. A spatially explicit analysis of the locus of these erosional and depositional events suggests a regime shift, during the onset of the transient state, from supply-limited to transport-limited fluvial channels. We document a characteristic scale-dependent signature of erosion at steady state (which we term the "E50-area curve") and show that during reorganization, its evolving shape reflects process and scales of geomorphic change. Finally, we document changes in the longitudinal river profiles, in response to increased precipitation rate, with the formation of abrupt gradient (knickpoints) that migrate upstream as time proceeds.

  2. Seasonal rainfall forecasting by adaptive network-based fuzzy inference system (ANFIS) using large scale climate signals

    Science.gov (United States)

    Mekanik, F.; Imteaz, M. A.; Talei, A.

    2016-05-01

    Accurate seasonal rainfall forecasting is an important step in the development of reliable runoff forecast models. The large scale climate modes affecting rainfall in Australia have recently been proven useful in rainfall prediction problems. In this study, adaptive network-based fuzzy inference systems (ANFIS) models are developed for the first time for southeast Australia in order to forecast spring rainfall. The models are applied in east, center and west Victoria as case studies. Large scale climate signals comprising El Nino Southern Oscillation (ENSO), Indian Ocean Dipole (IOD) and Inter-decadal Pacific Ocean (IPO) are selected as rainfall predictors. Eight models are developed based on single climate modes (ENSO, IOD, and IPO) and combined climate modes (ENSO-IPO and ENSO-IOD). Root Mean Square Error (RMSE), Mean Absolute Error (MAE), Pearson correlation coefficient (r) and root mean square error in probability (RMSEP) skill score are used to evaluate the performance of the proposed models. The predictions demonstrate that ANFIS models based on individual IOD index perform superior in terms of RMSE, MAE and r to the models based on individual ENSO indices. It is further discovered that IPO is not an effective predictor for the region and the combined ENSO-IOD and ENSO-IPO predictors did not improve the predictions. In order to evaluate the effectiveness of the proposed models a comparison is conducted between ANFIS models and the conventional Artificial Neural Network (ANN), the Predictive Ocean Atmosphere Model for Australia (POAMA) and climatology forecasts. POAMA is the official dynamic model used by the Australian Bureau of Meteorology. The ANFIS predictions certify a superior performance for most of the region compared to ANN and climatology forecasts. POAMA performs better in regards to RMSE and MAE in east and part of central Victoria, however, compared to ANFIS it shows weaker results in west Victoria in terms of prediction errors and RMSEP skill

  3. CRNET: An efficient sampling approach to infer functional regulatory networks by integrating large-scale ChIP-seq and time-course RNA-seq data.

    Science.gov (United States)

    Chen, Xi; Gu, Jinghua; Wang, Xiao; Jung, Jin-Gyoung; Wang, Tian-Li; Hilakivi-Clarke, Leena; Clarke, Robert; Xuan, Jianhua

    2017-12-21

    NGS techniques have been widely applied in genetic and epigenetic studies. Multiple ChIP-seq and RNA-seq profiles can now be jointly used to infer functional regulatory networks (FRNs). However, existing methods suffer from either oversimplified assumption on transcription factor (TF) regulation or slow convergence of sampling for FRN inference from large-scale ChIP-seq and time-course RNA-seq data. We developed an efficient Bayesian integration method (CRNET) for FRN inference using a two-stage Gibbs sampler to estimate iteratively hidden TF activities and the posterior probabilities of binding events. A novel statistic measure that jointly considers regulation strength and regression error enables the sampling process of CRNET to converge quickly, thus making CRNET very efficient for large-scale FRN inference. Experiments on synthetic and benchmark data showed a significantly improved performance of CRNET when compared with existing methods. CRNET was applied to breast cancer data to identify FRNs functional at promoter or enhancer regions in breast cancer MCF-7 cells. Transcription factor MYC is predicted as a key functional factor in both promoter and enhancer FRNs. We experimentally validated the regulation effects of MYC on CRNET-predicted target genes using appropriate RNAi approaches in MCF-7 cells. R scripts of CRNET are available at http://www.cbil.ece.vt.edu/software.htm. xuan@vt.edu. Supplementary data are available at Bioinformatics online.

  4. Head structures of Priacma serrata Leconte (Coleptera, Archostemata) inferred from X-ray tomography.

    Science.gov (United States)

    Hörnschemeyer, Thomas; Beutel, Rolf G; Pasop, Freek

    2002-06-01

    Internal and external features of the head of Priacma serrata were studied with X-ray microtomography and with histological methods. The comparison of both techniques shows that X-ray tomography is a promising new technique for the investigation of insect anatomy. The still somewhat coarse resolution of the X-ray data is compensated for by advantages like the nondestructive and artifact-free data acquisition. The head of P. serrata and other adults of Archostemata is characterized by many derived features. Muscular features of Priacma, especially muscles of the labium and pharynx, differ strongly from what is found in other groups of Coleoptera. Several character states are considered as autapomorphies of Archostemata: scale-like surface structures, constricted neck, strongly reduced tentorium, and the plate-like, enlarged prementum. The scales provide a protecting surface pattern and may have evolved with a more exposed lifestyle. The enlarged prementum forms a lid, which closes the mouth and covers the ligula when it is pulled back by contraction of the unusually strong submento-premental muscle. The presence of four cone-shaped protuberances on the dorsal side of the head is considered an autapomorphy of Cupedidae. The galea with a narrow stalk and a round and pubescent distal galeomere is another autapomorphy of this family. It has probably evolved as an adaptation to pollen-feeding. The shape of the mandible of Cupedidae is plesiomorphic compared to what is found in adults of Ommatidae. The vertical arrangement of apical teeth is an autapomorphy of the latter family. The lateral insertion of the antenna in Priacma is a groundplan feature of Cupedidae. The dorsal shift is a synapomorphy of all other cupedid genera. A cladistic analysis of characters of the head and additional data resulted in the following branching pattern: ((Crowsoniella + (Omma + Tetraphalerus)) + (Micromalthus + (Priacma + (Paracupes + (Cupes + Tenomerga + Prolixocupes + Rhipsideigma

  5. Beam Coupling to Optical Scale Accelerating Structures

    Energy Technology Data Exchange (ETDEWEB)

    Sears, C.M.; Byer, R.L.; Colby, E.R.; Cowan, B.M.; Ischebeck, R.; Lincoln, M.R.; Siemann, R.H.; Spencer, J.E.; /SLAC; Plettner, T.; /Stanford U., Phys. Dept.

    2007-03-27

    Current research efforts into structure based laser acceleration of electrons utilize beams from standard RF linacs. These beams must be coupled into very small structures with transverse dimensions comparable to the laser wavelength. To obtain decent transmission, a permanent magnet quadrupole (PMQ) triplet with a focusing gradient of 560 T/m is used to focus into the structure. Also of interest is the induced wakefield from the structure, useful for diagnosing potential accelerator structures or as novel radiation sources.

  6. Structural colors from Morpho peleides butterfly wing scales

    KAUST Repository

    Ding, Yong

    2009-01-01

    A male Morpho peleides butterfly wing is decorated by two types of scales, cover and ground scales. We have studied the optical properties of each type of scales in conjunction with the structural information provided by cross-sectional transmission electron microscopy and computer simulation. The shining blue color is mainly from the Bragg reflection of the one-dimensional photonic structure, e.g., the shelf structure packed regularly in each ridges on cover scales. A thin-film-like interference effect from the base plate of the cover scale enhances such blue color and further gives extra reflection peaks in the infrared and ultraviolet regions. The analogy in the spectra acquired from the original wing and that from the cover scales suggests that the cover scales take a dominant role in its structural color. This study provides insight of using the biotemplates for fabricating smart photonic structures. © 2009 American Institute of Physics.

  7. Structural colors from Morpho peleides butterfly wing scales

    Science.gov (United States)

    Ding, Yong; Xu, Sheng; Wang, Zhong Lin

    2009-10-01

    A male Morpho peleides butterfly wing is decorated by two types of scales, cover and ground scales. We have studied the optical properties of each type of scales in conjunction with the structural information provided by cross-sectional transmission electron microscopy and computer simulation. The shining blue color is mainly from the Bragg reflection of the one-dimensional photonic structure, e.g., the shelf structure packed regularly in each ridges on cover scales. A thin-film-like interference effect from the base plate of the cover scale enhances such blue color and further gives extra reflection peaks in the infrared and ultraviolet regions. The analogy in the spectra acquired from the original wing and that from the cover scales suggests that the cover scales take a dominant role in its structural color. This study provides insight of using the biotemplates for fabricating smart photonic structures.

  8. Small-scale longitudinal variations in the daytime equatorial thermospheric wave dynamics as inferred from oxygen dayglow emissions

    Science.gov (United States)

    Karan, Deepak K.; Pallamraju, Duggirala

    2017-06-01

    The equatorial upper atmospheric dynamic processes show both latitudinal and longitudinal variabilities. While the variability in latitudes can exist over small distances (approximately hundreds of kilometers), the longitudinal behavior has been shown to be existing mainly over large spatial separations (approximately thousands of kilometers). In the present work we have used variations in thermospheric optical dayglow emissions at OI 557.7, 630.0, and 777.4 nm, as tracers of neutral dynamics. These emissions are obtained simultaneously from a high-resolution slit spectrograph, Multi wavelength Imaging Spectrograph using Echelle grating, from a low-latitude location, Hyderabad (17.5°N, 78.4°E; 8.9°N magnetic latitude) in India, to investigate the longitudinal differences in the upper atmospheric processes over short separations. Spectral analyses of gravity waves carried out on the dayglow emission intensity variations for different independent viewing directions on some days show dissimilar periodicities suggesting the existence of longitudinal differences. Gravity wave scale sizes and the propagation characteristics on these days are different from those in which longitudinal differences are not seen. Further, the zenith diurnal emission intensity patterns are different on the days with and without the observed longitudinal variability. This work shows for the first time that longitudinal differences in upper atmospheric processes can exist at even as small as 3° longitude separations. Such longitudinal differences seen in the neutral dayglow emission intensities are attributed to the zonal variation in the daytime equatorial electrodynamics.type="synopsis">type="main">Plain Language SummaryThe longitudinal variability in the upper atmospheric phenomena has been reported over large distances in the literature that span greater than several thousands of kilometer. However, nothing is known as to what happens on the smaller distances. Using large field of view

  9. Inference regarding multiple structural changes in linear models with endogenous regressors☆

    Science.gov (United States)

    Hall, Alastair R.; Han, Sanggohn; Boldea, Otilia

    2012-01-01

    This paper considers the linear model with endogenous regressors and multiple changes in the parameters at unknown times. It is shown that minimization of a Generalized Method of Moments criterion yields inconsistent estimators of the break fractions, but minimization of the Two Stage Least Squares (2SLS) criterion yields consistent estimators of these parameters. We develop a methodology for estimation and inference of the parameters of the model based on 2SLS. The analysis covers the cases where the reduced form is either stable or unstable. The methodology is illustrated via an application to the New Keynesian Phillips Curve for the US. PMID:23805021

  10. Inferring 3D chromatin structure using a multiscale approach based on quaternions.

    Science.gov (United States)

    Caudai, Claudia; Salerno, Emanuele; Zoppè, Monica; Tonazzini, Anna

    2015-07-29

    The knowledge of the spatial organisation of the chromatin fibre in cell nuclei helps researchers to understand the nuclear machinery that regulates DNA activity. Recent experimental techniques of the type Chromosome Conformation Capture (3C, or similar) provide high-resolution, high-throughput data consisting in the number of times any possible pair of DNA fragments is found to be in contact, in a certain population of cells. As these data carry information on the structure of the chromatin fibre, several attempts have been made to use them to obtain high-resolution 3D reconstructions of entire chromosomes, or even an entire genome. The techniques proposed treat the data in different ways, possibly exploiting physical-geometric chromatin models. One popular strategy is to transform contact data into Euclidean distances between pairs of fragments, and then solve a classical distance-to-geometry problem. We developed and tested a reconstruction technique that does not require translating contacts into distances, thus avoiding a number of related drawbacks. Also, we introduce a geometrical chromatin chain model that allows us to include sound biochemical and biological constraints in the problem. This model can be scaled at different genomic resolutions, where the structures of the coarser models are influenced by the reconstructions at finer resolutions. The search in the solution space is then performed by a classical simulated annealing, where the model is evolved efficiently through quaternion operators. The presence of appropriate constraints permits the less reliable data to be overlooked, so the result is a set of plausible chromatin configurations compatible with both the data and the prior knowledge. To test our method, we obtained a number of 3D chromatin configurations from Hi-C data available in the literature for the long arm of human chromosome 1, and validated their features against known properties of gene density and transcriptional activity. Our

  11. Factor structure and measurement invariance of the Health Education Impact Questionnaire: Does the subjectivity of the response perspective threaten the contextual validity of inferences?

    Science.gov (United States)

    Elsworth, Gerald R; Nolte, Sandra; Osborne, Richard H

    2015-01-01

    On-going evidence is required to support the validity of inferences about change and group differences in the evaluation of health programs, particularly when self-report scales requiring substantial subjectivity in response generation are used as outcome measures. Following this reasoning, the aim of this study was to replicate the factor structure and investigate the measurement invariance of the latest version of the Health Education Impact Questionnaire, a widely used health program evaluation measure. An archived dataset of responses to the most recent version of the English-language Health Education Impact Questionnaire that uses four rather than six response options (N = 3221) was analysed using exploratory structural equation modelling and confirmatory factor analysis appropriate for ordered categorical data. Metric and scalar invariance were studied following recent recommendations in the literature to apply fully invariant unconditional models with minimum constraints necessary for model identification. The original eight-factor structure was replicated and all but one of the scales (Self Monitoring and Insight) was found to consist of unifactorial items with reliability of ⩾0.8 and satisfactory discriminant validity. Configural, metric and scalar invariance were established across pre-test to post-test and population sub-groups (sex, age, education, ethnic background). The results support the high level of interest in the Health Education Impact Questionnaire, particularly for use as a pre-test/post-test measure in experimental studies, other pre-post evaluation designs and system-level monitoring and evaluation.

  12. Large scale structure from viscous dark matter

    CERN Document Server

    Blas, Diego; Garny, Mathias; Tetradis, Nikolaos; Wiedemann, Urs Achim

    2015-01-01

    Cosmological perturbations of sufficiently long wavelength admit a fluid dynamic description. We consider modes with wavevectors below a scale $k_m$ for which the dynamics is only mildly non-linear. The leading effect of modes above that scale can be accounted for by effective non-equilibrium viscosity and pressure terms. For mildly non-linear scales, these mainly arise from momentum transport within the ideal and cold but inhomogeneous fluid, while momentum transport due to more microscopic degrees of freedom is suppressed. As a consequence, concrete expressions with no free parameters, except the matching scale $k_m$, can be derived from matching evolution equations to standard cosmological perturbation theory. Two-loop calculations of the matter power spectrum in the viscous theory lead to excellent agreement with $N$-body simulations up to scales $k=0.2 \\, h/$Mpc. The convergence properties in the ultraviolet are better than for standard perturbation theory and the results are robust with respect to varia...

  13. Spatial Structure and Scaling of Agricultural Networks

    CERN Document Server

    Sousa, Daniel

    2016-01-01

    Considering agricultural landscapes as networks can provide information about spatial connectivity relevant for a wide range of applications including pollination, pest management, and ecology. Global agricultural networks are well-described by power law rank-size distributions. However, regional analyses capture only a subset of the total global network. Most analyses are regional. In this paper, we seek to address the following questions: Does the globally observed scale-free property of agricultural networks hold over smaller spatial domains? Can similar properties be observed at kilometer to meter scales? We analyze 9 intensively cultivated Landsat scenes on 5 continents with a wide range of vegetation distributions. We find that networks of vegetation fraction within the domain of each of these Landsat scenes exhibit substantial variability - but still possess similar scaling properties to the global distribution of agriculture. We also find similar results using a 39 km2 IKONOS image. To illustrate an a...

  14. Inferring phylogenetic structure and ancient hybridization within Salmonidae using next-generation sequencing

    Directory of Open Access Journals (Sweden)

    Laurène Alicia Lecaudey

    2015-10-01

    Full Text Available Phylogenetic studies focusing on Salmonidae have thus far revealed significant drawbacks to elucidate some of the interspecific relationships within the family, due to limited number of markers, conflicting phylogenetic signals and hybridization events. In an attempt to resolve these issues, we applied restriction-site associated DNA sequencing (RAD-seq to 44 samples, including 23 different species across the family Salmonidae, with an emphasis on the genus Salvelinus. The aim of our study is to infer reliable interspecific phylogenetic relationships, evaluate several putative scenarios of ancient hybridization and detect possible reticulate patterns of evolution among salmonid fishes. RAD-seq can be particularly useful for systematic studies of closely related taxa, as it provides genome-wide informative characters and allows the detection of introgression. To our knowledge, this is the first next generation sequencing effort applied to salmonid phylogeny and related questions of their evolutionary history. Using the software pipeline pyRAD, we identified 28,402 orthologous loci, which were subsequently used in our downstream analyses. Phylogenetic inferences drawn from a maximum likelihood analysis reveal some interesting results. Salvelinus and Oncorhynchus appear as sister lineages, which contradicts some of the previous phylogenetic analyses. Additionally, despite constituting a separate genus, Salvethymus clusters within the genus Salvelinus, which is consistent with the findings of previous studies and therefore questions its taxonomic status. A monophylum of Salvelinus leucomaenis and Salvelinus levanidovi is the sister group to the remainder of the genus Salvelinus. The genus Parahucho appears as the sister clade to Salmo, which also contradicts some previously published inferences. Finally, we present a practical application of a relatively novel approach to test for putative ancient hybridization events. Since this is the first

  15. Genetic structure of Colletotrichum gloeosporioides sensu lato isolates infecting papaya inferred by multilocus ISSR markers.

    Science.gov (United States)

    Rampersad, Sephra N

    2013-02-01

    Colletotrichum gloeosporioides sensu lato is widely distributed throughout temperate and tropical regions and causes anthracnose disease in numerous plant species. Development of effective disease management strategies is dependent on, among other factors, an understanding of pathogen genetic diversity and population stratification at the intraspecific level. For 132 isolates of C. gloeosporioides sensu lato collected from papaya in Trinidad, inter-simple-sequence repeat-polymerase chain reaction (ISSR-PCR) generated 121 polymorphic loci from five ISSR primers selected from an initial screen of 22 ISSR primers. The mean percentage of polymorphic loci was 99.18%. Bayesian cluster analysis inferred three genetic subpopulations, where group 1 consisted exclusively of isolates collected in the southern part of Trinidad whereas groups 2 and 3, although genetically distinct, were mixtures of isolates collected from both the northern and southern parts of Trinidad. Principal coordinates analysis and unweighted pair-group method with arithmetic mean phylogeny were concordant with Bayesian cluster analysis and supported subdivision into the three subpopulations. Overall, the total mean gene diversity was 0.279, the mean within-population gene diversity was 0.2161, and genetic differentiation for the Trinidad population was 0.225. Regionally, northern isolates had a lower gene diversity compared with southern isolates. Nei's gene diversity was highest for group 1 (h = 0.231), followed by group 2 (h = 0.215) and group 3 (h = 0.202). Genotypic diversity was at or near maximum for all three subpopulations after clone correction. Pairwise estimates of differentiation indicated high and significant genetic differentiation among the inferred subpopulations (Weir's θ of 0.212 to 0.325). Pairwise comparisons among subpopulations suggested restricted gene flow between groups 1 and 2 and groups 1 and 3 but not between groups 2 and 3. The null hypothesis of random mating was rejected

  16. The effects of incomplete protein interaction data on structural and evolutionary inferences

    DEFF Research Database (Denmark)

    de Silva, E; Thorne, T; Ingram, P

    2006-01-01

    of the inherent noise in protein interaction data. The effects of the incomplete nature of network data become very noticeable, especially for so-called network motifs. We also consider the effect of incomplete network data on functional and evolutionary inferences. Conclusion Crucially, when only small, partial......Background Present protein interaction network data sets include only interactions among subsets of the proteins in an organism. Previously this has been ignored, but in principle any global network analysis that only looks at partial data may be biased. Here we demonstrate the need to consider...... network sampling properties explicitly and from the outset in any analysis. Results Here we study how properties of the yeast protein interaction network are affected by random and non-random sampling schemes using a range of different network statistics. Effects are shown to be independent...

  17. Factorial Structure of the Existence Scale

    NARCIS (Netherlands)

    Brouwers, Tomic, W. A.

    2015-01-01

    Existential meaning in life is becoming an increasingly important measure of personal assessment. In search of a suitable instrument to measure existential meaning, the authors reviewed several measures. Eventually, they selected the Existence Scale (ES), doing so on theoretical grounds. The ES is a

  18. The Large Scale Structure: Polarization Aspects

    Indian Academy of Sciences (India)

    Polarized radio emission is detected at various scales in the Universe. In this document, I will briefly review our knowledge on polarized radio sources in galaxy clusters and at their outskirts, emphasizing the crucial information provided by the polarized signal on the origin and evolution of such sources. Successively, I will ...

  19. Ultra-large-scale electronic structure theory and numerical algorithm

    OpenAIRE

    Hoshi, Takeo

    2008-01-01

    This article is composed of two parts; In the first part (Sec. 1), the ultra-large-scale electronic structure theory is reviewed for (i) its fundamental numerical algorithm and (ii) its role in nano-material science. The second part (Sec. 2) is devoted to the mathematical foundation of the large-scale electronic structure theory and their numerical aspects.

  20. Optimization of Large-Scale Structural Systems

    DEFF Research Database (Denmark)

    Jensen, F. M.

    solutions to small problems with one or two variables to the optimization of large structures such as bridges, ships and offshore structures. The methods used for salving these problems have evolved from being classical differential calculus and calculus of variation to very advanced numerical techniques....... In the same period of time the problems have grown in size and the ongoing research in the various engineering fields has introduced new areas to complicate the optimization task further. These are e.g. structural reliability theory (including new, more complex constraints), discrete optimization (introducing...... new narrow bounds on the optimization variables), s tachastic FEM, vibration theory or multiobjective optimization. At the same time researchers always try to salve problems ahead of to-day's capabilities, thereby utilising current mathematical programming (MP) methods to the limit. However, when...

  1. Inferred vs realized patterns of gene flow: an analysis of population structure in the Andros Island Rock Iguana.

    Directory of Open Access Journals (Sweden)

    Giuliano Colosimo

    Full Text Available Ecological data, the primary source of information on patterns and rates of migration, can be integrated with genetic data to more accurately describe the realized connectivity between geographically isolated demes. In this paper we implement this approach and discuss its implications for managing populations of the endangered Andros Island Rock Iguana, Cyclura cychlura cychlura. This iguana is endemic to Andros, a highly fragmented landmass of large islands and smaller cays. Field observations suggest that geographically isolated demes were panmictic due to high, inferred rates of gene flow. We expand on these observations using 16 polymorphic microsatellites to investigate the genetic structure and rates of gene flow from 188 Andros Iguanas collected across 23 island sites. Bayesian clustering of specimens assigned individuals to three distinct genotypic clusters. An analysis of molecular variance (AMOVA indicates that allele frequency differences are responsible for a significant portion of the genetic variance across the three defined clusters (Fst =  0.117, p<<0.01. These clusters are associated with larger islands and satellite cays isolated by broad water channels with strong currents. These findings imply that broad water channels present greater obstacles to gene flow than was inferred from field observation alone. Additionally, rates of gene flow were indirectly estimated using BAYESASS 3.0. The proportion of individuals originating from within each identified cluster varied from 94.5 to 98.7%, providing further support for local isolation. Our assessment reveals a major disparity between inferred and realized gene flow. We discuss our results in a conservation perspective for species inhabiting highly fragmented landscapes.

  2. The enzymatic nature of an anonymous protein sequence cannot reliably be inferred from superfamily level structural information alone.

    Science.gov (United States)

    Roche, Daniel Barry; Brüls, Thomas

    2015-05-01

    As the largest fraction of any proteome does not carry out enzymatic functions, and in order to leverage 3D structural data for the annotation of increasingly higher volumes of sequence data, we wanted to assess the strength of the link between coarse grained structural data (i.e., homologous superfamily level) and the enzymatic versus non-enzymatic nature of protein sequences. To probe this relationship, we took advantage of 41 phylogenetically diverse (encompassing 11 distinct phyla) genomes recently sequenced within the GEBA initiative, for which we integrated structural information, as defined by CATH, with enzyme level information, as defined by Enzyme Commission (EC) numbers. This analysis revealed that only a very small fraction (about 1%) of domain sequences occurring in the analyzed genomes was found to be associated with homologous superfamilies strongly indicative of enzymatic function. Resorting to less stringent criteria to define enzyme versus non-enzyme biased structural classes or excluding highly prevalent folds from the analysis had only modest effect on this proportion. Thus, the low genomic coverage by structurally anchored protein domains strongly associated to catalytic activities indicates that, on its own, the power of coarse grained structural information to infer the general property of being an enzyme is rather limited. © 2015 The Protein Society.

  3. Recent Progress in Large-Scale Structure

    CERN Multimedia

    CERN. Geneva

    2014-01-01

    I will discuss recent progress in the understanding of how to model galaxy clustering. While recent analyses have focussed on the baryon acoustic oscillations as a probe of cosmology, galaxy redshift surveys contain a lot more information than the acoustic scale. In extracting this additional information three main issues need to be well understood: nonlinear evolution of matter fluctuations, galaxy bias and redshift-space distortions. I will present recent progress in modeling these three effects that pave the way to constraining cosmology and galaxy formation with increased precision.

  4. Large-Scale Structures of Planetary Systems

    Science.gov (United States)

    Murray-Clay, Ruth; Rogers, Leslie A.

    2015-12-01

    A class of solar system analogs has yet to be identified among the large crop of planetary systems now observed. However, since most observed worlds are more easily detectable than direct analogs of the Sun's planets, the frequency of systems with structures similar to our own remains unknown. Identifying the range of possible planetary system architectures is complicated by the large number of physical processes that affect the formation and dynamical evolution of planets. I will present two ways of organizing planetary system structures. First, I will suggest that relatively few physical parameters are likely to differentiate the qualitative architectures of different systems. Solid mass in a protoplanetary disk is perhaps the most obvious possible controlling parameter, and I will give predictions for correlations between planetary system properties that we would expect to be present if this is the case. In particular, I will suggest that the solar system's structure is representative of low-metallicity systems that nevertheless host giant planets. Second, the disk structures produced as young stars are fed by their host clouds may play a crucial role. Using the observed distribution of RV giant planets as a function of stellar mass, I will demonstrate that invoking ice lines to determine where gas giants can form requires fine tuning. I will suggest that instead, disk structures built during early accretion have lasting impacts on giant planet distributions, and disk clean-up differentially affects the orbital distributions of giant and lower-mass planets. These two organizational hypotheses have different implications for the solar system's context, and I will suggest observational tests that may allow them to be validated or falsified.

  5. Determining protein structures by combining semireliable data with atomistic physical models by Bayesian inference.

    Science.gov (United States)

    MacCallum, Justin L; Perez, Alberto; Dill, Ken A

    2015-06-02

    More than 100,000 protein structures are now known at atomic detail. However, far more are not yet known, particularly among large or complex proteins. Often, experimental information is only semireliable because it is uncertain, limited, or confusing in important ways. Some experiments give sparse information, some give ambiguous or nonspecific information, and others give uncertain information-where some is right, some is wrong, but we don't know which. We describe a method called Modeling Employing Limited Data (MELD) that can harness such problematic information in a physics-based, Bayesian framework for improved structure determination. We apply MELD to eight proteins of known structure for which such problematic structural data are available, including a sparse NMR dataset, two ambiguous EPR datasets, and four uncertain datasets taken from sequence evolution data. MELD gives excellent structures, indicating its promise for experimental biomolecule structure determination where only semireliable data are available.

  6. Fine-Scale Genetic Structure in Finland

    Directory of Open Access Journals (Sweden)

    Sini Kerminen

    2017-10-01

    Full Text Available Coupling dense genotype data with new computational methods offers unprecedented opportunities for individual-level ancestry estimation once geographically precisely defined reference data sets become available. We study such a reference data set for Finland containing 2376 such individuals from the FINRISK Study survey of 1997 both of whose parents were born close to each other. This sampling strategy focuses on the population structure present in Finland before the 1950s. By using the recent haplotype-based methods ChromoPainter (CP and FineSTRUCTURE (FS we reveal a highly geographically clustered genetic structure in Finland and report its connections to the settlement history as well as to the current dialectal regions of the Finnish language. The main genetic division within Finland shows striking concordance with the 1323 borderline of the treaty of Nöteborg. In general, we detect genetic substructure throughout the country, which reflects stronger regional genetic differences in Finland compared to, for example, the UK, which in a similar analysis was dominated by a single unstructured population. We expect that similar population genetic reference data sets will become available for many more populations in the near future with important applications, for example, in forensic genetics and in genetic association studies. With this in mind, we report those extensions of the CP + FS approach that we found most useful in our analyses of the Finnish data.

  7. Local Large-Scale Structure and the Assumption of Homogeneity

    Science.gov (United States)

    Keenan, Ryan C.; Barger, Amy J.; Cowie, Lennox L.

    2016-10-01

    Our recent estimates of galaxy counts and the luminosity density in the near-infrared (Keenan et al. 2010, 2012) indicated that the local universe may be under-dense on radial scales of several hundred megaparsecs. Such a large-scale local under-density could introduce significant biases in the measurement and interpretation of cosmological observables, such as the inferred effects of dark energy on the rate of expansion. In Keenan et al. (2013), we measured the K-band luminosity density as a function of distance from us to test for such a local under-density. We made this measurement over the redshift range 0.01 0.07, we measure an increasing luminosity density that by z ~ 0.1 rises to a value of ~ 1.5 times higher than that measured locally. This implies that the stellar mass density follows a similar trend. Assuming that the underlying dark matter distribution is traced by this luminous matter, this suggests that the local mass density may be lower than the global mass density of the universe at an amplitude and on a scale that is sufficient to introduce significant biases into the measurement of basic cosmological observables. At least one study has shown that an under-density of roughly this amplitude and scale could resolve the apparent tension between direct local measurements of the Hubble constant and those inferred by Planck team. Other theoretical studies have concluded that such an under-density could account for what looks like an accelerating expansion, even when no dark energy is present.

  8. Small scale structures in coupled scalar field dark matter

    Directory of Open Access Journals (Sweden)

    J. Beyer

    2014-11-01

    Full Text Available We investigate structure formation for ultra-light scalar field dark matter coupled to quintessence, in particular the cosmon–bolon system. The linear power spectrum is computed by a numerical solution of the coupled field equations. We infer the substructure abundance within a Milky Way-like halo. Estimates of dark halo abundances from recent galaxy surveys imply a lower bound on the bolon mass of about 9×10−22 eV. This seems to exclude a possible detection of scalar field dark matter through time variation in pulsar timing signals in the near future.

  9. Evidence for multiple refugia at different time scales during Pleistocene climatic oscillations in southern Australia inferred from phylogeography

    Science.gov (United States)

    Byrne, M.

    2008-12-01

    Phylogeography uses the spatial distribution of genealogical lineages to deduce the influence of historical processes on the evolution of species, and can be informative in regard to location of refugia during extreme climatic conditions. Southern Australia is an ancient landscape with generally low geological relief that was not glaciated but did experience significant climatic oscillations from warm wet conditions in interglacials to cool dry environments during glacial maxima. Phylogeographic patterns in many of the biota of southern Australia reveal evidence of geographically structured divergent lineages indicative of contraction to, and expansion from, major refugia. The time frame for this divergence corresponds with mid Pleistocene climatic oscillations that became more extreme with greater amplitude, and with increased aridity and the formation of sandy deserts. Within lineages there is high haplotype diversity that is generally locally distributed, often specific to populations. These patterns do not reveal specific locations of major refugia that have high diversity and acted as an origin for recent range expansion, as has been observed in Northern Hemisphere glaciated regions. Rather it appears there have been multiple localised refugia throughout the distributions of the species, allowing them to persist through multiple climatic cycles in heterogeneous environments. Phylogeographic patterns in southern Australia indicate that major biotic responses to climatic change involve persistence and resilience rather than large-scale migration, indicating the importance of dynamic evolutionary processes and a mosaic of habitats in heterogeneous landscapes for species to persist though changing environmental conditions.

  10. Simultaneous inference for multilevel linear mixed models - with an application to a large-scale school meal study

    DEFF Research Database (Denmark)

    Ritz, Christian; Laursen, Rikke Pilmann; Damsgaard, Camilla Trab

    2017-01-01

    of a school meal programme. We propose a novel and versatile framework for simultaneous inference on parameters estimated from linear mixed models that were fitted separately for several outcomes from the same study, but did not necessarily contain the same fixed or random effects. By combining asymptotic...... sizes of practical relevance we studied simultaneous coverage through simulation, which showed that the approach achieved acceptable coverage probabilities even for small sample sizes (10 clusters) and for 2–16 outcomes. The approach also compared favourably with a joint modelling approach. We also...

  11. Multi-scale structural similarity index for motion detection

    Directory of Open Access Journals (Sweden)

    M. Abdel-Salam Nasr

    2017-07-01

    Full Text Available The most recent approach for measuring the image quality is the structural similarity index (SSI. This paper presents a novel algorithm based on the multi-scale structural similarity index for motion detection (MS-SSIM in videos. The MS-SSIM approach is based on modeling of image luminance, contrast and structure at multiple scales. The MS-SSIM has resulted in much better performance than the single scale SSI approach but at the cost of relatively lower processing speed. The major advantages of the presented algorithm are both: the higher detection accuracy and the quasi real-time processing speed.

  12. Problems in large-scale structural optimization

    Science.gov (United States)

    Arora, J. S.; Belegundu, A. D.

    1984-01-01

    A general design optimization model for large complex systems is defined. Major features of the model that challenge various optimization algorithms are discussed. Requirements of a model optimization algorithm are identified. Objectives of the study of various algorithms are defined and a basis for conducting such a study is developed. Primal as well as transformation methods are analytically studied and a unified viewpoint of various methods is presented. Several numerical examples are solved using different methods to study their performance. Conclusions drawn from the study are presented and discussed. Areas of future research in nonlinear programming as well as structural optimization are identified and discussed.

  13. A sequential point process model and Bayesian inference for spatial point patterns with linear structures

    DEFF Research Database (Denmark)

    Møller, Jesper; Rasmussen, Jakob Gulddahl

    2012-01-01

    We introduce a flexible spatial point process model for spatial point patterns exhibiting linear structures, without incorporating a latent line process. The model is given by an underlying sequential point process model. Under this model, the points can be of one of three types: a ‘background...... for producing point patterns with linear structures and propose to use the model as the likelihood in a Bayesian setting when analysing a spatial point pattern exhibiting linear structures. We illustrate this methodology by analysing two spatial point pattern datasets (locations of bronze age graves in Denmark...

  14. Optical Properties Of Nanometer-Scale Structures

    CERN Document Server

    Kudykina, T A

    2016-01-01

    Two approaches (micro- and macro- investigations) are used to determine the dimension dependences of the optical parameters of the nanometer-scale layers of materials. It is shown that both an index of refraction and coefficient of absorption depend strongly on the thickness of the layer. In this region of thicknesses, the dimension resonance occurs, where an index of refraction has a maximum and a coefficient of absorption has a minimum. The numerical calculation of the optical parameters of some materials (Ag, Al, Fe, Ge, Si, Se, Te) have been carried out with the use of the experimental data of reflection and transparency of thin layers, obtained in a series of works, and with our formulas for the wave amplitudes and the laws of refractions. The analogues of the Fresnel formulas and the Snell law have been derived from the Maxwell boundary conditions where the absorption and conductivity of media were taken into account. The use of our formulas for the wave amplitudes leads to the fulfillment of the conser...

  15. Inferring the mesoscale structure of layered, edge-valued and time-varying networks

    CERN Document Server

    Peixoto, Tiago P

    2015-01-01

    Many network systems are composed of interdependent but distinct types of interactions, which cannot be fully understood in isolation. These different types of interactions are often represented as layers, attributes on the edges or as a time-dependence of the network structure. Although they are crucial for a more comprehensive scientific understanding, these representations offer substantial challenges. Namely, it is an open problem how to precisely characterize the large or mesoscale structure of network systems in relation to these additional aspects. Furthermore, the direct incorporation of these features invariably increases the effective dimension of the network description, and hence aggravates the problem of overfitting, i.e. the use of overly-complex characterizations that mistake purely random fluctuations for actual structure. In this work, we propose a robust and principled method to tackle these problems, by constructing generative models of modular network structure, incorporating layered, attr...

  16. Structured ecosystem-scale approach to marine water quality management

    CSIR Research Space (South Africa)

    Taljaard, Susan

    2006-10-01

    Full Text Available and implement environmental management programmes. A structured ecosystem-scale approach for the design and implementation of marine water quality management programmes developed by the CSIR (South Africa) in response to recent advances in policies...

  17. Validity and factor structure of the bodybuilding dependence scale

    OpenAIRE

    Smith, D; Hale, B

    2004-01-01

    Objectives: To investigate the factor structure, validity, and reliability of the bodybuilding dependence scale and to investigate differences in bodybuilding dependence between men and women and competitive and non-competitive bodybuilders.

  18. Large and small-scale structures in Saturn's rings

    Science.gov (United States)

    Albers, N.; Rehnberg, M. E.; Brown, Z. L.; Sremcevic, M.; Esposito, L. W.

    2017-09-01

    Observations made by the Cassini spacecraft have revealed both large and small scale structures in Saturn's rings in unprecedented detail. Analysis of high-resolution measurements by the Cassini Ultraviolet Spectrograph (UVIS) High Speed Photometer (HSP) and the Imaging Science Subsystem (ISS) show an abundance of intrinsic small-scale structures (or clumping) seen across the entire ring system. These include self-gravity wakes (50-100m), sub-km structure at the A and B ring edges, and "straw"/"ropy" structures (1-3km).

  19. Probes of large-scale structure in the universe

    Science.gov (United States)

    Suto, Yasushi; Gorski, Krzysztof; Juszkiewicz, Roman; Silk, Joseph

    1988-01-01

    A general formalism is developed which shows that the gravitational instability theory for the origin of the large-scale structure of the universe is now capable of critically confronting observational results on cosmic background radiation angular anisotropies, large-scale bulk motions, and large-scale clumpiness in the galaxy counts. The results indicate that presently advocated cosmological models will have considerable difficulty in simultaneously explaining the observational results.

  20. Development of large-scale structure in the Universe

    CERN Document Server

    Ostriker, J P

    1991-01-01

    This volume grew out of the 1988 Fermi lectures given by Professor Ostriker, and is concerned with cosmological models that take into account the large scale structure of the universe. He starts with homogeneous isotropic models of the universe and then, by considering perturbations, he leads us to modern cosmological theories of the large scale, such as superconducting strings. This will be an excellent companion for all those interested in the cosmology and the large scale nature of the universe.

  1. The Large Scale Structure: Polarization Aspects R. F. Pizzo

    Indian Academy of Sciences (India)

    e-mail: pizzo@astron.nl. Abstract. Polarized radio emission is detected at various scales in the ... are located at the nodes of the filamentary large-scale structure of the cosmic web and form by subsequent merging .... After calibration, we produced Q and U channel images for each dataset and we inspected them to remove ...

  2. Factor Structure of Child Behavior Scale Scores in Peruvian Preschoolers

    Science.gov (United States)

    Meyer, Erin L.; Schaefer, Barbara A.; Soto, Cesar Merino; Simmons, Crystal S.; Anguiano, Rebecca; Brett, Jeremy; Holman, Alea; Martin, Justin F.; Hata, Heidi K.; Roberts, Kimberly J.; Mello, Zena R.; Worrell, Frank C.

    2011-01-01

    Behavior rating scales aid in the identification of problem behaviors, as well as the development of interventions to reduce such behavior. Although scores on many behavior rating scales have been validated in the United States, there have been few such studies in other cultural contexts. In this study, the structural validity of scores on a…

  3. A sequential point process model and Bayesian inference for spatial point patterns with linear structures

    DEFF Research Database (Denmark)

    Møller, Jesper; Rasmussen, Jakob Gulddahl

    We introduce a flexible spatial point process model for spatial point patterns exhibiting linear structures, without incorporating a latent line process. The model is given by an underlying sequential point process model, i.e. each new point is generated given the previous points. Under this model...... pattern exhibiting linear structures but where the exact mechanism responsible for the formations of lines is unknown. We illustrate this methodology by analyzing two spatial point pattern data sets (locations of bronze age graves in Denmark and locations of mountain tops in Spain) without knowing which...

  4. Bayesian inference of Earth's radial seismic structure from body-wave traveltimes using neural networks

    NARCIS (Netherlands)

    de Wit, R.W.L.; Valentine, A.P.; Trampert, J.

    2013-01-01

    How do body-wave traveltimes constrain the Earth's radial (1-D) seismic structure? Existing 1-D seismological models underpin 3-D seismic tomography and earthquake location algorithms. It is therefore crucial to assess the quality of such 1-D models, yet quantifying uncertainties in seismological

  5. Long term human impacts on genetic structure of Italian walnut inferred by SSR markers

    Science.gov (United States)

    Paola Pollegioni; Keith Woeste; Irene Olimpieri; Danilo Marandola; Francesco Cannata; Maria E Malvolti

    2011-01-01

    Life history traits, historic factors, and human activities can all shape the genetic diversity of a species. In Italy, walnut (Juglans regia L.) has a long history of cultivation both for wood and edible nuts. To better understand the genetic variability of current Italian walnut resources, we analyzed the relationships among the genetic structure...

  6. Large-scale inference of protein tissue origin in gram-positive sepsis plasma using quantitative targeted proteomics.

    Science.gov (United States)

    Malmström, Erik; Kilsgård, Ola; Hauri, Simon; Smeds, Emanuel; Herwald, Heiko; Malmström, Lars; Malmström, Johan

    2016-01-06

    The plasma proteome is highly dynamic and variable, composed of proteins derived from surrounding tissues and cells. To investigate the complex processes that control the composition of the plasma proteome, we developed a mass spectrometry-based proteomics strategy to infer the origin of proteins detected in murine plasma. The strategy relies on the construction of a comprehensive protein tissue atlas from cells and highly vascularized organs using shotgun mass spectrometry. The protein tissue atlas was transformed to a spectral library for highly reproducible quantification of tissue-specific proteins directly in plasma using SWATH-like data-independent mass spectrometry analysis. We show that the method can determine drastic changes of tissue-specific protein profiles in blood plasma from mouse animal models with sepsis. The strategy can be extended to several other species advancing our understanding of the complex processes that contribute to the plasma proteome dynamics.

  7. Local scale structures in Earth's thermospheric winds and their consequences for wind driven transport

    Science.gov (United States)

    Dhadly, Manbharat Singh

    In the traditional picture of Earth's upper thermosphere (~190--300 km), it is widely presumed that its convective stability and enormous kinematic viscosity attenuate wind gradients, and hence smooth out any structure present in the wind over scale size of several hundreds of kilometers. However, several independent experimental studies have shown that observed upper thermospheric wind fields at high latitudes contain stronger than expected local-scale spatial structures. The motivation of this dissertation is to investigate how the resulting local-scale gradients would distort neutral air masses and complicate thermospheric wind transport. To achieve this goal, we examined the behavior of a simple parameter that we refer to as the "distortion gradient". It incorporates all of the wind field's departures from uniformity, and is thus capable of representing all resulting contributions to the distortion or mixing of air masses. Climatological analysis of the distortion gradient using 2010, 2011, and 2012 wind data from the All-sky Scanning Doppler Imager (SDI) located at Poker Flat (65.12N, 147.47W) revealed the diurnal and seasonal trends in distortion of thermospheric masses. Distortion was observed to be dependent on geomagnetic activity and orientation of the interplanetary magnetic field. To understand the time-cumulative influence of these local-scale non-uniformities on thermospheric wind driven transport, time-resolved two-dimensional maps of the thermospheric vector wind fields were used to infer forward and backward air parcel trajectories. Tracing air parcel trajectories through a given geographic location indicates where they came from previously, and where they will go in the future. Results show that wind driven transport is very sensitive to small-scale details of the wind field. Any local-scale spatial wind gradients can significantly complicate air parcel trajectories. Transport of thermospheric neutral species in the presence of the local-scale

  8. Inferring global Upper-Mantle Shear Attenuation structure by waveform tomography using the Spectral Element Method

    Science.gov (United States)

    Karaoǧlu, Haydar; Romanowicz, Barbara

    2018-01-01

    We present a global upper-mantle shear wave attenuation model that is built through a hybrid full-waveform inversion algorithm applied to long-period waveforms, using the Spectral Element Method for wavefield computations. Our inversion strategy is based on an iterative approach that involves the inversion for successive updates in the attenuation parameter (δ Q^{-1}_μ) and elastic parameters (isotropic velocity VS, and radial anisotropy parameter ξ) through a Gauss-Newton type optimization scheme that employs envelope- and waveform-type misfit functionals for the two steps, respectively. We also include source and receiver terms in the inversion steps for attenuation structure. We conducted a total of 8 iterations (6 for attenuation and 2 for elastic structure), and one inversion for updates to source parameters. The starting model included the elastic part of the relatively high resolution 3-D whole mantle seismic velocity model, SEMUCB-WM1, which served to account for elastic focusing effects. The data set is a subset of the three component surface waveform data set, filtered between 400 and 60 s, that contributed to the construction of the whole-mantle tomographic model SEMUCB-WM1. We applied strict selection criteria to this data set for the attenuation iteration steps, and investigated the effect of attenuation crustal structure on the retrieved mantle attenuation structure. While a constant 1-D Qμ model with a constant value of 165 throughout the upper-mantle was used as starting model for attenuation inversion, we were able to recover, in depth extent and strength, the high attenuation zone present in the depth range 80-200 km. The final three-dimensional model, SEMUCB-UMQ, shows strong correlation with tectonic features down to 200˜250 km depth, with low attenuation beneath the cratons, stable parts of continents and regions of old oceanic crust, and high attenuation along mid-ocean ridges and back-arcs. Below 250 km, we observe strong attenuation in

  9. Inferring the interplay of network structure and market effects in Bitcoin

    CERN Document Server

    Kondor, Dániel; Szüle, János; Pósfai, Márton; Vattay, Gábor

    2014-01-01

    A main focus in economics research is understanding the time series of prices of goods and assets. While statistical models using only the properties of the time series itself have been successful in many aspects, we expect to gain a better understanding of the phenomena involved if we can model the underlying system of interacting agents. In this article, we consider the history of Bitcoin, a novel digital currency system, for which the complete list of transactions is available for analysis. Using this dataset, we reconstruct the transaction network between users and analyze changes in the structure of the subgraph induced by the most active users. Our approach is based on the unsupervised identification of important features of the time variation of the network. Applying the widely used method of Principal Component Analysis to the matrix constructed from snapshots of the network at different times, we are able to show how structural changes in the network accompany significant changes in the exchange pric...

  10. An empirical comparison of popular structure learning algorithms with a view to gene network inference

    Czech Academy of Sciences Publication Activity Database

    Djordjilović, V.; Chiogna, M.; Vomlel, Jiří

    2017-01-01

    Roč. 88, č. 1 (2017), s. 602-613 ISSN 0888-613X R&D Projects: GA ČR(CZ) GA16-12010S Institutional support: RVO:67985556 Keywords : Bayesian networks * Structure learning * Reverse engineering * Gene networks Subject RIV: JD - Computer Applications, Robotics Impact factor: 2.845, year: 2016 http:// library .utia.cas.cz/separaty/2017/MTR/vomlel-0477168.pdf

  11. Network structure from relational data: measurement and inference in four operational models

    OpenAIRE

    Bradley, Raymond Trevor; Roberts, Nancy C.

    1989-01-01

    An empirically-based assessment of the operational procedures routinely used in network analysis reveais serious measurement deficiencies that render spurious images of network structure. Based on explicit, exhaustive measurement along three basic relational dimensions, an alternative approach is described that resolves these problems. The three dimensions (type of relation, the relation’s existential status, and level of analysis) combine to create a general f...

  12. Inferring Action Structure and Causal Relationships in Continuous Sequences of Human Action

    Science.gov (United States)

    2014-01-01

    learning in infants and non-human animals , allowing them to extract useful sequences to imitate, or to predict the actor’s future behavior, without...Imitation without intentionality. using string parsing to copy the organization of behaviour. Animal Cognition, 2 (2), 63-72. Byrne, R. W. (2003). Imitation...segmentation of narrative cinema . Frontiers in Human Neuroscience, 4 (1-15). Zacks, J. M., & Tversky, B. (2001). Event structure in perception and

  13. structSSI: Simultaneous and Selective Inference for Grouped or Hierarchically Structured Data

    Directory of Open Access Journals (Sweden)

    Kris Sankaran

    2014-09-01

    We briefly describe the group Benjamini-Hochberg and hierarchical false discovery rate procedures and then illustrate them using two examples, one a measure of ecological microbial abundances and the other a global temperature time series. For both procedures, we detail the steps associated with the analysis of these particular data sets, including establishing the dependence structures, performing the test, and interpreting the results. These steps are encapsulated by R functions, and we explain their applicability to general data sets.

  14. Comparison of algorithms to infer genetic population structure from unlinked molecular markers.

    Science.gov (United States)

    Peña-Malavera, Andrea; Bruno, Cecilia; Fernandez, Elmer; Balzarini, Monica

    2014-08-01

    Identifying population genetic structure (PGS) is crucial for breeding and conservation. Several clustering algorithms are available to identify the underlying PGS to be used with genetic data of maize genotypes. In this work, six methods to identify PGS from unlinked molecular marker data were compared using simulated and experimental data consisting of multilocus-biallelic genotypes. Datasets were delineated under different biological scenarios characterized by three levels of genetic divergence among populations (low, medium, and high FST) and two numbers of sub-populations (K=3 and K=5). The relative performance of hierarchical and non-hierarchical clustering, as well as model-based clustering (STRUCTURE) and clustering from neural networks (SOM-RP-Q). We use the clustering error rate of genotypes into discrete sub-populations as comparison criterion. In scenarios with great level of divergence among genotype groups all methods performed well. With moderate level of genetic divergence (FST=0.2), the algorithms SOM-RP-Q and STRUCTURE performed better than hierarchical and non-hierarchical clustering. In all simulated scenarios with low genetic divergence and in the experimental SNP maize panel (largely unlinked), SOM-RP-Q achieved the lowest clustering error rate. The SOM algorithm used here is more effective than other evaluated methods for sparse unlinked genetic data.

  15. Long-term sunspot forcing of savanna structure inferred from carbon and oxygen isotopes

    Science.gov (United States)

    Woodborne, Stephan; Mélice, Jean-Luc; Scholes, Robert J.

    2008-01-01

    We used the δ 18O and δ 13C isotopes from a speleothem and Δ14C values from known age tree rings as proxies for vegetation structure, rainfall and sunspot activity over the last 10,000 years. The δ 18O and δ 13C signals are significantly correlated and wavelet coherence analysis shows that a phase locked responses is only found to occur over periods less than 150 years. The δ 13C and Δ14C signals are also significantly correlated but the wavelet coherence analysis shows phase locked responses at periods in the order of 320 and 1100 years at various times in the past. We conclude that savanna vegetation structure responds to rainfall over periods of decades to about 150 years, and to solar forcing over periods greater than 150 years. We propose that elevated UV-B radiation at the earth surface during periods of low sunspot activity favours the productivity of C4 plants over C3 plants possibly because of the metabolic cost of structural adaptive responses and of producing UV-B absorbing compounds in the latter.

  16. Hierarchical structure and cytocompatibility of fish scales from Carassius auratus.

    Science.gov (United States)

    Fang, Zhou; Wang, Yukun; Feng, Qingling; Kienzle, Arne; Müller, Werner E G

    2014-10-01

    To study the structure and the cytocompatibility of fish scales from Carassius auratus, scanning electron microscopy (SEM) was used to observe the morphology of fish scales treated with different processing methods. Based on varying morphologies and components, the fish scales can be divided into three regions on the surface and three layers in vertical. The functions of these three individual layers were analyzed. SEM results show that the primary inorganic components are spherical or cubic hydroxyapatite (HA) nanoparticles. The fish scales have an ~60° overlapped plywood structure of lamellas in the fibrillary plate. The plywood structure consists of co-aligned type I collagen fibers, which are parallel to the HA lamellas. X-ray diffraction (XRD), thermogravimetric analysis/differential scanning calorimetry (TGA/DSC) and Fourier transform infrared (FTIR) analysis indicate that the main components are HA and type I collagen fibers. MC3T3-E1 cell culture results show a high cytocompatibility and the ability to guide cell proliferation and migration along the scale ridge channels of the fish scales. This plywood structure provides inspiration for a structure-enhanced composite material. Copyright © 2014 Elsevier B.V. All rights reserved.

  17. Modeling Water Flow and Bromide Transport in a Two-Scale-Structured Lignitic Mine Soil

    Science.gov (United States)

    Dusek, J.; Gerke, H. H.; Vogel, T.; Maurer, T.; Buczko, U.

    2008-12-01

    Two-dimensional single- and dual-permeability simulations are used to analyze water and solute fluxes in heterogeneous lignitic mine soil at a forest-reclaimed mine spoil heap. The soil heterogeneity on this experimental site "Barenbrucker Hohe" resulted from inclined dumping structures and sediment mixtures that consist of sand with lignitic dust and embedded lignitic fragments. Observations on undisturbed field suction- cell lysimeters including tracer experiments revealed funneling-type preferential flow with lateral water and bromide movement along inclined sediment structures. The spatial distribution of soil structures and fragment distributions was acquired by a digital camera and identified by a supervised classification of the digital profile image. First, a classical single-domain modeling approach was proposed with spatially variable scaling factors inferred from image analyses. In the next step, a two-continuum scenario was constructed to examine additional effects of nonequilibrium on the flow regime. The scaling factors used for the preferential flow domain are here obtained from the gradient of the grayscale images. So far, the single domain scenarios failed to predict the bromide leaching patterns although water effluent could be described. Dual-permeability model allows the incorporation of structural effects and can be used as a tool to further testing other approaches that account for structure effects. The numerical study suggests that additional experiments are required to obtain better understanding of the highly complex transport processes on this experimental site.

  18. Inference of population structure of Leishmania donovani strains isolated from different Ethiopian visceral leishmaniasis endemic areas.

    Directory of Open Access Journals (Sweden)

    Tesfaye Gelanew

    Full Text Available BACKGROUND: Parasites' evolution in response to parasite-targeted control strategies, such as vaccines and drugs, is known to be influenced by their population genetic structure. The aim of this study was to describe the population structure of Ethiopian strains of Leishmania donovani derived from different areas endemic for visceral leishmaniasis (VL as a prerequisite for the design of effective control strategies against the disease. METHODOLOGY/PRINCIPAL FINDINGS: Sixty-three strains of L. donovani newly isolated from VL cases in the two main Ethiopian foci, in the north Ethiopia (NE and south Ethiopia (SE of the country were investigated by using 14 highly polymorphic microsatellite markers. The microsatellite profiles of 60 previously analysed L. donovani strains from Sudan, Kenya and India were included for comparison. Multilocus microsatellite typing placed strains from SE and Kenya (n = 30 in one population and strains from NE and Sudan (n = 65 in another. These two East African populations corresponded to the areas of distribution of two different sand fly vectors. In NE and Sudan Phlebotomus orientalis has been implicated to transmit the parasites and in SE and Kenya P. martini. The genetic differences between parasites from NE and SE are also congruent with some phenotypic differences. Each of these populations was further divided into two subpopulations. Interestingly, in one of the subpopulations of the population NE we observed predominance of strains isolated from HIV-VL co-infected patients and of strains with putative hybrid genotypes. Furthermore, high inbreeding irreconcilable from strict clonal reproduction was found for strains from SE and Kenya indicating a mixed-mating system. CONCLUSIONS/SIGNIFICANCE: This study identified a hierarchical population structure of L. donovani in East Africa. The existence of two main, genetically and geographically separated, populations could reflect different parasite-vector associations

  19. Crustal structure and tectonic history of the Kermadec arc inferred from MANGO seismic refraction profiles

    Science.gov (United States)

    Bassett, D.; Kopp, H.; Sutherland, R.; Henrys, S.; Watts, A. B.; Timm, C.; Scherwath, M.; Grevemeyer, I.; de Ronde, C. E. J.

    2016-12-01

    We have analyzed three wide-angle seismic reflection and refraction profiles and applied spectral averaging techniques to regional grids of bathymetry and free-air gravity anomaly to place the first regional constraints on the crustal structure of the Kermadec arc. These observations are used to test contrasting tectonic models for an along-strike transition in margin structure, across which, 1) the remnant Lau-Colville and active Kermadec arc ridges narrow by >50%; 2) the backarc and forearc deepen by 1 km, and 3) the active volcanic arc is deflected west into the deepest known backarc basin. We use residual bathymetric anomalies to constrain the geometry of this boundary and propose the name Central Kermadec Discontinuity (CKD). North of the CKD, the buried Tonga Ridge occupies the forearc with VP 6.5-7.3 km s-1 and residual free-air gravity anomalies constrain its latitudinal extent (north of 30.5°S), width (110±20 km) and strike ( 005° south of 25°S). South of the CKD the forearc is structurally homogeneous down-dip with VP 5.7-7.3 km s-1. Lower crustal velocities are similar to the northern Kermadec forearc, but there is no seismic or gravimetric evidence for an extinct arc ridge within the forearc. In the Havre Trough backarc, crustal thickness south of the CKD is 8-9 km, which is up-to 4 km thinner than the northern Havre Trough and at least 1 km thinner than the southern Havre Trough. The northern Kermadec/Tonga arc preserves a substrate of the Eocene arc, the southern Kermadec forearc preserves Mesozoic forearc rocks accreted at the Gondwana margin, and the central Kermadec arc may have fomed in the Kupe Abyssal Plain. The oldest arc related rocks recovered north and south of the CKD are 52 Ma and 16.7 Ma respectively, and plate tectonic reconstruction suggest the Eocene arc was originally conjoined with the Three Kings Ridge. The separation of these ridges during the early Oligocene likely formed the CKD. In contrast to previous interpretations, we

  20. From stratigraphy to (inferred) processes: development of the late Pleistocene Po Delta clinothems at millennial to centennial scales

    Science.gov (United States)

    Pellegrini, Claudio; Asioli, Alessandra; Drexler, Tina; Bohacs, Kevin; Sweet, Michael; Maselli, Vittorio; Gamberi, Fabiano; Rovere, Marzia; Dalla Valle, Giacomo; Trincardi, Fabio

    2017-04-01

    The 350-m thick succession of the late-Pleistocene Po River Lowstand Delta (PRLD) deposited in just 17 k.y. encompassing the Last Glacial Maximum and contains stratal architecture at a physical scale commonly attributed to much longer time intervals, with complex, systematically varying internal clinothem characteristics. We document clinothem characteristics, stacking patterns, and controls through the integration of seismic-reflection data with sediment attributes, micropaleontology, regional climate, eustacy, and high-resolution age control on the PRLD. Within the PRLD, three clinothem types are characterized by distinctive topset geometry, shelf-edge and onlap-point trajectory, internal seismic facies, and interpreted bottomset deposits: Type A) moderate topset aggradation, ascending shelf-edge trajectories, and thin mass-transport bottomset deposits; Type B) eroded topset, descending shelf-edge trajectories, and bottomset distributary channel-lobe complexes; and Type C) maximal topset aggradation, ascending shelf-edge trajectories, and draped concordant bottomsets. Measured sediment accumulation rates suggest that Type A and C clinothems experienced reduced sediment bypass and delivery to the basin, whereas, Type B clinothems were associated with short intervals of increased sediment export from the shelf to deep water and development of distributary channel-lobe complexes. This interpretation is supported by micropaleontological analyses that highlight increased delivery of sediment and fresh water to the basin during the progradation of Type B clinothems, as suggested by the reduced occurrence of Cassidulina laevigata carinata and the peak abundance of Nonion spp. Each clinothem formed in a very short interval, from 0.4 to 4.7 k.y., contemporaneous with significant eustatic and climate changes. While changes in stacking patterns at these temporal scales have previously been observed in modern deltaic clinothems, the significance of our study is that we have

  1. Inferring the interplay between network structure and market effects in Bitcoin

    Science.gov (United States)

    Kondor, Dániel; Csabai, István; Szüle, János; Pósfai, Márton; Vattay, Gábor

    2014-12-01

    A main focus in economics research is understanding the time series of prices of goods and assets. While statistical models using only the properties of the time series itself have been successful in many aspects, we expect to gain a better understanding of the phenomena involved if we can model the underlying system of interacting agents. In this article, we consider the history of Bitcoin, a novel digital currency system, for which the complete list of transactions is available for analysis. Using this dataset, we reconstruct the transaction network between users and analyze changes in the structure of the subgraph induced by the most active users. Our approach is based on the unsupervised identification of important features of the time variation of the network. Applying the widely used method of Principal Component Analysis to the matrix constructed from snapshots of the network at different times, we are able to show how structural changes in the network accompany significant changes in the exchange price of bitcoins.

  2. Advanced Large Scale Cross Domain Temporal Topic Modeling Algorithms to Infer the Influence of Recent Research on IPCC Assessment Reports

    Science.gov (United States)

    Sleeman, J.; Halem, M.; Finin, T.; Cane, M. A.

    2016-12-01

    topics, we establish which chapter-citation pairs are most similar. We will perform posterior inferences based on Hastings -Metropolis simulated annealing MCMC algorithm to infer, from the evolution of topics starting from AR1 to AR4, assertions of topics for AR5 and potentially AR6.

  3. Light trapping structures in wing scales of butterfly Trogonoptera brookiana.

    Science.gov (United States)

    Han, Zhiwu; Niu, Shichao; Shang, Chunhui; Liu, Zhenning; Ren, Luquan

    2012-04-28

    The fine optical structures in wing scales of Trogonoptera brookiana, a tropical butterfly exhibiting efficient light trapping effect, were carefully examined and the reflectivity was measured using reflectance spectrometry. The optimized 3D configuration of the coupling structure was determined using SEM and TEM data, and the light trapping mechanism of butterfly scales was studied. It is found that the front and back sides of butterfly wings possess different light trapping structures, but both can significantly increase the optical path and thus result in almost total absorption of all incident light. An optical model was created to check the properties of this light trapping structure. The simulated reflectance spectra are in concordance with the experimental ones. The results reliably confirm that these structures induce efficient light trapping effect. This functional "biomimetic structure" would have a potential value in wide engineering and optical applications. This journal is © The Royal Society of Chemistry 2012

  4. Graph-based linear scaling electronic structure theory.

    Science.gov (United States)

    Niklasson, Anders M N; Mniszewski, Susan M; Negre, Christian F A; Cawkwell, Marc J; Swart, Pieter J; Mohd-Yusof, Jamal; Germann, Timothy C; Wall, Michael E; Bock, Nicolas; Rubensson, Emanuel H; Djidjev, Hristo

    2016-06-21

    We show how graph theory can be combined with quantum theory to calculate the electronic structure of large complex systems. The graph formalism is general and applicable to a broad range of electronic structure methods and materials, including challenging systems such as biomolecules. The methodology combines well-controlled accuracy, low computational cost, and natural low-communication parallelism. This combination addresses substantial shortcomings of linear scaling electronic structure theory, in particular with respect to quantum-based molecular dynamics simulations.

  5. An Evaluation Framework for Large-Scale Network Structures

    DEFF Research Database (Denmark)

    Pedersen, Jens Myrup; Knudsen, Thomas Phillip; Madsen, Ole Brun

    2004-01-01

    An evaluation framework for large-scale network structures is presented, which facilitates evaluations and comparisons of different physical network structures. A number of quantitative and qualitative parameters are presented, and their importance to networks discussed. Choosing a network...... is closed by an example of how the framework can be used. The framework supports network planners in decision-making and researchers in evaluation and development of network structures....

  6. Data-Driven Inference on Sign Restrictions in Bayesian Structural Vector Autoregression

    DEFF Research Database (Denmark)

    Lanne, Markku; Luoto, Jani

    Sign-identified structural vector autoregressive (SVAR) models have recently become popular. However, the conventional approach to sign restrictions only yields set identification, and implicitly assumes an informative prior distribution of the impulse responses whose influence does not vanish...... a genuinely noninformative prior and thus learning from the data about the impulse responses. While the shocks are statistically identified, they carry no economic meaning as such, and we propose a procedure for labeling them by their probabilities of satisfying each of the given sign restrictions....... The impulse responses of the identified economic shocks can subsequently be computed in a straightforward manner. Our approach is quite flexible in that it facilitates labeling only a subset of the sign-restricted shocks, and also concluding that none of the sign restrictions is plausible. We illustrate...

  7. Multi-scale structures of turbulent magnetic reconnection

    Energy Technology Data Exchange (ETDEWEB)

    Nakamura, T. K. M., E-mail: takuma.nakamura@oeaw.ac.at; Nakamura, R.; Narita, Y.; Baumjohann, W. [Space Research Institute, Austrian Academy of Sciences, Graz 8042 (Austria); Daughton, W. [Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)

    2016-05-15

    We have analyzed data from a series of 3D fully kinetic simulations of turbulent magnetic reconnection with a guide field. A new concept of the guide filed reconnection process has recently been proposed, in which the secondary tearing instability and the resulting formation of oblique, small scale flux ropes largely disturb the structure of the primary reconnection layer and lead to 3D turbulent features [W. Daughton et al., Nat. Phys. 7, 539 (2011)]. In this paper, we further investigate the multi-scale physics in this turbulent, guide field reconnection process by introducing a wave number band-pass filter (k-BPF) technique in which modes for the small scale (less than ion scale) fluctuations and the background large scale (more than ion scale) variations are separately reconstructed from the wave number domain to the spatial domain in the inverse Fourier transform process. Combining with the Fourier based analyses in the wave number domain, we successfully identify spatial and temporal development of the multi-scale structures in the turbulent reconnection process. When considering a strong guide field, the small scale tearing mode and the resulting flux ropes develop over a specific range of oblique angles mainly along the edge of the primary ion scale flux ropes and reconnection separatrix. The rapid merging of these small scale modes leads to a smooth energy spectrum connecting ion and electron scales. When the guide field is sufficiently weak, the background current sheet is strongly kinked and oblique angles for the small scale modes are widely scattered at the kinked regions. Similar approaches handling both the wave number and spatial domains will be applicable to the data from multipoint, high-resolution spacecraft observations such as the NASA magnetospheric multiscale (MMS) mission.

  8. Distributional Inference

    NARCIS (Netherlands)

    Kroese, A.H.; van der Meulen, E.A.; Poortema, Klaas; Schaafsma, W.

    1995-01-01

    The making of statistical inferences in distributional form is conceptionally complicated because the epistemic 'probabilities' assigned are mixtures of fact and fiction. In this respect they are essentially different from 'physical' or 'frequency-theoretic' probabilities. The distributional form is

  9. Thermohaline structure of the Black Sea as inferred from Argo floats

    Science.gov (United States)

    Akpinar, Anil; Fach, Bettina; Oguz, Temel; Salihoglu, Baris

    2010-05-01

    The mixed layer, Cold Intermediate Layer (shallow temperature minimum) and the surface layer properties of the Black Sea have been examined using data available from seven Argo floats deployed in 2002-2009 by the Middle East Technical University (Turkey) in collaboration with the University of Washington (U.S.A) and the Marine Hydrophysical Institute (Ukraine) . Temperature data from these floats show distinct interannual variability in the surface layer of the Black Sea, whereas the salinity data reveals spatial changes due to freshwater input. The analyses of the Cold Intermediate Layer (CIL) demonstrates strong periodic variation in the depth of the CIL and changes in the mean temperature of the CIL over time. The CIL was detected down to over 100 meters depth which has not been observed before. The properties at 100 m and 200 m were also analyzed and this study showed distinct features depending on the float positions, which in comparison with satellite altimetry indicate that the features are observed when floats are entrained in cyclonic or anticyclonic eddies. This is the first time that such a comprehensive data set was available for the Black Sea and this data set allows us to see previously unknown features of the Black Sea thermohaline structure.

  10. Genetic structure in two northern muriqui populations (Brachyteles hypoxanthus, Primates, Atelidae as inferred from fecal DNA

    Directory of Open Access Journals (Sweden)

    Valéria Fagundes

    2008-01-01

    Full Text Available We assessed the genetic diversity of two northern muriqui (Brachyteles hypoxanthus Primata, Atelidae populations, the Feliciano Miguel Abdala population (FMA, n = 108 in the Brazilian state of Minas Gerais (19°44' S, 41°49' W and the Santa Maria de Jetibá population (SMJ, n = 18 in the Brazilian state of Espírito Santo (20°01' S, 40°44' W. Fecal DNA was isolated and PCR-RFLP analysis used to analyze 2160 bp of mitochondrial DNA, made up of an 820 bp segment of the gene cytochrome c oxidase subunit 2 (cox2, EC 1.9.3.1, an 880 bp segment of the gene cytochrome b (cytb, EC 1.10.2.2 and 460 bp of the hypervariable segment of the mtDNA control region (HVRI. The cox2 and cytb sequences were monomorphic within and between populations whereas the HVRI revealed three different population exclusive haplotypes, one unique to the SMJ population and two, present at similar frequencies, in the FMA population. Overall haplotype diversity (h = 0.609 and nucleotide diversity (pi = 0.181 were high but reduced within populations. The populations were genetically structured with a high fixation index (F ST = 0.725, possibly due to historical subdivision. These findings have conservation implications because they seem to indicate that the populations are distinct management units.

  11. Phylogeographic Structure in Anastrepha ludens (Diptera: Tephritidae) Populations Inferred With mtDNA Sequencing.

    Science.gov (United States)

    Ruiz-Arce, Raul; Owen, Christopher L; Thomas, Donald B; Barr, Norman B; McPheron, Bruce A

    2015-06-01

    Anastrepha ludens (Loew) (Diptera: Tephritidae), the Mexican fruit fly, is a major pest of citrus and mango. It has a wide distribution in Mexico and Central America, with infestations occurring in Texas, California, and Florida with origins believed to have been centered in northeastern Mexico. This research evaluates the utility of a sequence-based approach for two mitochondrial (COI and ND6) gene regions. We use these markers to examine genetic diversity, estimate population structure, and identify diagnostic information for A. ludens populations. We analyzed 543 individuals from 67 geographic collections and found one predominant haplotype occurring in the majority of specimens. We observed 68 haplotypes in all and see differences among haplotypes belonging to northern and southern collections. Mexico haplotypes differ by few bases possibly as a result of a recent bottleneck event. In contrast to the hypothesis suggesting northeastern Mexico as the origin of this species, we see that specimens from two southern collections show high genetic variability delineating three mitochondrial groups. These data suggest that Central America is the origin for A. ludens. We show that COI and ND6 are useful for phylogeographic studies of A. ludens. Published by Oxford University Press on behalf of Entomological Society of America 2015. This work is written by US Government employees and is in the public domain in the US.

  12. Crustal and uppermost mantle structures of Atlas Mountains of Morocco inferred from electromagnetic imaging

    Science.gov (United States)

    Kiyan, D.; Jones, A. G.; Fullea, J.; Ledo, J.; Siniscalchi, A.; Romano, G.

    2012-12-01

    The second phase of the PICASSO (Program to Investigate Convective Alboran Sea System Overturn) project and the concomitant TopoMed (Plate re-organization in the western Mediterranean: Lithospheric causes and topographic consequences - an ESF EUROCORES TOPO-EUROPE Collaborative Research Project) is designed to determine the internal structure of the crust and lithosphere of the Atlas Mountains of Morocco. A multi-institutional magnetotelluric (MT) experiment across the Atlas Mountains region comprises the acquisition of broadband and long period MT data along two profiles: a N-S oriented profile through Middle Atlas to the east and a NE-SW profile through Marrakech to the west. The preliminary results of interpretation of the MT data collected over the first profile were presented in the paper by Ledo et al. (2011). In this study, we present the results from 3D MT inversion using the codes WSINV3DMT (Siripunvaraporn et al., 2005) and Modular system for Electromagnetic Inversion (ModEM; Egbert and Kelbert, 2012). There is a general good agreement between the main features obtained from the 2D models and the new results of the 3D modelling. Models inverting for only off-diagonal tensor components showed a distinct conductivity contrast between Middle-High Atlas and Anti Atlas correlates with the South Atlas Front fault, the depth extent of which appears to be limited to uppermost mantle (approximately 55 km). The resistivity of the lithosphere is gradually increasing towards Anti Atlas. Beside this, a prominent conducting anomaly at the lower crust/uppermost mantle is imaged west of the profile in the junction between the High and Middle Atlas (Moulouya plain). The conductive body, which extends from the southern boundary of Middle Atlas to the northern boundary of High Atlas, is interpreted as due to the presence of partial melt and/or migrated fluids.

  13. Inferring latent task structure for Multitask Learning by Multiple Kernel Learning.

    Science.gov (United States)

    Widmer, Christian; Toussaint, Nora C; Altun, Yasemin; Rätsch, Gunnar

    2010-10-26

    The lack of sufficient training data is the limiting factor for many Machine Learning applications in Computational Biology. If data is available for several different but related problem domains, Multitask Learning algorithms can be used to learn a model based on all available information. In Bioinformatics, many problems can be cast into the Multitask Learning scenario by incorporating data from several organisms. However, combining information from several tasks requires careful consideration of the degree of similarity between tasks. Our proposed method simultaneously learns or refines the similarity between tasks along with the Multitask Learning classifier. This is done by formulating the Multitask Learning problem as Multiple Kernel Learning, using the recently published q-Norm MKL algorithm. We demonstrate the performance of our method on two problems from Computational Biology. First, we show that our method is able to improve performance on a splice site dataset with given hierarchical task structure by refining the task relationships. Second, we consider an MHC-I dataset, for which we assume no knowledge about the degree of task relatedness. Here, we are able to learn the task similarities ab initio along with the Multitask classifiers. In both cases, we outperform baseline methods that we compare against. We present a novel approach to Multitask Learning that is capable of learning task similarity along with the classifiers. The framework is very general as it allows to incorporate prior knowledge about tasks relationships if available, but is also able to identify task similarities in absence of such prior information. Both variants show promising results in applications from Computational Biology.

  14. Inferring latent task structure for Multitask Learning by Multiple Kernel Learning

    Directory of Open Access Journals (Sweden)

    Altun Yasemin

    2010-10-01

    Full Text Available Abstract Background The lack of sufficient training data is the limiting factor for many Machine Learning applications in Computational Biology. If data is available for several different but related problem domains, Multitask Learning algorithms can be used to learn a model based on all available information. In Bioinformatics, many problems can be cast into the Multitask Learning scenario by incorporating data from several organisms. However, combining information from several tasks requires careful consideration of the degree of similarity between tasks. Our proposed method simultaneously learns or refines the similarity between tasks along with the Multitask Learning classifier. This is done by formulating the Multitask Learning problem as Multiple Kernel Learning, using the recently published q-Norm MKL algorithm. Results We demonstrate the performance of our method on two problems from Computational Biology. First, we show that our method is able to improve performance on a splice site dataset with given hierarchical task structure by refining the task relationships. Second, we consider an MHC-I dataset, for which we assume no knowledge about the degree of task relatedness. Here, we are able to learn the task similarities ab initio along with the Multitask classifiers. In both cases, we outperform baseline methods that we compare against. Conclusions We present a novel approach to Multitask Learning that is capable of learning task similarity along with the classifiers. The framework is very general as it allows to incorporate prior knowledge about tasks relationships if available, but is also able to identify task similarities in absence of such prior information. Both variants show promising results in applications from Computational Biology.

  15. "HOOF-Print" Genotyping and Haplotype Inference Discriminates among Brucella spp Isolates From a Small Spatial Scale

    Science.gov (United States)

    We demonstrate that the “HOOF-Print” assay provides high power to discriminate among Brucella isolates collected on a small spatial scale (within Portugal). Additionally, we illustrate how haplotype identification using non-random association among markers allows resolution of B. melitensis biovars ...

  16. Multi-scale structural community organisation of the human genome.

    Science.gov (United States)

    Boulos, Rasha E; Tremblay, Nicolas; Arneodo, Alain; Borgnat, Pierre; Audit, Benjamin

    2017-04-11

    Structural interaction frequency matrices between all genome loci are now experimentally achievable thanks to high-throughput chromosome conformation capture technologies. This ensues a new methodological challenge for computational biology which consists in objectively extracting from these data the structural motifs characteristic of genome organisation. We deployed the fast multi-scale community mining algorithm based on spectral graph wavelets to characterise the networks of intra-chromosomal interactions in human cell lines. We observed that there exist structural domains of all sizes up to chromosome length and demonstrated that the set of structural communities forms a hierarchy of chromosome segments. Hence, at all scales, chromosome folding predominantly involves interactions between neighbouring sites rather than the formation of links between distant loci. Multi-scale structural decomposition of human chromosomes provides an original framework to question structural organisation and its relationship to functional regulation across the scales. By construction the proposed methodology is independent of the precise assembly of the reference genome and is thus directly applicable to genomes whose assembly is not fully determined.

  17. Structure and geological evolution of the island of Ponza, Italy: inferences from geological and gravimetric data

    Science.gov (United States)

    Bellucci, F.; Grimaldi, M.; Lirer, L.; Rapolla, A.

    1997-10-01

    A geological and a geophysical survey have been carried out at Ponza Island, Tyrrhenian sea, Italy. Geological and structural data allowed to identify three main tectonic systems: NW-SE, NE-SW and E-W trending. The first one is related to a pre-volcanic tectonic event, probably linked to the Pliocene extensional activity of the Tyrrhenian evolution; the other two systems affected the volcanic units in two different stages of the Lower Pleistocene, the earlier one after the rhyolitic hyaloclastic formation (HF) emplacement and the later one after the emplacement of older trachytic pyroclastic deposits (Lower Pyroclastic Units—LPU). The latter event was followed by the emersion of the whole Ponza area, as testified by a marked erosional surface and marine terrace deposits cropping out at the top of LPU. The Upper Pyroclastic Units (UPU) represent the younger trachytic activity of the island (1.3 Myr) and do not show evidence of tectonic activity. The NW-SE-trending tectonic system probably assisted the rhyolitic magma rise, while the NE-SW- and E-W-trending systems mainly assisted the trachytic magma rise, responsible for the explosive and effusive activity in the southern area and for the hydrothermal fluids that caused alteration processes in the northern area. A 161-station gravimetric survey was carried out on the island and surrounding islets. The geological data and the gravimetric survey have been used to propose a 2.5 D model in which rhyolitic hyaloclastic deposits (ρ = 1.7 g cm -3) overlay an articulated Meso-Cenozoic sedimentary substratum (ρ = 2.6 g cm -3) laying at a depth to 300 m below sea level. Both formations are crossed by rhyolitic dykes (ρ = 2.4 g cm -3) which mark feeder fractures. In the M. Guardia area, where a maximum is present, this model accounts for the presence of a horst of the rigid basement, a shallow trachytic lava flow and its feeder (ρ = 2.8 g cm -3).

  18. The scale dependence of single-nucleon shell structure

    Energy Technology Data Exchange (ETDEWEB)

    Somà, V., E-mail: vittorio.soma@cea.fr [Centre de Saclay, IRFU/Service de Physique Nucléaire, 91191 Gif-sur-Yvette (France); Duguet, T. [Centre de Saclay, IRFU/Service de Physique Nucléaire, 91191 Gif-sur-Yvette (France); KU Leuven, Instituut voor Kern-en Stralingsfysica, 3001 Leuven (Belgium); Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824-1321 (United States); NSCL, Michigan State University, East Lansing, Michigan 48824-1321 (United States); Hergert, H. [NSCL, Michigan State University, East Lansing, Michigan 48824-1321 (United States); The Ohio State University, Columbus, Ohio 43210 (United States); Holt, J. D. [TRIUMF, 4004 Wesbrook Mall, Vancouver, BC, V6T 2A3 (Canada)

    2015-10-15

    We address the scale dependence of (effective) single-particle energies, non-observable quantities that are commonly used for interpreting nuclear structure observables measured in experiments and computed in many-body theories. We first demonstrate their scale dependence on a formal level, making them intrinsically theoretical objects, before illustrating this point via ab initio calculations in the oxygen isotopes. Finally, we consider a modified definition of effective single-particle energy and investigate its running properties.

  19. Inferring social structure and its drivers from refuge use in the desert tortoise, a relatively solitary species

    Science.gov (United States)

    Sah, Pratha; Nussear, Kenneth E.; Esque, Todd C.; Aiello, Christina M.; Hudson, Peter J.; Bansal, Shweta

    2016-01-01

    For several species, refuges (such as burrows, dens, roosts, nests) are an essential resource for protection from predators and extreme environmental conditions. Refuges also serve as focal sites for social interactions, including mating, courtship, and aggression. Knowledge of refuge use patterns can therefore provide information about social structure, mating, and foraging success, as well as the robustness and health of wildlife populations, especially for species considered to be relatively solitary. In this study, we construct networks of burrow use to infer social associations in a threatened wildlife species typically considered solitary—the desert tortoise. We show that tortoise social networks are significantly different than null networks of random associations, and have moderate spatial constraints. We next use statistical models to identify major mechanisms behind individual-level variation in tortoise burrow use, popularity of burrows in desert tortoise habitat, and test for stressor-driven changes in refuge use patterns. We show that seasonal variation has a strong impact on tortoise burrow switching behavior. On the other hand, burrow age and topographical condition influence the number of tortoises visiting a burrow in desert tortoise habitat. Of three major population stressors affecting this species (translocation, drought, disease), translocation alters tortoise burrow switching behavior, with translocated animals visiting fewer unique burrows than residents. In a species that is not social, our study highlights the importance of leveraging refuge use behavior to study the presence of and mechanisms behind non-random social structure and individual-level variation. Our analysis of the impact of stressors on refuge-based social structure further emphasizes the potential of this method to detect environmental or anthropogenic disturbances.

  20. PERSISTENT ASYMMETRIC STRUCTURE OF SAGITTARIUS A* ON EVENT HORIZON SCALES

    Energy Technology Data Exchange (ETDEWEB)

    Fish, Vincent L.; Doeleman, Sheperd S.; Lu, Ru-Sen; Akiyama, Kazunori; Beaudoin, Christopher; Cappallo, Roger [Massachusetts Institute of Technology, Haystack Observatory, Route 40, Westford, MA 01886 (United States); Johnson, Michael D.; Blackburn, Lindy; Blundell, Ray; Chael, Andrew A. [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Broderick, Avery E. [Perimeter Institute for Theoretical Physics, 31 Caroline Street North, Waterloo, ON N2L 2Y5 (Canada); Psaltis, Dimitrios; Chan, Chi-Kwan [Steward Observatory and Department of Astronomy, University of Arizona, 933 North Cherry Ave., Tucson, AZ 85721-0065 (United States); Alef, Walter; Bertarini, Alessandra [Max-Planck-Institut für Radioastronomie, Auf dem Hügel 69, D-53121 Bonn (Germany); Algaba, Juan Carlos [Korea Astronomy and Space Science Institute, 776 Daedeokdae-ro, Yuseong-gu, Daejeon 305-348 (Korea, Republic of); Asada, Keiichi [Institute of Astronomy and Astrophysics, Academia Sinica, P.O. Box 23-141, Taipei 10617, Taiwan (China); Bower, Geoffrey C. [Academia Sinica Institute for Astronomy and Astrophysics, 645 N. A‘ohōkū Place, Hilo, HI 96720 (United States); Brinkerink, Christiaan [Department of Astrophysics/IMAPP, Radboud University Nijmegen, P.O. Box 9010, 6500 GL, Nijmegen (Netherlands); Chamberlin, Richard, E-mail: vfish@haystack.mit.edu [Caltech Submillimeter Observatory, 111 Nowelo Street, Hilo, HI 96720 (United States); and others

    2016-04-01

    The Galactic Center black hole Sagittarius A* (Sgr A*) is a prime observing target for the Event Horizon Telescope (EHT), which can resolve the 1.3 mm emission from this source on angular scales comparable to that of the general relativistic shadow. Previous EHT observations have used visibility amplitudes to infer the morphology of the millimeter-wavelength emission. Potentially much richer source information is contained in the phases. We report on 1.3 mm phase information on Sgr A* obtained with the EHT on a total of 13 observing nights over four years. Closure phases, which are the sum of visibility phases along a closed triangle of interferometer baselines, are used because they are robust against phase corruptions introduced by instrumentation and the rapidly variable atmosphere. The median closure phase on a triangle including telescopes in California, Hawaii, and Arizona is nonzero. This result conclusively demonstrates that the millimeter emission is asymmetric on scales of a few Schwarzschild radii and can be used to break 180° rotational ambiguities inherent from amplitude data alone. The stability of the sign of the closure phase over most observing nights indicates persistent asymmetry in the image of Sgr A* that is not obscured by refraction due to interstellar electrons along the line of sight.

  1. Multi-scale effects of nestling diet on breeding performance in a terrestrial top predator inferred from stable isotope analysis.

    Directory of Open Access Journals (Sweden)

    Jaime Resano-Mayor

    Full Text Available Inter-individual diet variation within populations is likely to have important ecological and evolutionary implications. The diet-fitness relationships at the individual level and the emerging population processes are, however, poorly understood for most avian predators inhabiting complex terrestrial ecosystems. In this study, we use an isotopic approach to assess the trophic ecology of nestlings in a long-lived raptor, the Bonelli's eagle Aquila fasciata, and investigate whether nestling dietary breath and main prey consumption can affect the species' reproductive performance at two spatial scales: territories within populations and populations over a large geographic area. At the territory level, those breeding pairs whose nestlings consumed similar diets to the overall population (i.e. moderate consumption of preferred prey, but complemented by alternative prey categories or those disproportionally consuming preferred prey were more likely to fledge two chicks. An increase in the diet diversity, however, related negatively with productivity. The age and replacements of breeding pair members had also an influence on productivity, with more fledglings associated to adult pairs with few replacements, as expected in long-lived species. At the population level, mean productivity was higher in those population-years with lower dietary breadth and higher diet similarity among territories, which was related to an overall higher consumption of preferred prey. Thus, we revealed a correspondence in diet-fitness relationships at two spatial scales: territories and populations. We suggest that stable isotope analyses may be a powerful tool to monitor the diet of terrestrial avian predators on large spatio-temporal scales, which could serve to detect potential changes in the availability of those prey on which predators depend for breeding. We encourage ecologists and evolutionary and conservation biologists concerned with the multi-scale fitness

  2. Intermittent structures at ion scales in the turbulent solar wind

    Science.gov (United States)

    Perrone, Denise; Alexandrova, Olga; Lion, Sonny; Roberts, Owen W.; Maksimovic, Milan; Escoubet, Philippe C.; Zouganelis, Yannis

    2017-04-01

    Understanding the physical mechanisms of dissipation, and the related heating, in turbulent collisionless plasmas (such as the solar wind) represents nowadays one of the key issues of plasma physics. Although the complex behavior of the solar wind has been matter of investigation of many years, some of the primary problems still remain a puzzle for the scientific community. Here, we study coherent structures responsible for solar wind intermittency around ion characteristic scales. We find that, in fast solar wind, intermittency is due to current sheets and Alfvén vortex-like structures. In slow solar wind, we observe as well compressive structures like magnetic solitons, holes and shocks. By using high-time resolution magnetic field data of multi-point measurements of Cluster spacecraft, we characterize the observed coherent structures in terms of topology and propagation speed. We show that all structures, both in fast and slow solar wind, are characterized by a strong wave-vector anisotropy in the perpendicular direction with respect to the local magnetic field and typical scales around ion characteristic scales. Moreover, some of them propagate in the plasma rest frame. Moreover, a further analysis on the ion velocity distribution shows a high variability; in particular, close to coherent structures the proton distribution function appears strongly deformed and far from the thermodynamic equilibrium. We discuss possible interpretation of the observed structures and their role in the heating process of the plasma.

  3. Structural Observability Analysis of Large Scale Systems Using Modelica and Python

    Directory of Open Access Journals (Sweden)

    M. Anushka S. Perera

    2015-01-01

    Full Text Available State observability of dynamic systems is a notion which determines how well the states can be inferred from input-output data. For small-scale systems, observability analysis can be done manually, while for large-scale systems an automated systematic approach is advantageous. Here we present an approach based on the concept of structural observability analysis, using graph theory. This approach can be automated and applied to large-scale, complex dynamic systems modeled using Modelica. Modelica models are imported into Python via the JModelica.org-CasADi interface, and the Python packages NetworkX (for graph-theoretic analysis and PyGraphviz (for graph layout and visualization are used to analyze the structural observability of the systems. The method is demonstrated with a Modelica model created for the Copper production plant at Glencore Nikkelverk, Kristiansand, Norway. The Copper plant model has 39 states, 11 disturbances and 5 uncertain parameters. The possibility of estimating disturbances and parameters in addition to estimating the states are also discussed from the graph-theory point of view. All the software tools used on the analysis are freely available.

  4. Inferring interdependencies in climate networks constructed at inter-annual, intra-season and longer time scales

    Science.gov (United States)

    Deza, J. I.; Barreiro, M.; Masoller, C.

    2013-06-01

    We study global climate networks constructed by means of ordinal time series analysis. Climate interdependencies among the nodes are quantified by the mutual information, computed from time series of monthly-averaged surface air temperature anomalies, and from their symbolic ordinal representation (OP). This analysis allows identifying topological changes in the network when varying the time-interval of the ordinal pattern. We consider intra-season time-intervals (e.g., the patterns are formed by anomalies in consecutive months) and inter-annual time-intervals (e.g., the patterns are formed by anomalies in consecutive years). We discuss how the network density and topology change with these time scales, and provide evidence of correlations between geographically distant regions that occur at specific time scales. In particular, we find that an increase in the ordinal pattern spacing (i.e., an increase in the timescale of the ordinal analysis), results in climate networks with increased connectivity on the equatorial Pacific area. On the contrary, the number of significant links decreases when the ordinal analysis is done with a shorter timescale (by comparing consecutive months), and interpret this effect as due to more stochasticity in the time-series in the short timescale. As the equatorial Pacific is known to be dominated by El Niño-Southern Oscillation (ENSO) on scales longer than several months, our methodology allows constructing climate networks where the effect of ENSO goes from mild (monthly OP) to intense (yearly OP), independently of the length of the ordinal pattern and of the thresholding method employed.

  5. Deep geoelectrical structure inferred from sea-effect-corrected magnetotelluric (MT) data obtained at Jeju Island, Korea

    Science.gov (United States)

    Yang, J.; Lee, H.; Yoo, H.

    2010-12-01

    Jeju Island, a volcanic island in South Korea, has been a main target of geophysical and/or geological studies because of tectonical importance associated with its volcanism and tentonical link with the southern Korean Peninsula. Recently, a number of natural-source magnetotelluric (MT) measurements, which is fairly effective to probe the deep part of Earth, were performed in the island, but shallow or middle rather than deep structures were mainly revealed. For the deeper structures such as the lower crust and the upper mantle, it is not easy to properly describe geoelectrical structures, because the observed low-frequency MT data seem to be strongly affected by the sea surrounding the island. We here reinterpret the deep subsurface structures of Jeju Island by applying an iterative sea-effect correction method to the existing MT data. A total of 11 MT sites, uniformly spread out across the island with good data quality down to 10-3 Hz, were selected for examining the 1-D deep structure. The sea effect correction made remarkable changes in the observed MT responses at frequencies below about 1 Hz, clearly indicating the existence of conductive bottom layer. The 1-D resistivity models obtained from sea-effect-corrected MT data of the 11 sites are greatly similar one another, commonly showing the discontinuity at a depth of 18 km on average. This discontinuity is thought of as transition zone separating resistive upper crust and conductive lower crust. Furthermore, in the southern part of the peninsula which seems to be tectonically linked to Jeju Island, the transition zone separating the upper and lower crusts has been also estimated to be approximately 18 km from the previous MT survey and 20 km from recent seismological study, respectively. This similarity indicates that 1-D resistivity model inferred form sea-effect-corrected MT responses is reliable enough to compatible with other geophysical data and also support the previous studies that Jeju Island is a

  6. A large-scale RF-based Indoor Localization System Using Low-complexity Gaussian filter and improved Bayesian inference

    Directory of Open Access Journals (Sweden)

    L. Xiao

    2013-04-01

    Full Text Available The growing convergence among mobile computing device and smart sensors boosts the development of ubiquitous computing and smart spaces, where localization is an essential part to realize the big vision. The general localization methods based on GPS and cellular techniques are not suitable for tracking numerous small size and limited power objects in the indoor case. In this paper, we propose and demonstrate a new localization method, this method is an easy-setup and cost-effective indoor localization system based on off-the-shelf active RFID technology. Our system is not only compatible with the future smart spaces and ubiquitous computing systems, but also suitable for large-scale indoor localization. The use of low-complexity Gaussian Filter (GF, Wheel Graph Model (WGM and Probabilistic Localization Algorithm (PLA make the proposed algorithm robust and suitable for large-scale indoor positioning from uncertainty, self-adjective to varying indoor environment. Using MATLAB simulation, we study the system performances, especially the dependence on a number of system and environment parameters, and their statistical properties. The simulation results prove that our proposed system is an accurate and cost-effective candidate for indoor localization.

  7. Constraining cosmological ultralarge scale structure using numerical relativity

    Science.gov (United States)

    Braden, Jonathan; Johnson, Matthew C.; Peiris, Hiranya V.; Aguirre, Anthony

    2017-07-01

    Cosmic inflation, a period of accelerated expansion in the early universe, can give rise to large amplitude ultralarge scale inhomogeneities on distance scales comparable to or larger than the observable universe. The cosmic microwave background (CMB) anisotropy on the largest angular scales is sensitive to such inhomogeneities and can be used to constrain the presence of ultralarge scale structure (ULSS). We numerically evolve nonlinear inhomogeneities present at the beginning of inflation in full general relativity to assess the CMB quadrupole constraint on the amplitude of the initial fluctuations and the size of the observable universe relative to a length scale characterizing the ULSS. To obtain a statistically meaningful ensemble of simulations, we adopt a toy model in which inhomogeneities are injected along a preferred direction. We compute the likelihood function for the CMB quadrupole including both ULSS and the standard quantum fluctuations produced during inflation. We compute the posterior given the observed CMB quadrupole, finding that when including gravitational nonlinearities, ULSS curvature perturbations of order unity are allowed by the data, even on length scales not too much larger than the size of the observable universe. To demonstrate the robustness of our conclusions, we also explore a semianalytic model for the ULSS which reproduces our numerical results for the case of planar symmetry, and which can be extended to ULSS with a three-dimensional inhomogeneity structure. Our results illustrate the utility and importance of numerical relativity for constraining early universe cosmology.

  8. INVESTIGATING THE FACTOR STRUCTURE OF THE BLOG ATTITUDE SCALE

    Directory of Open Access Journals (Sweden)

    Zahra SHAHSAVAR

    2010-10-01

    Full Text Available Due to the wide application of advanced technology in education, many attitude scales have been developed to evaluate learners’ attitudes toward educational tools. However, with the rapid development of emerging technologies, using blogs as one of the Web 2.0 tools is still in its infancy and few blog attitude scales have been developed yet. In view of this need, a lot of researchers like to design a new scale based on their conceptual and theoretical framework of their own study rather than using available scales. The present study reports the design and development of a blog attitude scale (BAS. The researchers developed a pool of items to capture the complexity of the blog attitude trait, selected 29 items in the content analysis, and assigned the scale comprising 29 items to 216 undergraduate students to explore the underlying structure of the BAS. In exploratory factor analysis, three factors were discovered: blog anxiety, blog desirability, and blog self-efficacy; 14 items were excluded. The extracted items were subjected to a confirmatory factor analysis which lent further support to the BAS underpinning structure.

  9. Atomic scale structures of interfaces between kaolinite edges and water

    NARCIS (Netherlands)

    Liu, X.; Lu, X.; Wang, R.; Meijer, E.J.; Zhou, H.; He, H.

    2012-01-01

    This paper reports the atomic scale structures of kaolinite edge surfaces in contact with water. The commonly occurring edge surfaces are investigated (i.e. (0 1 0) and (1 1 0)) by using first principles molecular dynamics (FPMD) technique. For (1 1 0)-type edge surface, there are two different

  10. Factor Structure of Japanese Versions of Two Emotional Intelligence Scales

    Science.gov (United States)

    Fukuda, Eriko; Saklofske, Donald H.; Tamaoka, Katsuo; Fung, Tak Shing; Miyaoka, Yayoi; Kiyama, Sachiko

    2011-01-01

    This article reports the psychometric properties of two emotional intelligence measures translated into Japanese. Confirmatory factor analysis (CFA) was conducted to examine the factor structure of a Japanese version of the Wong and Law Emotional Intelligence Scale (WLEIS) completed by 310 Japanese university students. A second study employed CFA…

  11. Random walk models of large-scale structure

    Indian Academy of Sciences (India)

    Abstract. This paper describes the insights gained from the excursion set approach, in which vari- ous questions about the phenomenology of large-scale structure formation can be mapped to problems associated with the first crossing distribution of appropriately defined barriers by random walks. Much of this is ...

  12. Gregory Research Beliefs Scale: Factor Structure and Internal Consistency

    Science.gov (United States)

    Gregory, Virgil L., Jr.

    2010-01-01

    Objective: This study evaluates the factor structure and internal consistency of the Gregory Research Beliefs Scale (GRBS). Method: Data were collected from subject matter experts, a pilot study, an online sample, and a classroom sample. Psychometric analyses were conducted after combining the online and classroom samples. Results: An a priori…

  13. A structured ecosystem-scale approach to marine water quality ...

    African Journals Online (AJOL)

    These, in turn, created the need for holistic and integrated frameworks within which to design and implement environmental management programmes. A structured ecosystem-scale approach for the design and implementation of marine water quality management programmes developed by the CSIR (South Africa) in ...

  14. Examining the factor structure of the Multiple Sclerosis Impact Scale.

    Science.gov (United States)

    Fitzgerald, Shawn M; Li, Jian; Rumrill, Phillip D; Merchant, William; Bishop, Malachy

    2014-01-01

    The purpose of this study was to investigate the factor structure of the Multiple Sclerosis Impact Scale (MSIS-29) to assess its suitability for modeling the impact of MS on a nation-wide sample of individuals from the United States. Investigators completed a Confirmatory Factor Analysis (CFA) to examine the two-factor structure proposed by Hobart et al. [17]. Although the original MSIS-29 factor structure did not fit the data exactly, the hypothesized two-factor model was partially supported in the current data. Implications for future instrument development and rehabilitation practice are discussed.

  15. The energy dependence of p_t angular correlations inferred frommean -pt fluctuation scale dependence in heavy ion collisions at the SPSand RHIC

    Energy Technology Data Exchange (ETDEWEB)

    Adams, J.; Aggarwal, M.M.; Ahammed, Z.; Amonett, J.; Anderson,B.D.; Anderson, M.; Arkhipkin, D.; Averichev, G.S.; Bai, Y.; Balewski,J.; Barannikova, O.; Barnby, L.S.; Baudot, J.; Bekele, S.; Belaga, V.V.; Bellingeri-Laurikainen, A.; Bellwied, R.; Benedosso, F.; Bhardwaj, S.; Bhasin, A.; Bhati, A.K.; Bichsel, H.; Bielcik, J.; Bielcikova, J.; Bland,L.C.; Blyth, S.-L.; Bonner, B.E.; Botje, M.; Bouchet, J.; Brandin, A.V.; Bravar, A.; Bystersky, M.; Cadman, R.V.; Cai, X.Z.; Caines, H.; Calderonde la Barca Sanchez, M.; Castillo, J.; Catu, O.; Cebra, D.; Chajecki, Z.; Chaloupka, P.; Chattopadhyay, S.; Chen, H.F.; Chen, J.H.; Cheng, J.; Cherney, M.; Chikanian, A.; Christie, W.; Coffin, J.P.; Cormier, T.M.; Cosentino, M.R.; Cramer, J.G.; Crawford, H.J.; Das, D.; Das, S.; Daugherity, M.; de Moura, M.M.; Dedovich, T.G.; DePhillips, M.; Derevschikov, A.A.; Didenko, L.; Dietel, T.; Djawotho, P.; Dogra, S.M.; Dong, W.J.; Dong, X.; Draper, J.E.; Du, F.; Dunin, V.B.; Dunlop, J.C.; Dutta Mazumdar, M.R.; Eckardt, V.; Edwards, W.R.; Efimov, L.G.; Emelianov, V.; Engelage, J.; Eppley, G.; Erazmus, B.; Estienne, M.; Fachini, P.; Fatemi, R.; Fedorisin, J.; Filimonov, K.; Filip, P.; Finch,E.; Fine, V.; Fisyak, Y.; Fu, J.; Gagliardi, C.A.; Gaillard, L.; Ganti,M.S.; Ghazikhanian, V.; Ghosh, P.; Gonzalez, J.S.; Gorbunov, Y.G.; Gos,H.; Grebenyuk, O.; Grosnick, D.; Guertin, S.M.; Guimaraes, K.S.F.F.; Guo,Y.; Gupta, N.; Gutierrez, T.D.; Haag, B.; Hallman, T.J.; Hamed, A.; Harris, J.W.; He, W.; Heinz, M.; Henry, T.W.; Hepplemann, S.; Hippolyte,B.; Hirsch, A.; Hjort, E.; Hoffman, A.M.; Hoffmann, G.W.; Horner, M.J.; Huang, H.Z.; Huang, S.L.; Hughes, E.W.; Humanic, T.J.; Igo, G.; Jacobs,P.; Jacobs, W.W.; Jakl, P.; Jia, F.; Jiang, H.; Jones, P.G.; Judd, E.G.; Kabana, S.; Kang, K.; Kapitan, J.; Kaplan, M.; Keane, D.; Kechechyan, A.; Khodyrev, V.Yu.; Kim, B.C.; Kiryluk, J.; Kisiel, A.; Kislov, E.M.; Klein,S.R.; Kocoloski, A.; Koetke, D.D.; Kollegger, T.; et al.

    2006-05-17

    We present the first study of the energy dependence of ptangular correlations inferred from event-wise mean transverse momentumfluctuations in heavy ion collisions. We compare ourlarge-acceptance measurements at CM energies sqrt sNN = 19.6, 62.4, 130and 200 GeV to SPS measurements at 12.3 and 17.3 GeV. pt angularcorrelation structure suggests that the principal source of ptcorrelations and fluctuations is minijets (minimum-bias partonfragments). We observe a dramatic increase in correlations andfluctuations from SPS to RHIC energies, increasing linearly with ln sqrtsNN from the onset of observable jet-related pt fluctuations near 10GeV.

  16. Inference of expanded Lrp-like feast/famine transcription factor targets in a non-model organism using protein structure-based prediction.

    Directory of Open Access Journals (Sweden)

    Justin Ashworth

    Full Text Available Widespread microbial genome sequencing presents an opportunity to understand the gene regulatory networks of non-model organisms. This requires knowledge of the binding sites for transcription factors whose DNA-binding properties are unknown or difficult to infer. We adapted a protein structure-based method to predict the specificities and putative regulons of homologous transcription factors across diverse species. As a proof-of-concept we predicted the specificities and transcriptional target genes of divergent archaeal feast/famine regulatory proteins, several of which are encoded in the genome of Halobacterium salinarum. This was validated by comparison to experimentally determined specificities for transcription factors in distantly related extremophiles, chromatin immunoprecipitation experiments, and cis-regulatory sequence conservation across eighteen related species of halobacteria. Through this analysis we were able to infer that Halobacterium salinarum employs a divergent local trans-regulatory strategy to regulate genes (carA and carB involved in arginine and pyrimidine metabolism, whereas Escherichia coli employs an operon. The prediction of gene regulatory binding sites using structure-based methods is useful for the inference of gene regulatory relationships in new species that are otherwise difficult to infer.

  17. Implementation of structure-mapping inference by event-file binding and action planning: a model of tool-improvisation analogies.

    Science.gov (United States)

    Fields, Chris

    2011-03-01

    Structure-mapping inferences are generally regarded as dependent upon relational concepts that are understood and expressible in language by subjects capable of analogical reasoning. However, tool-improvisation inferences are executed by members of a variety of non-human primate and other species. Tool improvisation requires correctly inferring the motion and force-transfer affordances of an object; hence tool improvisation requires structure mapping driven by relational properties. Observational and experimental evidence can be interpreted to indicate that structure-mapping analogies in tool improvisation are implemented by multi-step manipulation of event files by binding and action-planning mechanisms that act in a language-independent manner. A functional model of language-independent event-file manipulations that implement structure mapping in the tool-improvisation domain is developed. This model provides a mechanism by which motion and force representations commonly employed in tool-improvisation structure mappings may be sufficiently reinforced to be available to inwardly directed attention and hence conceptualization. Predictions and potential experimental tests of this model are outlined.

  18. A perspective on bridging scales and design of models using low-dimensional manifolds and data-driven model inference

    KAUST Repository

    Tegner, Jesper

    2016-10-04

    Systems in nature capable of collective behaviour are nonlinear, operating across several scales. Yet our ability to account for their collective dynamics differs in physics, chemistry and biology. Here, we briefly review the similarities and differences between mathematical modelling of adaptive living systems versus physico-chemical systems. We find that physics-based chemistry modelling and computational neuroscience have a shared interest in developing techniques for model reductions aiming at the identification of a reduced subsystem or slow manifold, capturing the effective dynamics. By contrast, as relations and kinetics between biological molecules are less characterized, current quantitative analysis under the umbrella of bioinformatics focuses on signal extraction, correlation, regression and machine-learning analysis. We argue that model reduction analysis and the ensuing identification of manifolds bridges physics and biology. Furthermore, modelling living systems presents deep challenges as how to reconcile rich molecular data with inherent modelling uncertainties (formalism, variables selection and model parameters). We anticipate a new generative data-driven modelling paradigm constrained by identified governing principles extracted from low-dimensional manifold analysis. The rise of a new generation of models will ultimately connect biology to quantitative mechanistic descriptions, thereby setting the stage for investigating the character of the model language and principles driving living systems.

  19. QuartetS-DB: a large-scale orthology database for prokaryotes and eukaryotes inferred by evolutionary evidence

    Directory of Open Access Journals (Sweden)

    Yu Chenggang

    2012-06-01

    Full Text Available Abstract Background The concept of orthology is key to decoding evolutionary relationships among genes across different species using comparative genomics. QuartetS is a recently reported algorithm for large-scale orthology detection. Based on the well-established evolutionary principle that gene duplication events discriminate paralogous from orthologous genes, QuartetS has been shown to improve orthology detection accuracy while maintaining computational efficiency. Description QuartetS-DB is a new orthology database constructed using the QuartetS algorithm. The database provides orthology predictions among 1621 complete genomes (1365 bacterial, 92 archaeal, and 164 eukaryotic, covering more than seven million proteins and four million pairwise orthologs. It is a major source of orthologous groups, containing more than 300,000 groups of orthologous proteins and 236,000 corresponding gene trees. The database also provides over 500,000 groups of inparalogs. In addition to its size, a distinguishing feature of QuartetS-DB is the ability to allow users to select a cutoff value that modulates the balance between prediction accuracy and coverage of the retrieved pairwise orthologs. The database is accessible at https://applications.bioanalysis.org/quartetsdb. Conclusions QuartetS-DB is one of the largest orthology resources available to date. Because its orthology predictions are underpinned by evolutionary evidence obtained from sequenced genomes, we expect its accuracy to continue to increase in future releases as the genomes of additional species are sequenced.

  20. Observer error structure in bull trout redd counts in Montana streams: Implications for inference on true redd numbers

    Science.gov (United States)

    Muhlfeld, Clint C.; Taper, Mark L.; Staples, David F.; Shepard, Bradley B.

    2006-01-01

    Despite the widespread use of redd counts to monitor trends in salmonid populations, few studies have evaluated the uncertainties in observed counts. We assessed the variability in redd counts for migratory bull trout Salvelinus confluentus among experienced observers in Lion and Goat creeks, which are tributaries to the Swan River, Montana. We documented substantially lower observer variability in bull trout redd counts than did previous studies. Observer counts ranged from 78% to 107% of our best estimates of true redd numbers in Lion Creek and from 90% to 130% of our best estimates in Goat Creek. Observers made both errors of omission and errors of false identification, and we modeled this combination by use of a binomial probability of detection and a Poisson count distribution of false identifications. Redd detection probabilities were high (mean = 83%) and exhibited no significant variation among observers (SD = 8%). We applied this error structure to annual redd counts in the Swan River basin (1982–2004) to correct for observer error and thus derived more accurate estimates of redd numbers and associated confidence intervals. Our results indicate that bias in redd counts can be reduced if experienced observers are used to conduct annual redd counts. Future studies should assess both sources of observer error to increase the validity of using redd counts for inferring true redd numbers in different basins. This information will help fisheries biologists to more precisely monitor population trends, identify recovery and extinction thresholds for conservation and recovery programs, ascertain and predict how management actions influence distribution and abundance, and examine effects of recovery and restoration activities.

  1. Mechanical properties and the laminate structure of Arapaima gigas scales.

    Science.gov (United States)

    Lin, Y S; Wei, C T; Olevsky, E A; Meyers, Marc A

    2011-10-01

    The Arapaima gigas scales play an important role in protecting this large Amazon basin fish against predators such as the piranha. They have a laminate composite structure composed of an external mineralized layer and internal lamellae with thickness of 50-60 μm each and composed of collagen fibers with ~1 μm diameter. The alignment of collagen fibers is consistent in each individual layer but varies from layer to layer, forming a non-orthogonal plywood structure, known as Bouligand stacking. X-ray diffraction revealed that the external surface of the scale contains calcium-deficient hydroxyapatite. EDS results confirm that the percentage of calcium is higher in the external layer. The micro-indentation hardness of the external layer (550 MPa) is considerably higher than that of the internal layer (200 MPa), consistent with its higher degree of mineralization. Tensile testing of the scales carried out in the dry and wet conditions shows that the strength and stiffness are hydration dependent. As is the case of most biological materials, the elastic modulus of the scale is strain-rate dependent. The strain-rate dependence of the elastic modulus, as expressed by the Ramberg-Osgood equation, is equal to 0.26, approximately ten times higher than that of bone. This is attributed to the higher fraction of collagen in the scales and to the high degree of hydration (30% H(2)O). Deproteinization of the scale reveals the structure of the mineral component consisting of an interconnected network of platelets with a thickness of ~50 nm and diameter of ~500 nm. Copyright © 2011 Elsevier Ltd. All rights reserved.

  2. Reliability Evaluation considering Structures of a Large Scale Wind Farm

    DEFF Research Database (Denmark)

    Shin, Je-Seok; Cha, Seung-Tae; Wu, Qiuwei

    2012-01-01

    Wind energy is one of the most widely used renewable energy resources. Wind power has been connected to the grid as large scale wind farm which is made up of dozens of wind turbines, and the scale of wind farm is more increased recently. Due to intermittent and variable wind source, reliability...... wind farm which is able to enhance a capability of delivering a power instead of controlling an uncontrollable output of wind power. Therefore, this paper introduces a method to evaluate the reliability depending upon structures of wind farm and to reflect the result to the planning stage of wind farm....

  3. Geophysical mapping of complex glaciogenic large-scale structures

    DEFF Research Database (Denmark)

    Høyer, Anne-Sophie

    2013-01-01

    is required to understand the structures. In practice, however, also the applicability and costs of the methods are crucial. The SkyTEM method is very cost-effective in providing dense data sets, and it is therefore recommendable to use this method initially in mapping campaigns. For more detailed structural...... information, seismic data can profitably be acquired in certain areas of interest, preferably selected on the basis of the SkyTEM data. In areas where extremely detailed information about the near-surface is required, geoelec¬tri¬cal data (resistivity information) and ground penetrating radar data (structural......This thesis presents the main results of a four year PhD study concerning the use of geophysical data in geological mapping. The study is related to the Geocenter project, “KOMPLEKS”, which focuses on the mapping of complex, large-scale geological structures. The study area is approximately 100 km2...

  4. Structure, inferred mechanical properties, and implications for fluid transport in the décollement zone, Costa Rica convergent margin

    Science.gov (United States)

    Tobin, Harold; Vannucchi, Paola; Meschede, Martin

    2001-10-01

    Faults in a variety of tectonic settings can act as both conduits for and barriers to fluid flow, sometimes simultaneously. Documenting the interaction between hydrologic and tectonic processes in active faults in situ is the key to understanding their mechanical behavior and large-scale fluid transport properties. We present observations of the plate boundary décollement zone at the Middle America Trench off Costa Rica, showing that it is structurally divisible into an upper brittle-fracture dominated domain overlying a lower, ductile domain. Pore-water geochemical evidence shows that along-fault flow is occurring specifically in the upper brittle domain, but is hydrologically isolated from fluids in the underlying footwall sediments. We propose a model for the mechanics of these contrasting domains in which differing stress paths coexist in the upper and lower parts of the décollement zone. The data suggest a mechanically controlled permeability anisotropy at a scale of several meters to ˜10 m across the décollement zone. This documentation of separate yet simultaneously active mechanical and hydrologic subregimes within a décollement provides a relatively simple explanation for enhanced along-fault permeability coexisting with reduced cross-fault permeability, without requiring matrix-scale permeability anisotropy.

  5. Scale and structure of capitated physician organizations in California.

    Science.gov (United States)

    Rosenthal, M B; Frank, R G; Buchanan, J L; Epstein, A M

    2001-01-01

    Physician organizations in California broke new ground in the 1980s by accepting capitated contracts and taking on utilization management functions. In this paper we present new data that document the scale, structure, and vertical affiliations of physician organizations that accept capitation in California. We provide information on capitated enrollment, the share of revenue derived by physician organizations from capitation contracts, and the scope of risk sharing with health maintenance organizations (HMOs). Capitation contracts and risk sharing dominate payment arrangements with HMOs. Physician organizations appear to have responded to capitation by affiliating with hospitals and management companies, adopting hybrid organizational structures, and consolidating into larger entities.

  6. Scaling laws of diffusion and time intermittency generated by coherent structures in atmospheric turbulence

    Directory of Open Access Journals (Sweden)

    P. Paradisi

    2012-02-01

    Full Text Available We investigate the time intermittency of turbulent transport associated with the birth-death of self-organized coherent structures in the atmospheric boundary layer. We apply a threshold analysis on the increments of turbulent fluctuations to extract sequences of rapid acceleration events, which is a marker of the transition between self-organized structures.

    The inter-event time distributions show a power-law decay ψ(τ ~ 1/τμ, with a strong dependence of the power-law index μ on the threshold.

    A recently developed method based on the application of event-driven walking rules to generate different diffusion processes is applied to the experimental event sequences. At variance with the power-law index μ estimated from the inter-event time distributions, the diffusion scaling H, defined by ⟨ X2⟩ ~ t2H, is independent from the threshold.

    From the analysis of the diffusion scaling it can also be inferred the presence of different kind of events, i.e. genuinely transition events and spurious events, which all contribute to the diffusion process but over different time scales. The great advantage of event-driven diffusion lies in the ability of separating different regimes of the scaling H. In fact, the greatest H, corresponding to the most anomalous diffusion process, emerges in the long time range, whereas the smallest H can be seen in the short time range if the time resolution of the data is sufficiently accurate.

    The estimated diffusion scaling is also robust under the change of the definition of turbulent fluctuations and, under the assumption of statistically independent events, it corresponds to a self-similar point process with a well-defined power-law index μD ~ 2.1, where D denotes that μD is derived from the diffusion scaling. We argue that

  7. Scaling laws of diffusion and time intermittency generated by coherent structures in atmospheric turbulence

    Science.gov (United States)

    Paradisi, P.; Cesari, R.; Donateo, A.; Contini, D.; Allegrini, P.

    2012-02-01

    We investigate the time intermittency of turbulent transport associated with the birth-death of self-organized coherent structures in the atmospheric boundary layer. We apply a threshold analysis on the increments of turbulent fluctuations to extract sequences of rapid acceleration events, which is a marker of the transition between self-organized structures. The inter-event time distributions show a power-law decay ψ(τ) ~ 1/τμ, with a strong dependence of the power-law index μ on the threshold. A recently developed method based on the application of event-driven walking rules to generate different diffusion processes is applied to the experimental event sequences. At variance with the power-law index μ estimated from the inter-event time distributions, the diffusion scaling H, defined by ⟨ X2⟩ ~ t2H, is independent from the threshold. From the analysis of the diffusion scaling it can also be inferred the presence of different kind of events, i.e. genuinely transition events and spurious events, which all contribute to the diffusion process but over different time scales. The great advantage of event-driven diffusion lies in the ability of separating different regimes of the scaling H. In fact, the greatest H, corresponding to the most anomalous diffusion process, emerges in the long time range, whereas the smallest H can be seen in the short time range if the time resolution of the data is sufficiently accurate. The estimated diffusion scaling is also robust under the change of the definition of turbulent fluctuations and, under the assumption of statistically independent events, it corresponds to a self-similar point process with a well-defined power-law index μD ~ 2.1, where D denotes that μD is derived from the diffusion scaling. We argue that this renewal point process can be associated to birth and death of coherent structures and to turbulent transport near the ground, where the contribution of turbulent coherent structures becomes dominant.

  8. The effective field theory of cosmological large scale structures

    Energy Technology Data Exchange (ETDEWEB)

    Carrasco, John Joseph M. [Stanford Univ., Stanford, CA (United States); Hertzberg, Mark P. [Stanford Univ., Stanford, CA (United States); SLAC National Accelerator Lab., Menlo Park, CA (United States); Senatore, Leonardo [Stanford Univ., Stanford, CA (United States); SLAC National Accelerator Lab., Menlo Park, CA (United States)

    2012-09-20

    Large scale structure surveys will likely become the next leading cosmological probe. In our universe, matter perturbations are large on short distances and small at long scales, i.e. strongly coupled in the UV and weakly coupled in the IR. To make precise analytical predictions on large scales, we develop an effective field theory formulated in terms of an IR effective fluid characterized by several parameters, such as speed of sound and viscosity. These parameters, determined by the UV physics described by the Boltzmann equation, are measured from N-body simulations. We find that the speed of sound of the effective fluid is c2s ≈ 10–6c2 and that the viscosity contributions are of the same order. The fluid describes all the relevant physics at long scales k and permits a manifestly convergent perturbative expansion in the size of the matter perturbations δ(k) for all the observables. As an example, we calculate the correction to the power spectrum at order δ(k)4. As a result, the predictions of the effective field theory are found to be in much better agreement with observation than standard cosmological perturbation theory, already reaching percent precision at this order up to a relatively short scale k ≃ 0.24h Mpc–1.

  9. Topological analysis of large-scale biomedical terminology structures.

    Science.gov (United States)

    Bales, Michael E; Lussier, Yves A; Johnson, Stephen B

    2007-01-01

    To characterize global structural features of large-scale biomedical terminologies using currently emerging statistical approaches. Given rapid growth of terminologies, this research was designed to address scalability. We selected 16 terminologies covering a variety of domains from the UMLS Metathesaurus, a collection of terminological systems. Each was modeled as a network in which nodes were atomic concepts and links were relationships asserted by the source vocabulary. For comparison against each terminology we created three random networks of equivalent size and density. Average node degree, node degree distribution, clustering coefficient, average path length. Eight of 16 terminologies exhibited the small-world characteristics of a short average path length and strong local clustering. An overlapping subset of nine exhibited a power law distribution in node degrees, indicative of a scale-free architecture. We attribute these features to specific design constraints. Constraints on node connectivity, common in more synthetic classification systems, localize the effects of changes and deletions. In contrast, small-world and scale-free features, common in comprehensive medical terminologies, promote flexible navigation and less restrictive organic-like growth. While thought of as synthetic, grid-like structures, some controlled terminologies are structurally indistinguishable from natural language networks. This paradoxical result suggests that terminology structure is shaped not only by formal logic-based semantics, but by rules analogous to those that govern social networks and biological systems. Graph theoretic modeling shows early promise as a framework for describing terminology structure. Deeper understanding of these techniques may inform the development of scalable terminologies and ontologies.

  10. Dark matter self-interactions and small scale structure

    Science.gov (United States)

    Tulin, Sean; Yu, Hai-Bo

    2018-02-01

    We review theories of dark matter (DM) beyond the collisionless paradigm, known as self-interacting dark matter (SIDM), and their observable implications for astrophysical structure in the Universe. Self-interactions are motivated, in part, due to the potential to explain long-standing (and more recent) small scale structure observations that are in tension with collisionless cold DM (CDM) predictions. Simple particle physics models for SIDM can provide a universal explanation for these observations across a wide range of mass scales spanning dwarf galaxies, low and high surface brightness spiral galaxies, and clusters of galaxies. At the same time, SIDM leaves intact the success of ΛCDM cosmology on large scales. This report covers the following topics: (1) small scale structure issues, including the core-cusp problem, the diversity problem for rotation curves, the missing satellites problem, and the too-big-to-fail problem, as well as recent progress in hydrodynamical simulations of galaxy formation; (2) N-body simulations for SIDM, including implications for density profiles, halo shapes, substructure, and the interplay between baryons and self-interactions; (3) semi-analytic Jeans-based methods that provide a complementary approach for connecting particle models with observations; (4) merging systems, such as cluster mergers (e.g., the Bullet Cluster) and minor infalls, along with recent simulation results for mergers; (5) particle physics models, including light mediator models and composite DM models; and (6) complementary probes for SIDM, including indirect and direct detection experiments, particle collider searches, and cosmological observations. We provide a summary and critical look for all current constraints on DM self-interactions and an outline for future directions.

  11. Structural Quality of Service in Large-Scale Networks

    DEFF Research Database (Denmark)

    Pedersen, Jens Myrup

    , telephony and data. To meet the requirements of the different applications, and to handle the increased vulnerability to failures, the ability to design robust networks providing good Quality of Service is crucial. However, most planning of large-scale networks today is ad-hoc based, leading to highly......Digitalization has created the base for co-existence and convergence in communications, leading to an increasing use of multi service networks. This is for example seen in the Fiber To The Home implementations, where a single fiber is used for virtually all means of communication, including TV...... complex networks lacking predictability and global structural properties. The thesis applies the concept of Structural Quality of Service to formulate desirable global properties, and it shows how regular graph structures can be used to obtain such properties....

  12. Structures, profile consistency, and transport scaling in electrostatic convection

    DEFF Research Database (Denmark)

    Bian, N.H.; Garcia, O.E.

    2005-01-01

    that for interchange modes, profile consistency is in fact due to mixing by persistent large-scale convective cells. This mechanism is not a turbulent diffusion, cannot occur in collisionless systems, and is the analog of the well-known laminar "magnetic flux expulsion" in magneiohydrodynamics. This expulsion process...... involves a "pinch" across closed streamlines and further results in the formation of pressure fingers along the-separatrix of the convective cells. By nature, these coherent structures are dissipative because the mixing process that leads to their formation relies on a finite amount of collisional...... diffusion. Numerical simulations of two-dimensional interchange modes confirm the role of laminar expulsion by convective cells, for profile consistency and structure formation. They also show that the fingerlike pressure structures ultimately control the rate of heat transport across the plasma layer...

  13. Admissibility of logical inference rules

    CERN Document Server

    Rybakov, VV

    1997-01-01

    The aim of this book is to present the fundamental theoretical results concerning inference rules in deductive formal systems. Primary attention is focused on: admissible or permissible inference rules the derivability of the admissible inference rules the structural completeness of logics the bases for admissible and valid inference rules. There is particular emphasis on propositional non-standard logics (primary, superintuitionistic and modal logics) but general logical consequence relations and classical first-order theories are also considered. The book is basically self-contained and

  14. Structures and microfabrics of the Franciscan Complex (California): Inferences on the rheology and kinematics of a subduction channel

    Science.gov (United States)

    Krohe, A.; Wassmann, S.; Trepmann, C.; Stoeckhert, B.

    2009-12-01

    The characteristic feature of the Franciscan Subduction Complex (FSC) is a chaotic mélange structure with centimeter- to about one kilometer-sized tectonic blocks composed of metabasalts, floating in a matrix of oceanic meta-sediments or, locally, serpentinites. Investigating map scale structures, microfabrics, and P-T-histories of the FSC, we try to gain information on the mechanical properties of rocks and their influence on the kinematics of material transport in a subduction channel. Structures and microfabrics indicate that metabasalts from the oceanic crust as well as mantle-derived ultramafic rocks (i) underwent fragmentation and sealing under high pore fluid pressure, (ii) remaining internally undeformed, or (iii) deform by dissolution precipitation creep. Importantly, microfabrics which would indicate crystal plastic deformation or dislocation creep are systematically absent. This means that, during the entire P-T history, differential stresses generally remained too low to activate crystal plastic deformation or dislocation creep. Hence the material in the subduction channel is characterized by a low strength, being either limited by brittle failure at high pore fluid pressure, or a Newton viscosity, which is expected for dissolution precipitation creep. We interpret the characteristic mélange structure as to reflect this mechanical state of the system: Brittle failure at quasi-lithostatic fluid pressures down to great depths is recorded in the tectonic blocks by the widespread occurrence of aragonite-bearing veins. This leads to fragmentation into the blocks of variable size and moderate aspect ratios, which behave as rigid inclusions in a flowing matrix with distributed deformation by dissolution precipitation creep. In contrast, a power law rheology characteristic for dislocation creep, would favor strain localization into shear zones at sites of stress concentration. However, such shear zones formed at high-P metamorphic conditions are not

  15. Genetic structuring and recent demographic history of red pandas (Ailurus fulgens) inferred from microsatellite and mitochondrial DNA.

    Science.gov (United States)

    Hu, Yibo; Guo, Yu; Qi, Dunwu; Zhan, Xiangjiang; Wu, Hua; Bruford, Michael W; Wei, Fuwen

    2011-07-01

    Clarification of the genetic structure and population history of a species can shed light on the impacts of landscapes, historical climate change and contemporary human activities and thus enables evidence-based conservation decisions for endangered organisms. The red panda (Ailurus fulgens) is an endangered species distributing at the edge of the Qinghai-Tibetan Plateau and is currently subject to habitat loss, fragmentation and population decline, thus representing a good model to test the influences of the above-mentioned factors on a plateau edge species. We combined nine microsatellite loci and 551 bp of mitochondrial control region (mtDNA CR) to explore the genetic structure and demographic history of this species. A total of 123 individuals were sampled from 23 locations across five populations. High levels of genetic variation were identified for both mtDNA and microsatellites. Phylogeographic analyses indicated little geographic structure, suggesting historically wide gene flow. However, microsatellite-based Bayesian clustering clearly identified three groups (Qionglai-Liangshan, Xiaoxiangling and Gaoligong-Tibet). A significant isolation-by-distance pattern was detected only after removing Xiaoxiangling. For mtDNA data, there was no statistical support for a historical population expansion or contraction for the whole sample or any population except Xiaoxiangling where a signal of contraction was detected. However, Bayesian simulations of population history using microsatellite data did pinpoint population declines for Qionglai, Xiaoxiangling and Gaoligong, demonstrating significant influences of human activity on demography. The unique history of the Xiaoxiangling population plays a critical role in shaping the genetic structure of this species, and large-scale habitat loss and fragmentation is hampering gene flow among populations. The implications of our findings for the biogeography of the Qinghai-Tibetan Plateau, subspecies classification and

  16. SCOWLP update: 3D classification of protein-protein, -peptide, -saccharide and -nucleic acid interactions, and structure-based binding inferences across folds

    Directory of Open Access Journals (Sweden)

    Schreiber Sven

    2011-10-01

    Full Text Available Abstract Background Protein interactions are essential for coordinating cellular functions. Proteomic studies have already elucidated a huge amount of protein-protein interactions that require detailed functional analysis. Understanding the structural basis of each individual interaction through their structural determination is necessary, yet an unfeasible task. Therefore, computational tools able to predict protein binding regions and recognition modes are required to rationalize putative molecular functions for proteins. With this aim, we previously created SCOWLP, a structural classification of protein binding regions at protein family level, based on the information obtained from high-resolution 3D protein-protein and protein-peptide complexes. Description We present here a new version of SCOWLP that has been enhanced by the inclusion of protein-nucleic acid and protein-saccharide interactions. SCOWLP takes interfacial solvent into account for a detailed characterization of protein interactions. In addition, the binding regions obtained per protein family have been enriched by the inclusion of predicted binding regions, which have been inferred from structurally related proteins across all existing folds. These inferences might become very useful to suggest novel recognition regions and compare structurally similar interfaces from different families. Conclusions The updated SCOWLP has new functionalities that allow both, detection and comparison of protein regions recognizing different types of ligands, which include other proteins, peptides, nucleic acids and saccharides, within a solvated environment. Currently, SCOWLP allows the analysis of predicted protein binding regions based on structure-based inferences across fold space. These predictions may have a unique potential in assisting protein docking, in providing insights into protein interaction networks, and in guiding rational engineering of protein ligands. The newly designed

  17. Statistical inference

    CERN Document Server

    Rohatgi, Vijay K

    2003-01-01

    Unified treatment of probability and statistics examines and analyzes the relationship between the two fields, exploring inferential issues. Numerous problems, examples, and diagrams--some with solutions--plus clear-cut, highlighted summaries of results. Advanced undergraduate to graduate level. Contents: 1. Introduction. 2. Probability Model. 3. Probability Distributions. 4. Introduction to Statistical Inference. 5. More on Mathematical Expectation. 6. Some Discrete Models. 7. Some Continuous Models. 8. Functions of Random Variables and Random Vectors. 9. Large-Sample Theory. 10. General Meth

  18. Kinetic Scale Structure of Low-frequency Waves and Fluctuations

    Energy Technology Data Exchange (ETDEWEB)

    López, Rodrigo A.; Yoon, Peter H. [Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742 (United States); Viñas, Adolfo F. [NASA Goddard Space Flight Center, Heliophysics Science Division, Geospace Physics Laboratory, Mail Code 673, Greenbelt, MD 20771 (United States); Araneda, Jaime A., E-mail: rlopezh@umd.edu, E-mail: yoonp@umd.edu [Departamento de Física, Facultad de Ciencias Físicas y Matemáticas, Universidad de Concepción, Concepción (Chile)

    2017-08-10

    The dissipation of solar wind turbulence at kinetic scales is believed to be important for the heating of the corona and for accelerating the wind. The linear Vlasov kinetic theory is a useful tool for identifying various wave modes, including kinetic Alfvén, fast magnetosonic/whistler, and ion-acoustic (or kinetic slow), and their possible roles in the dissipation. However, the kinetic mode structure in the vicinity of ion-cyclotron modes is not clearly understood. The present paper aims to further elucidate the structure of these low-frequency waves by introducing discrete particle effects through hybrid simulations and Klimontovich formalism of spontaneous emission theory. The theory and simulation of spontaneously emitted low-frequency fluctuations are employed to identify and distinguish the detailed mode structures associated with ion-Bernstein modes versus quasi-modes. The spontaneous emission theory and simulation also confirm the findings of the Vlasov theory in that the kinetic Alfvén waves can be defined over a wide range of frequencies, including the proton cyclotron frequency and its harmonics, especially for high-beta plasmas. This implies that these low-frequency modes may play predominant roles even in the fully kinetic description of kinetic scale turbulence and dissipation despite the fact that cyclotron harmonic and Bernstein modes may also play important roles in wave–particle interactions.

  19. Structural colour: Colour mixing in wing scales of a butterfly

    Science.gov (United States)

    Vukusic, P.; Sambles, J. R.; Lawrence, C. R.

    2000-03-01

    Green coloration in the animal kingdom, as seen in birds' feathers and reptile integument, is often an additive mixture of structurally effected blue and pigmentary yellow. Here we investigate the origin of the bright green coloration of the wing scales of the Indonesian male Papilio palinurus butterfly, the microstructure of which generates an extraordinary combination of both yellow and blue iridescence. The dual colour arises from a modulation imposed on the multilayer, producing the blue component as a result of a previously undiscovered retro-reflection process.

  20. Cosmological constraints from large-scale structure growth rate measurements

    Science.gov (United States)

    Pavlov, Anatoly; Farooq, Omer; Ratra, Bharat

    2014-07-01

    We compile a list of 14 independent measurements of a large-scale structure growth rate between redshifts 0.067≤z≤0.8 and use this to place constraints on model parameters of constant and time-evolving general-relativistic dark energy cosmologies. With the assumption that gravity is well modeled by general relativity, we discover that growth-rate data provide restrictive cosmological parameter constraints. In combination with type Ia supernova apparent magnitude versus redshift data and Hubble parameter measurements, the growth rate data are consistent with the standard spatially flat ΛCDM model, as well as with mildly evolving dark energy density cosmological models.

  1. Brittle fracture in structural steels: perspectives at different size-scales.

    Science.gov (United States)

    Knott, John

    2015-03-28

    This paper describes characteristics of transgranular cleavage fracture in structural steel, viewed at different size-scales. Initially, consideration is given to structures and the service duty to which they are exposed at the macroscale, highlighting failure by plastic collapse and failure by brittle fracture. This is followed by sections describing the use of fracture mechanics and materials testing in carrying-out assessments of structural integrity. Attention then focuses on the microscale, explaining how values of the local fracture stress in notched bars or of fracture toughness in pre-cracked test-pieces are related to features of the microstructure: carbide thicknesses in wrought material; the sizes of oxide/silicate inclusions in weld metals. Effects of a microstructure that is 'heterogeneous' at the mesoscale are treated briefly, with respect to the extraction of test-pieces from thick sections and to extrapolations of data to low failure probabilities. The values of local fracture stress may be used to infer a local 'work-of-fracture' that is found experimentally to be a few times greater than that of two free surfaces. Reasons for this are discussed in the conclusion section on nano-scale events. It is suggested that, ahead of a sharp crack, it is necessary to increase the compliance by a cooperative movement of atoms (involving extra work) to allow the crack-tip bond to displace sufficiently for the energy of attraction between the atoms to reduce to zero. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

  2. Linear scaling 3D fragment method for large-scale electronic structure calculations

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Lin-Wang; Wang, Lin-Wang; Lee, Byounghak; Shan, HongZhang; Zhao, Zhengji; Meza, Juan; Strohmaier, Erich; Bailey, David

    2008-07-11

    We present a new linearly scaling three-dimensional fragment (LS3DF) method for large scale ab initio electronic structure calculations. LS3DF is based on a divide-and-conquer approach, which incorporates a novel patching scheme that effectively cancels out the artificial boundary effects due to the subdivision of the system. As a consequence, the LS3DF program yields essentially the same results as direct density functional theory (DFT) calculations. The fragments of the LS3DF algorithm can be calculated separately with different groups of processors. This leads to almost perfect parallelization on tens of thousands of processors. After code optimization, we were able to achieve 35.1 Tflop/s, which is 39% of the theoretical speed on 17,280 Cray XT4 processor cores. Our 13,824-atom ZnTeO alloy calculation runs 400 times faster than a direct DFT calculation, even presuming that the direct DFT calculation can scale well up to 17,280 processor cores. These results demonstrate the applicability of the LS3DF method to material simulations, the advantage of using linearly scaling algorithms over conventional O(N{sup 3}) methods, and the potential for petascale computation using the LS3DF method.

  3. Linearly Scaling 3D Fragment Method for Large-Scale Electronic Structure Calculations

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Lin-Wang; Lee, Byounghak; Shan, Hongzhang; Zhao, Zhengji; Meza, Juan; Strohmaier, Erich; Bailey, David H.

    2008-07-01

    We present a new linearly scaling three-dimensional fragment (LS3DF) method for large scale ab initio electronic structure calculations. LS3DF is based on a divide-and-conquer approach, which incorporates a novel patching scheme that effectively cancels out the artificial boundary effects due to the subdivision of the system. As a consequence, the LS3DF program yields essentially the same results as direct density functional theory (DFT) calculations. The fragments of the LS3DF algorithm can be calculated separately with different groups of processors. This leads to almost perfect parallelization on tens of thousands of processors. After code optimization, we were able to achieve 35.1 Tflop/s, which is 39percent of the theoretical speed on 17,280 Cray XT4 processor cores. Our 13,824-atom ZnTeO alloy calculation runs 400 times faster than a direct DFTcalculation, even presuming that the direct DFT calculation can scale well up to 17,280 processor cores. These results demonstrate the applicability of the LS3DF method to material simulations, the advantage of using linearly scaling algorithms over conventional O(N3) methods, and the potential for petascale computation using the LS3DF method.

  4. Fine-Scale Structure Design for 3D Printing

    Science.gov (United States)

    Panetta, Francis Julian

    Modern additive fabrication technologies can manufacture shapes whose geometric complexities far exceed what existing computational design tools can analyze or optimize. At the same time, falling costs have placed these fabrication technologies within the average consumer's reach. Especially for inexpert designers, new software tools are needed to take full advantage of 3D printing technology. This thesis develops such tools and demonstrates the exciting possibilities enabled by fine-tuning objects at the small scales achievable by 3D printing. The thesis applies two high-level ideas to invent these tools: two-scale design and worst-case analysis. The two-scale design approach addresses the problem that accurately simulating--let alone optimizing--the full-resolution geometry sent to the printer requires orders of magnitude more computational power than currently available. However, we can decompose the design problem into a small-scale problem (designing tileable structures achieving a particular deformation behavior) and a macro-scale problem (deciding where to place these structures in the larger object). This separation is particularly effective, since structures for every useful behavior can be designed once, stored in a database, then reused for many different macroscale problems. Worst-case analysis refers to determining how likely an object is to fracture by studying the worst possible scenario: the forces most efficiently breaking it. This analysis is needed when the designer has insufficient knowledge or experience to predict what forces an object will undergo, or when the design is intended for use in many different scenarios unknown a priori. The thesis begins by summarizing the physics and mathematics necessary to rigorously approach these design and analysis problems. Specifically, the second chapter introduces linear elasticity and periodic homogenization. The third chapter presents a pipeline to design microstructures achieving a wide range of

  5. A large scale analysis of information-theoretic network complexity measures using chemical structures.

    Directory of Open Access Journals (Sweden)

    Matthias Dehmer

    Full Text Available This paper aims to investigate information-theoretic network complexity measures which have already been intensely used in mathematical- and medicinal chemistry including drug design. Numerous such measures have been developed so far but many of them lack a meaningful interpretation, e.g., we want to examine which kind of structural information they detect. Therefore, our main contribution is to shed light on the relatedness between some selected information measures for graphs by performing a large scale analysis using chemical networks. Starting from several sets containing real and synthetic chemical structures represented by graphs, we study the relatedness between a classical (partition-based complexity measure called the topological information content of a graph and some others inferred by a different paradigm leading to partition-independent measures. Moreover, we evaluate the uniqueness of network complexity measures numerically. Generally, a high uniqueness is an important and desirable property when designing novel topological descriptors having the potential to be applied to large chemical databases.

  6. Large-scale structure non-Gaussianities with modal methods

    Science.gov (United States)

    Schmittfull, Marcel

    2016-10-01

    Relying on a separable modal expansion of the bispectrum, the implementation of a fast estimator for the full bispectrum of a 3d particle distribution is presented. The computational cost of accurate bispectrum estimation is negligible relative to simulation evolution, so the bispectrum can be used as a standard diagnostic whenever the power spectrum is evaluated. As an application, the time evolution of gravitational and primordial dark matter bispectra was measured in a large suite of N-body simulations. The bispectrum shape changes characteristically when the cosmic web becomes dominated by filaments and halos, therefore providing a quantitative probe of 3d structure formation. Our measured bispectra are determined by ~ 50 coefficients, which can be used as fitting formulae in the nonlinear regime and for non-Gaussian initial conditions. We also compare the measured bispectra with predictions from the Effective Field Theory of Large Scale Structures (EFTofLSS).

  7. UCLA Loneliness Scale (Version 3): reliability, validity, and factor structure.

    Science.gov (United States)

    Russell, D W

    1996-02-01

    In this article I evaluated the psychometric properties of the UCLA Loneliness Scale (Version 3). Using data from prior studies of college students, nurses, teachers, and the elderly, analyses of the reliability, validity, and factor structure of this new version of the UCLA Loneliness Scale were conducted. Results indicated that the measure was highly reliable, both in terms of internal consistency (coefficient alpha ranging from .89 to .94) and test-retest reliability over a 1-year period (r = .73). Convergent validity for the scale was indicated by significant correlations with other measures of loneliness. Construct validity was supported by significant relations with measures of the adequacy of the individual's interpersonal relationships, and by correlations between loneliness and measures of health and well-being. Confirmatory factor analyses indicated that a model incorporating a global bipolar loneliness factor along with two method factor reflecting direction of item wording provided a very good fit to the data across samples. Implications of these results for future measurement research on loneliness are discussed.

  8. The scaling structure of the global road network.

    Science.gov (United States)

    Strano, Emanuele; Giometto, Andrea; Shai, Saray; Bertuzzo, Enrico; Mucha, Peter J; Rinaldo, Andrea

    2017-10-01

    Because of increasing global urbanization and its immediate consequences, including changes in patterns of food demand, circulation and land use, the next century will witness a major increase in the extent of paved roads built worldwide. To model the effects of this increase, it is crucial to understand whether possible self-organized patterns are inherent in the global road network structure. Here, we use the largest updated database comprising all major roads on the Earth, together with global urban and cropland inventories, to suggest that road length distributions within croplands are indistinguishable from urban ones, once rescaled to account for the difference in mean road length. Such similarity extends to road length distributions within urban or agricultural domains of a given area. We find two distinct regimes for the scaling of the mean road length with the associated area, holding in general at small and at large values of the latter. In suitably large urban and cropland domains, we find that mean and total road lengths increase linearly with their domain area, differently from earlier suggestions. Scaling regimes suggest that simple and universal mechanisms regulate urban and cropland road expansion at the global scale. As such, our findings bear implications for global road infrastructure growth based on land-use change and for planning policies sustaining urban expansions.

  9. Exploring the determinants of phylogenetic diversity and assemblage structure in conifers across temporal, spatial, and taxonomic scales

    DEFF Research Database (Denmark)

    Eiserhardt, Wolf L.; Borchsenius, Finn; Sandel, Brody Steven

    -environmental models are important elements in this framework. Here, we integrate both types of data in order to explore the determinants of forest tree diversity using the conifers as a model group. Conifers are an old, diverse (ca. 650 spp. in 6 families) and widespread group of woody plants of high ecological...... and economic importance. They are better studied than most other globally distributed groups of forest trees, allowing integrative studies with high phylogenetic and spatial resolution. We analyse phylogenetic diversity, assemblage structure, and diversification rates for regional conifer assemblages...... throughout the natural range of the group (269 TDWG3 “botanical countries”) to infer the effects of current and past climate . To explore the effects of taxonomic and spatial scale, we deconstruct the overall pattern into families and perform a fine-scale analysis for one particular lineage (the genus Pinus...

  10. Structural connectivity at a national scale: Wildlife corridors in Tanzania.

    Directory of Open Access Journals (Sweden)

    Jason Riggio

    Full Text Available Wildlife corridors can help maintain landscape connectivity but novel methods must be developed to assess regional structural connectivity quickly and cheaply so as to determine where expensive and time-consuming surveys of functional connectivity should occur. We use least-cost methods, the most accurate and up-to-date land conversion dataset for East Africa, and interview data on wildlife corridors, to develop a single, consistent methodology to systematically assess wildlife corridors at a national scale using Tanzania as a case study. Our research aimed to answer the following questions; (i which corridors may still remain open (i.e. structurally connected at a national scale, (ii which have been potentially severed by anthropogenic land conversion (e.g., agriculture and settlements, (iii where are other remaining potential wildlife corridors located, and (iv which protected areas with lower forms of protection (e.g., Forest Reserves and Wildlife Management Areas may act as stepping-stones linking more than one National Park and/or Game Reserve. We identify a total of 52 structural connections between protected areas that are potentially open to wildlife movement, and in so doing add 23 to those initially identified by other methods in Tanzanian Government reports. We find that the vast majority of corridors noted in earlier reports as "likely to be severed" have actually not been cut structurally (21 of 24. Nonetheless, nearly a sixth of all the wildlife corridors identified in Tanzania in 2009 have potentially been separated by land conversion, and a third now pass across lands likely to be converted to human use in the near future. Our study uncovers two reserves with lower forms of protection (Uvinza Forest Reserve in the west and Wami-Mbiki Wildlife Management Area in the east that act as apparently crucial stepping-stones between National Parks and/or Game Reserves and therefore require far more serious conservation support. Methods

  11. Structural connectivity at a national scale: Wildlife corridors in Tanzania.

    Science.gov (United States)

    Riggio, Jason; Caro, Tim

    2017-01-01

    Wildlife corridors can help maintain landscape connectivity but novel methods must be developed to assess regional structural connectivity quickly and cheaply so as to determine where expensive and time-consuming surveys of functional connectivity should occur. We use least-cost methods, the most accurate and up-to-date land conversion dataset for East Africa, and interview data on wildlife corridors, to develop a single, consistent methodology to systematically assess wildlife corridors at a national scale using Tanzania as a case study. Our research aimed to answer the following questions; (i) which corridors may still remain open (i.e. structurally connected) at a national scale, (ii) which have been potentially severed by anthropogenic land conversion (e.g., agriculture and settlements), (iii) where are other remaining potential wildlife corridors located, and (iv) which protected areas with lower forms of protection (e.g., Forest Reserves and Wildlife Management Areas) may act as stepping-stones linking more than one National Park and/or Game Reserve. We identify a total of 52 structural connections between protected areas that are potentially open to wildlife movement, and in so doing add 23 to those initially identified by other methods in Tanzanian Government reports. We find that the vast majority of corridors noted in earlier reports as "likely to be severed" have actually not been cut structurally (21 of 24). Nonetheless, nearly a sixth of all the wildlife corridors identified in Tanzania in 2009 have potentially been separated by land conversion, and a third now pass across lands likely to be converted to human use in the near future. Our study uncovers two reserves with lower forms of protection (Uvinza Forest Reserve in the west and Wami-Mbiki Wildlife Management Area in the east) that act as apparently crucial stepping-stones between National Parks and/or Game Reserves and therefore require far more serious conservation support. Methods used in this

  12. Scour around Support Structures of Scaled Model Marine Hydrokinetic Devices

    Science.gov (United States)

    Volpe, M. A.; Beninati, M. L.; Krane, M.; Fontaine, A.

    2013-12-01

    Experiments are presented to explore scour due to flows around support structures of marine hydrokinetic (MHK) devices. Three related studies were performed to understand how submergence, scour condition, and the presence of an MHK device impact scour around the support structure (cylinder). The first study focuses on clear-water scour conditions for a cylinder of varying submergence: surface-piercing and fully submerged. The second study centers on three separate scour conditions (clear-water, transitional and live-bed) around the fully submerged cylinder. Lastly, the third study emphasizes the impact of an MHK turbine on scour around the support structure, in live-bed conditions. Small-scale laboratory testing of model devices can be used to help predict the behavior of MHK devices at full-scale. Extensive studies have been performed on single cylinders, modeling bridge piers, though few have focused on fully submerged structures. Many of the devices being used to harness marine hydrokinetic energy are fully submerged in the flow. Additionally, scour hole dimensions and scour rates have not been addressed. Thus, these three studies address the effect of structure blockage/drag, and the ambient scour conditions on scour around the support structure. The experiments were performed in the small-scale testing platform in the hydraulic flume facility (9.8 m long, 1.2 m wide and 0.4 m deep) at Bucknell University. The support structure diameter (D = 2.54 cm) was held constant for all tests. The submerged cylinder (l/D = 5) and sediment size (d50 = 790 microns) were held constant for all three studies. The MHK device (Dturbine = 10.2 cm) is a two-bladed horizontal axis turbine and the rotating shaft is friction-loaded using a metal brush motor. For each study, bed form topology was measured after a three-hour time interval using a traversing two-dimensional bed profiler. During the experiments, scour hole depth measurements at the front face of the support structure

  13. Detecting small scale CO2 emission structures using OCO-2

    Science.gov (United States)

    Schwandner, Florian M.; Eldering, Annmarie; Verhulst, Kristal R.; Miller, Charles E.; Nguyen, Hai M.; Oda, Tomohiro; O'Dell, Christopher; Rao, Preeti; Kahn, Brian; Crisp, David; Gunson, Michael R.; Sanchez, Robert M.; Ashok, Manasa; Pieri, David; Linick, Justin P.; Yuen, Karen

    2016-04-01

    Localized carbon dioxide (CO2) emission structures cover spatial domains of less than 50 km diameter and include cities and transportation networks, as well as fossil fuel production, upgrading and distribution infra-structure. Anthropogenic sources increasingly upset the natural balance between natural carbon sources and sinks. Mitigation of resulting climate change impacts requires management of emissions, and emissions management requires monitoring, reporting and verification. Space-borne measurements provide a unique opportunity to detect, quantify, and analyze small scale and point source emissions on a global scale. NASA's first satellite dedicated to atmospheric CO2 observation, the July 2014 launched Orbiting Carbon Observatory (OCO-2), now leads the afternoon constellation of satellites (A-Train). Its continuous swath of 2 to 10 km in width and eight footprints across can slice through coincident emission plumes and may provide momentary cross sections. First OCO-2 results demonstrate that we can detect localized source signals in the form of urban total column averaged CO2 enhancements of ~2 ppm against suburban and rural backgrounds. OCO-2's multi-sounding swath observing geometry reveals intra-urban spatial structures reflected in XCO2 data, previously unobserved from space. The transition from single-shot GOSAT soundings detecting urban/rural differences (Kort et al., 2012) to hundreds of soundings per OCO-2 swath opens up the path to future capabilities enabling urban tomography of greenhouse gases. For singular point sources like coal fired power plants, we have developed proxy detections of plumes using bands of imaging spectrometers with sensitivity to SO2 in the thermal infrared (ASTER). This approach provides a means to automate plume detection with subsequent matching and mining of OCO-2 data for enhanced detection efficiency and validation. © California Institute of Technology

  14. Nonlinear Analysis and Scaling Laws for Noncircular Composite Structures Subjected to Combined Loads

    Science.gov (United States)

    Hilburger, Mark W.; Rose, Cheryl A.; Starnes, James H., Jr.

    2001-01-01

    Results from an analytical study of the response of a built-up, multi-cell noncircular composite structure subjected to combined internal pressure and mechanical loads are presented. Nondimensional parameters and scaling laws based on a first-order shear-deformation plate theory are derived for this noncircular composite structure. The scaling laws are used to design sub-scale structural models for predicting the structural response of a full-scale structure representative of a portion of a blended-wing-body transport aircraft. Because of the complexity of the full-scale structure, some of the similitude conditions are relaxed for the sub-scale structural models. Results from a systematic parametric study are used to determine the effects of relaxing selected similitude conditions on the sensitivity of the effectiveness of using the sub-scale structural model response characteristics for predicting the full-scale structure response characteristics.

  15. Improving the Factor Structure of Psychological Scales: The Expanded Format as an Alternative to the Likert Scale Format

    Science.gov (United States)

    Zhang, Xijuan; Savalei, Victoria

    2016-01-01

    Many psychological scales written in the Likert format include reverse worded (RW) items in order to control acquiescence bias. However, studies have shown that RW items often contaminate the factor structure of the scale by creating one or more method factors. The present study examines an alternative scale format, called the Expanded format,…

  16. Population structure of Atlantic Mackerel inferred from RAD-seq derived SNP markers: effects of sequence clustering parameters and hierarchical SNP selection

    KAUST Repository

    Rodríguez-Ezpeleta, Naiara

    2016-03-03

    Restriction-site associated DNA sequencing (RAD-seq) and related methods are revolutionizing the field of population genomics in non-model organisms as they allow generating an unprecedented number of single nucleotide polymorphisms (SNPs) even when no genomic information is available. Yet, RAD-seq data analyses rely on assumptions on nature and number of nucleotide variants present in a single locus, the choice of which may lead to an under- or overestimated number of SNPs and/or to incorrectly called genotypes. Using the Atlantic mackerel (Scomber scombrus L.) and a close relative, the Atlantic chub mackerel (Scomber colias), as case study, here we explore the sensitivity of population structure inferences to two crucial aspects in RAD-seq data analysis: the maximum number of mismatches allowed to merge reads into a locus and the relatedness of the individuals used for genotype calling and SNP selection. Our study resolves the population structure of the Atlantic mackerel, but, most importantly, provides insights into the effects of alternative RAD-seq data analysis strategies on population structure inferences that are directly applicable to other species.

  17. Testing Inflation with Large Scale Structure: Connecting Hopes with Reality

    Energy Technology Data Exchange (ETDEWEB)

    Alvarez, Marcello [Univ. of Toronto, ON (Canada); Baldauf, T. [Inst. of Advanced Studies, Princeton, NJ (United States); Bond, J. Richard [Univ. of Toronto, ON (Canada); Canadian Inst. for Advanced Research, Toronto, ON (Canada); Dalal, N. [Univ. of Illinois, Urbana-Champaign, IL (United States); Putter, R. D. [Jet Propulsion Lab., Pasadena, CA (United States); California Inst. of Technology (CalTech), Pasadena, CA (United States); Dore, O. [Jet Propulsion Lab., Pasadena, CA (United States); California Inst. of Technology (CalTech), Pasadena, CA (United States); Green, Daniel [Univ. of Toronto, ON (Canada); Canadian Inst. for Advanced Research, Toronto, ON (Canada); Hirata, Chris [The Ohio State Univ., Columbus, OH (United States); Huang, Zhiqi [Univ. of Toronto, ON (Canada); Huterer, Dragan [Univ. of Michigan, Ann Arbor, MI (United States); Jeong, Donghui [Pennsylvania State Univ., University Park, PA (United States); Johnson, Matthew C. [York Univ., Toronto, ON (Canada); Perimeter Inst., Waterloo, ON (Canada); Krause, Elisabeth [Stanford Univ., CA (United States); Loverde, Marilena [Univ. of Chicago, IL (United States); Meyers, Joel [Univ. of Toronto, ON (Canada); Meeburg, Daniel [Univ. of Toronto, ON (Canada); Senatore, Leonardo [Stanford Univ., CA (United States); Shandera, Sarah [Pennsylvania State Univ., University Park, PA (United States); Silverstein, Eva [Stanford Univ., CA (United States); Slosar, Anze [Brookhaven National Lab. (BNL), Upton, NY (United States); Smith, Kendrick [Perimeter Inst., Waterloo, Toronto, ON (Canada); Zaldarriaga, Matias [Univ. of Toronto, ON (Canada); Assassi, Valentin [Cambridge Univ. (United Kingdom); Braden, Jonathan [Univ. of Toronto, ON (Canada); Hajian, Amir [Univ. of Toronto, ON (Canada); Kobayashi, Takeshi [Perimeter Inst., Waterloo, Toronto, ON (Canada); Univ. of Toronto, ON (Canada); Stein, George [Univ. of Toronto, ON (Canada); Engelen, Alexander van [Univ. of Toronto, ON (Canada)

    2014-12-15

    The statistics of primordial curvature fluctuations are our window into the period of inflation, where these fluctuations were generated. To date, the cosmic microwave background has been the dominant source of information about these perturbations. Large-scale structure is, however, from where drastic improvements should originate. In this paper, we explain the theoretical motivations for pursuing such measurements and the challenges that lie ahead. In particular, we discuss and identify theoretical targets regarding the measurement of primordial non-Gaussianity. We argue that when quantified in terms of the local (equilateral) template amplitude f$loc\\atop{NL}$ (f$eq\\atop{NL}$), natural target levels of sensitivity are Δf$loc, eq\\atop{NL}$ ≃ 1. We highlight that such levels are within reach of future surveys by measuring 2-, 3- and 4-point statistics of the galaxy spatial distribution. This paper summarizes a workshop held at CITA (University of Toronto) on October 23-24, 2014.

  18. Breed locally, disperse globally: fine-scale genetic structure despite landscape-scale panmixia in a fire-specialist.

    Directory of Open Access Journals (Sweden)

    Jennifer C Pierson

    Full Text Available An exciting advance in the understanding of metapopulation dynamics has been the investigation of how populations respond to ephemeral patches that go 'extinct' during the lifetime of an individual. Previous research has shown that this scenario leads to genetic homogenization across large spatial scales. However, little is known about fine-scale genetic structuring or how this changes over time in ephemeral patches. We predicted that species that specialize on ephemeral habitats will delay dispersal to exploit natal habitat patches while resources are plentiful and thus display fine-scale structure. To investigate this idea, we evaluated the effect of frequent colonization of ephemeral habitats on the fine-scale genetic structure of a fire specialist, the black-backed woodpecker (Picoides arcticus and found a pattern of fine-scale genetic structure. We then tested for differences in spatial structure between sexes and detected a pattern consistent with male-biased dispersal. We also detected a temporal increase in relatedness among individuals within newly burned forest patches. Our results indicate that specialist species that outlive their ephemeral patches can accrue significant fine-scale spatial structure that does not necessarily affect spatial structure at larger scales. This highlights the importance of both spatial and temporal scale considerations in both sampling and data interpretation of molecular genetic results.

  19. Detection of Coherent Structures in Extreme-Scale Simulations

    Energy Technology Data Exchange (ETDEWEB)

    Kamath, C; Iverson, J; Kirk, R; Karypis, G

    2012-03-24

    The analysis of coherent structures is a common problem in many scientific domains ranging from astrophysics to combustion, fusion, and materials science. The data from three-dimensional simulations are analyzed to detect the structures, extract statistics on them, and track them over time to gain insights into the phenomenon being modeled. This analysis is typically done off-line, using data that have been written out by the simulations. However, the move towards extreme scale architectures, with multi-core processors and graphical processing units, will affect how such analysis is done as it is unlikely that the systems will support the I/O bandwidth required for off-line analysis. Moving the analysis in-situ is a solution only if we know a priori what analysis will be done, as well as the algorithms used and their parameter settings. Even then, we need to ensure that this will not substantially increase the memory requirements or the data movement as the former will be limited and the latter will be expensive. In the Exa-DM project, a collaboration between Lawrence Livermore National Laboratory and University of Minnesota, we are exploring ways in which we can address the conflicting demands of coherent structure analysis of simulation data and the architecture of modern parallel systems, while enabling scientific discovery at the exascale. In this paper, we describe our work in two areas: the in situ implementation of an existing algorithm for coherent structure analysis and the use of graph-based techniques to efficiently compress the data.

  20. Iron phosphate glasses: Bulk properties and atomic scale structure

    Energy Technology Data Exchange (ETDEWEB)

    Joseph, Kitheri; Stennett, Martin C.; Hyatt, Neil C.; Asuvathraman, R.; Dube, Charu L.; Gandy, Amy S.; Govindan Kutty, K. V.; Jolley, Kenny; Vasudeva Rao, P. R.; Smith, Roger

    2017-10-01

    Bulk properties such as glass transition temperature, density and thermal expansion of iron phosphate glass compositions, with replacement of Cs by Ba, are investigated as a surrogate for the transmutation of 137Cs to 137Ba, relevant to the immobilisation of Cs in glass. These studies are required to establish the appropriate incorporation rate of 137Cs in iron phosphate glass. Density and glass transition temperature increases with the addition of BaO indicating the shrinkage and reticulation of the iron phosphate glass network. The average thermal expansion coefficient reduces from 19.8 × 10-6 K-1 to 13.4 × 10-6 K-1, when 25 wt. % of Cs2O was replaced by 25 wt. % of BaO in caesium loaded iron phosphate glass. In addition to the above bulk properties, the role of Ba as a network modifier in the structure of iron phosphate glass is examined using various spectroscopic techniques. The FeII content and average coordination number of iron in the glass network was estimated using Mössbauer spectroscopy. The FeII content in the un-doped iron phosphate glass and barium doped iron phosphate glasses was 20, 21 and 22 ± 1% respectively and the average Fe coordination varied from 5.3 ± 0.2 to 5.7 ± 0.2 with increasing Ba content. The atomic scale structure was further probed by Fe K-edge X-ray absorption spectroscopy. The average coordination number provided by extended X-ray absorption fine structure spectroscopy and X-ray absorption near edge structure was in good agreement with that given by the Mössbauer data.

  1. Inflationary tensor fossils in large-scale structure

    Energy Technology Data Exchange (ETDEWEB)

    Dimastrogiovanni, Emanuela [School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455 (United States); Fasiello, Matteo [Department of Physics, Case Western Reserve University, Cleveland, OH 44106 (United States); Jeong, Donghui [Department of Astronomy and Astrophysics, The Pennsylvania State University, University Park, PA 16802 (United States); Kamionkowski, Marc, E-mail: ema@physics.umn.edu, E-mail: mrf65@case.edu, E-mail: duj13@psu.edu, E-mail: kamion@jhu.edu [Department of Physics and Astronomy, 3400 N. Charles St., Johns Hopkins University, Baltimore, MD 21218 (United States)

    2014-12-01

    Inflation models make specific predictions for a tensor-scalar-scalar three-point correlation, or bispectrum, between one gravitational-wave (tensor) mode and two density-perturbation (scalar) modes. This tensor-scalar-scalar correlation leads to a local power quadrupole, an apparent departure from statistical isotropy in our Universe, as well as characteristic four-point correlations in the current mass distribution in the Universe. So far, the predictions for these observables have been worked out only for single-clock models in which certain consistency conditions between the tensor-scalar-scalar correlation and tensor and scalar power spectra are satisfied. Here we review the requirements on inflation models for these consistency conditions to be satisfied. We then consider several examples of inflation models, such as non-attractor and solid-inflation models, in which these conditions are put to the test. In solid inflation the simplest consistency conditions are already violated whilst in the non-attractor model we find that, contrary to the standard scenario, the tensor-scalar-scalar correlator probes directly relevant model-dependent information. We work out the predictions for observables in these models. For non-attractor inflation we find an apparent local quadrupolar departure from statistical isotropy in large-scale structure but that this power quadrupole decreases very rapidly at smaller scales. The consistency of the CMB quadrupole with statistical isotropy then constrains the distance scale that corresponds to the transition from the non-attractor to attractor phase of inflation to be larger than the currently observable horizon. Solid inflation predicts clustering fossils signatures in the current galaxy distribution that may be large enough to be detectable with forthcoming, and possibly even current, galaxy surveys.

  2. Deep structure beneath Lake Ontario: Crustal-scale Grenville subdivisions

    Science.gov (United States)

    Forsyth, D. A.; Milkereit, B.; Zelt, Colin A.; White, D. J.; Easton, R. M.; Hutchinson, Deborah R.

    1994-01-01

    Lake Ontario marine seismic data reveal major Grenville crustal subdivisions beneath central and southern Lake Ontario separated by interpreted shear zones that extend to the lower crust. A shear zone bounded transition between the Elzevir and Frontenac terranes exposed north of Lake Ontario is linked to a seismically defined shear zone beneath central Lake Ontario by prominent aeromagnetic and gravity anomalies, easterly dipping wide-angle reflections, and fractures in Paleozoic strata. We suggest the central Lake Ontario zone represents crustal-scale deformation along an Elzevir–Frontenac boundary zone that extends from outcrop to the south shore of Lake Ontario.Seismic images from Lake Ontario and the exposed western Central Metasedimentary Belt are dominated by crustal-scale shear zones and reflection geometries featuring arcuate reflections truncated at their bases by apparent east-dipping linear reflections. The images show that zones analogous to the interpreted Grenville Front Tectonic Zone are also present within the Central Metasedimentary Belt and support models of northwest-directed crustal shortening for Grenvillian deep crustal deformation beneath most of southeastern Ontario.A Precambrian basement high, the Iroquoian high, is defined by a thinning of generally horizontal Paleozoic strata over a crestal area above the basement shear zone beneath central Lake Ontario. The Iroquoian high helps explain the peninsular extension into Lake Ontario forming Prince Edward County, the occurrence of Precambrian inlier outcrops in Prince Edward County, and Paleozoic fractures forming the Clarendon–Linden structure in New York.

  3. Validity and factor structure of the bodybuilding dependence scale

    Science.gov (United States)

    Smith, D; Hale, B

    2004-01-01

    Objectives: To investigate the factor structure, validity, and reliability of the bodybuilding dependence scale and to investigate differences in bodybuilding dependence between men and women and competitive and non-competitive bodybuilders. Methods: Seventy two male competitive bodybuilders, 63 female competitive bodybuilders, 87 male non-competitive bodybuilders, and 63 non-competitive female bodybuilders completed the bodybuilding dependence scale (BDS), the exercise dependence questionnaire (EDQ), and the muscle dysmorphia inventory (MDI). Results: Confirmatory factor analysis of the BDS supported a three factor model of bodybuilding dependence, consisting of social dependence, training dependence, and mastery dependence (Q = 3.16, CFI = 0.98, SRMR = 0.04). Internal reliability of all three subscales was high (Cronbach's α = 0.92, 0.92, and 0.93 respectively). Significant (p0.05). Conclusion: The three factor BDS appears to be a reliable and valid measure of bodybuilding dependence. Symptoms of bodybuilding dependence are more prevalent in competitive bodybuilders than non-competitive ones, but there are no significant sex differences in bodybuilding dependence. PMID:15039255

  4. Validity and factor structure of the bodybuilding dependence scale.

    Science.gov (United States)

    Smith, D; Hale, B

    2004-04-01

    To investigate the factor structure, validity, and reliability of the bodybuilding dependence scale and to investigate differences in bodybuilding dependence between men and women and competitive and non-competitive bodybuilders. Seventy two male competitive bodybuilders, 63 female competitive bodybuilders, 87 male non-competitive bodybuilders, and 63 non-competitive female bodybuilders completed the bodybuilding dependence scale (BDS), the exercise dependence questionnaire (EDQ), and the muscle dysmorphia inventory (MDI). Confirmatory factor analysis of the BDS supported a three factor model of bodybuilding dependence, consisting of social dependence, training dependence, and mastery dependence (Q = 3.16, CFI = 0.98, SRMR = 0.04). Internal reliability of all three subscales was high (Cronbach's alpha = 0.92, 0.92, and 0.93 respectively). Significant (pbodybuilders scored significantly (pbodybuilders. However, there were no significant sex differences on any of the BDS subscales (p>0.05). The three factor BDS appears to be a reliable and valid measure of bodybuilding dependence. Symptoms of bodybuilding dependence are more prevalent in competitive bodybuilders than non-competitive ones, but there are no significant sex differences in bodybuilding dependence.

  5. Towards a true vario-scale structure supporting smooth-zoom

    NARCIS (Netherlands)

    Van Oosterom, P.J.M.; Meijers, B.M.

    2011-01-01

    This paper presents the first true vario-scale structure for geographic information: a delta in scale leads to a delta in the map (and smaller scale deltas lead to smaller map deltas until and including the infinitesimal small delta) for all scales. The structure is called smooth tGAP and its

  6. Forearc structure in the Lesser Antilles inferred from depth to the Curie temperature and thermo-mechanical simulations

    Science.gov (United States)

    Gailler, Lydie; Arcay, Diane; Münch, Philippe; Martelet, Guillaume; Thinon, Isabelle; Lebrun, Jean-Frédéric

    2017-06-01

    Imaging deep active volcanic areas remains a challenge in our understanding of their activity and evolution, especially in subduction zones. Study of magnetic anomalies is appropriate to access such dynamics in depth. The magnetic anomaly pattern of the Lesser Antilles Arc (LAA) subduction is studied through Curie Point Depth (CPD), interpreted as the depth of the 580 °C isotherm, and developed to better assess the deep thermal structure of the arc. The depth of the estimated CPD exhibits a complex topography. Keeping in mind the overall uncertainty associated with this method, a main doming is evidenced below the Guadeloupe archipelago. Its apex is shifted towards the ancient arc, suggesting a very hot state of the fore-arc/arc domain. To better understand the LAA thermal state, we perform 2D thermo-mechanical simulations of the subduction zone. Recalling that magnetite is a serpentinization by-product, we simulate water transfer triggered by slab dehydration to test the assumption of fore-arc serpentinization suggested by the positive magnetic anomaly in the vicinity of the Guadeloupe archipelago. In this area, the subduction-induced arc lithosphere hydration and related weakening trigger a fast heating of the upper plate by basal convective removal. This process of fast arc lithosphere thinning may apply where simultaneously the volcanic arc is split in two and normal convergence is high enough. As serpentinization strongly decreases P-wave velocity, we propose a new interpretation of a published seismic profile below Guadeloupe. The seismic layer previously interpreted as the arc lower crust may rather be a layer of serpentinized mantle, as supported by spatial correlations between gravimetric and magnetic anomalies. Consequently, at the scale of Guadeloupe Island, the fore-arc Moho would be shallower than initially assumed, with a dome shape more consistent with both the extensive deformation active since the Oligocene in the inner fore-arc and the CPD doming.

  7. 2D dual permeability modeling of flow and transport in a two-scale structured lignitic mine soil

    Science.gov (United States)

    Dusek, J.; Gerke, H. H.; Vogel, T.; Maurer, T.; Buczko, U.

    2009-04-01

    Two-dimensional single- and dual-permeability simulations are used to analyze water and solute fluxes in heterogeneous lignitic mine soil at a forest-reclaimed mine spoil heap. The soil heterogeneity on this experimental site "Bärenbrücker Höhe" resulted from inclined dumping structures and sediment mixtures that consist of sand with lignitic dust and embedded lignitic fragments. Observations on undisturbed field suction-cell lysimeters including tracer experiments revealed funneling-type preferential flow with lateral water and bromide movement along inclined sediment structures. The spatial distribution of soil structures and fragment distributions was acquired by a digital camera and identified by a supervised classification of the digital profile image. First, a classical single-domain modeling approach was used, with spatially variable scaling factors inferred from image analyses. In the next step, a two-continuum scenario was constructed to examine additional effects of nonequilibrium on the flow regime. The scaling factors used for the preferential flow domain are here obtained from the gradient of the grayscale images. So far, the single domain scenarios failed to predict the bromide leaching patterns although water effluent could be described. Dual-permeability model allows the incorporation of structural effects and can be used as a tool to further testing other approaches that account for structure effects. The numerical study suggests that additional experiments are required to obtain better understanding of the highly complex transport processes on this experimental site.

  8. Using Artificial Intelligence to Retrieve the Optimal Parameters and Structures of Adaptive Network-Based Fuzzy Inference System for Typhoon Precipitation Forecast Modeling

    Directory of Open Access Journals (Sweden)

    Chien-Lin Huang

    2015-01-01

    Full Text Available This study aims to construct a typhoon precipitation forecast model providing forecasts one to six hours in advance using optimal model parameters and structures retrieved from a combination of the adaptive network-based fuzzy inference system (ANFIS and artificial intelligence. To enhance the accuracy of the precipitation forecast, two structures were then used to establish the precipitation forecast model for a specific lead-time: a single-model structure and a dual-model hybrid structure where the forecast models of higher and lower precipitation were integrated. In order to rapidly, automatically, and accurately retrieve the optimal parameters and structures of the ANFIS-based precipitation forecast model, a tabu search was applied to identify the adjacent radius in subtractive clustering when constructing the ANFIS structure. The coupled structure was also employed to establish a precipitation forecast model across short and long lead-times in order to improve the accuracy of long-term precipitation forecasts. The study area is the Shimen Reservoir, and the analyzed period is from 2001 to 2009. Results showed that the optimal initial ANFIS parameters selected by the tabu search, combined with the dual-model hybrid method and the coupled structure, provided the favors in computation efficiency and high-reliability predictions in typhoon precipitation forecasts regarding short to long lead-time forecasting horizons.

  9. Small-Scale Fabrication of Biomimetic Structures for Periodontal Regeneration

    Directory of Open Access Journals (Sweden)

    David William Green

    2016-02-01

    Full Text Available The periodontium is the supporting tissues for the tooth organ and is vulnerable to destruction, arising from overpopulating pathogenic bacteria and spirochaetes. The presence of microbes together with host responses can destroy large parts of the periodontium sometimes leading tooth loss. Permanent tissue replacements are made possible with tissue engineering techniques. However, existing periodontal biomaterials cannot promote proper tissue architectures, necessary tissue volumes within the periodontal pocket and a water-tight barrier, to become clinically acceptable. New kinds of small-scale engineered biomaterials, with increasing biological complexity are needed to guide proper biomimetic regeneration of periodontal tissues. So the ability to make compound structures with small modules, filled with tissue components, is a promising design strategy for simulating the anatomical complexity of the periodotium attachement complexes along the tooth root and the abutment with the tooth collar. Anatomical structures such as, intima, adventitia and special compartments such as the epithelial cell rests of Malassez or a stellate reticulum niche need to be engineered from the start of regeneration to produce proper periodontium replacement.. It is our contention that the positioning of tissue components at the origin is also necessary to promote self-organising cell-cell connections, cell-matrix connections. This leads to accelerated, synchronized and well-formed tissue architectures and anatomies. This strategy is a highly effective preparation for tackling periodontitis, periodontium tissue resorption and to ultimately prevent tooth loss. Furthermore, such biomimetic tissue replacements will tackle problems associated with dental implant support and perimimplantitis.

  10. Small-Scale Fabrication of Biomimetic Structures for Periodontal Regeneration

    Science.gov (United States)

    Green, David W.; Lee, Jung-Seok; Jung, Han-Sung

    2016-01-01

    The periodontium is the supporting tissues for the tooth organ and is vulnerable to destruction, arising from overpopulating pathogenic bacteria and spirochaetes. The presence of microbes together with host responses can destroy large parts of the periodontium sometimes leading tooth loss. Permanent tissue replacements are made possible with tissue engineering techniques. However, existing periodontal biomaterials cannot promote proper tissue architectures, necessary tissue volumes within the periodontal pocket and a “water-tight” barrier, to become clinically acceptable. New kinds of small-scale engineered biomaterials, with increasing biological complexity are needed to guide proper biomimetic regeneration of periodontal tissues. So the ability to make compound structures with small modules, filled with tissue components, is a promising design strategy for simulating the anatomical complexity of the periodotium attachment complexes along the tooth root and the abutment with the tooth collar. Anatomical structures such as, intima, adventitia, and special compartments such as the epithelial cell rests of Malassez or a stellate reticulum niche need to be engineered from the start of regeneration to produce proper periodontium replacement. It is our contention that the positioning of tissue components at the origin is also necessary to promote self-organizing cell–cell connections, cell–matrix connections. This leads to accelerated, synchronized and well-formed tissue architectures and anatomies. This strategy is a highly effective preparation for tackling periodontitis, periodontium tissue resorption, and to ultimately prevent tooth loss. Furthermore, such biomimetic tissue replacements will tackle problems associated with dental implant support and perimimplantitis. PMID:26903872

  11. Large scale structures in liquid crystal/clay colloids

    Science.gov (United States)

    van Duijneveldt, Jeroen S.; Klein, Susanne; Leach, Edward; Pizzey, Claire; Richardson, Robert M.

    2005-04-01

    Suspensions of three different clays in K15, a thermotropic liquid crystal, have been studied by optical microscopy and small angle x-ray scattering. The three clays were claytone AF, a surface treated natural montmorillonite, laponite RD, a synthetic hectorite, and mined sepiolite. The claytone and laponite were sterically stabilized whereas sepiolite formed a relatively stable suspension in K15 without any surface treatment. Micrographs of the different suspensions revealed that all three suspensions contained large scale structures. The nature of these aggregates was investigated using small angle x-ray scattering. For the clays with sheet-like particles, claytone and laponite, the flocs contain a mixture of stacked and single platelets. The basal spacing in the stacks was independent of particle concentration in the suspension and the phase of the solvent. The number of platelets in the stack and their percentage in the suspension varied with concentration and the aspect ratio of the platelets. The lath shaped sepiolite did not show any tendency to organize into ordered structures. Here the aggregates are networks of randomly oriented single rods.

  12. Scale-adaptive surface modeling of vascular structures

    Directory of Open Access Journals (Sweden)

    Ma Xin

    2010-11-01

    Full Text Available Abstract Background The effective geometric modeling of vascular structures is crucial for diagnosis, therapy planning and medical education. These applications require good balance with respect to surface smoothness, surface accuracy, triangle quality and surface size. Methods Our method first extracts the vascular boundary voxels from the segmentation result, and utilizes these voxels to build a three-dimensional (3D point cloud whose normal vectors are estimated via covariance analysis. Then a 3D implicit indicator function is computed from the oriented 3D point cloud by solving a Poisson equation. Finally the vessel surface is generated by a proposed adaptive polygonization algorithm for explicit 3D visualization. Results Experiments carried out on several typical vascular structures demonstrate that the presented method yields both a smooth morphologically correct and a topologically preserved two-manifold surface, which is scale-adaptive to the local curvature of the surface. Furthermore, the presented method produces fewer and better-shaped triangles with satisfactory surface quality and accuracy. Conclusions Compared to other state-of-the-art approaches, our method reaches good balance in terms of smoothness, accuracy, triangle quality and surface size. The vessel surfaces produced by our method are suitable for applications such as computational fluid dynamics simulations and real-time virtual interventional surgery.

  13. Temporal-spatial structure of magnetic merging at the magnetopause inferred from 557.7-nm all-sky images

    Directory of Open Access Journals (Sweden)

    N. C. Maynard

    2004-09-01

    Full Text Available We demonstrate that high-resolution 557.7-nm all-sky images are useful tools for investigating the spatial and temporal evolution of merging on the dayside magnetopause. Analysis of ground and satellite measurements leads us to conclude that high-latitude merging events can occur at multiple sites simultaneously and vary asynchronously on time scales of 30s to 3min. Variations of 557.7nm emissions were observed at a 10s cadence at Ny-Ålesund on 19 December 2001, while significant changes in the IMF clock angle were reaching the magnetopause. The optical patterns are consistent with a scenario in which merging occurs around the rim of the high-latitude cusp at positions dictated by the IMF clock angle. Electrons energized at merging sites represent plausible sources for 557.7nm emissions in the cusp. Polar observations at the magnetopause have directly linked enhanced fluxes of ≥0.5keV electrons with merging. Spectra of electrons responsible for some of the emissions, measured during a DMSP F15 overflight, exhibit "inverted-V" features, indicating further acceleration above the ionosphere. SuperDARN spectral width boundaries, characteristic of open-closed field line transitions, are located at the equatorward edge of the 557.7nm emissions. Optical data suggest that with IMF BY>0, the Northern Hemisphere cusp divides into three source regions. When the IMF clock angle was ~150° structured 557.7-nm emissions came from east of the 13:00 MLT meridian. At larger clock angles the emissions appeared between 12:00 and 13:00 MLT. No significant 557.7-nm emissions were detected in the prenoon MLT sector. MHD simulations corroborate our scenario, showing that with the observed large dipole-tilt and IMF clock angles, merging sites develop near the front and eastern portions of the high-altitude cusp rim in the Northern Hemisphere and near the western part of the cusp rim in the Southern Hemisphere.

  14. Cosmological parameters from large scale structure - geometric versus shape information

    Energy Technology Data Exchange (ETDEWEB)

    Hamann, Jan; Hannestad, Steen [Department of Physics and Astronomy, University of Aarhus, DK-8000 Århus C (Denmark); Lesgourgues, Julien [CERN, Theory Division, CH-1211 Geneva 23 (Switzerland); Rampf, Cornelius; Wong, Yvonne Y.Y., E-mail: hamann@phys.au.dk, E-mail: sth@phys.au.dk, E-mail: julien.lesgourgues@cern.ch, E-mail: rampf@physik.rwth-aachen.de, E-mail: ywong@physik.rwth-aachen.de [Institut für Theoretische Teilchenphysik und Kosmologie, RWTH Aachen, D-52056 Aachen (Germany)

    2010-07-01

    The matter power spectrum as derived from large scale structure (LSS) surveys contains two important and distinct pieces of information: an overall smooth shape and the imprint of baryon acoustic oscillations (BAO). We investigate the separate impact of these two types of information on cosmological parameter estimation for current data, and show that for the simplest cosmological models, the broad-band shape information currently contained in the SDSS DR7 halo power spectrum (HPS) is by far superseded by geometric information derived from the baryonic features. An immediate corollary is that contrary to popular beliefs, the upper limit on the neutrino mass m{sub ν} presently derived from LSS combined with cosmic microwave background (CMB) data does not in fact arise from the possible small-scale power suppression due to neutrino free-streaming, if we limit the model framework to minimal ΛCDM+m{sub ν}. However, in more complicated models, such as those extended with extra light degrees of freedom and a dark energy equation of state parameter w differing from -1, shape information becomes crucial for the resolution of parameter degeneracies. This conclusion will remain true even when data from the Planck spacecraft are combined with SDSS DR7 data. In the course of our analysis, we update both the BAO likelihood function by including an exact numerical calculation of the time of decoupling, as well as the HPS likelihood, by introducing a new dewiggling procedure that generalises the previous approach to models with an arbitrary sound horizon at decoupling. These changes allow a consistent application of the BAO and HPS data sets to a much wider class of models, including the ones considered in this work. All the cases considered here are compatible with the conservative 95%-bounds Σm{sub ν} < 1.16eV, N{sub eff} = 4.8±2.0.

  15. The structure of tubulin-binding cofactor A from Leishmania major infers a mode of association during the early stages of microtubule assembly

    Energy Technology Data Exchange (ETDEWEB)

    Barrack, Keri L.; Fyfe, Paul K.; Hunter, William N., E-mail: w.n.hunter@dundee.ac.uk [University of Dundee, Dow Street, Dundee DD1 5EH, Scotland (United Kingdom)

    2015-04-21

    The structure of a tubulin-binding cofactor from L. major is reported and compared with yeast, plant and human orthologues. Tubulin-binding cofactor A (TBCA) participates in microtubule formation, a key process in eukaryotic biology to create the cytoskeleton. There is little information on how TBCA might interact with β-tubulin en route to microtubule biogenesis. To address this, the protozoan Leishmania major was targeted as a model system. The crystal structure of TBCA and comparisons with three orthologous proteins are presented. The presence of conserved features infers that electrostatic interactions that are likely to involve the C-terminal tail of β-tubulin are key to association. This study provides a reagent and template to support further work in this area.

  16. Optimization methods for logical inference

    CERN Document Server

    Chandru, Vijay

    2011-01-01

    Merging logic and mathematics in deductive inference-an innovative, cutting-edge approach. Optimization methods for logical inference? Absolutely, say Vijay Chandru and John Hooker, two major contributors to this rapidly expanding field. And even though ""solving logical inference problems with optimization methods may seem a bit like eating sauerkraut with chopsticks. . . it is the mathematical structure of a problem that determines whether an optimization model can help solve it, not the context in which the problem occurs."" Presenting powerful, proven optimization techniques for logic in

  17. Structural characterization of genomes by large scale sequence-structure threading

    Directory of Open Access Journals (Sweden)

    Cherkasov Artem

    2004-04-01

    Full Text Available Abstract Background Using sequence-structure threading we have conducted structural characterization of complete proteomes of 37 archaeal, bacterial and eukaryotic organisms (including worm, fly, mouse and human totaling 167,888 genes. Results The reported data represent first rather general evaluation of performance of full sequence-structure threading on multiple genomes providing opportunity to evaluate its general applicability for large scale studies. According to the estimated results the sequence-structure threading has assigned protein folds to more then 60% of eukaryotic, 68% of archaeal and 70% of bacterial proteomes. The repertoires of protein classes, architectures, topologies and homologous superfamilies (according to the CATH 2.4 classification have been established for distant organisms and superkingdoms. It has been found that the average abundance of CATH classes decreases from "alpha and beta" to "mainly beta", followed by "mainly alpha" and "few secondary structures". 3-Layer (aba Sandwich has been characterized as the most abundant protein architecture and Rossman fold as the most common topology. Conclusion The analysis of genomic occurrences of CATH 2.4 protein homologous superfamilies and topologies has revealed the power-law character of their distributions. The corresponding double logarithmic "frequency – genomic occurrence" dependences characteristic of scale-free systems have been established for individual organisms and for three superkingdoms. Supplementary materials to this works are available at 1.

  18. Perfluoroalkyl Acids Shift Microbial Community Structure Across Experimental Scales

    Science.gov (United States)

    Weathers, T. S.; Sharp, J.

    2016-12-01

    Perfluoroalkyl acids (PFAAs) are contaminants of emerging concern that have increasingly been found in groundwater and drinking water systems. Previously, we demonstrated that PFAAs significantly alter the abundance of specific microbial clades in batch reductive dechlorinating systems, resulting in decreased chlorinated solvent attenuation capabilities. To further understand the impacts of PFAA exposure on subsurface microbial processes and PFAA transport, we investigated changes in microbial community structure as a function of PFAA presence in flow-through columns simulating aquifer transport. Phylogenetic analysis using high throughput, next generation sequencing performed after exposure to 250 pore volumes of source zone concentrations of PFAAs (10 mg/L each of 11 analytes including PFOS and PFOA) resulted in patterns that mirrored those observed in batch systems, demonstrating a conservation of community dynamics across experimental scales. Of the nine clades observed in both batch and flow-through systems, six were similarly impacted as a function of PFAA exposure, regardless of the experimental differences in transport and redox state. Specifically, the presence of PFAAs enhanced the relative abundance of Archaea, Bacteroidetes (phylum), and the family Veillonellaceae in both systems. Repressed clades include the genus Sedimentibacter, Ruminococcaceae (family), and the Anaerolineales, which contains Dehalococcoides, a genus known for its ability to fully dechlorinate TCE. As PFAAs are often co-located with TCE and BTEX, changes in microbial community structure can result in hindered bioremediation of these co-contaminants. Consideration of community shifts and corresponding changes in behavior, such as repressed reductive dechlorination or increased biofilm formation, will aid in the development of conceptual site models that account for co-contaminant bioremediation potential and PFAA transport.

  19. Factor Structure of the Conflict Tactics Scale 1

    Directory of Open Access Journals (Sweden)

    Kaori Baba

    2017-07-01

    Full Text Available Background: The Conflict Tactics Scale 1 (CTS1 is a widely used self-report measure of abusive attitudes of parents towards children. The factor structure of the CTS1 still remains to be clarified. The aim of this study was to examine the factor structure of the Japanese version of the CTS1 for postpartum women in community settings. Method: The data in this study came from the Okayama and Kumamoto’s study. These were part of a larger survey using longitudinal questionnaire studies conducted in Japan from 2001 to 2002 and in 2011, respectively. In both study sites, the participant mothers were asked to fill in the CTS1 one month after delivery when they attended for check-up at the out-patient clinic. Results: A total of 1,150 questionnaires were collected, excluding the participants with missing values in the CTS1. Finally, 1,078 were included in the statistical analyses. Data of 1,078 women were divided into two parts. In the first halved sample (n=578, an exploratory factor analysis was conducted for the CTS1 items after exluding nine items with extremely low prevalence. It revealed 2-factor or 3-factor models. Then, we conducted a model comparison with the second halved sample (n=500, using confirmatory factor analysis. In terms of goodness-of-fit indeces, the 2-factor model was superior. Its subscales were Reasoning and Psycholosical Aggression. Conclusion: The 2-factor model of the CTS1 consisting of Reasoning and Psychological Aggression was superior to the 3-factor model. This is not inconsistent with the original authors’ theoretical model.

  20. [Aging and spirituality: Factorial structure and reliability of 2 scales].

    Science.gov (United States)

    Galiana, Laura; Sancho, Patricia; Oliver, Amparo; Tomás, José Manuel; Calatayud, Pablo

    2016-01-01

    In the field of gerontology, the study of the improvement of health and quality of life, and «successfully aging», spirituality plays a key role and, is one of the current research approaches. However, its incorporation into scientific literature is arduous and slow, a fact that is in part due to the absence of developed and validated measurement tools, particularly, in the Spanish speaking area. This work aims to present evidence of the psychometric properties of two tools for the measurement of spirituality: the Functional Assessment of Chronic Illness Therapy Spiritual Well-Being (FACIT-Sp) and the GES Questionnaire. A sample of 224 elderly persons from Valencia (Spain) was recruited, on which two confirmatory factor analyses were estimated, with the proposed a priori structures for each tool, together with several reliability coefficients. Both models presented an good fit to the data: χ(2)51=104.97 (P.05); CFI=.996; RMSEA=.050 for the GES Questionnaire. Reliability indices also supported the use of the scales in elderly population, with alphas of .85 and .86, respectively. These results may be useful as a starting point to include spirituality in works that aim to discover the mechanisms involved in successful aging. Copyright © 2016 SEGG. Publicado por Elsevier España, S.L.U. All rights reserved.

  1. Large-Scale Structure of the Carina Nebula.

    Science.gov (United States)

    Smith; Egan; Carey; Price; Morse; Price

    2000-04-01

    Observations obtained with the Midcourse Space Experiment (MSX) satellite reveal for the first time the complex mid-infrared morphology of the entire Carina Nebula (NGC 3372). On the largest size scale of approximately 100 pc, the thermal infrared emission from the giant H ii region delineates one coherent structure: a (somewhat distorted) bipolar nebula with the major axis perpendicular to the Galactic plane. The Carina Nebula is usually described as an evolved H ii region that is no longer actively forming stars, clearing away the last vestiges of its natal molecular cloud. However, the MSX observations presented here reveal numerous embedded infrared sources that are good candidates for sites of current star formation. Several compact infrared sources are located at the heads of dust pillars or in dark globules behind ionization fronts. Because their morphology suggests a strong interaction with the peculiar collection of massive stars in the nebula, we speculate that these new infrared sources may be sites of triggered star formation in NGC 3372.

  2. Far field scattering pattern of differently structured butterfly scales

    NARCIS (Netherlands)

    Giraldo, M. A.; Yoshioka, S.; Stavenga, D. G.

    The angular and spectral reflectance of single scales of five different butterfly species was measured and related to the scale anatomy. The scales of the pierids Pieris rapae and Delias nigrina scatter white light randomly, in close agreement with Lambert's cosine law, which can be well understood

  3. Visualization of small scale structures on high resolution DEMs

    Science.gov (United States)

    Kokalj, Žiga; Zakšek, Klemen; Pehani, Peter; Čotar, Klemen; Oštir, Krištof

    2015-04-01

    Knowledge on the terrain morphology is very important for observation of numerous processes and events and digital elevation models are therefore one of the most important datasets in geographic analyses. Furthermore, recognition of natural and anthropogenic microrelief structures, which can be observed on detailed terrain models derived from aerial laser scanning (lidar) or structure-from-motion photogrammetry, is of paramount importance in many applications. In this paper we thus examine and evaluate methods of raster lidar data visualization for the determination (recognition) of microrelief features and present a series of strategies to assist selecting the preferred visualization of choice for structures of various shapes and sizes, set in varied landscapes. Often the answer is not definite and more frequently a combination of techniques has to be used to map a very diverse landscape. Researchers can only very recently benefit from free software for calculation of advanced visualization techniques. These tools are often difficult to understand, have numerous options that confuse the user, or require and produce non-standard data formats, because they were written for specific purposes. We therefore designed the Relief Visualization Toolbox (RVT) as a free, easy-to-use, standalone application to create visualisations from high-resolution digital elevation data. It is tailored for the very beginners in relief interpretation, but it can also be used by more advanced users in data processing and geographic information systems. It offers a range of techniques, such as simple hillshading and its derivatives, slope gradient, trend removal, positive and negative openness, sky-view factor, and anisotropic sky-view factor. All included methods have been proven to be effective for detection of small scale features and the default settings are optimised to accomplish this task. However, the usability of the tool goes beyond computation for visualization purposes, as sky

  4. SimulFold: simultaneously inferring RNA structures including pseudoknots, alignments, and trees using a Bayesian MCMC framework.

    Directory of Open Access Journals (Sweden)

    Irmtraud M Meyer

    2007-08-01

    Full Text Available Computational methods for predicting evolutionarily conserved rather than thermodynamic RNA structures have recently attracted increased interest. These methods are indispensable not only for elucidating the regulatory roles of known RNA transcripts, but also for predicting RNA genes. It has been notoriously difficult to devise them to make the best use of the available data and to predict high-quality RNA structures that may also contain pseudoknots. We introduce a novel theoretical framework for co-estimating an RNA secondary structure including pseudoknots, a multiple sequence alignment, and an evolutionary tree, given several RNA input sequences. We also present an implementation of the framework in a new computer program, called SimulFold, which employs a Bayesian Markov chain Monte Carlo method to sample from the joint posterior distribution of RNA structures, alignments, and trees. We use the new framework to predict RNA structures, and comprehensively evaluate the quality of our predictions by comparing our results to those of several other programs. We also present preliminary data that show SimulFold's potential as an alignment and phylogeny prediction method. SimulFold overcomes many conceptual limitations that current RNA structure prediction methods face, introduces several new theoretical techniques, and generates high-quality predictions of conserved RNA structures that may include pseudoknots. It is thus likely to have a strong impact, both on the field of RNA structure prediction and on a wide range of data analyses.

  5. Structure, evolution and functional inference on the Mildew Locus O (MLO) gene family in three cultivated Cucurbitaceae spp.

    Science.gov (United States)

    Iovieno, Paolo; Andolfo, Giuseppe; Schiavulli, Adalgisa; Catalano, Domenico; Ricciardi, Luigi; Frusciante, Luigi; Ercolano, Maria Raffaella; Pavan, Stefano

    2015-12-29

    The powdery mildew disease affects thousands of plant species and arguably represents the major fungal threat for many Cucurbitaceae crops, including melon (Cucumis melo L.), watermelon (Citrullus lanatus L.) and zucchini (Cucurbita pepo L.). Several studies revealed that specific members of the Mildew Locus O (MLO) gene family act as powdery mildew susceptibility factors. Indeed, their inactivation, as the result of gene knock-out or knock-down, is associated with a peculiar form of resistance, referred to as mlo resistance. We exploited recently available genomic information to provide a comprehensive overview of the MLO gene family in Cucurbitaceae. We report the identification of 16 MLO homologs in C. melo, 14 in C. lanatus and 18 in C. pepo genomes. Bioinformatic treatment of data allowed phylogenetic inference and the prediction of several ortholog pairs and groups. Comparison with functionally characterized MLO genes and, in C. lanatus, gene expression analysis, resulted in the detection of candidate powdery mildew susceptibility factors. We identified a series of conserved amino acid residues and motifs that are likely to play a major role for the function of MLO proteins. Finally, we performed a codon-based evolutionary analysis indicating a general high level of purifying selection in the three Cucurbitaceae MLO gene families, and the occurrence of regions under diversifying selection in candidate susceptibility factors. Results of this study may help to address further biological questions concerning the evolution and function of MLO genes. Moreover, data reported here could be conveniently used by breeding research, aiming to select powdery mildew resistant cultivars in Cucurbitaceae.

  6. Electrotonic Structure of Motoneurons in the Spinal Cord of the Turtle: Inferences for the Mechanisms of Bistability

    National Research Council Canada - National Science Library

    Gytis Svirskis; Aron Gutman; Jørn Hounsgaard

    2001-01-01

    .... A novel method based on weak DC field stimulation and the classical method based on current injection were used to obtain two independent estimates of the electrotonic structure of motoneurons...

  7. Migration, distribution and population (stock) structure of shallow-water hake (Merluccius capensis) in the Benguela Current Large Marine Ecosystem inferred using a geostatistical population model

    DEFF Research Database (Denmark)

    Jansen, Teunis; Kristensen, Kasper; Kainge, Paulus Inekela

    2016-01-01

    Shallow-water hake (Merluccius capensis) is of considerable ecological and economic importance in the Benguela Current Large Marine Ecosystem in South Africa and Namibia. Optimal management of the resource is currently constrained by the limited understanding of migration patterns and population...... (stock) structure. We combined data from multiple demersal trawl surveys from the entire distribution area to estimate growth rate, mortality and spatial and temporal patterns of M. capensis. Analyses were conducted using the geostatistical model GeoPop. The complexity of the model and the amount of data...... required a new level of soft- and hardware performance. This was achieved by utilizing Template Model Builder and high-end computational hardware (Amazon Elastic Compute Cloud, EC2). The data and the model enabled us to follow the distribution and infer movements of M. capensis from the recruitment...

  8. Criterion for the simultaneous selection of a working correlation structure and either generalized estimating equations or the quadratic inference function approach.

    Science.gov (United States)

    Westgate, Philip M

    2014-05-01

    Generalized estimating equations (GEE) are commonly used for the marginal analysis of correlated data, although the quadratic inference function (QIF) approach is an alternative that is increasing in popularity. This method optimally combines distinct sets of unbiased estimating equations that are based upon a working correlation structure, therefore asymptotically increasing or maintaining estimation efficiency relative to GEE. However, in finite samples, additional estimation variability arises when combining these sets of estimating equations, and therefore the QIF approach is not guaranteed to work as well as GEE. Furthermore, estimation efficiency can be improved for both analysis methods by accurate modeling of the correlation structure. Our goal is to improve parameter estimation, relative to existing methods, by simultaneously selecting a working correlation structure and choosing between GEE and two versions of the QIF approach. To do this, we propose the use of a criterion based upon the trace of the empirical covariance matrix (TECM). To make GEE and both QIF versions directly comparable for any given working correlation structure, the proposed TECM utilizes a penalty to account for the finite-sample variance inflation that can occur with either version of the QIF approach. Via a simulation study and in application to a longitudinal study, we show that penalizing the variance inflation that occurs with the QIF approach is necessary and that the proposed criterion works very well. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Planetary-scale streak structures produced in a high-resolution simulation of Venus atmosphere

    Science.gov (United States)

    Kashimura, H.; Sugimoto, N.; Takagi, M.; Matsuda, Y.; Ohfuchi, W.; Enomoto, T.; Nakajima, K.; Ishiwatari, M.; Sato, T. M.; Hashimoto, G. L.; Satoh, T.; Takahashi, Y. O.; Hayashi, Y.-Y.

    2017-09-01

    Planetary-scale streak structures captured by the IR2 camera onboard AKATSUKI was reproduced in a high-resolution simulation of Venus Atmosphere. We have found that the streak structures are extending from the polar vortices and synchronized in both hemispheres. Our experiments suggest that a low-stability layer is a key for forming the planetary-scale streak structures.

  10. Nanotechnology and statistical inference

    Science.gov (United States)

    Vesely, Sara; Vesely, Leonardo; Vesely, Alessandro

    2017-08-01

    We discuss some problems that arise when applying statistical inference to data with the aim of disclosing new func-tionalities. A predictive model analyzes the data taken from experiments on a specific material to assess the likelihood that another product, with similar structure and properties, will exhibit the same functionality. It doesn't have much predictive power if vari-ability occurs as a consequence of a specific, non-linear behavior. We exemplify our discussion on some experiments with biased dice.

  11. Stability-to-instability transition in the structure of large-scale networks.

    Science.gov (United States)

    Hu, Dandan; Ronhovde, Peter; Nussinov, Zohar

    2012-12-01

    We examine phase transitions between the "easy," "hard," and "unsolvable" phases when attempting to identify structure in large complex networks ("community detection") in the presence of disorder induced by network "noise" (spurious links that obscure structure), heat bath temperature T, and system size N. The partition of a graph into q optimally disjoint subgraphs or "communities" inherently requires Potts-type variables. In earlier work [Philos. Mag. 92, 406 (2012)], when examining power law and other networks (and general associated Potts models), we illustrated that transitions in the computational complexity of the community detection problem typically correspond to spin-glass-type transitions (and transitions to chaotic dynamics in mechanical analogs) at both high and low temperatures and/or noise. The computationally "hard" phase exhibits spin-glass type behavior including memory effects. The region over which the hard phase extends in the noise and temperature phase diagram decreases as N increases while holding the average number of nodes per community fixed. This suggests that in the thermodynamic limit a direct sharp transition may occur between the easy and unsolvable phases. When present, transitions at low temperature or low noise correspond to entropy driven (or "order by disorder") annealing effects, wherein stability may initially increase as temperature or noise is increased before becoming unsolvable at sufficiently high temperature or noise. Additional transitions between contending viable solutions (such as those at different natural scales) are also possible. Identifying community structure via a dynamical approach where "chaotic-type" transitions were found earlier. The correspondence between the spin-glass-type complexity transitions and transitions into chaos in dynamical analogs might extend to other hard computational problems. In this work, we examine large networks (with a power law distribution in cluster size) that have a large

  12. Otoliths versus scales: evaluating the most suitable structure for ...

    African Journals Online (AJOL)

    Otoliths (1.4% rejected) were more readable than scales (41.7% and 7.5% rejected) for Wriggleswade and Mankazana Impoundments respectively. Otolith readings were more precise (average percentage error (APE) = 13.6%; coefficient of variation (CV) = 15.8%) than scales (APE = 18.0%; CV = 21.9%) for the total sample ...

  13. Rich Linguistic Structure from Large-Scale Web Data

    Science.gov (United States)

    Yamangil, Elif

    2013-01-01

    The past two decades have shown an unexpected effectiveness of "Web-scale" data in natural language processing. Even the simplest models, when paired with unprecedented amounts of unstructured and unlabeled Web data, have been shown to outperform sophisticated ones. It has been argued that the effectiveness of Web-scale data has…

  14. Microsatellite analyses reveal fine-scale genetic structure in grey mouse lemurs (Microcebus murinus)

    DEFF Research Database (Denmark)

    Fredsted, T; Pertoldi, C; Schierup, MH

    2005-01-01

    Information on genetic structure can be used to complement direct inferences on social systems and behaviour. We studied the genetic structure of the solitary grey mouse lemur (Microcebus murinus), a small, nocturnal primate endemic to western Madagascar, with the aim of getting further insight...... distribution of identical homozygotes was found, supporting the notion that dispersal distance for breeding was shorter than that for foraging, i.e. the breeding neighbourhood size is smaller than the foraging neighbourhood size. In conclusion, we found a more complex population structure than what has been...

  15. Pseudoscorpion mitochondria show rearranged genes and genome-wide reductions of RNA gene sizes and inferred structures, yet typical nucleotide composition bias

    Science.gov (United States)

    2012-01-01

    Background Pseudoscorpions are chelicerates and have historically been viewed as being most closely related to solifuges, harvestmen, and scorpions. No mitochondrial genomes of pseudoscorpions have been published, but the mitochondrial genomes of some lineages of Chelicerata possess unusual features, including short rRNA genes and tRNA genes that lack sequence to encode arms of the canonical cloverleaf-shaped tRNA. Additionally, some chelicerates possess an atypical guanine-thymine nucleotide bias on the major coding strand of their mitochondrial genomes. Results We sequenced the mitochondrial genomes of two divergent taxa from the chelicerate order Pseudoscorpiones. We find that these genomes possess unusually short tRNA genes that do not encode cloverleaf-shaped tRNA structures. Indeed, in one genome, all 22 tRNA genes lack sequence to encode canonical cloverleaf structures. We also find that the large ribosomal RNA genes are substantially shorter than those of most arthropods. We inferred secondary structures of the LSU rRNAs from both pseudoscorpions, and find that they have lost multiple helices. Based on comparisons with the crystal structure of the bacterial ribosome, two of these helices were likely contact points with tRNA T-arms or D-arms as they pass through the ribosome during protein synthesis. The mitochondrial gene arrangements of both pseudoscorpions differ from the ancestral chelicerate gene arrangement. One genome is rearranged with respect to the location of protein-coding genes, the small rRNA gene, and at least 8 tRNA genes. The other genome contains 6 tRNA genes in novel locations. Most chelicerates with rearranged mitochondrial genes show a genome-wide reversal of the CA nucleotide bias typical for arthropods on their major coding strand, and instead possess a GT bias. Yet despite their extensive rearrangement, these pseudoscorpion mitochondrial genomes possess a CA bias on the major coding strand. Phylogenetic analyses of all 13

  16. Sample-Starved Large Scale Network Analysis

    Science.gov (United States)

    2016-05-05

    Applications to materials science 2.1 Foundational principles for large scale inference on structure of covariance We developed general principles for...concise but accessible format. These principles are applicable to large-scale complex network applications arising genomics , connectomics, eco-informatics...available to estimate or detect patterns in the matrix. 15. SUBJECT TERMS multivariate dependency structure multivariate spatio-temporal prediction

  17. Inferring coarse-grain histone-DNA interaction potentials from high-resolution structures of the nucleosome

    CERN Document Server

    Meyer, Sam

    2014-01-01

    The histone-DNA interaction in the nucleosome is a fundamental mechanism of genomic compaction and regulation, which remains largely unkown despite a growing structural knowledge of the complex. Here, we propose a framework for the extraction of a nanoscale histone-DNA force-field from a collection of high-resolution structures, which may be adapted to a larger class of protein-DNA complexes. We apply the procedure on a large crystallographic database extended by snapshots from molecular dynamics simulations. The comparison of the structural models first shows that, at the sites of histone-DNA contact, the DNA base-pairs are locally shifted outwards, consistent with locally repulsive forces exerted by the histones. In a second step, we show that the various force profiles of the analyzed structures derive locally from a unique, sequence-independent, quadratic repulsive force field, while the sequence preferences are entirely due to the internal DNA mechanics. We thus obtain the first knowledge-derived nanosca...

  18. Structure of a low-enthalpy geothermal system inferred from magnetotellurics - A case study from Sri Lanka

    Science.gov (United States)

    Nimalsiri, Thusitha Bandara; Suriyaarachchi, Nuwan Buddhika; Hobbs, Bruce; Manzella, Adele; Fonseka, Morrel; Dharmagunawardena, H. A.; Subasinghe, Nalaka Deepal

    2015-06-01

    First comprehensive geothermal exploration in Sri Lanka was conducted in 2010 encompassing seven thermal springs, of which Kapurella records the highest temperature. The study consisted of passive magnetotelluric (MT) soundings, in which static shifts were corrected using time domain electromagnetic method (TDEM). A frequency range of 12,500-0.001 Hz was used for MT acquisition and polar diagrams were employed for dimensionality determination. MT and TDEM data were jointly inverted and 2D models were created using both transverse electric and transverse magnetic modes. A conductive southeast dipping structure is revealed from both phase pseudosections and the preferred 2D inversion model. A conductive formation starting at a depth of 7.5 km shows a direct link with the dipping structure. We suggest that these conductive structures are accounted for deep circulation and accumulation of groundwater. Our results show the geothermal reservoir of Kapurella system with a lateral extension of around 2.5 km and a depth range of 3 km. It is further found that the associated dolerite dike is not the source of heat although it could be acting as an impermeable barrier to form the reservoir. The results have indicated the location of the deep reservoir and the possible fluid path of the Kapurella system, which could be utilized to direct future geothermal studies. This pioneering study makes suggestions to improve future MT data acquisition and to use boreholes and other geophysical methods to improve the investigation of structures at depth.

  19. Genetic structure of Octopus vulgaris (Cephalopoda, Octopodidae) in the central Mediterranean Sea inferred from the mitochondrial COIII gene.

    Science.gov (United States)

    Fadhlaoui-Zid, Karima; Knittweis, Leyla; Aurelle, Didier; Nafkha, Chaala; Ezzeddine, Soufia; Fiorentino, Fabio; Ghmati, Hisham; Ceriola, Luca; Jarboui, Othman; Maltagliati, Ferruccio

    2012-01-01

    The polymorphism of the mitochondrial gene cytochrome oxidase III was studied in the Mediterranean octopus, Octopus vulgaris Cuvier, 1797. A total of 202 specimens from seven sampling sites were analysed with the aim of elucidating patterns of genetic structure in the central Mediterranean Sea and to give an insight into the phylogeny of the Octopus genus. Phylogenetic analyses showed that individuals from the central Mediterranean belong to the O. vulgaris species whose limits should nevertheless be clarified. Concerning genetic structure, two high-frequency haplotypes were present in all locations. The overall genetic divergence (Φ(ST)=0.05, P<0.05) indicated a significant genetic structuring in the study area and an AMOVA highlighted a significant break between western and eastern Mediterranean basins (Φ(CT)=0.094, P<0.05). Possible explanations for the observed patterns of genetic structuring are discussed with reference to their relevance for fisheries management. Copyright © 2012. Published by Elsevier SAS.

  20. How CMB and large-scale structure constrain chameleon interacting dark energy

    Energy Technology Data Exchange (ETDEWEB)

    Boriero, Daniel [Fakultät für Physik, Universität Bielefeld, Universitätstr. 25, Bielefeld (Germany); Das, Subinoy [Indian Institute of Astrophisics, Bangalore, 560034 (India); Wong, Yvonne Y.Y., E-mail: boriero@physik.uni-bielefeld.de, E-mail: subinoy@iiap.res.in, E-mail: yvonne.y.wong@unsw.edu.au [School of Physics, The University of New South Wales, Sydney NSW 2052 (Australia)

    2015-07-01

    We explore a chameleon type of interacting dark matter-dark energy scenario in which a scalar field adiabatically traces the minimum of an effective potential sourced by the dark matter density. We discuss extensively the effect of this coupling on cosmological observables, especially the parameter degeneracies expected to arise between the model parameters and other cosmological parameters, and then test the model against observations of the cosmic microwave background (CMB) anisotropies and other cosmological probes. We find that the chameleon parameters α and β, which determine respectively the slope of the scalar field potential and the dark matter-dark energy coupling strength, can be constrained to α < 0.17 and β < 0.19 using CMB data and measurements of baryon acoustic oscillations. The latter parameter in particular is constrained only by the late Integrated Sachs-Wolfe effect. Adding measurements of the local Hubble expansion rate H{sub 0} tightens the bound on α by a factor of two, although this apparent improvement is arguably an artefact of the tension between the local measurement and the H{sub 0} value inferred from Planck data in the minimal ΛCDM model. The same argument also precludes chameleon models from mimicking a dark radiation component, despite a passing similarity between the two scenarios in that they both delay the epoch of matter-radiation equality. Based on the derived parameter constraints, we discuss possible signatures of the model for ongoing and future large-scale structure surveys.

  1. Genetic diversity and structure of wild populations of Carica papaya in Northern Mesoamerica inferred by nuclear microsatellites and chloroplast markers.

    Science.gov (United States)

    Chávez-Pesqueira, Mariana; Núñez-Farfán, Juan

    2016-12-01

    Few studies have evaluated the genetic structure and evolutionary history of wild varieties of important crop species. The wild papaya (Carica papaya) is a key element of early successional tropical and sub-tropical forests in Mexico, and constitutes the genetic reservoir for evolutionary potential of the species. In this study we aimed to determine how diverse and structured is the genetic variability of wild populations of C. papaya in Northern Mesoamerica. Moreover, we assessed if genetic structure and evolutionary history coincide with hypothetized (1) pre-Pleistocene events (Isthmus of Tehuantepec sinking), (2) Pleistocene refugia or (3) recent patterns. We used six nuclear and two chloroplast (cp) DNA markers to assess the genetic diversity and phylogeographical structure of 19 wild populations of C. papaya in its natural distribution in Northern Mesoamerica. We found high genetic diversity (H o = 0·681 for nuclear markers, and h = 0·701 for cpDNA markers) and gene flow between populations of C. papaya (migration r up to 420 km). A lack of phylogeographical structure was found with the cpDNA markers (NST papaya. Because of its life history characteristics and lack of an ancient phylogeographical structure found with the cpDNA markers, we suggest that C. papaya was dispersed throughout the lowland rain forests of Mexico (along the coastal plains and foothills of Sierras). This scenario supports the hypothesis that tropical forests in Northern Mesoamerica did not experience important climate fluctuations during the Pleistocene, and that the life history of C. papaya could have promoted long-distance dispersal and rapid colonization of lowland rainforests. Moreover, the results obtained with the nuclear markers suggest recent human disturbances. The fragmentation of tropical habitats in Northern Mesoamerica appears to be the main driver of genetic structuring, and the major threat to the dispersion and survival of the species in the wild. © The Author 2016

  2. Development of Computational Tools for the Inference of Protein Interaction Specificity Rules and Functional Annotation Using Structural Information

    Directory of Open Access Journals (Sweden)

    Manuela Helmer-Citterich

    2006-04-01

    Full Text Available Relatively few protein structures are known, compared to the enormous amount of sequence data produced in the sequencing of different genomes, and relatively few protein complexes are deposited in the PDB with respect to the great amount of interaction data coming from high-throughput experiments (two-hybrid or affinity purification of protein complexes and mass spectrometry. Nevertheless, we can rely on computational techniques for the extraction of high-quality and information-rich data from the known structures and for their spreading in the protein sequence space. We describe here the ongoing research projects in our group: we analyse the protein complexes stored in the PDB and, for each complex involving one domain belonging to a family of interaction domains for which some interaction data are available, we can calculate its probability of interaction with any protein sequence. We analyse the structures of proteins encoding a function specified in a PROSITE pattern, which exhibits relatively low selectivity and specificity, and build extended patterns. To this aim, we consider residues that are well-conserved in the structure, even if their conservation cannot easily be recognized in the sequence alignment of the proteins holding the function. We also analyse protein surface regions and, through the annotation of the solvent-exposed residues, we annotate protein surface patches via a structural comparison performed with stringent parameters and independently of the residue order in the sequence. Local surface comparison may also help in identifying new sequence patterns, which could not be highlighted with other sequence-based methods.

  3. Scale-invariant structure of energy fluctuations in real earthquakes

    Science.gov (United States)

    Wang, Ping; Chang, Zhe; Wang, Huanyu; Lu, Hong

    2017-11-01

    Earthquakes are obviously complex phenomena associated with complicated spatiotemporal correlations, and they are generally characterized by two power laws: the Gutenberg-Richter (GR) and the Omori-Utsu laws. However, an important challenge has been to explain two apparently contrasting features: the GR and Omori-Utsu laws are scale-invariant and unaffected by energy or time scales, whereas earthquakes occasionally exhibit a characteristic energy or time scale, such as with asperity events. In this paper, three high-quality datasets on earthquakes were used to calculate the earthquake energy fluctuations at various spatiotemporal scales, and the results reveal the correlations between seismic events regardless of their critical or characteristic features. The probability density functions (PDFs) of the fluctuations exhibit evidence of another scaling that behaves as a q-Gaussian rather than random process. The scaling behaviors are observed for scales spanning three orders of magnitude. Considering the spatial heterogeneities in a real earthquake fault, we propose an inhomogeneous Olami-Feder-Christensen (OFC) model to describe the statistical properties of real earthquakes. The numerical simulations show that the inhomogeneous OFC model shares the same statistical properties with real earthquakes.

  4. Micron-scale lens array having diffracting structures

    Science.gov (United States)

    Goldberg, Kenneth A

    2013-10-29

    A novel micron-scale lens, a microlens, is engineered to concentrate light efficiently onto an area of interest, such as a small, light-sensitive detector element in an integrated electronic device. Existing microlens designs imitate the form of large-scale lenses and are less effective at small sizes. The microlenses described herein have been designed to accommodate diffraction effects, which dominate the behavior of light at small length scales. Thus a new class of light-concentrating optical elements with much higher relative performance has been created. Furthermore, the new designs are much easier to fabricate than previous designs.

  5. Effects of structural connectivity on fine scale population genetic structure of muskrat, Ondatra zibethicus

    Science.gov (United States)

    Laurence, Sophie; Smith, Matthew J; Schulte-Hostedde, Albrecht I

    2013-01-01

    In heterogeneous landscapes, physical barriers and loss of structural connectivity have been shown to reduce gene flow and therefore lead to population structuring. In this study, we assessed the influence of landscape features on population genetic structure and gene flow of a semiaquatic species, the muskrat. A total of 97 muskrats were sampled from three watersheds near Sudbury, Ontario, Canada. We estimated population genetic structure using 11 microsatellite loci and identified a single genetic cluster and no genetic differences were found among the watersheds as a result of high levels of gene flow. At finer scales, we assessed the correlation between individual pairwise genetic distances and Euclidean distance as well as different models of least cost path (LCP). We used a range of cost values for the landscape types in order to build our LCP models. We found a positive relationship between genetic distance and least cost distance when we considered roads as corridors for movements. Open landscapes and urban areas seemed to restrict but not prevent gene flow within the study area. Our study underlines the high-dispersal ability of generalist species in their use of landscape and highlights how landscape features often considered barriers to animal movements are corridors for other species. PMID:24223287

  6. Fractals and the Large-Scale Structure in the Universe

    Indian Academy of Sciences (India)

    Gasket. Hence by definition, the self-similarity dimension of the. Sierpinski gasket is. (1). The n = 5 approximation of the Sierpinski gasket is shown in Fig1.LTe B. say .8 . ern. : If it is scaled down by a factor of 1/2 we win get a line segment of length 4 cm. Two such scaled down line segments 'put together produce the original.

  7. The vertical structure of Jupiter and Saturn zonal winds from nonlinear simulations of major vortices and planetary-scale disturbances

    Science.gov (United States)

    Garcia-Melendo, E.; Legarreta, J.; Sanchez-Lavega, A.

    2012-12-01

    Direct measurements of the structure of the zonal winds of Jupiter and Saturn below the upper cloud layer are very difficult to retrieve. Except from the vertical profile at a Jupiter hot spot obtained from the Galileo probe in 1995 and measurements from cloud tracking by Cassini instruments just below the upper cloud, no other data are available. We present here our inferences of the vertical structure of Jupiter and Saturn zonal wind across the upper troposphere (deep down to about 10 bar level) obtained from nonlinear simulations using the EPIC code of the stability and interactions of large-scale vortices and planetary-scale disturbances in both planets. Acknowledgements: This work has been funded by Spanish MICIIN AYA2009-10701 with FEDER support, Grupos Gobierno Vasco IT-464-07 and UPV/EHU UFI11/55. [1] García-Melendo E., Sánchez-Lavega A., Dowling T.., Icarus, 176, 272-282 (2005). [2] García-Melendo E., Sánchez-Lavega A., Hueso R., Icarus, 191, 665-677 (2007). [3] Sánchez-Lavega A., et al., Nature, 451, 437- 440 (2008). [4] Sánchez-Lavega A., et al., Nature, 475, 71-74 (2011).

  8. Magnetotelluric imaging of the resurgent caldera on the island of Ischia (southern Italy): inferences for its structure and activity

    Science.gov (United States)

    Di Giuseppe, M. G.; Troiano, A.; Carlino, S.

    2017-12-01

    The island of Ischia (located in the Bay of Naples, Italy) represents a peculiar case of a well-exposed caldera that has experienced a large (>800 m) and rapid resurgence, accompanied by volcanic activity. What drives the resurgence of calderas is a crucial issue to investigate, because this process is associated with potential eruptions and high risk to people living within and around such large active volcanic systems. To improve the knowledge of volcano-tectonic processes affecting the caldera of Ischia, electromagnetic imaging of the structures associated with its resurgence was performed and integrated with available geological information. A magnetotelluric (MT) survey of the island was carried out along two main profiles through the central-western sector, providing an electrical resistivity map to a depth of 3 km. These resistivity cross sections allowed us to identify the presence of a very shallow magmatic intrusion, possibly a laccolith, at a depth of about 1 km, which was responsible for both the resurgence and the volcanic activity. Furthermore, the tectonic structures bordering the resurgent area and the occurrence of a large thermal anomaly in the western sector of the caldera also provided a signature in the resistivity cross sections, with the magma intrusion producing advection of hot fluids with high geothermal gradients (>150 °C km-1) in the southern and western sectors. All of these data are fundamental for the assessment of the island's volcano-tectonic dynamics and their associated hazards. The structure and activity of the island have been controlled by the process of resurgence associated with the arrival of new magma and the progressive intrusion of a laccolith at a shallow depth. The reactivation of such a shallow system may imply imminent eruption which would pose a major volcanic hazard.

  9. The Effective Field Theory of Large Scale Structure at Two Loops: the apparent scale dependence of the speed of sound

    OpenAIRE

    Baldauf, Tobias; Mercolli, Lorenzo; Zaldarriaga, Matias

    2015-01-01

    We study the Effective Field Theory of Large Scale Structure for cosmic density and momentum fields. We show that the finite part of the two-loop calculation and its counterterms introduce an apparent scale dependence for the leading order parameter $c_\\text{s}^2$ of the EFT starting at k=0.1 h/Mpc. These terms limit the range over which one can trust the one-loop EFT calculation at the 1 % level to k

  10. Strain, nano-phase separation, multi-scale structures and function of advanced materials

    OpenAIRE

    Billinge, S. J. L.

    2002-01-01

    Recent atomic pair distribution function results from our group from manganites and cuprate systems are reviewed in light of the presence of multi-scale structures. These structures have a profound effect on the material properties

  11. Population genetic structure, genetic diversity, and natural history of the South American species of Nothofagus subgenus Lophozonia (Nothofagaceae) inferred from nuclear microsatellite data.

    Science.gov (United States)

    Vergara, Rodrigo; Gitzendanner, Matthew A; Soltis, Douglas E; Soltis, Pamela S

    2014-06-01

    The effect of glaciation on the levels and patterns of genetic variation has been well studied in the Northern Hemisphere. However, although glaciation has undoubtedly shaped the genetic structure of plants in the Southern Hemisphere, fewer studies have characterized the effect, and almost none of them using microsatellites. Particularly, complex patterns of genetic structure might be expected in areas such as the Andes, where both latitudinal and altitudinal glacial advance and retreat have molded modern plant communities. We therefore studied the population genetics of three closely related, hybridizing species of Nothofagus (N. obliqua, N. alpina, and N. glauca, all of subgenus Lophozonia; Nothofagaceae) from Chile. To estimate population genetic parameters and infer the influence of the last ice age on the spatial and genetic distribution of these species, we examined and analyzed genetic variability at seven polymorphic microsatellite DNA loci in 640 individuals from 40 populations covering most of the ranges of these species in Chile. Populations showed no significant inbreeding and exhibited relatively high levels of genetic diversity (H E = 0.502-0.662) and slight, but significant, genetic structure (R ST = 8.7-16.0%). However, in N. obliqua, the small amount of genetic structure was spatially organized into three well-defined latitudinal groups. Our data may also suggest some introgression of N. alpina genes into N. obliqua in the northern populations. These results allowed us to reconstruct the influence of the last ice age on the genetic structure of these species, suggesting several centers of genetic diversity for N. obliqua and N. alpina, in agreement with the multiple refugia hypothesis.

  12. The effect of proline on the network structure of major ampullate silks as inferred from their mechanical and optical properties.

    Science.gov (United States)

    Savage, Ken N; Gosline, John M

    2008-06-01

    The silk that orb-weaving spiders produce for use as dragline and for the frame of the web is spun from the major ampullate (MA) glands, and it is renowned for its exceptional toughness. The fibroins that make up MA silk have previously been organized into two major groupings, spidroin-1 and spidroin-2, based largely on differences in amino acid sequence. The most apparent difference between spidroin-1 and spidroin-2 fibroins is the lack of proline in spidroin-1. The MA silk of Araneus diadematus comprises two spidroin-2 fibroins, and is therefore proline-rich, whereas spidroin-1 is preferentially expressed in Nephila clavipes MA silk, and so this silk is proline deficient. Together, these two silks provide a system for testing the consequences of proline-rich and proline-deficient fibroin networks. This study measures the mechanical and optical properties of dry and hydrated Araneus and Nephila MA silks. Since proline acts to disrupt secondary structure, it is hypothesized that the fibroin network of Araneus MA silk will contain less secondary structure than the network of Nephila MA silk. Mechanical and optical studies clearly support this hypothesis. Although the dry properties of these two silks are indistinguishable, there are large differences between the hydrated silks. Nephila silk does not swell upon hydration to the same degree as Araneus silk. In addition, upon hydration, Nephila MA silk retains more of its initial dry stiffness, and retains more molecular order, as indicated by birefringence measurements.

  13. Size structure, not metabolic scaling rules, determines fisheries reference points

    DEFF Research Database (Denmark)

    Andersen, Ken Haste; Beyer, Jan

    2015-01-01

    these empirical relations is lacking. Here, we combine life-history invariants, metabolic scaling and size-spectrum theory to develop a general size- and trait-based theory for demography and recruitment of exploited fish stocks. Important concepts are physiological or metabolic scaled mortalities and flux...... of individuals or their biomass to size. The theory is based on classic metabolic relations at the individual level and uses asymptotic size W∞ as a trait. The theory predicts fundamental similarities and differences between small and large species in vital rates and response to fishing. The central result...... that even though small species have a higher productivity than large species their resilience towards fishing is lower than expected from metabolic scaling rules. Further, we show that the fishing mortality leading to maximum yield per recruit is an ill-suited reference point. The theory can be used...

  14. Spatial variation in Earth structure inferred by GNSS seasonal deformations due to snow loads in northeast Japan

    Science.gov (United States)

    Hirose, H.; Kurisu, R.; Nishimura, T.

    2016-12-01

    Seasonal variations are observed in GNSS site coordinate time series (e.g., Murakami and Miyazaki, 2001; Munekane et al., 2004). Heki (2001) showed that snow loads cause seasonal subsidence in winter in the Tohoku region, northeast Japan from the Geospatial Information Authority of Japan's GEONET GNSS daily site coordinates during the period 1999.0-2001.0. It becomes worth reevaluating this issue because the observed GNSS data are accumulated over 10 years and the amplitude of apparent seasonal components can be reduced with revised analysis strategies (e.g., Nakagawa et al., 2009). Here we show that the correlation between a seasonal variation in GNSS vertical displacement time-series and snow depth measured by Japan Meteorological Agency's AMeDAS over 10 years is good in some areas with the largest snow depths among the study areas, the ratio of seasonal subsidence to snow depth shows spatial variation, and the variation can be explained by spatial variation of underground structure.

  15. Systematic Review on Global Epidemiology of Methicillin-Resistant Staphylococcus pseudintermedius: Inference of Population Structure from Multilocus Sequence Typing Data

    DEFF Research Database (Denmark)

    dos Santos, Teresa Pires; Damborg, Peter; Moodley, Arshnee

    2016-01-01

    Background and rationale: Methicillin-resistant Staphylococcus pseudintermedius (MRSP) is a major cause of infections in dogs, also posing a zoonotic risk to humans. This systematic review aimed to determine the global epidemiology of MRSP and provide new insights into the population structure...... of this important veterinary pathogen. Methodology: Web of Science was searched systematically for articles reporting data on multilocus sequence typing (MLST) of S. pseudintermedius isolates from dogs or other animal or human patients and carriers. Data from the eligible studies were then integrated with data from....... In Europe, CC258, which is more frequently susceptible to enrofloxacin and aminoglycosides, and more frequently resistant to sulphonamides/trimethoprim than CC71, is increasingly reported in various countries. CC68, previously described as the epidemic North American clone, is frequently reported...

  16. Microplanktonic community structure in a coastal system relative to a Phaeocystis bloom inferred from morphological and tag pyrosequencing methods.

    Directory of Open Access Journals (Sweden)

    Sébastien Monchy

    Full Text Available BACKGROUND: Massive phytoplankton blooms, like the recurrent Phaeocystis proliferation observed every year in the Eastern English Channel (EEC, have a significant influence on the overall planktonic community structure and their food web dynamics. As well as being an important area for local fisheries, the EEC is an ideal ecosystem for work on microbial diversity. This is because, although its environmental context is relatively complex, it is reasonably well understood due to several years of monitoring and morphological observations of its planktonic organisms. The objective of our study was to better understand the under-explored microbial eukaryotic diversity relative to the Phaeocystis bloom. METHODOLOGY AND PRINCIPAL FINDINGS: The community structure of microplankton (diatoms, haptophytes, ciliates and dinoflagellates was studied through morphological observations and tag pyrosequencing. During the annual Phaeocystis spring bloom, the phytoplankton biomass increased by 34-fold, while the microzooplankton biomass showed a 4-fold increase, representing on average about 4.6% of the biomass of their phytoplankton prey. Tag pyrosequencing unveiled an extensive diversity of Gymnodiniaceae, with G. spirale and G. fusiformis representing the most abundant reads. An extended diversity of Phaeocystales, with partial 18S rDNA genes sequence identity as low as 85% was found, with taxa corresponding to P. globosa, but also to unknown Phaeocystaceae. CONCLUSIONS: Morphological analyses and pyrosequencing were generally in accordance with capturing frequency shifts of abundant taxa. Tag pyrosequencing allowed highlighting the maintenance of microplankton diversity during the Phaeocystis bloom and the increase of the taxa presenting low number of reads (minor taxa along with the dominant ones in response to biotic and/or abiotic changing conditions. Although molecular approaches have enhanced our perception on diversity, it has come to light that the

  17. Evolution of Wechsler's Memory Scales: Content and structural analysis.

    Science.gov (United States)

    Kent, Phillip L

    2017-01-01

    The Wechsler Memory Scale-1 was introduced to the professional community 70 years ago and has been the most widely used standardized memory battery for over 50 years. Since its introduction, the test has been revised three times, with the last revision occurring in 2009 . Few clinicians are aware that Wechsler developed a prior memory battery in 1917 , which was used to assess retention deficits in persons with Korsakoff psychosis. The purpose of the present article is to describe the development of Wechsler's memory scales from 1917 through 2009 . Suggestions for the next revision are offered.

  18. Structural genomics of eukaryotic targets at a laboratory scale.

    Science.gov (United States)

    Busso, Didier; Poussin-Courmontagne, Pierre; Rosé, David; Ripp, Raymond; Litt, Alain; Thierry, Jean-Claude; Moras, Dino

    2005-01-01

    Structural genomics programs are distributed worldwide and funded by large institutions such as the NIH in United-States, the RIKEN in Japan or the European Commission through the SPINE network in Europe. Such initiatives, essentially managed by large consortia, led to technology and method developments at the different steps required to produce biological samples compatible with structural studies. Besides specific applications, method developments resulted mainly upon miniaturization and parallelization. The challenge that academic laboratories faces to pursue structural genomics programs is to produce, at a higher rate, protein samples. The Structural Biology and Genomics Department (IGBMC - Illkirch - France) is implicated in a structural genomics program of high eukaryotes whose goal is solving crystal structures of proteins and their complexes (including large complexes) related to human health and biotechnology. To achieve such a challenging goal, the Department has established a medium-throughput pipeline for producing protein samples suitable for structural biology studies. Here, we describe the setting up of our initiative from cloning to crystallization and we demonstrate that structural genomics may be manageable by academic laboratories by strategic investments in robotic and by adapting classical bench protocols and new developments, in particular in the field of protein expression, to parallelization.

  19. Using genetic profiles of African forest elephants to infer population structure, movements, and habitat use in a conservation and development landscape in Gabon.

    Science.gov (United States)

    Eggert, L S; Buij, R; Lee, M E; Campbell, P; Dallmeier, F; Fleischer, R C; Alonso, A; Maldonado, J E

    2014-02-01

    Conservation of wide-ranging species, such as the African forest elephant (Loxodonta cyclotis), depends on fully protected areas and multiple-use areas (MUA) that provide habitat connectivity. In the Gamba Complex of Protected Areas in Gabon, which includes 2 national parks separated by a MUA containing energy and forestry concessions, we studied forest elephants to evaluate the importance of the MUA to wide-ranging species. We extracted DNA from elephant dung samples and used genetic information to identify over 500 individuals in the MUA and the parks. We then examined patterns of nuclear microsatellites and mitochondrial control-region sequences to infer population structure, movement patterns, and habitat use by age and sex. Population structure was weak but significant, and differentiation was more pronounced during the wet season. Within the MUA, males were more strongly associated with open habitats, such as wetlands and savannas, than females during the dry season. Many of the movements detected within and between seasons involved the wetlands and bordering lagoons. Our results suggest that the MUA provides year-round habitat for some elephants and additional habitat for others whose primary range is in the parks. With the continuing loss of roadless wilderness areas in Central Africa, well-managed MUAs will likely be important to the conservation of wide-ranging species. © 2013 Society for Conservation Biology.

  20. Inferring Trust Based on Similarity with TILLIT

    Science.gov (United States)

    Tavakolifard, Mozhgan; Herrmann, Peter; Knapskog, Svein J.

    A network of people having established trust relations and a model for propagation of related trust scores are fundamental building blocks in many of today’s most successful e-commerce and recommendation systems. However, the web of trust is often too sparse to predict trust values between non-familiar people with high accuracy. Trust inferences are transitive associations among users in the context of an underlying social network and may provide additional information to alleviate the consequences of the sparsity and possible cold-start problems. Such approaches are helpful, provided that a complete trust path exists between the two users. An alternative approach to the problem is advocated in this paper. Based on collaborative filtering one can exploit the like-mindedness resp. similarity of individuals to infer trust to yet unknown parties which increases the trust relations in the web. For instance, if one knows that with respect to a specific property, two parties are trusted alike by a large number of different trusters, one can assume that they are similar. Thus, if one has a certain degree of trust to the one party, one can safely assume a very similar trustworthiness of the other one. In an attempt to provide high quality recommendations and proper initial trust values even when no complete trust propagation path or user profile exists, we propose TILLIT — a model based on combination of trust inferences and user similarity. The similarity is derived from the structure of the trust graph and users’ trust behavior as opposed to other collaborative-filtering based approaches which use ratings of items or user’s profile. We describe an algorithm realizing the approach based on a combination of trust inferences and user similarity, and validate the algorithm using a real large-scale data-set.

  1. The deep structure of Gaussian scale space images

    NARCIS (Netherlands)

    Kuijper, Arjan

    2002-01-01

    In order to be able to deal with the discrete nature of images in a continuous way, one can use results of the mathematical field of 'distribution theory'. Under almost trivial assumptions, like 'we know nothing', one ends up with convolving the image with a Gaussian filter. In this manner scale is

  2. Structural Validity of the Fear of Success Scale

    Science.gov (United States)

    Metzler, Jonathan N.; Conroy, David E.

    2004-01-01

    Fear of success is a dispositional form of anxiety that can have harmful effects on athletes' motivation and performance; however, empirical research on fear of success in sport has been limited. Zuckerman and Allison's (1976) Fear of Success Scale (FOSS) has been the most popular fear of success measure used in sport, yet it is laden with…

  3. Population structure of the malaria vector Anopheles sinensis (Diptera: Culicidae) in China: two gene pools inferred by microsatellites.

    Science.gov (United States)

    Ma, Yajun; Yang, Manni; Fan, Yong; Wu, Jing; Ma, Ying; Xu, Jiannong

    2011-01-01

    Anopheles sinensis is a competent malaria vector in China. An understanding of vector population structure is important to the vector-based malaria control programs. However, there is no adequate data of A. sinensis population genetics available yet. This study used 5 microsatellite loci to estimate population genetic diversity, genetic differentiation and demographic history of A. sinensis from 14 representative localities in China. All 5 microsatellite loci were highly polymorphic across populations, with high allelic richness and heterozygosity. Hardy-Weinberg disequilibrium was found in 12 populations associated with heterozygote deficits, which was likely caused by the presence of null allele and the Wahlund effect. Bayesian clustering analysis revealed two gene pools, grouping samples into two population clusters; one includes six and the other includes eight populations. Out of 14 samples, six samples were mixed with individuals from both gene pools, indicating the coexistence of two genetic units in the areas sampled. The overall differentiation between two genetic pools was moderate (F(ST) = 0.156). Pairwise differentiation between populations were lower within clusters (F(ST) = 0.008-0.028 in cluster I and F(ST) = 0.004-0.048 in cluster II) than between clusters (F(ST) = 0.120-0.201). A reduced gene flow (Nm = 1-1.7) was detected between clusters. No evidence of isolation by distance was detected among populations neither within nor between the two clusters. There are differences in effective population size (Ne = 14.3-infinite) across sampled populations. Two genetic pools with moderate genetic differentiation were identified in the A. sinensis populations in China. The population divergence was not correlated with geographic distance or barrier in the range. Variable effective population size and other demographic effects of historical population perturbations could be the factors affecting the population differentiation. The

  4. Population structure of the malaria vector Anopheles sinensis (Diptera: Culicidae in China: two gene pools inferred by microsatellites.

    Directory of Open Access Journals (Sweden)

    Yajun Ma

    Full Text Available BACKGROUND: Anopheles sinensis is a competent malaria vector in China. An understanding of vector population structure is important to the vector-based malaria control programs. However, there is no adequate data of A. sinensis population genetics available yet. METHODOLOGY/PRINCIPAL FINDINGS: This study used 5 microsatellite loci to estimate population genetic diversity, genetic differentiation and demographic history of A. sinensis from 14 representative localities in China. All 5 microsatellite loci were highly polymorphic across populations, with high allelic richness and heterozygosity. Hardy-Weinberg disequilibrium was found in 12 populations associated with heterozygote deficits, which was likely caused by the presence of null allele and the Wahlund effect. Bayesian clustering analysis revealed two gene pools, grouping samples into two population clusters; one includes six and the other includes eight populations. Out of 14 samples, six samples were mixed with individuals from both gene pools, indicating the coexistence of two genetic units in the areas sampled. The overall differentiation between two genetic pools was moderate (F(ST = 0.156. Pairwise differentiation between populations were lower within clusters (F(ST = 0.008-0.028 in cluster I and F(ST = 0.004-0.048 in cluster II than between clusters (F(ST = 0.120-0.201. A reduced gene flow (Nm = 1-1.7 was detected between clusters. No evidence of isolation by distance was detected among populations neither within nor between the two clusters. There are differences in effective population size (Ne = 14.3-infinite across sampled populations. CONCLUSIONS/SIGNIFICANCE: Two genetic pools with moderate genetic differentiation were identified in the A. sinensis populations in China. The population divergence was not correlated with geographic distance or barrier in the range. Variable effective population size and other demographic effects of historical population

  5. The Student Perception of University Support and Structure Scale: Development and Validation

    Science.gov (United States)

    Wintre, Maxine G.; Gates, Shawn K. E.; Pancer, W. Mark; Pratt, Michael S.; Polivy, Janet; Birnie-Lefcovitch, S.; Adams, Gerald

    2009-01-01

    A new scale, the Student Perception of University Support and Structure Scale (SPUSS), was developed for research on the transition to university. The scale was based on concepts derived from Baumrind's (1971) theory of parenting styles. Data were obtained from two separate cohorts of freshmen (n=759 and 397) attending six Canadian universities of…

  6. Scaling the relative dominance of exogenous drivers in structuring desert small mammal assemblages

    Science.gov (United States)

    Rodríguez, Daniela; Ojeda, Ricardo A.

    2015-11-01

    Assemblage patterns could be primarily generated by two types of drivers: exogenous (such as environmental and climatic factors) and endogenous (interactions such as competition, predation, mutualism or herbivory). The most widely accepted hypothesis states that at smaller scales (such as patch scale), interspecific interactions are the major drivers structuring communities, whereas at larger regional scales, factors such as climate, topography and soil act as ecological filters that determine assemblage composition. The general aim of this paper is to compare different exogenous drivers in terms of their relative dominance in structuring desert small mammal communities across a range of spatial scales, from patch to regional, and compare them with previous results on endogenous drivers. Our results show that as spatial scale increases, the explanatory power of exogenous factors also increases, e.g. from 17% at the patch scale (i.e. abundance) to 99% at the regional scale (i.e. diversity). Moreover, environmental drivers vary in type and strength depending on the community estimator across several spatial scales. On the other hand, endogenous drivers such as interspecific interactions are more important at the patch scale, diminishing in importance towards the regional scale. Therefore, the relative importance of exogenous versus endogenous drivers affects small mammal assemblage structure at different spatial scales. Our results fill up a knowledge gap concerning ecological drivers of assemblage structure at intermediate spatial scales for Monte desert small mammals, and highlight the importance of dealing with multi-causal factors in explaining ecological patterns of assemblages.

  7. Causal Inference for Meta-Analysis and Multi-Level Data Structures, with Application to Randomized Studies of Vioxx.

    Science.gov (United States)

    Sobel, Michael; Madigan, David; Wang, Wei

    2017-06-01

    We construct a framework for meta-analysis and other multi-level data structures that codifies the sources of heterogeneity between studies or settings in treatment effects and examines their implications for analyses. The key idea is to consider, for each of the treatments under investigation, the subject's potential outcome in each study or setting were he to receive that treatment. We consider four sources of heterogeneity: (1) response inconsistency, whereby a subject's response to a given treatment would vary across different studies or settings, (2) the grouping of nonequivalent treatments, where two or more treatments are grouped and treated as a single treatment under the incorrect assumption that a subject's responses to the different treatments would be identical, (3) nonignorable treatment assignment, and (4) response-related variability in the composition of subjects in different studies or settings. We then examine how these sources affect heterogeneity/homogeneity of conditional and unconditional treatment effects. To illustrate the utility of our approach, we re-analyze individual participant data from 29 randomized placebo-controlled studies on the cardiovascular risk of Vioxx, a Cox-2 selective nonsteroidal anti-inflammatory drug approved by the FDA in 1999 for the management of pain and withdrawn from the market in 2004.

  8. Puf operon sequences and inferred structures of light-harvesting complexes of three closely related Chromatiaceae exhibiting different absorption characteristics.

    Science.gov (United States)

    Rücker, Ovidiu; Köhler, Anne; Behammer, Beate; Sichau, Katja; Overmann, Jörg

    2012-02-01

    Whole cells of the purple sulfur bacterium strain 970 exhibit an unusual absorption peak at 963 nm. Its closest relatives, Thiorhodovibrio (Trv.) winogradskyi DSM6702(T) and strain 06511 display a bacteriochlorophyll (BChl) a absorption peak at 867 nm that is characteristic for most light-harvesting complexes 1 (LHC1) of proteobacteria. The puf operons encoding the LHC1 and reaction center proteins were amplified, cloned, and sequenced, and for the Trv. winogradskyi, strains show the common pufBALMC gene arrangement, whereas strain 970 contains a second pufBA copy downstream of pufC. Only pufB(1)A(1) is transcribed, and the corresponding mRNA fragment had an increased stability. Alignments of the deduced protein sequences showed that the LHC1 polypeptides are closely related to those of Thermochromatium (Tch.) tepidum. A deletion between αHis(0) and αTrp(+11), thought to be responsible for the redshifted Q(y) absorption in Tch. tepidum, was also detected in strain 970 and Trv. winogradskyi, whereas αLys(+12) is replaced by histidine only in strain 970. Based on our structural modeling, the side chain of this αHis is predicted to be in close proximity to the BChl a, suggesting that it exerts a modulating effect on the spectral properties of the highly unusual LHC1 complex of strain 970.

  9. The 3-D structure of the Somma-Vesuvius volcanic complex (Italy) inferred from new and historic gravimetric data.

    Science.gov (United States)

    Linde, Niklas; Ricci, Tullio; Baron, Ludovic; Shakas, Alexis; Berrino, Giovanna

    2017-08-16

    Existing 3-D density models of the Somma-Vesuvius volcanic complex (SVVC), Italy, largely disagree. Despite the scientific and socioeconomic importance of Vesuvius, there is no reliable 3-D density model of the SVVC. A considerable uncertainty prevails concerning the presence (or absence) of a dense body underlying the Vesuvius crater (1944 eruption) that is implied from extensive seismic investigations. We have acquired relative gravity measurements at 297 stations, including measurements in difficult-to-access areas (e.g., the first-ever measurements in the crater). In agreement with seismic investigations, the simultaneous inversion of these and historic data resolves a high-density body that extends from the surface of the Vesuvius crater down to depths that exceed 2 km. A 1.5-km radius horseshoe-shaped dense feature (open in the southwestern sector) enforces the existing model of groundwater circulation within the SVVC. Based on its volcano-tectonic evolution, we interpret volcanic structures that have never been imaged before.

  10. Sperm ultra-structure of Odontosyllis ctenostoma (Polychaeta: Syllidae with inferences on syllid phylogeny and reproductive biology

    Directory of Open Access Journals (Sweden)

    Adriana Giangrande

    2008-09-01

    Full Text Available The analysis of the complex reproductive patterns of Syllidae may drastically change the taxonomic hierarchy of the family. To further contribute to the knowledge of Syllidae we have described the sperm ultra-structure and some steps of spermiogenesis of Odontosyllis ctenostoma Claparède, 1868, the first non interstitial eusylline investigated. The mature sperm has a bell-shaped acrosome and contains electron-dense granular material and thin filaments. The barrel-shaped nucleus bears two depressions: one anterior facing the acrosome and the other posterior partially containing the distal centriole and up to six mitochondria. Odontosyllis ctenostoma spermatozoa can be ascribed to the ect-aquasperm type typical of species practising external fertilisation. This morphology is not in complete accordance either with the particular brood protection reported for the species or the egg size. The sperm is similar to those of the Syllinae species thus far investigated, but the acrosome resembles that of the exogonine spermatid. Some authors consider Odontosyllis to be phylogenetically closer to Syllinae, though it shares epigamy with Exogoninae. Others have hypothesised that the exogonine sperm could have been derived from sylline sperm by simplification. In our hypothesis this could have happened through a gradual passage from an Odontosyllis-like eusylline ancestor.

  11. Seismic structure of the Longmenshan area in SW China inferred from receiver function analysis: Implications for future large earthquakes

    Science.gov (United States)

    He, Chuansong; Dong, Shuwen; Santosh, M.; Chen, Xuanhua

    2014-12-01

    Following the 2008 Mw 7.9 Wenchuan and 2013 Ms 7.0 Lushan earthquakes, the Longmenshan thrust-fault belt and the Songpan-Ganzi terrane have been the focus of several investigations. Here we use the H-k stacking technique and neighborhood algorithm to investigate the seismic structure of this area. Based on the presence of felsic lower crust and the Mesozoic crustal architecture of the Songpan-Ganzi and Longmenshan area, we exclude the model on the eastward flow of the middle and lower crust assigned as the cause for the crustal thickening in previous studies. In contrast, the E-W trending cumulative compression induced by the continued northward motion of the Indian plate and India-Asian collision are identified as the dominant factors leading to the crustal thickening in the Longmenshan thrust-fault region as well as the Songpan-Ganzi terrane. Particularly, the 2008 Mw 7.9 Wenchuan and 2013 Ms 7.0 Lushan earthquakes likely indicate the cumulative offsets and the E-W continuing compression.

  12. Relationships between avian richness and landscape structure at multiple scales using multiple landscapes

    Science.gov (United States)

    Michael S. Mitchell; Scott H. Rutzmoser; T. Bently Wigley; Craig Loehle; John A. Gerwin; Patrick D. Keyser; Richard A. Lancia; Roger W. Perry; Christopher L. Reynolds; Ronald E. Thill; Robert Weih; Don White; Petra Bohall Wood

    2006-01-01

    Little is known about factors that structure biodiversity on landscape scales, yet current land management protocols, such as forest certification programs, place an increasing emphasis on managing for sustainable biodiversity at landscape scales. We used a replicated landscape study to evaluate relationships between forest structure and avian diversity at both stand...

  13. Double inflation: A possible resolution of the large-scale structure problem

    Energy Technology Data Exchange (ETDEWEB)

    Turner, M.S.; Villumsen, J.V.; Vittorio, N.; Silk, J.; Juszkiewicz, R.

    1986-11-01

    A model is presented for the large-scale structure of the universe in which two successive inflationary phases resulted in large small-scale and small large-scale density fluctuations. This bimodal density fluctuation spectrum in an ..cap omega.. = 1 universe dominated by hot dark matter leads to large-scale structure of the galaxy distribution that is consistent with recent observational results. In particular, large, nearly empty voids and significant large-scale peculiar velocity fields are produced over scales of approx.100 Mpc, while the small-scale structure over less than or equal to 10 Mpc resembles that in a low density universe, as observed. Detailed analytical calculations and numerical simulations are given of the spatial and velocity correlations. 38 refs., 6 figs.

  14. Reconnaissance study of an inferred Quaternary maar structure in the western part of the Bohemian Massif near Neualbenreuth, NE-Bavaria (Germany)

    Science.gov (United States)

    Rohrmüller, J.; Kämpf, H.; Geiß, E.; Großmann, J.; Grun, I.; Mingram, J.; Mrlina, J.; Plessen, B.; Stebich, M.; Veress, C.; Wendt, A.; Nowaczyk, N.

    2017-10-01

    After a comprehensive geophysical prospecting the Quaternary Mýtina Maar, located on a line between the two Quaternary scoria cones Komorní hůrka/Kammerbühl and Železná hůrka/Eisenbühl, could be revealed by a scientific drilling at the German-Czech border in 2007. Further geophysical field investigations led to the discovery of another geological structure about 2.5 km ESE of the small town Neualbenreuth (NE-Bavaria, Germany), inferred to be also a maar structure, being the fourth volcanic feature aligned along the NW-SE trending Tachov fault zone. It is only faintly indicated as a partial circular rim in the digital elevation model. Though not expressed by a clear magnetic anomaly, geoelectric and refraction seismic tomography strongly indicates a bowl-shaped depression filled with low-resistivity and low-velocity material, correlating well with the well-defined negative gravity anomaly of - 2.5 mGal. Below ca. 15 m-thick debris layer, successions of mostly laminated sediments were recovered in a 100 m-long sediment core in 2015. Sections of finely laminated layers, likely varves, rich in organic matter and tree pollen, were recognized in the upper (22-30 m) and lower (70-86 m) part of the core, respectively, interpreted as interglacials, whereas mostly minerogenic laminated deposits, poor in organic matter, and (almost) barren of tree pollen are interpreted as clastic glacial deposits. According to a preliminary age model based on magnetostratigraphy, palynology, radiocarbon dating, and cyclostratigraphy, the recovered sediments span the time window from about 85 ka back to about 270 ka, covering marine isotope stages 5-8. Sedimentation rates are in the range of 10 cm ka-1 in interglacials and up to 100 cm ka-1 in glacial phases. The stratigraphic record resembles the one from Mýtina Maar, with its eruption date being derived from a nearby tephra deposit at 288 ± 17 ka, thus supporting the age model of the inferred Neualbenreuth Maar.

  15. Titanium alloy lattice structures with millimeter scale cell sizes

    Energy Technology Data Exchange (ETDEWEB)

    Moongkhamklang, Pimsiree; Wadley, Haydn N.G. [Department of Materials Science and Engineering, University of Virginia Charlottesville, VA 22904-4745 (United States)

    2010-11-15

    Titanium sandwich panels with cellular cores of a uniform 1-5 mm diameter open cell size are well suited for impact energy absorption and cross flow heat exchange applications. Periodic cellular structures (lattices) made from high specific strength, high temperature alloys are preferred for these multifunctional uses. A diffusion bonding method has been applied here to make cellular lattice structures from a Ti-6A1-4V alloy. To illustrate the approach, lattice structures with both square and diamond collinear topologies, a 2 mm open cell size, and a relative density of 15% were made from 254 {mu}m diameter titanium alloy wires. These structures were found to have a compressive strength of 40 {+-} 5 MPa that was controlled by plastic yield followed by buckling of the struts. The cellular structures have been brazed to titanium alloy face sheets to create sandwich panel structures that appear well suited for multifunctional applications up to 420 C. (Copyright copyright 2010 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  16. Fine-Scale Analysis Reveals Cryptic Landscape Genetic Structure in Desert Tortoises

    OpenAIRE

    Latch, Emily K.; William I Boarman; Andrew Walde; Robert C Fleischer

    2011-01-01

    Characterizing the effects of landscape features on genetic variation is essential for understanding how landscapes shape patterns of gene flow and spatial genetic structure of populations. Most landscape genetics studies have focused on patterns of gene flow at a regional scale. However, the genetic structure of populations at a local scale may be influenced by a unique suite of landscape variables that have little bearing on connectivity patterns observed at broader spatial scales. We inves...

  17. Hydrologic response to valley-scale structure in alpine headwaters

    Science.gov (United States)

    Weekes, Anne A.; Torgersen, Christian E.; Montgomery, David R.; Woodward, Andrea; Bolton, Susan M.

    2015-01-01

    Few systematic studies of valley-scale geomorphic drivers of streamflow regimes in complex alpine headwaters have compared response between catchments. As a result, little guidance is available for regional-scale hydrological research and monitoring efforts that include assessments of ecosystem function. Physical parameters such as slope, elevation range, drainage area and bedrock geology are often used to stratify differences in streamflow response between sampling sites within an ecoregion. However, these metrics do not take into account geomorphic controls on streamflow specific to glaciated mountain headwaters. The coarse-grained nature of depositional features in alpine catchments suggests that these landforms have little water storage capacity because hillslope runoff moves rapidly just beneath the rock mantle before emerging in fluvial networks. However, recent studies show that a range of depositional features, including talus slopes, protalus ramparts and 'rock-ice' features may have more storage capacity than previously thought.

  18. Multi-scale structural analysis of gas diffusion layers

    Science.gov (United States)

    Göbel, Martin; Godehardt, Michael; Schladitz, Katja

    2017-07-01

    The macroscopic properties of materials are strongly determined by their micro structure. Here, transport properties of gas diffusion layers (GDL) for fuel cells are considered. In order to simulate flow and thermal properties, detailed micro structural information is essential. 3D images obtained by high-resolution computed tomography using synchrotron radiation and scanning electron microscopy (SEM) combined with focused ion beam (FIB) serial slicing were used. A recent method for reconstruction of porous structures from FIB-SEM images and sophisticated morphological image transformations were applied to segment the solid structural components. The essential algorithmic steps for segmenting the different components in the tomographic data-sets are described and discussed. In this paper, two types of GDL, based on a non-woven substrate layer and a paper substrate layer were considered, respectively. More than three components are separated within the synchrotron radiation computed tomography data. That is, fiber system, polytetrafluoroethylene (PTFE) binder/impregnation, micro porous layer (MPL), inclusions within the latter, and pore space are segmented. The usage of the thus derived 3D structure data in different simulation applications can be demonstrated. Simulations of macroscopic properties such as thermal conductivity, depending on the flooding state of the GDL are possible.

  19. Optimal inference with suboptimal models: addiction and active Bayesian inference.

    Science.gov (United States)

    Schwartenbeck, Philipp; FitzGerald, Thomas H B; Mathys, Christoph; Dolan, Ray; Wurst, Friedrich; Kronbichler, Martin; Friston, Karl

    2015-02-01

    When casting behaviour as active (Bayesian) inference, optimal inference is defined with respect to an agent's beliefs - based on its generative model of the world. This contrasts with normative accounts of choice behaviour, in which optimal actions are considered in relation to the true structure of the environment - as opposed to the agent's beliefs about worldly states (or the task). This distinction shifts an understanding of suboptimal or pathological behaviour away from aberrant inference as such, to understanding the prior beliefs of a subject that cause them to behave less 'optimally' than our prior beliefs suggest they should behave. Put simply, suboptimal or pathological behaviour does not speak against understanding behaviour in terms of (Bayes optimal) inference, but rather calls for a more refined understanding of the subject's generative model upon which their (optimal) Bayesian inference is based. Here, we discuss this fundamental distinction and its implications for understanding optimality, bounded rationality and pathological (choice) behaviour. We illustrate our argument using addictive choice behaviour in a recently described 'limited offer' task. Our simulations of pathological choices and addictive behaviour also generate some clear hypotheses, which we hope to pursue in ongoing empirical work. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

  20. Recent Trends in Local-Scale Marine Biodiversity Reflect Community Structure and Human Impacts.

    Science.gov (United States)

    Elahi, Robin; O'Connor, Mary I; Byrnes, Jarrett E K; Dunic, Jillian; Eriksson, Britas Klemens; Hensel, Marc J S; Kearns, Patrick J

    2015-07-20

    The modern biodiversity crisis reflects global extinctions and local introductions. Human activities have dramatically altered rates and scales of processes that regulate biodiversity at local scales. Reconciling the threat of global biodiversity loss with recent evidence of stability at fine spatial scales is a major challenge and requires a nuanced approach to biodiversity change that integrates ecological understanding. With a new dataset of 471 diversity time series spanning from 1962 to 2015 from marine coastal ecosystems, we tested (1) whether biodiversity changed at local scales in recent decades, and (2) whether we can ignore ecological context (e.g., proximate human impacts, trophic level, spatial scale) and still make informative inferences regarding local change. We detected a predominant signal of increasing species richness in coastal systems since 1962 in our dataset, though net species loss was associated with localized effects of anthropogenic impacts. Our geographically extensive dataset is unlikely to be a random sample of marine coastal habitats; impacted sites (3% of our time series) were underrepresented relative to their global presence. These local-scale patterns do not contradict the prospect of accelerating global extinctions but are consistent with local species loss in areas with direct human impacts and increases in diversity due to invasions and range expansions in lower impact areas. Attempts to detect and understand local biodiversity trends are incomplete without information on local human activities and ecological context. Copyright © 2015 Elsevier Ltd. All rights reserved.

  1. Additive Manufacturing of Metal Structures at the Micrometer Scale.

    Science.gov (United States)

    Hirt, Luca; Reiser, Alain; Spolenak, Ralph; Zambelli, Tomaso

    2017-05-01

    Currently, the focus of additive manufacturing (AM) is shifting from simple prototyping to actual production. One driving factor of this process is the ability of AM to build geometries that are not accessible by subtractive fabrication techniques. While these techniques often call for a geometry that is easiest to manufacture, AM enables the geometry required for best performance to be built by freeing the design process from restrictions imposed by traditional machining. At the micrometer scale, the design limitations of standard fabrication techniques are even more severe. Microscale AM thus holds great potential, as confirmed by the rapid success of commercial micro-stereolithography tools as an enabling technology for a broad range of scientific applications. For metals, however, there is still no established AM solution at small scales. To tackle the limited resolution of standard metal AM methods (a few tens of micrometers at best), various new techniques aimed at the micrometer scale and below are presently under development. Here, we review these recent efforts. Specifically, we feature the techniques of direct ink writing, electrohydrodynamic printing, laser-assisted electrophoretic deposition, laser-induced forward transfer, local electroplating methods, laser-induced photoreduction and focused electron or ion beam induced deposition. Although these methods have proven to facilitate the AM of metals with feature sizes in the range of 0.1-10 µm, they are still in a prototype stage and their potential is not fully explored yet. For instance, comprehensive studies of material availability and material properties are often lacking, yet compulsory for actual applications. We address these items while critically discussing and comparing the potential of current microscale metal AM techniques. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Emergence of scale-free close-knit friendship structure in online social networks.

    Directory of Open Access Journals (Sweden)

    Ai-Xiang Cui

    Full Text Available Although the structural properties of online social networks have attracted much attention, the properties of the close-knit friendship structures remain an important question. Here, we mainly focus on how these mesoscale structures are affected by the local and global structural properties. Analyzing the data of four large-scale online social networks reveals several common structural properties. It is found that not only the local structures given by the indegree, outdegree, and reciprocal degree distributions follow a similar scaling behavior, the mesoscale structures represented by the distributions of close-knit friendship structures also exhibit a similar scaling law. The degree correlation is very weak over a wide range of the degrees. We propose a simple directed network model that captures the observed properties. The model incorporates two mechanisms: reciprocation and preferential attachment. Through rate equation analysis of our model, the local-scale and mesoscale structural properties are derived. In the local-scale, the same scaling behavior of indegree and outdegree distributions stems from indegree and outdegree of nodes both growing as the same function of the introduction time, and the reciprocal degree distribution also shows the same power-law due to the linear relationship between the reciprocal degree and in/outdegree of nodes. In the mesoscale, the distributions of four closed triples representing close-knit friendship structures are found to exhibit identical power-laws, a behavior attributed to the negligible degree correlations. Intriguingly, all the power-law exponents of the distributions in the local-scale and mesoscale depend only on one global parameter, the mean in/outdegree, while both the mean in/outdegree and the reciprocity together determine the ratio of the reciprocal degree of a node to its in/outdegree. Structural properties of numerical simulated networks are analyzed and compared with each of the four

  3. Critical Scales, Fundamental Structures and Inherent Instabilities of Turbulent Flames

    Science.gov (United States)

    2015-06-01

    turbulence scales were both analyzed. It was shown that in both limits interactions of detonations with non-uniform fluid density fields had greater...effects than interactions with non-uniform fluid velocity fields. High-speed turbulent-combustion dynamics thereby was shown to behave very...Williams,   “Ignition  Time  of  Hydrogen-­‐Air  Diffusion  Flames,”  Comptes  Rendus   Mecanique  340,  882-­‐893  (2012

  4. The scaling and structure of aquatic animal wakes

    NARCIS (Netherlands)

    Videler, JJ; Stamhuis, EJ; Muller, UK; van Duren, LA

    2002-01-01

    Animal generated water movements are visualized and quantified using two-dimensional particle image velocimetry (PIV). The resulting vector flow fields allow for the study of the distribution of velocity, vorticity and vortices. Structural and temporal aspects of animal-induced flows covering a

  5. Quantitative Structure-Activity Relationship Model for HCVNS5B inhibitors based on an Antlion Optimizer-Adaptive Neuro-Fuzzy Inference System.

    Science.gov (United States)

    Elaziz, Mohamed Abd; Moemen, Yasmine S; Hassanien, Aboul Ella; Xiong, Shengwu

    2018-01-24

    The global prevalence of hepatitis C Virus (HCV) is approximately 3% and one-fifth of all HCV carriers live in the Middle East, where Egypt has the highest global incidence of HCV infection. Quantitative structure-activity relationship (QSAR) models were used in many applications for predicting the potential effects of chemicals on human health and environment. The adaptive neuro-fuzzy inference system (ANFIS) is one of the most popular regression methods for building a nonlinear QSAR model. However, the quality of ANFIS is influenced by the size of the descriptors, so descriptor selection methods have been proposed, although these methods are affected by slow convergence and high time complexity. To avoid these limitations, the antlion optimizer was used to select relevant descriptors, before constructing a nonlinear QSAR model based on the PIC 50 and these descriptors using ANFIS. In our experiments, 1029 compounds were used, which comprised 579 HCVNS5B inhibitors (PIC 50   ~14). The experimental results showed that the proposed QSAR model obtained acceptable accuracy according to different measures, where [Formula: see text] was 0.952 and 0.923 for the training and testing sets, respectively, using cross-validation, while [Formula: see text] was 0.8822 using leave-one-out (LOO).

  6. Geographic genetic structure in two laticaudine sea kraits, Laticauda laticaudata and Laticauda semifasciata (Serpentes: Elapidae), in the Ryukyu-Taiwan region as inferred from mitochondrial cytochrome b sequences.

    Science.gov (United States)

    Tandavanitj, Nontivich; Ota, Hidetoshi; Cheng, Yuan-Cheng; Toda, Mamoru

    2013-08-01

    The Ryukyu-Taiwan region is an island arch with intervening waters of varying distances and depths. This study examines the geographic genetic structure of two sympatric sea kraits, Laticauda laticaudata and L. semifasciata, in the region, to infer factors affecting the extent of dispersal and other biogeographical traits of these amphibious reptiles. Sequence analyses of the mitochondrial cytochrome b gene revealed four and 16 haplotypes for L. laticaudata (136 individuals) and L. semifasciata (177 individuals), respectively. For both species, population pairwise F ST analyses revealed significant genetic differentiations among islands and island groups, which are separated by deep straits, suggesting that deep waters serve as obstacles for dispersal in both species. Significant genetic differentiation was detected even among islands of the same basin in L. laticaudata, but not in L. semifasciata, and the isolation by distance analyses revealed no significant correlation between geographic and genetic distances in the former species. These results further suggest that L. laticaudata has stronger site fidelity or degree of philopatry than L. semifasciata. Based on the geographic genetic patterns, the historical biogeography of the two species in the Ryukyu-Taiwan region is also discussed.

  7. Large-scale structure and gravitational waves. III. Tidal effects

    Science.gov (United States)

    Schmidt, Fabian; Pajer, Enrico; Zaldarriaga, Matias

    2014-04-01

    The leading locally observable effect of a long-wavelength metric perturbation corresponds to a tidal field. We derive the tidal field induced by scalar, vector, and tensor perturbations, and use second-order perturbation theory to calculate the effect on the locally measured small-scale density fluctuations. For subhorizon scalar perturbations, we recover the standard perturbation theory result (F2 kernel). For tensor modes of wavenumber kL, we find that effects persist for kLτ ≫1, i.e. even long after the gravitational wave has entered the horizon and redshifted away ("fossil effect"). We then use these results, combined with the "ruler perturbations" of F. Schmidt and D. Jeong [Phys. Rev. D 86, 083527 (2012)], to predict the observed distortion of the small-scale matter correlation function induced by a long-wavelength tensor mode. We also estimate the observed signal in the B mode of the cosmic shear from a gravitational wave background, including both tidal (intrinsic alignment) and projection (lensing) effects. The nonvanishing tidal effect in the kLτ≫1 limit significantly increases the intrinsic alignment contribution to shear B modes, especially at low redshifts z≲2.

  8. Loss of the flagellum happened only once in the fungal lineage: phylogenetic structure of Kingdom Fungi inferred from RNA polymerase II subunit genes

    Science.gov (United States)

    Liu, Yajuan J; Hodson, Matthew C; Hall, Benjamin D

    2006-01-01

    Background At present, there is not a widely accepted consensus view regarding the phylogenetic structure of kingdom Fungi although two major phyla, Ascomycota and Basidiomycota, are clearly delineated. Regarding the lower fungi, Zygomycota and Chytridiomycota, a variety of proposals have been advanced. Microsporidia may or may not be fungi; the Glomales (vesicular-arbuscular mycorrhizal fungi) may or may not constitute a fifth fungal phylum, and the loss of the flagellum may have occurred either once or multiple times during fungal evolution. All of these issues are capable of being resolved by a molecular phylogenetic analysis which achieves strong statistical support for major branches. To date, no fungal phylogeny based upon molecular characters has satisfied this criterion. Results Using the translated amino acid sequences of the RPB1 and RPB2 genes, we have inferred a fungal phylogeny that consists largely of well-supported monophyletic phyla. Our major results, each with significant statistical support, are: (1) Microsporidia are sister to kingdom Fungi and are not members of Zygomycota; that is, Microsporidia and fungi originated from a common ancestor. (2) Chytridiomycota, the only fungal phylum having a developmental stage with a flagellum, is paraphyletic and is the basal lineage. (3) Zygomycota is monophyletic based upon sampling of Trichomycetes, Zygomycetes, and Glomales. (4) Zygomycota, Basidiomycota, and Ascomycota form a monophyletic group separate from Chytridiomycota. (5) Basidiomycota and Ascomycota are monophyletic sister groups. Conclusion In general, this paper highlights the evolutionary position and significance of the lower fungi (Zygomycota and Chytridiomycota). Our results suggest that loss of the flagellum happened only once during early stages of fungal evolution; consequently, the majority of fungi, unlike plants and animals, are nonflagellated. The phylogeny we infer from gene sequences is the first one that is congruent with the

  9. An Inference Language for Imaging

    DEFF Research Database (Denmark)

    Pedemonte, Stefano; Catana, Ciprian; Van Leemput, Koen

    2014-01-01

    We introduce iLang, a language and software framework for probabilistic inference. The iLang framework enables the definition of directed and undirected probabilistic graphical models and the automated synthesis of high performance inference algorithms for imaging applications. The iLang framework...... is composed of a set of language primitives and of an inference engine based on a message-passing system that integrates cutting-edge computational tools, including proximal algorithms and high performance Hamiltonian Markov Chain Monte Carlo techniques. A set of domain-specific highly optimized GPU......-accelerated primitives specializes iLang to the spatial data-structures that arise in imaging applications. We illustrate the framework through a challenging application: spatio-temporal tomographic reconstruction with compressive sensing....

  10. Dark matter, long-range forces, and large-scale structure

    Science.gov (United States)

    Gradwohl, Ben-Ami; Frieman, Joshua A.

    1992-01-01

    If the dark matter in galaxies and clusters is nonbaryonic, it can interact with additional long-range fields that are invisible to experimental tests of the equivalence principle. We discuss the astrophysical and cosmological implications of a long-range force coupled only to the dark matter and find rather tight constraints on its strength. If the force is repulsive (attractive), the masses of galaxy groups and clusters (and the mean density of the universe inferred from them) have been systematically underestimated (overestimated). We explore the consequent effects on the two-point correlation function, large-scale velocity flows, and microwave background anisotropies, for models with initial scale-invariant adiabatic perturbations and cold dark matter.

  11. Evidence of variant intra- and interspecific scaling of tree crown structure and relevance for allometric theory.

    Science.gov (United States)

    Pretzsch, Hans; Dieler, Jochen

    2012-07-01

    General scaling rules or constants for metabolic and structural plant allometry as assumed by the theory of Euclidian geometric scaling (2/3-scaling) or metabolic scaling (3/4-scaling) may meet human's innate propensity for simplicity and generality of pattern and processes in nature. However, numerous empirical works show that variability of crown structure rather than constancy is essential for a tree's success in coping with crowding. In order to link theory and empiricism, we analyzed the intra- and inter-specific scaling of crown structure for 52 tree species. The basis is data from 84 long-term plots of temperate monospecific forests under survey since 1870 and a set of 126 yield tables of angiosperm and gymnosperm forest tree species across the world. The study draws attention to (1) the intra-specific variation and correlation of the three scaling relationships: tree height versus trunk diameter, crown cross-sectional area versus trunk diameter, and tree volume versus trunk diameter, and their dependence on competition, (2) the inter-specific variation and correlation of the same scaling exponents ([Formula: see text] and [Formula: see text]) across 52 tree species, and (3) the relevance of the revealed variable scaling of crown structure for leaf organs and metabolic scaling. Our results arrive at suggesting a more extended metabolic theory of ecology which includes variability and covariation between allometric relationships as prerequisite for the individual plant's competitiveness.

  12. Inferring coastal processes from regional-scale mapping of {sup 222}Radon and salinity: examples from the Great Barrier Reef, Australia

    Energy Technology Data Exchange (ETDEWEB)

    Stieglitz, Thomas C., E-mail: thomas.stieglitz@jcu.edu.a [AIMS-JCU, Townsville (Australia); Australian Institute of Marine Science, PMB NO 3, Townsville QLD 4810 (Australia); School of Engineering and Physical Sciences, James Cook University, Townsville QLD 4811 (Australia); Cook, Peter G., E-mail: peter.g.cook@csiro.a [CSIRO Land and Water, Private Bag 2, Glen Osmond SA 5064 (Australia); Burnett, William C., E-mail: wburnett@mailer.fsu.ed [Department of Oceanography, Florida State University, Tallahassee, FL 32306 (United States)

    2010-07-15

    The radon isotope {sup 222}Rn and salinity in coastal surface water were mapped on regional scales, to improve the understanding of coastal processes and their spatial variability. Radon was measured with a surface-towed, continuously recording multi-detector setup on a moving vessel. Numerous processes and locations of land-ocean interaction along the Central Great Barrier Reef coastline were identified and interpreted based on the data collected. These included riverine fluxes, terrestrially-derived fresh submarine groundwater discharge (SGD) and the tidal pumping of seawater through mangrove forests. Based on variations in the relationship of the tracers radon and salinity, some aspects of regional freshwater inputs to the coastal zone and to estuaries could be assessed. Concurrent mapping of radon and salinity allowed an efficient qualitative assessment of land-ocean interaction on various spatial and temporal scales, indicating that such surveys on coastal scales can be a useful tool to obtain an overview of SGD locations and processes.

  13. Sediment Scaling for Mud Mountain Fish Barrier Structure

    Science.gov (United States)

    2017-06-28

    Structure by Jeremy A. Sharp, Gary L. Brown, and Gary L. Bell PURPOSE: This Coastal and Hydraulics Laboratory technical note describes the process of... energy in the system (model) to keep the WL suspended until it encounters an area of momentum loss (e.g., behind the barrier). Satisfaction of Rouse...Seattle District hydraulic engineers and the fish barrier operators). At a flow of approximately 4,000 cubic feet/second, the bed mobilizes and readily

  14. Large scale structures and the cubic galileon model

    CERN Document Server

    Bhattacharya, Sourav; Tomaras, Theodore N

    2015-01-01

    The maximum size of a bound cosmic structure is computed perturbatively as a function of its mass in the framework of the cubic galileon, proposed recently to model the dark energy of our Universe. Comparison of our results with observations constrains the matter-galileon coupling of the model to $0.03\\lesssim \\alpha \\lesssim 0.17$, thus improving previous bounds based solely on solar system physics.

  15. Large Scale Structure From Motion for Autonomous Underwater Vehicle Surveys

    Science.gov (United States)

    2004-09-01

    and putting up with my bad movie choices. Thanks Charlie for defending your ideals, for the runs together, and for being Charlie. Mark Johnson to...mosaicing, the information from multiple underwater views can be used to extract structure and motion estimates using ideas from SFM and photogrammetry ...to use images to measure and come up with estimates of uncertainty will bring some of the fruits of photogrammetry to underwater archeology such as

  16. Equifinality and the Scaling Exponent of the Structure Function

    Science.gov (United States)

    Fitton, G. F.; Mezematy, Y.; Schertzer, D. J. M.; Tchiguirinskaia, I.

    2014-12-01

    In turbulence the structure function is by far the most widely used tool for the empirical analysis of the velocity field. This is due mainly to the work of Kolmogorov (1941) who hypothesised a homogeneous flux of energy and derived the famous 2/3 power law for the second-order structure function; — which corresponds to a 5/3 law for the energy spectrum (Obukhov, 1942). In 1962 Kolmogorov refined his hypothesis to take into account the intermittency of the flux, with the consequence that the exponent ξ(q) of the structure function is not longer proportional to its statistical order q. In this communication, we first show that the refined hypothesis can lead to different models that can have opposite intermittency corrections. Secondly, we demonstrate that the inverse problem, i.e., starting from a given expression of ξ(q) to recover the involved flux leads to an interesting problem of equifinality for the definition of this flux. This is done in particular in the framework of the Fractionally Integrated Flux model that gives a precise meaning to the refined hypothesis. The theoretical and practical consequences are illustrated with the help data analysis and simulations of turbulence in wind farms and urban lakes.

  17. Quantitative structure-activity relationship analysis of human neutrophil elastase inhibitors using shuffling classification and regression trees and adaptive neuro-fuzzy inference systems.

    Science.gov (United States)

    Asadollahi-Baboli, M

    2012-07-01

    The purpose of this study was to develop quantitative structure-activity relationship models for N-benzoylindazole derivatives as inhibitors of human neutrophil elastase. These models were developed with the aid of classification and regression trees (CART) and an adaptive neuro-fuzzy inference system (ANFIS) combined with a shuffling cross-validation technique using interpretable descriptors. More than one hundred meaningful descriptors, representing various structural characteristics for all 51 N-benzoylindazole derivatives in the data set, were calculated and used as the original variables for shuffling CART modelling. Five descriptors of average Wiener index, Kier benzene-likeliness index, subpolarity parameter, average shape profile index of order 2 and folding degree index selected by the shuffling CART technique have been used as inputs of the ANFIS for prediction of inhibition behaviour of N-benzoylindazole derivatives. The results of the developed shuffling CART-ANFIS model compared to other techniques, such as genetic algorithm (GA)-partial least square (PLS)-ANFIS and stepwise multiple linear regression (MLR)-ANFIS, are promising and descriptive. The satisfactory results r2p = 0.845, Q2(LOO) = 0.861, r2(L25%O) = 0.829, RMSE(LOO)  = 0.305 and RMSE(L25%O)  = 0.336) demonstrate that shuffling CART-ANFIS models present the relationship between human neutrophil elastase inhibitor activity and molecular descriptors, and they yield predictions in excellent agreement with the experimental values.

  18. Network-scale spatial and temporal variation in Chinook salmon (Oncorhynchus tshawytscha) redd distributions: patterns inferred from spatially continuous replicate surveys

    Science.gov (United States)

    Daniel J. Isaak; Russell F. Thurow

    2006-01-01

    Spatially continuous sampling designs, when temporally replicated, provide analytical flexibility and are unmatched in their ability to provide a dynamic system view. We have compiled such a data set by georeferencing the network-scale distribution of Chinook salmon (Oncorhynchus tshawytscha) redds across a large wilderness basin (7330 km2) in...

  19. Migration history of North Sea houting (Coregonus oxyrinchus L.) caught in Lake IJsselmeer (The Netherlands) inferred from scale transects of 88SR:44 Ca ratios

    NARCIS (Netherlands)

    Borcherding, J.; Pickhardt, C.; Winter, H.V.; Becker, J.S.

    2008-01-01

    North Sea houting, Coregonus oxyrinchus, became extinct in the River Rhine in the 1940 s and was reintroduced in the 1990 s. To study the migration history of individuals, the 88Sr:44Ca ratio of scales of 39 houting (10¿44 cm TL) caught in Lake IJsselmeer was analysed using laser ablation

  20. Thermal scaling laws of the optical Bragg acceleration structure

    Directory of Open Access Journals (Sweden)

    Vadim Karagodsky

    2006-05-01

    Full Text Available The temperature distribution and heat flow in the planar optical Bragg acceleration structure, fed by a train of high-power laser pulses, are analyzed. Dynamic analysis of a high-repetition rate train of pulses indicates that the stationary solution is an excellent approximation for the regime of interest. Analytic expressions for the temperature and heat distributions across the acceleration structure are developed. Assuming an accelerating gradient of 1  GV/m and a loss factor similar to that existing in communication optical fibers 1   dB/km (tan⁡δ∼10^{-11}, the temperature increase is less than 1 K and the heat flow is of the order of 1   W/cm^{2}, which is 3 orders of magnitude lower than the known technological limit for heat dissipation. Obviously, using materials with a significantly higher loss tangent may lead to unacceptable temperatures and temperature gradients as well as confinement difficulties and phase mismatch.

  1. Inferring large-scale patterns of niche evolution and dispersal limitation from the phylogenetic composition of assemblages: A case study on New World palms

    DEFF Research Database (Denmark)

    Eiserhardt, Wolf L.; Svenning, J.-C.; Baker, William J.

    How fast species’ environmental tolerances can evolve is crucial for their survival prospect under climate change. Phylogenetic information can yield insights into the tempo of niche evolution. Phylogenetic community structure (PCS) complements the more widely used approach of studying niche...

  2. Implementation of Grid-computing Framework for Simulation in Multi-scale Structural Analysis

    Directory of Open Access Journals (Sweden)

    Data Iranata

    2010-05-01

    Full Text Available A new grid-computing framework for simulation in multi-scale structural analysis is presented. Two levels of parallel processing will be involved in this framework: multiple local distributed computing environments connected by local network to form a grid-based cluster-to-cluster distributed computing environment. To successfully perform the simulation, a large-scale structural system task is decomposed into the simulations of a simplified global model and several detailed component models using various scales. These correlated multi-scale structural system tasks are distributed among clusters and connected together in a multi-level hierarchy and then coordinated over the internet. The software framework for supporting the multi-scale structural simulation approach is also presented. The program architecture design allows the integration of several multi-scale models as clients and servers under a single platform. To check its feasibility, a prototype software system has been designed and implemented to perform the proposed concept. The simulation results show that the software framework can increase the speedup performance of the structural analysis. Based on this result, the proposed grid-computing framework is suitable to perform the simulation of the multi-scale structural analysis.

  3. Deciphering Adsorption Structure on Insulators at the Atomic Scale

    Energy Technology Data Exchange (ETDEWEB)

    Thurmer, Konrad [Sandia National Lab. (SNL-CA), Livermore, CA (United States). Materials Physics; Feibelman, Peter J. [Sandia National Lab. (SNL-CA), Livermore, CA (United States). Integrated Nanotechnologies

    2014-09-01

    We applied Scanning Probe Microscopy and Density Functional Theory (DFT) to discover the basics of how adsorbates wet insulating substrates, addressing a key question in geochemistry. To allow experiments on insulating samples we added Atomic Force Microscopy (AFM) capability to our existing UHV Scanning Tunneling Microscope (STM). This was accomplished by integrating and debugging a commercial qPlus AFM upgrade. Examining up-to-40-nm-thick water films grown in vacuum we found that the exact nature of the growth spirals forming around dislocations determines what structure of ice, cubic or hexagonal, is formed at low temperature. DFT revealed that wetting of mica is controlled by how exactly a water layer wraps around (hydrates) the K+ ions that protrude from the mica surface. DFT also sheds light on the experimentally observed extreme sensitivity of the mica surface to preparation conditions: K atoms can easily be rinsed off by water flowing past the mica surface.

  4. Reliability of the factor structure of the Multidimensional Scale of Interpersonal Reactivity (EMRI

    Directory of Open Access Journals (Sweden)

    Nilton S. Formiga

    2013-10-01

    Full Text Available This study aims to check the internal consistency and factor structure evaluative of the empathy scale in a high school and college sample in the state of Minas Gerais. The instruments that measure empathy can be easily found, however, of the existing, just multidimensional scale of interpersonal reactivity (Emri is the theoretical framework that has far more and better organized, and the scale that is most commonly used to assess this construct. Participated 488 subjects, male and female, with ages from 14-54 years old, distributed in primary and college levels in Patrocínio-MG composed this study sample. The subjects answered the Multidimensional Scale of Interpersonal Reactivity and socio-demographic data. From an equation analysis and structural modeling were observed psychometric indicators that assured the structural consistency of the scale, promoting in the security of the measure theoretical construct of empathy.

  5. A divide-and-conquer linear scaling three dimensional fragment method for large scale electronic structure calculations

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Lin-Wang; Zhao, Zhengji; Meza, Juan; Wang, Lin-Wang

    2008-07-11

    We present a new linear scaling ab initio total energy electronic structure calculation method based on the divide-and-conquer strategy. This method is simple to implement, easily to parallelize, and produces very accurate results when compared with the direct ab initio method. The method has been tested using up to 8,000 processors, and has been used to calculate nanosystems up to 15,000 atoms.

  6. Femtosecond structural dynamics on the atomic length scale

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Dongfang

    2014-03-15

    This thesis reports on the development and application of two different but complementary ultrafast electron diffraction setups built at the Max Planck Research Department for Structural Dynamics. One is an ultra-compact femtosecond electron diffraction (FED) setup (Egun300), which is currently operational (with a maximum electron energy of 150 keV) and provides ultrashort (∝300 fs) and bright (∝10 e/μm{sup 2}) electron bunches. The other one, named as Relativistic Electron Gun for Atomic Exploration (REGAE) is a radio frequency driven 2 to 5 MeV FED setup built in collaboration with different groups from DESY. REGAE was developed as a facility that will provide high quality diffraction with sufficient coherence to even address structural protein dynamics and with electron pulses as short as 20 fs (FWHM). As one of the first students in Prof. R.J. Dwayne Miller's group, I led the femtosecond (fs) laser sub-group at REGAE being responsible for the construction of different key optical elements required to drive both of aforementioned FED systems. A third harmonic generation (THG) and a nonlinear optical parametric amplifier (NOPA) have been used for the photo-generation of ultrashort electron bursts as well as sample laser excitation. Different diagnostic tools have been constructed to monitor the performance of the fs optical system. A fast autocorrelator was developed to provide on the fly pulse duration correction. A transient-grating frequency-resolved optical gating (TG-FROG) was built to obtain detail information about the characteristics of fs optical pulse, i.e. phase and amplitude of its spectral components. In addition to these optical setups, I developed a fs optical pump-probe system, which supports broadband probe pulses. This setup was successfully applied to investigate the semiconductor-to-metal photoinduced phase transition in VO{sub 2} and the ultrafast photo-reduction mechanism of graphene oxide. In regard to FED setups, I have been

  7. Morphology Characterization of PP/Clay Nanocomposites Across the Length Scales of the Structural Architecture

    NARCIS (Netherlands)

    Szazdi, Laszlo; Abranyi, Agnes; Pukansky Jr, Bela; Vancso, Gyula J.; Pukanszky, B.; Pukanszky, Bela

    2006-01-01

    The structure and rheological properties of a large number of layered silicate poly(propylene) nanocomposites were studied with widely varying compositions. Morphology characterization at different length scales was achieved by SEM, TEM, and XRD. Rheological measurements supplied additional

  8. Gauged extended supergravity without cosmological constant no-scale structure and supersymmetry breaking

    CERN Document Server

    Andrianopoli, Laura; Ferrara, Sergio; Lledó, M A

    2003-01-01

    We consider the interplay of duality symmetries and gauged isometries of supergravity models giving N-extended, spontaneously broken supergravity with a no-scale structure. Some examples, motivated by superstring and M-theory compactifications are described.

  9. Genetic structure of Bemisia tabaci Med populations from home-range countries, inferred by nuclear and cytoplasmic markers: impact on the distribution of the insecticide resistance genes.

    Science.gov (United States)

    Gauthier, Nathalie; Clouet, Cécile; Perrakis, Andreas; Kapantaidaki, Despoina; Peterschmitt, Michel; Tsagkarakou, Anastasia

    2014-10-01

    Insecticide resistance management in Bemisia tabaci is one of the main issues facing agricultural production today. An extensive survey was undertaken in five Mediterranean countries to examine the resistance status of Med B. tabaci species in its range of geographic origin and the relationship between population genetic structure and the distribution of resistance genes. The investigation combined molecular diagnostic tests, sequence and microsatellite polymorphism studies and monitoring of endosymbionts. High frequencies of pyrethroid (L925I and T929V, VGSC gene) and organophosphate (F331W, ace1 gene) resistance mutations were found in France, Spain and Greece, but not in Morocco or Tunisia. Sequence analyses of the COI gene delineated two closely related mitochondrial groups (Q1 and Q2), which were found either sympatrically (Spain) or separately (France). Only Q1 was observed in Greece, Morocco and Tunisia. Bayesian analyses based on microsatellite loci revealed three geographically delineated genetic groups (France, Spain, Morocco/Greece/Tunisia) and high levels of genetic differentiation even between neighbouring samples. Evidence was also found for hybridisation and asymmetrical gene flow between Q1 and Q2. Med B. tabaci is more diverse and structured than reported so far. On a large geographic scale, resistance is affected by population genetic structure, whereas on a local scale, agricultural practices appear to play a major role. © 2014 Society of Chemical Industry.

  10. The Development of Large Scale Cosmic Structure:. A Theoretician's Approach

    Science.gov (United States)

    Ostriker, Jeremiah P.

    2001-03-01

    The study of cosmology, the origin, nature and future evolution of structure in the universe, has been totally transformed in the last decade, and computers have played a major role in the change. New theories have arisen from particle physics which make the subject, formerly almost a branch of philosophy, into quantitative science. Initial, semi-quantitative tests of these theories, either using data on galaxy distributions in the local universe or the cosmic background radiation fluctuations reaching us from the distant universe, indicate rough agreement with the simplest predictions of the theories. But now that fully three-dimensional, time-dependent numerical simulations can be made on modern, parallel architecture computers, we can examine (using good physical modelling) the detailed quantitative predictions of the various theories that have been proposed to see which, if any, can produce an output consistent with the real world being revealed to us by the latest ground-and space-based instruments. Using these tools, we have been able to reduce to a small number the currently viable options for the correct cosmological theory. At present, the most acceptable model, passing all presently applied tests, is the low density but flat Cold Dark Matter model with Ωbaryon = 0.04, ΩCDM = 0.26, ΩLambda = 0.70. The nature of the "cosmological constant" presents a challenging problem of physics.

  11. The Large-scale Coronal Structure of the 2017 August 21 Great American Eclipse: An Assessment of Solar Surface Flux Transport Model Enabled Predictions and Observations

    Science.gov (United States)

    Nandy, Dibyendu; Bhowmik, Prantika; Yeates, Anthony R.; Panda, Suman; Tarafder, Rajashik; Dash, Soumyaranjan

    2018-01-01

    On 2017 August 21, a total solar eclipse swept across the contiguous United States, providing excellent opportunities for diagnostics of the Sun’s corona. The Sun’s coronal structure is notoriously difficult to observe except during solar eclipses; thus, theoretical models must be relied upon for inferring the underlying magnetic structure of the Sun’s outer atmosphere. These models are necessary for understanding the role of magnetic fields in the heating of the corona to a million degrees and the generation of severe space weather. Here we present a methodology for predicting the structure of the coronal field based on model forward runs of a solar surface flux transport model, whose predicted surface field is utilized to extrapolate future coronal magnetic field structures. This prescription was applied to the 2017 August 21 solar eclipse. A post-eclipse analysis shows good agreement between model simulated and observed coronal structures and their locations on the limb. We demonstrate that slow changes in the Sun’s surface magnetic field distribution driven by long-term flux emergence and its evolution governs large-scale coronal structures with a (plausibly cycle-phase dependent) dynamical memory timescale on the order of a few solar rotations, opening up the possibility for large-scale, global corona predictions at least a month in advance.

  12. Coupling Fine-Scale Root and Canopy Structure Using Ground-Based Remote Sensing

    Directory of Open Access Journals (Sweden)

    Brady S. Hardiman

    2017-02-01

    Full Text Available Ecosystem physical structure, defined by the quantity and spatial distribution of biomass, influences a range of ecosystem functions. Remote sensing tools permit the non-destructive characterization of canopy and root features, potentially providing opportunities to link above- and belowground structure at fine spatial resolution in functionally meaningful ways. To test this possibility, we employed ground-based portable canopy LiDAR (PCL and ground penetrating radar (GPR along co-located transects in forested sites spanning multiple stages of ecosystem development and, consequently, of structural complexity. We examined canopy and root structural data for coherence (i.e., correlation in the frequency of spatial variation at multiple spatial scales ≤10 m within each site using wavelet analysis. Forest sites varied substantially in vertical canopy and root structure, with leaf area index and root mass more becoming even vertically as forests aged. In all sites, above- and belowground structure, characterized as mean maximum canopy height and root mass, exhibited significant coherence at a scale of 3.5–4 m, and results suggest that the scale of coherence may increase with stand age. Our findings demonstrate that canopy and root structure are linked at characteristic spatial scales, which provides the basis to optimize scales of observation. Our study highlights the potential, and limitations, for fusing LiDAR and radar technologies to quantitatively couple above- and belowground ecosystem structure.

  13. Structure, expression profile and phylogenetic inference of chalcone isomerase-like genes from the narrow-leafed lupin (Lupinus angustifolius L. genome

    Directory of Open Access Journals (Sweden)

    Łucja ePrzysiecka

    2015-04-01

    Full Text Available Lupins, like other legumes, have a unique biosynthesis scheme of 5-deoxy-type flavonoids and isoflavonoids. A key enzyme in this pathway is chalcone isomerase (CHI, a member of CHI-fold protein family, encompassing subfamilies of CHI1, CHI2, CHI-like (CHIL, and fatty acid-binding (FAP proteins. Here, two Lupinus angustifolius (narrow-leafed lupin CHILs, LangCHIL1 and LangCHIL2, were identified and characterized using DNA fingerprinting, cytogenetic and linkage mapping, sequencing and expression profiling. Clones carrying CHIL sequences were assembled into two contigs. Full gene sequences were obtained from these contigs, and mapped in two L. angustifolius linkage groups by gene-specific markers. Bacterial artificial chromosome fluorescence in situ hybridization approach confirmed the localization of two LangCHIL genes in distinct chromosomes. The expression profiles of both LangCHIL isoforms were very similar. The highest level of transcription was in the roots of the third week of plant growth; thereafter, expression declined. The expression of both LangCHIL genes in leaves and stems was similar and low. Comparative mapping to reference legume genome sequences revealed strong syntenic links; however, LangCHIL2 contig had a much more conserved structure than LangCHIL1. LangCHIL2 is assumed to be an ancestor gene, whereas LangCHIL1 probably appeared as a result of duplication. As both copies are transcriptionally active, questions arise concerning their hypothetical functional divergence. Screening of the narrow-leafed lupin genome and transcriptome with CHI-fold protein sequences, followed by Bayesian inference of phylogeny and cross-genera synteny survey, identified representatives of all but one (CHI1 main subfamilies. They are as follows: two copies of CHI2, FAPa2 and CHIL, and single copies of FAPb and FAPa1. Duplicated genes are remnants of whole genome duplication which is assumed to have occurred after the divergence of Lupinus, Arachis

  14. Structure, expression profile and phylogenetic inference of chalcone isomerase-like genes from the narrow-leafed lupin (Lupinus angustifolius L.) genome.

    Science.gov (United States)

    Przysiecka, Łucja; Książkiewicz, Michał; Wolko, Bogdan; Naganowska, Barbara

    2015-01-01

    Lupins, like other legumes, have a unique biosynthesis scheme of 5-deoxy-type flavonoids and isoflavonoids. A key enzyme in this pathway is chalcone isomerase (CHI), a member of CHI-fold protein family, encompassing subfamilies of CHI1, CHI2, CHI-like (CHIL), and fatty acid-binding (FAP) proteins. Here, two Lupinus angustifolius (narrow-leafed lupin) CHILs, LangCHIL1 and LangCHIL2, were identified and characterized using DNA fingerprinting, cytogenetic and linkage mapping, sequencing and expression profiling. Clones carrying CHIL sequences were assembled into two contigs. Full gene sequences were obtained from these contigs, and mapped in two L. angustifolius linkage groups by gene-specific markers. Bacterial artificial chromosome fluorescence in situ hybridization approach confirmed the localization of two LangCHIL genes in distinct chromosomes. The expression profiles of both LangCHIL isoforms were very similar. The highest level of transcription was in the roots of the third week of plant growth; thereafter, expression declined. The expression of both LangCHIL genes in leaves and stems was similar and low. Comparative mapping to reference legume genome sequences revealed strong syntenic links; however, LangCHIL2 contig had a much more conserved structure than LangCHIL1. LangCHIL2 is assumed to be an ancestor gene, whereas LangCHIL1 probably appeared as a result of duplication. As both copies are transcriptionally active, questions arise concerning their hypothetical functional divergence. Screening of the narrow-leafed lupin genome and transcriptome with CHI-fold protein sequences, followed by Bayesian inference of phylogeny and cross-genera synteny survey, identified representatives of all but one (CHI1) main subfamilies. They are as follows: two copies of CHI2, FAPa2 and CHIL, and single copies of FAPb and FAPa1. Duplicated genes are remnants of whole genome duplication which is assumed to have occurred after the divergence of Lupinus, Arachis, and Glycine.

  15. MMPI-A Scale-Level Factor Structure: Replication in a Clinical Sample.

    Science.gov (United States)

    Archer, Robert P.; Krishnamurthy, Radhika

    1997-01-01

    The scale-level factor structure of the adolescent form of the Minnesota Multiphasic Personality Inventory (MMPI-A) was examined in a clinical sample of 358 adolescents receiving psychiatric services. Nine factors accounted for 75.6% of total variance in scale and subscale raw scores. Findings support use of the MMPI-A for assessment of…

  16. Examination of the Spanish Trait Meta-Mood Scale-24 Factor Structure in a Mexican Setting

    Science.gov (United States)

    Valdivia Vázquez, Juan Antonio; Rubio Sosa, Juan Carlos A.; French, Brian F.

    2015-01-01

    The Trait Meta-Mood Scale (TMMS) is an emotional intelligence (EI) assessment originally developed for the U.S. population. This scale measures three EI factors--attention, clarity, and repair--to evaluate how an individual perceives one's own EI skills. Although the TMMS has been adapted for use in several languages and cultures, the structure of…

  17. A Structural Equation Modelling of the Academic Self-Concept Scale

    Science.gov (United States)

    Matovu, Musa

    2014-01-01

    The study aimed at validating the academic self-concept scale by Liu and Wang (2005) in measuring academic self-concept among university students. Structural equation modelling was used to validate the scale which was composed of two subscales; academic confidence and academic effort. The study was conducted on university students; males and…

  18. Relationship between microbial activity and microbial community structure in six full-scale anaerobic digesters

    NARCIS (Netherlands)

    Regueiro, L.; Veiga, P.; Figueroa, M.; Alonso-Gutierrez, J.; Stams, A.J.M.; Lema, J.M.; Carballa, M.

    2012-01-01

    High activity levels and balanced anaerobic microbial communities are necessary to attain proper anaerobic digestion performance. Therefore, this work was focused on the kinetic performance and the microbial community structure of six full-scale anaerobic digesters and one lab-scale co-digester.

  19. Factorial Structure of Rosenberg's Self-Esteem Scale among Crack-Cocaine Drug Users.

    Science.gov (United States)

    Wang, Jichuan; Siegal, Harvey A.; Falck, Russell S.; Carlson, Robert G.

    2001-01-01

    Used nine different confirmatory factor analysis models to test the factorial structure of Rosenberg's (M. Rosenberg, 1965) self-esteem scale with a sample of 430 crack-cocaine users. Results partly support earlier research to show a single global self-esteem factor underlying responses to the Rosenberg scale, method effects associated with item…

  20. Electrohydrodynamic jet printing of PZT thick film micro-scale structures

    OpenAIRE

    Wang, D; Zhu, X.; Liang, J.; Ren, T.; Zha, W.; Dong,W.; Rocks, SA; Dorey, RA; Xu, Z; Wang, X

    2015-01-01

    © 2015 Elsevier Ltd. This paper reports the use of a printing technique, called electrohydrodynamic jet printing, for producing PZT thick film micro-scale structures without additional material removing processes. The PZT powder was ball-milled and the effect of milling time on the particle size was examined. This ball-milling process can significantly reduce the PZT particle size and help to prepare stable composite slurry suitable for the E-Jet printing. The PZT micro-scale structures with ...

  1. Egg distribution, bottom topography and small-scale cod population structure in a coastal marine system

    OpenAIRE

    Knutsen, Halvor; Olsen, Espen Moland; Ciannelli, Lorenzo; Espeland, Sigurd Heiberg; Knutsen, Jan Atle; Simonsen, Jan Henrik; Skreslet, Stig; Stenseth, Nils Christian

    2007-01-01

    Coastal marine species with pelagic egg and larval stages, such as the Atlantic cod Gadus morhua, can be structured into genetically distinct local populations on a surprisingly small geographic scale considering their dispersal potential. Mechanisms responsible for such small-scale genetic structure may involve homing of adults to their natal spawning grounds, but also local retention of pelagic eggs and larvae. For example, spawning within sheltered fjord habitats is expected to favour loca...

  2. INTRINSIC FINE-SCALE STRUCTURE IN COMPLEX MATERIALS: BEYOND GLOBAL CRYSTALLOGRAPHIC ANALYSIS

    Energy Technology Data Exchange (ETDEWEB)

    A. MIGLIORI; ET AL

    2000-12-01

    Many important classes of materials owe their interesting properties to structures and patterns produced by local atomic deviations from ideal crystallographic positions. The pattern scale may vary from a few atomic spacings to many microns. In a macroscopic sample these deviations may still average to an ideal lattice while retaining the intrinsic fine-scale structures, or a phase transition may create a pattern of variants of a new crystallographic structure. We have carried out experiments on the formation of fine-scale structures in a range of materials, particularly those produced by phase transitions. We have used Resonant Ultrasound Spectroscopy for elastic properties and dissipation, neutron pair-distribution function, and electronic transport measurements to characterize samples. We have carried out extensive dynamical modeling based on Ginzberg-Landau formalisms to simulate the development and appearance of the structures. Our results highlight the importance of long-range strain fields and the intrinsic unstable equilibrium features of the materials studied.

  3. Contrasting effects of sampling scale on insect herbivores distribution in response to canopy structure

    Directory of Open Access Journals (Sweden)

    Frederico S. Neves

    2013-03-01

    Full Text Available Species diversity of insect herbivores associated to canopy may vary local and geographically responding to distinct factors at different spatial scales. The aim of this study was to investigate how forest canopy structure affects insect herbivore species richness and abundance depending on feeding guilds´ specificities. We tested the hypothesis that habitat structure affects insect herbivore species richness and abundance differently to sap-sucking and chewing herbivore guilds. Two spatial scales were evaluated: inside tree crowns (fine spatial scale and canopy regions (coarse spatial scale. In three sampling sites we measured 120 tree crowns, grouped in five points with four contiguous tree crowns. Insects were sampled by beating method from each crown and data were summed up for analyzing each canopy region. In crowns (fine spatial scale we measured habitat structure: trunk circumference, tree height, canopy depth, number of ramifications and maximum ramification level. In each point, defined as a canopy region (coarse spatial scale, we measured habitat structure using a vertical cylindrical transect: tree species richness, leaf area, sum of strata heights and maximum canopy height. A principal component analysis based on the measured variables for each spatial scale was run to estimate habitat structure parameters. To test the effects of habitat structure upon herbivores, different general linear models were adjusted using the first two principal components as explanatory variables. Sap-sucking insect species richness and all herbivore abundances increased with size of crown at fine spatial scale. On the other hand, chewer species richness and abundance increased with resource quantity at coarse scale. Feeding specialization, resources availability, and agility are discussed as ecological causes of the found pattern.

  4. AIRS-Observed Interrelationships of Anomaly Time-Series of Moist Process-Related Parameters and Inferred Feedback Values on Various Spatial Scales

    Science.gov (United States)

    Molnar, Gyula I.; Susskind, Joel; Iredell, Lena

    2011-01-01

    In the beginning, a good measure of a GMCs performance was their ability to simulate the observed mean seasonal cycle. That is, a reasonable simulation of the means (i.e., small biases) and standard deviations of TODAY?S climate would suffice. Here, we argue that coupled GCM (CG CM for short) simulations of FUTURE climates should be evaluated in much more detail, both spatially and temporally. Arguably, it is not the bias, but rather the reliability of the model-generated anomaly time-series, even down to the [C]GCM grid-scale, which really matter. This statement is underlined by the social need to address potential REGIONAL climate variability, and climate drifts/changes in a manner suitable for policy decisions.

  5. Engineering data management through different breakdown structures in a large-scale project

    CERN Document Server

    Hameri, A P

    2002-01-01

    This document discusses the benefits stemming from managing different project breakdown structures with an engineering data management system. The structures discussed are project breakdown structure (PBS), assembly breakdown structure (ABS), as-built structure and hardware breakdown. Each structure is presented from the quality management point of view and a practical example of each of the four structures is given to illustrate their differences, and to show what kind of engineering information is to be stored in these structures. The main underlying case is that of CERN and its global, over a decade-long Large Hadron Collider project. The approach used for managing the new particle accelerator project is benchmarked against the way large-scale shipbuilding projects are managed. It is concluded that several structures are needed to manage complex system projects, and that linking information between structures plays a crucial role for the overall success of the project. Information technology and the WWW ar...

  6. A four-scale homogenization analysis of creep of a nuclear containment structure

    Energy Technology Data Exchange (ETDEWEB)

    Tran, A.B. [Université Paris-Est, Laboratoire Modélisation et Simulation Multi Échelle, MSME UMR 8208 CNRS, 5 bd Descartes, F-77454 Marne-la-Vallée (France); EDF R and D – Département MMC Site des Renardières – Avenue des Renardières - Ecuelles, 77818 Moret sur Loing Cedex (France); Department of Applied Informatics in Construction, National University of Civil Engineering, 55 Giai Phong Road, Hai Ba Trung District, Hanoi (Viet Nam); Yvonnet, J., E-mail: julien.yvonnet@univ-paris-est.fr [Université Paris-Est, Laboratoire Modélisation et Simulation Multi Échelle, MSME UMR 8208 CNRS, 5 bd Descartes, F-77454 Marne-la-Vallée (France); He, Q.-C. [Université Paris-Est, Laboratoire Modélisation et Simulation Multi Échelle, MSME UMR 8208 CNRS, 5 bd Descartes, F-77454 Marne-la-Vallée (France); Toulemonde, C.; Sanahuja, J. [EDF R and D – Département MMC Site des Renardières – Avenue des Renardières - Ecuelles, 77818 Moret sur Loing Cedex (France)

    2013-12-15

    A four-scale approach is proposed to predict the creep behavior of a concrete structure. The behavior of concrete is modeled through a numerical multiscale methodology, by successively homogenizing the viscoelastic behavior at different scales, starting from the cement paste. The homogenization is carried out by numerically constructing an effective relaxation tensor at each scale. In this framework, the impact of modifying the microstructural parameters can be directly observed on the structure response, like the interaction of the creep of concrete with the prestressing tendons network, and the effects of an internal pressure which might occur during a nuclear accident.

  7. Apparent Dependence of Rate- and State-Dependent Friction Parameters on Loading Velocity and Cumulative Displacement Inferred from Large-Scale Biaxial Friction Experiments

    Science.gov (United States)

    Urata, Yumi; Yamashita, Futoshi; Fukuyama, Eiichi; Noda, Hiroyuki; Mizoguchi, Kazuo

    2017-06-01

    We investigated the constitutive parameters in the rate- and state-dependent friction (RSF) law by conducting numerical simulations, using the friction data from large-scale biaxial rock friction experiments for Indian metagabbro. The sliding surface area was 1.5 m long and 0.5 m wide, slid for 400 s under a normal stress of 1.33 MPa at a loading velocity of either 0.1 or 1.0 mm/s. During the experiments, many stick-slips were observed and those features were as follows. (1) The friction drop and recurrence time of the stick-slip events increased with cumulative slip displacement in an experiment before which the gouges on the surface were removed, but they became almost constant throughout an experiment conducted after several experiments without gouge removal. (2) The friction drop was larger and the recurrence time was shorter in the experiments with faster loading velocity. We applied a one-degree-of-freedom spring-slider model with mass to estimate the RSF parameters by fitting the stick-slip intervals and slip-weakening curves measured based on spring force and acceleration of the specimens. We developed an efficient algorithm for the numerical time integration, and we conducted forward modeling for evolution parameters ( b) and the state-evolution distances (L_{{c}}), keeping the direct effect parameter ( a) constant. We then identified the confident range of b and L_{{c}} values. Comparison between the results of the experiments and our simulations suggests that both b and L_{{c}} increase as the cumulative slip displacement increases, and b increases and L_{{c}} decreases as the loading velocity increases. Conventional RSF laws could not explain the large-scale friction data, and more complex state evolution laws are needed.

  8. NetView: a high-definition network-visualization approach to detect fine-scale population structures from genome-wide patterns of variation.

    Science.gov (United States)

    Neuditschko, Markus; Khatkar, Mehar S; Raadsma, Herman W

    2012-01-01

    High-throughput sequencing and single nucleotide polymorphism (SNP) genotyping can be used to infer complex population structures. Fine-scale population structure analysis tracing individual ancestry remains one of the major challenges. Based on network theory and recent advances in SNP chip technology, we investigated an unsupervised network clustering method called Super Paramagnetic Clustering (Spc). When applied to whole-genome marker data it identifies the natural divisions of groups of individuals into population clusters without use of prior ancestry information. Furthermore, we optimised an analysis pipeline called NetView, a high-definition network visualization, starting with computation of genetic distance, followed clustering using Spc and finally visualization of clusters with Cytoscape. We compared NetView against commonly used methodologies including Principal Component Analyses (PCA) and a model-based algorithm, Admixture, on whole-genome-wide SNP data derived from three previously described data sets: simulated (2.5 million SNPs, 5 populations), human (1.4 million SNPs, 11 populations) and cattle (32,653 SNPs, 19 populations). We demonstrate that individuals can be effectively allocated to their correct population whilst simultaneously revealing fine-scale structure within the populations. Analyzing the human HapMap populations, we identified unexpected genetic relatedness among individuals, and population stratification within the Indian, African and Mexican samples. In the cattle data set, we correctly assigned all individuals to their respective breeds and detected fine-scale population sub-structures reflecting different sample origins and phenotypes. The NetView pipeline is computationally extremely efficient and can be easily applied on large-scale genome-wide data sets to assign individuals to particular populations and to reproduce fine-scale population structures without prior knowledge of individual ancestry. NetView can be used on any

  9. A new scaling approach for the mesoscale simulation of magnetic domain structures using Monte Carlo simulations

    Energy Technology Data Exchange (ETDEWEB)

    Radhakrishnan, B., E-mail: radhakrishnb@ornl.gov; Eisenbach, M.; Burress, T.A.

    2017-06-15

    Highlights: • Developed new scaling technique for dipole–dipole interaction energy. • Developed new scaling technique for exchange interaction energy. • Used scaling laws to extend atomistic simulations to micrometer length scale. • Demonstrated transition from mono-domain to vortex magnetic structure. • Simulated domain wall width and transition length scale agree with experiments. - Abstract: A new scaling approach has been proposed for the spin exchange and the dipole–dipole interaction energy as a function of the system size. The computed scaling laws are used in atomistic Monte Carlo simulations of magnetic moment evolution to predict the transition from single domain to a vortex structure as the system size increases. The width of a 180° – domain wall extracted from the simulated structures is in close agreement with experimentally values for an F–Si alloy. The transition size from a single domain to a vortex structure is also in close agreement with theoretically predicted and experimentally measured values for Fe.

  10. Internal structure, fault rocks, and inferences regarding deformation, fluid flow, and mineralization in the seismogenic Stillwater normal fault, Dixie Valley, Nevada

    Science.gov (United States)

    Caine, Jonathan S.; Bruhn, R.L.; Forster, C.B.

    2010-01-01

    Outcrop mapping and fault-rock characterization of the Stillwater normal fault zone in Dixie Valley, Nevada are used to document and interpret ancient hydrothermal fluid flow and its possible relationship to seismic deformation. The fault zone is composed of distinct structural and hydrogeological components. Previous work on the fault rocks is extended to the map scale where a distinctive fault core shows a spectrum of different fault-related breccias. These include predominantly clast-supported breccias with angular clasts that are cut by zones containing breccias with rounded clasts that are also clast supported. These are further cut by breccias that are predominantly matrix supported with angular and rounded clasts. The fault-core breccias are surrounded by a heterogeneously fractured damage zone. Breccias are bounded between major, silicified slip surfaces, forming large pod-like structures, systematically oriented with long axes parallel to slip. Matrix-supported breccias have multiply brecciated, angular and rounded clasts revealing episodic deformation and fluid flow. These breccias have a quartz-rich matrix with microcrystalline anhedral, equant, and pervasively conformable mosaic texture. The breccia pods are interpreted to have formed by decompression boiling and rapid precipitation of hydrothermal fluids whose flow was induced by coseismic, hybrid dilatant-shear deformation and hydraulic connection to a geothermal reservoir. The addition of hydrothermal silica cement localized in the core at the map scale causes fault-zone widening, local sealing, and mechanical heterogeneities that impact the evolution of the fault zone throughout the seismic cycle. ?? 2010.

  11. Scale Issues in the Assessment of Pesticide Leaching Vulnerability for Loamy Structured Soils in Denmark

    DEFF Research Database (Denmark)

    van der Keur, Peter; Iversen, Bo Vangsø; Hollis, John

    Three approaches for vulnerability mapping of pesticide leaching for Denmark are considered. The first method is based on an approach developed at the European spatial scale, the second method relies on mapping soil hydraulic properties at a finer scale derived from a national soil property map...... for vulnerability due to change in climate and agricultural land management. In the European scale approach soil types in Denmark are classified using a decision tree structure that accounts for both soil texture as well as the lower boundary condition available from soil survey data at the European scale...... saturated conductivity. It is expected that loamy soils are vulnerable at both the low and high values as low values indicate risk for preferential flow, whereas high values correspond to a more coarse soil structure with high soil hydraulic conductivity. It appears that the coarse spatial scale of derived...

  12. Factorial Structure and Invariance Analysis of the Sense of Belonging Scales

    Science.gov (United States)

    Tovar, Esau; Simon, Merril A.

    2010-01-01

    Using a diverse sample of university students, this article describes outcomes of a confirmatory factor analysis and a group invariance analysis conducted to validate the factorial structure of the Sense of Belonging Scales. Accordingly, a modified factor structure departing significantly from that of the original authors is proposed. (Contains 5…

  13. Factorial Structure of the New Ecological Paradigm Scale in Two French Samples

    Science.gov (United States)

    Fleury-Bahi, Ghozlane; Marcouyeux, Aurore; Renard, Elise; Roussiau, Nicolas

    2015-01-01

    The principal objective of this research is to test the factorial structure of the New Ecological Paradigm scale on a population of men and women residing in France. The tested model is a second-order factorial model. This factorial structure is evaluated on two separate samples to test the stability of the solution (a first sample of 253…

  14. Initial condition effects on large scale structure in numerical simulations of plane mixing layers

    Science.gov (United States)

    McMullan, W. A.; Garrett, S. J.

    2016-01-01

    In this paper, Large Eddy Simulations are performed on the spatially developing plane turbulent mixing layer. The simulated mixing layers originate from initially laminar conditions. The focus of this research is on the effect of the nature of the imposed fluctuations on the large-scale spanwise and streamwise structures in the flow. Two simulations are performed; one with low-level three-dimensional inflow fluctuations obtained from pseudo-random numbers, the other with physically correlated fluctuations of the same magnitude obtained from an inflow generation technique. Where white-noise fluctuations provide the inflow disturbances, no spatially stationary streamwise vortex structure is observed, and the large-scale spanwise turbulent vortical structures grow continuously and linearly. These structures are observed to have a three-dimensional internal geometry with branches and dislocations. Where physically correlated provide the inflow disturbances a "streaky" streamwise structure that is spatially stationary is observed, with the large-scale turbulent vortical structures growing with the square-root of time. These large-scale structures are quasi-two-dimensional, on top of which the secondary structure rides. The simulation results are discussed in the context of the varying interpretations of mixing layer growth that have been postulated. Recommendations are made concerning the data required from experiments in order to produce accurate numerical simulation recreations of real flows.

  15. Factor Structure and Psychometric Properties of the Injection Phobia Scale-Anxiety

    Science.gov (United States)

    Olatunji, Bunmi O.; Sawchuk, Craig N.; Moretz, Melanie W.; David, Bieke; Armstrong, Thomas; Ciesielski, Bethany G.

    2010-01-01

    The present investigation examined the factor structure and psychometric properties of the Injection Phobia Scale-Anxiety (IPS-Anx). Principal components analysis of IPS-Anx items in Study 1 (n = 498) revealed a 2-factor structure consisting of Distal Fear and Contact Fear. However, CFA results in Study 2 (n = 567) suggest that a 1-factor…

  16. Application of Exploratory Structural Equation Modeling to Evaluate the Academic Motivation Scale

    Science.gov (United States)

    Guay, Frédéric; Morin, Alexandre J. S.; Litalien, David; Valois, Pierre; Vallerand, Robert J.

    2015-01-01

    In this research, the authors examined the construct validity of scores of the Academic Motivation Scale using exploratory structural equation modeling. Study 1 and Study 2 involved 1,416 college students and 4,498 high school students, respectively. First, results of both studies indicated that the factor structure tested with exploratory…

  17. Scale-dependent genetic structure of the Idaho giant salamander (Dicamptodon aterrimus) in stream networks

    Science.gov (United States)

    Lindy B. Mullen; H. Arthur Woods; Michael K. Schwartz; Adam J. Sepulveda; Winsor H. Lowe

    2010-01-01

    The network architecture of streams and rivers constrains evolutionary, demographic and ecological processes of freshwater organisms. This consistent architecture also makes stream networks useful for testing general models of population genetic structure and the scaling of gene flow. We examined genetic structure and gene flow in the facultatively paedomorphic Idaho...

  18. Inference in `poor` languages

    Energy Technology Data Exchange (ETDEWEB)

    Petrov, S.

    1996-10-01

    Languages with a solvable implication problem but without complete and consistent systems of inference rules (`poor` languages) are considered. The problem of existence of finite complete and consistent inference rule system for a ``poor`` language is stated independently of the language or rules syntax. Several properties of the problem arc proved. An application of results to the language of join dependencies is given.

  19. The Essentialist Inference

    NARCIS (Netherlands)

    Mulder, J.M.

    2013-01-01

    It is often claimed that principles of individuation imply essential properties of the things individuated. For example, sets are individuated by their members, hence sets have their members essentially. But how does this inference work? First I discuss the form of such inferences, and conclude that

  20. Stan: Statistical inference

    Science.gov (United States)

    Stan Development Team

    2018-01-01

    Stan facilitates statistical inference at the frontiers of applied statistics and provides both a modeling language for specifying complex statistical models and a library of statistical algorithms for computing inferences with those models. These components are exposed through interfaces in environments such as R, Python, and the command line.

  1. STRUCTURAL SCALE LIFE PREDICTION OF AERO STRUCTURES EXPERIENCING COMBINED EXTREME ENVIRONMENTS

    Science.gov (United States)

    2017-07-01

    Using Complex Variables to Estimate the Derivatives of Nonlinear Reduced-Order Models,” AIAA-2016-1707, 57th AIAA/ ASME /ASCE/AHS/ASC Structures, Structural Dynamics and Materials Conference, San Diego, CA, Jan 2016.

  2. Chameleon: Dynamic Color Mapping for Multi-Scale Structural Biology Models.

    Science.gov (United States)

    Waldin, Nicholas; Le Muzic, Mathieu; Waldner, Manuela; Gröller, Eduard; Goodsell, David; Ludovic, Autin; Viola, Ivan

    2016-09-01

    Visualization of structural biology data uses color to categorize or separate dense structures into particular semantic units. In multiscale models of viruses or bacteria, there are atoms on the finest level of detail, then amino-acids, secondary structures, macromolecules, up to the compartment level and, in all these levels, elements can be visually distinguished by color. However, currently only single scale coloring schemes are utilized that show information for one particular scale only. We present a novel technology which adaptively, based on the current scale level, adjusts the color scheme to depict or distinguish the currently best visible structural information. We treat the color as a visual resource that is distributed given a particular demand. The changes of the color scheme are seamlessly interpolated between the color scheme from the previous views into a given new one. With such dynamic multi-scale color mapping we ensure that the viewer is able to distinguish structural detail that is shown on any given scale. This technique has been tested by users with an expertise in structural biology and has been overall well received.

  3. Advancing multiscale structural mapping of the brain through fluorescence imaging and analysis across length scales

    Science.gov (United States)

    Hogstrom, L. J.; Guo, S. M.; Murugadoss, K.; Bathe, M.

    2016-01-01

    Brain function emerges from hierarchical neuronal structure that spans orders of magnitude in length scale, from the nanometre-scale organization of synaptic proteins to the macroscopic wiring of neuronal circuits. Because the synaptic electrochemical signal transmission that drives brain function ultimately relies on the organization of neuronal circuits, understanding brain function requires an understanding of the principles that determine hierarchical neuronal structure in living or intact organisms. Recent advances in fluorescence imaging now enable quantitative characterization of neuronal structure across length scales, ranging from single-molecule localization using super-resolution imaging to whole-brain imaging using light-sheet microscopy on cleared samples. These tools, together with correlative electron microscopy and magnetic resonance imaging at the nanoscopic and macroscopic scales, respectively, now facilitate our ability to probe brain structure across its full range of length scales with cellular and molecular specificity. As these imaging datasets become increasingly accessible to researchers, novel statistical and computational frameworks will play an increasing role in efforts to relate hierarchical brain structure to its function. In this perspective, we discuss several prominent experimental advances that are ushering in a new era of quantitative fluorescence-based imaging in neuroscience along with novel computational and statistical strategies that are helping to distil our understanding of complex brain structure. PMID:26855758

  4. Skin and scales of teleost fish: Simple structure but high performance and multiple functions

    Science.gov (United States)

    Vernerey, Franck J.; Barthelat, Francois

    2014-08-01

    Natural and man-made structural materials perform similar functions such as structural support or protection. Therefore they rely on the same types of properties: strength, robustness, lightweight. Nature can therefore provide a significant source of inspiration for new and alternative engineering designs. We report here some results regarding a very common, yet largely unknown, type of biological material: fish skin. Within a thin, flexible and lightweight layer, fish skins display a variety of strain stiffening and stabilizing mechanisms which promote multiple functions such as protection, robustness and swimming efficiency. We particularly discuss four important features pertaining to scaled skins: (a) a strongly elastic tensile behavior that is independent from the presence of rigid scales, (b) a compressive response that prevents buckling and wrinkling instabilities, which are usually predominant for thin membranes, (c) a bending response that displays nonlinear stiffening mechanisms arising from geometric constraints between neighboring scales and (d) a robust structure that preserves the above characteristics upon the loss or damage of structural elements. These important properties make fish skin an attractive model for the development of very thin and flexible armors and protective layers, especially when combined with the high penetration resistance of individual scales. Scaled structures inspired by fish skin could find applications in ultra-light and flexible armor systems, flexible electronics or the design of smart and adaptive morphing structures for aerospace vehicles.

  5. The response of relative humidity to centennial-scale warming over the southeastern Tibetan Plateau inferred from tree-ring width chronologies

    Science.gov (United States)

    Shi, Chunming; Daux, Valérie; Li, Zongshan; Wu, Xiuchen; Fan, Tianyi; Ma, Qian; Wu, Xiaoxu; Tian, Huaiyu; Carré, Matthieu; Ji, Duoying; Wang, Wenli; Rinke, Annette; Gong, Wei; Liu, Yan; Chen, Yating; Masson-Delmotte, Valérie

    2018-02-01

    Understanding the past variability in atmospheric moisture associated with global warming is essential for reducing the uncertainties in climate projections. Such understanding is especially necessary in the Asian monsoon region in the context of increasing anthropogenic forcing. Here, we average four tree-ring width chronologies from the southeastern Tibetan Plateau (TP) over their common intervals and reconstruct the variability in regional relative humidity (RH) from the previous May to the current March over 1751-2005. In contrast to the summer drying associated with centennial-scale warming and the weakening of the Asian summer monsoon, our RH reconstruction shows no significant centennial trend from the 1820s through the 2000s. This absence of a consistent signal is due to the combined effects of contrasting moisture trends during the monsoonal and non-monsoonal seasons, which are controlled by summer monsoon precipitation and local convective precipitation, respectively. The interannual and decadal variability of our RH reconstruction is modulated by El Niño-Southern Oscillation (ENSO) and the Pacific Decadal Oscillation (PDO); however, these links are unstable over time. Two rapid increases in moisture are found to have occurred around the 1820s and 1980s; the latter increase caused the variability in RH during the 1980s-2000s to be the largest over the entire reconstruction period.

  6. 29-Day Analysis of Scale Heights And The Inference of the Topside Ionosphere Over Millstone Hill During the 2002 Incoherent Scatter Radar Campaign

    Science.gov (United States)

    Meehan, Jennifer L.

    This study aims to characterize the topside ionospheric density and temperature profiles using readily available Global Positioning System (GPS) total electron content (TEC) and ionosonde bottomside profile of electron density. The aim of this study is to find a technique that can be applied globally rather than specific locations where a wealth of data exists. Knowledge of the distribution of electron density and its altitude dependence, known as scale height, is important for ionospheric empirical modeling and ionospheric studies, and for practical applications, such as time delay correction of radio-wave propagation through the ionosphere. Over the years, researchers have gathered information and developed several different methods to analyze the topside ionosphere, including: coherent scatter radar observations of underdense electron density irregularities, incoherent scatter radar (ISR) probing, topside sounders onboard satellites, in situ rocket and satellite observations, such as Global Positioning System (GPS),and occultation measurements. We were able to obtain topside information by an analysis of GPS TEC in combination with bottom side electron density profiles observed by ionosondes. This was verified by a study using one month's worth of data from Millstone Hill ISR observations.

  7. A new scaling approach for the mesoscale simulation of magnetic domain structures using Monte Carlo simulations

    Energy Technology Data Exchange (ETDEWEB)

    Radhakrishnan, B. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Eisenbach, M. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Burress, Timothy A. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2017-01-24

    A new scaling approach has been proposed for the spin exchange and the dipole–dipole interaction energy as a function of the system size. The computed scaling laws are used in atomistic Monte Carlo simulations of magnetic moment evolution to predict the transition from single domain to a vortex structure as the system size increases. The width of a 180° – domain wall extracted from the simulated structures is in close agreement with experimentally values for an F–Si alloy. In conclusion, the transition size from a single domain to a vortex structure is also in close agreement with theoretically predicted and experimentally measured values for Fe.

  8. Factor structure of the Italian version of the religious fundamentalism scale.

    Science.gov (United States)

    Carlucci, Leonardo; Tommasi, Marco; Saggino, Aristide

    2013-02-01

    The Religious Fundamentalism Scale was applied to an Italian group, composed of 250 participants, to assess if it could be considered a reliable measure of fundamentalism. All participants professed to be believers of the Catholic religion. The overall group was split randomly into two smaller groups. The data of the first group were analyzed with an exploratory factor analysis (EFA) to test the factor structure of the Italian version of the scale. The data of the second sample were analyzed with a confirmatory factor analysis, to test the factor structure that emerged from EFA. Results indicated a two-dimensional structure, composed of two correlated factors apparently representing believing and skeptical attitudes.

  9. Statistical Inference at Work: Statistical Process Control as an Example

    Science.gov (United States)

    Bakker, Arthur; Kent, Phillip; Derry, Jan; Noss, Richard; Hoyles, Celia

    2008-01-01

    To characterise statistical inference in the workplace this paper compares a prototypical type of statistical inference at work, statistical process control (SPC), with a type of statistical inference that is better known in educational settings, hypothesis testing. Although there are some similarities between the reasoning structure involved in…

  10. Possible uses of the layered structure found in the scales of Hoplia coerulea (Coleoptera)

    Science.gov (United States)

    Vigneron, Jean-Pol; Rassart, Marie; Simonis, Priscilla; Colomer, Jean-Francois; Bay, Annick

    2009-08-01

    The male of the beetle Hoplia coerulea is known for its spectacular blue-violet iridescence. The blue coloration is caused by the presence of an interesting photonic structure inside the scales which cover the dorsal parts of the insect's body. This structure can be described as the stacking of chitin plates supporting arrays of parallel rods. The change of colour of this structure with humidity is investigated, as well as its response to some other external conditions, such as mechanical strain.

  11. Mechanism and scaling for convection of isolated structures in nonuniformly magnetized plasmas

    DEFF Research Database (Denmark)

    Garcia, O.E.; Bian, N.H.; Naulin, V.

    2005-01-01

    Large-scale radial advection of isolated structures in nonuniformly magnetized plasmas is investigated. The underlying mechanism considered is due to the nonlinear evolution of interchange motions, without any presumption of plasma sheaths. Theoretical arguments supported by numerical simulations...... of the structures, compares favorably with recent experimental measurements of radially propagating blob structures in the scrape-off layer of magnetically confined plasmas. (C) 2005 American Institute of Physics....

  12. Structure function scaling in a Reλ = 250 turbulent mixing layer

    KAUST Repository

    Attili, Antonio

    2011-12-22

    A highly resolved Direct Numerical Simulation of a spatially developing turbulent mixing layer is presented. In the fully developed region, the flow achieves a turbulent Reynolds number Reλ = 250, high enough for a clear separation between large and dissipative scales, so for the presence of an inertial range. Structure functions have been calculated in the self-similar region using velocity time series and Taylor\\'s frozen turbulence hypothesis. The Extended Self-Similarity (ESS) concept has been employed to evaluate relative scaling exponents. A wide range of scales with scaling exponents and intermittency levels equal to homogeneous isotropic turbulence has been identified. Moreover an additional scaling range exists for larger scales; it is characterized by smaller exponents, similar to the values reported in the literature for flows with strong shear.

  13. Large-Scale Structure Effects on Particle Motion in a Spatialy Developing Mixing Layer

    Science.gov (United States)

    Nikitopoulos, Dimitris E.; Acharya, Sumanta; Ning, Hui

    1996-11-01

    We will present results from a simulation of particle motion in a spatially developing turbulent mixing layer forced by a single frequency. The simulation is based on a model which utilizes Eulerian formulation for the carrier phase flowfield and Lagrangian formulation for the dispersed particles. The carrier-phase mean flow is determined from the classical turbulent boundary layer equations and a traditional k-ɛ turbulence model modified to include interaction terms with the imposed large-scale structure. An integral energy method is used to determine the evolution of the large-scale structure which is modeled as a spatially growing wave. The effect of the carrier phase small-scale turbulent fluctuations is taken into account by using a classical stochastic model with a gaussian PDF. The effects of the particle time scale magnitude relative to the large-scale structure timescale (Stokes number) are discussed as well as the effects of the particle injection conditions. It is found that the Stokes number for which the cross-stream dispersion of the particles is maximized has a strong dependence on the particle injection conditions. The particle injection phase relative to the large-scale structure also has a profound influence on the motion of the particles and their distribution within the mixing layer.

  14. Identification of the underlying factor structure of the Derriford Appearance Scale 24

    Science.gov (United States)

    Lawson, Victoria; White, Paul

    2015-01-01

    Background. The Derriford Appearance Scale24 (DAS24) is a widely used measure of distress and dysfunction in relation to self-consciousness of appearance. It has been used in clinical and research settings, and translated into numerous European and Asian languages. Hitherto, no study has conducted an analysis to determine the underlying factor structure of the scale. Methods. A large (n = 1,265) sample of community and hospital patients with a visible difference were recruited face to face or by post, and completed the DAS24. Results. A two factor solution was generated. An evaluation of the congruence of the factor solutions on each of the the hospital and the community samples using Tucker’s Coefficient of Congruence (rc = .979) and confirmatory factor analysis, which demonstrated a consistent factor structure. A main factor, general self consciousness (GSC), was represented by 18 items. Six items comprised a second factor, sexual and body self-consciousness (SBSC). The SBSC scale demonstrated greater sensitivity and specificity in identifying distress for sexually significant areas of the body. Discussion. The factor structure of the DAS24 facilitates a more nuanced interpretation of scores using this scale. Two conceptually and statistically coherent sub-scales were identified. The SBSC sub-scale offers a means of identifying distress and dysfunction around sexually significant areas of the body not previously possible with this scale. PMID:26157633

  15. Identification of the underlying factor structure of the Derriford Appearance Scale 24

    Directory of Open Access Journals (Sweden)

    Timothy P. Moss

    2015-07-01

    Full Text Available Background. The Derriford Appearance Scale24 (DAS24 is a widely used measure of distress and dysfunction in relation to self-consciousness of appearance. It has been used in clinical and research settings, and translated into numerous European and Asian languages. Hitherto, no study has conducted an analysis to determine the underlying factor structure of the scale.Methods. A large (n = 1,265 sample of community and hospital patients with a visible difference were recruited face to face or by post, and completed the DAS24.Results. A two factor solution was generated. An evaluation of the congruence of the factor solutions on each of the the hospital and the community samples using Tucker’s Coefficient of Congruence (rc = .979 and confirmatory factor analysis, which demonstrated a consistent factor structure. A main factor, general self consciousness (GSC, was represented by 18 items. Six items comprised a second factor, sexual and body self-consciousness (SBSC. The SBSC scale demonstrated greater sensitivity and specificity in identifying distress for sexually significant areas of the body.Discussion. The factor structure of the DAS24 facilitates a more nuanced interpretation of scores using this scale. Two conceptually and statistically coherent sub-scales were identified. The SBSC sub-scale offers a means of identifying distress and dysfunction around sexually significant areas of the body not previously possible with this scale.

  16. RAD genotyping reveals fine-scale genetic structuring and provides powerful population assignment in a widely distributed marine species, the American lobster (Homarus americanus).

    Science.gov (United States)

    Benestan, Laura; Gosselin, Thierry; Perrier, Charles; Sainte-Marie, Bernard; Rochette, Rémy; Bernatchez, Louis

    2015-07-01

    Deciphering genetic structure and inferring connectivity in marine species have been challenging due to weak genetic differentiation and limited resolution offered by traditional genotypic methods. The main goal of this study was to assess how a population genomics framework could help delineate the genetic structure of the American lobster (Homarus americanus) throughout much of the species' range and increase the assignment success of individuals to their location of origin. We genotyped 10 156 filtered SNPs using RAD sequencing to delineate genetic structure and perform population assignment for 586 American lobsters collected in 17 locations distributed across a large portion of the species' natural distribution range. Our results revealed the existence of a hierarchical genetic structure, first separating lobsters from the northern and southern part of the range (FCT  = 0.0011; P-value = 0.0002) and then revealing a total of 11 genetically distinguishable populations (mean FST  = 0.00185; CI: 0.0007-0.0021, P-value < 0.0002), providing strong evidence for weak, albeit fine-scale population structuring within each region. A resampling procedure showed that assignment success was highest with a subset of 3000 SNPs having the highest FST . Applying Anderson's (Molecular Ecology Resources, 2010, 10, 701) method to avoid 'high-grading bias', 94.2% and 80.8% of individuals were correctly assigned to their region and location of origin, respectively. Lastly, we showed that assignment success was positively associated with sample size. These results demonstrate that using a large number of SNPs improves fine-scale population structure delineation and population assignment success in a context of weak genetic structure. We discuss the implications of these findings for the conservation and management of highly connected marine species, particularly regarding the geographic scale of demographic independence. © 2015 John Wiley & Sons Ltd.

  17. Compressive Coherent Structures at Ion Scales in the Slow Solar Wind

    Science.gov (United States)

    Perrone, D.; Alexandrova, O.; Mangeney, A.; Maksimovic, M.; Lacombe, C.; Rakoto, V.; Kasper, J. C.; Jovanovic, D.

    2016-08-01

    We present a study of magnetic field fluctuations in a slow solar wind stream, close to ion scales, where an increase of the level of magnetic compressibility is observed. Here, the nature of these compressive fluctuations is found to be characterized by coherent structures. Although previous studies have shown that current sheets can be considered the principal cause of intermittency at ion scales, here we show for the first time that, in the case of the slow solar wind, a large variety of coherent structures contributes to intermittency at proton scales, and current sheets are not the most common. Specifically, we find compressive (δ {b}\\parallel \\gg δ {b}\\perp ), linearly polarized structures in the form of magnetic holes, solitons, and shock waves. Examples of Alfvénic structures (δ {b}\\perp \\gt δ {b}\\parallel ) are identified as current sheets and vortex-like structures. Some of these vortices have δ {b}\\perp \\gg δ {b}\\parallel , as in the case of Alfvén vortices, but the majority of them are characterized by δ {b}\\perp ≳ δ {b}\\parallel . Thanks to multi-point measurements by the Cluster spacecraft, for about 100 structures we could determine the normal, the propagation velocity, and the spatial scale along this normal. Independently of the nature of the structures, the normal is always perpendicular to the local magnetic field, meaning that k ⊥ ≫ k ∥. The spatial scales of the studied structures are found to be between two and eight times the proton gyroradius. Most of them are simply convected by the wind, but 25% propagate in the plasma frame. Possible interpretations of the observed structures and the connection with plasma heating are discussed.

  18. Large-scale structural analysis: The structural analyst, the CSM Testbed and the NAS System

    Science.gov (United States)

    Knight, Norman F., Jr.; Mccleary, Susan L.; Macy, Steven C.; Aminpour, Mohammad A.

    1989-01-01

    The Computational Structural Mechanics (CSM) activity is developing advanced structural analysis and computational methods that exploit high-performance computers. Methods are developed in the framework of the CSM testbed software system and applied to representative complex structural analysis problems from the aerospace industry. An overview of the CSM testbed methods development environment is presented and some numerical methods developed on a CRAY-2 are described. Selected application studies performed on the NAS CRAY-2 are also summarized.

  19. Climate, habitat, and species interactions at different scales determine the structure of a Neotropical bat community.

    Science.gov (United States)

    Estrada-Villegas, Sergio; McGill, Brian J; Kalko, Elisabeth K V

    2012-05-01

    Climate, habitat, and species interactions are factors that control community properties (e.g., species richness, abundance) across various spatial scales. Usually, researchers study how a few properties are affected by one factor in isolation and at one scale. Hence, there are few multi-scale studies testing how multiple controlling factors simultaneously affect community properties at different scales. We ask whether climate, habitat structure, or insect resources at each of three spatial scales explains most of the variation in six community properties and which theory best explains the distribution of selected community properties across a rainfall gradient. We studied a Neotropical insectivorous bat ensemble in the Isthmus of Panama with acoustic monitoring techniques. Using climatological data, habitat surveys, and insect captures in a hierarchical sampling design we determined how much variation of the community properties was explained by the three factors employing two approaches for variance partitioning. Our results revealed that most of the variation in species richness, total abundance, and feeding activity occurred at the smallest spatial scale and was explained by habitat structure. In contrast, climate at large scales explained most of the variation in individual species' abundances. Although each species had an idiosyncratic response to the gradient, species richness peaked at intermediate levels of precipitation, whereas total abundance was very similar across sites, suggesting density compensation. All community properties responded in a different manner to the factor and scale under consideration.

  20. Gauging Variational Inference

    Energy Technology Data Exchange (ETDEWEB)

    Chertkov, Michael [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Ahn, Sungsoo [Korea Advanced Inst. Science and Technology (KAIST), Daejeon (Korea, Republic of); Shin, Jinwoo [Korea Advanced Inst. Science and Technology (KAIST), Daejeon (Korea, Republic of)

    2017-05-25

    Computing partition function is the most important statistical inference task arising in applications of Graphical Models (GM). Since it is computationally intractable, approximate methods have been used to resolve the issue in practice, where meanfield (MF) and belief propagation (BP) are arguably the most popular and successful approaches of a variational type. In this paper, we propose two new variational schemes, coined Gauged-MF (G-MF) and Gauged-BP (G-BP), improving MF and BP, respectively. Both provide lower bounds for the partition function by utilizing the so-called gauge transformation which modifies factors of GM while keeping the partition function invariant. Moreover, we prove that both G-MF and G-BP are exact for GMs with a single loop of a special structure, even though the bare MF and BP perform badly in this case. Our extensive experiments, on complete GMs of relatively small size and on large GM (up-to 300 variables) confirm that the newly proposed algorithms outperform and generalize MF and BP.

  1. Analysis of reactive bromine production and ozone depletion in the Arctic boundary layer using 3-D simulations with GEM-AQ: inference from synoptic-scale patterns

    Science.gov (United States)

    Toyota, K.; McConnell, J. C.; Lupu, A.; Neary, L.; McLinden, C. A.; Richter, A.; Kwok, R.; Semeniuk, K.; Kaminski, J. W.; Gong, S.-L.; Jarosz, J.; Chipperfield, M. P.; Sioris, C. E.

    2011-04-01

    Episodes of high bromine levels and surface ozone depletion in the springtime Arctic are simulated by an online air-quality model, GEM-AQ, with gas-phase and heterogeneous reactions of inorganic bromine species and a simple scheme of air-snowpack chemical interactions implemented for this study. Snowpack on sea ice is assumed to be the only source of bromine to the atmosphere and to be capable of converting relatively stable bromine species to photolabile Br2 via air-snowpack interactions. A set of sensitivity model runs are performed for April 2001 at a horizontal resolution of approximately 100 km×100 km in the Arctic, to provide insights into the effects of temperature and the age (first-year, FY, versus multi-year, MY) of sea ice on the release of reactive bromine to the atmosphere. The model simulations capture much of the temporal variations in surface ozone mixing ratios as observed at stations in the high Arctic and the synoptic-scale evolution of areas with enhanced BrO column amount ("BrO clouds") as estimated from satellite observations. The simulated "BrO clouds" are in modestly better agreement with the satellite measurements when the FY sea ice is assumed to be more efficient at releasing reactive bromine to the atmosphere than on the MY sea ice. Surface ozone data from coastal stations used in this study are not sufficient to evaluate unambiguously the difference between the FY sea ice and the MY sea ice as a source of bromine. The results strongly suggest that reactive bromine is released ubiquitously from the snow on the sea ice during the Arctic spring while the timing and location of the bromine release are largely controlled by meteorological factors. It appears that a rapid advection and an enhanced turbulent diffusion associated with strong boundary-layer winds drive transport and dispersion of ozone to the near-surface air over the sea ice, increasing the oxidation rate of bromide (Br-) in the surface snow. Also, if indeed the surface

  2. Analysis of reactive bromine production and ozone depletion in the Arctic boundary layer using 3-D simulations with GEM-AQ: inference from synoptic-scale patterns

    Directory of Open Access Journals (Sweden)

    K. Toyota

    2011-04-01

    Full Text Available Episodes of high bromine levels and surface ozone depletion in the springtime Arctic are simulated by an online air-quality model, GEM-AQ, with gas-phase and heterogeneous reactions of inorganic bromine species and a simple scheme of air-snowpack chemical interactions implemented for this study. Snowpack on sea ice is assumed to be the only source of bromine to the atmosphere and to be capable of converting relatively stable bromine species to photolabile Br2 via air-snowpack interactions. A set of sensitivity model runs are performed for April 2001 at a horizontal resolution of approximately 100 km×100 km in the Arctic, to provide insights into the effects of temperature and the age (first-year, FY, versus multi-year, MY of sea ice on the release of reactive bromine to the atmosphere. The model simulations capture much of the temporal variations in surface ozone mixing ratios as observed at stations in the high Arctic and the synoptic-scale evolution of areas with enhanced BrO column amount ("BrO clouds" as estimated from satellite observations. The simulated "BrO clouds" are in modestly better agreement with the satellite measurements when the FY sea ice is assumed to be more efficient at releasing reactive bromine to the atmosphere than on the MY sea ice. Surface ozone data from coastal stations used in this study are not sufficient to evaluate unambiguously the difference between the FY sea ice and the MY sea ice as a source of bromine. The results strongly suggest that reactive bromine is released ubiquitously from the snow on the sea ice during the Arctic spring while the timing and location of the bromine release are largely controlled by meteorological factors. It appears that a rapid advection and an enhanced turbulent diffusion associated with strong boundary-layer winds drive transport and dispersion of ozone to the near-surface air over the sea ice, increasing the oxidation rate of bromide (Br in the surface

  3. Characterization of multi-scale porous structure of fly ash/phosphate geopolymer hollow sphere structures: from submillimeter to nano-scale.

    Science.gov (United States)

    Li, Ruifeng; Wu, Gaohui; Jiang, Longtao; Sun, Dongli

    2015-01-01

    In the present work, the porous structure of fly ash/phosphate geopolymer hollow sphere structures (FPGHSS), prepared by pre-bonding and curing technology, has been characterized by multi-resolution methods from sub-millimeter to nano-scale. Micro-CT and confocal microscopy could provide the macroscopic distribution of porous structure on sub-millimeter scale, and hollow fly ashes with sphere shape and several sub-millimeter open cells with irregular shape were identified. SEM is more suitable to illustrate the distribution of micro-sized open and closed cells, and it was found that the open cells of FPGHSS were mainly formed in the interstitial porosity between fly ashes. Mercury porosimeter measurement showed that the micro-sized open cell of FPGHSS demonstrated a normal/bimodal distribution, and the peaks of pore size distribution were mainly around 100 and 10 μm. TEM observation revealed that the phosphate geopolymer was mainly composed of the porous area with nano-pores and dense areas, which were amorphous Al-O-P phase and α-Al2O3 respectively. The pore size of nano-pores demonstrated a quasi-normal distribution from about 10 to 100 nm. Therefore, detailed information of the porous structure of FPGHSS could be revealed using multiple methods. Copyright © 2014 Elsevier Ltd. All rights reserved.

  4. Probing Newton's constant on vast scales: Dvali-Gabadadze-Porrati gravity, cosmic acceleration, and large scale structure

    CERN Document Server

    Lue, Arthur; Starkman, G D

    2004-01-01

    The nature of the fuel that drives today's cosmic acceleration is an open and tantalizing mystery. The brane-world theory of Dvali, Gabadadze, and Porrati (DGP) provides a context where late-time acceleration is driven not by some energy-momentum component (dark energy), but rather is the manifestation of the excruciatingly slow leakage of gravity off our four-dimensional world into an extra dimension. At the same time, DGP gravity alters the gravitational force law in a specific and dramatic way at cosmologically accessible scales. We derive the DGP gravitational force law in a cosmological setting for spherical perturbations at subhorizon scales and compute the growth of large-scale structures. We find that a residual repulsive force at large distances gives rise to a suppression of the growth of density and velocity perturbations. Explaining the cosmic acceleration in this framework leads to a present day fluctuation power spectrum normalization sigma8<=0.8 at about the two-sigma level, in contrast with...

  5. Knowledge and inference

    CERN Document Server

    Nagao, Makoto

    1990-01-01

    Knowledge and Inference discusses an important problem for software systems: How do we treat knowledge and ideas on a computer and how do we use inference to solve problems on a computer? The book talks about the problems of knowledge and inference for the purpose of merging artificial intelligence and library science. The book begins by clarifying the concept of """"knowledge"""" from many points of view, followed by a chapter on the current state of library science and the place of artificial intelligence in library science. Subsequent chapters cover central topics in the artificial intellig

  6. Bayesian Computation Methods for Inferring Regulatory Network Models Using Biomedical Data.

    Science.gov (United States)

    Tian, Tianhai

    2016-01-01

    The rapid advancement of high-throughput technologies provides huge amounts of information for gene expression and protein activity in the genome-wide scale. The availability of genomics, transcriptomics, proteomics, and metabolomics dataset gives an unprecedented opportunity to study detailed molecular regulations that is very important to precision medicine. However, it is still a significant challenge to design effective and efficient method to infer the network structure and dynamic property of regulatory networks. In recent years a number of computing methods have been designed to explore the regulatory mechanisms as well as estimate unknown model parameters. Among them, the Bayesian inference method can combine both prior knowledge and experimental data to generate updated information regarding the regulatory mechanisms. This chapter gives a brief review for Bayesian statistical methods that are used to infer the network structure and estimate model parameters based on experimental data.

  7. Implications of a class of grand unified theories for large scale structure in the universe

    Science.gov (United States)

    Shafi, Q.; Stecker, F. W.

    1983-01-01

    A class of grand unified theories in which cosmologicaly significant axion and neutrino energy densities arise naturally is discussed. To obtain large scale structure three scenarios are considered: (1) an inflationary scenario; (2) inflation followed by string production; and (3) a non-inflationary scenario with density fluctuations caused solely by strings. Inflation may be compatible with the recent observational indications that mega 1 on the scale of superclusters, particularly if strings are present.

  8. Halo Models of Large Scale Structure and Reliability of Cosmological N-Body Simulations

    Directory of Open Access Journals (Sweden)

    José Gaite

    2013-05-01

    Full Text Available Halo models of the large scale structure of the Universe are critically examined, focusing on the definition of halos as smooth distributions of cold dark matter. This definition is essentially based on the results of cosmological N-body simulations. By a careful analysis of the standard assumptions of halo models and N-body simulations and by taking into account previous studies of self-similarity of the cosmic web structure, we conclude that N-body cosmological simulations are not fully reliable in the range of scales where halos appear. Therefore, to have a consistent definition of halos is necessary either to define them as entities of arbitrary size with a grainy rather than smooth structure or to define their size in terms of small-scale baryonic physics.

  9. Fine-scale analysis reveals cryptic landscape genetic structure in desert tortoises.

    Directory of Open Access Journals (Sweden)

    Emily K Latch

    Full Text Available Characterizing the effects of landscape features on genetic variation is essential for understanding how landscapes shape patterns of gene flow and spatial genetic structure of populations. Most landscape genetics studies have focused on patterns of gene flow at a regional scale. However, the genetic structure of populations at a local scale may be influenced by a unique suite of landscape variables that have little bearing on connectivity patterns observed at broader spatial scales. We investigated fine-scale spatial patterns of genetic variation and gene flow in relation to features of the landscape in desert tortoise (Gopherus agassizii, using 859 tortoises genotyped at 16 microsatellite loci with associated data on geographic location, sex, elevation, slope, and soil type, and spatial relationship to putative barriers (power lines, roads. We used spatially explicit and non-explicit Bayesian clustering algorithms to partition the sample into discrete clusters, and characterize the relationships between genetic distance and ecological variables to identify factors with the greatest influence on gene flow at a local scale. Desert tortoises exhibit weak genetic structure at a local scale, and we identified two subpopulations across the study area. Although genetic differentiation between the subpopulations was low, our landscape genetic analysis identified both natural (slope and anthropogenic (roads landscape variables that have significantly influenced gene flow within this local population. We show that desert tortoise movements at a local scale are influenced by features of the landscape, and that these features are different than those that influence gene flow at larger scales. Our findings are important for desert tortoise conservation and management, particularly in light of recent translocation efforts in the region. More generally, our results indicate that recent landscape changes can affect gene flow at a local scale and that their

  10. Towards a Gravity Dual for the Large Scale Structure of the Universe

    DEFF Research Database (Denmark)

    Kehagias, A.; Riotto, Antonio; Sloth, M. S.

    2016-01-01

    The dynamics of the large-scale structure of the universe enjoys at all scales, even in the highly non-linear regime, a Lifshitz symmetry during the matter-dominated period. In this paper we propose a general class of six-dimensional spacetimes which could be a gravity dual to the four-dimensiona......The dynamics of the large-scale structure of the universe enjoys at all scales, even in the highly non-linear regime, a Lifshitz symmetry during the matter-dominated period. In this paper we propose a general class of six-dimensional spacetimes which could be a gravity dual to the four......-dimensional large-scale structure of the universe. In this set-up, the Lifshitz symmetry manifests itself as an isometry in the bulk and our universe is a four-dimensional brane moving in such six-dimensional bulk. After finding the correspondence between the bulk and the brane dynamical Lifshitz exponents, we find...... the intriguing result that the preferred value of the dynamical Lifshitz exponent of our observed universe, at both linear and non-linear scales, corresponds to a fixed point of the RGE flow of the dynamical Lifshitz exponent in the dual system where the symmetry is enhanced to the Schrodinger group containing...

  11. Particle-scale structure in frozen colloidal suspensions from small-angle x-ray scattering

    KAUST Repository

    Spannuth, Melissa

    2011-02-01

    During directional solidification of the solvent in a colloidal suspension, the colloidal particles segregate from the growing solid, forming high-particle-density regions with structure on a hierarchy of length scales ranging from that of the particle-scale packing to the large-scale spacing between these regions. Previous work has concentrated mostly on the medium- to large-length scale structure, as it is the most accessible and thought to be more technologically relevant. However, the packing of the colloids at the particle scale is an important component not only in theoretical descriptions of the segregation process, but also to the utility of freeze-cast materials for new applications. Here we present the results of experiments in which we investigated this structure across a wide range of length scales using a combination of small-angle x-ray scattering and direct optical imaging. As expected, during freezing the particles were concentrated into regions between ice dendrites forming a microscopic pattern of high- and low-particle-density regions. X-ray scattering indicates that the particles in the high-density regions were so closely packed as to be touching. However, the arrangement of the particles does not conform to that predicted by standard interparticle pair potentials, suggesting that the particle packing induced by freezing differs from that formed during equilibrium densification processes. © 2011 American Physical Society.

  12. Practical guidelines to select and scale earthquake records for nonlinear response history analysis of structures

    Science.gov (United States)

    Kalkan, Erol; Chopra, Anil K.

    2010-01-01

    Earthquake engineering practice is increasingly using nonlinear response history analysis (RHA) to demonstrate performance of structures. This rigorous method of analysis requires selection and scaling of ground motions appropriate to design hazard levels. Presented herein is a modal-pushover-based scaling (MPS) method to scale ground motions for use in nonlinear RHA of buildings and bridges. In the MPS method, the ground motions are scaled to match (to a specified tolerance) a target value of the inelastic deformation of the first-'mode' inelastic single-degree-of-freedom (SDF) system whose properties are determined by first-'mode' pushover analysis. Appropriate for first-?mode? dominated structures, this approach is extended for structures with significant contributions of higher modes by considering elastic deformation of second-'mode' SDF system in selecting a subset of the scaled ground motions. Based on results presented for two bridges, covering single- and multi-span 'ordinary standard' bridge types, and six buildings, covering low-, mid-, and tall building types in California, the accuracy and efficiency of the MPS procedure are established and its superiority over the ASCE/SEI 7-05 scaling procedure is demonstrated.

  13. Manufacturing and design of the offshore structure Froude scale model related to basin restrictions

    Science.gov (United States)

    Scurtu, I. C.

    2015-11-01

    Manufacturing steps for a modern three - column semi-submersible structure are delivered using CFD/CAE software and actual Froude scaled model testing. The three- column offshore is part of the Wind Float Project already realized as prototype for wind energy extraction in water depths more than 40 meters, and the actual model will not consider the wind turbine. The model will have heave plates for a smaller heave motion in order to compare it with the case without heave plates. The heave plates will be part of the Froude scale model.. Using a smaller model will determine a smaller heave motion and this will affect predictions of the vertical movement of the three- column offshore structure in real sea. The Froude criterion is used for the time, speed and acceleration scale. The scale model is manufactured from steel and fiberglass and all parts are subjected to software analysis in order to get the smallest stress in connections inside the model. The model mass was restricted by scale dimensions and also the vertical position of centre gravity will be considered during the manufacturing and design process of the Froude scale offshore structure. All conditions must converge in model manufacturing and design in order to get the best results to compare with real sea states and heave motion data.

  14. Assessment of the confiability and factorial structure of three scales measuring chronic procrastination

    Directory of Open Access Journals (Sweden)

    Doris Argumedo Bustinza

    2005-06-01

    Full Text Available This study explores the confiability and factorial structure of three scales measuring chronic procrastination: Scale of General Procrastination (EPG. Lay. 1986. Adult Procrastinatio Inventory (lPA. McCown & Johnson as cited in Ferrari. Johnson & McCown. 1995 and the Scale of Procrastination in Decision-Making (PTF. Mann. 1982. The sample included 514 adults between 20 and 65 years of age from Lima. The three scales showed high levels of intemal consistency and factorial analysis showed three factors for EPG and IPA and one factor for PTD A second degree factorial analysis suggested the presence of only one factor based on the grouping of items of the EPG and IPA scales The study did not find theoretically relevant dlfferences in chronic procrastination according to gender, age or education level. However,with respect to socioeconomic status. there were higher levels of chronic procrastmation in the poorest sector

  15. Decomposition of multi-scale coherent structures in a turbulent boundary layer by variational mode decomposition

    Science.gov (United States)

    Wang, Wenkang; Pan, Chong; Wang, Jinjun

    2016-11-01

    Turbulent boundary layer (TBL) is believed to contain a wide spectrum of coherent structures, from near-wall low-speed streaks characterized by inner scale to log-layer large-scale coherent motions (LSM and VLSM) characterized by outer scale. Recent studies have evidenced the interaction between these multi-scale structures via either bottom-up or top-down mechanisms, which implies the possibility of identifying the coexistence of their footprints at medium flow layer. Here, we propose a Quasi-Bivariate Variational Mode Decomposition method (QB-VMD), which is an update of the traditional Empirical Mode Decomposition (EMD) with bandwidth limitation, for the decomposition of the PIV measured 2D flow fields with large ROI (Δx × Δz 4 δ × 1 . 5 δ) at specified wall-normal heights (y / δ = 0 . 05 0 . 2) of a turbulent boundary layer with Reτ = 3460 . The empirical modes identified by QB-VMD well capture the characteristics of log-layer LSMs as well as that of near-wall streak-like structures. The lateral scales of these structures are analyzed and their respective energy contribution are evaluated. Supported by both the National Natural Science Foundation of China (Grant Nos. 11372001 and 11490552) and the Fundamental Research Funds for the Central Universities of China (No. YWF-16-JCTD-A-05).

  16. Bridging scales from satellite to grains: Structural mapping aided by tablet and photogrammetry

    Science.gov (United States)

    Hawemann, Friedrich; Mancktelow, Neil; Pennacchioni, Giorgio; Wex, Sebastian; Camacho, Alfredo

    2016-04-01

    Bridging scales from satellite to grains: Structural mapping aided by tablet and photogrammetry A fundamental problem in small-scale mapping is linking outcrop observations to the large scale deformation pattern. The evolution of handheld devices such as tablets with integrated GPS and the availability of airborne imagery allows a precise localization of outcrops. Detailed structural geometries can be analyzed through ortho-rectified photo mosaics generated by photogrammetry software. In this study, we use a cheap standard Samsung-tablet (used for photogrammetry. The software PhotoScan from Agisoft matches the photographs in a fully automated manner, calculates a 3D model of the outcrop, and has the option to project this as an orthophoto onto a flat surface. This allows original orientations of grain-scale structures to be recorded over areas on a scale up to tens to hundreds of metres. The photo mosaics can then be georeferenced with the aid of the GPS-tracks of the shear zones and included in a GIS. This provides a cheap recording of the structures in high detail. The great advantages over mapping with UAVs (drones) is the resolution (1cm), the independence from weather and energy source, and the low cost.

  17. Extending the scope of models for large-scale structure formation in the Universe

    CERN Document Server

    Buchert, T; Pérez-Mercader, J; Buchert, Thomas; Dominguez, Alvaro; Perez-Mercader, Juan

    1999-01-01

    We propose a phenomenological generalization of the models of large-scale structure formation in the Universe by gravitational instability in two ways: we include pressure forces to model multi-streaming, and noise to model fluctuations due to neglected short-scale physical processes. We show that pressure gives rise to a viscous-like force of the same character as that one introduced in the ``adhesion model'', while noise leads to a roughening of the density field yielding a scaling behavior of its correlations.

  18. Shear viscosity and structural scalings in model adhesive hard-sphere gels

    Science.gov (United States)

    Eberle, Aaron P. R.; Martys, Nicos; Porcar, Lionel; Kline, Steven R.; George, William L.; Kim, Jung M.; Butler, Paul D.; Wagner, Norman J.

    2014-05-01

    We present experiments and simulations that show a fundamental scaling for both the rheology and microstructure of flowing gels. Unique flow-SANS measurements demonstrate that the structure orients along both the neutral and compression axis. We quantify the anisotropy using a single parameter, αn, that scales by a dimensionless number, M', that arises from a force balance on a particle. Simulations support the scalings and confirm the results are independent of the shape and range of the potential suggesting a universal for colloidal gels with short-ranged attractions.

  19. Statistical inferences in phylogeography

    DEFF Research Database (Denmark)

    Nielsen, Rasmus; Beaumont, Mark A

    2009-01-01

    In conventional phylogeographic studies, historical demographic processes are elucidated from the geographical distribution of individuals represented on an inferred gene tree. However, the interpretation of gene trees in this context can be difficult as the same demographic/geographical process ...

  20. Horizontal Structure of Turbulence on Decimeter to 10m Scales in Fast Tidal Flows

    Science.gov (United States)

    Horwitz, R.; Hay, A. E.

    2016-02-01

    We characterize the structure of turbulence in a very fast tidal channel in the Bay of Fundy, Nova Scotia that has been identified for development as a commercial tidal power resource. A subsurface mooring that orients into the flow was equipped with a horizontally-aimed AD2CP, and upward- and downward-looking ADCPs. Two week-long deployments provide velocity measurements of tidal flows up to 4 m/s that are used to describe the spatial (lateral) and temporal structure of turbulent fluctuations on decimeter to 10m scales. The spatial scales and temporal intermittency vary with both speed of the flow and the effects of upstream topography.

  1. Primordial Non-Gaussianity in the Large-Scale Structure of the Universe

    Directory of Open Access Journals (Sweden)

    Vincent Desjacques

    2010-01-01

    generated the cosmological fluctuations observed today. Any detection of significant non-Gaussianity would thus have profound implications for our understanding of cosmic structure formation. The large-scale mass distribution in the Universe is a sensitive probe of the nature of initial conditions. Recent theoretical progress together with rapid developments in observational techniques will enable us to critically confront predictions of inflationary scenarios and set constraints as competitive as those from the Cosmic Microwave Background. In this paper, we review past and current efforts in the search for primordial non-Gaussianity in the large-scale structure of the Universe.

  2. Universal small-scale structure in turbulence driven by magnetorotational instability

    Science.gov (United States)

    Zhdankin, Vladimir; Walker, Justin; Boldyrev, Stanislav; Lesur, Geoffroy

    2017-05-01

    The intermittent small-scale structure of turbulence governs energy dissipation in many astrophysical plasmas and is often believed to have universal properties for sufficiently large systems. In this work, we argue that small-scale turbulence in accretion discs is universal in the sense that it is insensitive to the magnetorotational instability (MRI) and background shear, and therefore indistinguishable from standard homogeneous magnetohydrodynamic (MHD) turbulence at small scales. We investigate the intermittency of current density, vorticity and energy dissipation in numerical simulations of incompressible MHD turbulence driven by the MRI in a shearing box. We find that the simulations exhibit a similar degree of intermittency as in standard MHD turbulence. We perform a statistical analysis of intermittent dissipative structures and find that energy dissipation is concentrated in thin sheet-like structures that span a wide range of scales up to the box size. We show that these structures exhibit strikingly similar statistical properties to those in standard MHD turbulence. Additionally, the structures are oriented in the toroidal direction with a characteristic tilt of approximately 17.^{circ}5, implying an effective guide field in that direction.

  3. An Examination of the Structure and Construct Validity of the Wender Utah Rating Scale.

    Science.gov (United States)

    Stanton, Kasey; Watson, David

    2016-01-01

    The Wender Utah Rating Scale (Ward, Wender, & Reimherr, 1993 ) has been widely used in adult attention-deficit/hyperactivity disorder (ADHD) research to assess childhood symptoms retrospectively, but little research has examined its factor structure and specificity in predicting ADHD versus other psychopathology. Consequently, this study had 2 goals: (a) to examine the Wender Utah Rating Scale's structure, and (b) to explicate the construct validity of this measure by relating factors from our structural analyses to other ADHD, psychopathology, and personality measures. Structural analyses in an adult community sample (N = 294) yielded a 3-factor structure of aggression (e.g., angry), internalizing distress (e.g., depressed), and academic difficulties (e.g., underachiever). Correlational and regression analyses indicated that these factors failed to display specificity in their associations with ADHD versus other psychopathology. Aggression and internalizing distress associated most strongly with indicators of externalizing (e.g., ill temper, manipulativeness) and internalizing psychopathology (e.g., depression, anxiety), respectively. Academic difficulties associated most strongly with ADHD symptoms, but these relations were relatively weak. Taken together, these findings raise concerns about the Wender Utah Rating Scale's construct validity, although additional longitudinal research is needed to clarify to what extent the Wender Utah Rating Scale validly assesses childhood ADHD symptoms.

  4. Swift: Compiled Inference for Probabilistic Programming Languages

    OpenAIRE

    Wu, Yi; Li, Lei; Russell, Stuart; Bodik, Rastislav

    2016-01-01

    A probabilistic program defines a probability measure over its semantic structures. One common goal of probabilistic programming languages (PPLs) is to compute posterior probabilities for arbitrary models and queries, given observed evidence, using a generic inference engine. Most PPL inference engines---even the compiled ones---incur significant runtime interpretation overhead, especially for contingent and open-universe models. This paper describes Swift, a compiler for the BLOG PPL. Swift-...

  5. Accelerating large-scale protein structure alignments with graphics processing units

    Directory of Open Access Journals (Sweden)

    Pang Bin

    2012-02-01

    Full Text Available Abstract Background Large-scale protein structure alignment, an indispensable tool to structural bioinformatics, poses a tremendous challenge on computational resources. To ensure structure alignment accuracy and efficiency, efforts have been made to parallelize traditional alignment algorithms in grid environments. However, these solutions are costly and of limited accessibility. Others trade alignment quality for speedup by using high-level characteristics of structure fragments for structure comparisons. Findings We present ppsAlign, a parallel protein structure Alignment framework designed and optimized to exploit the parallelism of Graphics Processing Units (GPUs. As a general-purpose GPU platform, ppsAlign could take many concurrent methods, such as TM-align and Fr-TM-align, into the parallelized algorithm design. We evaluated ppsAlign on an NVIDIA Tesla C2050 GPU card, and compared it with existing software solutions running on an AMD dual-core CPU. We observed a 36-fold speedup over TM-align, a 65-fold speedup over Fr-TM-align, and a 40-fold speedup over MAMMOTH. Conclusions ppsAlign is a high-performance protein structure alignment tool designed to tackle the computational complexity issues from protein structural data. The solution presented in this paper allows large-scale structure comparisons to be performed using massive parallel computing power of GPU.

  6. Using LiDAR Metrics to Characterize Forest Structural Complexity at Multiple Scales

    Science.gov (United States)

    Kane, V. R.; McGaughey, R. J.; Gersonde, R.; Franklin, J. F.

    2007-12-01

    Forest structure - the size and arrangement of trees and foliage - reflects a stand's history of initiation, growth, disturbance, and mortality. Because of this, studying the structure of forests can provide key insights into ecological processes, guides to silvicultural prescriptions to improve habitat, and assessments of forested landscapes. This study tested LiDAR metrics to characterize stands based on canopy structure. The study site was the 34,591 ha of forests in the Cedar River Watershed in western Washington State, USA. Stands ranged in age from 350 years old (including old-growth). Study sites spanned the western hemlock- Douglas fir (Tsuga heterophylla-Pseudotsuga menziesii), Pacific silver fir (Abies amabilis), and mountain hemlock (Tsuga mertansiana) forest zones. Eighty sample plots were used to ground truth the LiDAR data. A variety of structural indices were used to study canopy structural variations at the plot, stand, and landscape scales. The two most successful indices used the exposed geometry of the canopy surface: (1) the ratio of the canopy surface area to ground surface area (rumple index), and (2) the ratio of the volume beneath the canopy surface to maximum volume beneath the 95th percentile height (modified canopy volume method). These two indices integrated the spatial effects of tree heights, foliage distribution, and tree arrangement within 15m pixels. Variation between pixels revealed structural complexity at larger scales. Results: At the plot scale (~4 pixels), correlations with standard plot metrics (e.g., diameter at breast height) were similar to those reported by other studies. Comparison of structural complexity with age and height revealed a diversity of development pathways. The relationship between height and complexity allowed stands to be classified by the degree to which they have achieved their potential structural complexity, a new way to examine forest development. At the stand scale, the indices allowed spatial

  7. Full-scale performance assessment of aircraft secondary sandwich structure using thermoelastic stress analysis

    OpenAIRE

    Crump, D.A.; Dulieu-Barton, J.M.; Savage, J

    2009-01-01

    The use of resin film infusion (RFI) has been proven to reduce the cost of production of aircraft secondary sandwich structure. In this paper thermoelastic stress analysis (TSA) is used to assess the performance of full scale aircraft sandwich structure panels produced using both the conventional autoclave process and RFI. Finite element (FE) models of both panel types are developed and TSA is used to validate the models.

  8. Large-Scale Computations Leading to a First-Principles Approach to Nuclear Structure

    Energy Technology Data Exchange (ETDEWEB)

    Ormand, W E; Navratil, P

    2003-08-18

    We report on large-scale applications of the ab initio, no-core shell model with the primary goal of achieving an accurate description of nuclear structure from the fundamental inter-nucleon interactions. In particular, we show that realistic two-nucleon interactions are inadequate to describe the low-lying structure of {sup 10}B, and that realistic three-nucleon interactions are essential.

  9. Lack of sex-biased dispersal promotes fine-scale genetic structure in alpine ungulates

    Science.gov (United States)

    Roffler, Gretchen H.; Talbot, Sandra L.; Luikart, Gordon; Sage, George K.; Pilgrim, Kristy L.; Adams, Layne G.; Schwartz, Michael K.

    2014-01-01

    Identifying patterns of fine-scale genetic structure in natural populations can advance understanding of critical ecological processes such as dispersal and gene flow across heterogeneous landscapes. Alpine ungulates generally exhibit high levels of genetic structure due to female philopatry and patchy configuration of mountain habitats. We assessed the spatial scale of genetic structure and the amount of gene flow in 301 Dall’s sheep (Ovis dalli dalli) at the landscape level using 15 nuclear microsatellites and 473 base pairs of the mitochondrial (mtDNA) control region. Dall’s sheep exhibited significant genetic structure within contiguous mountain ranges, but mtDNA structure occurred at a broader geographic scale than nuclear DNA within the study area, and mtDNA structure for other North American mountain sheep populations. No evidence of male-mediated gene flow or greater philopatry of females was observed; there was little difference between markers with different modes of inheritance (pairwise nuclear DNA F ST = 0.004–0.325; mtDNA F ST = 0.009–0.544), and males were no more likely than females to be recent immigrants. Historical patterns based on mtDNA indicate separate northern and southern lineages and a pattern of expansion following regional glacial retreat. Boundaries of genetic clusters aligned geographically with prominent mountain ranges, icefields, and major river valleys based on Bayesian and hierarchical modeling of microsatellite and mtDNA data. Our results suggest that fine-scale genetic structure in Dall’s sheep is influenced by limited dispersal, and structure may be weaker in populations occurring near ancestral levels of density and distribution in continuous habitats compared to other alpine ungulates that have experienced declines and marked habitat fragmentation.

  10. Scaling of velocity and scalar structure functions in ac electrokinetic turbulence

    Science.gov (United States)

    Zhao, Wei; Wang, Guiren

    2017-02-01

    Electrokinetic (EK) turbulence or electrohydrodynamic (EHD) turbulence has been recently achieved in different fluids under both ac [G. Wang et al., Lab Chip 14, 1452 (2014), 10.1039/C3LC51403J; Phys. Rev. E 93, 013106 (2016), 10.1103/PhysRevE.93.013106] and dc electric fields [A. Varshney et al., Soft Matter 12, 1759 (2016), 10.1039/C5SM02316E]. Here, through dimensional analysis, scaling laws of both velocity and electric conductivity structure functions in the forced cascade region of ac EK turbulence can be predicated (similar to Bolgiano-Obukhov scaling law in turbulent Rayleigh-Bénard convection), in either macroscale or microscale flows. In the forced cascade region, EK force, which relies on the direct cascade of conductivity structures, injects energy directly into a wide spectral region to sustain the flow disturbance. The scaling exponents of the second-order velocity and conductivity structures are 2/5 and 4/5, respectively. In addition to the scaling regions, two characteristic small length scales are derived for both weak and strong electric body forces, respectively. This theoretical investigation can significantly enhance our understanding of EK or EHD turbulence while forced by an ac electric field. It can further broaden our understanding of the forced cascade region of forced turbulence and make the manipulation of the turbulent cascade process more flexible and controllable.

  11. The natural armors of fish: A comparison of the lamination pattern and structure of scales

    Energy Technology Data Exchange (ETDEWEB)

    Murcia, Sandra; Lavoie, Ellen; Linley, Tim; Devaraj, Arun; Ossa, E. Alex; Arola, D.

    2017-09-01

    Fish scales exhibit a unique balance of flexibility, strength and toughness, which is essential to provide protection without encumbering locomotion. Although the mechanical behavior and structure of this natural armor are of recent interest, a comparison of these qualities from scales of different fish species has not been reported. In this investigation the armor of fish with different locomotion, size and protection needs were analyzed. Scales from the Arapaima gigas, the tarpon (Megalops atlanticus) and the carp (Cyprinus carpio) were compared in terms of the stacking sequence of individual plies and their microstructure. The scales were also compared with respect to anatomical position to distinguish site-specific functional differences. Results show that the lamination sequence of plies for the carp and tarpon exhibit a Bouligand structure with relative rotation of 75° between consecutive plies. The arapaima scales exhibit a cross-ply structure, with 90° rotation between adjacent plies. In addition, results indicate that the volume fraction of reinforcement, the number of plies and the variations in thickness with anatomical position are unique amongst the three fish. These characteristics should be considered in evaluations focused on the mechanical behavior.

  12. The natural armors of fish: A comparison of the lamination pattern and structure of scales.

    Science.gov (United States)

    Murcia, Sandra; Lavoie, Ellen; Linley, Tim; Devaraj, Arun; Ossa, E Alex; Arola, D

    2017-09-01

    Fish scales exhibit a unique balance of flexibility, strength and toughness, which is essential to provide protection without encumbering locomotion. Although the mechanical behavior and structure of this natural armor are of recent interest, a comparison of these qualities from scales of different fish species has not been reported. In this investigation the armor of fish with different locomotion, size and protection needs were analyzed. Scales from the Arapaima gigas, the tarpon (Megalops atlanticus) and the carp (Cyprinus carpio) were compared in terms of the stacking sequence of individual plies and their microstructure. The scales were also compared with respect to anatomical position to distinguish site-specific functional differences. Results show that the lamination sequence of plies for the carp and tarpon exhibit a Bouligand structure with relative rotation of 75° between consecutive plies. The arapaima scales exhibit a cross-ply structure, with 90° rotation between adjacent plies. In addition, results indicate that the volume fraction of reinforcement, the number of plies and the variations in thickness with anatomical position are unique amongst the three fish. These characteristics should be considered in evaluations focused on the mechanical behavior. Copyright © 2016 Elsevier Ltd. All rights reserved.

  13. 3D multi-scale velocity structure of an active seismogenic normal fault zone (Central Apennines, Italy)

    Science.gov (United States)

    Fondriest, Michele; Mitchell, Tom; Vassallo, Maurizio; Di Giulio, Giuseppe; Balsamo, Fabrizio; Passelegue, Francois; Pischiutta, Marta; Di Toro, Giulio

    2017-04-01

    the sample and outcrop scale) were performed to investigate the scaling relation between laboratory and field measurements. These results were then coupled with ultrasonic velocity vs. confining pressure (0-30 MPa) profiles measured in the laboratory to extrapolate the subsurface velocity structure of the fault zone to larger depths (up to 1 km). The final dataset of physical properties was used to build a three dimensional velocity-elastic model of the Vado di Corno fault zone based on the fault zone structure inferred from the mapping. This type of studies are extremely relevant to better understand the petrophysical evolution and geophysical expression of active fault zones during the seismic cycle and represent the base for modern and robust fault mechanics models developed both in quasi-static or dynamic rupture scenarios.

  14. Item-level and scale-level factor structures of the MMPI-A.

    Science.gov (United States)

    Archer, R P; Belevich, J K; Elkins, D E

    1994-04-01

    The Minnesota Multiphasic Personality Inventory-Adolescent (MMPI-A) is a 478-item test that represents a substantial revision of the original form of the MMPI. This investigation sought to identify the item-level factor structure of the MMPI-A and also examined the scale-level factor structure of the 69 scales and subscales of this instrument. The study utilized the 1,620 normal adolescents (805 boys and 815 girls) of the normative sample for the MMPI-A. These adolescents ranged in age from 14 to 18, inclusive, with a mean age of 15.54 for boys and 15.60 for girls. A principal factor analysis of item-level responses resulted in extraction of 14 factors that were subjected to promax (oblique) rotation procedures. These 14 factors incorporated 81% of the total MMPI-A item pool and accounted for 44% of the total item-level response variance. For the scale-level analysis, 8 factors were selected for extraction and submitted to promax rotation procedures. These eight factors accounted for a total of 93.5% of the total variance in MMPI-A scale and subscale raw scores. Item-level results were discussed in terms of areas of congruence and dissimilarities from previously reported MMPI factor analyses in adolescent and adult samples, and scale-level factor results were presented in terms of clinical implications for the interpretation of MMPI-A scales and subscales.

  15. Patch-Scale Effects of Equine Disturbance on Arthropod Assemblages and Vegetation Structure in Subalpine Wetlands

    Science.gov (United States)

    Holmquist, Jeffrey G.; Schmidt-Gengenbach, Jutta; Ballenger, Elizabeth A.

    2014-06-01

    Assessments of vertebrate disturbance to plant and animal assemblages often contrast grazed versus ungrazed meadows or other larger areas of usage, and this approach can be powerful. Random sampling of such habitats carries the potential, however, for smaller, more intensely affected patches to be missed and for other responses that are only revealed at smaller scales to also escape detection. We instead sampled arthropod assemblages and vegetation structure at the patch scale (400-900 m2 patches) within subalpine wet meadows of Yosemite National Park (USA), with the goal of determining if there were fine-scale differences in magnitude and directionality of response at three levels of grazing intensity. Effects were both stronger and more nuanced than effects evidenced by previous random sampling of paired grazed and ungrazed meadows: (a) greater negative effects on vegetation structure and fauna in heavily used patches, but (b) some positive effects on fauna in lightly grazed patches, suggested by trends for mean richness and total and population abundances. Although assessment of disturbance at either patch or landscape scales should be appropriate, depending on the management question at hand, our patch-scale work demonstrated that there can be strong local effects on the ecology of these wetlands that may not be detected by comparing larger scale habitats.

  16. German National Proficiency Scales in Biology: Internal Structure, Relations to General Cognitive Abilities and Verbal Skills

    Science.gov (United States)

    Kampa, Nele; Köller, Olaf

    2016-01-01

    National and international large-scale assessments (LSA) have a major impact on educational systems, which raises fundamental questions about the validity of the measures regarding their internal structure and their relations to relevant covariates. Given its importance, research on the validity of instruments specifically developed for LSA is…

  17. Clonal growth and fine-scale genetic structure in tanoak (Notholithocarpus densiflorus: Fagaceae)

    Science.gov (United States)

    Richard S. Dodd; Wasima Mayer; Alejandro Nettel; Zara. Afzal-Rafii

    2013-01-01

    The combination of sprouting and reproduction by seed can have important consequences on fine-scale spatial distribution of genetic structure (SGS). SGS is an important consideration for species’ restoration because it determines the minimum distance among seed trees to maximize genetic diversity while not prejudicing locally adapted genotypes. Local environmental...

  18. Bacterial community structure of a full-scale biofilter treating pig house exhaust air

    DEFF Research Database (Denmark)

    Kristiansen, Anja; Pedersen, Kristina Hadulla; Nielsen, Per Halkjær

    2011-01-01

    Biological air filters represent a promising tool for treating emissions of ammonia and odor from pig facilities. Quantitative fluorescence in situ hybridization (FISH) and 16S rRNA gene sequencing were used to investigate the bacterial community structure and diversity in a full-scale biofilter...

  19. Factor structure and measurement invariance of a multidimensional loneliness scale : Comparisons across gender and age

    NARCIS (Netherlands)

    Maes, Marlies; Klimstra, T.A.; Van den Noortgate, Wim; Goossens, Luc

    2015-01-01

    This study focuses on the factor structure of a multidimensional loneliness measure, that is, the Loneliness and Aloneness Scale for Children and Adolescents (LACA). Confirmatory factor analyses were conducted on a large sample of children and adolescents (N = 9,676) in Belgium. Results indicated

  20. Atomic-scale structure of single-layer MoS2 nanoclusters

    DEFF Research Database (Denmark)

    Helveg, S.; Lauritsen, J. V.; Lægsgaard, E.

    2000-01-01

    We have studied using scanning tunneling microscopy (STM) the atomic-scale realm of molybdenum disulfide (MoS2) nanoclusters, which are of interest as a model system in hydrodesulfurization catalysis. The STM gives the first real space images of the shape and edge structure of single-layer MoS2...

  1. Structure of isolated large-scale inhomogeneities in the outer ionosphere

    Science.gov (United States)

    Kalinin, Iu. K.; Romanchuk, A. A.

    1991-03-01

    The structure of large-scale inhomogeneities in the outer ionosphere is examined with reference to Thomson scattering data. The dependence of delta Ne/Ne and delta Ne on the local coordinates is established. The shape function is also examined.

  2. Factor Structure of the Social Appearance Anxiety Scale in Turkish Early Adolescents

    Science.gov (United States)

    Sahin, Ertugrul; Topkaya, Nursel

    2015-01-01

    Although the Social Appearance Anxiety Scale (SAAS) is most often validated with the use of confirmatory factor analysis (CFA) on undergraduate students, exploratory factor analysis and multiple factor retention decision criteria necessitate the analysis of underlying factor structure to prevent over and under factoring as well as to reveal…

  3. Homework Management Scale: Confirming the Factor Structure with Middle School Students in China

    Science.gov (United States)

    Xu, Jianzhong; Fan, Xitao; Du, Jianxia

    2015-01-01

    This study presents a psychometric evaluation of the Homework Management Scale (HMS) for mathematics, consisting of five subscales for measuring homework management strategies. Confirmatory factor analyses were conducted with a sample of middle school students (N = 796). Results indicated that the factor structure of the Chinese version of the HMS…

  4. Factor Structure of the Korean Version of Wong and Law's Emotional Intelligence Scale

    Science.gov (United States)

    Fukuda, Eriko; Saklofske, Donald H.; Tamaoka, Katsuo; Lim, Hyunjung

    2012-01-01

    This study reports the factor structure of a Korean version of the 16-item Wong and Law Emotional Intelligence Scale (WLEIS) for a sample of 161 Korean university students. Confirmatory factor analysis supported the four-factor model of the WLEIS: (1) self-emotional appraisal, (2) others' emotional appraisal, (3) use of emotion, and (4) regulation…

  5. The Factor Structure of Preschool Learning Behaviors Scale Scores in Peruvian Children

    Science.gov (United States)

    Hahn, Kathryn R.; Schaefer, Barbara A.; Merino, Cesar; Worrell, Frank C.

    2009-01-01

    The factor structure of the Escala de Conductas de Aprendizaje Preescolar (ECAP), a Spanish translation of the Preschool Learning Behaviors Scale (PLBS), was examined in this study. Children aged 2 to 6 years (N = 328) enrolled in public and private preschools in the Republic of Peru were rated by classroom teachers on the frequency of observable,…

  6. Phase transitions as the origin of large scale structure in the universe

    Science.gov (United States)

    Turok, Neil

    1989-01-01

    A review of the formation of large scale structure through gravitational growth of primordial perturbations is given. This is followed by a discussion of how symmetry breaking phase transitions in the early universe might have produced the required perturbations, in particular through the formation and evolution of a network of cosmic strings.

  7. Mapping the MMPI-2-RF Specific Problems Scales Onto Extant Psychopathology Structures.

    Science.gov (United States)

    Sellbom, Martin

    2017-01-01

    A main objective in developing the Minnesota Multiphasic Personality Inventory-2-Restructured Form (MMPI-2-RF; Ben-Porath & Tellegen, 2008 ) was to link the hierarchical structure of the instrument's scales to contemporary psychopathology and personality models for greater enhancement of construct validity. Initial evidence published with the Restructured Clinical scales has indicated promising results in that the higher order structure of these measures maps onto those reported in the extant psychopathology literature. This study focused on evaluating the internal structure of the Specific Problems and Interest scales, which have not yet been examined in this manner. Two large, mixed-gender outpatient and correctional samples were used. Exploratory factor analyses revealed consistent evidence for a 4-factor structure representing somatization, negative affect, externalizing, and social detachment. Convergent and discriminant validity analyses in the outpatient sample yielded a pattern of results consistent with expectations. These findings add further evidence to indicate that the MMPI-2-RF hierarchy of scales map onto extant psychopathology literature, and also add support to the notion that somatization and detachment should be considered important higher order domains in the psychopathology literature.

  8. The structural and hydration properties of heat-treated rice studied at multiple lenght scales

    NARCIS (Netherlands)

    Witek, M.M.; Weglarz, W.; Jong, de L.; Dalen, van G.; Blonk, J.C.G.; Heussen, P.; Velzen, van E.; As, van H.; Duynhoven, van J.P.M.

    2010-01-01

    The impact of heat-treatment on structure and hydration properties of rice was studied at different length scales (µm–nm). Heat-treatment introduced micro- and macro-pores within rice kernels (µCT) and, within intact cell walls, disintegrated starch granules were observed (SEM, CSLM). In native

  9. Wavelength-Scale Structures as Extremely High Haze Films for Efficient Polymer Solar Cells.

    Science.gov (United States)

    Ham, Juyoung; Dong, Wan Jae; Jung, Gwan Ho; Lee, Jong-Lam

    2016-03-09

    Wavelength-scale inverted pyramid structures with low reflectance and excellent haze have been designed for application to polymer solar cells (PSCs). The wavelength-scale structured haze films are fabricated on the back surface of glass without damages to organic active layer by using a soft lithographic technique with etched GaN molds. With a rigorous coupled-wave analysis of optical modeling, we find the shift of resonance peaks with the increase of pattern's diameter. Wavelength-scale structures could provide the number of resonances at the long wavelength spectrum (λ = 650-800 nm), yielding enhancement of power conversion efficiency (PCE) in the PSCs. Compared with a flat device (PCE = 7.12%, Jsc = 15.6 mA/cm(2)), improved PCE of 8.41% is achieved in a haze film, which is mainly due to the increased short circuit current density (Jsc) of 17.5 mA/cm(2). Hence, it opens up exciting opportunities for a variety of PSCs with wavelength-scale structures to further improve performance, simplify complicated process, and reduce costs.

  10. Factor Structure of the Kessler Psychological Distress Scale (K6) among Emerging Adults

    Science.gov (United States)

    Bessaha, Melissa L.

    2017-01-01

    Objective: Confirmatory factor analysis was used to assess the factor structure of the 6-item version of the Kessler Psychological Distress Scale (K6). Methods: A subsample of emerging adults, aged 18-29 (n = 20,699), from the 2013 National Survey of Drug Use and Health were used in this study. Results: Each of the models (one-factor, two-factor…

  11. Examining the Emergence of Large-Scale Structures in Collaboration Networks: Methods in Sociological Analysis

    Science.gov (United States)

    Ghosh, Jaideep; Kshitij, Avinash

    2017-01-01

    This article introduces a number of methods that can be useful for examining the emergence of large-scale structures in collaboration networks. The study contributes to sociological research by investigating how clusters of research collaborators evolve and sometimes percolate in a collaboration network. Typically, we find that in our networks,…

  12. Factor Structure of the Rorschach Prognostic Rating Scale and Its Relation to Therapeutic Outcome

    Science.gov (United States)

    Auerbach, Stephen M.; Edinger, Jack D.

    1976-01-01

    This study evaluated the factor structure of the Rorschach Prognostic Rating Scale (RPRS) in order to: (a) test the assumption that the RPRS represents a unitary response system and (b) determine the efficacy of employing population specific factor scores as predictors of therapy outcome. (Author/NG)

  13. Fractals and the Large-Scale Structure in the Universe-Is the ...

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 7; Issue 4. Fractals and the Large-Scale Structure in the Universe - Is the Cosmological Principle Valid? A K Mittal T R Seshadri. General Article Volume 7 Issue 4 April 2002 pp 39-47 ...

  14. Fractals and the Large-Scale Structure in the Universe-Introduction ...

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 7; Issue 2. Fractals and the Large-Scale Structure in the Universe - Introduction and Basic Concepts. A K Mittal T R Seshadri. General Article Volume 7 Issue 2 February 2002 pp 6-19 ...

  15. Anatomically diverse butterfly scales all produce structural colours by coherent scattering.

    Science.gov (United States)

    Prum, Richard O; Quinn, Tim; Torres, Rodolfo H

    2006-02-01

    The structural colours of butterflies and moths (Lepidoptera) have been attributed to a diversity of physical mechanisms, including multilayer interference, diffraction, Bragg scattering, Tyndall scattering and Rayleigh scattering. We used fibre optic spectrophotometry, transmission electron microscopy (TEM) and 2D Fourier analysis to investigate the physical mechanisms of structural colour production in twelve lepidopteran species from four families, representing all of the previously proposed anatomical and optical classes of butterfly nanostructure. The 2D Fourier analyses of TEMs of colour producing butterfly scales document that all species are appropriately nanostructured to produce visible colours by coherent scattering, i.e. differential interference and reinforcement of scattered, visible wavelengths. Previously hypothesized to produce a blue colour by incoherent, Tyndall scattering, the scales of Papilio zalmoxis are not appropriately nanostructured for incoherent scattering. Rather, available data indicate that the blue of P. zalmoxis is a fluorescent pigmentary colour. Despite their nanoscale anatomical diversity, all structurally coloured butterfly scales share a single fundamental physical color production mechanism - coherent scattering. Recognition of this commonality provides a new perspective on how the nanostructure and optical properties of structurally coloured butterfly scales evolved and diversified among and within lepidopteran clades.

  16. Large-scale structural alteration of brain in epileptic children with SCN1A mutation

    Directory of Open Access Journals (Sweden)

    Yun-Jeong Lee

    2017-01-01

    Significance: This study showed large-scale developmental brain changes in patients with epilepsy and SCN1A gene mutation, which may be associated with the core symptoms of the patients. Further longitudinal MRI studies with larger cohorts are required to confirm the effect of SCN1A gene mutation on structural brain development.

  17. Factor Structure of the Acute Stress Disorder Scale in a Sample of Hurricane Katrina Evacuees

    Science.gov (United States)

    Edmondson, Donald; Mills, Mary Alice; Park, Crystal L.

    2010-01-01

    Acute stress disorder (ASD) is a poorly understood and controversial diagnosis (A. G. Harvey & R. A. Bryant, 2002). The present study used confirmatory factor analysis (CFA) to test the factor structure of the most widely used self-report measure of ASD, the Acute Stress Disorder Scale (R. A. Bryant, M. L. Moulds, & R. M. Guthrie, 2000),…

  18. Factorial Structure of the French Version of the Rosenberg Self-Esteem Scale among the Elderly

    Science.gov (United States)

    Gana, Kamel; Alaphilippe, Daniel; Bailly, Nathalie

    2005-01-01

    Ten different confirmatory factor analysis models, including ones with correlated traits correlated methods, correlated traits correlated uniqueness, and correlated traits uncorrelated methods, were proposed to examine the factorial structure of the French version of the Rosenberg Self-Esteem Scale (Rosenberg, 1965). In line with previous studies…

  19. Self-Preservation of Large-Scale Structures in Burgers' Turbulence

    CERN Document Server

    Aurell, E; Wertgeim, I I; Aurell, Erik; Gurbatov, Sergey N.; Wertgeim, Igor I.

    1993-01-01

    Abstract:We investigate the stability of large-scale structures in Burgers' equation under the perturbation of high wave-number noise in the initial conditions. Analytical estimates are obtained for random initial data with spatial spectral density k^n, n < 1. Numerical investigations are performed for the case n=0, using a parallel implementation of the Fast Legendre Transform.

  20. Factor Structure, Reliability and Validity of the Taiwanese Version of the Multidimensional Anxiety Scale for Children

    Science.gov (United States)

    Yen, Cheng-Fang; Yang, Pinchen; Wu, Yu-Yu; Hsu, Fan-Ching; Cheng, Chung-Ping

    2010-01-01

    The aims of this study were to examine the factor structure, internal consistency 1 month test-retest reliability and the discriminant validity for the diagnosis of anxiety disorder of the Taiwanese version of the Multidimensional Anxiety Scale for Children (MASC-T). A total of 12,536 Taiwanese children and adolescents in the community were…