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Sample records for acyclic graphs dags

  1. Directed Acyclic Graphs for Oral Disease Research.

    PubMed

    Akinkugbe, A A; Sharma, S; Ohrbach, R; Slade, G D; Poole, C

    2016-07-01

    Directed acyclic graphs (DAGs) are nonparametric graphical tools used to depict causal relations in the epidemiologic assessment of exposure-outcome associations. Although their use in dental research was first advocated in 2002, DAGs have yet to be widely adopted in this field. DAGs help identify threats to causal inference such as confounders, bias due to subject selection, and inappropriate handling of missing data. DAGs can also inform the data analysis strategy based on relations among variables depicted on it. This article uses the example of a study of temporomandibular disorders (TMDs), investigating causal effects of facial injury on subsequent risk of TMD. We illustrate how DAGs can be used to identify 1) potential confounders, 2) mediators and the consequences of attempt to estimate direct causal effects, 3) colliders and the consequences of conditioning on colliders, and 4) variables that are simultaneously mediators and confounders and the consequences of adjustment for such variables. For example, one DAG shows that statistical adjustment for the pressure pain threshold would necessarily bias the causal relation between facial injury and TMD. Finally, we discuss the usefulness of DAGs during study design, subject selection, and choosing variables to be measured in a study. PMID:27000052

  2. Acyclic colorings of graphs with bounded degree

    NASA Astrophysics Data System (ADS)

    Fiedorowicz, Anna; Sidorowicz, Elżbieta

    2016-07-01

    A $k$-colouring (not necessarily proper) of vertices of a graph is called {\\it acyclic}, if for every pair of distinct colours $i$ and $j$ the subgraph induced by the edges whose endpoints have colours $i$ and $j$ is acyclic. In the paper we consider some generalised acyclic $k$-colourings, namely, we require that each colour class induces an acyclic or bounded degree graph. Mainly we focus on graphs with maximum degree 5. We prove that any such graph has an acyclic $5$-colouring such that each colour class induces an acyclic graph with maximum degree at most 4. We prove that the problem of deciding whether a graph $G$ has an acyclic 2-colouring in which each colour class induces a graph with maximum degree at most 3 is NP-complete, even for graphs with maximum degree 5. We also give a linear-time algorithm for an acyclic $t$-improper colouring of any graph with maximum degree $d$ assuming that the number of colors is large enough.

  3. Analyzing microarray data with transitive directed acyclic graphs.

    PubMed

    Phan, Vinhthuy; Olusegun George, E; Tran, Quynh T; Goodwin, Shirlean; Bodreddigari, Sridevi; Sutter, Thomas R

    2009-02-01

    Post hoc assignment of patterns determined by all pairwise comparisons in microarray experiments with multiple treatments has been proven to be useful in assessing treatment effects. We propose the usage of transitive directed acyclic graphs (tDAG) as the representation of these patterns and show that such representation can be useful in clustering treatment effects, annotating existing clustering methods, and analyzing sample sizes. Advantages of this approach include: (1) unique and descriptive meaning of each cluster in terms of how genes respond to all pairs of treatments; (2) insensitivity of the observed patterns to the number of genes analyzed; and (3) a combinatorial perspective to address the sample size problem by observing the rate of contractible tDAG as the number of replicates increases. The advantages and overall utility of the method in elaborating drug structure activity relationships are exemplified in a controlled study with real and simulated data. PMID:19226664

  4. A Directed Acyclic Graph-Large Margin Distribution Machine Model for Music Symbol Classification.

    PubMed

    Wen, Cuihong; Zhang, Jing; Rebelo, Ana; Cheng, Fanyong

    2016-01-01

    Optical Music Recognition (OMR) has received increasing attention in recent years. In this paper, we propose a classifier based on a new method named Directed Acyclic Graph-Large margin Distribution Machine (DAG-LDM). The DAG-LDM is an improvement of the Large margin Distribution Machine (LDM), which is a binary classifier that optimizes the margin distribution by maximizing the margin mean and minimizing the margin variance simultaneously. We modify the LDM to the DAG-LDM to solve the multi-class music symbol classification problem. Tests are conducted on more than 10000 music symbol images, obtained from handwritten and printed images of music scores. The proposed method provides superior classification capability and achieves much higher classification accuracy than the state-of-the-art algorithms such as Support Vector Machines (SVMs) and Neural Networks (NNs). PMID:26985826

  5. A Directed Acyclic Graph-Large Margin Distribution Machine Model for Music Symbol Classification

    PubMed Central

    Wen, Cuihong; Zhang, Jing; Rebelo, Ana; Cheng, Fanyong

    2016-01-01

    Optical Music Recognition (OMR) has received increasing attention in recent years. In this paper, we propose a classifier based on a new method named Directed Acyclic Graph-Large margin Distribution Machine (DAG-LDM). The DAG-LDM is an improvement of the Large margin Distribution Machine (LDM), which is a binary classifier that optimizes the margin distribution by maximizing the margin mean and minimizing the margin variance simultaneously. We modify the LDM to the DAG-LDM to solve the multi-class music symbol classification problem. Tests are conducted on more than 10000 music symbol images, obtained from handwritten and printed images of music scores. The proposed method provides superior classification capability and achieves much higher classification accuracy than the state-of-the-art algorithms such as Support Vector Machines (SVMs) and Neural Networks (NNs). PMID:26985826

  6. Analytic Bounds on Causal Risk Differences in Directed Acyclic Graphs Involving Three Observed Binary Variables

    PubMed Central

    Kaufman, Sol; Kaufman, Jay S.; MacLehose, Richard F.

    2009-01-01

    We apply a linear programming approach which uses the causal risk difference (RDC) as the objective function and provides minimum and maximum values that RDC can achieve under any set of linear constraints on the potential response type distribution. We consider two scenarios involving binary exposure X, covariate Z and outcome Y. In the first, Z is not affected by X, and is a potential confounder of the causal effect of X on Y. In the second, Z is affected by X and intermediate in the causal pathway between X and Y. For each scenario we consider various linear constraints corresponding to the presence or absence of arcs in the associated directed acyclic graph (DAG), monotonicity assumptions, and presence or absence of additive-scale interactions. We also estimate Z-stratum-specific bounds when Z is a potential effect measure modifier and bounds for both controlled and natural direct effects when Z is affected by X. In the absence of any additional constraints deriving from background knowledge, the well-known bounds on RDc are duplicated: −Pr(Y≠X) ≤ RDC ≤ Pr(Y=X). These bounds have unit width, but can be narrowed by background knowledge-based assumptions. We provide and compare bounds and bound widths for various combinations of assumptions in the two scenarios and apply these bounds to real data from two studies. PMID:20161106

  7. Acyclic and star colorings of joins of graphs and an algorithm for cographs.

    SciTech Connect

    Lyons, A.; Mathematics and Computer Science; Univ. of Chicago

    2009-01-01

    An acyclic coloring of a graph is a proper vertex coloring such that the subgraph induced by the union of any two color classes is a disjoint collection of trees. The more restricted notion of star coloring requires that the union of any two color classes induces a disjoint collection of stars. The acyclic and star chromatic numbers of a graph G are defined analogously to the chromatic number {chi}(G) and are denoted by {chi}{sub a}(G) and {chi}{sub s}(G), respectively. In this paper, we consider acyclic and star colorings of graphs that are decomposable with respect to the join operation, which builds a new graph from a collection of two or more disjoint graphs by adding all possible edges between them. In particular, we present a recursive formula for the acyclic chromatic number of joins of graphs and show that a similar formula holds for the star chromatic number. We also demonstrate the algorithmic implications of our results for the cographs, which have the unique property that they are recursively decomposable with respect to the join and disjoint union operations.

  8. A DAG Scheduling Scheme on Heterogeneous Computing Systems Using Tuple-Based Chemical Reaction Optimization

    PubMed Central

    Jiang, Yuyi; Shao, Zhiqing; Guo, Yi

    2014-01-01

    A complex computing problem can be solved efficiently on a system with multiple computing nodes by dividing its implementation code into several parallel processing modules or tasks that can be formulated as directed acyclic graph (DAG) problems. The DAG jobs may be mapped to and scheduled on the computing nodes to minimize the total execution time. Searching an optimal DAG scheduling solution is considered to be NP-complete. This paper proposed a tuple molecular structure-based chemical reaction optimization (TMSCRO) method for DAG scheduling on heterogeneous computing systems, based on a very recently proposed metaheuristic method, chemical reaction optimization (CRO). Comparing with other CRO-based algorithms for DAG scheduling, the design of tuple reaction molecular structure and four elementary reaction operators of TMSCRO is more reasonable. TMSCRO also applies the concept of constrained critical paths (CCPs), constrained-critical-path directed acyclic graph (CCPDAG) and super molecule for accelerating convergence. In this paper, we have also conducted simulation experiments to verify the effectiveness and efficiency of TMSCRO upon a large set of randomly generated graphs and the graphs for real world problems. PMID:25143977

  9. Cell Tracking Accuracy Measurement Based on Comparison of Acyclic Oriented Graphs.

    PubMed

    Matula, Pavel; Maška, Martin; Sorokin, Dmitry V; Matula, Petr; Ortiz-de-Solórzano, Carlos; Kozubek, Michal

    2015-01-01

    Tracking motile cells in time-lapse series is challenging and is required in many biomedical applications. Cell tracks can be mathematically represented as acyclic oriented graphs. Their vertices describe the spatio-temporal locations of individual cells, whereas the edges represent temporal relationships between them. Such a representation maintains the knowledge of all important cellular events within a captured field of view, such as migration, division, death, and transit through the field of view. The increasing number of cell tracking algorithms calls for comparison of their performance. However, the lack of a standardized cell tracking accuracy measure makes the comparison impracticable. This paper defines and evaluates an accuracy measure for objective and systematic benchmarking of cell tracking algorithms. The measure assumes the existence of a ground-truth reference, and assesses how difficult it is to transform a computed graph into the reference one. The difficulty is measured as a weighted sum of the lowest number of graph operations, such as split, delete, and add a vertex and delete, add, and alter the semantics of an edge, needed to make the graphs identical. The measure behavior is extensively analyzed based on the tracking results provided by the participants of the first Cell Tracking Challenge hosted by the 2013 IEEE International Symposium on Biomedical Imaging. We demonstrate the robustness and stability of the measure against small changes in the choice of weights for diverse cell tracking algorithms and fluorescence microscopy datasets. As the measure penalizes all possible errors in the tracking results and is easy to compute, it may especially help developers and analysts to tune their algorithms according to their needs. PMID:26683608

  10. Cell Tracking Accuracy Measurement Based on Comparison of Acyclic Oriented Graphs

    PubMed Central

    Sorokin, Dmitry V.; Matula, Petr; Ortiz-de-Solórzano, Carlos; Kozubek, Michal

    2015-01-01

    Tracking motile cells in time-lapse series is challenging and is required in many biomedical applications. Cell tracks can be mathematically represented as acyclic oriented graphs. Their vertices describe the spatio-temporal locations of individual cells, whereas the edges represent temporal relationships between them. Such a representation maintains the knowledge of all important cellular events within a captured field of view, such as migration, division, death, and transit through the field of view. The increasing number of cell tracking algorithms calls for comparison of their performance. However, the lack of a standardized cell tracking accuracy measure makes the comparison impracticable. This paper defines and evaluates an accuracy measure for objective and systematic benchmarking of cell tracking algorithms. The measure assumes the existence of a ground-truth reference, and assesses how difficult it is to transform a computed graph into the reference one. The difficulty is measured as a weighted sum of the lowest number of graph operations, such as split, delete, and add a vertex and delete, add, and alter the semantics of an edge, needed to make the graphs identical. The measure behavior is extensively analyzed based on the tracking results provided by the participants of the first Cell Tracking Challenge hosted by the 2013 IEEE International Symposium on Biomedical Imaging. We demonstrate the robustness and stability of the measure against small changes in the choice of weights for diverse cell tracking algorithms and fluorescence microscopy datasets. As the measure penalizes all possible errors in the tracking results and is easy to compute, it may especially help developers and analysts to tune their algorithms according to their needs. PMID:26683608

  11. DagStream: locality aware and failure resilient peer-to-peer streaming

    NASA Astrophysics Data System (ADS)

    Liang, Jin; Nahrstedt, Klara

    2006-01-01

    Live peer to peer (P2P) media streaming faces many challenges such as peer unreliability and bandwidth heterogeneity. To effectively address these challenges, general "mesh" based P2P streaming architectures have recently been adopted. Mesh-based systems allow peers to aggregate bandwidth from multiple neighbors, and dynamically adapt to changing network conditions and neighbor failures. However, a drawback of mesh-based overlays is that it is difficult to guarantee network connectivity in a distributed fashion, especially when network locality needs to be optimized. This paper introduces a new P2P streaming framework called DagStream, which (1) organizes peers into a directed acyclic graph (DAG) where each node maintains at least k parents, thus has provable network connectivity (and hence failure resilience), and (2) enables peers to quickly achieve locality awareness in a distributed fashion, thus ensures efficient network resource usage. Our experiment results in both simulation and wide area environment show that with our DagStream protocol, peers can quickly self-organize into a locality aware DAG. Further, by selecting additional parents as needed, peers can achieve good streaming quality commensurate with their downlink bandwidth.

  12. Defining order and timing of mutations during cancer progression: the TO-DAG probabilistic graphical model

    PubMed Central

    Lecca, Paola; Casiraghi, Nicola; Demichelis, Francesca

    2015-01-01

    Somatic mutations arise and accumulate both during tumor genesis and progression. However, the order in which mutations occur is an open question and the inference of the temporal ordering at the gene level could potentially impact on patient treatment. Thus, exploiting recent observations suggesting that the occurrence of mutations is a non-memoryless process, we developed a computational approach to infer timed oncogenetic directed acyclic graphs (TO-DAGs) from human tumor mutation data. Such graphs represent the path and the waiting times of alterations during tumor evolution. The probability of occurrence of each alteration in a path is the probability that the alteration occurs when all alterations prior to it have occurred. The waiting time between an alteration and the subsequent is modeled as a stochastic function of the conditional probability of the event given the occurrence of the previous one. TO-DAG performances have been evaluated both on synthetic data and on somatic non-silent mutations from prostate cancer and melanoma patients and then compared with those of current well-established approaches. TO-DAG shows high performance scores on synthetic data and recognizes mutations in gatekeeper tumor suppressor genes as trigger for several downstream mutational events in the human tumor data. PMID:26528329

  13. Indexing hierarchical structures using graph spectra.

    PubMed

    Shokoufandeh, Ali; Macrini, Diego; Dickinson, Sven; Siddiqi, Kaleem; Zucker, Steven W

    2005-07-01

    Hierarchical image structures are abundant in computer vision and have been used to encode part structure, scale spaces, and a variety of multiresolution features. In this paper, we describe a framework for indexing such representations that embeds the topological structure of a directed acyclic graph (DAG) into a low-dimensional vector space. Based on a novel spectral characterization of a DAG, this topological signature allows us to efficiently retrieve a promising set of candidates from a database of models using a simple nearest-neighbor search. We establish the insensitivity of the signature to minor perturbation of graph structure due to noise, occlusion, or node split/merge. To accommodate large-scale occlusion, the DAG rooted at each nonleaf node of the query "votes" for model objects that share that "part," effectively accumulating local evidence in a model DAG's topological subspaces. We demonstrate the approach with a series of indexing experiments in the domain of view-based 3D object recognition using shock graphs. PMID:16013759

  14. Dynamic Uncertain Causality Graph for Knowledge Representation and Probabilistic Reasoning: Directed Cyclic Graph and Joint Probability Distribution.

    PubMed

    Zhang, Qin

    2015-07-01

    Probabilistic graphical models (PGMs) such as Bayesian network (BN) have been widely applied in uncertain causality representation and probabilistic reasoning. Dynamic uncertain causality graph (DUCG) is a newly presented model of PGMs, which can be applied to fault diagnosis of large and complex industrial systems, disease diagnosis, and so on. The basic methodology of DUCG has been previously presented, in which only the directed acyclic graph (DAG) was addressed. However, the mathematical meaning of DUCG was not discussed. In this paper, the DUCG with directed cyclic graphs (DCGs) is addressed. In contrast, BN does not allow DCGs, as otherwise the conditional independence will not be satisfied. The inference algorithm for the DUCG with DCGs is presented, which not only extends the capabilities of DUCG from DAGs to DCGs but also enables users to decompose a large and complex DUCG into a set of small, simple sub-DUCGs, so that a large and complex knowledge base can be easily constructed, understood, and maintained. The basic mathematical definition of a complete DUCG with or without DCGs is proved to be a joint probability distribution (JPD) over a set of random variables. The incomplete DUCG as a part of a complete DUCG may represent a part of JPD. Examples are provided to illustrate the methodology. PMID:25781960

  15. Cardioleader use in acyclic types of sports

    NASA Technical Reports Server (NTRS)

    Bondin, V. I.

    1980-01-01

    The use of the cardioleader method in regulating training loads and tests for athletes in acyclic sports was investigated. It was found that the use of this method increases the effectiveness of the training process.

  16. Fast Reachability Test on DAGs for XML

    NASA Astrophysics Data System (ADS)

    Nakamura, Yusaku; Maita, Tetsuya; Sakamoto, Hiroshi

    We propose an efficient algorithm for deciding the reachability between any nodes on XML data represented by connected directed graphs. We develop a technique to reduce the size of the reference table for the reachability test. Using the small table and the standard range labeling method for rooted ordered trees, we show that our algorithm answers almost queries in a constant time preserving the space efficiency and a reasonable preprocessing time.

  17. Inferring Pedigree Graphs from Genetic Distances

    NASA Astrophysics Data System (ADS)

    Tamura, Takeyuki; Ito, Hiro

    In this paper, we study a problem of inferring blood relationships which satisfy a given matrix of genetic distances between all pairs of n nodes. Blood relationships are represented by our proposed graph class, which is called a pedigree graph. A pedigree graph is a directed acyclic graph in which the maximum indegree is at most two. We show that the number of pedigree graphs which satisfy the condition of given genetic distances may be exponential, but they can be represented by one directed acyclic graph with n nodes. Moreover, an O(n3) time algorithm which solves the problem is also given. Although phylogenetic trees and phylogenetic networks are similar data structures to pedigree graphs, it seems that inferring methods for phylogenetic trees and networks cannot be applied to infer pedigree graphs since nodes of phylogenetic trees and networks represent species whereas nodes of pedigree graphs represent individuals. We also show an O(n2) time algorithm which detects a contradiction between a given pedigreee graph and distance matrix of genetic distances.

  18. FIRE near-infrared spectroscopic classifications of SN 2016dag

    NASA Astrophysics Data System (ADS)

    Morrell, N.; Phillips, M. M.; Contreras, C.; Hsia, E. Y.

    2016-07-01

    We report the spectroscopic classification of SN 2016dag, discovered by the Backyard Observatory Supernova Search (BOSS), using a near-infrared spectrum (range 800-2500 nm) obtained on Jul 14.95 UT with the FoldedPort Infrared Echellette (FIRE) spectrograph on the 6.5-m Magellan Baade Telescope at Las Campanas Observatory.

  19. Biodegradation of acyclic isoprenoids by Pseudomonas species.

    PubMed Central

    Cantwell, S G; Lau, E P; Watt, D S; Fall, R R

    1978-01-01

    The ability of various pseudomonads to utilize acyclic isoprenoids as a sole carbon source was investigated. Tests for utilization of acyclic isoprenols such as citronellol and geraniol were complicated by toxic effects of these alcohols, and most species tested were killed by exposure to citronellol or geraniol (0.1%, vol/vol) in liquid culture. In the case of Pseudomonas citronellolis, sensitivity to isoprenols is reduced by prior induction of the isoprenoid degradative pathway via either growth on succinate in the presence of citronellol or growth on citronellic acid. For this species, citronellic acid proved to be the best isoprenoid growth substrate tested. Geraniol utilization as a taxonomic indicator for different subgroups of pseudomonads is discussed. Only a few of the species tested were able to utilize acyclic isoprenoids. Two species which utilize C10 acyclic isoprenoids, P. aeruginosa and P. mendocina, were shown to contain the inducible enzyme geranyl-coenzyme A carboxylase, one of the unique enzymes in the isoprenol degradative pathway known to occur in P. citronellolis. Of the species which utilized geranitol, none showed definite growth on the homologous C15 and C20 isoprenols. PMID:681275

  20. CHARMM Additive All-Atom Force Field for Acyclic Polyalcohols, Acyclic Carbohydrates and Inositol

    PubMed Central

    Hatcher, Elizabeth; Guvench, Olgun; MacKerell, Alexander D.

    2009-01-01

    Parametrization of the additive all-atom CHARMM force field for acyclic polyalcohols, acyclic carbohydrates and inositol is conducted. Initial parameters were transferred from the alkanes and hexopyranose carbohydrates, with subsequent development and optimization of parameters unique to the molecules considered in this study. Using the model compounds acetone and acetaldehyde, nonbonded parameters for carbonyls were optimized targeting quantum mechanical interaction data for solute-water pairs and pure solvent thermodynamic data. Bond and angle parameters were adjusted by comparing optimized geometries to small molecule crystal survey data and by performing vibrational analyses on acetone, acetaldehyde and glycerol. C-C-C-C, C-C-C-O, C-C-OH and O-C-C-O torsional parameters for polyol chains were fit to quantum mechanical dihedral potential energy scans comprising over 1500 RIMP2/cc-pVTZ//MP2/6-31G(d) conformations using an automated Monte Carlo simulated annealing procedure. Comparison of computed condensed-phase data, including crystal lattice parameters and densities, NMR proton-proton couplings, densities and diffusion coefficients of aqueous solutions, to experimental data validated the optimized parameters. Parameter development for these compounds proved particularly challenging because of the flexibility of the acyclic sugars and polyalcohols as well as the intramolecular hydrogen bonding between vicinal hydroxyls for all of the compounds. The newly optimized additive CHARMM force field parameters are anticipated to be of utility for atomic level of detail simulations of acyclic polyalcohols, acyclic carbohydrates and inositol in solution. PMID:20160980

  1. Turkey's next big science project: DAG the 4 meter telescope

    NASA Astrophysics Data System (ADS)

    Keskin, O.; Yesilyaprak, C.; Yerli, S. K.; Zago, L.; Jolissaint, L.

    2014-07-01

    The DAG (Turkish for Eastern Anatolia Observatory) 4-m telescope project has been formally launched in 2012, being fully funded by the Government of Turkey. This new observatory is to be located on a 3170 m altitude ridge near the town of Erzurum in Eastern Anatolia. First light is scheduled for late 2017. The DAG team's baseline design of the telescope consists of a Ritchey-Chretien type with alt-az mount, a focal length of 56 m and a field of view up to 30 arcmin. Multiple instruments will be located at the Nasmyth foci. The optical specifications of the telescope are set by DAG team for diffraction limited performance with active and adaptive optics. Modern mirror control technologies will allow defining in a most cost effective way the figuring requirements of the optical surfaces: the low order figuring errors of the combined optical train constituted of M1-M2-M3 are defined in terms of Zernike coefficients and referred to the M1 surface area. The high order figuring errors are defined using the phase structure functions. Daytime chilling of the closed enclosure volume and natural ventilation through suitable openings during observations will be used to ensure optimal mirror and dome seeing. A design of a ground layer adaptive optics (GLAO) subsystem is developed concurrently with the telescope. In this paper, main design aspects, the optical design and expected performance analysis of the telescope will be presented.

  2. Impossible Graphs.

    ERIC Educational Resources Information Center

    Noble, Tracy; And Others

    Graphs without a time axis, such as velocity-versus-position graphs, offer interesting possibilities for exploring graphing and motion. Relations depicted by these graphs are not limited to functions. Interviews with a high school student named Olivia, who uses a motion detector to create such graphs, indicate that she uses thought experiments as…

  3. Acyclic Lipids in Amazon Shelf Waters

    NASA Astrophysics Data System (ADS)

    Elias, V. O.; Cardoso, J. N.; Simoneit, B. R. T.

    2000-02-01

    Acyclic lipids were analysed for dissolved (<1·2 μm) and particulate (>1·2 μm) material from surface water of the Amazon continental shelf to correlate the direct inputs with diagenetic processes of the organic matter and to assess the differences in compound distribution patterns of the samples. The dissolved samples contained n -alkanes with an unusual even-to-odd carbon number predominance acyclic lipids indicates an origin from micro-organisms, probably diatoms. Although minor, a contribution of components derived from plant waxes are more abundant in the particulate phase with profiles indicating a remineralized residue. Plant waxes are effectively biodegraded in the shelf waters during downstream transport in the Amazon River. Furthermore, the Pr/Ph ratios calculated for the dissolved samples indicate that the organic matter in the surface of the highly turbid waters passed through an anaerobic stage. The differences in the acyclic hydrocarbon profiles of the dissolved and particulate phases show that organic inputs are preserved differently in smaller and larger particles.

  4. Graphing Predictions

    ERIC Educational Resources Information Center

    Connery, Keely Flynn

    2007-01-01

    Graphing predictions is especially important in classes where relationships between variables need to be explored and derived. In this article, the author describes how his students sketch the graphs of their predictions before they begin their investigations on two laboratory activities: Distance Versus Time Cart Race Lab and Resistance; and…

  5. User-friendly graph editing for procedural modeling of buildings.

    PubMed

    Patow, Gustavo

    2012-01-01

    A proposed rule-based editing metaphor intuitively lets artists create buildings without changing their workflow. It's based on the realization that the rule base represents a directed acyclic graph and on a shift in the development paradigm from product-based to rule-based representations. Users can visually add or edit rules, connect them to control the workflow, and easily create commands that expand the artist's toolbox (for example, Boolean operations or local controlling operators). This approach opens new possibilities, from model verification to model editing through graph rewriting. PMID:24804948

  6. On the acyclicity of the solution sets of operator equations

    SciTech Connect

    Gel'man, Boris D

    2010-12-07

    A parameter-dependent completely continuous map is considered. The acyclicity of the set of fixed points of this map is proved for some fixed value of the parameter under the assumption that for close values of the parameter the map has a unique fixed point. The results obtained are used to prove the acyclicity of the set of fixed points of a 'nonscattering' map, as well as to study the topological structure of the set of fixed points of an abstract Volterra map. Bibliography: 13 titles.

  7. Labeling RDF Graphs for Linear Time and Space Querying

    NASA Astrophysics Data System (ADS)

    Furche, Tim; Weinzierl, Antonius; Bry, François

    Indices and data structures for web querying have mostly considered tree shaped data, reflecting the view of XML documents as tree-shaped. However, for RDF (and when querying ID/IDREF constraints in XML) data is indisputably graph-shaped. In this chapter, we first study existing indexing and labeling schemes for RDF and other graph datawith focus on support for efficient adjacency and reachability queries. For XML, labeling schemes are an important part of the widespread adoption of XML, in particular for mapping XML to existing (relational) database technology. However, the existing indexing and labeling schemes for RDF (and graph data in general) sacrifice one of the most attractive properties of XML labeling schemes, the constant time (and per-node space) test for adjacency (child) and reachability (descendant). In the second part, we introduce the first labeling scheme for RDF data that retains this property and thus achieves linear time and space processing of acyclic RDF queries on a significantly larger class of graphs than previous approaches (which are mostly limited to tree-shaped data). Finally, we show how this labeling scheme can be applied to (acyclic) SPARQL queries to obtain an evaluation algorithm with time and space complexity linear in the number of resources in the queried RDF graph.

  8. Graph Theory

    SciTech Connect

    Sanfilippo, Antonio P.

    2005-12-27

    Graph theory is a branch of discrete combinatorial mathematics that studies the properties of graphs. The theory was pioneered by the Swiss mathematician Leonhard Euler in the 18th century, commenced its formal development during the second half of the 19th century, and has witnessed substantial growth during the last seventy years, with applications in areas as diverse as engineering, computer science, physics, sociology, chemistry and biology. Graph theory has also had a strong impact in computational linguistics by providing the foundations for the theory of features structures that has emerged as one of the most widely used frameworks for the representation of grammar formalisms.

  9. New acyclic diterpenic acids from yacon (Smallanthus sonchifolius) leaves.

    PubMed

    Mercado, María I; Coll Aráoz, María V; Grau, Alfredo; Catalán, César A N

    2010-11-01

    Two new acyclic diterpenoids, smaditerpenic acid E (1a) and F (2a), along with nineteen melampolide-type sesquiterpene lactones, six of them not previously reported in yacon, were isolated from the methylene chloride leaf rinse extract. Their structures were elucidated from 1D and 2D NMR experiments and gas chromatography coupled to mass spectrometry. PMID:21213966

  10. DAG-TM Concept Element 11 CNS Performance Assessment: ADS-B Performance in the TRACON

    NASA Technical Reports Server (NTRS)

    Raghavan, Rajesh S.

    2004-01-01

    Distributed Air/Ground (DAG) Traffic Management (TM) is an integrated operational concept in which flight deck crews, air traffic service providers and aeronautical operational control personnel use distributed decision-making to enable user preferences and increase system capacity, while meeting air traffic management (ATM) safety requirements. It is a possible operational mode under the Free Flight concept outlined by the RTCA Task Force 3. The goal of DAG-TM is to enhance user flexibility/efficiency and increase system capacity, without adversely affecting system safety or restricting user accessibility to the National Airspace System (NAS). DAG-TM will be accomplished with a human-centered operational paradigm enabled by procedural and technological innovations. These innovations include automation aids, information sharing and Communication, Navigation, and Surveillance (CNS) / ATM technologies. The DAG-TM concept is intended to eliminate static restrictions to the maximum extent possible. In this paradigm, users may plan and operate according to their preferences - as the rule rather than the exception - with deviations occurring only as necessary. The DAG-TM concept elements aim to mitigate the extent and impact of dynamic NAS constraints, while maximizing the flexibility of airspace operations

  11. Human CalDAG-GEFI gene (RASGRP2) mutation affects platelet function and causes severe bleeding

    PubMed Central

    Canault, Matthias; Ghalloussi, Dorsaf; Grosdidier, Charlotte; Guinier, Marie; Perret, Claire; Chelghoum, Nadjim; Germain, Marine; Raslova, Hana; Peiretti, Franck; Morange, Pierre E.; Saut, Noemie; Pillois, Xavier; Nurden, Alan T.; Cambien, François; Pierres, Anne; van den Berg, Timo K.; Kuijpers, Taco W.; Tregouet, David-Alexandre

    2014-01-01

    The nature of an inherited platelet disorder was investigated in three siblings affected by severe bleeding. Using whole-exome sequencing, we identified the culprit mutation (cG742T) in the RAS guanyl-releasing protein-2 (RASGRP2) gene coding for calcium- and DAG-regulated guanine exchange factor-1 (CalDAG-GEFI). Platelets from individuals carrying the mutation present a reduced ability to activate Rap1 and to perform proper αIIbβ3 integrin inside-out signaling. Expression of CalDAG-GEFI mutant in HEK293T cells abolished Rap1 activation upon stimulation. Nevertheless, the PKC- and ADP-dependent pathways allow residual platelet activation in the absence of functional CalDAG-GEFI. The mutation impairs the platelet’s ability to form thrombi under flow and spread normally as a consequence of reduced Rac1 GTP-binding. Functional deficiencies were confined to platelets and megakaryocytes with no leukocyte alteration. This contrasts with the phenotype seen in type III leukocyte adhesion deficiency caused by the absence of kindlin-3. Heterozygous did not suffer from bleeding and have normal platelet aggregation; however, their platelets mimicked homozygous ones by failing to undergo normal adhesion under flow and spreading. Rescue experiments on cultured patient megakaryocytes corrected the functional deficiency after transfection with wild-type RASGRP2. Remarkably, the presence of a single normal allele is sufficient to prevent bleeding, making CalDAG-GEFI a novel and potentially safe therapeutic target to prevent thrombosis. PMID:24958846

  12. Graphing Reality

    NASA Astrophysics Data System (ADS)

    Beeken, Paul

    2014-11-01

    Graphing is an essential skill that forms the foundation of any physical science.1 Understanding the relationships between measurements ultimately determines which modeling equations are successful in predicting observations.2 Over the years, science and math teachers have approached teaching this skill with a variety of techniques. For secondary school instruction, the job of graphing skills falls heavily on physics teachers. By virtue of the nature of the topics we cover, it is our mission to develop this skill to the fine art that it is.

  13. Graphing Reality

    ERIC Educational Resources Information Center

    Beeken, Paul

    2014-01-01

    Graphing is an essential skill that forms the foundation of any physical science. Understanding the relationships between measurements ultimately determines which modeling equations are successful in predicting observations. Over the years, science and math teachers have approached teaching this skill with a variety of techniques. For secondary…

  14. Medicinal chemistry of fluorinated cyclic and acyclic nucleoside phosphonates.

    PubMed

    Baszczyňski, Ondřej; Janeba, Zlatko

    2013-11-01

    The fluorine atom plays an important role in medicinal chemistry because fluorine substitution has a strong impact on the physical, chemical, and biological properties of bioactive compounds. Such fluorine modifications have also been extensively studied among the pharmaceutically important class of nucleoside phosphonates, nucleotide analogues in which the phosphate group is replaced by the enzymatically and chemically stable phosphonate moiety. The fluorinated nucleoside phosphonates abound with antiviral, antiparasitic, and anticancer properties because they are able to act as inhibitors of important enzymes of nucleoside/nucleotide metabolism. In this paper, we review the biological properties of cyclic and acyclic nucleoside phosphonates modified by the attachment of one or more fluorine atoms to various parts of the molecule, namely to nucleobases, alkylphosphonate groups, cyclic or acyclic linkers, or to prodrug moieties. PMID:23893552

  15. Quantification of TAG and DAG in lesquerella (Physaria fendleri) oil by HPLC and MS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Castor oil has many industrial uses because of its high content (90%) of the hydroxy fatty acid, ricinoleic acid (OH1218:19). Lesquerella oil containing lesquerolic acid (Ls, OH1420:111, 56.5%) is potentially useful in industry. Ten diacylglycerols (DAG) and 74 triacylglycerols (TAG) in the seed oil...

  16. Tyrosinase kinetics in epidermal melanocytes: analysis of DAG-PKC-dependent signaling pathway

    NASA Astrophysics Data System (ADS)

    Stolnitz, Mikhail M.; Peshkova, Anna Y.

    2001-05-01

    Tyrosinase is the key enzyme of melanogenesis with unusual enzyme kinetics. Protein kinase C plays an important role in regulating of tyrosinase activity. In the paper the mathematical model of PKC-DAG-dependent signal transduction pathway for UV-radiation is presented.

  17. Design and synthesis of protein kinase C epsilon selective diacylglycerol lactones (DAG-lactones).

    PubMed

    Ann, Jihyae; Yoon, Suyoung; Baek, Jisoo; Kim, Da Hye; Lewin, Nancy E; Hill, Colin S; Blumberg, Peter M; Lee, Jeewoo

    2015-01-27

    DAG-lactones afford a synthetically accessible, high affinity platform for probing structure activity relationships at the C1 regulatory domain of protein kinase C (PKC). Given the central role of PKC isoforms in cellular signaling, along with their differential biological activities, a critical objective is the design of isoform selective ligands. Here, we report the synthesis of a series of DAG-lactones varying in their side chains, with a particular focus on linoleic acid derivatives. We evaluated their selectivity for PKC epsilon versus PKC alpha both under standard lipid conditions (100% phosphatidylserine, PS) as well as in the presence of a nuclear membrane mimetic lipid mixture (NML). We find that selectivity for PKC epsilon versus PKC alpha tended to be enhanced in the presence of the nuclear membrane mimetic lipid mixture and, for our lead compound, report a selectivity of 32-fold. PMID:25437619

  18. Acyclic nucleoside/nucleotide analogues with an imidazole ring skeleton.

    PubMed

    Chen, H M; Hosmane, R S

    2001-08-01

    Syntheses of a few acyclic nucleoside and acyclic nucleoside phosphonate analogues containing an imidazole ring have been reported. These analogues include methyl 1-(2-hydroxyethoxymethyl)imidazole-4, 5-dicarbo-xylate (1), 4,5-dicarbamoyl-1-(2-hydroxyethoxymethyl)imidazole (2), 4,5-dicyano-1-(2-hydroxyethoxymethyl)imidazole (4), Methyl 1-(2-bromoethoxymethyl)imidazole-4,5-dicarboxylate (7), 4,5-dicyano-(2-bromoethoxymethyl)imidazole (8), and Methyl 1-(2-phosphonomethoxyethyl)imidazole (10). Also reported are a few potential prodrugs of the above compounds, including the acetyl derivatives 5 and 6 (of 1 and 4, respectively), and the diethyl phosphonate ester 9 (of 10). In addition, the corresponding benzyl-protected precursors 11 and 12 (of 1 and 4, respectively), along with their common hydrolysis product, 1-(2-benzyloxy-ethoxymethyl)-4,5-imidazoledicarboxylic acid (3), are reported. Another potential prodrug included in the list is 1-(2-acetoxyethyl)-4,5-dicyanoimidazole (15). The compounds were screened for in vitro antiviral activity against a wide variety of herpes and respiratory viruses. The most active compound was the phosphonate analogue 9 which exhibited an anti-measles virus activity with an EC50 of <2.5 microg/mL and an SI value of > 176. PMID:11554548

  19. Des-acyl-ghrelin (DAG) normalizes hyperlactacidemia and improves survival in a lethal rat model of burn trauma.

    PubMed

    Sheriff, Sulaiman; Kadeer, Nijiati; Friend, Lou Ann; James, J Howard; Alexander, J Wesley; Balasubramaniam, Ambikaipakan

    2014-10-01

    Critical illness, including burn injury, results in elevated plasma lactate levels. Dysregulation of PI3K/Akt signaling has been shown to play a predominant role in the inactivation of skeletal muscle PDC and, hence, in hyperlactacidemia in rat models of sepsis and endotoxemia. This observation, and our previous finding that DAG can reverse burn-induced skeletal muscle proteolysis through the activation of PI3K/Akt pathway, led us to hypothesize that DAG may also attenuate hyperlactacidemia in burn injury. Our investigations revealed that burn injury significantly elevated both skeletal muscle lactate production and plasma lactate levels. Moreover, this was accompanied in skeletal muscle by a 5-7 fold increase in mRNA expression of pyruvate dehydrogenase kinases (PDK) 2 and 4, and a ∼30% reduction in PDC activity. DAG treatment of burn rats completely normalized not only the mRNA expression of the PDKs and PDC activity, but also hyperlactacidemia within 24h of burn injury. DAG also normalized epinephrine-induced lactate production by isolated skeletal muscles from normal rats. Moreover, DAG also improved survival in a lethal rat model of burn trauma. These findings with DAG may have clinical implications because chances of survival for critically ill patients are greatly improved if plasma lactate levels are normalized within 24h of injury. PMID:25063053

  20. Nemrud Dag

    NASA Astrophysics Data System (ADS)

    Belmonte, Juan Antonio; González-García, A. César

    The World Heritage Site of the hierothesion of Antiochos I, King of Commagene, at Mount Nemrud (Turkey) certainly constitutes one of the most fascinating historical enigmas in human culture. The monument includes the famous lion "horoscope" which has often been used in various attempts to interpret and date the ruins with controversial results. According to recent analyses, Antiochos' monument reflects the situation of the skies at exclusive moments of the year 49 BC, when the monument would have been started. This alternative explanation considers the lion slab together with the orientation of the eastern and western terraces of the hierothesion and the inscriptions on the monument.

  1. Graphing Polar Curves

    ERIC Educational Resources Information Center

    Lawes, Jonathan F.

    2013-01-01

    Graphing polar curves typically involves a combination of three traditional techniques, all of which can be time-consuming and tedious. However, an alternative method--graphing the polar function on a rectangular plane--simplifies graphing, increases student understanding of the polar coordinate system, and reinforces graphing techniques learned…

  2. Path Separability of Graphs

    NASA Astrophysics Data System (ADS)

    Diot, Emilie; Gavoille, Cyril

    In this paper we investigate the structural properties of k-path separable graphs, that are the graphs that can be separated by a set of k shortest paths. We identify several graph families having such path separability, and we show that this property is closed under minor taking. In particular we establish a list of forbidden minors for 1-path separable graphs.

  3. Graphing for Any Grade.

    ERIC Educational Resources Information Center

    Nibbelink, William

    1982-01-01

    An instructional sequence for teaching graphing that has been extensively field tested in kindergarten through grade six is detailed. The material begins with point graphs, employs a movable y-axis to begin with minimal clutter, and has graphs constructed before reading graphs is required. (MP)

  4. Iridium-Catalyzed Diastereoselective and Enantioselective Allylic Substitutions with Acyclic α-Alkoxy Ketones.

    PubMed

    Jiang, Xingyu; Chen, Wenyong; Hartwig, John F

    2016-05-01

    The asymmetric alkylation of acyclic ketones is a longstanding challenge in organic synthesis. Reported herein are diastereoselective and enantioselective allylic substitutions with acyclic α-alkoxy ketones catalyzed by a metallacyclic iridium complex to form products with contiguous stereogenic centers derived from the nucleophile and electrophile. These reactions occur between allyl methyl carbonates and unstabilized copper(I) enolates generated in situ from acyclic α-alkoxy ketones. The resulting products can be readily converted into enantioenriched tertiary alcohols and tetrahydrofuran derivatives without erosion of enantiomeric purity. PMID:27038004

  5. Forming Stereogenic Centers in Acyclic Systems from Alkynes.

    PubMed

    Vabre, Roxane; Island, Biana; Diehl, Claudia J; Schreiner, Peter R; Marek, Ilan

    2015-08-17

    The combined carbometalation/zinc homologation followed by reactions with α-heterosubstituted aldehydes and imines proceed through a chair-like transition structure with the substituent of the incoming aldehyde residue preferentially occupying a pseudo-axial position to avoid the two gauche interactions. The heteroatom in the axial position produces a chelated intermediate (and not a Cornforth-Evans transition structure for α-chloro aldehydes and imines) leading to a face differentiation in the allylation reaction. This method provides access to functionalized products in which three new carbon-carbon bonds and two to three stereogenic centers, including a quaternary one, were created in acyclic systems in a single-pot operation from simple alkynes. PMID:26130570

  6. Tautomerism and stereodynamics of acyclic. beta. -diketo esters

    SciTech Connect

    Romas, A.D.; Esakov, S.M.; Petrov, Al.An.; Ershov, B.A.

    1986-04-10

    The tautomeric transformations and stereodynamics of a series of ring-substituted acyclic ..beta..-diketo esters p-XC/sub 6/H/sub 4/COCH(CH/sub 3/CO)CO/sub 2/CH/sub 3/ in hexachlorobutadiene and nitrobenzene were investigated by proton and carbon magnetic resonance spectroscopy. The enolization of the compounds is accompanied by the formation of two cis-enol forms (of the three theoretically possible forms) with nonchelated benzene of methoxycarbonyl groups respectively. The form with the nonchelated methoxycarbonyl group predominates in the equilibrium on account of the smaller loss of entropy during its formation compared with the enol containing the nonchelated benzoyl group. The kinetic characteristics of the mutual transformations of the enolic forms in hexachlorobutadiene and nitrobenzene respectively were determined by integration and dynamic nuclear magnetic resonance.

  7. Biochemical Properties and Structure Analysis of a DAG-Like Lipase from Malassezia globosa

    PubMed Central

    Xu, Huan; Lan, Dongming; Yang, Bo; Wang, Yonghua

    2015-01-01

    Diacylglycerol (DAG)-like lipases are found to play an important role in the life sciences and industrial fields. A putative DAG-like lipase (MgMDL2) from Malassezia globosa was cloned and expressed in recombinant Pichia pastoris. The recombinant MgMDL2 was expressed as a glycosylated protein and purified into homogeneity by anion exchange chromatography. The activity of recombinant MgMDL2 was optimal at 15 °C and pH 6.0, and it keeps over 50% of relative activity at 5 °C, suggesting that MgMDL2 was a cold active lipase. MgMDL2 retained over 80% of initial activity after incubation at 30 and 40 °C for 2.5 h, but it was not stable at 50 °C. Incubation of methanol and ethanol at a concentration of 30% for 2 h did not affect the recombinant enzyme activity, while metal ions, including Ca2+, Mn2+ and Ni2+, sharply inhibited the MgMDL2 activity at 5 mM by 42%, 35% and 36%, respectively. MgMDL2 exhibited a preference for medium chain-length esters with highest activity toward p-nitrophenyl caprylate, while it was active on mono- and diacylglycerol but not on triacylglycerol, indicating that it was a typical DAG-like lipase. By homology modeling, Phe278 was predicted to be involved in the preference of MgMDL2 for monoacyl- and diacyl-glyceride substrates, but not triglycerides. PMID:25749469

  8. Diagnostic Analyzer for Gearboxes (DAG): User's Guide. Version 3.1 for Microsoft Windows 3.1

    NASA Technical Reports Server (NTRS)

    Jammu, Vinay B.; Kourosh, Danai

    1997-01-01

    This documentation describes the Diagnostic Analyzer for Gearboxes (DAG) software for performing fault diagnosis of gearboxes. First, the user would construct a graphical representation of the gearbox using the gear, bearing, shaft, and sensor tools contained in the DAG software. Next, a set of vibration features obtained by processing the vibration signals recorded from the gearbox using a signal analyzer is required. Given this information, the DAG software uses an unsupervised neural network referred to as the Fault Detection Network (FDN) to identify the occurrence of faults, and a pattern classifier called Single Category-Based Classifier (SCBC) for abnormality scaling of individual vibration features. The abnormality-scaled vibration features are then used as inputs to a Structure-Based Connectionist Network (SBCN) for identifying faults in gearbox subsystems and components. The weights of the SBCN represent its diagnostic knowledge and are derived from the structure of the gearbox graphically presented in DAG. The outputs of SBCN are fault possibility values between 0 and 1 for individual subsystems and components in the gearbox with a 1 representing a definite fault and a 0 representing normality. This manual describes the steps involved in creating the diagnostic gearbox model, along with the options and analysis tools of the DAG software.

  9. A novel DAG-dependent mechanism links PKCa and Cyclin B1 regulating cell cycle progression

    PubMed Central

    Poli, Alessandro; Ramazzotti, Giulia; Matteucci, Alessandro; Manzoli, Lucia; Lonetti, Annalisa; Suh, Pann-Ghill; McCubrey, James A.; Cocco, Lucio

    2014-01-01

    Through the years, different studies showed the involvement of Protein Kinase C (PKC) in cell cycle control, in particular during G1/S transition. Little is known about their role at G2/M checkpoint. In this study, using K562 human erythroleukemia cell line, we found a novel and specific mechanism through which the conventional isoform PKC⍺ positively affects Cyclin B1 modulating G2/M progression of cell cycle. Since the kinase activity of this PKC isoform was not necessary in this process, we demonstrated that PKC⍺, physically interacting with Cyclin B1, avoided its degradation and stimulated its nuclear import at mitosis. Moreover, the process resulted to be strictly connected with the increase in nuclear diacylglycerol levels (DAG) at G2/M checkpoint, due to the activity of nuclear Phospholipase C β1 (PLCβ1), the only PLC isoform mainly localized in the nucleus of K562 cells. Taken together, our findings indicated a novel DAG dependent mechanism able to regulate the G2/M progression of the cell cycle. PMID:25362646

  10. Fast synthesis of 1,3-DAG by Lecitase® Ultra-catalyzed esterification in solvent-free system.

    PubMed

    Liu, Ning; Wang, Yong; Zhao, Qiangzhong; Zhang, Qingli; Zhao, Mouming

    2011-08-01

    Lecitase® Ultra, a phospholipase, was explored as an effective biocatalyst for direct esterification of glycerol with oleic acid to produce 1,3-DAG. Experiments were carried out in batch mode, and optimal reaction conditions were evaluated. In comparison with several organic solvent mediums, the solvent-free system was found to be more beneficial for this esterification reaction, which was further studied to investigate the reaction conditions including oleic acid/glycerol mole ratio, temperature, initial water content, enzyme load, and operating time. The results showed that Lecitase® Ultra catalyzed a fast synthesis of 1,3-DAG by direct esterification in a solvent-free medium. Under the optimal reaction conditions, a short reaction time 1.5 h was found to achieve the fatty acid esterification efficiency of 80.3 ± 1.2% and 1,3-DAG content of 54.8 ± 1.6 wt% (lipid layer of reaction mixture mass). The reusability of Lecitase® Ultra was evaluated via recycling the excess glycerol layer in the reaction system. DAG in the upper lipid layer of reaction mixture was purified by molecular distillation and the 1,3-DAG-enriched oil with a purity of about 75 wt% was obtained.Practical applications: The new Lecitase® Ultra catalyzed process for production of 1,3-DAG from glycerol and oleic acid described in this study provides several advantages over conventional methods including short reaction time, the absence of a solvents and a high product yield. PMID:21966255

  11. Fast synthesis of 1,3-DAG by Lecitase® Ultra-catalyzed esterification in solvent-free system

    PubMed Central

    Liu, Ning; Wang, Yong; Zhao, Qiangzhong; Zhang, Qingli; Zhao, Mouming

    2011-01-01

    Lecitase® Ultra, a phospholipase, was explored as an effective biocatalyst for direct esterification of glycerol with oleic acid to produce 1,3-DAG. Experiments were carried out in batch mode, and optimal reaction conditions were evaluated. In comparison with several organic solvent mediums, the solvent-free system was found to be more beneficial for this esterification reaction, which was further studied to investigate the reaction conditions including oleic acid/glycerol mole ratio, temperature, initial water content, enzyme load, and operating time. The results showed that Lecitase® Ultra catalyzed a fast synthesis of 1,3-DAG by direct esterification in a solvent-free medium. Under the optimal reaction conditions, a short reaction time 1.5 h was found to achieve the fatty acid esterification efficiency of 80.3 ± 1.2% and 1,3-DAG content of 54.8 ± 1.6 wt% (lipid layer of reaction mixture mass). The reusability of Lecitase® Ultra was evaluated via recycling the excess glycerol layer in the reaction system. DAG in the upper lipid layer of reaction mixture was purified by molecular distillation and the 1,3-DAG-enriched oil with a purity of about 75 wt% was obtained. Practical applications: The new Lecitase® Ultra catalyzed process for production of 1,3-DAG from glycerol and oleic acid described in this study provides several advantages over conventional methods including short reaction time, the absence of a solvents and a high product yield. PMID:21966255

  12. Are Graphs Finally Surfacing?

    ERIC Educational Resources Information Center

    Beineke, Lowell W.

    1989-01-01

    Explored are various aspects of drawing graphs on surfaces. The Euler's formula, Kuratowski's theorem and the drawing of graphs in the plane with as few crossings as possible are discussed. Some applications including embedding of graphs and coloring of maps are included. (YP)

  13. Graph-Plotting Routine

    NASA Technical Reports Server (NTRS)

    Kantak, Anil V.

    1987-01-01

    Plotter routine for IBM PC (AKPLOT) designed for engineers and scientists who use graphs as integral parts of their documentation. Allows user to generate graph and edit its appearance on cathode-ray tube. Graph may undergo many interactive alterations before finally dumped from screen to be plotted by printer. Written in BASIC.

  14. Graphing Important People

    ERIC Educational Resources Information Center

    Reading Teacher, 2012

    2012-01-01

    The "Toolbox" column features content adapted from ReadWriteThink.org lesson plans and provides practical tools for classroom teachers. This issue's column features a lesson plan adapted from "Graphing Plot and Character in a Novel" by Lisa Storm Fink and "Bio-graph: Graphing Life Events" by Susan Spangler. Students retell biographic events…

  15. Graphing Inequalities, Connecting Meaning

    ERIC Educational Resources Information Center

    Switzer, J. Matt

    2014-01-01

    Students often have difficulty with graphing inequalities (see Filloy, Rojano, and Rubio 2002; Drijvers 2002), and J. Matt Switzer's students were no exception. Although students can produce graphs for simple inequalities, they often struggle when the format of the inequality is unfamiliar. Even when producing a correct graph of an…

  16. Structural Interactions within Lithium Salt Solvates. Acyclic Carbonates and Esters

    SciTech Connect

    Afroz, Taliman; Seo, D. M.; Han, Sang D.; Boyle, Paul D.; Henderson, Wesley A.

    2015-03-06

    Solvate crystal structures serve as useful models for the molecular-level interactions within the diverse solvates present in liquid electrolytes. Although acyclic carbonate solvents are widely used for Li-ion battery electrolytes, only three solvate crystal structures with lithium salts are known for these and related solvents. The present work, therefore, reports six lithium salt solvate structures with dimethyl and diethyl carbonate: (DMC)2:LiPF6, (DMC)1:LiCF3SO3, (DMC)1/4:LiBF4, (DEC)2:LiClO4, (DEC)1:LiClO4 and (DEC)1:LiCF3SO3 and four with the structurally related methyl and ethyl acetate: (MA)2:LiClO4, (MA)1:LiBF4, (EA)1:LiClO4 and (EA)1:LiBF4.

  17. On the Feasibility of Dynamically Scheduling DAG Applications on Shared Heterogeneous Systems

    NASA Astrophysics Data System (ADS)

    Nascimento, Aline P.; Sena, Alexandre; Boeres, Cristina; Rebello, Vinod E. F.

    Grid and Internet Computing have proved their worth executing large-scale bag-of-task class applications. Numerous middlewares have been developed to manage their execution in either dedicated environments or opportunistic and shared ad-hoc grids. While job dependencies are now being resolved by middleware capable of scheduling workflows, these environments have yet to be shown beneficial for message passing parallel applications. Obtaining high performance in these widely available environments without rewriting existing parallel applications is of up most importance to e-Science. The key to an efficient solution may be an alternative execution model and the efficient dynamic scheduling of application processes. This paper presents a hierarchical scheme for dynamically scheduling parallel DAG applications across a set of non-dedicated heterogeneous resources. In order to efficiently tackle process dependencies and adapt to varying system characteristics, dynamic schedulers are distributed within the application and operate in a collaborative and pro-active fashion to keep overheads low.

  18. Study of the recent geodynamic processes in the Kopet-Dag region

    NASA Astrophysics Data System (ADS)

    Izyumov, S. F.; Kuzmin, Yu. O.

    2014-11-01

    The time series of the uniquely long geodetic observations of recent geodynamic processes in the Kopet-Dag region are analyzed. The regional observations of contemporary vertical movements cover a 75-year period; the zonal and local systems of leveling measurements, which provide an increased degree of spatiotemporal detail (the distance between the benchmarks is less than 1 km and the measurements are repeated with a frequency of once per month to two times per annum), have been functioning for 50 years. It is shown that during the last 40-50 years, the regional stress field in the forefront of the Main Kopet-Dag thrust and collision zone of the Turanian and Iranian plates is quasi static. The annual average trend rate of strains estimated from a set of the time series of uniquely long geodetic observations is (3-5) × 10-8 yr-1, which is only one to two amplitudes of tidal deformations of the solid Earth. The local deformations in the fault zone reach the rates that are by 1.5-2 orders of magnitude higher than in the block part of the region. It is found that the segments of the Earth's surface within the axial part of the depression experience persistent uplifting, which indicates that they do not follow the scheme of inherited evolution characteristic of the fault-block structures of the region. It is demonstrated that these anomalous uplifts can be caused by the variations in the weak seismicity in the zone of the North Ashgabat Fault.

  19. Methods of visualizing graphs

    DOEpatents

    Wong, Pak C.; Mackey, Patrick S.; Perrine, Kenneth A.; Foote, Harlan P.; Thomas, James J.

    2008-12-23

    Methods for visualizing a graph by automatically drawing elements of the graph as labels are disclosed. In one embodiment, the method comprises receiving node information and edge information from an input device and/or communication interface, constructing a graph layout based at least in part on that information, wherein the edges are automatically drawn as labels, and displaying the graph on a display device according to the graph layout. In some embodiments, the nodes are automatically drawn as labels instead of, or in addition to, the label-edges.

  20. Hyperbolic graph generator

    NASA Astrophysics Data System (ADS)

    Aldecoa, Rodrigo; Orsini, Chiara; Krioukov, Dmitri

    2015-11-01

    Networks representing many complex systems in nature and society share some common structural properties like heterogeneous degree distributions and strong clustering. Recent research on network geometry has shown that those real networks can be adequately modeled as random geometric graphs in hyperbolic spaces. In this paper, we present a computer program to generate such graphs. Besides real-world-like networks, the program can generate random graphs from other well-known graph ensembles, such as the soft configuration model, random geometric graphs on a circle, or Erdős-Rényi random graphs. The simulations show a good match between the expected values of different network structural properties and the corresponding empirical values measured in generated graphs, confirming the accurate behavior of the program.

  1. Fostered to Internationalism and Peace: Biographical Notes on UN General Secretary Dag Hammarskjold. Peace Education Miniprints No. 97.

    ERIC Educational Resources Information Center

    Thelin, Bengt

    This paper presents some biographical glimpses of Dag Hammarskjold's childhood and youth. It is a period of the life of the late United Nations (UN) Secretary General (1905-1961) that has been dealt with very little by his biographers. Hammarskjold's private archives at the Royal Library in Stockholm are now available for research. These sources…

  2. Enzymatic selective synthesis of 1,3-DAG based on deep eutectic solvent acting as substrate and solvent.

    PubMed

    Zeng, Chao-Xi; Qi, Sui-Jian; Xin, Rui-Pu; Yang, Bo; Wang, Yong-Hua

    2015-11-01

    In this study, enzymatic selective esterification of oleic acid with glycerol based on deep eutectic solvent acting as substrate and solvent was studied. As choline chloride (ChCl) or betaine can effectively change the chemical reaction characteristics of glycerol when they are mixed with a certain molar ratio of glycerol, several factors crucial to the lipase catalytic esterification of glycerol with oleic acid was investigated. Results showed that, betaine had more moderate effects than ChCl on the lipase, and water content had an important influence of the esterification and the enzyme selectivity. Significant changes of the glyceride compositions and enzyme selectivity were found in ChCl adding system compared with pure glycerol system; optimum accumulation of DAG especially 1,3-DAG because of the eutectic effect of ChCl was found in this system. Furthermore, in a model 1,3-DAG esterification synthesis system catalyzed by Novozym 435, high content (42.9 mol%) of the 1,3-DAG could be obtained in ChCl adding system within 1 h. PMID:26210852

  3. Novel mutations in RASGRP2, which encodes CalDAG-GEFI, abrogate Rap1 activation, causing platelet dysfunction.

    PubMed

    Lozano, María Luisa; Cook, Aaron; Bastida, José María; Paul, David S; Iruin, Gemma; Cid, Ana Rosa; Adan-Pedroso, Rosa; Ramón González-Porras, José; Hernández-Rivas, Jesús María; Fletcher, Sarah J; Johnson, Ben; Morgan, Neil; Ferrer-Marin, Francisca; Vicente, Vicente; Sondek, John; Watson, Steve P; Bergmeier, Wolfgang; Rivera, José

    2016-09-01

    In addition to mutations in ITG2B or ITGB3 genes that cause defective αIIbβ3 expression and/or function in Glanzmann's thrombasthenia patients, platelet dysfunction can be a result of genetic variability in proteins that mediate inside-out activation of αIIbβ3 The RASGRP2 gene is strongly expressed in platelets and neutrophils, where its encoded protein CalDAG-GEFI facilitates the activation of Rap1 and subsequent activation of integrins. We used next-generation sequencing (NGS) and whole-exome sequencing (WES) to identify 2 novel function-disrupting mutations in RASGRP2 that account for bleeding diathesis and platelet dysfunction in 2 unrelated families. By using a panel of 71 genes, we identified a homozygous change (c.1142C>T) in exon 10 of RASGRP2 in a 9-year-old child of Chinese origin (family 1). This variant led to a p.Ser381Phe substitution in the CDC25 catalytic domain of CalDAG-GEFI. In 2 Spanish siblings from family 2, WES identified a nonsense homozygous variation (c.337C>T) (p.Arg113X) in exon 5 of RASGRP2 CalDAG-GEFI expression was markedly reduced in platelets from all patients, and by using a novel in vitro assay, we found that the nucleotide exchange activity was dramatically reduced in CalDAG-GEFI p.Ser381Phe. Platelets from homozygous patients exhibited agonist-specific defects in αIIbβ3 integrin activation and aggregation. In contrast, α- and δ-granule secretion, platelet spreading, and clot retraction were not markedly affected. Integrin activation in the patients' neutrophils was also impaired. These patients are the first cases of a CalDAG-GEFI deficiency due to homozygous RASGRP2 mutations that are linked to defects in both leukocyte and platelet integrin activation. PMID:27235135

  4. Acyclic cucurbit[n]uril molecular containers enhance the solubility and bioactivity of poorly soluble pharmaceuticals

    NASA Astrophysics Data System (ADS)

    Ma, Da; Hettiarachchi, Gaya; Nguyen, Duc; Zhang, Ben; Wittenberg, James B.; Zavalij, Peter Y.; Briken, Volker; Isaacs, Lyle

    2012-06-01

    The solubility characteristics of 40-70% of new drug candidates are so poor that they cannot be formulated on their own, so new methods for increasing drug solubility are highly prized. Here, we describe a new class of general-purpose solubilizing agents—acyclic cucurbituril-type containers—which increase the solubility of ten insoluble drugs by a factor of between 23 and 2,750 by forming container-drug complexes. The containers exhibit low in vitro toxicity in human liver, kidney and monocyte cell lines, and outbred Swiss Webster mice tolerate high doses of the container without sickness or weight loss. Paclitaxel solubilized by the acyclic cucurbituril-type containers kills cervical and ovarian cancer cells more efficiently than paclitaxel alone. The acyclic cucurbituril-type containers preferentially bind cationic and aromatic drugs, but also solubilize neutral drugs such as paclitaxel, and represent an attractive extension of cyclodextrin-based technology for drug solubilization and delivery.

  5. Topologies on directed graphs

    NASA Technical Reports Server (NTRS)

    Lieberman, R. N.

    1972-01-01

    Given a directed graph, a natural topology is defined and relationships between standard topological properties and graph theoretical concepts are studied. In particular, the properties of connectivity and separatedness are investigated. A metric is introduced which is shown to be related to separatedness. The topological notions of continuity and homeomorphism. A class of maps is studied which preserve both graph and topological properties. Applications involving strong maps and contractions are also presented.

  6. A new efficient algorithm generating all minimal S-T cut-sets in a graph-modeled network

    NASA Astrophysics Data System (ADS)

    Malinowski, Jacek

    2016-06-01

    A new algorithm finding all minimal s-t cut-sets in a graph-modeled network with failing links and nodes is presented. It is based on the analysis of the tree of acyclic s-t paths connecting a given pair of nodes in the considered structure. The construction of such a tree is required by many existing algorithms for s-t cut-sets generation in order to eliminate "stub" edges or subgraphs through which no acyclic path passes. The algorithm operates on the acyclic paths tree alone, i.e. no other analysis of the network's topology is necessary. It can be applied to both directed and undirected graphs, as well as partly directed ones. It is worth noting that the cut-sets can be composed of both links and failures, while many known algorithms do not take nodes into account, which is quite restricting from the practical point of view. The developed cut-sets generation technique makes the algorithm significantly faster than most of the previous methods, as proved by the experiments.

  7. Graph Generator Survey

    SciTech Connect

    Lothian, Josh; Powers, Sarah S; Sullivan, Blair D; Baker, Matthew B; Schrock, Jonathan; Poole, Stephen W

    2013-12-01

    The benchmarking effort within the Extreme Scale Systems Center at Oak Ridge National Laboratory seeks to provide High Performance Computing benchmarks and test suites of interest to the DoD sponsor. The work described in this report is a part of the effort focusing on graph generation. A previously developed benchmark, SystemBurn, allowed the emulation of dierent application behavior profiles within a single framework. To complement this effort, similar capabilities are desired for graph-centric problems. This report examines existing synthetic graph generator implementations in preparation for further study on the properties of their generated synthetic graphs.

  8. mpiGraph

    2007-05-22

    MpiGraph consists of an MPI application called mpiGraph written in C to measure message bandwidth and an associated crunch_mpiGraph script written in Perl to process the application output into an HTMO report. The mpiGraph application is designed to inspect the health and scalability of a high-performance interconnect while under heavy load. This is useful to detect hardware and software problems in a system, such as slow nodes, links, switches, or contention in switch routing. Itmore » is also useful to characterize how interconnect performance changes with different settings or how one interconnect type compares to another.« less

  9. Coloring random graphs.

    PubMed

    Mulet, R; Pagnani, A; Weigt, M; Zecchina, R

    2002-12-23

    We study the graph coloring problem over random graphs of finite average connectivity c. Given a number q of available colors, we find that graphs with low connectivity admit almost always a proper coloring, whereas graphs with high connectivity are uncolorable. Depending on q, we find the precise value of the critical average connectivity c(q). Moreover, we show that below c(q) there exists a clustering phase c in [c(d),c(q)] in which ground states spontaneously divide into an exponential number of clusters and where the proliferation of metastable states is responsible for the onset of complexity in local search algorithms. PMID:12484862

  10. mpiGraph

    SciTech Connect

    Moody, Adam

    2007-05-22

    MpiGraph consists of an MPI application called mpiGraph written in C to measure message bandwidth and an associated crunch_mpiGraph script written in Perl to process the application output into an HTMO report. The mpiGraph application is designed to inspect the health and scalability of a high-performance interconnect while under heavy load. This is useful to detect hardware and software problems in a system, such as slow nodes, links, switches, or contention in switch routing. It is also useful to characterize how interconnect performance changes with different settings or how one interconnect type compares to another.

  11. Stereodefined acyclic trisubstituted metal enolates towards the asymmetric formation of quaternary carbon stereocentres.

    PubMed

    Minko, Yury; Marek, Ilan

    2014-10-28

    Reactions that involve metal enolate species are amongst the most versatile carbon-carbon bond forming processes available to synthetic chemists. Enolate species are involved in a multitude of powerful applications in asymmetric organic synthesis, but the generation of fully substituted enolates in a geometrically defined form is not easily achieved especially in acyclic systems. In this Feature Article we focus on the most prominent examples reported in the literature describing the formation of highly diastereo- and enantiomerically enriched quaternary stereocentres in acyclic molecules derived from stereodefined non-cyclic trisubstituted metal enolates. PMID:25054432

  12. Graphs, matrices, and the GraphBLAS: Seven good reasons

    SciTech Connect

    Kepner, Jeremy; Bader, David; Buluç, Aydın; Gilbert, John; Mattson, Timothy; Meyerhenke, Henning

    2015-01-01

    The analysis of graphs has become increasingly important to a wide range of applications. Graph analysis presents a number of unique challenges in the areas of (1) software complexity, (2) data complexity, (3) security, (4) mathematical complexity, (5) theoretical analysis, (6) serial performance, and (7) parallel performance. Implementing graph algorithms using matrix-based approaches provides a number of promising solutions to these challenges. The GraphBLAS standard (istcbigdata.org/GraphBlas) is being developed to bring the potential of matrix based graph algorithms to the broadest possible audience. The GraphBLAS mathematically defines a core set of matrix-based graph operations that can be used to implement a wide class of graph algorithms in a wide range of programming environments. This paper provides an introduction to the GraphBLAS and describes how the GraphBLAS can be used to address many of the challenges associated with analysis of graphs.

  13. Graphs, matrices, and the GraphBLAS: Seven good reasons

    DOE PAGESBeta

    Kepner, Jeremy; Bader, David; Buluç, Aydın; Gilbert, John; Mattson, Timothy; Meyerhenke, Henning

    2015-01-01

    The analysis of graphs has become increasingly important to a wide range of applications. Graph analysis presents a number of unique challenges in the areas of (1) software complexity, (2) data complexity, (3) security, (4) mathematical complexity, (5) theoretical analysis, (6) serial performance, and (7) parallel performance. Implementing graph algorithms using matrix-based approaches provides a number of promising solutions to these challenges. The GraphBLAS standard (istcbigdata.org/GraphBlas) is being developed to bring the potential of matrix based graph algorithms to the broadest possible audience. The GraphBLAS mathematically defines a core set of matrix-based graph operations that can be used to implementmore » a wide class of graph algorithms in a wide range of programming environments. This paper provides an introduction to the GraphBLAS and describes how the GraphBLAS can be used to address many of the challenges associated with analysis of graphs.« less

  14. Property Graph vs RDF Triple Store: A Comparison on Glycan Substructure Search

    PubMed Central

    Alocci, Davide; Mariethoz, Julien; Horlacher, Oliver; Bolleman, Jerven T.; Campbell, Matthew P.; Lisacek, Frederique

    2015-01-01

    Resource description framework (RDF) and Property Graph databases are emerging technologies that are used for storing graph-structured data. We compare these technologies through a molecular biology use case: glycan substructure search. Glycans are branched tree-like molecules composed of building blocks linked together by chemical bonds. The molecular structure of a glycan can be encoded into a direct acyclic graph where each node represents a building block and each edge serves as a chemical linkage between two building blocks. In this context, Graph databases are possible software solutions for storing glycan structures and Graph query languages, such as SPARQL and Cypher, can be used to perform a substructure search. Glycan substructure searching is an important feature for querying structure and experimental glycan databases and retrieving biologically meaningful data. This applies for example to identifying a region of the glycan recognised by a glycan binding protein (GBP). In this study, 19,404 glycan structures were selected from GlycomeDB (www.glycome-db.org) and modelled for being stored into a RDF triple store and a Property Graph. We then performed two different sets of searches and compared the query response times and the results from both technologies to assess performance and accuracy. The two implementations produced the same results, but interestingly we noted a difference in the query response times. Qualitative measures such as portability were also used to define further criteria for choosing the technology adapted to solving glycan substructure search and other comparable issues. PMID:26656740

  15. Making "Photo" Graphs

    ERIC Educational Resources Information Center

    Doto, Julianne; Golbeck, Susan

    2007-01-01

    Collecting data and analyzing the results of experiments is difficult for children. The authors found a surprising way to help their third graders make graphs and draw conclusions from their data: digital photographs. The pictures bridged the gap between an abstract graph and the plants it represented. With the support of the photos, students…

  16. Reflections on "The Graph"

    ERIC Educational Resources Information Center

    Petrosino, Anthony

    2012-01-01

    This article responds to arguments by Skidmore and Thompson (this issue of "Educational Researcher") that a graph published more than 10 years ago was erroneously reproduced and "gratuitously damaged" perceptions of the quality of education research. After describing the purpose of the original graph, the author counters assertions that the graph…

  17. Exploring Graphs: WYSIWYG.

    ERIC Educational Resources Information Center

    Johnson, Millie

    1997-01-01

    Graphs from media sources and questions developed from them can be used in the middle school mathematics classroom. Graphs depict storage temperature on a milk carton; air pressure measurements on a package of shock absorbers; sleep-wake patterns of an infant; a dog's breathing patterns; and the angle, velocity, and radius of a leaning bicyclist…

  18. Walking Out Graphs

    ERIC Educational Resources Information Center

    Shen, Ji

    2009-01-01

    In the Walking Out Graphs Lesson described here, students experience several types of representations used to describe motion, including words, sentences, equations, graphs, data tables, and actions. The most important theme of this lesson is that students have to understand the consistency among these representations and form the habit of…

  19. Real World Graph Connectivity

    ERIC Educational Resources Information Center

    Lind, Joy; Narayan, Darren

    2009-01-01

    We present the topic of graph connectivity along with a famous theorem of Menger in the real-world setting of the national computer network infrastructure of "National LambdaRail". We include a set of exercises where students reinforce their understanding of graph connectivity by analysing the "National LambdaRail" network. Finally, we give…

  20. Graphing Electric Potential.

    ERIC Educational Resources Information Center

    De Jong, Marvin L.

    1993-01-01

    Describes the powerful graphing ability of computer algebra systems (CAS) to create three-dimensional graphs or surface graphics of electric potentials. Provides equations along with examples of the printouts. Lists the programs Mathematica, Maple, Derive, Theorist, MathCad, and MATLAB as promising CAS systems. (MVL)

  1. ACTIVITIES: Graphs and Games

    ERIC Educational Resources Information Center

    Hirsch, Christian R.

    1975-01-01

    Using a set of worksheets, students will discover and apply Euler's formula regarding connected planar graphs and play and analyze the game of Sprouts. One sheet leads to the discovery of Euler's formula; another concerns traversability of a graph; another gives an example and a game involving these ideas. (Author/KM)

  2. Let's Do It: Making Graphs.

    ERIC Educational Resources Information Center

    Shaw, Jean M.

    1984-01-01

    Reasons for having students make graphs are noted. Then specific graphing topics and materials appropriate for young learners are presented, including life-sized, floor, clothespin, felt-face, block, and magnetic graphs, and polls of pupils. (MNS)

  3. Evolutionary stability on graphs

    PubMed Central

    Ohtsuki, Hisashi; Nowak, Martin A.

    2008-01-01

    Evolutionary stability is a fundamental concept in evolutionary game theory. A strategy is called an evolutionarily stable strategy (ESS), if its monomorphic population rejects the invasion of any other mutant strategy. Recent studies have revealed that population structure can considerably affect evolutionary dynamics. Here we derive the conditions of evolutionary stability for games on graphs. We obtain analytical conditions for regular graphs of degree k > 2. Those theoretical predictions are compared with computer simulations for random regular graphs and for lattices. We study three different update rules: birth-death (BD), death-birth (DB), and imitation (IM) updating. Evolutionary stability on sparse graphs does not imply evolutionary stability in a well-mixed population, nor vice versa. We provide a geometrical interpretation of the ESS condition on graphs. PMID:18295801

  4. 77 FR 38391 - Mercedes-Benz USA, LLC, and Daimler AG (DAG), Receipt of Petition for Decision of Inconsequential...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-06-27

    ...Mercedes-Benz USA, LLC \\1\\ (MBUSA) and its parent company Daimler AG (DAG)(collectively referred to as ``MB'') have determined that certain model year 2011 and 2012 Mercedes-Benz S-Class (221 platform) passenger cars do not fully comply with paragraph S4.4 TPMS Malfunction of Federal Motor Vehicle Safety Standard (FMVSS) No. 138, Tire Pressure Monitoring Systems. MB has filed an appropriate......

  5. The Effect of Using Graphing Calculators in Complex Function Graphs

    ERIC Educational Resources Information Center

    Ocak, Mehmet Akif

    2008-01-01

    This study investigates the role of graphing calculators in multiple representations for knowledge transfer and the omission of oversimplification in complex function graphs. The main aim is to examine whether graphing calculators were used efficiently to see different cases and multiple perspectives among complex function graphs, or whether…

  6. A study on vague graphs.

    PubMed

    Rashmanlou, Hossein; Samanta, Sovan; Pal, Madhumangal; Borzooei, R A

    2016-01-01

    The main purpose of this paper is to introduce the notion of vague h-morphism on vague graphs and regular vague graphs. The action of vague h-morphism on vague strong regular graphs are studied. Some elegant results on weak and co weak isomorphism are derived. Also, [Formula: see text]-complement of highly irregular vague graphs are defined. PMID:27536517

  7. A Semantic Graph Query Language

    SciTech Connect

    Kaplan, I L

    2006-10-16

    Semantic graphs can be used to organize large amounts of information from a number of sources into one unified structure. A semantic query language provides a foundation for extracting information from the semantic graph. The graph query language described here provides a simple, powerful method for querying semantic graphs.

  8. Direct reciprocity on graphs

    PubMed Central

    Ohtsuki, Hisashi; Nowak, Martin A.

    2008-01-01

    Direct reciprocity is a mechanism for the evolution of cooperation based on the idea of repeated encounters between the same two individuals. Here we examine direct reciprocity in structured populations, where individuals occupy the vertices of a graph. The edges denote who interacts with whom. The graph represents spatial structure or a social network. For birth-death or pairwise comparison updating, we find that evolutionary stability of direct reciprocity is more restrictive on a graph than in a well-mixed population, but the condition for reciprocators to be advantageous is less restrictive on a graph. For death-birth and imitation updating, in contrast, both conditions are easier to fulfill on a graph. Moreover, for all four update mechanisms, reciprocators can dominate defectors on a graph, which is never possible in a well-mixed population. We also study the effect of an error rate, which increases with the number of links per individual; interacting with more people simultaneously enhances the probability of making mistakes. We provide analytic derivations for all results. PMID:17466339

  9. Commuting projections on graphs

    SciTech Connect

    Vassilevski, Panayot S.; Zikatanov, Ludmil T.

    2013-02-19

    For a given (connected) graph, we consider vector spaces of (discrete) functions defined on its vertices and its edges. These two spaces are related by a discrete gradient operator, Grad and its adjoint, ₋Div, referred to as (negative) discrete divergence. We also consider a coarse graph obtained by aggregation of vertices of the original one. Then a coarse vertex space is identified with the subspace of piecewise constant functions over the aggregates. We consider the ℓ2-projection QH onto the space of these piecewise constants. In the present paper, our main result is the construction of a projection π H from the original edge-space onto a properly constructed coarse edge-space associated with the edges of the coarse graph. The projections π H and QH commute with the discrete divergence operator, i.e., we have div π H = QH div. The respective pair of coarse edge-space and coarse vertexspace offer the potential to construct two-level, and by recursion, multilevel methods for the mixed formulation of the graph Laplacian which utilizes the discrete divergence operator. The performance of one two-level method with overlapping Schwarz smoothing and correction based on the constructed coarse spaces for solving such mixed graph Laplacian systems is illustrated on a number of graph examples.

  10. Clique graphs and overlapping communities

    NASA Astrophysics Data System (ADS)

    Evans, T. S.

    2010-12-01

    It is shown how to construct a clique graph in which properties of cliques of a fixed order in a given graph are represented by vertices in a weighted graph. Various definitions and motivations for these weights are given. The detection of communities or clusters is used to illustrate how a clique graph may be exploited. In particular a benchmark network is shown where clique graphs find the overlapping communities accurately while vertex partition methods fail.

  11. Higher-order graph wavelets and sparsity on circulant graphs

    NASA Astrophysics Data System (ADS)

    Kotzagiannidis, Madeleine S.; Dragotti, Pier Luigi

    2015-08-01

    The notion of a graph wavelet gives rise to more advanced processing of data on graphs due to its ability to operate in a localized manner, across newly arising data-dependency structures, with respect to the graph signal and underlying graph structure, thereby taking into consideration the inherent geometry of the data. In this work, we tackle the problem of creating graph wavelet filterbanks on circulant graphs for a sparse representation of certain classes of graph signals. The underlying graph can hereby be data-driven as well as fixed, for applications including image processing and social network theory, whereby clusters can be modelled as circulant graphs, respectively. We present a set of novel graph wavelet filter-bank constructions, which annihilate higher-order polynomial graph signals (up to a border effect) defined on the vertices of undirected, circulant graphs, and are localised in the vertex domain. We give preliminary results on their performance for non-linear graph signal approximation and denoising. Furthermore, we provide extensions to our previously developed segmentation-inspired graph wavelet framework for non-linear image approximation, by incorporating notions of smoothness and vanishing moments, which further improve performance compared to traditional methods.

  12. Cascade Cyclizations of Acyclic and Macrocyclic Alkynones: Studies toward the Synthesis of Phomactin A

    PubMed Central

    Ciesielski, Jennifer; Gandon, Vincent; Frontier, Alison J.

    2013-01-01

    A study of the reactivity and diastereoselectivity of the Lewis acid-promoted cascade cyclizations of both acyclic and macrocyclic alkynones is described. In these reactions, a β-iodoallenolate intermediate is generated via conjugate addition of iodide to an alkynone, followed by an intramolecular aldol reaction with a tethered aldehyde to afford a cyclohexenyl alcohol. The Lewis acid magnesium iodide (MgI2) was found to promote irreversible ring closure, while cyclizations using BF3·OEt2 as promoter occurred reversibly. For both acyclic and macrocyclic ynones, high diastereoselectivity was observed in the intramolecular aldol reaction. The MgI2 protocol for cyclization was applied to the synthesis of advanced intermediates relevant to the synthesis of phomactin natural products, during which a novel transannular cation-olefin cyclization was observed. DFT calculations were conducted to analyze the mechanism of this unusual MgI2-promoted process. PMID:23724905

  13. N-Branched acyclic nucleoside phosphonates as monomers for the synthesis of modified oligonucleotides.

    PubMed

    Hocková, Dana; Rosenbergová, Šárka; Ménová, Petra; Páv, Ondřej; Pohl, Radek; Novák, Pavel; Rosenberg, Ivan

    2015-04-21

    Protected N-branched nucleoside phosphonates containing adenine and thymine bases were prepared as the monomers for the introduction of aza-acyclic nucleotide units into modified oligonucleotides. The phosphotriester and phosphoramidite methods were used for the incorporation of modified and natural units, respectively. The solid phase synthesis of a series of nonamers containing one central modified unit was successfully performed in both 3'→5' and 5'→3' directions. Hybridization properties of the prepared oligoribonucleotides and oligodeoxyribonucleotides were evaluated. The measurement of thermal characteristics of the complexes of modified nonamers with the complementary strand revealed a considerable destabilizing effect of the introduced units. We also examined the substrate/inhibitory properties of aza-acyclic nucleoside phosphono-diphosphate derivatives (analogues of nucleoside triphosphates) but neither inhibition of human and bacterial DNA polymerases nor polymerase-mediated incorporation of these triphosphate analogues into short DNA was observed. PMID:25766752

  14. Acyclic monoterpenes in tree essential oils as a shrinking agent for waste-expanded polystyrene.

    PubMed

    Shimotori, Yasutaka; Hattori, Kazuyuki; Aoyama, Masakazu; Miyakoshi, Tetsuo

    2011-01-01

    We examined the dissolution of polystyrene (PS) into acyclic monoterpenes present in tree essential oils, to develop an environmentally friendly shrinking agent for waste-expanded polystyrene (EPS). The dissolving powers of geranyl acetate, geranylacetone, and geranyl formate [221.8-241.2 g PS (100 g solvent)(-1)] compared favorably with that of (R)-limonene [181.7 g PS (100 g solvent)(-1)]. Their favorable dissolving powers for PS can be explained by their flexible linear structures, which may be more accessible to the inside of bulk PS compared with cyclic monoterpenes. These acyclic monoterpenes and PS were recovered almost quantitatively by simple steam distillation of the PS solution. PMID:21644162

  15. Regulation of the survival and differentiation of hepatic stem/progenitor cells by acyclic retinoid.

    PubMed

    Kamiya, Akihide

    2015-01-01

    During embryonic liver development, hepatic stem/progenitor cells (HpSCs) have a high proliferative ability and bipotency to differentiate into hepatocytes and cholangiocytes. Retinoic acid is a derivative of vitamin A and is involved in the proliferation and differentiation of stem/progenitor cells in several tissues. However, whether retinoic acid regulates the characteristics of HpSCs in the normal liver is still unknown. A recent study has shown that acyclic retinoid regulates the survival and proliferation of HpSCs derived from mouse foetal liver. Acyclic retinoid suppressed the expansion of CD29(+)CD49f(+) HpSCs through the induction of hepatocytic differentiation and progression of apoptosis. PMID:26021438

  16. [Synthesis of acyclic 1,3-polyols and its application to structural study of natural products].

    PubMed

    Mori, Y

    1993-06-01

    A 1,3-polyhydroxylated chain is often found on the backbone of biologically important natural products. The acyclic nature and the regular array of many hydroxyl groups are main obstacles to structural and synthetic studies, and many efforts have been made to this end. We have developed a new general synthetic method of 1,3-polyols based on the coupling of a chiral dithiane, a four-carbon unit, and an epoxide, followed by 1,3-diastereoselective reduction. We applied the method to the synthesis of polymethoxy-1-alkenes isolated from blue-green algae to establish their absolute stereochemistry. Moreover, a general procedure for assigning the absolute stereochemistry of acyclic 1,3-polyols by the difference circular dichroism (CD) method have been established. Combination of the method and a reiterative degradation enables one to determine the absolute configuration of 1,3-polyols, even if the relative stereochemistry is unknown. PMID:8355146

  17. ASK-GraphView: A large scale graph visualization system.

    PubMed

    Abello, James; van Ham, Frank; Krishnan, Neeraj

    2006-01-01

    We describe ASK-GraphView, a node-link-based graph visualization system that allows clustering and interactive navigation of large graphs, ranging in size up to 16 million edges. The system uses a scalable architecture and a series of increasingly sophisticated clustering algorithms to construct a hierarchy on an arbitrary, weighted undirected input graph. By lowering the interactivity requirements we can scale to substantially bigger graphs. The user is allowed to navigate this hierarchy in a top down manner by interactively expanding individual clusters. ASK-GraphView also provides facilities for filtering and coloring, annotation and cluster labeling. PMID:17080786

  18. New Graph Calculi for Planar Non-3-Colorable Graphs

    NASA Astrophysics Data System (ADS)

    Hanatani, Yoichi; Horiyama, Takashi; Iwama, Kazuo; Tamaki, Suguru

    The Hajós calculus is a nondeterministic procedure which generates the class of non-3-colorable graphs. If all non-3-colorable graphs can be constructed in polynomial steps by the calculus, then NP=co-NP holds. Up to date, however, it remains open whether there exists a family of graphs that cannot be generated in polynomial steps. To attack this problem, we propose two graph calculi PHC and PHC* that generate non-3-colorable planar graphs, where intermediate graphs in the calculi are also restricted to be planar. Then we prove that PHC and PHC* are sound and complete. We also show that PHC* can polynomially simulate PHC.

  19. Graphing. USMES Beginning "How To" Set.

    ERIC Educational Resources Information Center

    Agro, Sally; And Others

    In this set of eight booklets on graphing, primary grade students learn how to choose which graph to make and how to make a bar graph, bar graph histogram, conversion graph, line chart, line graph, scatter graph, and slope diagram. The major emphasis in all Unified Sciences and Mathematics for Elementary Schools (USMES) units is on open-ended,…

  20. Triphosgene-Pyridine Mediated Stereoselective Chlorination of Acyclic Aliphatic 1,3-Diols†

    PubMed Central

    Villalpando, Andrés; Saputra, Mirza A.; Tugwell, Thomas H.; Kartika, Rendy

    2015-01-01

    We describe a strategy to chlorinate stereocomplementary acyclic aliphatic 1,3-diols using a mixture of triphosgene and pyridine. While 1,3-anti diols readily led to 1,3-anti dichlorides, 1,3-syn diols must be converted to 1,3-syn diol monosilylethers to access the corresponding 1,3-syn dichlorides. These dichlorination protocols were operationally simple, very mild, and readily tolerated by advanced synthetic intermediates. PMID:26323232

  1. Algebraic distance on graphs.

    SciTech Connect

    Chen, J.; Safro, I.

    2011-01-01

    Measuring the connection strength between a pair of vertices in a graph is one of the most important concerns in many graph applications. Simple measures such as edge weights may not be sufficient for capturing the effects associated with short paths of lengths greater than one. In this paper, we consider an iterative process that smooths an associated value for nearby vertices, and we present a measure of the local connection strength (called the algebraic distance; see [D. Ron, I. Safro, and A. Brandt, Multiscale Model. Simul., 9 (2011), pp. 407-423]) based on this process. The proposed measure is attractive in that the process is simple, linear, and easily parallelized. An analysis of the convergence property of the process reveals that the local neighborhoods play an important role in determining the connectivity between vertices. We demonstrate the practical effectiveness of the proposed measure through several combinatorial optimization problems on graphs and hypergraphs.

  2. Quantum Ergodicity on Graphs

    NASA Astrophysics Data System (ADS)

    Gnutzmann, S.; Keating, J. P.; Piotet, F.

    2008-12-01

    We investigate the equidistribution of the eigenfunctions on quantum graphs in the high-energy limit. Our main result is an estimate of the deviations from equidistribution for large well-connected graphs. We use an exact field-theoretic expression in terms of a variant of the supersymmetric nonlinear σ model. Our estimate is based on a saddle-point analysis of this expression and leads to a criterion for when equidistribution emerges asymptotically in the limit of large graphs. Our theory predicts a rate of convergence that is a significant refinement of previous estimates, long assumed to be valid for quantum chaotic systems, agreeing with them in some situations but not all. We discuss specific examples for which the theory is tested numerically.

  3. Subdominant pseudoultrametric on graphs

    SciTech Connect

    Dovgoshei, A A; Petrov, E A

    2013-08-31

    Let (G,w) be a weighted graph. We find necessary and sufficient conditions under which the weight w:E(G)→R{sup +} can be extended to a pseudoultrametric on V(G), and establish a criterion for the uniqueness of such an extension. We demonstrate that (G,w) is a complete k-partite graph, for k≥2, if and only if for any weight that can be extended to a pseudoultrametric, among all such extensions one can find the least pseudoultrametric consistent with w. We give a structural characterization of graphs for which the subdominant pseudoultrametric is an ultrametric for any strictly positive weight that can be extended to a pseudoultrametric. Bibliography: 14 titles.

  4. Martian Pyroxenes in the Shergottite Meteorites; Zagami, SAU005, DAG476 and EETA79001

    NASA Astrophysics Data System (ADS)

    Stephen, N.; Benedix, G. K.; Bland, P.; Hamilton, V. E.

    2010-12-01

    The geology and surface mineralogy of Mars is characterised using remote sensing techniques such as thermal emission spectroscopy (TES) from instruments on a number of spacecraft currently orbiting Mars or gathered from roving missions on the Martian surface. However, the study of Martian meteorites is also important in efforts to further understand the geological history of Mars or to interpret mission data as they are believed to be the only available samples that give us direct clues as to Martian igneous processes [1]. We have recently demonstrated that the spectra of Martian-specific minerals can be determined using micro-spectroscopy [2] and that these spectra can be reliably obtained from thin sections of Martian meteorites [3]. Accurate modal mineralogy of these meteorites is also important [4]. In this study we are using a variety of techniques to build upon previous studies of these particular samples in order to fully characterise the nature of the 2 common pyroxenes found in Martian Shergottites; pigeonite and augite [5], [6]. Previous studies have shown that the Shergottite meteorites are dominated by pyroxene (pigeonite and augite in varying quantities) [4], [5], commonly but not always olivine, plagioclase or maskelynite/glass and also hydrous minerals, which separate the Martian meteorites from other achondrites [7]. Our microprobe study of meteorites Zagami, EETA79001, SAU005 and DAG476 in thin-section at the Natural History Museum, London shows a chemical variability within both the pigeonite and augite composition across individual grains in all thin sections; variation within either Mg or Ca concentration varies from core to rim within the grains. This variation can also be seen in modal mineralogy maps using SEM-derived element maps and the Photoshop® technique previously described [4], and in new micro-spectroscopy data, particularly within the Zagami meteorite. New mineral spectra have been gathered from the Shergottite thin-sections by

  5. A new monoclonal antibody DAG-6F4 against human alpha-dystroglycan reveals reduced core protein in some, but not all, dystroglycanopathy patients.

    PubMed

    Humphrey, Emma L; Lacey, Erica; Le, Lam T; Feng, Lucy; Sciandra, Francesca; Morris, Charlotte R; Hewitt, Jane E; Holt, Ian; Brancaccio, Andrea; Barresi, Rita; Sewry, Caroline A; Brown, Susan C; Morris, Glenn E

    2015-01-01

    We generated a novel monoclonal antibody, DAG-6F4, against alpha-dystroglycan which immunolabels the sarcolemma in human muscle biopsies. Its seven amino-acid epitope, PNQRPEL, was identified using phage-displayed peptides and is located immediately after the highly-glycosylated mucin domain of alpha-dystroglycan. On Western blots of recombinant alpha-dystroglycan, epitope accessibility was reduced, but not entirely prevented, by glycosylation. DAG-6F4 immunolabelling was markedly reduced in muscle biopsies from Duchenne muscular dystrophy patients consistent with disruption of the dystroglycan complex. In a range of dystroglycanopathy patients with reduced/altered glycosylation, staining by DAG-6F4 was often less reduced than staining by IIH6 (antibody against the glycan epitope added by LARGE and commonly used to identify glycosylated alpha-dystroglycan). Whereas IIH6 was reduced in all patients, DAG-6F4 was hardly changed in a LARGE patient, less reduced than IIH6 in limb-girdle muscular dystrophy type 2I, but as reduced as IIH6 in some congenital muscular dystrophy patients. Although absence of the LARGE-dependent laminin-binding site appears not to affect alpha-dystroglycan stability at the sarcolemma, the results suggest that further reduction in aDG glycosylation may reduce its stability. These studies suggest that DAG-6F4 may be a useful addition to the antibody repertoire for evaluating the dystroglycan complex in neuromuscular disorders. PMID:25387694

  6. Graphing Calculator Mini Course

    NASA Technical Reports Server (NTRS)

    Karnawat, Sunil R.

    1996-01-01

    The "Graphing Calculator Mini Course" project provided a mathematically-intensive technologically-based summer enrichment workshop for teachers of American Indian students on the Turtle Mountain Indian Reservation. Eleven such teachers participated in the six-day workshop in summer of 1996 and three Sunday workshops in the academic year. The project aimed to improve science and mathematics education on the reservation by showing teachers effective ways to use high-end graphing calculators as teaching and learning tools in science and mathematics courses at all levels. In particular, the workshop concentrated on applying TI-82's user-friendly features to understand the various mathematical and scientific concepts.

  7. Graph for locked rotor current

    NASA Technical Reports Server (NTRS)

    Peck, R. R.

    1972-01-01

    Graph determines effect of stalled motor on a distribution system and eliminates hand calculation of amperage in emergencies. Graph is useful to any manufacturer, contractor, or maintenance department involved in electrical technology.

  8. Inactivation of the Phloem-Specific Dof Zinc Finger Gene DAG1 Affects Response to Light and Integrity of the Testa of Arabidopsis Seeds1

    PubMed Central

    Papi, Maura; Sabatini, Sabrina; Altamura, Maria Maddalena; Hennig, Lars; Schäfer, Eberhard; Costantino, Paolo; Vittorioso, Paola

    2002-01-01

    We show here that seeds from the knockout mutant of the Arabidopsis DAG1 gene encoding a Dof zinc finger transcription factor have an altered response to red and far-red light. Mutant dag1 seeds are induced to germinate by much lower red light fluence rates, and germination reaches more quickly a point where it is independent of phytochrome signaling. Moreover, although microscopic analysis reveals no obvious structural alterations in the seed coat (testa) of dag1 seeds, staining assays with different dyes point to an abnormal fragility of the testa. By extensive in situ mRNA hybridization analysis we show here that the gene, which is not expressed in the embryo, is specifically expressed in the phloem of all organs of the mother plant. PMID:11842145

  9. Coloring geographical threshold graphs

    SciTech Connect

    Bradonjic, Milan; Percus, Allon; Muller, Tobias

    2008-01-01

    We propose a coloring algorithm for sparse random graphs generated by the geographical threshold graph (GTG) model, a generalization of random geometric graphs (RGG). In a GTG, nodes are distributed in a Euclidean space, and edges are assigned according to a threshold function involving the distance between nodes as well as randomly chosen node weights. The motivation for analyzing this model is that many real networks (e.g., wireless networks, the Internet, etc.) need to be studied by using a 'richer' stochastic model (which in this case includes both a distance between nodes and weights on the nodes). Here, we analyze the GTG coloring algorithm together with the graph's clique number, showing formally that in spite of the differences in structure between GTG and RGG, the asymptotic behavior of the chromatic number is identical: {chi}1n 1n n / 1n n (1 + {omicron}(1)). Finally, we consider the leading corrections to this expression, again using the coloring algorithm and clique number to provide bounds on the chromatic number. We show that the gap between the lower and upper bound is within C 1n n / (1n 1n n){sup 2}, and specify the constant C.

  10. Body Motion and Graphing.

    ERIC Educational Resources Information Center

    Nemirovsky, Ricardo; Tierney, Cornelia; Wright, Tracy

    1998-01-01

    Analyzed two children's use of a computer-based motion detector to make sense of symbolic expressions (Cartesian graphs). Found three themes: (1) tool perspectives, efforts to understand graphical responses to body motion; (2) fusion, emergent ways of talking and behaving that merge symbols and referents; and (3) graphical spaces, when changing…

  11. Graphs in Real Time.

    ERIC Educational Resources Information Center

    Beckmann, Charlene E.; Rozanski, Kara

    1999-01-01

    Presents a lesson that uses a motion detector in order for students to experience the interplay between motion and its graphical representation of the slope. Focuses on the change in the appearance of the graph with regard to changing speed. (ASK)

  12. Line Graph Learning

    ERIC Educational Resources Information Center

    Pitts Bannister, Vanessa R.; Jamar, Idorenyin; Mutegi, Jomo W.

    2007-01-01

    In this article, the learning progress of one fifth-grade student is examined with regard to the development of her graph interpretation skills as she participated in the Junior Science Institute (JSI), a two-week, science intensive summer camp in which participants engaged in microbiology research and application. By showcasing the student's…

  13. Straight Line Graphs

    ERIC Educational Resources Information Center

    Krueger, Tom

    2010-01-01

    In this article, the author shares one effective lesson idea on straight line graphs that he applied in his lower ability Y9 class. The author wanted something interesting for his class to do, something that was fun and engaging with direct feedback, and something that worked because someone else had tried it before. In a word, the author admits…

  14. Cookies and Graphs

    ERIC Educational Resources Information Center

    Cooper, Carol

    1975-01-01

    Teachers of an integrated elementary classroom used cookie-sharing time as a learning experience for students. Responsible for dividing varying amounts of cookies daily, the students learned to translate their experiences to graphs of differing sophistication and analyses. Further interpretation and application were done by individual students…

  15. GraphLib

    2013-02-19

    This library is used in several LLNL projects, including STAT (the Stack Trace Analysis Tool for scalable debugging) and some modules in P^nMPI (a tool MPI tool infrastructure). It can also be used standalone for creating and manipulationg graphs, but its API is primarily tuned to support these other projects

  16. Graph-theoretical exorcism

    SciTech Connect

    Simmons, G.J.

    1985-01-01

    Given a graph G and an ordering phi of the vertices, V(G), we define a parsimonious proper coloring (PPC) of V(G) under phi to be a proper coloring of V(G) in the order phi, where a new color is introduced only when a vertex cannot be properly colored in its order with any of the colors already used.

  17. Physics on Graphs

    NASA Astrophysics Data System (ADS)

    Schrader, Robert

    This is an extended version of the talk given at the Nato Advanced Research Workshop: New Challenges in Complex System Physics, May 20-24, 2013 in Samarkand (Uzbekistan). We report on results on three topics in joint work with V. Kostrykin (Mainz, Germany) and J. Potthoff (Mannheim, Germany): Propagation of waves on graphs,

  18. Temporal Representation in Semantic Graphs

    SciTech Connect

    Levandoski, J J; Abdulla, G M

    2007-08-07

    A wide range of knowledge discovery and analysis applications, ranging from business to biological, make use of semantic graphs when modeling relationships and concepts. Most of the semantic graphs used in these applications are assumed to be static pieces of information, meaning temporal evolution of concepts and relationships are not taken into account. Guided by the need for more advanced semantic graph queries involving temporal concepts, this paper surveys the existing work involving temporal representations in semantic graphs.

  19. Quantum walks on quotient graphs

    SciTech Connect

    Krovi, Hari; Brun, Todd A.

    2007-06-15

    A discrete-time quantum walk on a graph {gamma} is the repeated application of a unitary evolution operator to a Hilbert space corresponding to the graph. If this unitary evolution operator has an associated group of symmetries, then for certain initial states the walk will be confined to a subspace of the original Hilbert space. Symmetries of the original graph, given by its automorphism group, can be inherited by the evolution operator. We show that a quantum walk confined to the subspace corresponding to this symmetry group can be seen as a different quantum walk on a smaller quotient graph. We give an explicit construction of the quotient graph for any subgroup H of the automorphism group and illustrate it with examples. The automorphisms of the quotient graph which are inherited from the original graph are the original automorphism group modulo the subgroup H used to construct it. The quotient graph is constructed by removing the symmetries of the subgroup H from the original graph. We then analyze the behavior of hitting times on quotient graphs. Hitting time is the average time it takes a walk to reach a given final vertex from a given initial vertex. It has been shown in earlier work [Phys. Rev. A 74, 042334 (2006)] that the hitting time for certain initial states of a quantum walks can be infinite, in contrast to classical random walks. We give a condition which determines whether the quotient graph has infinite hitting times given that they exist in the original graph. We apply this condition for the examples discussed and determine which quotient graphs have infinite hitting times. All known examples of quantum walks with hitting times which are short compared to classical random walks correspond to systems with quotient graphs much smaller than the original graph; we conjecture that the existence of a small quotient graph with finite hitting times is necessary for a walk to exhibit a quantum speedup.

  20. A Clustering Graph Generator

    SciTech Connect

    Winlaw, Manda; De Sterck, Hans; Sanders, Geoffrey

    2015-10-26

    In very simple terms a network can be de ned as a collection of points joined together by lines. Thus, networks can be used to represent connections between entities in a wide variety of elds including engi- neering, science, medicine, and sociology. Many large real-world networks share a surprising number of properties, leading to a strong interest in model development research and techniques for building synthetic networks have been developed, that capture these similarities and replicate real-world graphs. Modeling these real-world networks serves two purposes. First, building models that mimic the patterns and prop- erties of real networks helps to understand the implications of these patterns and helps determine which patterns are important. If we develop a generative process to synthesize real networks we can also examine which growth processes are plausible and which are not. Secondly, high-quality, large-scale network data is often not available, because of economic, legal, technological, or other obstacles [7]. Thus, there are many instances where the systems of interest cannot be represented by a single exemplar network. As one example, consider the eld of cybersecurity, where systems require testing across diverse threat scenarios and validation across diverse network structures. In these cases, where there is no single exemplar network, the systems must instead be modeled as a collection of networks in which the variation among them may be just as important as their common features. By developing processes to build synthetic models, so-called graph generators, we can build synthetic networks that capture both the essential features of a system and realistic variability. Then we can use such synthetic graphs to perform tasks such as simulations, analysis, and decision making. We can also use synthetic graphs to performance test graph analysis algorithms, including clustering algorithms and anomaly detection algorithms.

  1. Topic Model for Graph Mining.

    PubMed

    Xuan, Junyu; Lu, Jie; Zhang, Guangquan; Luo, Xiangfeng

    2015-12-01

    Graph mining has been a popular research area because of its numerous application scenarios. Many unstructured and structured data can be represented as graphs, such as, documents, chemical molecular structures, and images. However, an issue in relation to current research on graphs is that they cannot adequately discover the topics hidden in graph-structured data which can be beneficial for both the unsupervised learning and supervised learning of the graphs. Although topic models have proved to be very successful in discovering latent topics, the standard topic models cannot be directly applied to graph-structured data due to the "bag-of-word" assumption. In this paper, an innovative graph topic model (GTM) is proposed to address this issue, which uses Bernoulli distributions to model the edges between nodes in a graph. It can, therefore, make the edges in a graph contribute to latent topic discovery and further improve the accuracy of the supervised and unsupervised learning of graphs. The experimental results on two different types of graph datasets show that the proposed GTM outperforms the latent Dirichlet allocation on classification by using the unveiled topics of these two models to represent graphs. PMID:25616091

  2. Random Walks on Random Graphs

    NASA Astrophysics Data System (ADS)

    Cooper, Colin; Frieze, Alan

    The aim of this article is to discuss some of the notions and applications of random walks on finite graphs, especially as they apply to random graphs. In this section we give some basic definitions, in Section 2 we review applications of random walks in computer science, and in Section 3 we focus on walks in random graphs.

  3. Editing graphs for maximum effect

    SciTech Connect

    Murphy, P.W.; Rhiner, R.W.

    1991-01-08

    The paper contains over eighty rules for editing graphs, arranged under nine major headings in a logical sequence for editing all the graphs in a manuscript. It is excerpted from a monograph used at the Lawrence Livermore National Laboratory to train beginning technical editors in editing graphs; a corresponding Hypercard stack is also used in this training. 6 refs., 4 figs.

  4. Mining and Indexing Graph Databases

    ERIC Educational Resources Information Center

    Yuan, Dayu

    2013-01-01

    Graphs are widely used to model structures and relationships of objects in various scientific and commercial fields. Chemical molecules, proteins, malware system-call dependencies and three-dimensional mechanical parts are all modeled as graphs. In this dissertation, we propose to mine and index those graph data to enable fast and scalable search.…

  5. Kevin Bacon and Graph Theory

    ERIC Educational Resources Information Center

    Hopkins, Brian

    2004-01-01

    The interconnected world of actors and movies is a familiar, rich example for graph theory. This paper gives the history of the "Kevin Bacon Game" and makes extensive use of a Web site to analyze the underlying graph. The main content is the classroom development of the weighted average to determine the best choice of "center" for the graph. The…

  6. Recursive Feature Extraction in Graphs

    2014-08-14

    ReFeX extracts recursive topological features from graph data. The input is a graph as a csv file and the output is a csv file containing feature values for each node in the graph. The features are based on topological counts in the neighborhoods of each nodes, as well as recursive summaries of neighbors' features.

  7. A Note on Hamiltonian Graphs

    ERIC Educational Resources Information Center

    Skurnick, Ronald; Davi, Charles; Skurnick, Mia

    2005-01-01

    Since 1952, several well-known graph theorists have proven numerous results regarding Hamiltonian graphs. In fact, many elementary graph theory textbooks contain the theorems of Ore, Bondy and Chvatal, Chvatal and Erdos, Posa, and Dirac, to name a few. In this note, the authors state and prove some propositions of their own concerning Hamiltonian…

  8. What is a complex graph?

    NASA Astrophysics Data System (ADS)

    Kim, Jongkwang; Wilhelm, Thomas

    2008-04-01

    Many papers published in recent years show that real-world graphs G(n,m) ( n nodes, m edges) are more or less “complex” in the sense that different topological features deviate from random graphs. Here we narrow the definition of graph complexity and argue that a complex graph contains many different subgraphs. We present different measures that quantify this complexity, for instance C1e, the relative number of non-isomorphic one-edge-deleted subgraphs (i.e. DECK size). However, because these different subgraph measures are computationally demanding, we also study simpler complexity measures focussing on slightly different aspects of graph complexity. We consider heuristically defined “product measures”, the products of two quantities which are zero in the extreme cases of a path and clique, and “entropy measures” quantifying the diversity of different topological features. The previously defined network/graph complexity measures Medium Articulation and Offdiagonal complexity ( OdC) belong to these two classes. We study OdC measures in some detail and compare it with our new measures. For all measures, the most complex graph G has a medium number of edges, between the edge numbers of the minimum and the maximum connected graph n-1graph complexity measures are characterized with the help of different example graphs. For all measures the corresponding time complexity is given. Finally, we discuss the complexity of 33 real-world graphs of different biological, social and economic systems with the six computationally most simple measures (including OdC). The complexities of the real graphs are compared with average complexities of two different random graph versions: complete random graphs (just fixed n,m) and rewired graphs with fixed node degrees.

  9. Graphing. USMES Intermediate "How To" Set.

    ERIC Educational Resources Information Center

    Agro, Sally; And Others

    In this set of six booklets on graphing, intermediate grade students learn how to choose which kind of graph to make; make bar graphs, histograms, line graphs, and conversion graphs; and use graphs to compare two sets of data. The major emphasis in all Unified Sciences and Mathematics for Elementary Schools (USMES) units is on open-ended,…

  10. Random graphs with hidden color.

    PubMed

    Söderberg, Bo

    2003-07-01

    We propose and investigate a unifying class of sparse random graph models, based on a hidden coloring of edge-vertex incidences, extending an existing approach, random graphs with a given degree distribution, in a way that admits a nontrivial correlation structure in the resulting graphs. The approach unifies a number of existing random graph ensembles within a common general formalism, and allows for the analytic calculation of observable graph characteristics. In particular, generating function techniques are used to derive the size distribution of connected components (clusters) as well as the location of the percolation threshold where a giant component appears. PMID:12935185

  11. Spectral fluctuations of quantum graphs

    SciTech Connect

    Pluhař, Z.; Weidenmüller, H. A.

    2014-10-15

    We prove the Bohigas-Giannoni-Schmit conjecture in its most general form for completely connected simple graphs with incommensurate bond lengths. We show that for graphs that are classically mixing (i.e., graphs for which the spectrum of the classical Perron-Frobenius operator possesses a finite gap), the generating functions for all (P,Q) correlation functions for both closed and open graphs coincide (in the limit of infinite graph size) with the corresponding expressions of random-matrix theory, both for orthogonal and for unitary symmetry.

  12. Synthesis, biological, and biophysical studies of DAG-indololactones designed as selective activators of RasGRP.

    PubMed

    Garcia, Lia C; Donadío, Lucia Gandolfi; Mann, Ella; Kolusheva, Sofiya; Kedei, Noemi; Lewin, Nancy E; Hill, Colin S; Kelsey, Jessica S; Yang, Jing; Esch, Timothy E; Santos, Marina; Peach, Megan L; Kelley, James A; Blumberg, Peter M; Jelinek, Raz; Marquez, Victor E; Comin, Maria J

    2014-06-15

    The development of selective agents capable of discriminating between protein kinase C (PKC) isoforms and other diacylglycerol (DAG)-responsive C1 domain-containing proteins represents an important challenge. Recent studies have highlighted the role that Ras guanine nucleotide-releasing protein (RasGRP) isoforms play both in immune responses as well as in the development of prostate cancer and melanoma, suggesting that the discovery of selective ligands could have potential therapeutic value. Thus far, the N-methyl-substituted indololactone 1 is the agonist with the highest reported potency and selectivity for RasGRP relative to PKC. Here we present the synthesis, binding studies, cellular assays and biophysical analysis of interactions with model membranes of a family of regioisomers of 1 (compounds 2-5) that differ in the position of the linkage between the indole ring and the lactone moiety. These structural variations were studied to explore the interaction of the active complex (C1 domain-ligand) with cellular membranes, which is believed to be an important factor for selectivity in the activation of DAG-responsive C1 domain containing signaling proteins. All compounds were potent and selective activators of RasGRP when compared to PKCα with selectivities ranging from 6 to 65 fold. However, the parent compound 1 was appreciably more selective than any of the other isomers. In intact cells, modest differences in the patterns of translocation of the C1 domain targets were observed. Biophysical studies using giant vesicles as model membranes did show substantial differences in terms of molecular interactions impacting lipid organization, dynamics and membrane insertion. However, these differences did not yield correspondingly large changes in patterns of biological response, at least for the parameters examined. PMID:24794745

  13. Synthesis, Biological, and Biophysical Studies of DAG-indololactones Designed as Selective Activators of RasGRP

    PubMed Central

    Garcia, Lia C.; Donadío, Lucia Gandolfi; Mann, Ella; Kolusheva, Sofiya; Kedei, Noemi; Lewin, Nancy E.; Hill, Colin S.; Kelsey, Jessica S.; Yang, Jing; Esch, Timothy E.; Santos, Marina; Peach, Megan L.; Kelley, James A.; Blumberg, Peter M.; Jelinek, Raz; Marquez, Victor E.; Comin, Maria J.

    2014-01-01

    The development of selective agents capable of discriminating between protein kinase C (PKC) isoforms and other diacylglycerol (DAG)-responsive C1 domain-containing proteins represents an important challenge. Recent studies have highlighted the role that Ras guanine nucleotide-releasing protein (RasGRP) isoforms play both in immune responses as well as in the development of prostate cancer and melanoma, suggesting that the discovery of selective ligands could have potential therapeutic value. Thus far, the N-methyl-substituted indololactone 1 is the agonist with the highest reported potency and selectivity for RasGRP relative to PKC. Here we present the synthesis, binding studies, cellular assays and biophysical analysis of interactions with model membranes of a family of regioisomers of 1 (compounds 2 to 5) that differ in the position of the linkage between the indole ring and the lactone moiety. These structural variations were studied to explore the interaction of the active complex (C1 domain-ligand) with cellular membranes, which is believed to be an important factor for selectivity in the activation of DAG-responsive C1 domain containing signaling proteins. All compounds were potent and selective activators of RasGRP when compared to PKCα with selectivities ranging from 6 to 65 fold. However, the parent compound 1 was appreciably more selective than any of the other isomers. In intact cells, modest differences in the patterns of translocation of the C1 domain targets were observed. Biophysical studies using giant vesicles as model membranes did show substantial differences in terms of molecular interactions impacting lipid organization, dynamics and membrane insertion. However, these differences did not yield correspondingly large changes in patterns of biological response, at least for the parameters examined. PMID:24794745

  14. An Unusual Exponential Graph

    ERIC Educational Resources Information Center

    Syed, M. Qasim; Lovatt, Ian

    2014-01-01

    This paper is an addition to the series of papers on the exponential function begun by Albert Bartlett. In particular, we ask how the graph of the exponential function y = e[superscript -t/t] would appear if y were plotted versus ln t rather than the normal practice of plotting ln y versus t. In answering this question, we find a new way to…

  15. Graphs in molecular biology

    PubMed Central

    Huber, Wolfgang; Carey, Vincent J; Long, Li; Falcon, Seth; Gentleman, Robert

    2007-01-01

    Graph theoretical concepts are useful for the description and analysis of interactions and relationships in biological systems. We give a brief introduction into some of the concepts and their areas of application in molecular biology. We discuss software that is available through the Bioconductor project and present a simple example application to the integration of a protein-protein interaction and a co-expression network. PMID:17903289

  16. Characterization of cyclic and acyclic alkanes in Forties and Kuwait petroleum crudes

    SciTech Connect

    Jones, D.W. ); Pakdel, H. ); Bartle, K.D. )

    1990-01-01

    Alkane hydrocarbon fractions from Forties (North Sea) and Kuwait petroleum crudes, separated by distillation, solvent extraction and silicagel column chromatography and sub-fractionated by molecular-sieve adsorption, have been examined by gas chromatography (GC), {sup 1}H and {sup 13}C NMR spectroscopy, GC-mass spectrometry (MS) and field desorption (FD)MS. GC indicates that Forties contains rather more acyclic isoprenoids and cyclic alkanes than Kuwait; FDMS of Kuwait shows molecular-weight ranges for mono-, di-, tri-, tetra-, and pentacyclic alkanes. {sup 13}C NMR spectra provide evidence of higher aromatic carbon, C{sub A}, in Forties than Kuwait and longer T{sub 1} relaxation times.

  17. Recent Applications of Acyclic (Diene)iron Complexes and (Dienyl)iron Cations in Organic Synthesis

    PubMed Central

    Chaudhury, Subhabrata

    2009-01-01

    Complexation of (tricarbonyl)iron to an acyclic diene serves to protect the ligand against oxidation, reduction and cycloaddition reactions while the steric bulk of this adjunct serves to direct the approach reagents to unsaturated groups attached to the diene onto the face opposite to iron. Furthermore, the Fe(CO)3 moiety can serve to stabilize carbocation centers adjacent to the diene (i.e. pentadienyl-iron cations). Recent applications of these reactivities to the synthesis of polyene, cyclopropane, cycloheptadiene and cyclohexenone containing natural products or analogs will be presented. PMID:21709767

  18. Acyclic phosph(on)ate inhibitors of Plasmodium falciparum hypoxanthine-guanine-xanthine phosphoribosyltransferase

    PubMed Central

    Clinch, Keith; Crump, Douglas R.; Evans, Gary B.; Hazleton, Keith Z.; Mason, Jennifer M.; Schramm, Vern L.

    2013-01-01

    The pathogenic protozoa responsible for malaria lack enzymes for the de novo synthesis of purines and rely on purine salvage from the host. In Plasmodium falciparum (Pf), hypoxanthine-guanine-xanthine phosphoribosyltransferase (HGXPRT) converts hypoxanthine to inosine monophosphate and is essential for purine salvage making the enzyme an anti-malarial drug target. We have synthesized a number of simple acyclic aza-C- nucleosides and shown that some are potent inhibitors of Pf HGXPRT while showing excellent selectivity for the Pf versus the human enzyme. PMID:23810424

  19. A Practical Approach for Scalable Conjunctive Query Answering on Acyclic {EL}^+ Knowledge Base

    NASA Astrophysics Data System (ADS)

    Mei, Jing; Liu, Shengping; Xie, Guotong; Kalyanpur, Aditya; Fokoue, Achille; Ni, Yuan; Li, Hanyu; Pan, Yue

    Conjunctive query answering for {EL}^{++} ontologies has recently drawn much attention, as the Description Logic {EL}^{++} captures the expressivity of many large ontologies in the biomedical domain and is the foundation for the OWL 2 EL profile. In this paper, we propose a practical approach for conjunctive query answering in a fragment of {EL}^{++}, namely acyclic {EL}^+, that supports role inclusions. This approach can be implemented with low cost by leveraging any existing relational database management system to do the ABox data completion and query answering. We conducted a preliminary experiment to evaluate our approach using a large clinical data set and show our approach is practical.

  20. Community detection in graphs

    NASA Astrophysics Data System (ADS)

    Fortunato, Santo

    2010-02-01

    The modern science of networks has brought significant advances to our understanding of complex systems. One of the most relevant features of graphs representing real systems is community structure, or clustering, i.e. the organization of vertices in clusters, with many edges joining vertices of the same cluster and comparatively few edges joining vertices of different clusters. Such clusters, or communities, can be considered as fairly independent compartments of a graph, playing a similar role like, e.g., the tissues or the organs in the human body. Detecting communities is of great importance in sociology, biology and computer science, disciplines where systems are often represented as graphs. This problem is very hard and not yet satisfactorily solved, despite the huge effort of a large interdisciplinary community of scientists working on it over the past few years. We will attempt a thorough exposition of the topic, from the definition of the main elements of the problem, to the presentation of most methods developed, with a special focus on techniques designed by statistical physicists, from the discussion of crucial issues like the significance of clustering and how methods should be tested and compared against each other, to the description of applications to real networks.

  1. A novel intramolecular through-space interaction between F and CN: a strategy for the conformational control of an acyclic system.

    PubMed

    Nishide, K; Hagimoto, Y; Hasegawa, H; Shiro, M; Node, M

    2001-11-21

    X-Ray crystallographic analyses of fluorocyanides anti-1 and 2 revealed a novel intramolecular through-space interaction between F and CN in an acyclic system, which was applied to a stereoselective protonation of acyclic fluorocyanides 2 having flexible conformation. PMID:12240092

  2. A new strategy to construct acyclic nucleosides via Ag(I)-catalyzed addition of pronucleophiles to 9-allenyl-9H-purines.

    PubMed

    Wei, Tao; Xie, Ming-Sheng; Qu, Gui-Rong; Niu, Hong-Ying; Guo, Hai-Ming

    2014-02-01

    A new strategy to construct acyclic nucleosides with diverse side chains was developed. With Ag(I) salts as catalysts, the hydrocarboxylation, hydroamination, and hydrocarbonation reactions proceeded well, affording acyclic nucleosides in good yields (41 examples, 60-98% yields). Meanwhile, these reactions exhibited high chemoselectivities and E-selectivities. PMID:24437554

  3. The Story of a Seminar in Applied Communication. The Dag Hammarskjold Seminar on "Communication--An Essential Component in Development Work" (Uppsala, Sweden, August 27-September 9, 1972).

    ERIC Educational Resources Information Center

    Fuglesang, Andreas, Ed.

    The objective of the two week long 1972 Dag Hammarskjold Seminar was to break away from traditional and theoretical concepts of information work in order to gain a practical insight into communication, especially as it applies to social and economic development. Fifty participants and lecturers from developed and developing countries in Europe and…

  4. Evaluation of Graph Pattern Matching Workloads in Graph Analysis Systems

    SciTech Connect

    Hong, Seokyong; Sukumar, Sreenivas Rangan; Vatsavai, Raju

    2016-01-01

    Graph analysis has emerged as a powerful method for data scientists to represent, integrate, query, and explore heterogeneous data sources. As a result, graph data management and mining became a popular area of research, and led to the development of plethora of systems in recent years. Unfortunately, the number of emerging graph analysis systems and the wide range of applications, coupled with a lack of apples-to-apples comparisons, make it difficult to understand the trade-offs between different systems and the graph operations for which they are designed. A fair comparison of these systems is a challenging task for the following reasons: multiple data models, non-standardized serialization formats, various query interfaces to users, and diverse environments they operate in. To address these key challenges, in this paper we present a new benchmark suite by extending the Lehigh University Benchmark (LUBM) to cover the most common capabilities of various graph analysis systems. We provide the design process of the benchmark, which generalizes the workflow for data scientists to conduct the desired graph analysis on different graph analysis systems. Equipped with this extended benchmark suite, we present performance comparison for nine subgraph pattern retrieval operations over six graph analysis systems, namely NetworkX, Neo4j, Jena, Titan, GraphX, and uRiKA. Through the proposed benchmark suite, this study reveals both quantitative and qualitative findings in (1) implications in loading data into each system; (2) challenges in describing graph patterns for each query interface; and (3) different sensitivity of each system to query selectivity. We envision that this study will pave the road for: (i) data scientists to select the suitable graph analysis systems, and (ii) data management system designers to advance graph analysis systems.

  5. Graph Coarsening for Path Finding in Cybersecurity Graphs

    SciTech Connect

    Hogan, Emilie A.; Johnson, John R.; Halappanavar, Mahantesh

    2013-01-01

    n the pass-the-hash attack, hackers repeatedly steal password hashes and move through a computer network with the goal of reaching a computer with high level administrative privileges. In this paper we apply graph coarsening in network graphs for the purpose of detecting hackers using this attack or assessing the risk level of the network's current state. We repeatedly take graph minors, which preserve the existence of paths in the graph, and take powers of the adjacency matrix to count the paths. This allows us to detect the existence of paths as well as find paths that have high risk of being used by adversaries.

  6. Investigation of diastereoselective acyclic α-alkoxydithioacetal substitutions involving thiacarbenium intermediates.

    PubMed

    Prévost, Michel; Dostie, Starr; Waltz, Marie-Ève; Guindon, Yvan

    2014-11-01

    Reported herein is an experimental and theoretical study that elucidates why silylated nucleobase additions to acyclic α-alkoxythiacarbenium intermediates proceed with high 1,2-syn stereocontrol (anti-Felkin-Anh), which is opposite to what would be expected with corresponding activated aldehydes. The acyclic thioaminals formed undergo intramolecular cyclizations to provide nucleoside analogues with anticancer and antiviral properties. The factors influencing the selectivity of the substitution reaction have been examined thoroughly. Halothioether species initially form, ionize in the presence (low dielectric media) or absence (higher dielectric media) of the nucleophile, and react through SN2-like transition structures (TS A and D), where the α-alkoxy group is gauche to the thioether moiety. An important, and perhaps counterintuitive, observation in this work was that calculations done in the gas phase or low dielectric media (toluene) are essential to locate the product- and rate-determining transition structures (C-N bond formation) that allow the most reasonable prediction of selectivity and isotope effects for more polar solvents (THF, MeCN). The ΔΔG(⧧) (G(TSA-TSD)) obtained in silico are consistent with the preferential formation of 1,2-syn product and with the trends of stereocontrol displayed by 2,3-anti and 2,3-syn α,β-bis-alkoxydithioacetals. PMID:25280088

  7. Cactus Graphs for Genome Comparisons

    NASA Astrophysics Data System (ADS)

    Paten, Benedict; Diekhans, Mark; Earl, Dent; St. John, John; Ma, Jian; Suh, Bernard; Haussler, David

    We introduce a data structure, analysis and visualization scheme called a cactus graph for comparing sets of related genomes. Cactus graphs capture some of the advantages of de Bruijn and breakpoint graphs in one unified framework. They naturally decompose the common substructures in a set of related genomes into a hierarchy of chains that can be visualized as multiple alignments and nets that can be visualized in circular genome plots.

  8. Contact Graph Routing

    NASA Technical Reports Server (NTRS)

    Burleigh, Scott C.

    2011-01-01

    Contact Graph Routing (CGR) is a dynamic routing system that computes routes through a time-varying topology of scheduled communication contacts in a network based on the DTN (Delay-Tolerant Networking) architecture. It is designed to enable dynamic selection of data transmission routes in a space network based on DTN. This dynamic responsiveness in route computation should be significantly more effective and less expensive than static routing, increasing total data return while at the same time reducing mission operations cost and risk. The basic strategy of CGR is to take advantage of the fact that, since flight mission communication operations are planned in detail, the communication routes between any pair of bundle agents in a population of nodes that have all been informed of one another's plans can be inferred from those plans rather than discovered via dialogue (which is impractical over long one-way-light-time space links). Messages that convey this planning information are used to construct contact graphs (time-varying models of network connectivity) from which CGR automatically computes efficient routes for bundles. Automatic route selection increases the flexibility and resilience of the space network, simplifying cross-support and reducing mission management costs. Note that there are no routing tables in Contact Graph Routing. The best route for a bundle destined for a given node may routinely be different from the best route for a different bundle destined for the same node, depending on bundle priority, bundle expiration time, and changes in the current lengths of transmission queues for neighboring nodes; routes must be computed individually for each bundle, from the Bundle Protocol agent's current network connectivity model for the bundle s destination node (the contact graph). Clearly this places a premium on optimizing the implementation of the route computation algorithm. The scalability of CGR to very large networks remains a research topic

  9. Graph Visualization for RDF Graphs with SPARQL-EndPoints

    2014-07-11

    RDF graphs are hard to visualize as triples. This software module is a web interface that connects to a SPARQL endpoint and retrieves graph data that the user can explore interactively and seamlessly. The software written in python and JavaScript has been tested to work on screens as little as the smart phones to large screens such as EVEREST.

  10. Quantum Graph Analysis

    SciTech Connect

    Maunz, Peter Lukas Wilhelm; Sterk, Jonathan David; Lobser, Daniel; Parekh, Ojas D.; Ryan-Anderson, Ciaran

    2016-01-01

    In recent years, advanced network analytics have become increasingly important to na- tional security with applications ranging from cyber security to detection and disruption of ter- rorist networks. While classical computing solutions have received considerable investment, the development of quantum algorithms to address problems, such as data mining of attributed relational graphs, is a largely unexplored space. Recent theoretical work has shown that quan- tum algorithms for graph analysis can be more efficient than their classical counterparts. Here, we have implemented a trapped-ion-based two-qubit quantum information proces- sor to address these goals. Building on Sandia's microfabricated silicon surface ion traps, we have designed, realized and characterized a quantum information processor using the hyperfine qubits encoded in two 171 Yb + ions. We have implemented single qubit gates using resonant microwave radiation and have employed Gate set tomography (GST) to characterize the quan- tum process. For the first time, we were able to prove that the quantum process surpasses the fault tolerance thresholds of some quantum codes by demonstrating a diamond norm distance of less than 1 . 9 x 10 [?] 4 . We used Raman transitions in order to manipulate the trapped ions' motion and realize two-qubit gates. We characterized the implemented motion sensitive and insensitive single qubit processes and achieved a maximal process infidelity of 6 . 5 x 10 [?] 5 . We implemented the two-qubit gate proposed by Molmer and Sorensen and achieved a fidelity of more than 97 . 7%.

  11. Detecting alternative graph clusterings.

    PubMed

    Mandala, Supreet; Kumara, Soundar; Yao, Tao

    2012-07-01

    The problem of graph clustering or community detection has enjoyed a lot of attention in complex networks literature. A quality function, modularity, quantifies the strength of clustering and on maximization yields sensible partitions. However, in most real world networks, there are an exponentially large number of near-optimal partitions with some being very different from each other. Therefore, picking an optimal clustering among the alternatives does not provide complete information about network topology. To tackle this problem, we propose a graph perturbation scheme which can be used to identify an ensemble of near-optimal and diverse clusterings. We establish analytical properties of modularity function under the perturbation which ensures diversity. Our approach is algorithm independent and therefore can leverage any of the existing modularity maximizing algorithms. We numerically show that our methodology can systematically identify very different partitions on several existing data sets. The knowledge of diverse partitions sheds more light into the topological organization and helps gain a more complete understanding of the underlying complex network. PMID:23005495

  12. Detecting alternative graph clusterings

    NASA Astrophysics Data System (ADS)

    Mandala, Supreet; Kumara, Soundar; Yao, Tao

    2012-07-01

    The problem of graph clustering or community detection has enjoyed a lot of attention in complex networks literature. A quality function, modularity, quantifies the strength of clustering and on maximization yields sensible partitions. However, in most real world networks, there are an exponentially large number of near-optimal partitions with some being very different from each other. Therefore, picking an optimal clustering among the alternatives does not provide complete information about network topology. To tackle this problem, we propose a graph perturbation scheme which can be used to identify an ensemble of near-optimal and diverse clusterings. We establish analytical properties of modularity function under the perturbation which ensures diversity. Our approach is algorithm independent and therefore can leverage any of the existing modularity maximizing algorithms. We numerically show that our methodology can systematically identify very different partitions on several existing data sets. The knowledge of diverse partitions sheds more light into the topological organization and helps gain a more complete understanding of the underlying complex network.

  13. Synthesis and antiviral activity evaluation of acyclic 2'-azanucleosides bearing a phosphonomethoxy function in the side chain.

    PubMed

    Koszytkowska-Stawińska, Mariola; De Clercq, Erik; Balzarini, Jan

    2009-06-01

    Acyclic 2'-azanucleosides with a phosphonomethoxy function in the side chain were obtained by coupling of diethyl {2-[N-(pivaloyloxymethyl)-N-(p-toluenesulfonyl)amino]ethoxymethyl}phosphonate with the pyrimidine nucleobases via the Vorbrüggen-type protocol. The compounds were evaluated in vitro for activity against a broad variety of RNA and DNA viruses. PMID:19442526

  14. Anomalous Reactivity and Selectivity in the Intermolecular Diels-Alder Reactions of Multisubstituted Acyclic Dienes with Geometrical Isomers of Enals.

    PubMed

    Zhou, Jia-Hui; Cai, Sai-Hu; Xu, Yun-He; Loh, Teck-Peng

    2016-05-20

    A Lewis-acid catalyzed intermolecular Diels-Alder reaction between multisubstituted acyclic dienes and the E and Z isomers of α,β-enals was studied. It was found that the diene reacted selectively with the Z-isomer of the α,β-enal. PMID:27132468

  15. Quantization of gauge fields, graph polynomials and graph homology

    SciTech Connect

    Kreimer, Dirk; Sars, Matthias; Suijlekom, Walter D. van

    2013-09-15

    We review quantization of gauge fields using algebraic properties of 3-regular graphs. We derive the Feynman integrand at n loops for a non-abelian gauge theory quantized in a covariant gauge from scalar integrands for connected 3-regular graphs, obtained from the two Symanzik polynomials. The transition to the full gauge theory amplitude is obtained by the use of a third, new, graph polynomial, the corolla polynomial. This implies effectively a covariant quantization without ghosts, where all the relevant signs of the ghost sector are incorporated in a double complex furnished by the corolla polynomial–we call it cycle homology–and by graph homology. -- Highlights: •We derive gauge theory Feynman from scalar field theory with 3-valent vertices. •We clarify the role of graph homology and cycle homology. •We use parametric renormalization and the new corolla polynomial.

  16. Resistance of human immunodeficiency virus type 1 to acyclic 6-phenylselenenyl- and 6-phenylthiopyrimidines.

    PubMed Central

    Nguyen, M H; Schinazi, R F; Shi, C; Goudgaon, N M; McKenna, P M; Mellors, J W

    1994-01-01

    Acyclic 6-phenylselenenyl- and 6-phenylthiopyrimidine derivatives are potent and specific inhibitors of human immunodeficiency virus type 1 (HIV-1). The development of in vitro resistance to two derivatives, 5-ethyl-1-(ethoxymethyl)-(6-phenylthio)-uracil (E-EPU), was evaluated by serial passage of HIV-1 in increasing concentrations of inhibitor. HIV-1 variants exhibiting > 500-fold resistance to E-EPSeU and E-EPU were isolated after sequential passage in 1, 5, and 10 microM inhibitor. The resistant variants exhibited coresistance to related acyclic 6-substituted pyrimidines and the HIV-1-specific inhibitors (+)-(5S)-4,5,6,7-tetrahydro-5- pyrimidines and the HIV-1-specific inhibitors (+)-(5S)-4,5,6,7-tetrahydro-5- methyl-6-(3-methyl-2-butenyl)imidazo[4,5,1-jk]benzodiazepin-2(1H)- thione (TIBO R82150) and nevirapine, but remained susceptible to 3'-azido-3'-deoxythymidine, 2',3'-dideoxycytidine, 2',3'-dideoxyinosine, and phosphonoformic acid. DNA sequence analysis of reverse transcriptase (RT) derived from E-EPSeU-resistant virus identified a Tyr (TAT)-to-Cys (TGT) mutation at either codon 188 (Cys-188; 9 of 15 clones) or codon 181 (Cys-181; 5 of 15 clones). The same amino acid changes were found in RT from E-EPU-resistant virus, but the Cys-181 mutation was more common (9 of 10 clones) than the Cys-188 mutation (1 of 10 clones). Site-specific mutagenesis and production of mutant recombinant viruses demonstrated that both the Cys-181 and Cys-188 mutations cause resistance to E-EPSeU and E-EPU. Of the two mutations, the Cys-188 substitution produced greater E-EPSeU and E-EPU resistance. The predominance of the Cys-188 mutation in E-EPSeU-resistant variants has not been noted for other classes of HIV-1 specific RT inhibitors. HIV-1 resistance is likely to limit the therapeutic efficacy of acyclic 6-substituted pyrimidines if they are used as monotherapy. PMID:7840579

  17. CANCER MORTALITY MAPS AND GRAPHS

    EPA Science Inventory

    The Cancer Mortality Maps & Graph Web Site provides interactive maps, graphs (which are accessible to the blind and visually-impaired), text, tables and figures showing geographic patterns and time trends of cancer death rates for the time period 1950-1994 for more than 40 cancer...

  18. Graphs as Statements of Belief.

    ERIC Educational Resources Information Center

    Lake, David

    2002-01-01

    Identifies points where beliefs are important when making decisions about how graphs are drawn. Describes a simple case of the reaction between 'bicarb soda' and orange or lemon juice and discusses how drawing a graph becomes a statement of belief. (KHR)

  19. A PVS Graph Theory Library

    NASA Technical Reports Server (NTRS)

    Butler, Ricky W.; Sjogren, Jon A.

    1998-01-01

    This paper documents the NASA Langley PVS graph theory library. The library provides fundamental definitions for graphs, subgraphs, walks, paths, subgraphs generated by walks, trees, cycles, degree, separating sets, and four notions of connectedness. Theorems provided include Ramsey's and Menger's and the equivalence of all four notions of connectedness.

  20. Graph models of habitat mosaics.

    PubMed

    Urban, Dean L; Minor, Emily S; Treml, Eric A; Schick, Robert S

    2009-03-01

    Graph theory is a body of mathematics dealing with problems of connectivity, flow, and routing in networks ranging from social groups to computer networks. Recently, network applications have erupted in many fields, and graph models are now being applied in landscape ecology and conservation biology, particularly for applications couched in metapopulation theory. In these applications, graph nodes represent habitat patches or local populations and links indicate functional connections among populations (i.e. via dispersal). Graphs are models of more complicated real systems, and so it is appropriate to review these applications from the perspective of modelling in general. Here we review recent applications of network theory to habitat patches in landscape mosaics. We consider (1) the conceptual model underlying these applications; (2) formalization and implementation of the graph model; (3) model parameterization; (4) model testing, insights, and predictions available through graph analyses; and (5) potential implications for conservation biology and related applications. In general, and for a variety of ecological systems, we find the graph model a remarkably robust framework for applications concerned with habitat connectivity. We close with suggestions for further work on the parameterization and validation of graph models, and point to some promising analytic insights. PMID:19161432

  1. Graphs and Zero-Divisors

    ERIC Educational Resources Information Center

    Axtell, M.; Stickles, J.

    2010-01-01

    The last ten years have seen an explosion of research in the zero-divisor graphs of commutative rings--by professional mathematicians "and" undergraduates. The objective is to find algebraic information within the geometry of these graphs. This topic is approachable by anyone with one or two semesters of abstract algebra. This article gives the…

  2. A Collection of Features for Semantic Graphs

    SciTech Connect

    Eliassi-Rad, T; Fodor, I K; Gallagher, B

    2007-05-02

    Semantic graphs are commonly used to represent data from one or more data sources. Such graphs extend traditional graphs by imposing types on both nodes and links. This type information defines permissible links among specified nodes and can be represented as a graph commonly referred to as an ontology or schema graph. Figure 1 depicts an ontology graph for data from National Association of Securities Dealers. Each node type and link type may also have a list of attributes. To capture the increased complexity of semantic graphs, concepts derived for standard graphs have to be extended. This document explains briefly features commonly used to characterize graphs, and their extensions to semantic graphs. This document is divided into two sections. Section 2 contains the feature descriptions for static graphs. Section 3 extends the features for semantic graphs that vary over time.

  3. A parallel graph coloring heuristic

    SciTech Connect

    Jones, M.T.; Plassmann, P.E. )

    1993-05-01

    The problem of computing good graph colorings arises in many diverse applications, such as in the estimation of sparse Jacobians and in the development of efficient, parallel iterative methods for solving sparse linear systems. This paper presents an asynchronous graph coloring heuristic well suited to distributed memory parallel computers. Experimental results obtained on an Intel iPSC/860 are presented, which demonstrate that, for graphs arising from finite element applications, the heuristic exhibits scalable performance and generates colorings usually within three or four colors of the best-known linear time sequential heuristics. For bounded degree graphs, it is shown that the expected running time of the heuristic under the P-Ram computation model is bounded by EO(log(n)/log log(n)). This bound is an improvement over the previously known best upper bound for the expected running time of a random heuristic for the graph coloring problem.

  4. Semi-Markov Graph Dynamics

    PubMed Central

    Raberto, Marco; Rapallo, Fabio; Scalas, Enrico

    2011-01-01

    In this paper, we outline a model of graph (or network) dynamics based on two ingredients. The first ingredient is a Markov chain on the space of possible graphs. The second ingredient is a semi-Markov counting process of renewal type. The model consists in subordinating the Markov chain to the semi-Markov counting process. In simple words, this means that the chain transitions occur at random time instants called epochs. The model is quite rich and its possible connections with algebraic geometry are briefly discussed. Moreover, for the sake of simplicity, we focus on the space of undirected graphs with a fixed number of nodes. However, in an example, we present an interbank market model where it is meaningful to use directed graphs or even weighted graphs. PMID:21887245

  5. Graph Partitioning and Sequencing Software

    1995-09-19

    Graph partitioning is a fundemental problem in many scientific contexts. CHACO2.0 is a software package designed to partition and sequence graphs. CHACO2.0 allows for recursive application of several methods for finding small edge separators in weighted graphs. These methods include inertial, spectral, Kernighan Lin and multilevel methods in addition to several simpler strategies. Each of these approaches can be used to partition the graph into two, four, or eight pieces at each level of recursion.more » In addition, the Kernighan Lin method can be used to improve partitions generated by any of the other algorithms. CHACO2.0 can also be used to address various graph sequencing problems, with applications to scientific computing, database design, gene sequencing and other problems.« less

  6. Reduced expression of CDP-DAG synthase changes lipid composition and leads to male sterility in Drosophila

    PubMed Central

    Laurinyecz, Barbara; Péter, Mária; Vedelek, Viktor; Kovács, Attila L.; Juhász, Gábor; Maróy, Péter; Vígh, László; Balogh, Gábor; Sinka, Rita

    2016-01-01

    Drosophila spermatogenesis is an ideal system to study the effects of changes in lipid composition, because spermatid elongation and individualization requires extensive membrane biosynthesis and remodelling. The bulk of transcriptional activity is completed with the entry of cysts into meiotic division, which makes post-meiotic stages of spermatogenesis very sensitive to even a small reduction in gene products. In this study, we describe the effect of changes in lipid composition during spermatogenesis using a hypomorphic male sterile allele of the Drosophila CDP-DAG synthase (CdsA) gene. We find that the CdsA mutant shows defects in spermatid individualization and enlargement of mitochondria and the axonemal sheath of the spermatids. Furthermore, we could genetically rescue the male sterile phenotype by overexpressing Phosphatidylinositol synthase (dPIS) in a CdsA mutant background. The results of lipidomic and genetic analyses of the CdsA mutant highlight the importance of correct lipid composition during sperm development and show that phosphatidic acid levels are crucial in late stages of spermatogenesis. PMID:26791243

  7. Graph hierarchies for phylogeography.

    PubMed

    Cybis, Gabriela B; Sinsheimer, Janet S; Lemey, Philippe; Suchard, Marc A

    2013-03-19

    Bayesian phylogeographic methods simultaneously integrate geographical and evolutionary modelling, and have demonstrated value in assessing spatial spread patterns of measurably evolving organisms. We improve on existing phylogeographic methods by combining information from multiple phylogeographic datasets in a hierarchical setting. Consider N exchangeable datasets or strata consisting of viral sequences and locations, each evolving along its own phylogenetic tree and according to a conditionally independent geographical process. At the hierarchical level, a random graph summarizes the overall dispersion process by informing which migration rates between sampling locations are likely to be relevant in the strata. This approach provides an efficient and improved framework for analysing inherently hierarchical datasets. We first examine the evolutionary history of multiple serotypes of dengue virus in the Americas to showcase our method. Additionally, we explore an application to intrahost HIV evolution across multiple patients. PMID:23382428

  8. Diversity-oriented synthesis of acyclic nucleosides via ring-opening of vinyl cyclopropanes with purines.

    PubMed

    Niu, Hong-Ying; Du, Cong; Xie, Ming-Sheng; Wang, Yong; Zhang, Qian; Qu, Gui-Rong; Guo, Hai-Ming

    2015-02-25

    The diversity-oriented synthesis of acyclic nucleosides has been achieved via ring-opening of vinyl cyclopropanes with purines. With Pd2(dba)3·CHCl3 as a catalyst, the 1,5-ring-opening reaction proceeded well and afforded N9 adducts as the major form, in which the C=C bonds in the side chain were exclusively E-form. In the presence of AlCl3, the 1,3-ring-opening reaction occurred smoothly, giving N9 adducts as the dominate products. Meanwhile, when MgI2 was used as the catalyst, the 1,3-ring-opening reaction also worked well to form N7 adducts. PMID:25572827

  9. Antimalarial activity of prodrugs of N-branched acyclic nucleoside phosphonate inhibitors of 6-oxopurine phosphoribosyltransferases.

    PubMed

    Hocková, Dana; Janeba, Zlatko; Naesens, Lieve; Edstein, Michael D; Chavchich, Marina; Keough, Dianne T; Guddat, Luke W

    2015-09-01

    Acyclic nucleoside phosphonates (ANPs) that contain a 6-oxopurine base are good inhibitors of the human and Plasmodium falciparum 6-oxopurine phosphoribosyltransferases (PRTs), key enzymes of the purine salvage pathway. Chemical modifications, based on the crystal structures of several inhibitors in complex with the human PRTase, led to the design of a new class of inhibitors--the aza-ANPs. Because of the negative charges of the phosphonic acid moiety, their ability to cross cell membranes is, however, limited. Thus, phosphoramidate prodrugs of the aza-ANPs were prepared to improve permeability. These prodrugs arrest parasitemia with IC50 values in the micromolar range against Plasmodium falciparum-infected erythrocyte cultures (both chloroquine-sensitive and chloroquine-resistant Pf strains). The prodrugs exhibit low cytotoxicity in several human cell lines. Thus, they fulfill two essential criteria to qualify them as promising antimalarial drug leads. PMID:26275679

  10. Molecular Motion of the Junction Points in Model Networks Prepared by Acyclic Triene Metathesis.

    PubMed

    da Silva, Lucas Caire; Bowers, Clifford R; Graf, Robert; Wagener, Kenneth B

    2016-03-01

    The junction dynamics in a selectively deuterated model polymer network containing junctions on every 21st chain carbon is studied by solid state (2) H echo NMR. Polymer networks are prepared via acyclic triene metathesis of deuteron-labeled symmetric trienes with deuteron probes precisely placed at the alpha carbon relative to the junction point. The effect of decreasing the cross-link density on the junction dynamics is studied by introduction of polybutadiene chains in-between junctions. The networks are characterized by swelling, gel content, and solid state (1) H MAS NMR. Line shape analysis of the (2) H quadrupolar echo spectra reveals that the degree of motion anisotropy and the distribution of motion correlation times depend on the cross-link density and structural heterogeneity of the polymer networks. A detailed model of the junction dynamics at different temperatures is proposed and explained in terms of the intermolecular cooperativity in densely-packed systems. PMID:26787457

  11. The Acyclic Retinoid Peretinoin Inhibits Hepatitis C Virus Replication and Infectious Virus Release in Vitro

    NASA Astrophysics Data System (ADS)

    Shimakami, Tetsuro; Honda, Masao; Shirasaki, Takayoshi; Takabatake, Riuta; Liu, Fanwei; Murai, Kazuhisa; Shiomoto, Takayuki; Funaki, Masaya; Yamane, Daisuke; Murakami, Seishi; Lemon, Stanley M.; Kaneko, Shuichi

    2014-04-01

    Clinical studies suggest that the oral acyclic retinoid Peretinoin may reduce the recurrence of hepatocellular carcinoma (HCC) following surgical ablation of primary tumours. Since hepatitis C virus (HCV) infection is a major cause of HCC, we assessed whether Peretinoin and other retinoids have any effect on HCV infection. For this purpose, we measured the effects of several retinoids on the replication of genotype 1a, 1b, and 2a HCV in vitro. Peretinoin inhibited RNA replication for all genotypes and showed the strongest antiviral effect among the retinoids tested. Furthermore, it reduced infectious virus release by 80-90% without affecting virus assembly. These effects could be due to reduced signalling from lipid droplets, triglyceride abundance, and the expression of mature sterol regulatory element-binding protein 1c and fatty acid synthase. These negative effects of Peretinoin on HCV infection may be beneficial in addition to its potential for HCC chemoprevention in HCV-infected patients.

  12. Halogen bonding in water results in enhanced anion recognition in acyclic and rotaxane hosts.

    PubMed

    Langton, Matthew J; Robinson, Sean W; Marques, Igor; Félix, Vítor; Beer, Paul D

    2014-12-01

    Halogen bonding (XB), the attractive interaction between an electron-deficient halogen atom and a Lewis base, has undergone a dramatic development as an intermolecular force analogous to hydrogen bonding (HB). However, its utilization in the solution phase remains underdeveloped. Furthermore, the design of receptors capable of strong and selective recognition of anions in water remains a significant challenge. Here we demonstrate the superiority of halogen bonding over hydrogen bonding for strong anion binding in water, to the extent that halide recognition by a simple acyclic mono-charged receptor is achievable. Quantification of iodide binding by rotaxane hosts reveals the strong binding by the XB-rotaxane is driven exclusively by favourable enthalpic contributions arising from the halogen-bonding interactions, whereas weaker association with the HB-rotaxanes is entropically driven. These observations demonstrate the unique nature of halogen bonding in water as a strong alternative interaction to the ubiquitous hydrogen bonding in molecular recognition and assembly. PMID:25411880

  13. Generation and exploitation of acyclic azomethine imines in chiral Brønsted acid catalysis

    NASA Astrophysics Data System (ADS)

    Hashimoto, Takuya; Kimura, Hidenori; Kawamata, Yu; Maruoka, Keiji

    2011-08-01

    Successful implementation of a catalytic asymmetric synthesis strategy to produce enantiomerically enriched compounds requires the adoption of suitable prochiral substrates. The combination of an azomethine imine electrophile with various nucleophiles could give straightforward access to a number of synthetically useful chiral hydrazines, but is used rarely. Here we report the exploitation of acyclic azomethine imines as a new type of prochiral electrophile. They can be generated in situ by the condensation of N‧-benzylbenzoylhydrazide with a variety of aldehydes in the presence of a catalytic amount of an axially chiral dicarboxylic acid. By trapping these electrophiles with alkyl diazoacetate or (diazomethyl)phosphonate nucleophiles, we produced a diverse array of chiral α-diazo-β-hydrazino esters and phosphonates with excellent enantioselectivities.

  14. Versatile synthesis of oxime-containing acyclic nucleoside phosphonates--synthetic solutions and antiviral activity.

    PubMed

    Solyev, Pavel N; Jasko, Maxim V; Kleymenova, Alla A; Kukhanova, Marina K; Kochetkov, Sergey N

    2015-11-28

    New oxime-containing acyclic nucleoside phosphonates 9-{2-[(phosphonomethyl)oximino]ethyl}adenine (1), -guanine (2) and 9-{2-[(phosphonomethyl)oximino]propyl}adenine (3) with wide spectrum activity against different types of viruses were synthesized. The key intermediate, diethyl aminooxymethylphosphonate, was obtained by the Mitsunobu reaction. Modified conditions for the by-product separation (without chromatography and distillation) allowed us to obtain 85% yield of the aminooxy intermediate. The impact of DBU and Cs2CO3 on the N(9)/N(7) product ratio for adenine and guanine alkylation was studied. A convenient procedure for aminooxy group detection was found. The synthesized phosphonates were tested and they appeared to display moderate activity against different types of viruses (HIV, herpes viruses in cell cultures, and hepatitis C virus in the replicon system) without toxicity up to 1000 μM. PMID:26383895

  15. Acyclic N-halamine-immobilized polyurethane: Preparation and antimicrobial and biofilm-controlling functions

    PubMed Central

    Luo, Jie; Porteous, Nuala; Lin, Jiajin; Sun, Yuyu

    2015-01-01

    Hydroxyl groups were introduced onto polyurethane surfaces through 1,6-hexamethylene diisocyanate activation, followed by diethanolamine hydroxylation. Polymethacrylamide was covalently attached to the hydroxylated polyurethane through surface grafting polymerization of methacrylamide using cerium (IV) ammonium nitrate as an initiator. After bleach treatment, the amide groups of the covalently bound polymethacrylamide chains were transformed into N-halamines. The new N-halamine-immobilized polyurethane provided a total sacrifice of 107–108 colony forming units per milliliter of Staphylococcus aureus (Gram-positive bacteria), Escherichia coli (Gram-negative bacteria), and Candida albicans (fungi) within 10 min and successfully prevented bacterial and fungal biofilm formation. The antimicrobial and biofilm-controlling effects were both durable and rechargeable, pointing to great potentials of the new acyclic N-halamine-immobilized polyurethane for a broad range of related applications. PMID:26089593

  16. Acyclic Immucillin Phosphonates. Second-Generation Inhibitors of Plasmodium falciparum Hypoxanthine- Guanine-Xanthine Phosphoribosyltransferase

    SciTech Connect

    Hazelton, Keith Z.; Ho, Meng-Chaio; Cassera, Maria B.; Clinch, Keith; Crump, Douglas R.; Rosario Jr., Irving; Merino, Emilio F.; Almo, Steve C.; Tyler, Peter C.; Schramm, Vern L.

    2012-06-22

    We found that Plasmodium falciparum is the primary cause of deaths from malaria. It is a purine auxotroph and relies on hypoxanthine salvage from the host purine pool. Purine starvation as an antimalarial target has been validated by inhibition of purine nucleoside phosphorylase. Hypoxanthine depletion kills Plasmodium falciparum in cell culture and in Aotus monkey infections. Hypoxanthine-guanine-xanthine phosphoribosyltransferase (HGXPRT) from P. falciparum is required for hypoxanthine salvage by forming inosine 5'-monophosphate, a branchpoint for all purine nucleotide synthesis in the parasite. We present a class of HGXPRT inhibitors, the acyclic immucillin phosphonates (AIPs), and cell permeable AIP prodrugs. The AIPs are simple, potent, selective, and biologically stable inhibitors. The AIP prodrugs block proliferation of cultured parasites by inhibiting the incorporation of hypoxanthine into the parasite nucleotide pool and validates HGXPRT as a target in malaria.

  17. Acyclic hydrocarbon environments ⩾ n-C 18 on the early terrestrial planets

    NASA Astrophysics Data System (ADS)

    Marcano, Vicente; Benitez, Pedro; Palacios-Prü, Ernesto

    2003-03-01

    The possible occurrence on the surface of the early Earth, Mars and Venus of hydrocarbon environments mainly composed by acyclic alkane molecules ⩾ n-C 18 has been revised. These hydrocarbons could be accumulated from the contribution of endogenous Fischer-Tropsh-type reactions and post-impact recombination reactions, as well as from exogenous sources such as comets, meteorites and dust particles. Such heavy alkane environments could offer protection for the synthesis and survival of biomolecules on the early terrestrial planets. Amounts of heavy n-alkanes delivered by large impactors, dust particles or produced by post-impact recombination on Venus would have been higher than those delivered or produced by the same sources on Earth and Mars before 3600 Myr ago. However, the high values of the total frequency of impacts by bolides >14-km in diameter estimated in this time period (viz. 3.9×10 3, Mars; 2.2×10 4, Earth, and 3.8×10 4 Venus) and the high surface temperatures generated by those impactors suggest the existence of very unstable conditions on the early terrestrial planets for the survival and long-term accumulation of acyclic hydrocarbons. Therefore, the most significant accumulation of n-alkanes could have occurred only during the longer intervals (10 5- 10 7 yr) between each impact through the contribution mainly of IDPs, and thereby a high decomposition rate would be expected for the accumulated n-alkanes by successive impacts. Amounts of n-alkanes accumulated from IDPs in these intervals have been estimated between 2.3×10 9 and 2.2×10 10 kg 3600- 3800 Myr ago. These processes are expected to occur on other planetary bodies or satellites belonging to our solar system and probably in analogs of the early solar system.

  18. Flying through Graphs: An Introduction to Graph Theory.

    ERIC Educational Resources Information Center

    McDuffie, Amy Roth

    2001-01-01

    Presents an activity incorporating basic terminology, concepts, and solution methods of graph theory in the context of solving problems related to air travel. Discusses prerequisite knowledge and resources and includes a teacher's guide with a student worksheet. (KHR)

  19. Multigraph: Reusable Interactive Data Graphs

    NASA Astrophysics Data System (ADS)

    Phillips, M. B.

    2010-12-01

    There are surprisingly few good software tools available for presenting time series data on the internet. The most common practice is to use a desktop program such as Excel or Matlab to save a graph as an image which can be included in a web page like any other image. This disconnects the graph from the data in a way that makes updating a graph with new data a cumbersome manual process, and it limits the user to one particular view of the data. The Multigraph project defines an XML format for describing interactive data graphs, and software tools for creating and rendering those graphs in web pages and other internet connected applications. Viewing a Multigraph graph is extremely simple and intuitive, and requires no instructions; the user can pan and zoom by clicking and dragging, in a familiar "Google Maps" kind of way. Creating a new graph for inclusion in a web page involves writing a simple XML configuration file. Multigraph can read data in a variety of formats, and can display data from a web service, allowing users to "surf" through large data sets, downloading only those the parts of the data that are needed for display. The Multigraph XML format, or "MUGL" for short, provides a concise description of the visual properties of a graph, such as axes, plot styles, data sources, labels, etc, as well as interactivity properties such as how and whether the user can pan or zoom along each axis. Multigraph reads a file in this format, draws the described graph, and allows the user to interact with it. Multigraph software currently includes a Flash application for embedding graphs in web pages, a Flex component for embedding graphs in larger Flex/Flash applications, and a plugin for creating graphs in the WordPress content management system. Plans for the future include a Java version for desktop viewing and editing, a command line version for batch and server side rendering, and possibly Android and iPhone versions. Multigraph is currently in use on several web

  20. n-Nucleotide circular codes in graph theory.

    PubMed

    Fimmel, Elena; Michel, Christian J; Strüngmann, Lutz

    2016-03-13

    The circular code theory proposes that genes are constituted of two trinucleotide codes: the classical genetic code with 61 trinucleotides for coding the 20 amino acids (except the three stop codons {TAA,TAG,TGA}) and a circular code based on 20 trinucleotides for retrieving, maintaining and synchronizing the reading frame. It relies on two main results: the identification of a maximal C(3) self-complementary trinucleotide circular code X in genes of bacteria, eukaryotes, plasmids and viruses (Michel 2015 J. Theor. Biol. 380, 156-177. (doi:10.1016/j.jtbi.2015.04.009); Arquès & Michel 1996 J. Theor. Biol. 182, 45-58. (doi:10.1006/jtbi.1996.0142)) and the finding of X circular code motifs in tRNAs and rRNAs, in particular in the ribosome decoding centre (Michel 2012 Comput. Biol. Chem. 37, 24-37. (doi:10.1016/j.compbiolchem.2011.10.002); El Soufi & Michel 2014 Comput. Biol. Chem. 52, 9-17. (doi:10.1016/j.compbiolchem.2014.08.001)). The univerally conserved nucleotides A1492 and A1493 and the conserved nucleotide G530 are included in X circular code motifs. Recently, dinucleotide circular codes were also investigated (Michel & Pirillo 2013 ISRN Biomath. 2013, 538631. (doi:10.1155/2013/538631); Fimmel et al. 2015 J. Theor. Biol. 386, 159-165. (doi:10.1016/j.jtbi.2015.08.034)). As the genetic motifs of different lengths are ubiquitous in genes and genomes, we introduce a new approach based on graph theory to study in full generality n-nucleotide circular codes X, i.e. of length 2 (dinucleotide), 3 (trinucleotide), 4 (tetranucleotide), etc. Indeed, we prove that an n-nucleotide code X is circular if and only if the corresponding graph [Formula: see text] is acyclic. Moreover, the maximal length of a path in [Formula: see text] corresponds to the window of nucleotides in a sequence for detecting the correct reading frame. Finally, the graph theory of tournaments is applied to the study of dinucleotide circular codes. It has full equivalence between the combinatorics

  1. Mineralogical and Geochemical Analysis of Howardite DaG 779: understanding geological evolution of asteroid (4) Vesta

    NASA Astrophysics Data System (ADS)

    Marcel Müller, Christian; Mengel, Kurt; Singh Thangjam, Guneshwar; Weckwerth, Gerd

    2016-04-01

    The HED meteorites, a clan of stony achondrites, are believed to originate from asteroid (4) Vesta (e.g. Mittlefehldt et al. (2015)). Recent evolution models (e.g. Toplis et al. (2013)) and observations from Dawn spacecraft data (e.g., Prettyman et al. (2013)) indicate that diogenites form the lower crust and uppermost mantle of (4) Vesta. Deep seated material excavated by large impacts such as the Rheasilvia- and Veneneiaforming event should be present in howardites. We analysed a slice of howardite DaG 779 which had been recovered from the Libyan Desert in 1999 and was briefly described by Grossmann (2000). The data presented here include electron microprobe, bulk-rock XRD and XRF as well as trace element analysis by ICP-MS and INA. The petrographic results confirm earlier observations that DaG 779 is polymict and mainly contains diogenite and eucrite clasts. Mass balance calculations using bulk-rock and microprobe major element data reveal a modal mineralogy of 77% orthopyroxene, 8% plagioclase, 7% clinopyroxene and 2% spinels, the rest being olivine, SiO2-phases, sulphides, and native Fe(Ni). When compared with the element compilation recently reported by Mittlefehldt (2015) the 39 trace element analysed here (including REE and PGE) confirm that this howardite is clearly dominated by diogenite. Beside the modal petrographic information, a number of more detailed observations obtained from microprobe investigations reveal fresh and recrystallized glasses, troilite-orthopyroxene symplectites from a mixed silicate-sulphide melt giving rise to graphic intergrowths as well as vermicular and reticular FeS in highly disrupted clasts. While the origin of the FeS in these clasts is not clear yet, its particular shape and distribution indicates that this mineral has been (partially) molten and recrystallized from a sulphide melt. The silicate minerals around these FeS occurrences are recrystallized but there is no indication for a partial silicate melt. Further

  2. Evolutionary games on graphs

    NASA Astrophysics Data System (ADS)

    Szabó, György; Fáth, Gábor

    2007-07-01

    Game theory is one of the key paradigms behind many scientific disciplines from biology to behavioral sciences to economics. In its evolutionary form and especially when the interacting agents are linked in a specific social network the underlying solution concepts and methods are very similar to those applied in non-equilibrium statistical physics. This review gives a tutorial-type overview of the field for physicists. The first four sections introduce the necessary background in classical and evolutionary game theory from the basic definitions to the most important results. The fifth section surveys the topological complications implied by non-mean-field-type social network structures in general. The next three sections discuss in detail the dynamic behavior of three prominent classes of models: the Prisoner's Dilemma, the Rock-Scissors-Paper game, and Competing Associations. The major theme of the review is in what sense and how the graph structure of interactions can modify and enrich the picture of long term behavioral patterns emerging in evolutionary games.

  3. Stacked graphs--geometry & aesthetics.

    PubMed

    Byron, Lee; Wattenberg, Martin

    2008-01-01

    In February 2008, the New York Times published an unusual chart of box office revenues for 7500 movies over 21 years. The chart was based on a similar visualization, developed by the first author, that displayed trends in music listening. This paper describes the design decisions and algorithms behind these graphics, and discusses the reaction on the Web. We suggest that this type of complex layered graph is effective for displaying large data sets to a mass audience. We provide a mathematical analysis of how this layered graph relates to traditional stacked graphs and to techniques such as ThemeRiver, showing how each method is optimizing a different "energy function". Finally, we discuss techniques for coloring and ordering the layers of such graphs. Throughout the paper, we emphasize the interplay between considerations of aesthetics and legibility. PMID:18988970

  4. Graph anomalies in cyber communications

    SciTech Connect

    Vander Wiel, Scott A; Storlie, Curtis B; Sandine, Gary; Hagberg, Aric A; Fisk, Michael

    2011-01-11

    Enterprises monitor cyber traffic for viruses, intruders and stolen information. Detection methods look for known signatures of malicious traffic or search for anomalies with respect to a nominal reference model. Traditional anomaly detection focuses on aggregate traffic at central nodes or on user-level monitoring. More recently, however, traffic is being viewed more holistically as a dynamic communication graph. Attention to the graph nature of the traffic has expanded the types of anomalies that are being sought. We give an overview of several cyber data streams collected at Los Alamos National Laboratory and discuss current work in modeling the graph dynamics of traffic over the network. We consider global properties and local properties within the communication graph. A method for monitoring relative entropy on multiple correlated properties is discussed in detail.

  5. Constructing Dense Graphs with Unique Hamiltonian Cycles

    ERIC Educational Resources Information Center

    Lynch, Mark A. M.

    2012-01-01

    It is not difficult to construct dense graphs containing Hamiltonian cycles, but it is difficult to generate dense graphs that are guaranteed to contain a unique Hamiltonian cycle. This article presents an algorithm for generating arbitrarily large simple graphs containing "unique" Hamiltonian cycles. These graphs can be turned into dense graphs…

  6. Finding long cycles in graphs

    NASA Astrophysics Data System (ADS)

    Marinari, Enzo; Semerjian, Guilhem; van Kerrebroeck, Valery

    2007-06-01

    We analyze the problem of discovering long cycles inside a graph. We propose and test two algorithms for this task. The first one is based on recent advances in statistical mechanics and relies on a message passing procedure. The second follows a more standard Monte Carlo Markov chain strategy. Special attention is devoted to Hamiltonian cycles of (nonregular) random graphs of minimal connectivity equal to 3.

  7. Zeta functions of quantum graphs

    NASA Astrophysics Data System (ADS)

    Harrison, J. M.; Kirsten, K.

    2011-06-01

    In this paper, we construct zeta functions of quantum graphs using a contour integral technique based on the argument principle. We start by considering the special case of the star graph with Neumann matching conditions at the center of the star. We then extend the technique to allow any matching conditions at the center for which the Laplace operator is self-adjoint and finally obtain an expression for the zeta function of any graph with general vertex matching conditions. In the process, it is convenient to work with new forms for the secular equation of a quantum graph that extend the well-known secular equation of the Neumann star graph. In the second half of this paper, we apply the zeta function to obtain new results for the spectral determinant, vacuum energy and heat kernel coefficients of quantum graphs. These have all been topics of current research in their own right and in each case this unified approach significantly expands results in the literature.

  8. Uptake of Hydrocarbons in Aqueous Solution by Encapsulation in Acyclic Cucurbit[n]uril-Type Molecular Containers.

    PubMed

    Lu, Xiaoyong; Isaacs, Lyle

    2016-07-01

    The ability of two water-soluble acyclic cucurbit[n]uril (CB[n]) type containers, whose hydrophobic cavity is defined by a glycoluril tetramer backbone and terminal aromatic (benzene, naphthalene) sidewalls, to act as solubilizing agents for hydrocarbons in water is described. (1) H NMR spectroscopy studies and phase-solubility diagrams establish that the naphthalene-walled container performs as well as, or better than, CB[7] and CB[8] in promoting the uptake of poorly soluble hydrocarbons into aqueous solution through formation of host-hydrocarbon complexes. The naphthalene-walled acyclic CB[n] container is able to extract large hydrocarbons from crude oil into aqueous solution. PMID:27169688

  9. Dual Catalysis Using Boronic Acid and Chiral Amine: Acyclic Quaternary Carbons via Enantioselective Alkylation of Branched Aldehydes with Allylic Alcohols.

    PubMed

    Mo, Xiaobin; Hall, Dennis G

    2016-08-31

    A ferrocenium boronic acid salt activates allylic alcohols to generate transient carbocations that react with in situ-generated chiral enamines from branched aldehydes. The optimized conditions afford the desired acyclic products embedding a methyl-aryl quaternary carbon center with up to 90% yield and 97:3 enantiomeric ratio, with only water as the byproduct. This noble-metal-free method complements alternative methods that are incompatible with carbon-halogen bonds and other sensitive functional groups. PMID:27518200

  10. Investigating temporary acyclicity in a captive group of Asian elephants (Elephas maximus): Relationship between management, adrenal activity and social factors.

    PubMed

    Edwards, Katie L; Trotter, Jessica; Jones, Martin; Brown, Janine L; Steinmetz, Hanspeter W; Walker, Susan L

    2016-01-01

    Routine faecal steroid monitoring has been used to aid the management of five captive Asian elephant (Elephas maximus) females at Chester Zoo, UK, since 2007. Progestagen analysis initially revealed synchronised oestrous cycles among all females. However, a 14- to 20-week period of temporary acyclicity subsequently occurred in three females, following several management changes (increased training, foot-care and intermittent matriarch removal for health reasons) and the initiation of pregnancy in another female. The aim of this study was to retrospectively investigate whether these management changes were related to increased adrenal activity and disruption of ovarian activity, or whether social factors may have been involved in the temporary cessation of cyclicity. Faecal samples collected every other day were analysed to investigate whether glucocorticoid metabolites were related to reproductive status (pregnant, cycling, acyclic) or management (training, foot-care, matriarch presence). Routine training and foot-care were not associated with adrenal activity; however, intensive foot-care to treat an abscess in one female was associated with increased glucocorticoid concentration. Matriarch presence influenced adrenal activity in three females, being lower when the matriarch was separated from the group at night compared to being always present. However, in the females that exhibited temporary acyclicity, there was no consistent relationship between glucocorticoids and cyclicity state. Although the results of this study do not fully explain this occurrence, the highly synchronised nature of oestrous cycles within this group, and the concurrent acyclicity in three females, raises the question of whether social factors could have been involved in the temporary disruption of ovarian activity. PMID:26393308

  11. Iterative Coupling of Two Different Enones by Nitromethane Using Bifunctional Thiourea Organocatalysts. Stereocontrolled Assembly of Cyclic and Acyclic Structures.

    PubMed

    Varga, Szilárd; Jakab, Gergely; Csámpai, Antal; Soós, Tibor

    2015-09-18

    An organocatalytic iterative assembly line has been developed in which nitromethane was sequentially coupled with two different enones using a combination of pseudoenantiomeric cinchona-based thiourea catalysts. Application of unsaturated aldehydes and ketones in the second step of the iterative sequence allows the construction of cyclic syn-ketols and acyclic compounds with multiple contiguous stereocenters. The combination of the multifunctional substrates and ambident electrophiles rendered some organocatalytic transformations possible that have not yet been realized in bifunctional noncovalent organocatalysis. PMID:26301563

  12. Khovanov homology of graph-links

    SciTech Connect

    Nikonov, Igor M

    2012-08-31

    Graph-links arise as the intersection graphs of turning chord diagrams of links. Speaking informally, graph-links provide a combinatorial description of links up to mutations. Many link invariants can be reformulated in the language of graph-links. Khovanov homology, a well-known and useful knot invariant, is defined for graph-links in this paper (in the case of the ground field of characteristic two). Bibliography: 14 titles.

  13. Transition state analogue inhibitors of human methylthioadenosine phosphorylase and bacterial methylthioadenosine/S-adenosylhomocysteine nucleosidase incorporating acyclic ribooxacarbenium ion mimics

    PubMed Central

    Clinch, Keith; Evans, Gary B.; Fröhlich, Richard F. G.; Gulab, Shivali A.; Gutierrez, Jemy A.; Mason, Jennifer M.; Schramm, Vern L.; Tyler, Peter C.; Woolhouse, Anthony D.

    2012-01-01

    Several acyclic hydroxy-methylthio-amines with 3 to 5 carbon atoms were prepared and coupled via a methylene link to 9-deazaadenine. The products were tested for inhibition against human MTAP and E. coli and N. meningitidis MTANs and gave Ki values as low as 0.23 nM. These results were compared to those obtained with 1st and 2nd generation inhibitors (1S)-1-(9-deazaadenin-9-yl)-1,4-dideoxy-1,4-imino-5-methylthio-d-ribitol (MT-Immucillin-A, 3) and (3R,4S)-1-[9-deazaadenin-9-yl)methyl]3-hydroxy-4-methylthiomethylpyrrolidine (MT-DADMe-Immucillin-A, 4). The best inhibitors were found to exhibit binding affinities of approximately 2- to 4-fold those of 3 but were significantly weaker than 4. Cleavage of the 2,3 carbon–carbon bond in MT-Immucillin-A (3) gave an acyclic product (79) with a 21,500 fold loss of activity against E. coli MTAN. In another case, N-methylation of a side chain secondary amine resulted in a 250-fold loss of activity against the same enzyme [(±)-65 vs (±)-68]. The inhibition results were also contrasted with those acyclic derivatives previously prepared as inhibitors for a related enzyme, purine nucleoside phosphorylase (PNP), where some inhibitors in the latter case were found to be more potent than their cyclic counterparts. PMID:22854195

  14. Private Graphs - Access Rights on Graphs for Seamless Navigation

    NASA Astrophysics Data System (ADS)

    Dorner, W.; Hau, F.; Pagany, R.

    2016-06-01

    After the success of GNSS (Global Navigational Satellite Systems) and navigation services for public streets, indoor seems to be the next big development in navigational services, relying on RTLS - Real Time Locating Services (e.g. WIFI) and allowing seamless navigation. In contrast to navigation and routing services on public streets, seamless navigation will cause an additional challenge: how to make routing data accessible to defined users or restrict access rights for defined areas or only to parts of the graph to a defined user group? The paper will present case studies and data from literature, where seamless and especially indoor navigation solutions are presented (hospitals, industrial complexes, building sites), but the problem of restricted access rights was only touched from a real world, but not a technical perspective. The analysis of case studies will show, that the objective of navigation and the different target groups for navigation solutions will demand well defined access rights and require solutions, how to make only parts of a graph to a user or application available to solve a navigational task. The paper will therefore introduce the concept of private graphs, which is defined as a graph for navigational purposes covering the street, road or floor network of an area behind a public street and suggest different approaches how to make graph data for navigational purposes available considering access rights and data protection, privacy and security issues as well.

  15. Subvoxel accurate graph search using non-Euclidean graph space.

    PubMed

    Abràmoff, Michael D; Wu, Xiaodong; Lee, Kyungmoo; Tang, Li

    2014-01-01

    Graph search is attractive for the quantitative analysis of volumetric medical images, and especially for layered tissues, because it allows globally optimal solutions in low-order polynomial time. However, because nodes of graphs typically encode evenly distributed voxels of the volume with arcs connecting orthogonally sampled voxels in Euclidean space, segmentation cannot achieve greater precision than a single unit, i.e. the distance between two adjoining nodes, and partial volume effects are ignored. We generalize the graph to non-Euclidean space by allowing non-equidistant spacing between nodes, so that subvoxel accurate segmentation is achievable. Because the number of nodes and edges in the graph remains the same, running time and memory use are similar, while all the advantages of graph search, including global optimality and computational efficiency, are retained. A deformation field calculated from the volume data adaptively changes regional node density so that node density varies with the inverse of the expected cost. We validated our approach using optical coherence tomography (OCT) images of the retina and 3-D MR of the arterial wall, and achieved statistically significant increased accuracy. Our approach allows improved accuracy in volume data acquired with the same hardware, and also, preserved accuracy with lower resolution, more cost-effective, image acquisition equipment. The method is not limited to any specific imaging modality and readily extensible to higher dimensions. PMID:25314272

  16. Sharing Teaching Ideas: Graphing Families of Curves Using Transformations of Reference Graphs

    ERIC Educational Resources Information Center

    Kukla, David

    2007-01-01

    This article provides for a fast extremely accurate approach to graphing functions that is based on learning function reference graphs and then applying algebraic transformations to these reference graphs.

  17. Airborne Conflict Management within Confined Airspace in a Piloted Simulation of DAG-TM Autonomous Aircraft Operations

    NASA Technical Reports Server (NTRS)

    Barmore, Bryan; Johnson, Edward; Wing, David J.; Barhydt, Richard

    2003-01-01

    A human-in-the-loop experiment was performed at the NASA Langley Research Center to study the feasibility of Distributed Air/Ground Traffic Management (DAG-TM) autonomous aircraft operations in highly constrained airspace. The airspace was constrained by a pair of special use airspace (SUA) regions on either side of the pilot s planned route. The available airspace was further varied by changing the separation standard for lateral separation between 3 nm and 5 nm. The pilot had to maneuver through the corridor between the SUA s, avoid other traffic and meet flow management constraints. Traffic flow management (TFM) constraints were imposed as a required time of arrival and crossing altitude at an en route fix. This is a follow-up study to work presented at the 4th USA/Europe Air Traffic Management R&D Seminar in December 2001. Nearly all of the pilots were able to meet their TFM constraints while maintaining adequate separation from other traffic. In only 3 out of 59 runs were the pilots unable to meet their required time of arrival. Two loss of separation cases are studied and it is found that the pilots need conflict prevention information presented in a clearer manner. No degradation of performance or safety was seen between the wide and narrow corridors. Although this was not a thorough study of the consequences of reducing the en route lateral separation, nothing was found that would refute the feasibility of reducing the separation requirement from 5 nm to 3 nm. The creation of additional, second-generation conflicts is also investigated. Two resolution methods were offered to the pilots: strategic and tactical. The strategic method is a closed-loop alteration to the Flight Management System (FMS) active route that considers other traffic as well as TFM constraints. The tactical resolutions are short-term resolutions that leave avoiding other traffic conflicts and meeting the TFM constraints to the pilot. Those that made use of the strategic tools avoided

  18. Computer simulations of cyclic and acyclic cholinergic agonists: conformational search and molecular dynamics simulations.

    PubMed Central

    McGroddy, K A; Brady, J W; Oswald, R E

    1994-01-01

    Molecular dynamics simulations have been performed on aqueous solutions of two chemically similar nicotinic cholinergic agonists in order to compare their structural and dynamical differences. The cyclic 1,1-dimethyl-4-acetylpiperazinium iodide (HPIP) molecule was previously shown to be a strong agonist for nicotinic acetylcholine receptors (McGroddy et al., 1993), while the acyclic N,N,N,N'-tetramethyl-N'-acetylethylenediamine iodide (HTED) derivative is much less potent. These differences were expected to arise from differences in the solution structures and internal dynamics of the two molecules. HPIP was originally thought to be relatively rigid; however, molecular dynamics simulations suggest that the acetyl portion of the molecule undergoes significant ring dynamics on a psec timescale. The less constrained HTED molecule is relatively rigid, with only one transition observed about any of the major dihedrals in four 100 psec simulations, each started from a different conformation. The average structures obtained from the simulations are very similar to the starting minimized structure in each case, except for the HTED simulation where a single rotation about the N-C-C-N(+) backbone occurred. In each case, HTED had three to five more water molecules in its primary solvation shell than HPIP, indicating that differences in the energetics of desolvation before binding may partially explain the increased potency of HPIP as compared to HTED. Images FIGURE 1 FIGURE 2 PMID:8161685

  19. Amino acids of the Murchison meteorite. I - Six carbon acyclic primary alpha-amino alkanoic acids

    NASA Technical Reports Server (NTRS)

    Cronin, J. R.; Gandy, W. E.; Pizzarello, S.

    1981-01-01

    Six of the seven chain isomers of six-carbon acyclic primary alpha-amino alkanoic acids (leucine isomers) have been either identified or confirmed in hot-water extracts of the Murchison meteorite using combined gas chromatography-mass spectrometry (GC-MS) and ion exchange chromatography. 2-Amino-2-ethylbutyric acid, 2-amino-2,3-dimethylbutyric acid, pseudoleucine, and 2-methylnorvaline were positively identified by GC-MS. These amino acids have not been previously reported to occur in natural materials and may be uniquely meteoritic in origin. The presence of leucine and isoleucine (including the diastereoisomer, alloisoleucine) was confirmed. Peaks corresponding to norleucine were seen by ion-exchange and gas chromatography but characteristic mass spectra were not obtained. The alpha-branched chain isomers in this series are quantitatively the most significant. These results are compared with literature data on amino acid synthesis by electrical discharge and Fischer-Tropsch-type catalysis. Neither model system produces an amino acid suite that is completely comparable to that found in the Murchison meteorite.

  20. Amino acids of the Murchison meteorite. III - Seven carbon acyclic primary alpha-amino alkanoic acids

    NASA Technical Reports Server (NTRS)

    Cronin, John R.; Pizzarello, Sandra

    1986-01-01

    All of the eighteen possible seven-carbon acyclic primary alpha-amino alkanoic acids have been positively identified in a hot-water extract of the Murchison meteorite by the combined use of gas chromatography-mass spectrometry, ion exchange chromatography and reversed-phase chromatography. None of these amino acids has previously been found in meteorites or in any other natural material. They range in concentration from less than or equal to 0.5 to 5.3 nmol/g. Configuration assignments were made for 2-amino-3,4-dimethylpentanoic acid and allo-2-amino-3,4-dimethylpentanoic acid and the diasteromer ratio was determined. Fifty-five amino acids have now been positively identified in the Murchison meteorite, 36 of which are unknown in terrestrial materials. This unique suite of amino acids is characterized by the occurrence of all structural isomers within the two major classes of amino acids represented, by the predominance of branched chain isomers, and by an exponential decline in amount with increasing carbon chain length within homologous series. These characteristics of the Murchison amino acids are suggestive of synthesis before incorporation into a parent body.

  1. Source diagnostic and weathering indicators of tar balls utilizing acyclic, polycyclic and S-heterocyclic components.

    PubMed

    Hegazi, A H; Andersson, J T; Abu-Elgheit, M A; El-Gayar, M Sh

    2004-05-01

    This study represents a forensic chemical analysis to define the liability for the coastal bitumens polluting the beaches of the Mediterranean city of Alexandria. Six tar balls collected from several locations along the coast of the city were analyzed for their acyclic and polycyclic hydrocarbons as well as sulfur heterocycles using GC/FID, GC/AED and gas chromatography/mass spectrometry techniques. The analysis of one Egyptian crude oil is also included as a possible source oil. The tar ball samples were at early stages of weathering. Based on the GC traces and biomarker signatures, the tar balls could be genetically different. One sample collected from the Eastern Harbor region appears to be a Bunker C type fuel produced from Egyptian crudes. The refining process has removed the low molecular weight components. On the other hand, the wide n-alkane distribution together with the absence of an unresolved complex mixture suggests that crude oils probably from tank washings, ballast discharges or accident spills from tankers could have contributed significantly to the other tar ball samples. The distribution of source specific hopane and sterane markers revealed that the tar samples probably originate from different oil fields. PMID:15051374

  2. In vitro susceptibility of fungi to acyclic inhibitors of 2,3-oxidosqualene cyclases.

    PubMed

    Airaudi, D; Ceruti, M; Bianco, C; Filipello Marchisio, V

    1996-01-01

    In the present study we determine the antifungal properties of two acyclic inhibitors of 2,3-oxidosqualene cyclases: 22,23-epoxy-2-aza-2,3-dihydrosqualene (EAS) and azasqualene alcohol (ASA). Fungistatic and fungicidal activity towards dermatophytes and other fungi involved in cutaneous and systemic infections was tested (48 isolates from 10 species). The tests were carried out by inoculating 10 microliters of mycelial homogenate in 1 ml of Sabouraud glucose liquid medium containing serial dilutions of 100 to 0.25 micrograms ml-1 of the substance. For each isolate, the minimum inhibitory concentration (MIC) and the minimum fungicidal concentration (MFC) of both compounds were determined. EAS was more active (MIC range 1.5-25 micrograms ml-1) than ASA (MIC range 3-50 micrograms ml-1). At the highest concentration tested, EAS also showed fungicidal action towards some isolates of Trichophyton mentagrophytes, T. terrestre, Epidermophyton floccosum, Microsporum canis and Scopulariopsis brumptii. The most sensitive species was T. mentagrophytes, the most resistant T. rubrum. PMID:8786759

  3. Executive Summary of Ares V: Lunar Capabilities Concept Review Through Phase A-Cycle 3

    NASA Technical Reports Server (NTRS)

    Holladay, J. B.; Baggett, K. E.; Feldman, S. M.

    2011-01-01

    This Technical Memorandum (TM) was generated as an overall Ares V summary from the Lunar Capabilities Concept Review (LCCR) through Phase A-Cycle 3 (PA-C3) with the intent that it may be coupled with separately published appendices for a more detailed, integrated narrative. The Ares V has evolved from the initial point of departure (POD) 51.00.48 LCCR configuration to the current candidate POD, PA-C3D, and the family of vehicles concept that contains vehicles PA-C3A through H. The logical progression from concept to POD vehicles is summarized in this TM and captures the trade space and performance of each. The family-of-vehicles concept was assessed during PA-C3 and offered flexibility in the path forward with the ability to add options deemed appropriate. A description of each trade space is given in addition to a summary of each Ares V element. The Ares V contributions to a Mars campaign are also highlighted with the goal of introducing Ares V capabilities within the trade space. The assessment of the Ares V vehicle as it pertains to Mars missions remained locked to the architecture presented in Mars Design Reference Authorization 5.0 using the PA-C3D vehicle configuration to assess Mars transfer vehicle options, in-space EDS capabilities, docking adaptor and propellant transfer assessments, and lunar and Mars synergistic potential.

  4. Phosphonylated Acyclic Guanosine Analogues with the 1,2,3-Triazole Linker.

    PubMed

    Głowacka, Iwona E; Andrei, Graciela; Schols, Dominique; Snoeck, Robert; Piotrowska, Dorota G

    2015-01-01

    A novel series of {4-[(2-amino-6-chloro-9H-purin-9-yl)methyl]-1H-1,2,3-triazol-1-yl}alkylphosphonates and {4-[(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)methyl]-1H-1,2,3-triazol-1-yl}alkylphosphonates as acyclic analogues of guanosine were synthesized and assessed for antiviral activity against a broad range of DNA and RNA viruses and for their cytostatic activity toward three cancerous cell lines (HeLa, L1210 and CEM). They were devoid of antiviral activity; however, several phosphonates were found slightly cytostatic against HeLa cells at an IC50 in the 80-210 µM range. Compounds (1R,2S)-17k and (1S,2S)-17k showed the highest inhibitory effects (IC50=15-30 µM) against the proliferation of murine leukemia (L1210) and human T-lymphocyte (CEM) cell lines. PMID:26501246

  5. Flotation properties of some oxygen-containing compounds of the acyclic series

    SciTech Connect

    Shreider, E.M.; Para, S.F.; Galanov, M.E.; Trachik, T.L.; Lagutina, L.V.

    1981-01-01

    In the monatomic alcohols series, maximum flotation activity is reached at 6 to 8 carbon atoms in the radical. It was decided to investigate the reagent properties of some other substances containing hydroxyl radicals which have not previously been considered. Oxygen-containing compounds in the acyclic series were examined, including alcohols: I - ethanol, ethylene-glycol, glycerol, pentaerythrytol, D-mannitol; II - dulcitol, D-sorbitol, D-mannitol, xylitol; glycols - monoethyleneglycol, diethyleneglycol, triethyleneglycol, polyethyleneglycol; and ethanolamines - ethanolamine, triethanolamine. The flotation properties of the reagents were determined in a Mekhanobr laboratory flotation machine with a chamber volume of 1.5 liter and an impeller speed of 1800 rpm. The materials tested were the <1 mm size fractions from run-of-plant charge and slurry from the radial thickeners. The samples were first dried and averaged. The pulp density was 200 g/l. The reagent conditions were kept constant throughout (50% of the total added at the start of a test, 25% after 2 min and 25% after 4 min from the start). The reagent additions were 1.0 to 1.4 kg/ton. All of these compounds had a very weak flotation activity.

  6. Polarizable Empirical Force Field for Acyclic Poly-Alcohols Based on the Classical Drude Oscillator

    PubMed Central

    He, Xibing; Lopes, Pedro E. M.; MacKerell, Alexander D.

    2014-01-01

    A polarizable empirical force field for acyclic polyalcohols based on the classical Drude oscillator is presented. The model is optimized with an emphasis on the transferability of the developed parameters among molecules of different sizes in this series and on the condensed-phase properties validated against experimental data. The importance of the explicit treatment of electronic polarizability in empirical force fields is demonstrated in the cases of this series of molecules with vicinal hydroxyl groups that can form cooperative intra- and intermolecular hydrogen bonds. Compared to the CHARMM additive force field, improved treatment of the electrostatic interactions avoids overestimation of the gas-phase dipole moments, results in significant improvement in the treatment of the conformational energies, and leads to the correct balance of intra- and intermolecular hydrogen bonding of glycerol as evidenced by calculated heat of vaporization being in excellent agreement with experiment. Computed condensed phase data, including crystal lattice parameters and volumes and densities of aqueous solutions are in better agreement with experimental data as compared to the corresponding additive model. Such improvements are anticipated to significantly improve the treatment of polymers in general, including biological macromolecules. PMID:23703219

  7. beta-Lactamase-catalyzed hydrolysis of acyclic depsipeptides and acyl transfer to specific amino acid acceptors.

    PubMed Central

    Pratt, R F; Govardhan, C P

    1984-01-01

    beta-Lactamases from all three classes, A, B, and C, catalyze the hydrolysis of specific acyclic depsipeptide (PhCH2CONHCR1R2CO2CHR3CO2H) analogs of acyl-D-alanyl-D-alanine peptides. The depsipeptides investigated, which are chemically as reactive toward nucleophiles as penicillins, are in general poor substrates, although differences between the classes of beta-lactamases have been observed: the order of effectiveness seems to be C greater than B greater than A. Certain class A and C beta-lactamases also catalyze phenylacetylglycyl transfer between phenylacetylglycyl depsipeptides and specific amino acid acceptors, a type of reaction hitherto identified more closely with D-alanyl-D-alanine transpeptidases than with beta-lactamases. Preliminary indications of an acyl-enzyme intermediate in these reactions have been obtained. These results support the suggestion [Tipper, D.J. and Strominger, J.L. (1965) Proc. Natl. Acad. Sci. USA 54, 1133-1141] that beta-lactamases are evolutionary descendants of bacterial cell wall D-alanyl-D-alanine transpeptidases. PMID:6424114

  8. Ester prodrugs of acyclic nucleoside thiophosphonates compared to phosphonates: synthesis, antiviral activity and decomposition study.

    PubMed

    Roux, Loïc; Priet, Stéphane; Payrot, Nadine; Weck, Clément; Fournier, Maëlenn; Zoulim, Fabien; Balzarini, Jan; Canard, Bruno; Alvarez, Karine

    2013-05-01

    9-[2-(Thiophosphonomethoxy)ethyl]adenine [S-PMEA, 8] and (R)-9-[2-(Thiophosphonomethoxy)propyl]adenine [S-PMPA, 9] are acyclic nucleoside thiophosphonates we described recently that display the same antiviral spectrum (DNA viruses) as approved and potent phosphonates PMEA and (R)-PMPA. Here, we describe the synthesis, antiviral activities in infected cell cultures and decomposition study of bis(pivaloyloxymethoxy)-S-PMEA [Bis-POM-S-PMEA, 13] and bis(isopropyloxymethylcarbonyl)-S-PMPA [Bis-POC-S-PMPA, 14] as orally bioavailable prodrugs of the S-PMEA 8 and S-PMPA 9, in comparison to the equivalent "non-thio" derivatives [Bis-POM-PMEA, 11] and [Bis-POC-PMPA, 12]. Compounds 11, 12, 13 and 14 were evaluated for their in vitro antiviral activity against HIV-1-, HIV-2-, HBV- and a broad panel of DNA viruses, and found to exhibit moderate to potent antiviral activity. In order to determine the decomposition pathway of the prodrugs 11, 12, 13 and 14 into parent compounds PMEA, PMPA, 8 and 9, kinetic data and decomposition pathways in several media are presented. As expected, bis-POM-S-PMEA 13 and bis-POC-S-PMPA 14 behaved as prodrugs of S-PMEA 8 and S-PMPA 9. However, thiophosphonates 8 and 9 were released very smoothly in cell extracts, in contrast to the release of PMEA and PMPA from "non-thio" prodrugs 11 and 12. PMID:23603046

  9. Graph transformation expert system (GTES)

    NASA Astrophysics Data System (ADS)

    Li, Guiquing; Ge, Qihong; Zhong, Luo; Xie, Weiping

    1996-03-01

    The design of many industrial and engineering systems can often be accomplished using flow graphs of various types. Examples include manufacturing processes and data processing applications, Graph Transformation Expert System, is an expert system which has been developed by WUT for applying techniques of artificial intelligence to the architectural design of data and signal processing systems. Software and hardware architectures may be defined for such systems using data flow graphs, in which nodes represent data processing steps and directed areas represent the `flow' of data between the processing steps. Starting with a user- defined generic processing graphic, this expert will transform the graph by applying transformation rules in order to specialize the processing graph to satisfy specified design goals and/or hardware constraints. Although the particular application for which this expert is designed is that of data and signal processing systems, it can provide an expert system framework for other problems specified graphically; for example, manufacturing systems, information systems, and product distribution systems.

  10. Eigenfunction statistics on quantum graphs

    SciTech Connect

    Gnutzmann, S.; Keating, J.P.; Piotet, F.

    2010-12-15

    We investigate the spatial statistics of the energy eigenfunctions on large quantum graphs. It has previously been conjectured that these should be described by a Gaussian Random Wave Model, by analogy with quantum chaotic systems, for which such a model was proposed by Berry in 1977. The autocorrelation functions we calculate for an individual quantum graph exhibit a universal component, which completely determines a Gaussian Random Wave Model, and a system-dependent deviation. This deviation depends on the graph only through its underlying classical dynamics. Classical criteria for quantum universality to be met asymptotically in the large graph limit (i.e. for the non-universal deviation to vanish) are then extracted. We use an exact field theoretic expression in terms of a variant of a supersymmetric {sigma} model. A saddle-point analysis of this expression leads to the estimates. In particular, intensity correlations are used to discuss the possible equidistribution of the energy eigenfunctions in the large graph limit. When equidistribution is asymptotically realized, our theory predicts a rate of convergence that is a significant refinement of previous estimates. The universal and system-dependent components of intensity correlation functions are recovered by means of an exact trace formula which we analyse in the diagonal approximation, drawing in this way a parallel between the field theory and semiclassics. Our results provide the first instance where an asymptotic Gaussian Random Wave Model has been established microscopically for eigenfunctions in a system with no disorder.

  11. Box graphs and resolutions I

    NASA Astrophysics Data System (ADS)

    Braun, Andreas P.; Schäfer-Nameki, Sakura

    2016-04-01

    Box graphs succinctly and comprehensively characterize singular fibers of elliptic fibrations in codimension two and three, as well as flop transitions connecting these, in terms of representation theoretic data. We develop a framework that provides a systematic map between a box graph and a crepant algebraic resolution of the singular elliptic fibration, thus allowing an explicit construction of the fibers from a singular Weierstrass or Tate model. The key tool is what we call a fiber face diagram, which shows the relevant information of a (partial) toric triangulation and allows the inclusion of more general algebraic blowups. We shown that each such diagram defines a sequence of weighted algebraic blowups, thus providing a realization of the fiber defined by the box graph in terms of an explicit resolution. We show this correspondence explicitly for the case of SU (5) by providing a map between box graphs and fiber faces, and thereby a sequence of algebraic resolutions of the Tate model, which realizes each of the box graphs.

  12. Discrete Signal Processing on Graphs: Sampling Theory

    NASA Astrophysics Data System (ADS)

    Chen, Siheng; Varma, Rohan; Sandryhaila, Aliaksei; Kovacevic, Jelena

    2015-12-01

    We propose a sampling theory for signals that are supported on either directed or undirected graphs. The theory follows the same paradigm as classical sampling theory. We show that perfect recovery is possible for graph signals bandlimited under the graph Fourier transform. The sampled signal coefficients form a new graph signal, whose corresponding graph structure preserves the first-order difference of the original graph signal. For general graphs, an optimal sampling operator based on experimentally designed sampling is proposed to guarantee perfect recovery and robustness to noise; for graphs whose graph Fourier transforms are frames with maximal robustness to erasures as well as for Erd\\H{o}s-R\\'enyi graphs, random sampling leads to perfect recovery with high probability. We further establish the connection to the sampling theory of finite discrete-time signal processing and previous work on signal recovery on graphs. To handle full-band graph signals, we propose a graph filter bank based on sampling theory on graphs. Finally, we apply the proposed sampling theory to semi-supervised classification on online blogs and digit images, where we achieve similar or better performance with fewer labeled samples compared to previous work.

  13. Algebraic connectivity and graph robustness.

    SciTech Connect

    Feddema, John Todd; Byrne, Raymond Harry; Abdallah, Chaouki T.

    2009-07-01

    Recent papers have used Fiedler's definition of algebraic connectivity to show that network robustness, as measured by node-connectivity and edge-connectivity, can be increased by increasing the algebraic connectivity of the network. By the definition of algebraic connectivity, the second smallest eigenvalue of the graph Laplacian is a lower bound on the node-connectivity. In this paper we show that for circular random lattice graphs and mesh graphs algebraic connectivity is a conservative lower bound, and that increases in algebraic connectivity actually correspond to a decrease in node-connectivity. This means that the networks are actually less robust with respect to node-connectivity as the algebraic connectivity increases. However, an increase in algebraic connectivity seems to correlate well with a decrease in the characteristic path length of these networks - which would result in quicker communication through the network. Applications of these results are then discussed for perimeter security.

  14. Quantum snake walk on graphs

    SciTech Connect

    Rosmanis, Ansis

    2011-02-15

    I introduce a continuous-time quantum walk on graphs called the quantum snake walk, the basis states of which are fixed-length paths (snakes) in the underlying graph. First, I analyze the quantum snake walk on the line, and I show that, even though most states stay localized throughout the evolution, there are specific states that most likely move on the line as wave packets with momentum inversely proportional to the length of the snake. Next, I discuss how an algorithm based on the quantum snake walk might potentially be able to solve an extended version of the glued trees problem, which asks to find a path connecting both roots of the glued trees graph. To the best of my knowledge, no efficient quantum algorithm solving this problem is known yet.

  15. Graph Analytics for Signature Discovery

    SciTech Connect

    Hogan, Emilie A.; Johnson, John R.; Halappanavar, Mahantesh; Lo, Chaomei

    2013-06-01

    Within large amounts of seemingly unstructured data it can be diffcult to find signatures of events. In our work we transform unstructured data into a graph representation. By doing this we expose underlying structure in the data and can take advantage of existing graph analytics capabilities, as well as develop new capabilities. Currently we focus on applications in cybersecurity and communication domains. Within cybersecurity we aim to find signatures for perpetrators using the pass-the-hash attack, and in communications we look for emails or phone calls going up or down a chain of command. In both of these areas, and in many others, the signature we look for is a path with certain temporal properties. In this paper we discuss our methodology for finding these temporal paths within large graphs.

  16. Optimal preparation of graph states

    SciTech Connect

    Cabello, Adan; Lopez-Tarrida, Antonio J.; Danielsen, Lars Eirik; Portillo, Jose R.

    2011-04-15

    We show how to prepare any graph state of up to 12 qubits with (a) the minimum number of controlled-Z gates and (b) the minimum preparation depth. We assume only one-qubit and controlled-Z gates. The method exploits the fact that any graph state belongs to an equivalence class under local Clifford operations. We extend up to 12 qubits the classification of graph states according to their entanglement properties, and identify each class using only a reduced set of invariants. For any state, we provide a circuit with both properties (a) and (b), if it does exist, or, if it does not, one circuit with property (a) and one with property (b), including the explicit one-qubit gates needed.

  17. Graph modeling systems and methods

    DOEpatents

    Neergaard, Mike

    2015-10-13

    An apparatus and a method for vulnerability and reliability modeling are provided. The method generally includes constructing a graph model of a physical network using a computer, the graph model including a plurality of terminating vertices to represent nodes in the physical network, a plurality of edges to represent transmission paths in the physical network, and a non-terminating vertex to represent a non-nodal vulnerability along a transmission path in the physical network. The method additionally includes evaluating the vulnerability and reliability of the physical network using the constructed graph model, wherein the vulnerability and reliability evaluation includes a determination of whether each terminating and non-terminating vertex represents a critical point of failure. The method can be utilized to evaluate wide variety of networks, including power grid infrastructures, communication network topologies, and fluid distribution systems.

  18. Sequential visibility-graph motifs

    NASA Astrophysics Data System (ADS)

    Iacovacci, Jacopo; Lacasa, Lucas

    2016-04-01

    Visibility algorithms transform time series into graphs and encode dynamical information in their topology, paving the way for graph-theoretical time series analysis as well as building a bridge between nonlinear dynamics and network science. In this work we introduce and study the concept of sequential visibility-graph motifs, smaller substructures of n consecutive nodes that appear with characteristic frequencies. We develop a theory to compute in an exact way the motif profiles associated with general classes of deterministic and stochastic dynamics. We find that this simple property is indeed a highly informative and computationally efficient feature capable of distinguishing among different dynamics and robust against noise contamination. We finally confirm that it can be used in practice to perform unsupervised learning, by extracting motif profiles from experimental heart-rate series and being able, accordingly, to disentangle meditative from other relaxation states. Applications of this general theory include the automatic classification and description of physical, biological, and financial time series.

  19. Conformationally Constrained Analogues of Diacylglycerol (DAG). 25. Exploration of the sn-1 and sn-2 carbonyl functionality reveals the essential role of the sn-1 carbonyl at the lipid interface in the binding of DAG-lactones to protein kinase C

    PubMed Central

    Kang, Ji-Hye; Peach, Megan L.; Pu, Yongmei; Lewin, Nancy E.; Nicklaus, Marc C.; Blumberg, Peter M.; Marquez, Victor E.

    2008-01-01

    A group of DAG-lactones with altered functionality (C=O → CH2 or C=O → C=S) at the sn-1 and sn-2 carbonyl pharmacophores was synthesized and used as probes to dissect the individual role of each carbonyl in binding to protein kinase C (PKC). The results suggest that the hydrated sn-1 carbonyl is engaged in very strong hydrogen bonding interactions with the charged lipid headgroups and organized water molecules at the lipid interface. Conversely, the sn-2 carbonyl has a more modest contribution to the binding process as a result of its involvement with the receptor (C1 domain) via conventional hydrogen bonding to the protein. The parent DAG-lactones, E-6 and Z-7, were designed to bind exclusively in the sn-2 binding mode to insure the correct orientation and disposition of pharmacophores at the binding site. PMID:16134942

  20. Interacting particle systems on graphs

    NASA Astrophysics Data System (ADS)

    Sood, Vishal

    In this dissertation, the dynamics of socially or biologically interacting populations are investigated. The individual members of the population are treated as particles that interact via links on a social or biological network represented as a graph. The effect of the structure of the graph on the properties of the interacting particle system is studied using statistical physics techniques. In the first chapter, the central concepts of graph theory and social and biological networks are presented. Next, interacting particle systems that are drawn from physics, mathematics and biology are discussed in the second chapter. In the third chapter, the random walk on a graph is studied. The mean time for a random walk to traverse between two arbitrary sites of a random graph is evaluated. Using an effective medium approximation it is found that the mean first-passage time between pairs of sites, as well as all moments of this first-passage time, are insensitive to the density of links in the graph. The inverse of the mean-first passage time varies non-monotonically with the density of links near the percolation transition of the random graph. Much of the behavior can be understood by simple heuristic arguments. Evolutionary dynamics, by which mutants overspread an otherwise uniform population on heterogeneous graphs, are studied in the fourth chapter. Such a process underlies' epidemic propagation, emergence of fads, social cooperation or invasion of an ecological niche by a new species. The first part of this chapter is devoted to neutral dynamics, in which the mutant genotype does not have a selective advantage over the resident genotype. The time to extinction of one of the two genotypes is derived. In the second part of this chapter, selective advantage or fitness is introduced such that the mutant genotype has a higher birth rate or a lower death rate. This selective advantage leads to a dynamical competition in which selection dominates for large populations

  1. Synchronizability of random rectangular graphs

    SciTech Connect

    Estrada, Ernesto Chen, Guanrong

    2015-08-15

    Random rectangular graphs (RRGs) represent a generalization of the random geometric graphs in which the nodes are embedded into hyperrectangles instead of on hypercubes. The synchronizability of RRG model is studied. Both upper and lower bounds of the eigenratio of the network Laplacian matrix are determined analytically. It is proven that as the rectangular network is more elongated, the network becomes harder to synchronize. The synchronization processing behavior of a RRG network of chaotic Lorenz system nodes is numerically investigated, showing complete consistence with the theoretical results.

  2. Graphs for Early Elementary Social Studies.

    ERIC Educational Resources Information Center

    Freeland, Kent; Brewer, Samrie

    1989-01-01

    Describes a lesson plan that instructs third graders to use graphs. Explains learning objectives, motivating students, conducting a class activity that includes graph construction, and concluding and evaluating the lesson. Lists materials needed. (GG)

  3. Comparison Graph of Sea Ice Minimum - 2010

    NASA Video Gallery

    This animated graph tracks the retreat of sea ice, measured in millions of square kilometers, averaged from the start of the satellite record in 1979 through 2000 (white). Next, the graph follows t...

  4. Dr.L: Distributed Recursive (Graph) Layout

    2007-11-19

    Dr. L provides two-dimensional visualizations of very large abstract graph structures. it can be used for data mining applications including biology, scientific literature, and social network analysis. Dr. L is a graph layout program that uses a multilevel force-directed algorithm. A graph is input and drawn using a force-directed algorithm based on simulated annealing. The resulting layout is clustered using a single link algorithm. This clustering is used to produce a coarsened graph (fewer nodes)more » which is then re-drawn. this process is repeated until a sufficiently small graph is produced. The smallest graph is drawn and then used as a basis for drawing the original graph by refining the series of coarsened graphs that were produced. The layout engine can be run in serial or in parallel.« less

  5. Graphing and Social Studies: An Interdisciplinary Activity.

    ERIC Educational Resources Information Center

    Brehm, Julia L.

    1996-01-01

    Describes a graphing activity that promotes mathematical connections with social studies lessons. Students should be familiar with graphing on the Cartesian coordinate system to play this variation of the game Battleship on maps of various regions of the world. (AIM)

  6. Mathematical Minute: Rotating a Function Graph

    ERIC Educational Resources Information Center

    Bravo, Daniel; Fera, Joseph

    2013-01-01

    Using calculus only, we find the angles you can rotate the graph of a differentiable function about the origin and still obtain a function graph. We then apply the solution to odd and even degree polynomials.

  7. Standard Distributions: One Graph Fits All

    ERIC Educational Resources Information Center

    Wagner, Clifford H.

    2007-01-01

    Standard distributions are ubiquitous but not unique. With suitable scaling, the graph of a standard distribution serves as the graph for every distribution in the family. The standard exponential can easily be taught in elementary statistics courses.

  8. A functional interaction between TRPC/NCKX induced by DAG plays a role in determining calcium influx independently from PKC activation.

    PubMed

    Pulcinelli, Fabio M; Trifirò, Elisabetta; Massimi, Isabella; Di Renzo, Livia

    2013-01-01

    Ca(2+)influx might occur through K(+)-dependent Na(+)/Ca(2+) exchanger operating in reverse mode (rNCKX). In a cellular model different from platelets, an interaction between canonical transient receptor potential cation (TRPC) channels and NCX has been found. The aim of this study was to verify whether the TRPC/NCKX interaction operates in human platelets. Our results showed that the diacylglycerol (DAG) analogue, 1-oleoyl-2-acetyl-sn-glycerol (OAG) induced rNCKX-mediated Ca(2+) influx through TRPC-mediated Na(+) influx. DAG-induced activation of TRPC/NCKX occurs independently of protein kinase C (PKC) activation, as PKC inhibitor did not modify OAG-mediated Ca(2+) influx. Moreover, as both rNCKX and TRPC inhibitors reduced OAG-induced platelet aggregation which, conversely, was increased by flufenamic acid, known to develop TRPC activity, it could be suggested that the TRPC/NCKX interaction has a role in OAG-dependent platelet aggregation. PMID:23249278

  9. Fibonacci Identities, Matrices, and Graphs

    ERIC Educational Resources Information Center

    Huang, Danrun

    2005-01-01

    General strategies used to help discover, prove, and generalize identities for Fibonacci numbers are described along with some properties about the determinants of square matrices. A matrix proof for identity (2) that has received immense attention from many branches of mathematics, like linear algebra, dynamical systems, graph theory and others…

  10. Two-Player Graph Pebbling

    NASA Astrophysics Data System (ADS)

    Prudente, Matthew James

    Given a graph G with pebbles on the vertices, we define a pebbling move as removing two pebbles from a vertex u, placing one pebble on a neighbor v, and discarding the other pebble, like a toll. The pebbling number pi( G) is the least number of pebbles needed so that every arrangement of pi(G) pebbles can place a pebble on any vertex through a sequence of pebbling moves. We introduce a new variation on graph pebbling called two-player pebbling. In this, players called the mover and the defender alternate moves, with the stipulation that the defender cannot reverse the previous move. The mover wins only if they can place a pebble on a specified vertex and the defender wins if the mover cannot. We define η(G), analogously, as the minimum number of pebbles such that given every configuration of the η( G) pebbles and every specified vertex r, the mover has a winning strategy. First, we will investigate upper bounds for η( G) on various classes of graphs and find a certain structure for which the defender has a winning strategy, no matter how many pebbles are in a configuration. Then, we characterize winning configurations for both players on a special class of diameter 2 graphs. Finally, we show winning configurations for the mover on paths using a recursive argument.

  11. Graphs and Enhancing Maple Multiplication.

    ERIC Educational Resources Information Center

    Cecil, David R.; Wang, Rongdong

    2002-01-01

    Description of a technique in Maple programming language that automatically prints all paths of any desired length along with the name of each vertex, proceeding in order from the beginning vertex to the ending vertex for a given graph. (Author/MM)

  12. Situating Graphs as Workplace Knowledge

    ERIC Educational Resources Information Center

    Noss, Richard; Bakker, Arthur; Hoyles, Celia; Kent, Phillip

    2007-01-01

    We investigate the use and knowledge of graphs in the context of a large industrial factory. We are particularly interested in the question of "transparency", a question that has been extensively considered in the general literature on tool use and, more recently, by Michael Roth and his colleagues in the context of scientific work. Roth uses the…

  13. Affect and Graphing Calculator Use

    ERIC Educational Resources Information Center

    McCulloch, Allison W.

    2011-01-01

    This article reports on a qualitative study of six high school calculus students designed to build an understanding about the affect associated with graphing calculator use in independent situations. DeBellis and Goldin's (2006) framework for affect as a representational system was used as a lens through which to understand the ways in which…

  14. Humidity Graphs for All Seasons.

    ERIC Educational Resources Information Center

    Esmael, F.

    1982-01-01

    In a previous article in this journal (Vol. 17, p358, 1979), a wet-bulb depression table was recommended for two simple experiments to determine relative humidity. However, the use of a graph is suggested because it gives the relative humidity directly from the wet and dry bulb readings. (JN)

  15. Ancestral Genres of Mathematical Graphs

    ERIC Educational Resources Information Center

    Gerofsky, Susan

    2011-01-01

    Drawing from sources in gesture studies, cognitive science, the anthropology of religion and art/architecture history, this article explores cultural, bodily and cosmological resonances carried (unintentionally) by mathematical graphs on Cartesian coordinates. Concepts of asymmetric bodily spaces, grids, orthogonality, mapping and sacred spaces…

  16. Alteration in substrate specificity of horse liver alcohol dehydrogenase by an acyclic nicotinamide analog of NAD(+).

    PubMed

    Malver, Olaf; Sebastian, Mina J; Oppenheimer, Norman J

    2014-11-01

    A new, acyclic NAD-analog, acycloNAD(+) has been synthesized where the nicotinamide ribosyl moiety has been replaced by the nicotinamide (2-hydroxyethoxy)methyl moiety. The chemical properties of this analog are comparable to those of β-NAD(+) with a redox potential of -324mV and a 341nm λmax for the reduced form. Both yeast alcohol dehydrogenase (YADH) and horse liver alcohol dehydrogenase (HLADH) catalyze the reduction of acycloNAD(+) by primary alcohols. With HLADH 1-butanol has the highest Vmax at 49% that of β-NAD(+). The primary deuterium kinetic isotope effect is greater than 3 indicating a significant contribution to the rate limiting step from cleavage of the carbon-hydrogen bond. The stereochemistry of the hydride transfer in the oxidation of stereospecifically deuterium labeled n-butanol is identical to that for the reaction with β-NAD(+). In contrast to the activity toward primary alcohols there is no detectable reduction of acycloNAD(+) by secondary alcohols with HLADH although these alcohols serve as competitive inhibitors. The net effect is that acycloNAD(+) has converted horse liver ADH from a broad spectrum alcohol dehydrogenase, capable of utilizing either primary or secondary alcohols, into an exclusively primary alcohol dehydrogenase. This is the first example of an NAD analog that alters the substrate specificity of a dehydrogenase and, like site-directed mutagenesis of proteins, establishes that modifications of the coenzyme distance from the active site can be used to alter enzyme function and substrate specificity. These and other results, including the activity with α-NADH, clearly demonstrate the promiscuity of the binding interactions between dehydrogenases and the riboside phosphate of the nicotinamide moiety, thus greatly expanding the possibilities for the design of analogs and inhibitors of specific dehydrogenases. PMID:25280628

  17. Chemical Applications of Graph Theory: Part II. Isomer Enumeration.

    ERIC Educational Resources Information Center

    Hansen, Peter J.; Jurs, Peter C.

    1988-01-01

    Discusses the use of graph theory to aid in the depiction of organic molecular structures. Gives a historical perspective of graph theory and explains graph theory terminology with organic examples. Lists applications of graph theory to current research projects. (ML)

  18. Around the Sun in a Graphing Calculator.

    ERIC Educational Resources Information Center

    Demana, Franklin; Waits, Bert K.

    1989-01-01

    Discusses the use of graphing calculators for polar and parametric equations. Presents eight lines of the program for the graph of a parametric equation and 11 lines of the program for a graph of a polar equation. Illustrates the application of the programs for planetary motion and free-fall motion. (YP)

  19. 47 CFR 80.761 - Conversion graphs.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 5 2010-10-01 2010-10-01 false Conversion graphs. 80.761 Section 80.761... MARITIME SERVICES Standards for Computing Public Coast Station VHF Coverage § 80.761 Conversion graphs. The following graphs must be employed where conversion from one to the other of the indicated types of units...

  20. My Bar Graph Tells a Story

    ERIC Educational Resources Information Center

    McMillen, Sue; McMillen, Beth

    2010-01-01

    Connecting stories to qualitative coordinate graphs has been suggested as an effective instructional strategy. Even students who are able to "create" bar graphs may struggle to correctly "interpret" them. Giving children opportunities to work with qualitative graphs can help them develop the skills to interpret, describe, and compare information…

  1. 47 CFR 80.761 - Conversion graphs.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 47 Telecommunication 5 2014-10-01 2014-10-01 false Conversion graphs. 80.761 Section 80.761... MARITIME SERVICES Standards for Computing Public Coast Station VHF Coverage § 80.761 Conversion graphs. The following graphs must be employed where conversion from one to the other of the indicated types of units...

  2. So Many Graphs, So Little Time

    ERIC Educational Resources Information Center

    Wall, Jennifer J.; Benson, Christine C.

    2009-01-01

    Interpreting graphs found in various content areas is an important skill for students, especially in light of high-stakes testing. In addition, reading and understanding graphs is an important part of numeracy, or numeric literacy, a skill necessary for informed citizenry. This article explores the different categories of graphs, provides…

  3. 47 CFR 80.761 - Conversion graphs.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 47 Telecommunication 5 2011-10-01 2011-10-01 false Conversion graphs. 80.761 Section 80.761... MARITIME SERVICES Standards for Computing Public Coast Station VHF Coverage § 80.761 Conversion graphs. The following graphs must be employed where conversion from one to the other of the indicated types of units...

  4. 47 CFR 80.761 - Conversion graphs.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 47 Telecommunication 5 2012-10-01 2012-10-01 false Conversion graphs. 80.761 Section 80.761... MARITIME SERVICES Standards for Computing Public Coast Station VHF Coverage § 80.761 Conversion graphs. The following graphs must be employed where conversion from one to the other of the indicated types of units...

  5. 47 CFR 80.761 - Conversion graphs.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 47 Telecommunication 5 2013-10-01 2013-10-01 false Conversion graphs. 80.761 Section 80.761... MARITIME SERVICES Standards for Computing Public Coast Station VHF Coverage § 80.761 Conversion graphs. The following graphs must be employed where conversion from one to the other of the indicated types of units...

  6. Some Applications of Graph Theory to Clustering

    ERIC Educational Resources Information Center

    Hubert, Lawrence J.

    1974-01-01

    The connection between graph theory and clustering is reviewed and extended. Major emphasis is on restating, in a graph-theoretic context, selected past work in clustering, and conversely, developing alternative strategies from several standard concepts used in graph theory per se. (Author/RC)

  7. Collaborative Robotic Instruction: A Graph Teaching Experience

    ERIC Educational Resources Information Center

    Mitnik, Ruben; Recabarren, Matias; Nussbaum, Miguel; Soto, Alvaro

    2009-01-01

    Graphing is a key skill in the study of Physics. Drawing and interpreting graphs play a key role in the understanding of science, while the lack of these has proved to be a handicap and a limiting factor in the learning of scientific concepts. It has been observed that despite the amount of previous graph-working experience, students of all ages…

  8. Acyclic CB[n]-Type Molecular Containers: Effect of Solubilizing Group on their Function as Solubilizing Excipients

    PubMed Central

    Zhang, Ben; Zavalij, Peter Y.; Isaacs, Lyle

    2014-01-01

    We report the synthesis and x-ray crystal structures of three acyclic CB[n]-type molecular containers (2a, 2h, 2f) that differ in the charge on their solubilizing groups (SO3−, OH, NH3+). The x-ray crystal structures of compounds 2h and 2f reveal a self-folding of the ArOCH2CH2X wall into the cavity driven by π–π interactions, H-bonds and ion-dipole interactions. The need to reverse this self-folding phenomenon upon guest binding decreases the affinity of 2h and 2f toward cationic guests in water relative to 2a as revealed by direct 1H NMR and UV/Vis titrations as well as UV/Vis competition experiments. We determined the pKa of 6-aminocoumarin 7 (pKa = 3.6) on its own and in the presence anionic, neutral, and cationic hosts (2a: pKa = 4.9; 2h: pKa = 4.1; 2f, pKa = 3.4) which reflect in part the relevance of direct ion-ion interactions between the arms of the host and the guest toward the recognition properties of acyclic CB[n]-type containers. Finally, we showed that the weaker binding affinities measured for neutral and positively charged hosts 2h and 2f compared to anionic 2a results in a decreased ability to act as solubilizing agents for either cationic (tamoxifen), neutral (17α–ethynylestradiol), or anionic (indomethacin) drugs in water. The results establish that acyclic CB[n] compounds that bear anionic solubilizing groups are most suitable for development as general purpose solubilizing excipients for insoluble pharmaceutical agents. PMID:24595500

  9. Amino acids of the Murchison meteorite. II - Five carbon acyclic primary beta-, gamma-, and delta-amino alkanoic acids

    NASA Technical Reports Server (NTRS)

    Cronin, J. R.; Pizzarello, S.; Yuen, G. U.

    1985-01-01

    The five-carbon acyclic primary beta, gamma, and delta amino alkanoic acids of the Murchison meteorite are studied using gas chromatography-mass spectrometry and ion exchange chromatography. The chromatograms reveal that alpha is the most abundant monoamino alkanoic acid followed by gamma and beta, and an exponential increase in the amount of amino acid is observed as the carbon number increases in the homologous series. The influence of frictional heating, spontaneous thermal decomposition, and radiation of the synthesis of amino acids is examined. The data obtained support an amino acid synthesis process involving random combination of single-carbon precursors.

  10. A graph edit dictionary for correcting errors in roof topology graphs reconstructed from point clouds

    NASA Astrophysics Data System (ADS)

    Xiong, B.; Oude Elberink, S.; Vosselman, G.

    2014-07-01

    In the task of 3D building model reconstruction from point clouds we face the problem of recovering a roof topology graph in the presence of noise, small roof faces and low point densities. Errors in roof topology graphs will seriously affect the final modelling results. The aim of this research is to automatically correct these errors. We define the graph correction as a graph-to-graph problem, similar to the spelling correction problem (also called the string-to-string problem). The graph correction is more complex than string correction, as the graphs are 2D while strings are only 1D. We design a strategy based on a dictionary of graph edit operations to automatically identify and correct the errors in the input graph. For each type of error the graph edit dictionary stores a representative erroneous subgraph as well as the corrected version. As an erroneous roof topology graph may contain several errors, a heuristic search is applied to find the optimum sequence of graph edits to correct the errors one by one. The graph edit dictionary can be expanded to include entries needed to cope with errors that were previously not encountered. Experiments show that the dictionary with only fifteen entries already properly corrects one quarter of erroneous graphs in about 4500 buildings, and even half of the erroneous graphs in one test area, achieving as high as a 95% acceptance rate of the reconstructed models.

  11. Fast graph operations in quantum computation

    NASA Astrophysics Data System (ADS)

    Zhao, Liming; Pérez-Delgado, Carlos A.; Fitzsimons, Joseph F.

    2016-03-01

    The connection between certain entangled states and graphs has been heavily studied in the context of measurement-based quantum computation as a tool for understanding entanglement. Here we show that this correspondence can be harnessed in the reverse direction to yield a graph data structure, which allows for more efficient manipulation and comparison of graphs than any possible classical structure. We introduce efficient algorithms for many transformation and comparison operations on graphs represented as graph states, and prove that no classical data structure can have similar performance for the full set of operations studied.

  12. Generalized graph states based on Hadamard matrices

    SciTech Connect

    Cui, Shawn X.; Yu, Nengkun; Zeng, Bei

    2015-07-15

    Graph states are widely used in quantum information theory, including entanglement theory, quantum error correction, and one-way quantum computing. Graph states have a nice structure related to a certain graph, which is given by either a stabilizer group or an encoding circuit, both can be directly given by the graph. To generalize graph states, whose stabilizer groups are abelian subgroups of the Pauli group, one approach taken is to study non-abelian stabilizers. In this work, we propose to generalize graph states based on the encoding circuit, which is completely determined by the graph and a Hadamard matrix. We study the entanglement structures of these generalized graph states and show that they are all maximally mixed locally. We also explore the relationship between the equivalence of Hadamard matrices and local equivalence of the corresponding generalized graph states. This leads to a natural generalization of the Pauli (X, Z) pairs, which characterizes the local symmetries of these generalized graph states. Our approach is also naturally generalized to construct graph quantum codes which are beyond stabilizer codes.

  13. Constrained Graph Optimization: Interdiction and Preservation Problems

    SciTech Connect

    Schild, Aaron V

    2012-07-30

    The maximum flow, shortest path, and maximum matching problems are a set of basic graph problems that are critical in theoretical computer science and applications. Constrained graph optimization, a variation of these basic graph problems involving modification of the underlying graph, is equally important but sometimes significantly harder. In particular, one can explore these optimization problems with additional cost constraints. In the preservation case, the optimizer has a budget to preserve vertices or edges of a graph, preventing them from being deleted. The optimizer wants to find the best set of preserved edges/vertices in which the cost constraints are satisfied and the basic graph problems are optimized. For example, in shortest path preservation, the optimizer wants to find a set of edges/vertices within which the shortest path between two predetermined points is smallest. In interdiction problems, one deletes vertices or edges from the graph with a particular cost in order to impede the basic graph problems as much as possible (for example, delete edges/vertices to maximize the shortest path between two predetermined vertices). Applications of preservation problems include optimal road maintenance, power grid maintenance, and job scheduling, while interdiction problems are related to drug trafficking prevention, network stability assessment, and counterterrorism. Computational hardness results are presented, along with heuristic methods for approximating solutions to the matching interdiction problem. Also, efficient algorithms are presented for special cases of graphs, including on planar graphs. The graphs in many of the listed applications are planar, so these algorithms have important practical implications.

  14. Fast Approximate Quadratic Programming for Graph Matching

    PubMed Central

    Vogelstein, Joshua T.; Conroy, John M.; Lyzinski, Vince; Podrazik, Louis J.; Kratzer, Steven G.; Harley, Eric T.; Fishkind, Donniell E.; Vogelstein, R. Jacob; Priebe, Carey E.

    2015-01-01

    Quadratic assignment problems arise in a wide variety of domains, spanning operations research, graph theory, computer vision, and neuroscience, to name a few. The graph matching problem is a special case of the quadratic assignment problem, and graph matching is increasingly important as graph-valued data is becoming more prominent. With the aim of efficiently and accurately matching the large graphs common in big data, we present our graph matching algorithm, the Fast Approximate Quadratic assignment algorithm. We empirically demonstrate that our algorithm is faster and achieves a lower objective value on over 80% of the QAPLIB benchmark library, compared with the previous state-of-the-art. Applying our algorithm to our motivating example, matching C. elegans connectomes (brain-graphs), we find that it efficiently achieves performance. PMID:25886624

  15. Fast approximate quadratic programming for graph matching.

    PubMed

    Vogelstein, Joshua T; Conroy, John M; Lyzinski, Vince; Podrazik, Louis J; Kratzer, Steven G; Harley, Eric T; Fishkind, Donniell E; Vogelstein, R Jacob; Priebe, Carey E

    2015-01-01

    Quadratic assignment problems arise in a wide variety of domains, spanning operations research, graph theory, computer vision, and neuroscience, to name a few. The graph matching problem is a special case of the quadratic assignment problem, and graph matching is increasingly important as graph-valued data is becoming more prominent. With the aim of efficiently and accurately matching the large graphs common in big data, we present our graph matching algorithm, the Fast Approximate Quadratic assignment algorithm. We empirically demonstrate that our algorithm is faster and achieves a lower objective value on over 80% of the QAPLIB benchmark library, compared with the previous state-of-the-art. Applying our algorithm to our motivating example, matching C. elegans connectomes (brain-graphs), we find that it efficiently achieves performance. PMID:25886624

  16. Subgraph-Based Filterbanks for Graph Signals

    NASA Astrophysics Data System (ADS)

    Tremblay, Nicolas; Borgnat, Pierre

    2016-08-01

    We design a critically-sampled compact-support biorthogonal transform for graph signals, via graph filterbanks. Instead of partitioning the nodes in two sets so as to remove one every two nodes in the filterbank downsampling operations, the design is based on a partition of the graph in connected subgraphs. Coarsening is achieved by defining one "supernode" for each subgraph and the edges for this coarsened graph derives from the connectivity between the subgraphs. Unlike the "one every two nodes" downsampling on bipartite graphs, this coarsening operation does not have an exact formulation in the graph Fourier domain. Instead, we rely on the local Fourier bases of each subgraph to define filtering operations. We apply successfully this method to decompose graph signals, and show promising performance on compression and denoising.

  17. Hierarchical structure of the logical Internet graph

    NASA Astrophysics Data System (ADS)

    Ge, Zihui; Figueiredo, Daniel R.; Jaiswal, Sharad; Gao, Lixin

    2001-07-01

    The study of the Internet topology has recently received much attention from the research community. In particular, the observation that the network graph has interesting properties, such as power laws, that might be explored in a myriad of ways. Most of the work in characterizing the Internet graph is based on the physical network graph, i.e., the connectivity graph. In this paper we investigate how logical relationships between nodes of the AS graph can be used to gain insight to its structure. We characterize the logical graph using various metrics and identify the presence of power laws in the number of customers that a provider has. Using these logical relationships we define a structural model of the AS graph. The model highlights the hierarchical nature of logical relationships and the preferential connection to larger providers. We also investigate the consistency of this model over time and observe interesting properties of the hierarchical structure.

  18. On a programming language for graph algorithms

    NASA Technical Reports Server (NTRS)

    Rheinboldt, W. C.; Basili, V. R.; Mesztenyi, C. K.

    1971-01-01

    An algorithmic language, GRAAL, is presented for describing and implementing graph algorithms of the type primarily arising in applications. The language is based on a set algebraic model of graph theory which defines the graph structure in terms of morphisms between certain set algebraic structures over the node set and arc set. GRAAL is modular in the sense that the user specifies which of these mappings are available with any graph. This allows flexibility in the selection of the storage representation for different graph structures. In line with its set theoretic foundation, the language introduces sets as a basic data type and provides for the efficient execution of all set and graph operators. At present, GRAAL is defined as an extension of ALGOL 60 (revised) and its formal description is given as a supplement to the syntactic and semantic definition of ALGOL. Several typical graph algorithms are written in GRAAL to illustrate various features of the language and to show its applicability.

  19. The Feynman Identity for Planar Graphs

    NASA Astrophysics Data System (ADS)

    da Costa, G. A. T. F.

    2016-08-01

    The Feynman identity (FI) of a planar graph relates the Euler polynomial of the graph to an infinite product over the equivalence classes of closed nonperiodic signed cycles in the graph. The main objectives of this paper are to compute the number of equivalence classes of nonperiodic cycles of given length and sign in a planar graph and to interpret the data encoded by the FI in the context of free Lie superalgebras. This solves in the case of planar graphs a problem first raised by Sherman and sets the FI as the denominator identity of a free Lie superalgebra generated from a graph. Other results are obtained. For instance, in connection with zeta functions of graphs.

  20. Choosability of P 5-Free Graphs

    NASA Astrophysics Data System (ADS)

    Golovach, Petr A.; Heggernes, Pinar

    A graph is k-choosable if it admits a proper coloring of its vertices for every assignment of k (possibly different) allowed colors to choose from for each vertex. It is NP-hard to decide whether a given graph is k-choosable for k ≥ 3, and this problem is considered strictly harder than the k-coloring problem. Only few positive results are known on input graphs with a given structure. Here, we prove that the problem is fixed parameter tractable on P 5-free graphs when parameterized by k. This graph class contains the well known and widely studied class of cographs. Our result is surprising since the parameterized complexity of k-coloring is still open on P 5-free graphs. To give a complete picture, we show that the problem remains NP-hard on P 5-free graphs when k is a part of the input.

  1. Duplex-tetraplex equilibrium between a hairpin and two interacting hairpins of d(A-G)10 at neutral pH.

    PubMed Central

    Shiber, M C; Braswell, E H; Klump, H; Fresco, J R

    1996-01-01

    d(A-G)10 forms two helical structures at neutrality, at low ionic strength a single-hairpin duplex, and at higher ionic strength a double-hairpin tetraplex. An ionic strength-dependent equilibrium between these forms is indicated by native PAGE, which also reveals additional single-stranded species below 0.3 M Na+, probably corresponding to partially denatured states. The equilibrium also depends upon oligomer concentration: at very low concentrations, d(A-G)10 migrates faster than the random coil d(C-T)10, probably because it is a more compact single hairpin; at high concentrations, it co-migrates with the linear duplex d(A-G)10 x d(C-T)10, probably because it is a two-hairpin tetraplex. Molecular weights measured by equilibrium sedimentation in 0.1 M Na+, pH 7, reveal a mixture of monomer and dimer species at 1 degree C, but only a monomer at 40 degrees C; in 0.6 M Na+, pH 7, only a dimer species is observed at 4 degrees C. That the single- and double-stranded species are hairpin helices, is indicated by preferential S1 nuclease cleavage at the center of the oligomer(s), i.e., the loop of the hairpin(s). The UV melting transition below 0.3 M Na+ or K+, exhibits a dTm/dlog[Na+/K+] of 33 or 36 degrees C, respectively, consistent with conversion of a two-hairpin tetraplex to a single-hairpin duplex with extrahelical residues. When [Na+/K+] > or = 0.3 M, dTm/dlog [Na+/K+] is 19 or 17 degrees C, respectively, consistent with conversion of a two-hairpin tetraplex directly to single strands. A two-hairpin structure stabilized by G-tetrads is indicated by differential scanning calorimetry in 0.15 M Na+/5 mM Mg2+, with deltaH of formation per mole of the two-hairpin tetraplex of -116.9 kcal or -29.2 kcal/mol of G-tetrad. PMID:9016673

  2. The weighted random graph model

    NASA Astrophysics Data System (ADS)

    Garlaschelli, Diego

    2009-07-01

    We introduce the weighted random graph (WRG) model, which represents the weighted counterpart of the Erdos-Renyi random graph and provides fundamental insights into more complicated weighted networks. We find analytically that the WRG is characterized by a geometric weight distribution, a binomial degree distribution and a negative binomial strength distribution. We also characterize exactly the percolation phase transitions associated with edge removal and with the appearance of weighted subgraphs of any order and intensity. We find that even this completely null model displays a percolation behaviour similar to what is observed in real weighted networks, implying that edge removal cannot be used to detect community structure empirically. By contrast, the analysis of clustering successfully reveals different patterns between the WRG and real networks.

  3. Relativity on Rotated Graph Paper

    NASA Astrophysics Data System (ADS)

    Salgado, Roberto

    2011-11-01

    We present visual calculations in special relativity using spacetime diagrams drawn on graph paper that has been rotated by 45 degrees. The rotated lines represent lightlike directions in Minkowski spacetime, and the boxes in the grid (called light-clock diamonds) represent ticks of an inertial observer's lightclock. We show that many quantitative results can be read off a spacetime diagram by counting boxes, using a minimal amount of algebra.

  4. The Effect of Acyclic Retinoid on the Metabolomic Profiles of Hepatocytes and Hepatocellular Carcinoma Cells

    PubMed Central

    Qin, Xian-Yang; Wei, Feifei; Tanokura, Masaru; Ishibashi, Naoto; Shimizu, Masahito; Moriwaki, Hisataka; Kojima, Soichi

    2013-01-01

    Background/Purpose Acyclic retinoid (ACR) is a promising chemopreventive agent for hepatocellular carcinoma (HCC) that selectively inhibits the growth of HCC cells (JHH7) but not normal hepatic cells (Hc). To better understand the molecular basis of the selective anti-cancer effect of ACR, we performed nuclear magnetic resonance (NMR)-based and capillary electrophoresis time-of-flight mass spectrometry (CE-TOFMS)-based metabolome analyses in JHH7 and Hc cells after treatment with ACR. Methodology/Principal Findings NMR-based metabolomics revealed a distinct metabolomic profile of JHH7 cells at 18 h after ACR treatment but not at 4 h after ACR treatment. CE-TOFMS analysis identified 88 principal metabolites in JHH7 and Hc cells after 24 h of treatment with ethanol (EtOH) or ACR. The abundance of 71 of these metabolites was significantly different between EtOH-treated control JHH7 and Hc cells, and 49 of these metabolites were significantly down-regulated in the ACR-treated JHH7 cells compared to the EtOH-treated JHH7 cells. Of particular interest, the increase in adenosine-5′-triphosphate (ATP), the main cellular energy source, that was observed in the EtOH-treated control JHH7 cells was almost completely suppressed in the ACR-treated JHH7 cells; treatment with ACR restored ATP to the basal levels observed in both EtOH-control and ACR-treated Hc cells (0.72-fold compared to the EtOH control-treated JHH7 cells). Moreover, real-time PCR analyses revealed that ACR significantly increased the expression of pyruvate dehydrogenase kinases 4 (PDK4), a key regulator of ATP production, in JHH7 cells but not in Hc cells (3.06-fold and 1.20-fold compared to the EtOH control, respectively). Conclusions/Significance The results of the present study suggest that ACR may suppress the enhanced energy metabolism of JHH7 cells but not Hc cells; this occurs at least in part via the cancer-selective enhancement of PDK4 expression. The cancer-selective metabolic pathways identified in

  5. Topological structure of dictionary graphs

    NASA Astrophysics Data System (ADS)

    Fukś, Henryk; Krzemiński, Mark

    2009-09-01

    We investigate the topological structure of the subgraphs of dictionary graphs constructed from WordNet and Moby thesaurus data. In the process of learning a foreign language, the learner knows only a subset of all words of the language, corresponding to a subgraph of a dictionary graph. When this subgraph grows with time, its topological properties change. We introduce the notion of the pseudocore and argue that the growth of the vocabulary roughly follows decreasing pseudocore numbers—that is, one first learns words with a high pseudocore number followed by smaller pseudocores. We also propose an alternative strategy for vocabulary growth, involving decreasing core numbers as opposed to pseudocore numbers. We find that as the core or pseudocore grows in size, the clustering coefficient first decreases, then reaches a minimum and starts increasing again. The minimum occurs when the vocabulary reaches a size between 103 and 104. A simple model exhibiting similar behavior is proposed. The model is based on a generalized geometric random graph. Possible implications for language learning are discussed.

  6. Models of random graph hierarchies

    NASA Astrophysics Data System (ADS)

    Paluch, Robert; Suchecki, Krzysztof; Hołyst, Janusz A.

    2015-10-01

    We introduce two models of inclusion hierarchies: random graph hierarchy (RGH) and limited random graph hierarchy (LRGH). In both models a set of nodes at a given hierarchy level is connected randomly, as in the Erdős-Rényi random graph, with a fixed average degree equal to a system parameter c. Clusters of the resulting network are treated as nodes at the next hierarchy level and they are connected again at this level and so on, until the process cannot continue. In the RGH model we use all clusters, including those of size 1, when building the next hierarchy level, while in the LRGH model clusters of size 1 stop participating in further steps. We find that in both models the number of nodes at a given hierarchy level h decreases approximately exponentially with h. The height of the hierarchy H, i.e. the number of all hierarchy levels, increases logarithmically with the system size N, i.e. with the number of nodes at the first level. The height H decreases monotonically with the connectivity parameter c in the RGH model and it reaches a maximum for a certain c max in the LRGH model. The distribution of separate cluster sizes in the LRGH model is a power law with an exponent about - 1.25. The above results follow from approximate analytical calculations and have been confirmed by numerical simulations.

  7. Synthesis and Evaluation of Novel Acyclic Nucleoside Phosphonates as Inhibitors of Plasmodium falciparum and Human 6-Oxopurine Phosphoribosyltransferases.

    PubMed

    Kaiser, Martin M; Hocková, Dana; Wang, Tzu-Hsuan; Dračínský, Martin; Poštová-Slavětínská, Lenka; Procházková, Eliška; Edstein, Michael D; Chavchich, Marina; Keough, Dianne T; Guddat, Luke W; Janeba, Zlatko

    2015-10-01

    Acyclic nucleoside phosphonates (ANPs) are a promising class of antimalarial therapeutic drug leads that exhibit a wide variety of Ki values for Plasmodium falciparum (Pf) and human hypoxanthine-guanine-(xanthine) phosphoribosyltransferases [HG(X)PRTs]. A novel series of ANPs, analogues of previously reported 2-(phosphonoethoxy)ethyl (PEE) and (R,S)-3-hydroxy-2-(phosphonomethoxy)propyl (HPMP) derivatives, were designed and synthesized to evaluate their ability to act as inhibitors of these enzymes and to extend our ongoing antimalarial structure-activity relationship studies. In this series, (S)-3-hydroxy-2-(phosphonoethoxy)propyl (HPEP), (S)-2-(phosphonomethoxy)propanoic acid (CPME), or (S)-2-(phosphonoethoxy)propanoic acid (CPEE) are the acyclic moieties. Of this group, (S)-3-hydroxy-2-(phosphonoethoxy)propylguanine (HPEPG) exhibits the highest potency for PfHGXPRT, with a Ki value of 0.1 μM and a Ki value for human HGPRT of 0.6 μM. The crystal structures of HPEPG and HPEPHx (where Hx=hypoxanthine) in complex with human HGPRT were obtained, showing specific interactions with active site residues. Prodrugs for the HPEP and CPEE analogues were synthesized and tested for in vitro antimalarial activity. The lowest IC50 value (22 μM) in a chloroquine-resistant strain was observed for the bis-amidate prodrug of HPEPG. PMID:26368337

  8. Helping Students Make Sense of Graphs: An Experimental Trial of SmartGraphs Software

    NASA Astrophysics Data System (ADS)

    Zucker, Andrew; Kay, Rachel; Staudt, Carolyn

    2014-06-01

    Graphs are commonly used in science, mathematics, and social sciences to convey important concepts; yet students at all ages demonstrate difficulties interpreting graphs. This paper reports on an experimental study of free, Web-based software called SmartGraphs that is specifically designed to help students overcome their misconceptions regarding graphs. SmartGraphs allows students to interact with graphs and provides hints and scaffolding to help students, if they need help. SmartGraphs activities can be authored to be useful in teaching and learning a variety of topics that use graphs (such as slope, velocity, half-life, and global warming). A 2-year experimental study in physical science classrooms was conducted with dozens of teachers and thousands of students. In the first year, teachers were randomly assigned to experimental or control conditions. Data show that students of teachers who use SmartGraphs as a supplement to normal instruction make greater gains understanding graphs than control students studying the same content using the same textbooks, but without SmartGraphs. Additionally, teachers believe that the SmartGraphs activities help students meet learning goals in the physical science course, and a great majority reported they would use the activities with students again. In the second year of the study, several specific variations of SmartGraphs were researched to help determine what makes SmartGraphs effective.

  9. Computational Genomics Using Graph Theory

    NASA Astrophysics Data System (ADS)

    Schlick, Tamar

    2005-03-01

    With exciting new discoveries concerning RNA's regulatory cellular roles in gene expression, structural and functional problems associated with DNA's venerable cousin have come to the forefront. RNA folding, for example, is analogous to the well-known protein folding problem, and seeks to link RNA's primary sequence with secondary and tertiary structures. As a single-stranded polynucleotide, RNA's secondary structures are defined by a network of hydrogen bonds, which lead to a variety of stems, loops, junctions, bulges, and other motifs. Supersecondary pseudoknot structures can also occur and, together, lead to RNA's complex tertiary interactions stabilized by salt and solvent ions in the natural cellular milieu. Besides folding, challenges in RNA research include identifying locations and functions of RNA genes, discovering RNA's structural repertoire (folding motifs), designing novel RNAs, and developing new antiviral and antibiotic compounds composed of, or targeting, RNAs. In this talk, I will describe some of these new biological findings concerning RNA and present an approach using graph theory (network theory) to represent RNA secondary structures. Because the RNA motif space using graphs is vastly smaller than RNA's sequence space, many problems related to analyzing and discovering new RNAs can be simplified and studied systematically. Some preliminary applications to designing novel RNAs will also be described.Related ReadingH. H. Gan, S. Pasquali, and T. Schlick, ``A Survey of Existing RNAs using Graph Theory with Implications to RNA Analysis and Design,'' Nuc. Acids Res. 31: 2926--2943 (2003). J. Zorn, H. H. Gan, N. Shiffeldrim, and T. Schlick, ``Structural Motifs in Ribosomal RNAs: Implications for RNA Design and Genomics,'' Biopolymers 73: 340--347 (2004). H. H. Gan, D. Fera, J. Zorn, M. Tang, N. Shiffeldrim, U. Laserson, N. Kim, and T. Schlick,``RAG: RNA-As-Graphs Database -- Concepts, Analysis, and Features,'' Bioinformatics 20: 1285--1291 (2004). U

  10. Computing Information Value from RDF Graph Properties

    SciTech Connect

    al-Saffar, Sinan; Heileman, Gregory

    2010-11-08

    Information value has been implicitly utilized and mostly non-subjectively computed in information retrieval (IR) systems. We explicitly define and compute the value of an information piece as a function of two parameters, the first is the potential semantic impact the target information can subjectively have on its recipient's world-knowledge, and the second parameter is trust in the information source. We model these two parameters as properties of RDF graphs. Two graphs are constructed, a target graph representing the semantics of the target body of information and a context graph representing the context of the consumer of that information. We compute information value subjectively as a function of both potential change to the context graph (impact) and the overlap between the two graphs (trust). Graph change is computed as a graph edit distance measuring the dissimilarity between the context graph before and after the learning of the target graph. A particular application of this subjective information valuation is in the construction of a personalized ranking component in Web search engines. Based on our method, we construct a Web re-ranking system that personalizes the information experience for the information-consumer.

  11. Components in time-varying graphs.

    PubMed

    Nicosia, Vincenzo; Tang, John; Musolesi, Mirco; Russo, Giovanni; Mascolo, Cecilia; Latora, Vito

    2012-06-01

    Real complex systems are inherently time-varying. Thanks to new communication systems and novel technologies, today it is possible to produce and analyze social and biological networks with detailed information on the time of occurrence and duration of each link. However, standard graph metrics introduced so far in complex network theory are mainly suited for static graphs, i.e., graphs in which the links do not change over time, or graphs built from time-varying systems by aggregating all the links as if they were concurrent in time. In this paper, we extend the notion of connectedness, and the definitions of node and graph components, to the case of time-varying graphs, which are represented as time-ordered sequences of graphs defined over a fixed set of nodes. We show that the problem of finding strongly connected components in a time-varying graph can be mapped into the problem of discovering the maximal-cliques in an opportunely constructed static graph, which we name the affine graph. It is, therefore, an NP-complete problem. As a practical example, we have performed a temporal component analysis of time-varying graphs constructed from three data sets of human interactions. The results show that taking time into account in the definition of graph components allows to capture important features of real systems. In particular, we observe a large variability in the size of node temporal in- and out-components. This is due to intrinsic fluctuations in the activity patterns of individuals, which cannot be detected by static graph analysis. PMID:22757508

  12. Components in time-varying graphs

    NASA Astrophysics Data System (ADS)

    Nicosia, Vincenzo; Tang, John; Musolesi, Mirco; Russo, Giovanni; Mascolo, Cecilia; Latora, Vito

    2012-06-01

    Real complex systems are inherently time-varying. Thanks to new communication systems and novel technologies, today it is possible to produce and analyze social and biological networks with detailed information on the time of occurrence and duration of each link. However, standard graph metrics introduced so far in complex network theory are mainly suited for static graphs, i.e., graphs in which the links do not change over time, or graphs built from time-varying systems by aggregating all the links as if they were concurrent in time. In this paper, we extend the notion of connectedness, and the definitions of node and graph components, to the case of time-varying graphs, which are represented as time-ordered sequences of graphs defined over a fixed set of nodes. We show that the problem of finding strongly connected components in a time-varying graph can be mapped into the problem of discovering the maximal-cliques in an opportunely constructed static graph, which we name the affine graph. It is, therefore, an NP-complete problem. As a practical example, we have performed a temporal component analysis of time-varying graphs constructed from three data sets of human interactions. The results show that taking time into account in the definition of graph components allows to capture important features of real systems. In particular, we observe a large variability in the size of node temporal in- and out-components. This is due to intrinsic fluctuations in the activity patterns of individuals, which cannot be detected by static graph analysis.

  13. JavaGenes: Evolving Graphs with Crossover

    NASA Technical Reports Server (NTRS)

    Globus, Al; Atsatt, Sean; Lawton, John; Wipke, Todd

    2000-01-01

    Genetic algorithms usually use string or tree representations. We have developed a novel crossover operator for a directed and undirected graph representation, and used this operator to evolve molecules and circuits. Unlike strings or trees, a single point in the representation cannot divide every possible graph into two parts, because graphs may contain cycles. Thus, the crossover operator is non-trivial. A steady-state, tournament selection genetic algorithm code (JavaGenes) was written to implement and test the graph crossover operator. All runs were executed by cycle-scavagging on networked workstations using the Condor batch processing system. The JavaGenes code has evolved pharmaceutical drug molecules and simple digital circuits. Results to date suggest that JavaGenes can evolve moderate sized drug molecules and very small circuits in reasonable time. The algorithm has greater difficulty with somewhat larger circuits, suggesting that directed graphs (circuits) are more difficult to evolve than undirected graphs (molecules), although necessary differences in the crossover operator may also explain the results. In principle, JavaGenes should be able to evolve other graph-representable systems, such as transportation networks, metabolic pathways, and computer networks. However, large graphs evolve significantly slower than smaller graphs, presumably because the space-of-all-graphs explodes combinatorially with graph size. Since the representation strongly affects genetic algorithm performance, adding graphs to the evolutionary programmer's bag-of-tricks should be beneficial. Also, since graph evolution operates directly on the phenotype, the genotype-phenotype translation step, common in genetic algorithm work, is eliminated.

  14. Multi-Resolution Dynamic Meshes with Arbitrary Deformations

    SciTech Connect

    Shamir, A.; Pascucci, V.; Bajaj, C.

    2000-07-10

    Multi-resolution techniques and models have been shown to be effective for the display and transmission of large static geometric object. Dynamic environments with internally deforming models and scientific simulations using dynamic meshes pose greater challenges in terms of time and space, and need the development of similar solutions. In this paper we introduce the T-DAG, an adaptive multi-resolution representation for dynamic meshes with arbitrary deformations including attribute, position, connectivity and topology changes. T-DAG stands for Time-dependent Directed Acyclic Graph which defines the structure supporting this representation. We also provide an incremental algorithm (in time) for constructing the T-DAG representation of a given input mesh. This enables the traversal and use of the multi-resolution dynamic model for partial playback while still constructing new time-steps.

  15. Nonpreemptive run-time scheduling issues on a multitasked, multiprogrammed multiprocessor with dependencies, bidimensional tasks, folding and dynamic graphs

    SciTech Connect

    Miller, Allan Ray

    1987-05-01

    Increases in high speed hardware have mandated studies in software techniques to exploit the parallel capabilities. This thesis examines the effects a run-time scheduler has on a multiprocessor. The model consists of directed, acyclic graphs, generated from serial FORTRAN benchmark programs by the parallel compiler Parafrase. A multitasked, multiprogrammed environment is created. Dependencies are generated by the compiler. Tasks are bidimensional, i.e., they may specify both time and processor requests. Processor requests may be folded into execution time by the scheduler. The graphs may arrive at arbitrary time intervals. The general case is NP-hard, thus, a variety of heuristics are examined by a simulator. Multiprogramming demonstrates a greater need for a run-time scheduler than does monoprogramming for a variety of reasons, e.g., greater stress on the processors, a larger number of independent control paths, more variety in the task parameters, etc. The dynamic critical path series of algorithms perform well. Dynamic critical volume did not add much. Unfortunately, dynamic critical path maximizes turnaround time as well as throughput. Two schedulers are presented which balance throughput and turnaround time. The first requires classification of jobs by type; the second requires selection of a ratio value which is dependent upon system parameters. 45 refs., 19 figs., 20 tabs.

  16. A new class of acyclic nucleoside phosphonates: synthesis and biological activity of 9-[[(phosphonomethyl)aziridin-1-yl]methyl]guanine (PMAMG) and analogues.

    PubMed

    Abu Sheikha, Ghassan; La Colla, Paolo; Loi, Anna Giulia

    2002-10-01

    A new class of acyclic nucleoside phosphonates PMAMG, PMAMA, PMAMC, and PMAMT (compounds 1, 2, 3 and 4) have been synthesized and tested in vitro against a wide variety of viruses, fungi and bacteria. PMAMG (1) was synthesized by the alkylation reaction of acetylguanine with the phosphonate side-chain, diisopropyl [[2-(bromomethyl)aziridin-1-yl

  17. API Requirements for Dynamic Graph Prediction

    SciTech Connect

    Gallagher, B; Eliassi-Rad, T

    2006-10-13

    Given a large-scale time-evolving multi-modal and multi-relational complex network (a.k.a., a large-scale dynamic semantic graph), we want to implement algorithms that discover patterns of activities on the graph and learn predictive models of those discovered patterns. This document outlines the application programming interface (API) requirements for fast prototyping of feature extraction, learning, and prediction algorithms on large dynamic semantic graphs. Since our algorithms must operate on large-scale dynamic semantic graphs, we have chosen to use the graph API developed in the CASC Complex Networks Project. This API is supported on the back end by a semantic graph database (developed by Scott Kohn and his team). The advantages of using this API are (i) we have full-control of its development and (ii) the current API meets almost all of the requirements outlined in this document.

  18. Fast generation of sparse random kernel graphs

    DOE PAGESBeta

    Hagberg, Aric; Lemons, Nathan; Du, Wen -Bo

    2015-09-10

    The development of kernel-based inhomogeneous random graphs has provided models that are flexible enough to capture many observed characteristics of real networks, and that are also mathematically tractable. We specify a class of inhomogeneous random graph models, called random kernel graphs, that produces sparse graphs with tunable graph properties, and we develop an efficient generation algorithm to sample random instances from this model. As real-world networks are usually large, it is essential that the run-time of generation algorithms scales better than quadratically in the number of vertices n. We show that for many practical kernels our algorithm runs in timemore » at most ο(n(logn)²). As an example, we show how to generate samples of power-law degree distribution graphs with tunable assortativity.« less

  19. Fast generation of sparse random kernel graphs

    SciTech Connect

    Hagberg, Aric; Lemons, Nathan; Du, Wen -Bo

    2015-09-10

    The development of kernel-based inhomogeneous random graphs has provided models that are flexible enough to capture many observed characteristics of real networks, and that are also mathematically tractable. We specify a class of inhomogeneous random graph models, called random kernel graphs, that produces sparse graphs with tunable graph properties, and we develop an efficient generation algorithm to sample random instances from this model. As real-world networks are usually large, it is essential that the run-time of generation algorithms scales better than quadratically in the number of vertices n. We show that for many practical kernels our algorithm runs in time at most ο(n(logn)²). As an example, we show how to generate samples of power-law degree distribution graphs with tunable assortativity.

  20. Fast Generation of Sparse Random Kernel Graphs

    PubMed Central

    2015-01-01

    The development of kernel-based inhomogeneous random graphs has provided models that are flexible enough to capture many observed characteristics of real networks, and that are also mathematically tractable. We specify a class of inhomogeneous random graph models, called random kernel graphs, that produces sparse graphs with tunable graph properties, and we develop an efficient generation algorithm to sample random instances from this model. As real-world networks are usually large, it is essential that the run-time of generation algorithms scales better than quadratically in the number of vertices n. We show that for many practical kernels our algorithm runs in time at most 𝒪(n(logn)2). As a practical example we show how to generate samples of power-law degree distribution graphs with tunable assortativity. PMID:26356296

  1. Weight of quadratic forms and graph states

    NASA Astrophysics Data System (ADS)

    Cosentino, Alessandro; Severini, Simone

    2009-11-01

    We prove a connection between Schmidt rank and weight of quadratic forms. This provides a new tool for the classification of graph states based on entanglement. Our main tool arises from a reformulation of previously known results concerning the weight of quadratic forms in terms of graph states properties. As a byproduct, we obtain a straightforward characterization of the weight of functions associated with pivot-minor of bipartite graphs.

  2. Speed of evolution on graphs

    NASA Astrophysics Data System (ADS)

    Sui, Xiukai; Wu, Bin; Wang, Long

    2015-12-01

    The likelihood that a mutant fixates in the wild population, i.e., fixation probability, has been intensively studied in evolutionary game theory, where individuals' fitness is frequency dependent. However, it is of limited interest when it takes long to take over. Thus the speed of evolution becomes an important issue. In general, it is still unclear how fixation times are affected by the population structure, although the fixation times have already been addressed in the well-mixed populations. Here we theoretically address this issue by pair approximation and diffusion approximation on regular graphs. It is shown (i) that under neutral selection, both unconditional and conditional fixation time are shortened by increasing the number of neighbors; (ii) that under weak selection, for the simplified prisoner's dilemma game, if benefit-to-cost ratio exceeds the degree of the graph, then the unconditional fixation time of a single cooperator is slower than that in the neutral case; and (iii) that under weak selection, for the conditional fixation time, limited neighbor size dilutes the counterintuitive stochastic slowdown which was found in well-mixed populations. Interestingly, we find that all of our results can be interpreted as that in the well-mixed population with a transformed payoff matrix. This interpretation is also valid for both death-birth and birth-death processes on graphs. This interpretation bridges the fixation time in the structured population and that in the well-mixed population. Thus it opens the avenue to investigate the challenging fixation time in structured populations by the known results in well-mixed populations.

  3. Graph-matching based CTA.

    PubMed

    Maksimov, Dmitry; Hesser, Jürgen; Brockmann, Carolin; Jochum, Susanne; Dietz, Tiina; Schnitzer, Andreas; Düber, Christoph; Schoenberg, Stefan O; Diehl, Steffen

    2009-12-01

    Separating bone, calcification, and vessels in computer tomography angiography (CTA) allows for a detailed diagnosis of vessel stenosis. This paper presents a new, graph-based technique that solves this difficult problem with high accuracy. The approach requires one native data set and one that is contrast enhanced. On each data set, an attributed level-graph is derived and both graphs are matched by dynamic programming to differentiate between bone, on one hand side, and vessel/calcification on the other hand side. Lumen and calcified regions are then separated by a profile technique. Evaluation is based on data from vessels of pelvis and lower extremities of elderly patients. Due to substantial calcification and motion of patients between and during the acquisitions, the underlying approach is tested on a class of difficult cases. Analysis requires 3-5 min on a Pentium IV 3 GHz for a 700 MByte data set. Among 37 patients, our approach correctly identifies all three components in 80% of cases correctly compared to visual control. Critical inconsistencies with visual inspection were found in 6% of all cases; 70% of these inconsistencies are due to small vessels that have 1) a diameter near the resolution of the CT and 2) are passing next to bony structures. All other remaining deviations are found in an incorrect handling of the iliac artery since the slice thickness is near the diameter of this vessel and since the orientation is not in cranio-caudal direction. Increasing resolution is thus expected to solve many the aforementioned difficulties. PMID:19574161

  4. Breddin's graph for tectonic regimes

    NASA Astrophysics Data System (ADS)

    Célérier, Bernard; Séranne, Michel

    2001-05-01

    A simple graphical method is proposed to infer the tectonic regime from a fault and slip data set. An abacus is overlaid on a plot of the rake versus strike of the data. This yields the horizontal principal stress directions and a constraint on the stress tensor aspect ratio, in a manner similar to Breddin's graph for two-dimensional strain analysis. The main requirement is that one of the principal stress directions is close to the vertical. This method is illustrated on monophase synthetic and natural data, but is also expected to help sort out multiphase data sets.

  5. Naming on a Directed Graph

    NASA Astrophysics Data System (ADS)

    Gosti, Giorgio; Batchelder, William H.

    We address how the structure of a social communication system affects language coordination. The naming game is an abstraction of lexical acquisition dynamics, in which N agents try to find an agreement on the names to give to objects. Most results on naming games are specific to certain communication network topologies. We present two important results that are general to any graph topology: the first proves that under certain topologies the system always converges to a name-object agreement; the second proves that if these conditions are not met the system may end up in a state in which sub-networks with different competing object-name associations coexist.

  6. The alignment-distribution graph

    NASA Technical Reports Server (NTRS)

    Chatterjee, Siddhartha; Gilbert, John R.; Schreiber, Robert

    1993-01-01

    Implementing a data-parallel language such as Fortran 90 on a distributed-memory parallel computer requires distributing aggregate data objects (such as arrays) among the memory modules attached to the processors. The mapping of objects to the machine determines the amount of residual communication needed to bring operands of parallel operations into alignment with each other. We present a program representation called the alignment distribution graph that makes these communication requirements explicit. We describe the details of the representation, show how to model communication cost in this framework, and outline several algorithms for determining object mappings that approximately minimize residual communication.

  7. The alignment-distribution graph

    NASA Technical Reports Server (NTRS)

    Chatterjee, Siddhartha; Gilbert, John R.; Schreiber, Robert

    1993-01-01

    Implementing a data-parallel language such as Fortran 90 on a distributed-memory parallel computer requires distributing aggregate data objects (such as arrays) among the memory modules attached to the processors. The mapping of objects to the machine determines the amount of residual communication needed to bring operands of parallel operations into alignment with each other. We present a program representation called the alignment-distribution graph that makes these communication requirements explicit. We describe the details of the representation, show how to model communication cost in this framework, and outline several algorithms for determining object mappings that approximately minimize residual communication.

  8. Recurrence of hyperprolactinemia and continuation of ovarian acyclicity in captive African elephants (Loxodonta africana) treated with cabergoline.

    PubMed

    Morfeld, Kari A; Ball, Ray L; Brown, Janine L

    2014-09-01

    Hyperprolactinemia is associated with reproductive acyclicity in zoo African elephants (Loxodonta africana) and may contribute to the non-self-sustainability of the captive population in North America. It is a common cause of infertility in women and other mammals and can be treated with the dopamine agonist cabergoline. The objectives of this study were to assess prolactin responses to cabergoline treatment in hyperprolactinemic, acyclic African elephants and to determine the subsequent impact on ovarian cyclic activity. Five elephants, diagnosed as hyperprolactinemic (>11 ng/ml prolactin) and acyclic (maintenance of baseline progestagens for at least 1 yr), were treated with 1-2 mg cabergoline orally twice weekly for 16-82 wk. Cabergoline reduced (P < 0.05) serum prolactin concentrations during the treatment period compared to pretreatment levels in four of five elephants (11.5 +/- 3.2 vs. 9.1 +/- 3.4 ng/ml; 20.3 +/- 16.7 vs. 7.9 +/- 9.8 ng/ml; 26.4 +/- 15.0 vs. 6.8 +/- 1.5 ng/ml; 42.2 +/- 22.6 vs. 18.6 +/- 8.9 ng/ml). However, none of the females resumed ovarian cyclicity based on serum progestagen analyses up to 1 yr posttreatment. In addition, within 1 to 6 wk after cessation of oral cabergoline, serum prolactin concentrations returned to concentrations that were as high as or higher than before treatment (P < 0.05). One elephant that exhibited the highest pretreatment prolactin concentration (75.2 +/- 10.5 ng/ml) did not respond to cabergoline and maintained elevated levels throughout the study. Thus, oral cabergoline administration reduced prolactin concentrations in elephants with hyperprolactinemia, but there was no resumption of ovarian cyclicity, and a significant prolactin rebound effect was observed. It is possible that higher doses or longer treatment intervals may be required for cabergoline treatment to result in permanent suppression of prolactin secretion and to mitigate associated ovarian cycle problems. PMID:25314824

  9. On designing heteroclinic networks from graphs

    NASA Astrophysics Data System (ADS)

    Ashwin, Peter; Postlethwaite, Claire

    2013-12-01

    Robust heteroclinic networks are invariant sets that can appear as attractors in symmetrically coupled or otherwise constrained dynamical systems. These networks may have a complicated structure determined to a large extent by the constraints and dimension of the system. As these networks are of great interest as dynamical models of biological and cognitive processes, it is useful to understand how particular directed graphs can be realised as attracting robust heteroclinic networks between states in phase space. This paper presents two methods of realising arbitrarily complex directed graphs as robust heteroclinic networks for flows generated by ODEs-we say the ODEs realise the graphs as heteroclinic networks between equilibria that represent the vertices. Suppose we have a directed graph on nv vertices with ne edges. The “simplex realisation” embeds the graph as an invariant set of a flow on an (nv-1)-simplex. This method realises the graph as long as it is one- and two-cycle free. The “cylinder realisation” embeds a graph as an invariant set of a flow on a (ne+1)-dimensional space. This method realises the graph as long as it is one-cycle free. In both cases we realise the graph as an invariant set within an attractor, and discuss some illustrative examples, including the influence of noise and parameters on the dynamics. In particular we show that the resulting heteroclinic network may or may not display “memory” of the vertices visited.

  10. Evolutionary Games of Multiplayer Cooperation on Graphs

    PubMed Central

    Arranz, Jordi; Traulsen, Arne

    2016-01-01

    There has been much interest in studying evolutionary games in structured populations, often modeled as graphs. However, most analytical results so far have only been obtained for two-player or linear games, while the study of more complex multiplayer games has been usually tackled by computer simulations. Here we investigate evolutionary multiplayer games on graphs updated with a Moran death-Birth process. For cycles, we obtain an exact analytical condition for cooperation to be favored by natural selection, given in terms of the payoffs of the game and a set of structure coefficients. For regular graphs of degree three and larger, we estimate this condition using a combination of pair approximation and diffusion approximation. For a large class of cooperation games, our approximations suggest that graph-structured populations are stronger promoters of cooperation than populations lacking spatial structure. Computer simulations validate our analytical approximations for random regular graphs and cycles, but show systematic differences for graphs with many loops such as lattices. In particular, our simulation results show that these kinds of graphs can even lead to more stringent conditions for the evolution of cooperation than well-mixed populations. Overall, we provide evidence suggesting that the complexity arising from many-player interactions and spatial structure can be captured by pair approximation in the case of random graphs, but that it need to be handled with care for graphs with high clustering. PMID:27513946

  11. Evolutionary Games of Multiplayer Cooperation on Graphs.

    PubMed

    Peña, Jorge; Wu, Bin; Arranz, Jordi; Traulsen, Arne

    2016-08-01

    There has been much interest in studying evolutionary games in structured populations, often modeled as graphs. However, most analytical results so far have only been obtained for two-player or linear games, while the study of more complex multiplayer games has been usually tackled by computer simulations. Here we investigate evolutionary multiplayer games on graphs updated with a Moran death-Birth process. For cycles, we obtain an exact analytical condition for cooperation to be favored by natural selection, given in terms of the payoffs of the game and a set of structure coefficients. For regular graphs of degree three and larger, we estimate this condition using a combination of pair approximation and diffusion approximation. For a large class of cooperation games, our approximations suggest that graph-structured populations are stronger promoters of cooperation than populations lacking spatial structure. Computer simulations validate our analytical approximations for random regular graphs and cycles, but show systematic differences for graphs with many loops such as lattices. In particular, our simulation results show that these kinds of graphs can even lead to more stringent conditions for the evolution of cooperation than well-mixed populations. Overall, we provide evidence suggesting that the complexity arising from many-player interactions and spatial structure can be captured by pair approximation in the case of random graphs, but that it need to be handled with care for graphs with high clustering. PMID:27513946

  12. Generation of graph-state streams

    SciTech Connect

    Ballester, Daniel; Cho, Jaeyoon; Kim, M. S.

    2011-01-15

    We propose a protocol to generate a stream of mobile qubits in a graph state through a single stationary parent qubit and discuss two types of its physical implementation, namely, the generation of photonic graph states through an atomlike qubit and the generation of flying atoms through a cavity-mode photonic qubit. The generated graph states fall into an important class that can hugely reduce the resource requirement of fault-tolerant linear optics quantum computation, which was previously known to be far from realistic. In regard to the flying atoms, we also propose a heralded generation scheme, which allows for high-fidelity graph states even under the photon loss.

  13. Graph algorithms in the titan toolkit.

    SciTech Connect

    McLendon, William Clarence, III; Wylie, Brian Neil

    2009-10-01

    Graph algorithms are a key component in a wide variety of intelligence analysis activities. The Graph-Based Informatics for Non-Proliferation and Counter-Terrorism project addresses the critical need of making these graph algorithms accessible to Sandia analysts in a manner that is both intuitive and effective. Specifically we describe the design and implementation of an open source toolkit for doing graph analysis, informatics, and visualization that provides Sandia with novel analysis capability for non-proliferation and counter-terrorism.

  14. Simple scale interpolator facilitates reading of graphs

    NASA Technical Reports Server (NTRS)

    Fetterman, D. E., Jr.

    1965-01-01

    Simple transparent overlay with interpolation scale facilitates accurate, rapid reading of graph coordinate points. This device can be used for enlarging drawings and locating points on perspective drawings.

  15. DAG/PKCδ and IP3/Ca2+/CaMK IIβ Operate in Parallel to Each Other in PLCγ1-Driven Cell Proliferation and Migration of Human Gastric Adenocarcinoma Cells, through Akt/mTOR/S6 Pathway

    PubMed Central

    Dai, Lianzhi; Zhuang, Luhua; Zhang, Bingchang; Wang, Fen; Chen, Xiaolei; Xia, Chun; Zhang, Bing

    2015-01-01

    Phosphoinositide specific phospholipase Cγ (PLCγ) activates diacylglycerol (DAG)/protein kinase C (PKC) and inositol 1,4,5-trisphosphate (IP3)/Ca2+/calmodulin-dependent protein kinase II (CaMK II) axes to regulate import events in some cancer cells, including gastric adenocarcinoma cells. However, whether DAG/PKCδ and IP3/Ca2+/CaMK IIβ axes are simultaneously involved in PLCγ1-driven cell proliferation and migration of human gastric adenocarcinoma cells and the underlying mechanism are not elucidated. Here, we investigated the role of DAG/PKCδ or CaMK IIβ in PLCγ1-driven cell proliferation and migration of human gastric adenocarcinoma cells, using the BGC-823 cell line. The results indicated that the inhibition of PKCδ and CaMK IIβ could block cell proliferation and migration of BGC-823 cells as well as the effect of inhibiting PLCγ1, including the decrease of cell viability, the increase of apoptotic index, the down-regulation of matrix metalloproteinase (MMP) 9 expression level, and the decrease of cell migration rate. Both DAG/PKCδ and CaMK IIβ triggered protein kinase B (Akt)/mammalian target of rapamycin (mTOR)/S6 pathway to regulate protein synthesis. The data indicate that DAG/PKCδ and IP3/Ca2+/CaMK IIβ operate in parallel to each other in PLCγ1-driven cell proliferation and migration of human gastric adenocarcinoma cells through Akt/mTOR/S6 pathway, with important implication for validating PLCγ1 as a molecular biomarker in early gastric cancer diagnosis and disease surveillance. PMID:26633375

  16. GPD: a graph pattern diffusion kernel for accurate graph classification with applications in cheminformatics.

    PubMed

    Smalter, Aaron; Huan, Jun Luke; Jia, Yi; Lushington, Gerald

    2010-01-01

    Graph data mining is an active research area. Graphs are general modeling tools to organize information from heterogeneous sources and have been applied in many scientific, engineering, and business fields. With the fast accumulation of graph data, building highly accurate predictive models for graph data emerges as a new challenge that has not been fully explored in the data mining community. In this paper, we demonstrate a novel technique called graph pattern diffusion (GPD) kernel. Our idea is to leverage existing frequent pattern discovery methods and to explore the application of kernel classifier (e.g., support vector machine) in building highly accurate graph classification. In our method, we first identify all frequent patterns from a graph database. We then map subgraphs to graphs in the graph database and use a process we call "pattern diffusion" to label nodes in the graphs. Finally, we designed a graph alignment algorithm to compute the inner product of two graphs. We have tested our algorithm using a number of chemical structure data. The experimental results demonstrate that our method is significantly better than competing methods such as those kernel functions based on paths, cycles, and subgraphs. PMID:20431140

  17. Aspects of Performance on Line Graph Description Tasks: Influenced by Graph Familiarity and Different Task Features

    ERIC Educational Resources Information Center

    Xi, Xiaoming

    2010-01-01

    Motivated by cognitive theories of graph comprehension, this study systematically manipulated characteristics of a line graph description task in a speaking test in ways to mitigate the influence of graph familiarity, a potential source of construct-irrelevant variance. It extends Xi (2005), which found that the differences in holistic scores on…

  18. Helping Students Make Sense of Graphs: An Experimental Trial of SmartGraphs Software

    ERIC Educational Resources Information Center

    Zucker, Andrew; Kay, Rachel; Staudt, Carolyn

    2014-01-01

    Graphs are commonly used in science, mathematics, and social sciences to convey important concepts; yet students at all ages demonstrate difficulties interpreting graphs. This paper reports on an experimental study of free, Web-based software called SmartGraphs that is specifically designed to help students overcome their misconceptions regarding…

  19. Feature Tracking Using Reeb Graphs

    SciTech Connect

    Weber, Gunther H.; Bremer, Peer-Timo; Day, Marcus S.; Bell, John B.; Pascucci, Valerio

    2010-08-02

    Tracking features and exploring their temporal dynamics can aid scientists in identifying interesting time intervals in a simulation and serve as basis for performing quantitative analyses of temporal phenomena. In this paper, we develop a novel approach for tracking subsets of isosurfaces, such as burning regions in simulated flames, which are defined as areas of high fuel consumption on a temperature isosurface. Tracking such regions as they merge and split over time can provide important insights into the impact of turbulence on the combustion process. However, the convoluted nature of the temperature isosurface and its rapid movement make this analysis particularly challenging. Our approach tracks burning regions by extracting a temperature isovolume from the four-dimensional space-time temperature field. It then obtains isosurfaces for the original simulation time steps and labels individual connected 'burning' regions based on the local fuel consumption value. Based on this information, a boundary surface between burning and non-burning regions is constructed. The Reeb graph of this boundary surface is the tracking graph for burning regions.

  20. Phase unwrapping via graph cuts.

    PubMed

    Bioucas-Dias, José M; Valadão, Gonçalo

    2007-03-01

    Phase unwrapping is the inference of absolute phase from modulo-2pi phase. This paper introduces a new energy minimization framework for phase unwrapping. The considered objective functions are first-order Markov random fields. We provide an exact energy minimization algorithm, whenever the corresponding clique potentials are convex, namely for the phase unwrapping classical Lp norm, with p > or = 1. Its complexity is KT (n, 3n), where K is the length of the absolute phase domain measured in 2pi units and T (n, m) is the complexity of a max-flow computation in a graph with n nodes and m edges. For nonconvex clique potentials, often used owing to their discontinuity preserving ability, we face an NP-hard problem for which we devise an approximate solution. Both algorithms solve integer optimization problems by computing a sequence of binary optimizations, each one solved by graph cut techniques. Accordingly, we name the two algorithms PUMA, for phase unwrappping max-flow/min-cut. A set of experimental results illustrates the effectiveness of the proposed approach and its competitiveness in comparison with state-of-the-art phase unwrapping algorithms. PMID:17357730

  1. Clique percolation in random graphs.

    PubMed

    Li, Ming; Deng, Youjin; Wang, Bing-Hong

    2015-10-01

    As a generation of the classical percolation, clique percolation focuses on the connection of cliques in a graph, where the connection of two k cliques means that they share at least lgraphs, which gives not only the exact solutions of the critical point, but also the corresponding order parameter. Based on this, we prove theoretically that the fraction ψ of cliques in the giant clique cluster always makes a continuous phase transition as the classical percolation. However, the fraction ϕ of vertices in the giant clique cluster for l>1 makes a step-function-like discontinuous phase transition in the thermodynamic limit and a continuous phase transition for l=1. More interesting, our analysis shows that at the critical point, the order parameter ϕ(c) for l>1 is neither 0 nor 1, but a constant depending on k and l. All these theoretical findings are in agreement with the simulation results, which give theoretical support and clarification for previous simulation studies of clique percolation. PMID:26565177

  2. Multithreaded Algorithms for Graph Coloring

    SciTech Connect

    Catalyurek, Umit V.; Feo, John T.; Gebremedhin, Assefaw H.; Halappanavar, Mahantesh; Pothen, Alex

    2012-10-21

    Graph algorithms are challenging to parallelize when high performance and scalability are primary goals. Low concurrency, poor data locality, irregular access pattern, and high data access to computation ratio are among the chief reasons for the challenge. The performance implication of these features is exasperated on distributed memory machines. More success is being achieved on shared-memory, multi-core architectures supporting multithreading. We consider a prototypical graph problem, coloring, and show how a greedy algorithm for solving it can be e*ectively parallelized on multithreaded architectures. We present in particular two di*erent parallel algorithms. The first relies on speculation and iteration, and is suitable for any shared-memory, multithreaded system. The second uses data ow principles and is targeted at the massively multithreaded Cray XMT system. We benchmark the algorithms on three di*erent platforms and demonstrate scalable runtime performance. In terms of quality of solution, both algorithms use nearly the same number of colors as the serial algorithm.

  3. Clique percolation in random graphs

    NASA Astrophysics Data System (ADS)

    Li, Ming; Deng, Youjin; Wang, Bing-Hong

    2015-10-01

    As a generation of the classical percolation, clique percolation focuses on the connection of cliques in a graph, where the connection of two k cliques means that they share at least l graphs, which gives not only the exact solutions of the critical point, but also the corresponding order parameter. Based on this, we prove theoretically that the fraction ψ of cliques in the giant clique cluster always makes a continuous phase transition as the classical percolation. However, the fraction ϕ of vertices in the giant clique cluster for l >1 makes a step-function-like discontinuous phase transition in the thermodynamic limit and a continuous phase transition for l =1 . More interesting, our analysis shows that at the critical point, the order parameter ϕc for l >1 is neither 0 nor 1, but a constant depending on k and l . All these theoretical findings are in agreement with the simulation results, which give theoretical support and clarification for previous simulation studies of clique percolation.

  4. On the strong difference in reactivity of acyclic and cyclic diazodiketones with thioketones: experimental results and quantum-chemical interpretation

    PubMed Central

    Mereshchenko, Andrey S; Ivanov, Alexey V; Baranovskii, Viktor I; Rodina, Ludmila L

    2015-01-01

    Summary The 1,3-dipolar cycloaddition of acyclic 2-diazo-1,3-dicarbonyl compounds (DDC) and thioketones preferably occurs with Z,E-conformers and leads to the formation of transient thiocarbonyl ylides in two stages. The thermodynamically favorable further transformation of C=S ylides bearing at least one acyl group is identified as the 1,5-electrocyclization into 1,3-oxathioles. However, in the case of diazomalonates, the dominating process is 1,3-cyclization into thiiranes followed by their spontaneous desulfurization yielding the corresponding alkenes. Finally, carbocyclic diazodiketones are much less reactive under similar conditions due to the locked cyclic structure and are unfavorable for the 1,3-dipolar cycloaddition due to the Z,Z-conformation of the diazo molecule. This structure results in high, positive values of the Gibbs free energy change for the first stage of the cycloaddition process. PMID:25977725

  5. Synthesis and antiviral activity of novel acyclic nucleoside analogues of 5-(1-azido-2-haloethyl)uracils.

    PubMed

    Kumar, R; Sharma, N; Nath, M; Saffran, H A; Tyrrell, D L

    2001-11-22

    We present the discovery of a novel category of 5-substituted acyclic pyrimidine nucleosides as potent antiviral agents. A series of 1-[(2-hydroxyethoxy)methyl] (5-7), 1-[(2-hydroxy-1-(hydroxymethyl)ethoxy)methyl] (8-10), and 1-[4-hydroxy-3-(hydroxymethyl)-1-butyl] (11-13) derivatives of 5-(1-azido-2-haloethyl)uracil were synthesized and evaluated for their biological activity in cell culture. 1-[4-Hydroxy-3-(hydroxymethyl)-1-butyl]-5-(1-azido-2-chloroethyl)uracil (12) was the most effective antiviral agent in the in vitro assays against DHBV (EC(50) = 0.31-1.55 microM) and HCMV (EC(50) = 3.1 microM). None of the compounds investigated showed any detectable toxicity to several stationary and proliferating host cells. PMID:11708924

  6. Enabling Graph Appliance for Genome Assembly

    SciTech Connect

    Singh, Rina; Graves, Jeffrey A; Lee, Sangkeun; Sukumar, Sreenivas R; Shankar, Mallikarjun

    2015-01-01

    In recent years, there has been a huge growth in the amount of genomic data available as reads generated from various genome sequencers. The number of reads generated can be huge, ranging from hundreds to billions of nucleotide, each varying in size. Assembling such large amounts of data is one of the challenging computational problems for both biomedical and data scientists. Most of the genome assemblers developed have used de Bruijn graph techniques. A de Bruijn graph represents a collection of read sequences by billions of vertices and edges, which require large amounts of memory and computational power to store and process. This is the major drawback to de Bruijn graph assembly. Massively parallel, multi-threaded, shared memory systems can be leveraged to overcome some of these issues. The objective of our research is to investigate the feasibility and scalability issues of de Bruijn graph assembly on Cray s Urika-GD system; Urika-GD is a high performance graph appliance with a large shared memory and massively multithreaded custom processor designed for executing SPARQL queries over large-scale RDF data sets. However, to the best of our knowledge, there is no research on representing a de Bruijn graph as an RDF graph or finding Eulerian paths in RDF graphs using SPARQL for potential genome discovery. In this paper, we address the issues involved in representing a de Bruin graphs as RDF graphs and propose an iterative querying approach for finding Eulerian paths in large RDF graphs. We evaluate the performance of our implementation on real world ebola genome datasets and illustrate how genome assembly can be accomplished with Urika-GD using iterative SPARQL queries.

  7. Feynman graph generation and calculations in the Hopf algebra of Feynman graphs

    NASA Astrophysics Data System (ADS)

    Borinsky, Michael

    2014-12-01

    Two programs for the computation of perturbative expansions of quantum field theory amplitudes are provided. feyngen can be used to generate Feynman graphs for Yang-Mills, QED and φk theories. Using dedicated graph theoretic tools feyngen can generate graphs of comparatively high loop orders. feyncop implements the Hopf algebra of those Feynman graphs which incorporates the renormalization procedure necessary to calculate finite results in perturbation theory of the underlying quantum field theory. feyngen is validated by comparison to explicit calculations of zero dimensional quantum field theories and feyncop is validated using a combinatorial identity on the Hopf algebra of graphs.

  8. Stereo Vision By Pyramidal Bli Graph Matching

    NASA Astrophysics Data System (ADS)

    Shen, Jun; Castan, Serge; Zhao, Jian

    1988-04-01

    We propose the pyramidal BLI (Binary Laplacian Image) graph matching method for stereo vision, which uses the local as well as the global similarities to assure a good precision of matching results and to eliminate the ambiguities. Because the BLI is detected by DRF method which has a fast realization and matching between graphs is fast, a pseudo-real time system is possible.

  9. This Is Us! Great Graphs for Kids.

    ERIC Educational Resources Information Center

    Sullivan, Delia; O'Neil, Mary Ann

    1980-01-01

    Described are graphing activities which can be instrumental in introducing the mathematics concepts of counting, sorting, grouping, and comparing on the primary level. On the intermediate level, these activites can be used to introduce collecting and sorting unorganized data, and creating graphs to represent the data. (Author/TG)

  10. Student Reasoning about Graphs in Different Contexts

    ERIC Educational Resources Information Center

    Ivanjek, Lana; Susac, Ana; Planinic, Maja; Andrasevic, Aneta; Milin-Sipus, Zeljka

    2016-01-01

    This study investigates university students' graph interpretation strategies and difficulties in mathematics, physics (kinematics), and contexts other than physics. Eight sets of parallel (isomorphic) mathematics, physics, and other context questions about graphs, which were developed by us, were administered to 385 first-year students at the…

  11. Body Motion and Graphing. Working Paper.

    ERIC Educational Resources Information Center

    Nemirovsky, Ricardo; Tierney, Cornelia; Wright, Tracey

    This paper explores children's efforts to make sense of graphs by analyzing two students' use of a computer-based motion detector. The analysis focuses on the students' growing understanding of the motion detector which enables them to plan their movements in order to create graphs and interpret them in terms of kinesthetic actions. Students…

  12. TI-83 Graphing Calculator Keystroke Guide.

    ERIC Educational Resources Information Center

    Panik, Cathy

    This document presents keystrokes for the Texas Instrument (TI-83) graphing calculator. After presenting some basic TI-83 keystrokes, activities for student practice are listed. This is followed by keystrokes for TI-83 advanced functions such as evaluating function values, finding the zero of a function, finding the intersection of two graphs,…

  13. Generative Graph Prototypes from Information Theory.

    PubMed

    Han, Lin; Wilson, Richard C; Hancock, Edwin R

    2015-10-01

    In this paper we present a method for constructing a generative prototype for a set of graphs by adopting a minimum description length approach. The method is posed in terms of learning a generative supergraph model from which the new samples can be obtained by an appropriate sampling mechanism. We commence by constructing a probability distribution for the occurrence of nodes and edges over the supergraph. We encode the complexity of the supergraph using an approximate Von Neumann entropy. A variant of the EM algorithm is developed to minimize the description length criterion in which the structure of the supergraph and the node correspondences between the sample graphs and the supergraph are treated as missing data. To generate new graphs, we assume that the nodes and edges of graphs arise under independent Bernoulli distributions and sample new graphs according to their node and edge occurrence probabilities. Empirical evaluations on real-world databases demonstrate the practical utility of the proposed algorithm and show the effectiveness of the generative model for the tasks of graph classification, graph clustering and generating new sample graphs. PMID:26340255

  14. Multi-A Graph Patrolling and Partitioning

    NASA Astrophysics Data System (ADS)

    Elor, Y.; Bruckstein, A. M.

    2012-12-01

    We introduce a novel multi agent patrolling algorithm inspired by the behavior of gas filled balloons. Very low capability ant-like agents are considered with the task of patrolling an unknown area modeled as a graph. While executing the proposed algorithm, the agents dynamically partition the graph between them using simple local interactions, every agent assuming the responsibility for patrolling his subgraph. Balanced graph partition is an emergent behavior due to the local interactions between the agents in the swarm. Extensive simulations on various graphs (environments) showed that the average time to reach a balanced partition is linear with the graph size. The simulations yielded a convincing argument for conjecturing that if the graph being patrolled contains a balanced partition, the agents will find it. However, we could not prove this. Nevertheless, we have proved that if a balanced partition is reached, the maximum time lag between two successive visits to any vertex using the proposed strategy is at most twice the optimal so the patrol quality is at least half the optimal. In case of weighted graphs the patrol quality is at least (1)/(2){lmin}/{lmax} of the optimal where lmax (lmin) is the longest (shortest) edge in the graph.

  15. Using a Microcomputer for Graphing Practice.

    ERIC Educational Resources Information Center

    Beichner, Robert J.

    1986-01-01

    Describes a laboratory exercise that introduces physics students to graphing. Presents the program format and sample output of a computer simulation of an experiment which tests the effects of sound intensity on the crawling speed of a snail. Provides students with practice in making exponential or logarithmic graphs. (ML)

  16. Qualitative Graphing: A Construction in Mathematics.

    ERIC Educational Resources Information Center

    Narode, Ronald

    This document argues that qualitative graphing is an effective introduction to mathematics as a construction for communication of ideas involving quantitative relationships. It is suggested that with little or no prior knowledge of Cartesian coordinates or analytic descriptions of graphs using equations students can successfully grasp concepts of…

  17. Graph Coloring Used to Model Traffic Lights.

    ERIC Educational Resources Information Center

    Williams, John

    1992-01-01

    Two scheduling problems, one involving setting up an examination schedule and the other describing traffic light problems, are modeled as colorings of graphs consisting of a set of vertices and edges. The chromatic number, the least number of colors necessary for coloring a graph, is employed in the solutions. (MDH)

  18. Cognitive Aids for Guiding Graph Comprehension

    ERIC Educational Resources Information Center

    Mautone, Patricia D.; Mayer, Richard E.

    2007-01-01

    This study sought to improve students' comprehension of scientific graphs by adapting scaffolding techniques used to aid text comprehension. In 3 experiments involving 121 female and 88 male college students, some students were shown cognitive aids prior to viewing 4 geography graphs whereas others were not; all students were then asked to write a…

  19. A Ring Construction Using Finite Directed Graphs

    ERIC Educational Resources Information Center

    Bardzell, Michael

    2012-01-01

    In this paper we discuss an interesting class of noncommutative rings which can be constructed using finite directed graphs. This construction also creates a vector space. These structures provide undergraduate students connections between ring theory and graph theory and, among other things, allow them to see a ring unity element that looks quite…

  20. Critiquing the Culture of Computer Graphing Practices.

    ERIC Educational Resources Information Center

    Brasseur, Lee

    2001-01-01

    Argues that current approaches to computer graphing practices are ill suited to meet the complex needs of real users. Offers an overview of work in two major areas of graphing theory and research: the sociology of science and the educational research of mathematics and scientific students. Suggests what technical communicators can do to improve…

  1. Developing Data Graph Comprehension. Third Edition

    ERIC Educational Resources Information Center

    Curcio, Frances

    2010-01-01

    Since the dawn of civilization, pictorial representations and symbols have been used to communicate simple statistics. Efficient and effective, they are still used today in the form of pictures and graphs to record and present data. Who can tie their shoes? How many calories are in your favorite food? Make data and graphs relevant and interesting…

  2. Adolescents' Graphing Skills: A Descriptive Analysis.

    ERIC Educational Resources Information Center

    Clement, John; And Others

    Clinical interviews were conducted with 25 seventh- and eighth-grade students to determine: (1) the extent to which they could produce correct graphical representations of familiar situations; (2) to what extent they could infer relationships from graphs; (3) what are the most commonly held graphing misconceptions and how stable they are; and (4)…

  3. Pattern vectors from algebraic graph theory.

    PubMed

    Wilson, Richard C; Hancock, Edwin R; Luo, Bin

    2005-07-01

    Graph structures have proven computationally cumbersome for pattern analysis. The reason for this is that, before graphs can be converted to pattern vectors, correspondences must be established between the nodes of structures which are potentially of different size. To overcome this problem, in this paper, we turn to the spectral decomposition of the Laplacian matrix. We show how the elements of the spectral matrix for the Laplacian can be used to construct symmetric polynomials that are permutation invariants. The coefficients of these polynomials can be used as graph features which can be encoded in a vectorial manner. We extend this representation to graphs in which there are unary attributes on the nodes and binary attributes on the edges by using the spectral decomposition of a Hermitian property matrix that can be viewed as a complex analogue of the Laplacian. To embed the graphs in a pattern space, we explore whether the vectors of invariants can be embedded in a low-dimensional space using a number of alternative strategies, including principal components analysis (PCA), multidimensional scaling (MDS), and locality preserving projection (LPP). Experimentally, we demonstrate that the embeddings result in well-defined graph clusters. Our experiments with the spectral representation involve both synthetic and real-world data. The experiments with synthetic data demonstrate that the distances between spectral feature vectors can be used to discriminate between graphs on the basis of their structure. The real-world experiments show that the method can be used to locate clusters of graphs. PMID:16013758

  4. ON CLUSTERING TECHNIQUES OF CITATION GRAPHS.

    ERIC Educational Resources Information Center

    CHIEN, R.T.; PREPARATA, F.P.

    ONE OF THE PROBLEMS ENCOUNTERED IN CLUSTERING TECHNIQUES AS APPLIED TO DOCUMENT RETRIEVAL SYSTEMS USING BIBLIOGRAPHIC COUPLING DEVICES IS THAT THE COMPUTATIONAL EFFORT REQUIRED GROWS ROUGHLY AS THE SQUARE OF THE COLLECTION SIZE. IN THIS STUDY GRAPH THEORY IS APPLIED TO THIS PROBLEM BY FIRST MAPPING THE CITATION GRAPH OF THE DOCUMENT COLLECTION…

  5. Attitudes towards Graphing Calculators in Developmental Mathematics

    ERIC Educational Resources Information Center

    Rajan, Shaun Thomas

    2013-01-01

    The purpose of this exploratory study was to examine instructor and student attitudes towards the use of the graphing calculator in the developmental mathematics classroom. A focus of the study was to see if instructors or students believed there were changes in the conceptual understanding of mathematics as a result of graphing calculator…

  6. Graphing Calculators: The Newest Revolution in Mathematics.

    ERIC Educational Resources Information Center

    Clutter, Martha

    1999-01-01

    Asserts that there are numerous advantages to using graphing calculators, including the teaching of higher-level thinking skills and allowing students to draw conclusions about what they are learning. However, mathematics educators face such challenges as teaching students when it is appropriate to use graphing calculators, course-content…

  7. Teaching Discrete Mathematics with Graphing Calculators.

    ERIC Educational Resources Information Center

    Masat, Francis E.

    Graphing calculator use is often thought of in terms of pre-calculus or continuous topics in mathematics. This paper contains examples and activities that demonstrate useful, interesting, and easy ways to use a graphing calculator with discrete topics. Examples are given for each of the following topics: functions, mathematical induction and…

  8. On linear area embedding of planar graphs

    NASA Astrophysics Data System (ADS)

    Dolev, D.; Trickey, H.

    1981-09-01

    Planar embedding with minimal area of graphs on an integer grid is one of the major issues in VLSI. Valiant (V) gave an algorithm to construct a planar embedding for trees in linear area; he also proved that there are planar graphs that require quadratic area. An algorithm to embed outerplanar graphs in linear area is given. This algorithm is extended to work for every planar graph that has the following property: for every vertex there exists a path of length less than K to the exterior face, where K is a constant. Finally, finding a minimal embedding area is shown to be NP-complete for forests, and hence more general types of graphs.

  9. Quantum graphs and random-matrix theory

    NASA Astrophysics Data System (ADS)

    Pluhař, Z.; Weidenmüller, H. A.

    2015-07-01

    For simple connected graphs with incommensurate bond lengths and with unitary symmetry we prove the Bohigas-Giannoni-Schmit (BGS) conjecture in its most general form. Using supersymmetry and taking the limit of infinite graph size, we show that the generating function for every (P,Q) correlation function for both closed and open graphs coincides with the corresponding expression of random-matrix theory. We show that the classical Perron-Frobenius operator is bistochastic and possesses a single eigenvalue +1. In the quantum case that implies the existence of a zero (or massless) mode of the effective action. That mode causes universal fluctuation properties. Avoiding the saddle-point approximation we show that for graphs that are classically mixing (i.e. for which the spectrum of the classical Perron-Frobenius operator possesses a finite gap) and that do not carry a special class of bound states, the zero mode dominates in the limit of infinite graph size.

  10. Vortices and superfields on a graph

    SciTech Connect

    Kan, Nahomi; Kobayashi, Koichiro; Shiraishi, Kiyoshi

    2009-08-15

    We extend the dimensional deconstruction by utilizing the knowledge of graph theory. In the dimensional deconstruction, one uses the moose diagram to exhibit the structure of the 'theory space'. We generalize the moose diagram to a general graph with oriented edges. In the present paper, we consider only the U(1) gauge symmetry. We also introduce supersymmetry into our model by use of superfields. We suppose that vector superfields reside at the vertices and chiral superfields at the edges of a given graph. Then we can consider multivector, multi-Higgs models. In our model, [U(1)]{sup p} (where p is the number of vertices) is broken to a single U(1). Therefore, for specific graphs, we get vortexlike classical solutions in our model. We show some examples of the graphs admitting the vortex solutions of simple structure as the Bogomolnyi solution.

  11. Vortices and superfields on a graph

    NASA Astrophysics Data System (ADS)

    Kan, Nahomi; Kobayashi, Koichiro; Shiraishi, Kiyoshi

    2009-08-01

    We extend the dimensional deconstruction by utilizing the knowledge of graph theory. In the dimensional deconstruction, one uses the moose diagram to exhibit the structure of the “theory space.” We generalize the moose diagram to a general graph with oriented edges. In the present paper, we consider only the U(1) gauge symmetry. We also introduce supersymmetry into our model by use of superfields. We suppose that vector superfields reside at the vertices and chiral superfields at the edges of a given graph. Then we can consider multivector, multi-Higgs models. In our model, [U(1)]p (where p is the number of vertices) is broken to a single U(1). Therefore, for specific graphs, we get vortexlike classical solutions in our model. We show some examples of the graphs admitting the vortex solutions of simple structure as the Bogomolnyi solution.

  12. Graph Mining Meets the Semantic Web

    SciTech Connect

    Lee, Sangkeun; Sukumar, Sreenivas R; Lim, Seung-Hwan

    2015-01-01

    The Resource Description Framework (RDF) and SPARQL Protocol and RDF Query Language (SPARQL) were introduced about a decade ago to enable flexible schema-free data interchange on the Semantic Web. Today, data scientists use the framework as a scalable graph representation for integrating, querying, exploring and analyzing data sets hosted at different sources. With increasing adoption, the need for graph mining capabilities for the Semantic Web has emerged. We address that need through implementation of three popular iterative Graph Mining algorithms (Triangle count, Connected component analysis, and PageRank). We implement these algorithms as SPARQL queries, wrapped within Python scripts. We evaluate the performance of our implementation on 6 real world data sets and show graph mining algorithms (that have a linear-algebra formulation) can indeed be unleashed on data represented as RDF graphs using the SPARQL query interface.

  13. Structure and strategy in encoding simplified graphs

    NASA Technical Reports Server (NTRS)

    Schiano, Diane J.; Tversky, Barbara

    1992-01-01

    Tversky and Schiano (1989) found a systematic bias toward the 45-deg line in memory for the slopes of identical lines when embedded in graphs, but not in maps, suggesting the use of a cognitive reference frame specifically for encoding meaningful graphs. The present experiments explore this issue further using the linear configurations alone as stimuli. Experiments 1 and 2 demonstrate that perception and immediate memory for the slope of a test line within orthogonal 'axes' are predictable from purely structural considerations. In Experiments 3 and 4, subjects were instructed to use a diagonal-reference strategy in viewing the stimuli, which were described as 'graphs' only in Experiment 3. Results for both studies showed the diagonal bias previously found only for graphs. This pattern provides converging evidence for the diagonal as a cognitive reference frame in encoding linear graphs, and demonstrates that even in highly simplified displays, strategic factors can produce encoding biases not predictable solely from stimulus structure alone.

  14. Quantum walk search on Johnson graphs

    NASA Astrophysics Data System (ADS)

    Wong, Thomas G.

    2016-05-01

    The Johnson graph J(n,k) is defined by n symbols, where vertices are k-element subsets of the symbols, and vertices are adjacent if they differ in exactly one symbol. In particular, J(n,1) is the complete graph K n , and J(n,2) is the strongly regular triangular graph T n , both of which are known to support fast spatial search by continuous-time quantum walk. In this paper, we prove that J(n,3), which is the n-tetrahedral graph, also supports fast search. In the process, we show that a change of basis is needed for degenerate perturbation theory to accurately describe the dynamics. This method can also be applied to general Johnson graphs J(n,k) with fixed k.

  15. GraphReduce: Large-Scale Graph Analytics on Accelerator-Based HPC Systems

    SciTech Connect

    Sengupta, Dipanjan; Agarwal, Kapil; Song, Shuaiwen; Schwan, Karsten

    2015-09-30

    Recent work on real-world graph analytics has sought to leverage the massive amount of parallelism offered by GPU devices, but challenges remain due to the inherent irregularity of graph algorithms and limitations in GPU-resident memory for storing large graphs. We present GraphReduce, a highly efficient and scalable GPU-based framework that operates on graphs that exceed the device’s internal memory capacity. GraphReduce adopts a combination of both edge- and vertex-centric implementations of the Gather-Apply-Scatter programming model and operates on multiple asynchronous GPU streams to fully exploit the high degrees of parallelism in GPUs with efficient graph data movement between the host and the device.

  16. GraphReduce: Processing Large-Scale Graphs on Accelerator-Based Systems

    SciTech Connect

    Sengupta, Dipanjan; Song, Shuaiwen; Agarwal, Kapil; Schwan, Karsten

    2015-11-15

    Recent work on real-world graph analytics has sought to leverage the massive amount of parallelism offered by GPU devices, but challenges remain due to the inherent irregularity of graph algorithms and limitations in GPU-resident memory for storing large graphs. We present GraphReduce, a highly efficient and scalable GPU-based framework that operates on graphs that exceed the device’s internal memory capacity. GraphReduce adopts a combination of edge- and vertex-centric implementations of the Gather-Apply-Scatter programming model and operates on multiple asynchronous GPU streams to fully exploit the high degrees of parallelism in GPUs with efficient graph data movement between the host and device.

  17. Join-Graph Propagation Algorithms

    PubMed Central

    Mateescu, Robert; Kask, Kalev; Gogate, Vibhav; Dechter, Rina

    2010-01-01

    The paper investigates parameterized approximate message-passing schemes that are based on bounded inference and are inspired by Pearl's belief propagation algorithm (BP). We start with the bounded inference mini-clustering algorithm and then move to the iterative scheme called Iterative Join-Graph Propagation (IJGP), that combines both iteration and bounded inference. Algorithm IJGP belongs to the class of Generalized Belief Propagation algorithms, a framework that allowed connections with approximate algorithms from statistical physics and is shown empirically to surpass the performance of mini-clustering and belief propagation, as well as a number of other state-of-the-art algorithms on several classes of networks. We also provide insight into the accuracy of iterative BP and IJGP by relating these algorithms to well known classes of constraint propagation schemes. PMID:20740057

  18. Balanced Paths in Colored Graphs

    NASA Astrophysics Data System (ADS)

    Bianco, Alessandro; Faella, Marco; Mogavero, Fabio; Murano, Aniello

    We consider finite graphs whose edges are labeled with elements, called colors, taken from a fixed finite alphabet. We study the problem of determining whether there is an infinite path where either (i) all colors occur with the same asymptotic frequency, or (ii) there is a constant which bounds the difference between the occurrences of any two colors for all prefixes of the path. These two notions can be viewed as refinements of the classical notion of fair path, whose simplest form checks whether all colors occur infinitely often. Our notions provide stronger criteria, particularly suitable for scheduling applications based on a coarse-grained model of the jobs involved. We show that both problems are solvable in polynomial time, by reducing them to the feasibility of a linear program.

  19. Relativity on rotated graph paper

    NASA Astrophysics Data System (ADS)

    Salgado, Roberto B.

    2016-05-01

    We demonstrate a method for constructing spacetime diagrams for special relativity on graph paper that has been rotated by 45°. The diagonal grid lines represent light-flash worldlines in Minkowski spacetime, and the boxes in the grid (called "clock diamonds") represent units of measurement corresponding to the ticks of an inertial observer's light clock. We show that many quantitative results can be read off a spacetime diagram simply by counting boxes, with very little algebra. In particular, we show that the squared interval between two events is equal to the signed area of the parallelogram on the grid (called the "causal diamond") with opposite vertices corresponding to those events. We use the Doppler effect—without explicit use of the Doppler formula—to motivate the method.

  20. Degree distribution and assortativity in line graphs of complex networks

    NASA Astrophysics Data System (ADS)

    Wang, Xiangrong; Trajanovski, Stojan; Kooij, Robert E.; Van Mieghem, Piet

    2016-03-01

    Topological characteristics of links of complex networks influence the dynamical processes executed on networks triggered by links, such as cascading failures triggered by links in power grids and epidemic spread due to link infection. The line graph transforms links in the original graph into nodes. In this paper, we investigate how graph metrics in the original graph are mapped into those for its line graph. In particular, we study the degree distribution and the assortativity of a graph and its line graph. Specifically, we show, both analytically and numerically, the degree distribution of the line graph of an Erdős-Rényi graph follows the same distribution as its original graph. We derive a formula for the assortativity of line graphs and indicate that the assortativity of a line graph is not linearly related to its original graph. Additionally, line graphs of various graphs, e.g. Erdős-Rényi graphs, scale-free graphs, show positive assortativity. In contrast, we find certain types of trees and non-trees whose line graphs have negative assortativity.

  1. Approximate von Neumann entropy for directed graphs.

    PubMed

    Ye, Cheng; Wilson, Richard C; Comin, César H; Costa, Luciano da F; Hancock, Edwin R

    2014-05-01

    In this paper, we develop an entropy measure for assessing the structural complexity of directed graphs. Although there are many existing alternative measures for quantifying the structural properties of undirected graphs, there are relatively few corresponding measures for directed graphs. To fill this gap in the literature, we explore an alternative technique that is applicable to directed graphs. We commence by using Chung's generalization of the Laplacian of a directed graph to extend the computation of von Neumann entropy from undirected to directed graphs. We provide a simplified form of the entropy which can be expressed in terms of simple node in-degree and out-degree statistics. Moreover, we find approximate forms of the von Neumann entropy that apply to both weakly and strongly directed graphs, and that can be used to characterize network structure. We illustrate the usefulness of these simplified entropy forms defined in this paper on both artificial and real-world data sets, including structures from protein databases and high energy physics theory citation networks. PMID:25353841

  2. Graph isomorphism and adiabatic quantum computing

    NASA Astrophysics Data System (ADS)

    Gaitan, Frank; Clark, Lane

    2014-03-01

    In the Graph Isomorphism (GI) problem two N-vertex graphs G and G' are given and the task is to determine whether there exists a permutation of the vertices of G that preserves adjacency and maps G --> G'. If yes (no), then G and G' are said to be isomorphic (non-isomorphic). The GI problem is an important problem in computer science and is thought to be of comparable difficulty to integer factorization. We present a quantum algorithm that solves arbitrary instances of GI, and which provides a novel approach to determining all automorphisms of a graph. The algorithm converts a GI instance to a combinatorial optimization problem that can be solved using adiabatic quantum evolution. Numerical simulation of the algorithm's quantum dynamics shows that it correctly distinguishes non-isomorphic graphs; recognizes isomorphic graphs; and finds the automorphism group of a graph. We also discuss the algorithm's experimental implementation and show how it can be leveraged to solve arbitrary instances of the NP-Complete Sub-Graph Isomorphism problem.

  3. Object Discovery: Soft Attributed Graph Mining.

    PubMed

    Zhang, Quanshi; Song, Xuan; Shao, Xiaowei; Zhao, Huijing; Shibasaki, Ryosuke

    2016-03-01

    We categorize this research in terms of its contribution to both graph theory and computer vision. From the theoretical perspective, this study can be considered as the first attempt to formulate the idea of mining maximal frequent subgraphs in the challenging domain of messy visual data, and as a conceptual extension to the unsupervised learning of graph matching. We define a soft attributed pattern (SAP) to represent the common subgraph pattern among a set of attributed relational graphs (ARGs), considering both their structure and attributes. Regarding the differences between ARGs with fuzzy attributes and conventional labeled graphs, we propose a new mining strategy that directly extracts the SAP with the maximal graph size without applying node enumeration. Given an initial graph template and a number of ARGs, we develop an unsupervised method to modify the graph template into the maximal-size SAP. From a practical perspective, this research develops a general platform for learning the category model (i.e., the SAP) from cluttered visual data (i.e., the ARGs) without labeling "what is where," thereby opening the possibility for a series of applications in the era of big visual data. Experiments demonstrate the superior performance of the proposed method on RGB/RGB-D images and videos. PMID:27046496

  4. Partitioning sparse matrices with eigenvectors of graphs

    NASA Technical Reports Server (NTRS)

    Pothen, Alex; Simon, Horst D.; Liou, Kang-Pu

    1990-01-01

    The problem of computing a small vertex separator in a graph arises in the context of computing a good ordering for the parallel factorization of sparse, symmetric matrices. An algebraic approach for computing vertex separators is considered in this paper. It is shown that lower bounds on separator sizes can be obtained in terms of the eigenvalues of the Laplacian matrix associated with a graph. The Laplacian eigenvectors of grid graphs can be computed from Kronecker products involving the eigenvectors of path graphs, and these eigenvectors can be used to compute good separators in grid graphs. A heuristic algorithm is designed to compute a vertex separator in a general graph by first computing an edge separator in the graph from an eigenvector of the Laplacian matrix, and then using a maximum matching in a subgraph to compute the vertex separator. Results on the quality of the separators computed by the spectral algorithm are presented, and these are compared with separators obtained from other algorithms for computing separators. Finally, the time required to compute the Laplacian eigenvector is reported, and the accuracy with which the eigenvector must be computed to obtain good separators is considered. The spectral algorithm has the advantage that it can be implemented on a medium-size multiprocessor in a straightforward manner.

  5. Massive graph visualization : LDRD final report.

    SciTech Connect

    Wylie, Brian Neil; Moreland, Kenneth D.

    2007-10-01

    Graphs are a vital way of organizing data with complex correlations. A good visualization of a graph can fundamentally change human understanding of the data. Consequently, there is a rich body of work on graph visualization. Although there are many techniques that are effective on small to medium sized graphs (tens of thousands of nodes), there is a void in the research for visualizing massive graphs containing millions of nodes. Sandia is one of the few entities in the world that has the means and motivation to handle data on such a massive scale. For example, homeland security generates graphs from prolific media sources such as television, telephone, and the Internet. The purpose of this project is to provide the groundwork for visualizing such massive graphs. The research provides for two major feature gaps: a parallel, interactive visualization framework and scalable algorithms to make the framework usable to a practical application. Both the frameworks and algorithms are designed to run on distributed parallel computers, which are already available at Sandia. Some features are integrated into the ThreatView{trademark} application and future work will integrate further parallel algorithms.

  6. Lamplighter groups, de Brujin graphs, spider-web graphs and their spectra

    NASA Astrophysics Data System (ADS)

    Grigorchuk, R.; Leemann, P.-H.; Nagnibeda, T.

    2016-05-01

    We study the infinite family of spider-web graphs \\{{{ S }}k,N,M\\}, k≥slant 2, N≥slant 0 and M≥slant 1, initiated in the 50s in the context of network theory. It was later shown in physical literature that these graphs have remarkable percolation and spectral properties. We provide a mathematical explanation of these properties by putting the spider-web graphs in the context of group theory and algebraic graph theory. Namely, we realize them as tensor products of the well-known de Bruijn graphs \\{{{ B }}k,N\\} with cyclic graphs \\{{C}M\\} and show that these graphs are described by the action of the lamplighter group {{ L }}k={Z}/k{Z}\\wr {Z} on the infinite binary tree. Our main result is the identification of the infinite limit of \\{{{ S }}k,N,M\\}, as N,M\\to ∞ , with the Cayley graph of the lamplighter group {{ L }}k which, in turn, is one of the famous Diestel–Leader graphs {{DL}}k,k. As an application we compute the spectra of all spider-web graphs and show their convergence to the discrete spectral distribution associated with the Laplacian on the lamplighter group.

  7. BioGraphE: High-performance bionetwork analysis using the Biological Graph Environment

    SciTech Connect

    Chin, George; Chavarría-Miranda, Daniel; Nakamura, Grant C.; Sofia, Heidi J.

    2008-05-28

    Graphs and networks are common analysis representations for biological systems. Many traditional graph algorithms such as k-clique, k-coloring, and subgraph matching have great potential as analysis techniques for newly available data in biology. Yet, as the amount of genomic and bionetwork information rapidly grows, scientists need advanced new computational strategies and tools for dealing with the complexities of the bionetwork analysis and the volume of the data. We introduce a computational framework for graph analysis called the Biological Graph Environment (BioGraphE), which provides a general, scalable integration platform for connecting graph problems in biology to optimized computational solvers and high-performance systems. This framework enables biology researchers and computational scientists to identify and deploy network analysis applications and to easily connect them to efficient and powerful computational software and hardware that are specifically designed and tuned to solve complex graph problems. In our particular application of BioGraphE to support network analysis in genome biology, we investigate the use of a Boolean satisfiability solver known as Survey Propagation as a core computational solver and high-performance parallel systems that utilize multi-threaded architectures. In our application of BioGraphE to conduct bionetwork analysis of homology networks, we found that BioGraphE and a custom, parallel implementation of the Survey Propagation SAT solver were capable of solving very large bionetwork problems at high rates of execution on different high-performance computing platforms.

  8. Enabling Graph Mining in RDF Triplestores using SPARQL for Holistic In-situ Graph Analysis

    DOE PAGESBeta

    Lee, Sangkeun; Sukumar, Sreenivas R; Hong, Seokyong; Lim, Seung-Hwan

    2016-01-01

    The graph analysis is now considered as a promising technique to discover useful knowledge in data with a new perspective. We envi- sion that there are two dimensions of graph analysis: OnLine Graph Analytic Processing (OLGAP) and Graph Mining (GM) where each respectively focuses on subgraph pattern matching and automatic knowledge discovery in graph. Moreover, as these two dimensions aim to complementarily solve complex problems, holistic in-situ graph analysis which covers both OLGAP and GM in a single system is critical for minimizing the burdens of operating multiple graph systems and transferring intermediate result-sets between those systems. Nevertheless, most existingmore » graph analysis systems are only capable of one dimension of graph analysis. In this work, we take an approach to enabling GM capabilities (e.g., PageRank, connected-component analysis, node eccentricity, etc.) in RDF triplestores, which are originally developed to store RDF datasets and provide OLGAP capability. More specifically, to achieve our goal, we implemented six representative graph mining algorithms using SPARQL. The approach allows a wide range of available RDF data sets directly applicable for holistic graph analysis within a system. For validation of our approach, we evaluate performance of our implementations with nine real-world datasets and three different computing environments - a laptop computer, an Amazon EC2 instance, and a shared-memory Cray XMT2 URIKA-GD graph-processing appliance. The experimen- tal results show that our implementation can provide promising and scalable performance for real world graph analysis in all tested environments. The developed software is publicly available in an open-source project that we initiated.« less

  9. Enabling Graph Mining in RDF Triplestores using SPARQL for Holistic In-situ Graph Analysis

    SciTech Connect

    Lee, Sangkeun; Sukumar, Sreenivas R; Hong, Seokyong; Lim, Seung-Hwan

    2016-01-01

    The graph analysis is now considered as a promising technique to discover useful knowledge in data with a new perspective. We envi- sion that there are two dimensions of graph analysis: OnLine Graph Analytic Processing (OLGAP) and Graph Mining (GM) where each respectively focuses on subgraph pattern matching and automatic knowledge discovery in graph. Moreover, as these two dimensions aim to complementarily solve complex problems, holistic in-situ graph analysis which covers both OLGAP and GM in a single system is critical for minimizing the burdens of operating multiple graph systems and transferring intermediate result-sets between those systems. Nevertheless, most existing graph analysis systems are only capable of one dimension of graph analysis. In this work, we take an approach to enabling GM capabilities (e.g., PageRank, connected-component analysis, node eccentricity, etc.) in RDF triplestores, which are originally developed to store RDF datasets and provide OLGAP capability. More specifically, to achieve our goal, we implemented six representative graph mining algorithms using SPARQL. The approach allows a wide range of available RDF data sets directly applicable for holistic graph analysis within a system. For validation of our approach, we evaluate performance of our implementations with nine real-world datasets and three different computing environments - a laptop computer, an Amazon EC2 instance, and a shared-memory Cray XMT2 URIKA-GD graph-processing appliance. The experimen- tal results show that our implementation can provide promising and scalable performance for real world graph analysis in all tested environments. The developed software is publicly available in an open-source project that we initiated.

  10. Encoding the core electrons with graph concepts.

    PubMed

    Pogliani, Lionello

    2004-01-01

    The core electron problem of atoms in chemical graph studies has always been considered as a minor problem. Usually, chemical graphs had to encode just a small set of second row atoms, i.e., C, N, O, and F, thus, graph and, in some cases, pseudograph concepts were enough to "graph" encode the molecules at hand. Molecular connectivity theory, together with its side-branch the electrotopological state, introduced two "ad hoc" algorithms for the core electrons of higher-row atoms based, mainly, on quantum concepts alike. Recently, complete graphs, and, especially, odd complete graphs have been introduced to encode the core electrons of higher-row atoms. By the aid of these types of graphs a double-valued algorithm has been proposed for the valence delta, deltav, of any type of atoms of the periodic table with a principal quantum number n > or =2. The new algorithm is centered on an invariant suggested by the hand-shaking theorem, and the values it gives rise to parallel in some way the values derived by the aid of the two old "quantum" algorithms. A thorough comparative analysis of the newly proposed algorithms has been undertaken for atoms of the group 1A-7A of the periodic table. This comparative study includes the electronegativity, the size of the atoms, the first ionization energy, and the electron affinity. The given algorithm has also been tested with sequential complete graphs, while the even complete graphs give rise to conceptual difficulties. QSAR/QSPR studies do not show a clear-cut preference for any of the two values the algorithm gives rise to, even if recent results seem to prefer one of the two values. PMID:14741009

  11. The role of minerals in the thermal alteration of organic matter. IV - Generation of n-alkanes, acyclic isoprenoids, and alkenes in laboratory experiments

    NASA Technical Reports Server (NTRS)

    Huizinga, Bradley J.; Tannenbaum, Eli; Kaplan, Isaac R.

    1987-01-01

    The effect of common sedimentary minerals (illite, Na-montmorillonite, or calcite) under different water concentrations on the generation and release of n-alkanes, acyclic isoprenoids, and select alkenes from oil-prone kerogens was investigated. Matrices containing Green River Formation kerogen or Monterey Formation kerogen, alone or in the presence of minerals, were heated at 200 or 300 C for periods of up to 1000 hours, and the pyrolysis products were analyzed. The influence of the first two clay minerals was found to be critically dependent on the water content. Under the dry pyrolysis conditions, both minerals significantly reduced alkene formation; the C12+ n-alkanes and acyclic isoprenoids were mostly destroyed by montmorillonite, but underwent only minor alteration with illite. Under hydrous conditions (mineral/water of 2/1), the effects of both minerals were substantially reduced. Calcite had no significant effect on the thermal evolution of the hydrocarbons.

  12. Scale-invariant geometric random graphs

    NASA Astrophysics Data System (ADS)

    Xie, Zheng; Rogers, Tim

    2016-03-01

    We introduce and analyze a class of growing geometric random graphs that are invariant under rescaling of space and time. Directed connections between nodes are drawn according to influence zones that depend on node position in space and time, mimicking the heterogeneity and increased specialization found in growing networks. Through calculations and numerical simulations we explore the consequences of scale invariance for geometric random graphs generated this way. Our analysis reveals a dichotomy between scale-free and Poisson distributions of in- and out-degree, the existence of a random number of hub nodes, high clustering, and unusual percolation behavior. These properties are similar to those of empirically observed web graphs.

  13. Line graphs for a multiplex network.

    PubMed

    Criado, Regino; Flores, Julio; García Del Amo, Alejandro; Romance, Miguel; Barrena, Eva; Mesa, Juan A

    2016-06-01

    It is well known that line graphs offer a good summary of the graphs properties, which make them easier to analyze and highlight the desired properties. We extend the concept of line graph to multiplex networks in order to analyze multi-plexed and multi-layered networked systems. As these structures are very rich, different approaches to this notion are required to capture a variety of situations. Some relationships between these approaches are established. Finally, by means of some simulations, the potential utility of this concept is illustrated. PMID:27368798

  14. A heterogeneous graph-based recommendation simulator

    SciTech Connect

    Yeonchan, Ahn; Sungchan, Park; Lee, Matt Sangkeun; Sang-goo, Lee

    2013-01-01

    Heterogeneous graph-based recommendation frameworks have flexibility in that they can incorporate various recommendation algorithms and various kinds of information to produce better results. In this demonstration, we present a heterogeneous graph-based recommendation simulator which enables participants to experience the flexibility of a heterogeneous graph-based recommendation method. With our system, participants can simulate various recommendation semantics by expressing the semantics via meaningful paths like User Movie User Movie. The simulator then returns the recommendation results on the fly based on the user-customized semantics using a fast Monte Carlo algorithm.

  15. Intelligent Graph Layout Using Many Users' Input.

    PubMed

    Yuan, Xiaoru; Che, Limei; Hu, Yifan; Zhang, Xin

    2012-12-01

    In this paper, we propose a new strategy for graph drawing utilizing layouts of many sub-graphs supplied by a large group of people in a crowd sourcing manner. We developed an algorithm based on Laplacian constrained distance embedding to merge subgraphs submitted by different users, while attempting to maintain the topological information of the individual input layouts. To facilitate collection of layouts from many people, a light-weight interactive system has been designed to enable convenient dynamic viewing, modification and traversing between layouts. Compared with other existing graph layout algorithms, our approach can achieve more aesthetic and meaningful layouts with high user preference. PMID:26357179

  16. Spectral statistics of nearly unidirectional quantum graphs

    NASA Astrophysics Data System (ADS)

    Akila, Maram; Gutkin, Boris

    2015-08-01

    The energy levels of a quantum graph with time reversal symmetry and unidirectional classical dynamics are doubly degenerate and obey the spectral statistics of the Gaussian unitary ensemble. These degeneracies, however, are lifted when the unidirectionality is broken in one of the graph’s vertices by a singular perturbation. Based on a random matrix model we derive an analytic expression for the nearest neighbour distribution between energy levels of such systems. As we demonstrate the result agrees excellently with the actual statistics for graphs with a uniform distribution of eigenfunctions. Yet, it exhibits quite substantial deviations for classes of graphs which show strong scarring.

  17. The MultiThreaded Graph Library (MTGL)

    SciTech Connect

    Berry, Jonathan; Leung, Vitus; McLendon, III, William; & Madduri, Kamesh

    2008-07-17

    The MultiThreaded Graph Library (MTGL) is a set of header files that implement graph algorithm in such a way that they can run on massively multithreaded architectures. It is based upon the Boost Graph Library, but doesn’t use Boost since the latter doesn’t run well on these architectures.

  18. Coloring random graphs and maximizing local diversity.

    PubMed

    Bounkong, S; van Mourik, J; Saad, D

    2006-11-01

    We study a variation of the graph coloring problem on random graphs of finite average connectivity. Given the number of colors, we aim to maximize the number of different colors at neighboring vertices (i.e., one edge distance) of any vertex. Two efficient algorithms, belief propagation and Walksat, are adapted to carry out this task. We present experimental results based on two types of random graphs for different system sizes and identify the critical value of the connectivity for the algorithms to find a perfect solution. The problem and the suggested algorithms have practical relevance since various applications, such as distributed storage, can be mapped onto this problem. PMID:17280022

  19. Loops in Reeb Graphs of 2-Manifolds

    SciTech Connect

    Cole-McLaughlin, K; Edelsbrunner, H; Harer, J; Natarajan, V; Pascucci, V

    2004-12-16

    Given a Morse function f over a 2-manifold with or without boundary, the Reeb graph is obtained by contracting the connected components of the level sets to points. We prove tight upper and lower bounds on the number of loops in the Reeb graph that depend on the genus, the number of boundary components, and whether or not the 2-manifold is orientable. We also give an algorithm that constructs the Reeb graph in time O(n log n), where n is the number of edges in the triangulation used to represent the 2-manifold and the Morse function.

  20. Loops in Reeb Graphs of 2-Manifolds

    SciTech Connect

    Cole-McLaughlin, K; Edelsbrunner, H; Harer, J; Natarajan, V; Pascucci, V

    2003-02-11

    Given a Morse function f over a 2-manifold with or without boundary, the Reeb graph is obtained by contracting the connected components of the level sets to points. We prove tight upper and lower bounds on the number of loops in the Reeb graph that depend on the genus, the number of boundary components, and whether or not the 2-manifold is orientable. We also give an algorithm that constructs the Reeb graph in time O(n log n), where n is the number of edges in the triangulation used to represent the 2-manifold and the Morse function.

  1. Finite Frames and Graph Theoretic Uncertainty Principles

    NASA Astrophysics Data System (ADS)

    Koprowski, Paul J.

    The subject of analytical uncertainty principles is an important field within harmonic analysis, quantum physics, and electrical engineering. We explore uncertainty principles in the context of the graph Fourier transform, and we prove additive results analogous to the multiplicative version of the classical uncertainty principle. We establish additive uncertainty principles for finite Parseval frames. Lastly, we examine the feasibility region of simultaneous values of the norms of a graph differential operator acting on a function f ∈ l2(G) and its graph Fourier transform.

  2. Line graphs for a multiplex network

    NASA Astrophysics Data System (ADS)

    Criado, Regino; Flores, Julio; García del Amo, Alejandro; Romance, Miguel; Barrena, Eva; Mesa, Juan A.

    2016-06-01

    It is well known that line graphs offer a good summary of the graphs properties, which make them easier to analyze and highlight the desired properties. We extend the concept of line graph to multiplex networks in order to analyze multi-plexed and multi-layered networked systems. As these structures are very rich, different approaches to this notion are required to capture a variety of situations. Some relationships between these approaches are established. Finally, by means of some simulations, the potential utility of this concept is illustrated.

  3. Phenylalanine Ammonia-Lyase-Catalyzed Deamination of an Acyclic Amino Acid: Enzyme Mechanistic Studies Aided by a Novel Microreactor Filled with Magnetic Nanoparticles.

    PubMed

    Weiser, Diána; Bencze, László Csaba; Bánóczi, Gergely; Ender, Ferenc; Kiss, Róbert; Kókai, Eszter; Szilágyi, András; Vértessy, Beáta G; Farkas, Ödön; Paizs, Csaba; Poppe, László

    2015-11-01

    Phenylalanine ammonia-lyase (PAL), found in many organisms, catalyzes the deamination of l-phenylalanine (Phe) to (E)-cinnamate by the aid of its MIO prosthetic group. By using PAL immobilized on magnetic nanoparticles and fixed in a microfluidic reactor with an in-line UV detector, we demonstrated that PAL can catalyze ammonia elimination from the acyclic propargylglycine (PG) to yield (E)-pent-2-ene-4-ynoate. This highlights new opportunities to extend MIO enzymes towards acyclic substrates. As PG is acyclic, its deamination cannot involve a Friedel-Crafts-type attack at an aromatic ring. The reversibility of the PAL reaction, demonstrated by the ammonia addition to (E)-pent-2-ene-4-ynoate yielding enantiopure l-PG, contradicts the proposed highly exothermic single-step mechanism. Computations with the QM/MM models of the N-MIO intermediates from L-PG and L-Phe in PAL show similar arrangements within the active site, thus supporting a mechanism via the N-MIO intermediate. PMID:26345352

  4. Anti-EGFRvIII monoclonal antibody armed with 177Lu: in vivo comparison of macrocyclic and acyclic ligands

    PubMed Central

    Hens, Marc; Vaidyanathan, Ganesan; Zhao, Xiao-Guang; Bigner, Darell D.; Zalutsky, Michael R.

    2010-01-01

    Introduction Monoclonal antibody (mAb) L8A4 binds specifically to the epidermal growth factor receptor variant III (EGFRvIII) that is present on gliomas but not normal tissues, and is internalized rapidly after receptor binding. Because of the short range of its β-emissions, labeling this mAb with177Lu would be an attractive approach for the treatment of residual tumor margins remaining after surgical debulking of brain tumors. Materials and Methods L8A4 mAb was labeled with 177Lu using the acyclic ligands [(R)-2-Amino-3-(4-isothiocyanatophenyl)propyl]-trans-(S,S)-cyclohexane-1,2-diamine- pentaacetic acid (CHX-A″-DTPA) and 2-(4-Isothiocyanatobenzyl)-6-methyldiethylene- triaminepentaacetic acid (1B4M-DTPA), and the macrocyclic ligands S-2-(4- Isothiocyanatobenzyl)-1,4,7,10-tetraazacyclododecane-tetraacetic acid (C-DOTA) and α-(5-isothiocyanato-2-methoxyphenyl)-1,4,7,10-tetraazacyclododecane-1,4,7,10- tetraacetic acid (MeO-DOTA). Paired-label tissue distribution experiments were performed in athymic mice bearing subcutaneous EGFRvIII-expressing U87.)EGFR glioma xenografts over a period of 1 to 8 days to directly compare 177Lu-labeled L8A4 to L8A4 labeled with 125I using N-succinimidyl 4-guanidinomethyl-3-[125I]iodobenzoate ([125I]SGMIB). Results Except with C-DOTA, tumor uptake for the 177Lu-labeled mAb was significantly higher than the co-administered radioiodinated preparation; however, this was also the case for spleen, liver, bone and kidneys. Tumor:normal tissue ratios for 177Lu-1B4M-DTPA-L8A4 and to an even greater extent, 177Lu-MeO-DOTA-L8A4, were higher than those for [125I]SGMIB-L8A4 in most other tissues. Conclusions Tumor and normal tissue distribution patterns for this anti-EGFRvIII mAb were dependent on the nature of the bifunctional chelate used for 177Lu labeling. Optimal results were obtained with 1B4M-DTPA and MeO-DOTA, suggesting no clear advantage for acyclic vs. macrocyclic ligands for this application. PMID:20870149

  5. Analysis of cyclic and acyclic nicotinic cholinergic agonists using radioligand binding, single channel recording, and nuclear magnetic resonance spectroscopy.

    PubMed Central

    McGroddy, K A; Carter, A A; Tubbert, M M; Oswald, R E

    1993-01-01

    The relationship between the structure and function of a series of nicotinic cholinergic agonists has been studied using radioligand binding, single channel recording, and nuclear magnetic resonance spectroscopy. The cyclic compound 1,1-dimethyl-4-acetylpiperazinium iodide and its trifluoromethyl analogue (F3-PIP) interact with nicotinic acetylcholine receptors (nAChRs) from both Torpedo electroplaque and BC3H-1 cells at lower concentrations than the acyclic derivatives, N,N,N,N'-tetramethyl-N'-acetylethylenediamine iodide and its fluorinated analogue (F3-TED). The magnitude of the difference in potencies depends on the type of measurement. In binding experiments, the differences between the two classes of compounds depends mainly on the conditions of the experiment. In measurements of the initial interaction with the nAChR, the PIP compounds have an affinity approximately one order of magnitude higher than that of the TED compounds. Longer incubations indicated that the PIP compounds were able to induce a time-dependent shift in receptor affinity consistent with desensitization, whereas the TED compounds were unable to induce such a shift. The activation of single channel currents by the cyclic compounds occurs at concentrations approximately two orders of magnitude lower than for the acyclic compounds, but the TED compounds exhibit a larger degree of channel blockade than the PIP compounds. Previous work (McGroddy, K.A., and R.E. Oswald. 1992. Biophys. J. 64:314-324) has shown that the TED compounds can exist in two energetically distinct conformational states related by an isomerization of the amide bond. 19F nuclear magnetic resonance experiments suggest that the higher energy population of the TED compounds may interact preferentially with the ACh binding sites on the nAChRs and that a significant fraction of the difference between the initial affinity of the PIP and TED compounds may be accounted for by the predominance in solution of a conformational state

  6. Design and synthesis of novel 5-substituted acyclic pyrimidine nucleosides as potent and selective inhibitors of hepatitis B virus.

    PubMed

    Kumar, Rakesh; Nath, Mahendra; Tyrrell, D Lorne J

    2002-05-01

    A novel class of 5-substituted acyclic pyrimidine nucleosides, 1-[(2-hydroxyethoxy)methyl]-5-(1-azidovinyl)uracil (9a), 1-[(2-hydroxy-1-(hydroxymethyl)ethoxy)methyl]-5-(1-azidovinyl)uracil (9b), and 1-[4-hydroxy-3-(hydroxymethyl)-1-butyl]-5-(1-azidovinyl)uracil (9c), were synthesized by regiospecific addition of bromine azide to the 5-vinyl substituent of the respective 5-vinyluracils (2a-c) followed by treatment of the obtained 5-(1-azido-2-bromoethyl) compounds (3a-c) with t-BuOK, to affect the base-catalyzed elimination of HBr. Thermal decomposition of 9b and 9c at 110 degrees C in dioxane yielded corresponding 5-[2-(1-azirinyl)]uracil analogues (10b,c). The 5-(1-azidovinyl)uracil derivatives 9a-c were found to exhibit potent and selective in vitro anti-HBV activity against duck hepatitis B virus (DHBV) infected primary duck hepatocytes at low concentrations (EC(50) = 0.01-0.1 microg/mL range). The most active anti-DHBV agent (9c), possessing a [4-hydroxy-3-(hydroxymethyl)-1-butyl] substituent at N-1, exhibited an activity (EC(50) of 0.01-0.05 microg/mL) comparable to that of reference compound (-)-beta-L-2',3'-dideoxy-3'-thiacytidine (3-TC) (EC(50) = 0.01-0.05 microg/mL). In contrast, related 5-[2-(1-azirinyl)]uracil analogues (10b,c) were devoid of anti-DHBV activity, indicating that an acyclic side chain at C-5 position of the pyrimidine ring is essential for anti-HBV activity. The pyrimidine nucleosides (9a-c, 10b,c) exhibited no cytotoxic activity against a panel of 60 human cancer cell lines. All of the compounds investigated did not show any detectable toxicity to several stationary and proliferating host cell lines or to mitogen stimulated proliferating human T lymphocytes, up to the highest concentration tested. PMID:11985471

  7. Data graphs and mechanistic explanation.

    PubMed

    Burnston, Daniel C

    2016-06-01

    It is a widespread assumption in philosophy of science that representations of data are not explanatory-that they are mere stepping stones towards an explanation, such as a representation of a mechanism. I draw on instances of representational and explanatory practice from mammalian chronobiology to suggest that this assumption is unsustainable. In many instances, biologists employ representations of data in explanatory ways that are not reducible to constraints on or evidence for representations of mechanisms. Data graphs are used to represent relationships between quantities across conditions, and often these representations are necessary for explaining particular aspects of the phenomena under study. The benefit of the analysis is two-fold. First, it provides a more accurate account of explanatory practice in broadly mechanistic investigation in biology. Second, it suggests that there is not an explanatorily "fundamental" type of representation in biology. Rather, the practice of explanation consists in the construction of different types of representations and their employment for distinct explanatory purposes. PMID:26871740

  8. Fast Robust PCA on Graphs

    NASA Astrophysics Data System (ADS)

    Shahid, Nauman; Perraudin, Nathanael; Kalofolias, Vassilis; Puy, Gilles; Vandergheynst, Pierre

    2016-06-01

    Mining useful clusters from high dimensional data has received significant attention of the computer vision and pattern recognition community in the recent years. Linear and non-linear dimensionality reduction has played an important role to overcome the curse of dimensionality. However, often such methods are accompanied with three different problems: high computational complexity (usually associated with the nuclear norm minimization), non-convexity (for matrix factorization methods) and susceptibility to gross corruptions in the data. In this paper we propose a principal component analysis (PCA) based solution that overcomes these three issues and approximates a low-rank recovery method for high dimensional datasets. We target the low-rank recovery by enforcing two types of graph smoothness assumptions, one on the data samples and the other on the features by designing a convex optimization problem. The resulting algorithm is fast, efficient and scalable for huge datasets with O(nlog(n)) computational complexity in the number of data samples. It is also robust to gross corruptions in the dataset as well as to the model parameters. Clustering experiments on 7 benchmark datasets with different types of corruptions and background separation experiments on 3 video datasets show that our proposed model outperforms 10 state-of-the-art dimensionality reduction models. Our theoretical analysis proves that the proposed model is able to recover approximate low-rank representations with a bounded error for clusterable data.

  9. Signals on graphs: Transforms and tomograms

    NASA Astrophysics Data System (ADS)

    Vilela Mendes, R.; Mendes, Hugo C.; Araújo, Tanya

    2016-05-01

    Development of efficient tools for the representation of large datasets is a precondition for the study of dynamics on networks. Generalizations of the Fourier transform on graphs have been constructed through projections on the eigenvectors of graph matrices. By exploring mappings of the spectrum of these matrices we show how to construct more general transforms, in particular wavelet-like transforms on graphs. For time-series, tomograms, a generalization of the Radon transforms to arbitrary pairs of non-commuting operators, are positive bilinear transforms with a rigorous probabilistic interpretation which provide a full characterization of the signals and are robust in the presence of noise. Here the notion of tomogram is also extended to signals on arbitrary graphs.

  10. Trivalent Graphs, Volume Conjectures and Character Varieties

    NASA Astrophysics Data System (ADS)

    Nawata, Satoshi; Pichai, Ramadevi; Zodinmawia

    2014-10-01

    The generalized volume conjecture and the AJ conjecture (a.k.a. the quantum volume conjecture) are extended to colored quantum invariants of the theta and tetrahedron graph. The character variety of the fundamental group of the complement of a trivalent graph with E edges in S 3 is a Lagrangian subvariety of the Hitchin moduli space over the Riemann surface of genus g = E/3 + 1. For the theta and tetrahedron graph, we conjecture that the configuration of the character variety is locally determined by large color asymptotics of the quantum invariants of the trivalent graph in terms of complex Fenchel-Nielsen coordinates. Moreover, the q-holonomic difference equation of the quantum invariants provides the quantization of the character variety.

  11. Bipartite graph partitioning and data clustering

    SciTech Connect

    Zha, Hongyuan; He, Xiaofeng; Ding, Chris; Gu, Ming; Simon, Horst D.

    2001-05-07

    Many data types arising from data mining applications can be modeled as bipartite graphs, examples include terms and documents in a text corpus, customers and purchasing items in market basket analysis and reviewers and movies in a movie recommender system. In this paper, the authors propose a new data clustering method based on partitioning the underlying biopartite graph. The partition is constructed by minimizing a normalized sum of edge weights between unmatched pairs of vertices of the bipartite graph. They show that an approximate solution to the minimization problem can be obtained by computing a partial singular value decomposition (SVD) of the associated edge weight matrix of the bipartite graph. They point out the connection of their clustering algorithm to correspondence analysis used in multivariate analysis. They also briefly discuss the issue of assigning data objects to multiple clusters. In the experimental results, they apply their clustering algorithm to the problem of document clustering to illustrate its effectiveness and efficiency.

  12. Experiments on parallel graph coloring and applications

    SciTech Connect

    Lewandowski, G.; Condon, A.

    1994-12-31

    The graph coloring problem is an NP-Complete problem with a wide array of applications, such as course scheduling, exam scheduling, register allocation, and parallelizing solutions for sparse systems of linear equations. Much theoretical effort has been put into designing heuristics that perform well on randomly generated graphs. The best sequential heuristics require large amounts of time and tuning of various parameters in the heuristics. We have used parallelism to combine exhaustive search with successful heuristic strategies to create a new heuristic, Hybrid, which does well on a wide variety of graphs, without any tuning of parameters. We have also gathered real application data and tested several heuristics on this data. Our study of real data points out some flaws in studying only random graphs and also suggests interesting new problems for study.

  13. An Investigation of the Coauthor Graph.

    ERIC Educational Resources Information Center

    Logan, Elisabeth L.; Shaw, W. M., Jr.

    1987-01-01

    The role of the coauthor relationship in the structure of informal communications networks within disciplines is explored, and the validity of coauthor graphs used to map these relationships is tested for both small and large databases. (CLB)

  14. Bipartite Graphs of Large Clique-Width

    NASA Astrophysics Data System (ADS)

    Korpelainen, Nicholas; Lozin, Vadim V.

    Recently, several constructions of bipartite graphs of large clique-width have been discovered in the literature. In the present paper, we propose a general framework for developing such constructions and use it to obtain new results on this topic.

  15. Graph Theory and the High School Student.

    ERIC Educational Resources Information Center

    Chartrand, Gary; Wall, Curtiss E.

    1980-01-01

    Graph theory is presented as a tool to instruct high school mathematics students. A variety of real world problems can be modeled which help students recognize the importance and difficulty of applying mathematics. (MP)

  16. Graph500 in OpenSHMEM

    SciTech Connect

    D'Azevedo, Ed F; Imam, Neena

    2015-01-01

    This document describes the effort to implement the Graph 500 benchmark using OpenSHMEM based on the MPI-2 one-side version. The Graph 500 benchmark performs a breadth-first search in parallel on a large randomly generated undirected graph and can be implemented using basic MPI-1 and MPI-2 one-sided communication. Graph 500 requires atomic bit-wise operations on unsigned long integers but neither atomic bit-wise operations nor OpenSHMEM for unsigned long are available in OpenSHEM. Such needed bit-wise atomic operations and support for unsigned long are implemented using atomic condition swap (CSWAP) on signed long integers. Preliminary results on comparing the OpenSHMEM and MPI-2 one-sided implementations on a Silicon Graphics Incorporated (SGI) cluster and the Cray XK7 are presented.

  17. Fault-tolerant dynamic task graph scheduling

    SciTech Connect

    Kurt, Mehmet C.; Krishnamoorthy, Sriram; Agrawal, Kunal; Agrawal, Gagan

    2014-11-16

    In this paper, we present an approach to fault tolerant execution of dynamic task graphs scheduled using work stealing. In particular, we focus on selective and localized recovery of tasks in the presence of soft faults. We elicit from the user the basic task graph structure in terms of successor and predecessor relationships. The work stealing-based algorithm to schedule such a task graph is augmented to enable recovery when the data and meta-data associated with a task get corrupted. We use this redundancy, and the knowledge of the task graph structure, to selectively recover from faults with low space and time overheads. We show that the fault tolerant design retains the essential properties of the underlying work stealing-based task scheduling algorithm, and that the fault tolerant execution is asymptotically optimal when task re-execution is taken into account. Experimental evaluation demonstrates the low cost of recovery under various fault scenarios.

  18. Exploring Hill Ciphers with Graphing Calculators.

    ERIC Educational Resources Information Center

    St. John, Dennis

    1998-01-01

    Explains how to code and decode messages using Hill ciphers which combine matrix multiplication and modular arithmetic. Discusses how a graphing calculator can facilitate the matrix and modular arithmetic used in the coding and decoding procedures. (ASK)

  19. Note on resolution, connection graphs, and subsumption

    SciTech Connect

    De Champeaux, D.

    1982-07-01

    Completeness is endangered by the combination in connection graph of subsumption deletion rules and the run time pure literal rule. With some care completeness can be restored. How this can be achieved is briefly discussed. 3 references.

  20. Pre-Service Elementary Teachers' Understandings of Graphs

    ERIC Educational Resources Information Center

    Alacaci, Cengiz; Lewis, Scott; O'Brien, George E.; Jiang, Zhonghong

    2011-01-01

    Choosing graphs to display quantitative information is a component of "graph sense". An important aspect of pre-service elementary teachers' content knowledge; ability to choose appropriate graphs in applied contexts is investigated in this study. They were given three scenarios followed by four graphs representing the same quantitative data. They…

  1. Continuous Time Group Discovery in Dynamic Graphs

    SciTech Connect

    Miller, K; Eliassi-Rad, T

    2010-11-04

    With the rise in availability and importance of graphs and networks, it has become increasingly important to have good models to describe their behavior. While much work has focused on modeling static graphs, we focus on group discovery in dynamic graphs. We adapt a dynamic extension of Latent Dirichlet Allocation to this task and demonstrate good performance on two datasets. Modeling relational data has become increasingly important in recent years. Much work has focused on static graphs - that is fixed graphs at a single point in time. Here we focus on the problem of modeling dynamic (i.e. time-evolving) graphs. We propose a scalable Bayesian approach for community discovery in dynamic graphs. Our approach is based on extensions of Latent Dirichlet Allocation (LDA). LDA is a latent variable model for topic modeling in text corpora. It was extended to deal with topic changes in discrete time and later in continuous time. These models were referred to as the discrete Dynamic Topic Model (dDTM) and the continuous Dynamic Topic Model (cDTM), respectively. When adapting these models to graphs, we take our inspiration from LDA-G and SSN-LDA, applications of LDA to static graphs that have been shown to effectively factor out community structure to explain link patterns in graphs. In this paper, we demonstrate how to adapt and apply the cDTM to the task of finding communities in dynamic networks. We use link prediction to measure the quality of the discovered community structure and apply it to two different relational datasets - DBLP author-keyword and CAIDA autonomous systems relationships. We also discuss a parallel implementation of this approach using Hadoop. In Section 2, we review LDA and LDA-G. In Section 3, we review the cDTM and introduce cDTMG, its adaptation to modeling dynamic graphs. We discuss inference for the cDTM-G and details of our parallel implementation in Section 4 and present its performance on two datasets in Section 5 before concluding in

  2. Understanding graphs with two independent variables

    NASA Astrophysics Data System (ADS)

    Cooper, Jennifer L.

    Adults are not necessarily competent users of graphs with two independent variables, despite the frequency of this representational format. The three tasks in this thesis address the impact of interpretation statements and graph patterns. Interpretation statements were based on the statistical effects -- simple effects, main effects, and interactions. Graph patterns were systematically varied based on a novel classification scheme of graphs with two IVs. I suggest that the complexity of a graph's data pattern depends on the consistency of the simple effects' directions and magnitudes. In the first study, undergraduates constructed graphs based on statements about data patterns. Errors reflected a misunderstanding of how two IVs could be combined and represented graphically. When the experimental group had graph-relevant information added (variable labels spatially located on axes), the ability to represent the relationships among the IVs significantly increased. The ability to satisfy the constraints imposed by the statements was not affected. Adding labels specifically targeted skills relevant to graphical literacy. Transfer to a third trial was stronger for those of higher math abilities. The second study focused on the effect of an introductory statistics course. Overall, undergraduates performed well on statements describing the simple effects of the IVs. However, even though they improved from Time 1 to Time 2 for interaction statements, performance on statements about main effects and interactions still showed considerable room for improvement. In the third study, repeated trials of the 20 patterns proposed by the simple effects consistency model established that the proposed classification scheme addresses additional sources of variability in reasoning with graphs (i.e., sources not captured by traditional classification schemes). As the complexity level of the data pattern increased, performance (based on accuracy and RT) decreased, with parallel impacts on

  3. Accelerating semantic graph databases on commodity clusters

    SciTech Connect

    Morari, Alessandro; Castellana, Vito G.; Haglin, David J.; Feo, John T.; Weaver, Jesse R.; Tumeo, Antonino; Villa, Oreste

    2013-10-06

    We are developing a full software system for accelerating semantic graph databases on commodity cluster that scales to hundreds of nodes while maintaining constant query throughput. Our framework comprises a SPARQL to C++ compiler, a library of parallel graph methods and a custom multithreaded runtime layer, which provides a Partitioned Global Address Space (PGAS) programming model with fork/join parallelism and automatic load balancing over a commodity clusters. We present preliminary results for the compiler and for the runtime.

  4. On the Kirchhoff Index of Graphs

    NASA Astrophysics Data System (ADS)

    Das, Kinkar C.

    2013-09-01

    Let G be a connected graph of order n with Laplacian eigenvalues μ1 ≥ μ2 ≥ ... ≥ μn-1 > mn = 0. The Kirchhoff index of G is defined as [xxx] In this paper. we give lower and upper bounds on Kf of graphs in terms on n, number of edges, maximum degree, and number of spanning trees. Moreover, we present lower and upper bounds on the Nordhaus-Gaddum-type result for the Kirchhoff index.

  5. Capacitated max -Batching with Interval Graph Compatibilities

    NASA Astrophysics Data System (ADS)

    Nonner, Tim

    We consider the problem of partitioning interval graphs into cliques of bounded size. Each interval has a weight, and the weight of a clique is the maximum weight of any interval in the clique. This natural graph problem can be interpreted as a batch scheduling problem. Solving a long-standing open problem, we show NP-hardness, even if the bound on the clique sizes is constant. Moreover, we give a PTAS based on a novel dynamic programming technique for this case.

  6. Inverse scattering problem for quantum graph vertices

    SciTech Connect

    Cheon, Taksu; Turek, Ondrej; Exner, Pavel

    2011-06-15

    We demonstrate how the inverse scattering problem of a quantum star graph can be solved by means of diagonalization of the Hermitian unitary matrix when the vertex coupling is of the scale-invariant (or Fueloep-Tsutsui) form. This enables the construction of quantum graphs with desired properties in a tailor-made fashion. The procedure is illustrated on the example of quantum vertices with equal transmission probabilities.

  7. A software tool for dataflow graph scheduling

    NASA Technical Reports Server (NTRS)

    Jones, Robert L., III

    1994-01-01

    A graph-theoretic design process and software tool is presented for selecting a multiprocessing scheduling solution for a class of computational problems. The problems of interest are those that can be described using a dataflow graph and are intended to be executed repetitively on multiple processors. The dataflow paradigm is very useful in exposing the parallelism inherent in algorithms. It provides a graphical and mathematical model which describes a partial ordering of algorithm tasks based on data precedence.

  8. Program for Generating Graphs and Charts

    NASA Technical Reports Server (NTRS)

    Ackerson, C. T.

    1986-01-01

    Office Automation Pilot (OAP) Graphics Database system offers IBM personal computer user assistance in producing wide variety of graphs and charts and convenient data-base system, called chart base, for creating and maintaining data associated with graphs and charts. Thirteen different graphics packages available. Access graphics capabilities obtained in similar manner. User chooses creation, revision, or chartbase-maintenance options from initial menu; Enters or modifies data displayed on graphic chart. OAP graphics data-base system written in Microsoft PASCAL.

  9. On Ramsey (P3, P6)-minimal graphs

    NASA Astrophysics Data System (ADS)

    Rahmadani, Desi; Baskoro, Edy Tri; Assiyatun, Hilda

    2016-02-01

    Finding all Ramsey (G, H)-minimal graphs for a certain pair of graphs G and H is an interesting and difficult problem. Even though, it is just for small graphs G and H. In this paper, we determine some Ramsey (P3, P6)-minimal graphs of small order. We also characterize all such Ramsey minimal graphs of order 6 by using their degree sequences. We prove that Ramsey (P3, P6)-minimal graphs have diameter at least two. We construct an infinite class of trees [6] which provides Ramsey (P3, P6)-minimal graphs.

  10. Student reasoning about graphs in different contexts

    NASA Astrophysics Data System (ADS)

    Ivanjek, Lana; Susac, Ana; Planinic, Maja; Andrasevic, Aneta; Milin-Sipus, Zeljka

    2016-06-01

    This study investigates university students' graph interpretation strategies and difficulties in mathematics, physics (kinematics), and contexts other than physics. Eight sets of parallel (isomorphic) mathematics, physics, and other context questions about graphs, which were developed by us, were administered to 385 first-year students at the Faculty of Science, University of Zagreb. Students were asked to provide explanations and/or mathematical procedures with their answers. Students' main strategies and difficulties identified through the analysis of those explanations and procedures are described. Student strategies of graph interpretation were found to be largely context dependent and domain specific. A small fraction of students have used the same strategy in all three domains (mathematics, physics, and other contexts) on most sets of parallel questions. Some students have shown indications of transfer of knowledge in the sense that they used techniques and strategies developed in physics for solving (or attempting to solve) other context problems. In physics, the preferred strategy was the use of formulas, which sometimes seemed to block the use of other, more productive strategies which students displayed in other domains. Students' answers indicated the presence of slope-height confusion and interval-point confusion in all three domains. Students generally better interpreted graph slope than the area under a graph, although the concept of slope still seemed to be quite vague for many. The interpretation of the concept of area under a graph needs more attention in both physics and mathematics teaching.

  11. Graph representation of protein free energy landscape

    SciTech Connect

    Li, Minghai; Duan, Mojie; Fan, Jue; Huo, Shuanghong; Han, Li

    2013-11-14

    The thermodynamics and kinetics of protein folding and protein conformational changes are governed by the underlying free energy landscape. However, the multidimensional nature of the free energy landscape makes it difficult to describe. We propose to use a weighted-graph approach to depict the free energy landscape with the nodes on the graph representing the conformational states and the edge weights reflecting the free energy barriers between the states. Our graph is constructed from a molecular dynamics trajectory and does not involve projecting the multi-dimensional free energy landscape onto a low-dimensional space defined by a few order parameters. The calculation of free energy barriers was based on transition-path theory using the MSMBuilder2 package. We compare our graph with the widely used transition disconnectivity graph (TRDG) which is constructed from the same trajectory and show that our approach gives more accurate description of the free energy landscape than the TRDG approach even though the latter can be organized into a simple tree representation. The weighted-graph is a general approach and can be used on any complex system.

  12. Bipartite separability and nonlocal quantum operations on graphs

    NASA Astrophysics Data System (ADS)

    Dutta, Supriyo; Adhikari, Bibhas; Banerjee, Subhashish; Srikanth, R.

    2016-07-01

    In this paper we consider the separability problem for bipartite quantum states arising from graphs. Earlier it was proved that the degree criterion is the graph-theoretic counterpart of the familiar positive partial transpose criterion for separability, although there are entangled states with positive partial transpose for which the degree criterion fails. Here we introduce the concept of partially symmetric graphs and degree symmetric graphs by using the well-known concept of partial transposition of a graph and degree criteria, respectively. Thus, we provide classes of bipartite separable states of dimension m ×n arising from partially symmetric graphs. We identify partially asymmetric graphs that lack the property of partial symmetry. We develop a combinatorial procedure to create a partially asymmetric graph from a given partially symmetric graph. We show that this combinatorial operation can act as an entanglement generator for mixed states arising from partially symmetric graphs.

  13. The role of PIP2 and the IP3/DAG pathway in intracellular calcium release and cell survival during nanosecond electric pulse exposures

    NASA Astrophysics Data System (ADS)

    Steelman, Zachary A.; Tolstykh, Gleb P.; Estlack, Larry E.; Roth, Caleb C.; Ibey, Bennett L.

    2015-03-01

    Phosphatidylinositol4,5-biphosphate (PIP2) is a membrane phospholipid of particular importance in cell-signaling pathways. Hydrolysis of PIP2 releases inositol-1,4,5-triphosphate (IP3) from the membrane, activating IP3 receptors on the smooth endoplasmic reticulum (ER) and facilitating a release of intracellular calcium stores and activation of protein kinase C (PKC). Recent studies suggest that nanosecond pulsed electric fields (nsPEF) cause depletion of PIP2 in the cellular membrane, activating the IP3 signaling pathway. However, the exact mechanism(s) causing this observed depletion of PIP2 are unknown. Complicating the matter, nsPEF create nanopores in the plasma membrane, allowing calcium to enter the cell and thus causing an increase in intracellular calcium. While elevated intracellular calcium can cause activation of phospholipase C (PLC) (a known catalyst of PIP2 hydrolysis), PIP2 depletion has been shown to occur in the absence of both extracellular and intracellular calcium. These observations have led to the hypothesis that the high electric field itself may be playing a direct role in the hydrolysis of PIP2 from the plasma membrane. To support this hypothesis, we used edelfosine to block PLC and prevent activation of the IP3/DAG pathway in Chinese Hamster Ovarian (CHO) cells prior to applying nsPEF. Fluorescence microscopy was used to monitor intracellular calcium bursts during nsPEF, while MTT (3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) survivability assays were utilized to determine whether edelfosine improved cell survival during nsPEF exposure. This work is critical to refine the role of PIP2 in the cellular response to nsPEF, and also to determine the fundamental biological effects of high electric field exposures.

  14. InSAR analysis of the 2000 - 2002 earthquake sequence along the Sultan Dag front in the Isparta Angle (southern Turkey)

    NASA Astrophysics Data System (ADS)

    Manjunath, D. V.; Gomez, F. G.; Brooks, B. A.

    2009-12-01

    The Sultan Dag range of southern Turkey is a fault-block mountain range that has developed within or at the edge of the Isparta Angle - a region of the Anatolian plate situated near a tear in the subducting slab of the African plate. The mountain range is bounded on the northeast by the Sultandagi-Aksehir fault and the Aksehir-Afyon graben. A sequence of moderate earthquakes that occurred between 2000 and 2002 provides insight into the incremental growth of the mountain front through individual seismic events. The earthquake sequence consists of three moderate size events: a Mw 5.1 and a Mw 6.0 earthquake (December 15, 2000) and a Mw 6.5 earthquake (February 3, 2002). Surface deformations corresponding with the individual earthquakes were imaged using Interferometric Synthetic Aperture Radar (InSAR). The resulting displacement maps were used with elastic dislocation models to estimate faulting parameters associated with each earthquake (fault orientation and slip). These fault models were subsequently used to estimate static coulomb stress changes resulting from the earthquakes. The findings suggest that the two events of December 15, 2000, were not directly related to one another in terms of stress triggering. However, both events from 2000 appear to influence the extent of the 2002 earthquake. The larger event increased the stress on the segment ruptured in 2002, whereas the stress shadow from smaller event, which occurred on an antithetic fault, appears to have unloaded the stress at the termination of the 2002 rupture. Furthermore, the uplift and subsidence patterns associated with the earthquakes closely mimic overall geologic structure and general topography. Hence, these results permit exploring the extrapolation of coseismic displacements to understand the long-term growth of the mountain front.

  15. Synthesis, spectroscopic and biological activities studies of acyclic and macrocyclic mono and binuclear metal complexes containing a hard-soft Schiff base

    NASA Astrophysics Data System (ADS)

    Abou-Hussein, Azza A. A.; Linert, Wolfgang

    Mono- and bi-nuclear acyclic and macrocyclic complexes with hard-soft Schiff base, H2L, ligand derived from the reaction of 4,6-diacetylresorcinol and thiocabohydrazide, in the molar ratio 1:2 have been prepared. The H2L ligand reacts with Co(II), Ni(II), Cu(II), Zn(II), Mn(II) and UO2(VI) nitrates, VO(IV) sulfate and Ru(III) chloride to get acyclic binuclear complexes except for VO(IV) and Ru(III) which gave acyclic mono-nuclear complexes. Reaction of the acyclic mono-nuclear VO(IV) and Ru(III) complexes with 4,6-diacetylresorcinol afforded the corresponding macrocyclic mono-nuclear VO(IV) and Ru(IIII) complexes. Template reactions of the 4,6-diacetylresorcinol and thiocarbohydrazide with either VO(IV) or Ru(III) salts afforded the macrocyclic binuclear VO(IV) and Ru(III) complexes. The Schiff base, H2L, ligand acts as dibasic with two NSO-tridentate sites and can coordinate with two metal ions to form binuclear complexes after the deprotonation of the hydrogen atoms of the phenolic groups in all the complexes, except in the case of the acyclic mononuclear Ru(III) and VO(IV) complexes, where the Schiff base behaves as neutral tetradentate chelate with N2S2 donor atoms. The ligands and the metal complexes were characterized by elemental analysis, IR, UV-vis 1H-NMR, thermal gravimetric analysis (TGA) and ESR, as well as the measurements of conductivity and magnetic moments at room temperature. Electronic spectra and magnetic moments of the complexes indicate the geometries of the metal centers are either tetrahedral, square planar or octahedral. Kinetic and thermodynamic parameters were calculated using Coats-Redfern equation, for the different thermal decomposition steps of the complexes. The ligands and the metal complexes were screened for their antimicrobial activity against Staphylococcus aureus as Gram-positive bacteria, and Pseudomonas fluorescens as Gram-negative bacteria in addition to Fusarium oxysporum fungus. Most of the complexes exhibit mild

  16. Molecular mechanism by which acyclic retinoid induces nuclear localization of transglutaminase 2 in human hepatocellular carcinoma cells

    PubMed Central

    Shrestha, R; Tatsukawa, H; Shrestha, R; Ishibashi, N; Matsuura, T; Kagechika, H; Kose, S; Hitomi, K; Imamoto, N; Kojima, S

    2015-01-01

    Nuclear accumulation of transglutaminase 2 (TG2) is an important step in TG2-dependent cell death. However, the underlying molecular mechanisms for nuclear translocation of TG2 are still poorly understood. In this study, we demonstrated that acyclic retinoid (ACR) induced nuclear accumulation of TG2 in JHH-7 cells, a hepatocellular carcinoma (HCC) leading to their apoptosis. We further demonstrated molecular mechanism in nuclear-cytoplasmic trafficking of TG2 and an effect of ACR on it. We identified a novel 14-amino acid nuclear localization signal (NLS) 466AEKEETGMAMRIRV479 in the ‘C' domain and a leucine-rich nuclear export signal (NES) 657LHMGLHKL664 in the ‘D' domain that allowed TG2 to shuttle between the nuclear and cytosolic milieu. Increased nuclear import of GAPDH myc-HIS fused with the identified NLS was observed, confirming its nuclear import ability. Leptomycin B, an inhibitor of exportin-1 as well as point mutation of all leucine residues to glutamine residues in the NES of TG2 demolished its nuclear export. TG2 formed a trimeric complex with importin-α and importin-β independently from transamidase activity which strongly suggested the involvement of a NLS-based translocation of TG2 to the nucleus. ACR accelerated the formation of the trimeric complex and that may be at least in part responsible for enhanced nuclear localization of TG2 in HCC cells treated with ACR. PMID:26633708

  17. Acyclic monoterpene primary alcohol:NADP+ oxidoreductase of Rauwolfia serpentina cells: the key enzyme in biosynthesis of monoterpene alcohols.

    PubMed

    Ikeda, H; Esaki, N; Nakai, S; Hashimoto, K; Uesato, S; Soda, K; Fujita, T

    1991-02-01

    Acyclic monoterpene primary alcohol:NADP+ oxidoreductase, a key enzyme in the biosynthesis of monoterpene alcohols in plants, is unstable and has been only poorly characterized. However we have established conditions which stabilize the enzyme from Rauwolfia serpentina cells, and then purified it to homogeneity. It is a monomer with a molecular weight of about 44,000 and contains zinc ions. Various branched-chain allylic primary alcohols such as nerol, geraniol, and 10-hydroxygeraniol were substrates, but ethanol was inert. The enzyme exclusively requires NADP+ or NADPH as the cofactor. Steady-state kinetic studies showed that the nerol dehydrogenation proceeds by an ordered Bi-Bi mechanism. NADP+ binds the enzyme first and then NADPH is the second product released from it. Gas chromatography-mass spectrometric analysis of the reaction products showed that 10-hydroxygeraniol undergoes a reversible dehydrogenation to produce 10-oxogeraniol or 10-hydroxygeranial, which are oxidized further to give 10-oxogeranial, the direct precursor of iridodial. The enzyme has been found to exclusively transfer the pro-R hydrogen of NADPH to neral. The N-terminal sequence of the first 21 amino acids revealed no significant homology with those of various other proteins including the NAD(P)(+)-dependent alcohol dehydrogenases registered in a protein data bank. PMID:1864846

  18. Intramolecular OH⋅⋅⋅Fluorine Hydrogen Bonding in Saturated, Acyclic Fluorohydrins: The γ-Fluoropropanol Motif

    PubMed Central

    Linclau, Bruno; Peron, Florent; Bogdan, Elena; Wells, Neil; Wang, Zhong; Compain, Guillaume; Fontenelle, Clement Q; Galland, Nicolas; LeQuestel, Jean-Yves; Graton, Jérôme

    2015-01-01

    Fluorination is commonly exercised in compound property optimization. However, the influence of fluorination on hydrogen-bond (HB) properties of adjacent functional groups, as well as the HB-accepting capacity of fluorine itself, is still not completely understood. Although the formation of OH⋅⋅⋅F intramolecular HBs (IMHBs) has been established for conformationally restricted fluorohydrins, such interaction in flexible compounds remained questionable. Herein is demonstrated for the first time—and in contrast to earlier reports—the occurrence of OH⋅⋅⋅F IMHBs in acyclic saturated γ-fluorohydrins, even for the parent 3-fluoropropan-1-ol. The relative stereochemistry is shown to have a crucial influence on the corresponding h1JOH⋅⋅⋅F values, as illustrated by syn- and anti-4-fluoropentan-2-ol (6.6 and 1.9Hz). The magnitude of OH⋅⋅⋅F IMHBs and their strong dependence on the overall molecular conformational profile, fluorination motif, and alkyl substitution level, is rationalized by quantum chemical calculations. For a given alkyl chain, the “rule of shielding” applies to OH⋅⋅⋅F IMHB energies. Surprisingly, the predicted OH⋅⋅⋅F IMHB energies are only moderately weaker than these of the corresponding OH⋅⋅⋅OMe. These results provide new insights of the impact of fluorination of aliphatic alcohols, with attractive perspectives for rational drug design. PMID:26494542

  19. H4octapa-Trastuzumab: Versatile Acyclic Chelate System for 111In and 177Lu Imaging and Therapy

    PubMed Central

    Price, Eric W.; Zeglis, Brian M.; Cawthray, Jacqueline F.; Ramogida, Caterina F.; Ramos, Nicholas

    2013-01-01

    A bifunctional derivative of the versatile acyclic chelator H4octapa, p-SCNBn- H4octapa, has been synthesized for the first time. The chelator was conjugated to the HER2/neu-targeting antibody trastuzumab and labeled in high radiochemical purity and specific activity with the radioisotopes 111In and 177Lu. The in vivo behavior of the resulting radioimmunoconjugates was investigated in mice bearing ovarian cancer xenografts and compared to analogous radioimmunoconjugates employing the ubiquitous chelator DOTA. The H4octapa-trastuzumab conjugates displayed faster radiolabeling kinetics with more reproducible yields under milder conditions (15 min, RT, ~94–95%) than those based on DOTA-trastuzumab (60 min, 37 °C ~50–88%). Further, antibody integrity was better preserved in the 111In- and 177Lu-octapatrastuzumab constructs, with immunoreactive fractions of 0.99 for each compared to 0.93–0.95 for 111In- and 177Lu-DOTA-trastuzumab. These results translated to improved in vivo biodistribution profiles and SPECT imaging results for 111In- and 177Lu-octapa-trastuzumab compared to 111In- and 177Lu-DOTA-trastuzumab, with increased tumor uptake and higher tumor-to-tissue activity ratios. PMID:23901833

  20. Enzymatic synthesis of acyclic nucleoside thiophosphonate diphosphates: effect of the α-phosphorus configuration on HIV-1 RT activity.

    PubMed

    Priet, Stéphane; Roux, Loic; Saez-Ayala, Magali; Ferron, François; Canard, Bruno; Alvarez, Karine

    2015-05-01

    The acyclic nucleosides thiophosphonates (9-[2-(thiophosphonomethoxy)ethyl]adenine (S-PMEA) and (R)-9-[2-(thiophosphonomethoxy)propyl]adenine (S-PMPA), exhibit antiviral activity against HIV-1, -2 and HBV. Their diphosphate forms S-PMEApp and S-PMPApp, synthesized as stereoisomeric mixture, are potent inhibitors of wild-type (WT) HIV-1 RT. Understanding HIV-1 RT stereoselectivity, however, awaits resolution of the diphosphate forms into defined stereoisomers. To this aim, thiophosphonate monophosphates S-PMEAp and S-PMPAp were synthesized and used in a stereocontrolled enzyme-catalyzed phosphoryl transfer reaction involving either nucleoside diphosphate kinase (NDPK) or creatine kinase (CK) to obtain thiophosphonate diphosphates as separated isomers. We then quantified substrate preference of recombinant WT HIV-1 RT toward pure stereoisomers using in vitro steady-state kinetic analyses. The crystal structure of a complex between Dictyostelium NDPK and S-PMPApp at 2.32Å allowed to determine the absolute configuration at the α-phosphorus atom in relation to the stereo-preference of studied enzymes. The RP isomer of S-PMPApp and S-PMEApp are the preferred substrate over SP for both NDPK and HIV-1 RT. PMID:25766862

  1. Continuous-time quantum walks on star graphs

    SciTech Connect

    Salimi, S.

    2009-06-15

    In this paper, we investigate continuous-time quantum walk on star graphs. It is shown that quantum central limit theorem for a continuous-time quantum walk on star graphs for N-fold star power graph, which are invariant under the quantum component of adjacency matrix, converges to continuous-time quantum walk on K{sub 2} graphs (complete graph with two vertices) and the probability of observing walk tends to the uniform distribution.

  2. Preserving Differential Privacy in Degree-Correlation based Graph Generation

    PubMed Central

    Wang, Yue; Wu, Xintao

    2014-01-01

    Enabling accurate analysis of social network data while preserving differential privacy has been challenging since graph features such as cluster coefficient often have high sensitivity, which is different from traditional aggregate functions (e.g., count and sum) on tabular data. In this paper, we study the problem of enforcing edge differential privacy in graph generation. The idea is to enforce differential privacy on graph model parameters learned from the original network and then generate the graphs for releasing using the graph model with the private parameters. In particular, we develop a differential privacy preserving graph generator based on the dK-graph generation model. We first derive from the original graph various parameters (i.e., degree correlations) used in the dK-graph model, then enforce edge differential privacy on the learned parameters, and finally use the dK-graph model with the perturbed parameters to generate graphs. For the 2K-graph model, we enforce the edge differential privacy by calibrating noise based on the smooth sensitivity, rather than the global sensitivity. By doing this, we achieve the strict differential privacy guarantee with smaller magnitude noise. We conduct experiments on four real networks and compare the performance of our private dK-graph models with the stochastic Kronecker graph generation model in terms of utility and privacy tradeoff. Empirical evaluations show the developed private dK-graph generation models significantly outperform the approach based on the stochastic Kronecker generation model. PMID:24723987

  3. Labeled Graph Kernel for Behavior Analysis.

    PubMed

    Zhao, Ruiqi; Martinez, Aleix M

    2016-08-01

    Automatic behavior analysis from video is a major topic in many areas of research, including computer vision, multimedia, robotics, biology, cognitive science, social psychology, psychiatry, and linguistics. Two major problems are of interest when analyzing behavior. First, we wish to automatically categorize observed behaviors into a discrete set of classes (i.e., classification). For example, to determine word production from video sequences in sign language. Second, we wish to understand the relevance of each behavioral feature in achieving this classification (i.e., decoding). For instance, to know which behavior variables are used to discriminate between the words apple and onion in American Sign Language (ASL). The present paper proposes to model behavior using a labeled graph, where the nodes define behavioral features and the edges are labels specifying their order (e.g., before, overlaps, start). In this approach, classification reduces to a simple labeled graph matching. Unfortunately, the complexity of labeled graph matching grows exponentially with the number of categories we wish to represent. Here, we derive a graph kernel to quickly and accurately compute this graph similarity. This approach is very general and can be plugged into any kernel-based classifier. Specifically, we derive a Labeled Graph Support Vector Machine (LGSVM) and a Labeled Graph Logistic Regressor (LGLR) that can be readily employed to discriminate between many actions (e.g., sign language concepts). The derived approach can be readily used for decoding too, yielding invaluable information for the understanding of a problem (e.g., to know how to teach a sign language). The derived algorithms allow us to achieve higher accuracy results than those of state-of-the-art algorithms in a fraction of the time. We show experimental results on a variety of problems and datasets, including multimodal data. PMID:26415154

  4. Graph theory and the Virasoro master equation

    SciTech Connect

    Obers, N.A.J.

    1991-01-01

    A brief history of affine Lie algebra, the Virasoro algebra and its culmination in the Virasoro master equation is given. By studying ansaetze of the master equation, the author obtains exact solutions and gains insight in the structure of large slices of affine-Virasoro space. He finds an isomorphism between the constructions in the ansatz SO(n){sub diag}, which is a set of unitary, generically irrational affine-Virasoro constructions on SO(n), and the unlabeled graphs of order n. On the one hand, the conformal constructions, are classified by the graphs, while, conversely, a group-theoretic and conformal field-theoretic identification is obtained for every graph of graph theory. He also defines a class of magic Lie group bases in which the Virasoro master equation admits a simple metric ansatz {l brace}g{sub metric}{r brace}, whose structure is visible in the high-level expansion. When a magic basis is real on compact g, the corresponding g{sub metric} is a large system of unitary, generically irrational conformal field theories. Examples in this class include the graph-theory ansatz SO(n){sub diag} in the Cartesian basis of SO(n), and the ansatz SU(n){sub metric} in the Pauli-like basis of SU(n). Finally, he defines the sine-area graphs' of SU(n), which label the conformal field theories of SU(n){sub metric}, and he notes that, in similar fashion, each magic basis of g defines a generalized graph theory on g which labels the conformal field theories of g{sub metric}.

  5. A graph theoretic approach to scene matching

    NASA Technical Reports Server (NTRS)

    Ranganath, Heggere S.; Chipman, Laure J.

    1991-01-01

    The ability to match two scenes is a fundamental requirement in a variety of computer vision tasks. A graph theoretic approach to inexact scene matching is presented which is useful in dealing with problems due to imperfect image segmentation. A scene is described by a set of graphs, with nodes representing objects and arcs representing relationships between objects. Each node has a set of values representing the relations between pairs of objects, such as angle, adjacency, or distance. With this method of scene representation, the task in scene matching is to match two sets of graphs. Because of segmentation errors, variations in camera angle, illumination, and other conditions, an exact match between the sets of observed and stored graphs is usually not possible. In the developed approach, the problem is represented as an association graph, in which each node represents a possible mapping of an observed region to a stored object, and each arc represents the compatibility of two mappings. Nodes and arcs have weights indicating the merit or a region-object mapping and the degree of compatibility between two mappings. A match between the two graphs corresponds to a clique, or fully connected subgraph, in the association graph. The task is to find the clique that represents the best match. Fuzzy relaxation is used to update the node weights using the contextual information contained in the arcs and neighboring nodes. This simplifies the evaluation of cliques. A method of handling oversegmentation and undersegmentation problems is also presented. The approach is tested with a set of realistic images which exhibit many types of sementation errors.

  6. Graph optimized Laplacian eigenmaps for face recognition

    NASA Astrophysics Data System (ADS)

    Dornaika, F.; Assoum, A.; Ruichek, Y.

    2015-01-01

    In recent years, a variety of nonlinear dimensionality reduction techniques (NLDR) have been proposed in the literature. They aim to address the limitations of traditional techniques such as PCA and classical scaling. Most of these techniques assume that the data of interest lie on an embedded non-linear manifold within the higher-dimensional space. They provide a mapping from the high-dimensional space to the low-dimensional embedding and may be viewed, in the context of machine learning, as a preliminary feature extraction step, after which pattern recognition algorithms are applied. Laplacian Eigenmaps (LE) is a nonlinear graph-based dimensionality reduction method. It has been successfully applied in many practical problems such as face recognition. However the construction of LE graph suffers, similarly to other graph-based DR techniques from the following issues: (1) the neighborhood graph is artificially defined in advance, and thus does not necessary benefit the desired DR task; (2) the graph is built using the nearest neighbor criterion which tends to work poorly due to the high-dimensionality of original space; and (3) its computation depends on two parameters whose values are generally uneasy to assign, the neighborhood size and the heat kernel parameter. To address the above-mentioned problems, for the particular case of the LPP method (a linear version of LE), L. Zhang et al.1 have developed a novel DR algorithm whose idea is to integrate graph construction with specific DR process into a unified framework. This algorithm results in an optimized graph rather than a predefined one.

  7. A graph theoretic approach to scene matching

    NASA Astrophysics Data System (ADS)

    Ranganath, Heggere S.; Chipman, Laure J.

    1991-08-01

    The ability to match two scenes is a fundamental requirement in a variety of computer vision tasks. A graph theoretic approach to inexact scene matching is presented which is useful in dealing with problems due to imperfect image segmentation. A scene is described by a set of graphs, with nodes representing objects and arcs representing relationships between objects. Each node has a set of values representing the relations between pairs of objects, such as angle, adjacency, or distance. With this method of scene representation, the task in scene matching is to match two sets of graphs. Because of segmentation errors, variations in camera angle, illumination, and other conditions, an exact match between the sets of observed and stored graphs is usually not possible. In the developed approach, the problem is represented as an association graph, in which each node represents a possible mapping of an observed region to a stored object, and each arc represents the compatibility of two mappings. Nodes and arcs have weights indicating the merit or a region-object mapping and the degree of compatibility between two mappings. A match between the two graphs corresponds to a clique, or fully connected subgraph, in the association graph. The task is to find the clique that represents the best match. Fuzzy relaxation is used to update the node weights using the contextual information contained in the arcs and neighboring nodes. This simplifies the evaluation of cliques. A method of handling oversegmentation and undersegmentation problems is also presented. The approach is tested with a set of realistic images which exhibit many types of sementation errors.

  8. Graph ranking for exploratory gene data analysis

    PubMed Central

    2009-01-01

    Background Microarray technology has made it possible to simultaneously monitor the expression levels of thousands of genes in a single experiment. However, the large number of genes greatly increases the challenges of analyzing, comprehending and interpreting the resulting mass of data. Selecting a subset of important genes is inevitable to address the challenge. Gene selection has been investigated extensively over the last decade. Most selection procedures, however, are not sufficient for accurate inference of underlying biology, because biological significance does not necessarily have to be statistically significant. Additional biological knowledge needs to be integrated into the gene selection procedure. Results We propose a general framework for gene ranking. We construct a bipartite graph from the Gene Ontology (GO) and gene expression data. The graph describes the relationship between genes and their associated molecular functions. Under a species condition, edge weights of the graph are assigned to be gene expression level. Such a graph provides a mathematical means to represent both species-independent and species-dependent biological information. We also develop a new ranking algorithm to analyze the weighted graph via a kernelized spatial depth (KSD) approach. Consequently, the importance of gene and molecular function can be simultaneously ranked by a real-valued measure, KSD, which incorporates the global and local structure of the graph. Over-expressed and under-regulated genes also can be separately ranked. Conclusion The gene-function bigraph integrates molecular function annotations into gene expression data. The relevance of genes is described in the graph (through a common function). The proposed method provides an exploratory framework for gene data analysis. PMID:19811684

  9. Interpreting a Graph and Constructing Its Derivative Graph: Stability and Change in Students' Conceptions

    ERIC Educational Resources Information Center

    Ubuz, Behiye

    2007-01-01

    This present study investigated engineering students' conceptions and misconceptions related to derivative, particularly interpreting the graph of a function and constructing its derivative graph. Participants were 147 first year engineering students from four universities enrolled in first year undergraduate calculus courses with or without the…

  10. Efficient Sampling Set Selection for Bandlimited Graph Signals Using Graph Spectral Proxies

    NASA Astrophysics Data System (ADS)

    Anis, Aamir; Gadde, Akshay; Ortega, Antonio

    2016-07-01

    We study the problem of selecting the best sampling set for bandlimited reconstruction of signals on graphs. A frequency domain representation for graph signals can be defined using the eigenvectors and eigenvalues of variation operators that take into account the underlying graph connectivity. Smoothly varying signals defined on the nodes are of particular interest in various applications, and tend to be approximately bandlimited in the frequency basis. Sampling theory for graph signals deals with the problem of choosing the best subset of nodes for reconstructing a bandlimited signal from its samples. Most approaches to this problem require a computation of the frequency basis (i.e., the eigenvectors of the variation operator), followed by a search procedure using the basis elements. This can be impractical, in terms of storage and time complexity, for real datasets involving very large graphs. We circumvent this issue in our formulation by introducing quantities called graph spectral proxies, defined using the powers of the variation operator, in order to approximate the spectral content of graph signals. This allows us to formulate a direct sampling set selection approach that does not require the computation and storage of the basis elements. We show that our approach also provides stable reconstruction when the samples are noisy or when the original signal is only approximately bandlimited. Furthermore, the proposed approach is valid for any choice of the variation operator, thereby covering a wide range of graphs and applications. We demonstrate its effectiveness through various numerical experiments.

  11. Supporting Fourth Graders' Ability to Interpret Graphs through Real-Time Graphing Technology: A Preliminary Study

    ERIC Educational Resources Information Center

    Deniz, Hasan; Dulger, Mehmet F.

    2012-01-01

    This study examined to what extent inquiry-based instruction supported with real-time graphing technology improves fourth grader's ability to interpret graphs as representations of physical science concepts such as motion and temperature. This study also examined whether there is any difference between inquiry-based instruction supported with…

  12. GrouseFlocks: steerable exploration of graph hierarchy space.

    PubMed

    Archambault, Daniel; Munzner, Tamara; Auber, David

    2008-01-01

    Several previous systems allow users to interactively explore a large input graph through cuts of a superimposed hierarchy. This hierarchy is often created using clustering algorithms or topological features present in the graph. However, many graphs have domain-specific attributes associated with the nodes and edges, which could be used to create many possible hierarchies providing unique views of the input graph. GrouseFlocks is a system for the exploration of this graph hierarchy space. By allowing users to see several different possible hierarchies on the same graph, the system helps users investigate graph hierarchy space instead of a single fixed hierarchy. GrouseFlocks provides a simple set of operations so that users can create and modify their graph hierarchies based on selections. These selections can be made manually or based on patterns in the attribute data provided with the graph. It provides feedback to the user within seconds, allowing interactive exploration of this space. PMID:18467763

  13. Application of graph colouring to biological networks.

    PubMed

    Khor, S

    2010-05-01

    The author explores the application of graph colouring to biological networks, specifically protein-protein interaction (PPI) networks. First, the author finds that given similar conditions (i.e. graph size, degree distribution and clustering), fewer colours are needed to colour disassortative than assortative networks. Fewer colours create fewer independent sets which in turn imply higher concurrency potential for a network. Since PPI networks tend to be disassortative, the author suggests that in addition to functional specificity and stability proposed previously by Maslov and Sneppen (Science, 296, 2002), the disassortative nature of PPI networks may promote the ability of cells to perform multiple, crucial and functionally diverse tasks concurrently. Second, because graph colouring is closely related to the presence of cliques in a graph, the significance of node colouring information to the problem of identifying protein complexes (dense subgraphs in PPI networks), is investigated. The author finds that for PPI networks where 1-11% of nodes participate in at least one identified protein complex, such as H. sapien, DSATUR (a well-known complete graph colouring algorithm) node colouring information can improve the quality (homogeneity and separation) of initial candidate complexes. This finding may help improve existing protein complex detection methods, and/or suggest new methods. [Includes supplementary material]. PMID:20499999

  14. Modeling Transmission Line Networks Using Quantum Graphs

    NASA Astrophysics Data System (ADS)

    Koch, Trystan; Antonsen, Thomas

    Quantum graphs--one dimensional edges, connecting nodes, that support propagating Schrödinger wavefunctions--have been studied extensively as tractable models of wave chaotic behavior (Smilansky and Gnutzmann 2006, Berkolaiko and Kuchment 2013). Here we consider the electrical analog, in which the graph represents an electrical network where the edges are transmission lines (Hul et. al. 2004) and the nodes contain either discrete circuit elements or intricate circuit elements best represented by arbitrary scattering matrices. Including these extra degrees of freedom at the nodes leads to phenomena that do not arise in simpler graph models. We investigate the properties of eigenfrequencies and eigenfunctions on these graphs, and relate these to the statistical description of voltages on the transmission lines when driving the network externally. The study of electromagnetic compatibility, the effect of external radiation on complicated systems with numerous interconnected cables, motivates our research into this extension of the graph model. Work supported by the Office of Naval Research (N0014130474) and the Air Force Office of Scientific Research.

  15. DT-MRI segmentation using graph cuts

    NASA Astrophysics Data System (ADS)

    Weldeselassie, Yonas T.; Hamarneh, Ghassan

    2007-03-01

    An important problem in medical image analysis is the segmentation of anatomical regions of interest. Once regions of interest are segmented, one can extract shape, appearance, and structural features that can be analyzed for disease diagnosis or treatment evaluation. Diffusion tensor magnetic resonance imaging (DT-MRI) is a relatively new medical imaging modality that captures unique water diffusion properties and fiber orientation information of the imaged tissues. In this paper, we extend the interactive multidimensional graph cuts segmentation technique to operate on DT-MRI data by utilizing latest advances in tensor calculus and diffusion tensor dissimilarity metrics. The user interactively selects certain tensors as object ("obj") or background ("bkg") to provide hard constraints for the segmentation. Additional soft constraints incorporate information about both regional tissue diffusion as well as boundaries between tissues of different diffusion properties. Graph cuts are used to find globally optimal segmentation of the underlying 3D DT-MR image among all segmentations satisfying the constraints. We develop a graph structure from the underlying DT-MR image with the tensor voxels corresponding to the graph vertices and with graph edge weights computed using either Log-Euclidean or the J-divergence tensor dissimilarity metric. The topology of our segmentation is unrestricted and both obj and bkg segments may consist of several isolated parts. We test our method on synthetic DT data and apply it to real 2D and 3D MRI, providing segmentations of the corpus callosum in the brain and the ventricles of the heart.

  16. Linear Time Vertex Partitioning on Massive Graphs

    PubMed Central

    Mell, Peter; Harang, Richard; Gueye, Assane

    2016-01-01

    The problem of optimally removing a set of vertices from a graph to minimize the size of the largest resultant component is known to be NP-complete. Prior work has provided near optimal heuristics with a high time complexity that function on up to hundreds of nodes and less optimal but faster techniques that function on up to thousands of nodes. In this work, we analyze how to perform vertex partitioning on massive graphs of tens of millions of nodes. We use a previously known and very simple heuristic technique: iteratively removing the node of largest degree and all of its edges. This approach has an apparent quadratic complexity since, upon removal of a node and adjoining set of edges, the node degree calculations must be updated prior to choosing the next node. However, we describe a linear time complexity solution using an array whose indices map to node degree and whose values are hash tables indicating the presence or absence of a node at that degree value. This approach also has a linear growth with respect to memory usage which is surprising since we lowered the time complexity from quadratic to linear. We empirically demonstrate linear scalability and linear memory usage on random graphs of up to 15000 nodes. We then demonstrate tractability on massive graphs through execution on a graph with 34 million nodes representing Internet wide router connectivity. PMID:27336059

  17. Visualizing intelligence information using correlation graphs

    NASA Astrophysics Data System (ADS)

    Verma, Vivek; Gagvani, Nikhil

    2005-03-01

    This paper presents a new information model to help intelligence analysts in organizing, querying, and visualizing the information present in large volumes of unstructured data sources such as text reports, multi-media, and human discourse. Our primary goal is to create a system that would combine the human pattern recognition abilities of intelligence analysis with the storage and processing capabilities of computers. Our system models the collective mental map of intelligence analysts in the form of the Correlation Graph, a modified graph data structure with objects and events as nodes and subjective probabilistic correlations between them as edges. Objects are entities such as people, places, and things. Events are actions that involve the objects. A taxonomy is also associated with the model to enable intelligence domain specific querying of the data. Graph drawing techniques are used to visualize the information represented by the correlation graph. Through real world examples, we demonstrate that the resulting information model can be used for efficient representation, presentation, and querying to discover novel patterns in the intelligence data via graph visualization techniques.

  18. Exploiting graph properties of game trees

    SciTech Connect

    Plaat, A.; Pijls, W.; Bruin, A. de; Schaeffer, J.

    1996-12-31

    The state space of most adversary games is a directed graph. However, due to the success of simple recursive algorithms based on alpha-beta, theoreticians and practitioners have concentrated on the traversal of trees, giving the field the name {open_quotes}game-tree search,{close_quotes} This paper shows that the focus on trees has obscured some important properties of the underlying graphs. One of the hallmarks of the field of game-tree search has been the notion of the minimal tree, the smallest tree that has to be searched by any algorithm to find the minimax value. In fact, for most games it is a directed graph. As demonstrated in chess and checkers, we show that the minimal graph is significantly smaller than previously thought, proving that there is more room for improvement of current algorithms. We exploit the graph properties of the search space to reduce the size of trees built in practice by at least 25%. For over a decade, fixed-depth alpha-beta searching has been considered a closed subject, with research moving on to more application-dependent techniques. This work opens up new avenues of research for further application-independent improvements.

  19. Towards Scalable Graph Computation on Mobile Devices

    PubMed Central

    Chen, Yiqi; Lin, Zhiyuan; Pienta, Robert; Kahng, Minsuk; Chau, Duen Horng

    2015-01-01

    Mobile devices have become increasingly central to our everyday activities, due to their portability, multi-touch capabilities, and ever-improving computational power. Such attractive features have spurred research interest in leveraging mobile devices for computation. We explore a novel approach that aims to use a single mobile device to perform scalable graph computation on large graphs that do not fit in the device's limited main memory, opening up the possibility of performing on-device analysis of large datasets, without relying on the cloud. Based on the familiar memory mapping capability provided by today's mobile operating systems, our approach to scale up computation is powerful and intentionally kept simple to maximize its applicability across the iOS and Android platforms. Our experiments demonstrate that an iPad mini can perform fast computation on large real graphs with as many as 272 million edges (Google+ social graph), at a speed that is only a few times slower than a 13″ Macbook Pro. Through creating a real world iOS app with this technique, we demonstrate the strong potential application for scalable graph computation on a single mobile device using our approach. PMID:25859564

  20. An analysis of spectral transformation techniques on graphs

    NASA Astrophysics Data System (ADS)

    Djurović, Igor; Sejdić, Ervin; Bulatović, Nikola; Simeunović, Marko

    2015-05-01

    Emerging methods for the spectral analysis of graphs are analyzed in this paper, as graphs are currently used to study interactions in many fields from neuroscience to social networks. There are two main approaches related to the spectral transformation of graphs. The first approach is based on the Laplacian matrix. The graph Fourier transform is defined as an expansion of a graph signal in terms of eigenfunctions of the graph Laplacian. The calculated eigenvalues carry the notion of frequency of graph signals. The second approach is based on the graph weighted adjacency matrix, as it expands the graph signal into a basis of eigenvectors of the adjacency matrix instead of the graph Laplacian. Here, the notion of frequency is then obtained from the eigenvalues of the adjacency matrix or its Jordan decomposition. In this paper, advantages and drawbacks of both approaches are examined. Potential challenges and improvements to graph spectral processing methods are considered as well as the generalization of graph processing techniques in the spectral domain. Its generalization to the time-frequency domain and other potential extensions of classical signal processing concepts to graph datasets are also considered. Lastly, it is given an overview of the compressive sensing on graphs concepts.

  1. Polynomial Kernels for Hard Problems on Disk Graphs

    NASA Astrophysics Data System (ADS)

    Jansen, Bart

    Kernelization is a powerful tool to obtain fixed-parameter tractable algorithms. Recent breakthroughs show that many graph problems admit small polynomial kernels when restricted to sparse graph classes such as planar graphs, bounded-genus graphs or H-minor-free graphs. We consider the intersection graphs of (unit) disks in the plane, which can be arbitrarily dense but do exhibit some geometric structure. We give the first kernelization results on these dense graph classes. Connected Vertex Cover has a kernel with 12k vertices on unit-disk graphs and with 3k 2 + 7k vertices on disk graphs with arbitrary radii. Red-Blue Dominating Set parameterized by the size of the smallest color class has a linear-vertex kernel on planar graphs, a quadratic-vertex kernel on unit-disk graphs and a quartic-vertex kernel on disk graphs. Finally we prove that H -Matching on unit-disk graphs has a linear-vertex kernel for every fixed graph H.

  2. Directed transport in quantum star graphs

    NASA Astrophysics Data System (ADS)

    Yusupov, Jambul; Dolgushev, Maxim; Blumen, Alexander; Mülken, Oliver

    2016-04-01

    We study the quantum dynamics of Gaussian wave packets on star graphs whose arms feature each a periodic potential and an external time-dependent field. Assuming that the potentials and the field can be manipulated separately for each arm of the star, we show that it is possible to manipulate the direction of the motion of a Gaussian wave packet through the bifurcation point by a suitable choice of the parameters of the external fields. In doing so, one can achieve a transmission of the wave packet into the desired arm with nearly 70 % while also keeping the shape of the wave packet approximately intact. Since a star graph is the simplest element of many other complex graphs, the obtained results can be considered as the first step to wave packet manipulations on complex networks.

  3. A Gradient Descent Approximation for Graph Cuts

    NASA Astrophysics Data System (ADS)

    Yildiz, Alparslan; Akgul, Yusuf Sinan

    Graph cuts have become very popular in many areas of computer vision including segmentation, energy minimization, and 3D reconstruction. Their ability to find optimal results efficiently and the convenience of usage are some of the factors of this popularity. However, there are a few issues with graph cuts, such as inherent sequential nature of popular algorithms and the memory bloat in large scale problems. In this paper, we introduce a novel method for the approximation of the graph cut optimization by posing the problem as a gradient descent formulation. The advantages of our method is the ability to work efficiently on large problems and the possibility of convenient implementation on parallel architectures such as inexpensive Graphics Processing Units (GPUs). We have implemented the proposed method on the Nvidia 8800GTS GPU. The classical segmentation experiments on static images and video data showed the effectiveness of our method.

  4. Clustering gene expression data using graph separators.

    PubMed

    Kaba, Bangaly; Pinet, Nicolas; Lelandais, Gaëlle; Sigayret, Alain; Berry, Anne

    2007-01-01

    Recent work has used graphs to modelize expression data from microarray experiments, in view of partitioning the genes into clusters. In this paper, we introduce the use of a decomposition by clique separators. Our aim is to improve the classical clustering methods in two ways: first we want to allow an overlap between clusters, as this seems biologically sound, and second we want to be guided by the structure of the graph to define the number of clusters. We test this approach with a well-known yeast database (Saccharomyces cerevisiae). Our results are good, as the expression profiles of the clusters we find are very coherent. Moreover, we are able to organize into another graph the clusters we find, and order them in a fashion which turns out to respect the chronological order defined by the the sporulation process. PMID:18391236

  5. Dynamic graph system for a semantic database

    SciTech Connect

    Mizell, David

    2015-01-27

    A method and system in a computer system for dynamically providing a graphical representation of a data store of entries via a matrix interface is disclosed. A dynamic graph system provides a matrix interface that exposes to an application program a graphical representation of data stored in a data store such as a semantic database storing triples. To the application program, the matrix interface represents the graph as a sparse adjacency matrix that is stored in compressed form. Each entry of the data store is considered to represent a link between nodes of the graph. Each entry has a first field and a second field identifying the nodes connected by the link and a third field with a value for the link that connects the identified nodes. The first, second, and third fields represent the rows, column, and elements of the adjacency matrix.

  6. Dynamic graph system for a semantic database

    DOEpatents

    Mizell, David

    2016-04-12

    A method and system in a computer system for dynamically providing a graphical representation of a data store of entries via a matrix interface is disclosed. A dynamic graph system provides a matrix interface that exposes to an application program a graphical representation of data stored in a data store such as a semantic database storing triples. To the application program, the matrix interface represents the graph as a sparse adjacency matrix that is stored in compressed form. Each entry of the data store is considered to represent a link between nodes of the graph. Each entry has a first field and a second field identifying the nodes connected by the link and a third field with a value for the link that connects the identified nodes. The first, second, and third fields represent the rows, column, and elements of the adjacency matrix.

  7. Interactive Web Graphs with Fewer Restrictions

    NASA Technical Reports Server (NTRS)

    Fiedler, James

    2012-01-01

    There is growing popularity for interactive, statistical web graphs and programs to generate them. However, it seems that these programs tend to be somewhat restricted in which web browsers and statistical software are supported. For example, the software might use SVG (e.g., Protovis, gridSVG) or HTML canvas, both of which exclude most versions of Internet Explorer, or the software might be made specifically for R (gridSVG, CRanvas), thus excluding users of other stats software. There are more general tools (d3, Rapha lJS) which are compatible with most browsers, but using one of these to make statistical graphs requires more coding than is probably desired, and requires learning a new tool. This talk will present a method for making interactive web graphs, which, by design, attempts to support as many browsers and as many statistical programs as possible, while also aiming to be relatively easy to use and relatively easy to extend.

  8. Quantum Ergodicity for Quantum Graphs without Back-Scattering

    NASA Astrophysics Data System (ADS)

    Brammall, Matthew; Winn, B.

    2016-06-01

    We give an estimate of the quantum variance for $d$-regular graphs quantised with boundary scattering matrices that prohibit back-scattering. For families of graphs that are expanders, with few short cycles, our estimate leads to quantum ergodicity for these families of graphs. Our proof is based on a uniform control of an associated random walk on the bonds of the graph. We show that recent constructions of Ramanujan graphs, and asymptotically almost surely, random $d$-regular graphs, satisfy the necessary conditions to conclude that quantum ergodicity holds.

  9. Aligning graphs and finding substructures by a cavity approach

    NASA Astrophysics Data System (ADS)

    Bradde, S.; Braunstein, A.; Mahmoudi, H.; Tria, F.; Weigt, M.; Zecchina, R.

    2010-02-01

    We introduce a new distributed algorithm for aligning graphs or finding substructures within a given graph. It is based on the cavity method and is used to study the maximum-clique and the graph-alignment problems in random graphs. The algorithm allows to analyze large graphs and may find applications in fields such as computational biology. As a proof of concept we use our algorithm to align the similarity graphs of two interacting protein families involved in bacterial signal transduction, and to predict actually interacting protein partners between these families.

  10. The uniqueness of DMAX-matrix graph invariants.

    PubMed

    Dehmer, Matthias; Shi, Yongtang

    2014-01-01

    In this paper, we examine the uniqueness (discrimination power) of a newly proposed graph invariant based on the matrix DMAX defined by Randić et al. In order to do so, we use exhaustively generated graphs instead of special graph classes such as trees only. Using these graph classes allow us to generalize the findings towards complex networks as they usually do not possess any structural constraints. We obtain that the uniqueness of this newly proposed graph invariant is approximately as low as the uniqueness of the Balaban J index on exhaustively generated (general) graphs. PMID:24392099

  11. Acyclic Cucurbit[n]uril-Type Molecular Containers: Influence of Linker Length on Their Function as Solubilizing Agents.

    PubMed

    Sigwalt, David; Moncelet, Damien; Falcinelli, Shane; Mandadapu, Vijaybabu; Zavalij, Peter Y; Day, Anthony; Briken, Volker; Isaacs, Lyle

    2016-05-01

    Two acyclic cucurbit[n]uril (CB[n])-type molecular containers that differ in the length of the (CH2 )n linker (M2C2: n=2, M2C4: n=4) between their aromatic sidewalls and sulfonate solubilizing groups were prepared and studied. The inherent solubilities of M2C2 (68 mm) and M2C4 (196 mm) are higher than the analogue with a (CH2 )3 linker (M2, 14 mm) studied previously. (1) H NMR dilution experiments show that M2C2 and M2C4 do not self-associate in water, which enables their use as solubilizing excipients. We used phase solubility diagrams (PSDs) to compare the solubilizing capacities of M2, M2C2, M2C4, hydroxypropyl-β-cyclodextrin (HP-β-CD), and sulfobutylether-β-cyclodextrin (SBE-β-CD) toward 15 insoluble drugs. We found that M2C2 and M2C4-as gauged by the slope of their PSDs-are less potent solubilizing agents than M2. However, the higher inherent solubility of M2C2 allows higher concentrations of drug to be formulated using M2C2 than with M2 in several cases. The solubilizing ability of M2C2 and SBE-β-CD were similar in many cases, with Krel values averaging 23 and 12, respectively, relative to HP-β-CD. In vitro cytotoxicity and in vivo maximum tolerated dose studies document the biocompatibility of M2C2. PMID:26990780

  12. Acyclic Identification of Aptamers for Human alpha-Thrombin Using Over-Represented Libraries and Deep Sequencing

    PubMed Central

    Kupakuwana, Gillian V.; Crill, James E.; McPike, Mark P.; Borer, Philip N.

    2011-01-01

    Background Aptamers are oligonucleotides that bind proteins and other targets with high affinity and selectivity. Twenty years ago elements of natural selection were adapted to in vitro selection in order to distinguish aptamers among randomized sequence libraries. The primary bottleneck in traditional aptamer discovery is multiple cycles of in vitro evolution. Methodology/Principal Findings We show that over-representation of sequences in aptamer libraries and deep sequencing enables acyclic identification of aptamers. We demonstrated this by isolating a known family of aptamers for human α-thrombin. Aptamers were found within a library containing an average of 56,000 copies of each possible randomized 15mer segment. The high affinity sequences were counted many times above the background in 2–6 million reads. Clustering analysis of sequences with more than 10 counts distinguished two sequence motifs with candidates at high abundance. Motif I contained the previously observed consensus 15mer, Thb1 (46,000 counts), and related variants with mostly G/T substitutions; secondary analysis showed that affinity for thrombin correlated with abundance (Kd = 12 nM for Thb1). The signal-to-noise ratio for this experiment was roughly 10,000∶1 for Thb1. Motif II was unrelated to Thb1 with the leading candidate (29,000 counts) being a novel aptamer against hexose sugars in the storage and elution buffers for Concanavilin A (Kd = 0.5 µM for α-methyl-mannoside); ConA was used to immobilize α-thrombin. Conclusions/Significance Over-representation together with deep sequencing can dramatically shorten the discovery process, distinguish aptamers having a wide range of affinity for the target, allow an exhaustive search of the sequence space within a simplified library, reduce the quantity of the target required, eliminate cycling artifacts, and should allow multiplexing of sequencing experiments and targets. PMID:21625587

  13. New acyclic bis phenylpropanoid and neolignans, from Myristica fragrans Houtt., exhibiting PARP-1 and NF-κB inhibitory effects.

    PubMed

    Muñoz Acuña, Ulyana; Carcache, Peter J Blanco; Matthew, Susan; Carcache de Blanco, Esperanza J

    2016-07-01

    The bioassay-guided fractionation of the aril of Myristica fragrans (mace spice) yielded five phenolic compounds, one new acyclic bis phenylpropanoid (1) and four previously known phenolic compounds: compounds (1) (S) 1-(3,4,5-trimethoxyphenyl)-2-(3-methoxy-5-(prop-1-yl) phenyl)-propan-1-ol, (2) benzenemethanol; α-[1-[2,6-dimethoxy-4-(2-propen-1-yl)phenoxy]ethyl]-3,4-dimethoxy-1-acetate, (3) odoratisol A, phenol, 4-[(2S,3S)-2,3-dihydro-7-methoxy-3-methyl-5-(1E)-1-propenyl-2-benzofuranyl]-2,6-dimethoxy, (4) 1,3-benzodioxate-5-methanol,α-[1-[2,6-dimethoxy-4-(2-propenyl)phenoxy]ethyl]-acetate, (5) licarin C; benzofuran,2,3-dihydro-7-methoxy-3-methyl-5-(1E)-1-yl-2-(3,4,5-trimethoxyphenyl). An NMR tube Mosher ester reaction was used in an approach to characterize and determine the assignment of the absolute configuration of the new isolated chiral alcohol (1). The PARP-1 inhibitory activity was evaluated for compound (1) (IC50=3.04μM), compound (2) (IC50=0.001μM), compound (4) (IC50=22.07μM) and compound (5) (IC50=3.11μM). Furthermore, the isolated secondary metabolites were tested for NF-κB and K-Ras inhibitory activities. When tested in the p65 assay, compounds (2) and (4) displayed potent NF-κB inhibition (IC50=1.5 nM and 3.4nM, respectively). PMID:26920294

  14. Graph isomorphism and adiabatic quantum computing

    NASA Astrophysics Data System (ADS)

    Gaitan, Frank; Clark, Lane

    2014-02-01

    In the graph isomorphism (GI) problem two N-vertex graphs G and G' are given and the task is to determine whether there exists a permutation of the vertices of G that preserves adjacency and transforms G →G'. If yes, then G and G' are said to be isomorphic; otherwise they are nonisomorphic. The GI problem is an important problem in computer science and is thought to be of comparable difficulty to integer factorization. In this paper we present a quantum algorithm that solves arbitrary instances of GI and which also provides an approach to determining all automorphisms of a given graph. We show how the GI problem can be converted to a combinatorial optimization problem that can be solved using adiabatic quantum evolution. We numerically simulate the algorithm's quantum dynamics and show that it correctly (i) distinguishes nonisomorphic graphs; (ii) recognizes isomorphic graphs and determines the permutation(s) that connect them; and (iii) finds the automorphism group of a given graph G. We then discuss the GI quantum algorithm's experimental implementation, and close by showing how it can be leveraged to give a quantum algorithm that solves arbitrary instances of the NP-complete subgraph isomorphism problem. The computational complexity of an adiabatic quantum algorithm is largely determined by the minimum energy gap Δ (N) separating the ground and first-excited states in the limit of large problem size N ≫1. Calculating Δ (N) in this limit is a fundamental open problem in adiabatic quantum computing, and so it is not possible to determine the computational complexity of adiabatic quantum algorithms in general, nor consequently, of the specific adiabatic quantum algorithms presented here. Adiabatic quantum computing has been shown to be equivalent to the circuit model of quantum computing, and so development of adiabatic quantum algorithms continues to be of great interest.

  15. Graph theory and the Virasoro master equation

    SciTech Connect

    Obers, N.A.J.

    1991-04-01

    A brief history of affine Lie algebra, the Virasoro algebra and its culmination in the Virasoro master equations is given. By studying ansaetze of the master equation, we obtain exact solutions and gain insight in the structure of large slices of affine-Virasoro space. We find an isomorphism between the constructions in the ansatz SO(n){sub diag}, which is a set of unitary, generically irrational affine-Virasoro constructions on SO(n), and the unlabelled graphs, while, conversely, a group-theoretic and conformal field-theoretic identification is obtained for every graph of graph theory. We also define a class of magic'' Lie group bases in which the Virasoro master equation admits a simple metric ansatz (gmetric), whose structure is visible in the high-level expansion. When a magic basis is real on compact g, the corresponding g{sub metric} is a large system of unitary, generically irrational conformal field theories. Examples in this class include the graph-theory ansatz SO(n){sub diag} in the Cartesian basis of SO(n), and the ansatz SU(n){sub metric} in the Pauli-like basis of SU(n). Finally, we define the sine-area graphs'' of SU(n), which label the conformal field theories of SU(n){sub metric}, and we note that, in similar fashion, each magic basis of g defines a generalized graph theory on g which labels the conformal field theories of g{sub metric}. 24 figs., 4 tabs.

  16. Graph certificates, lookahead in dynamic graph problems, and assembly planning in robotics

    SciTech Connect

    Khanna, S.; Motwani, R.; Wilson, R.H.

    1994-12-31

    Despite intensive efforts in the area of dynamic graph algorithms, no efficient algorithms are known for the dynamic versions of some basic graph problems such as strong connectivity and transitive closure. We provide some explanation for this lack of success by presenting quadratic lower bounds on the strong certificate complexity of such problems, thereby establishing the inapplicability of the only known general technique for designing dynamic graph algorithms, viz., sparsification. These results also provide evidence of the inherent intractability of such dynamic graph problems. Some of our results are based on a general technique for obtaining lower bounds on the strong certificate complexity for a class of graph properties by establishing a relationship with the witness complexity. In many real applications of dynamic graph problems, a certain amount of lookahead is available. Specifically, we consider the problems of assembly planning in robotics and the maintenance of relations in databases which, respectively, give rise to dynamic strong connectivity and transitive closure. We exploit the (naturally available) lookahead in these two applications to circumvent the inherent complexity of the dynamic graph problems. We propose a variant of sparsification, viz., lookahead based sparsification, and apply it to obtain the first efficient fully dynamic algorithms for strong connectivity and transitive closure.

  17. Towards information inequalities for generalized graph entropies.

    PubMed

    Sivakumar, Lavanya; Dehmer, Matthias

    2012-01-01

    In this article, we discuss the problem of establishing relations between information measures for network structures. Two types of entropy based measures namely, the Shannon entropy and its generalization, the Rényi entropy have been considered for this study. Our main results involve establishing formal relationships, by means of inequalities, between these two kinds of measures. Further, we also state and prove inequalities connecting the classical partition-based graph entropies and partition-independent entropy measures. In addition, several explicit inequalities are derived for special classes of graphs. PMID:22715375

  18. Percolation threshold on planar Euclidean Gabriel graphs

    NASA Astrophysics Data System (ADS)

    Norrenbrock, Christoph

    2016-04-01

    In the present article, numerical simulations have been performed to find the bond and site percolation thresholds on two-dimensional Gabriel graphs (GG) for Poisson point processes. GGs belong to the family of "proximity graphs" and are discussed, e.g., in context of the construction of backbones for wireless ad-hoc networks. Finite-size scaling analyses have been performed to find the critical points and critical exponents ν, β and γ. The critical exponents obtained this way verify that the associated universality class is that of standard 2D percolation.

  19. Percolation threshold on planar Euclidean Gabriel graphs

    NASA Astrophysics Data System (ADS)

    Norrenbrock, Christoph

    2016-05-01

    In the present article, numerical simulations have been performed to find the bond and site percolation thresholds on two-dimensional Gabriel graphs (GG) for Poisson point processes. GGs belong to the family of "proximity graphs" and are discussed, e.g., in context of the construction of backbones for wireless ad-hoc networks. Finite-size scaling analyses have been performed to find the critical points and critical exponents ν, β and γ. The critical exponents obtained this way verify that the associated universality class is that of standard 2D percolation.

  20. From cognitive maps to cognitive graphs.

    PubMed

    Chrastil, Elizabeth R; Warren, William H

    2014-01-01

    We investigate the structure of spatial knowledge that spontaneously develops during free exploration of a novel environment. We present evidence that this structure is similar to a labeled graph: a network of topological connections between places, labeled with local metric information. In contrast to route knowledge, we find that the most frequent routes and detours to target locations had not been traveled during learning. Contrary to purely topological knowledge, participants typically traveled the shortest metric distance to a target, rather than topologically equivalent but longer paths. The results are consistent with the proposal that people learn a labeled graph of their environment. PMID:25389769

  1. Graph-state basis for Pauli channels

    SciTech Connect

    Chen Xiaoyu; Jiang Lizhen

    2011-05-15

    Quantum capacities of Pauli channels are not additive, a degenerate quantum code may improve the hashing bound of the capacity. The difficulty in approaching the capacity is how to calculate the coherent information of a generic degenerate quantum code. Using graph state basis, we greatly reduce the problem for the input of quantum error-correcting code. We show that for a graph diagonal state passing through a Pauli channel the output state is diagonalizable and the joint output state of the system and ancilla is block diagonalizable. When the input state is an equal probable mixture of codewords of a stabilizer code, the coherent information can be analytically obtained.

  2. Random graph coloring: statistical physics approach.

    PubMed

    van Mourik, J; Saad, D

    2002-11-01

    The problem of vertex coloring in random graphs is studied using methods of statistical physics and probability. Our analytical results are compared to those obtained by exact enumeration and Monte Carlo simulations. We critically discuss the merits and shortcomings of the various methods, and interpret the results obtained. We present an exact analytical expression for the two-coloring problem as well as general replica symmetric approximated solutions for the thermodynamics of the graph coloring problem with p colors and K-body edges. PMID:12513569

  3. Isomorphisms between petri nets and dataflow graphs

    SciTech Connect

    Kavi, K.M.; Buckles, B.P.; Bhat, U.N.

    1987-10-01

    Dataflow graphs are a generalized model of computation. Uninterpreted dataflow graphs with nondeterminism resolved via probabilities are shown to be isomorphic to a class of Petri nets known as free choice nets. Petri net analysis methods are readily available in the literature and this result makes those methods accessible to dataflow research. Nevertheless, combinatorial explosion can render Petri net analysis inoperative. Using a previously known technique for decomposing free choice nets into smaller components, it is demonstrated that, in principle, it is possible to determine aspects of the overall behavior from the particular behavior of components.

  4. Graphing techniques for materials laboratory using Excel

    NASA Technical Reports Server (NTRS)

    Kundu, Nikhil K.

    1994-01-01

    Engineering technology curricula stress hands on training and laboratory practices in most of the technical courses. Laboratory reports should include analytical as well as graphical evaluation of experimental data. Experience shows that many students neither have the mathematical background nor the expertise for graphing. This paper briefly describes the procedure and data obtained from a number of experiments such as spring rate, stress concentration, endurance limit, and column buckling for a variety of materials. Then with a brief introduction to Microsoft Excel the author explains the techniques used for linear regression and logarithmic graphing.

  5. Quasiperiodic graphs at the onset of chaos.

    PubMed

    Luque, B; Cordero-Gracia, M; Gómez, M; Robledo, A

    2013-12-01

    We examine the connectivity fluctuations across networks obtained when the horizontal visibility (HV) algorithm is used on trajectories generated by nonlinear circle maps at the quasiperiodic transition to chaos. The resultant HV graph is highly anomalous as the degrees fluctuate at all scales with amplitude that increases with the size of the network. We determine families of Pesin-like identities between entropy growth rates and generalized graph-theoretical Lyapunov exponents. An irrational winding number with pure periodic continued fraction characterizes each family. We illustrate our results for the so-called golden, silver, and bronze numbers. PMID:24483542

  6. Isomorphisms between Petri nets and dataflow graphs

    NASA Technical Reports Server (NTRS)

    Kavi, Krishna M.; Buckles, Billy P.; Bhat, U. Narayan

    1987-01-01

    Dataflow graphs are a generalized model of computation. Uninterpreted dataflow graphs with nondeterminism resolved via probabilities are shown to be isomorphic to a class of Petri nets known as free choice nets. Petri net analysis methods are readily available in the literature and this result makes those methods accessible to dataflow research. Nevertheless, combinatorial explosion can render Petri net analysis inoperative. Using a previously known technique for decomposing free choice nets into smaller components, it is demonstrated that, in principle, it is possible to determine aspects of the overall behavior from the particular behavior of components.

  7. Generalized graph manifolds and their effective recognition

    SciTech Connect

    Matveev, S V

    1998-10-31

    A generalized graph manifold is a three-dimensional manifold obtained by gluing together elementary blocks, each of which is either a Seifert manifold or contains no essential tori or annuli. By a well-known result on torus decomposition each compact three-dimensional manifold with boundary that is either empty or consists of tori has a canonical representation as a generalized graph manifold. A short simple proof of the existence of a canonical representation is presented and a (partial) algorithm for its construction is described. A simple hyperbolicity test for blocks that are not Seifert manifolds is also presented.

  8. Selective electrochemical discrimination between dopamine and phenethylamine-derived psychotropic drugs using electrodes modified with an acyclic receptor containing two terminal 3-alkoxy-5-nitroindazole rings.

    PubMed

    Doménech, Antonio; Navarro, Pilar; Arán, Vicente J; Muro, Beatriz; Montoya, Noemí; García-España, Enrique

    2010-06-01

    Electrochemical discrimination between dopamine and psychotropic drugs which have in common a skeletal structure of phenethylamine, can be obtained using acyclic receptors L(1) and L(2), containing two terminal 3-alkoxy-5-nitroindazole rings. Upon attachment to graphite electrodes, L(1) and L(2) exhibit a well-defined, essentially reversible solid state electrochemistry in contact with aqueous media, based on electrolyte-assisted reduction processes involving successive cation and anion insertion/binding. As a result, a distinctive, essentially Nernstian electrochemical response is obtained for phenethylammonium ions of methamphetamine (METH), p-methoxyamphetamine (PMA), amphetamine (AMPH), mescaline (MES), homoveratrylamine (HOM), phenethylamine (PEA) and dopamine (DA) in aqueous media. PMID:20407681

  9. On Ramsey (3K2, K3) - minimal graphs

    NASA Astrophysics Data System (ADS)

    Wijaya, Kristiana; Baskoro, Edy Tri; Assiyatun, Hilda; Suprijanto, Djoko

    2016-02-01

    The Ramsey graph theory has many interesting applications, such as in the fields of communications, information retrieval, and decision making. One of growing topics in Ramsey theory is Ramsey minimal graph. For any given graphs G and H, find graphs F such that any red-blue coloring of all edges of F contains either a red copy of G or a blue copy of H. If this condition is not satisfied by the graph F - e, then we call the graph F as a Ramsey (G, H) - minimal. In this paper, we derive the properties of (3K2, K3) - minimal graphs. We, then, characterize all Ramsey (3K2, K3) - minimal graphs.

  10. Manipulations of Cartesian Graphs: A First Introduction to Analysis.

    ERIC Educational Resources Information Center

    Lowenthal, Francis; Vandeputte, Christiane

    1989-01-01

    Introduces an introductory module for analysis. Describes stock of basic functions and their graphs as part one and three methods as part two: transformations of simple graphs, the sum of stock functions, and upper and lower bounds. (YP)

  11. Evolving Polygons Revisited: Inequalities and Computer Graphing

    ERIC Educational Resources Information Center

    Abramovich, Sergei; Brouwer, Peter

    2009-01-01

    This paper was developed with the goal of enhancing the mathematical preparation of secondary school teachers in the technological paradigm. It shows how two-variable inequalities can be utilized as models for the construction of geometric objects using the software Graphing Calculator 3.5 (produced by Pacific Tech) as a relation grapher. An…

  12. Interactive Web Graphs for Economic Principles.

    ERIC Educational Resources Information Center

    Kaufman, Dennis A.; Kaufman, Rebecca S.

    2002-01-01

    Describes a Web site with animation and interactive activities containing graphs and basic economics concepts. Features changes in supply and market equilibrium, the construction of the long-run average cost curve, short-run profit maximization, long-run market equilibrium, and changes in aggregate demand and aggregate supply. States the…

  13. Quantum secret sharing with qudit graph states

    SciTech Connect

    Keet, Adrian; Fortescue, Ben; Sanders, Barry C.; Markham, Damian

    2010-12-15

    We present a unified formalism for threshold quantum secret sharing using graph states of systems with prime dimension. We construct protocols for three varieties of secret sharing: with classical and quantum secrets shared between parties over both classical and quantum channels.

  14. Colour mathematics: with graphs and numbers

    NASA Astrophysics Data System (ADS)

    Lo Presto, Michael C.

    2009-07-01

    The different combinations involved in additive and subtractive colour mixing can often be difficult for students to remember. Using transmission graphs for filters of the primary colours and a numerical scheme to write out the relationships are good exercises in analytical thinking that can help students recall the combinations rather than just attempting to memorize them.

  15. Negative dimensional integrals. I. Feynman graphs

    NASA Astrophysics Data System (ADS)

    Halliday, I. G.; Ricotta, R. M.

    1987-07-01

    We propose a new method of evaluating integrals based on negative dimensional integration. We compute Feynman graphs by considering analytic extensions. Propagators are raised to negative integer powers and integrated over negative integer dimensions. We are left with the problem of computing polynomial integrals and summing finite series.

  16. Signals on Graphs: Uncertainty Principle and Sampling

    NASA Astrophysics Data System (ADS)

    Tsitsvero, Mikhail; Barbarossa, Sergio; Di Lorenzo, Paolo

    2016-09-01

    In many applications, the observations can be represented as a signal defined over the vertices of a graph. The analysis of such signals requires the extension of standard signal processing tools. In this work, first, we provide a class of graph signals that are maximally concentrated on the graph domain and on its dual. Then, building on this framework, we derive an uncertainty principle for graph signals and illustrate the conditions for the recovery of band-limited signals from a subset of samples. We show an interesting link between uncertainty principle and sampling and propose alternative signal recovery algorithms, including a generalization to frame-based reconstruction methods. After showing that the performance of signal recovery algorithms is significantly affected by the location of samples, we suggest and compare a few alternative sampling strategies. Finally, we provide the conditions for perfect recovery of a useful signal corrupted by sparse noise, showing that this problem is also intrinsically related to vertex-frequency localization properties.

  17. Marking Student Programs Using Graph Similarity

    ERIC Educational Resources Information Center

    Naude, Kevin A.; Greyling, Jean H.; Vogts, Dieter

    2010-01-01

    We present a novel approach to the automated marking of student programming assignments. Our technique quantifies the structural similarity between unmarked student submissions and marked solutions, and is the basis by which we assign marks. This is accomplished through an efficient novel graph similarity measure ("AssignSim"). Our experiments…

  18. Graph pyramids for protein function prediction

    PubMed Central

    2015-01-01

    Background Uncovering the hidden organizational characteristics and regularities among biological sequences is the key issue for detailed understanding of an underlying biological phenomenon. Thus pattern recognition from nucleic acid sequences is an important affair for protein function prediction. As proteins from the same family exhibit similar characteristics, homology based approaches predict protein functions via protein classification. But conventional classification approaches mostly rely on the global features by considering only strong protein similarity matches. This leads to significant loss of prediction accuracy. Methods Here we construct the Protein-Protein Similarity (PPS) network, which captures the subtle properties of protein families. The proposed method considers the local as well as the global features, by examining the interactions among 'weakly interacting proteins' in the PPS network and by using hierarchical graph analysis via the graph pyramid. Different underlying properties of the protein families are uncovered by operating the proposed graph based features at various pyramid levels. Results Experimental results on benchmark data sets show that the proposed hierarchical voting algorithm using graph pyramid helps to improve computational efficiency as well the protein classification accuracy. Quantitatively, among 14,086 test sequences, on an average the proposed method misclassified only 21.1 sequences whereas baseline BLAST score based global feature matching method misclassified 362.9 sequences. With each correctly classified test sequence, the fast incremental learning ability of the proposed method further enhances the training model. Thus it has achieved more than 96% protein classification accuracy using only 20% per class training data. PMID:26044522

  19. Graph theory in structure-property correlations

    NASA Astrophysics Data System (ADS)

    Vinogradova, M. G.; Fedina, Yu. A.; Papulov, Yu. G.

    2016-02-01

    The possibilities of the theoretical graph approach to the construction and interpretation of additive schemes for calculation and prediction are discussed. Working formulas are derived for calculating the thermodynamic properties of alkanes and their substitutes. The obtained algorithms are used to calculate thermodynamic properties of chloroalkanes that correspond to experimental values.

  20. Movement Forms: A Graph-Dynamic Perspective

    PubMed Central

    Saltzman, Elliot; Holt, Ken

    2014-01-01

    The focus of this paper is on characterizing the physical movement forms (e.g., walk, crawl, roll, etc.) that can be used to actualize abstract, functionally-specified behavioral goals (e.g., locomotion). Emphasis is placed on how such forms are distinguished from one another, in part, by the set of topological patterns of physical contact between agent and environment (i.e., the set of physical graphs associated with each form) and the transitions among these patterns displayed over the course of performance (i.e., the form’s physical graph dynamics). Crucial in this regard is the creation and dissolution of loops in these graphs, which can be related to the distinction between open and closed kinematic chains. Formal similarities are described within the theoretical framework of task-dynamics between physically-closed kinematic chains (physical loops) that are created during various movement forms and functionally-closed kinematic chains (functional loops) that are associated with task-space control of end-effectors; it is argued that both types of loop must be flexibly incorporated into the coordinative structures that govern skilled action. Final speculation is focused on the role of graphs and their dynamics, not only in processes of coordination and control for individual agents, but also in processes of inter-agent coordination and the coupling of agents with (non-sentient) environmental objects. PMID:24910507

  1. An Ellipse Morphs to a Cosine Graph!

    ERIC Educational Resources Information Center

    King, L .R.

    2013-01-01

    We produce a continuum of curves all of the same length, beginning with an ellipse and ending with a cosine graph. The curves in the continuum are made by cutting and unrolling circular cones whose section is the ellipse; the initial cone is degenerate (it is the plane of the ellipse); the final cone is a circular cylinder. The curves of the…

  2. Using Tables and Graphs for Reporting Data.

    PubMed

    Bavdekar, Sandeep B

    2015-10-01

    For presenting the study results, authors need to choose from one of the three formats: text, tables and graphs. The underlying consideration of any author while making the choice is to ensure that readers find it easy to understand, to assist the author present data in a way that would catch the reader's eye, hold his interest and enhance his understanding. The choice should, therefore, be based on the advantages and limitations of each of these formats. Most of the observations are reported in textual format. Tables are useful when comparisons are to be shown. Graphs attract readers' attention better and the data they depict remains in the reader's memory. The type of graph used is dependent upon the nature of data that is to be shown. Every research paper has a lot to say through the data that has been collected and analyzed. However, this data needs to be presented in a logical, coherent and easy-to-understand manner. The way data is presented can influence the reviewers' and editors' decision. It can also make the difference between a paper being appreciated by the readers or being neglected or even trashed by them. Tables and Graphs are the two important tools that authors use to make the data more presentable and easy to read and understand. PMID:27608693

  3. Graphing Calculator Use in Algebra Teaching

    ERIC Educational Resources Information Center

    Dewey, Brenda L.; Singletary, Ted J.; Kinzel, Margaret T.

    2009-01-01

    This study examines graphing calculator technology availability, characteristics of teachers who use it, teacher attitudes, and how use reflects changes to algebra curriculum and instructional practices. Algebra I and Algebra II teachers in 75 high school and junior high/middle schools in a diverse region of a northwestern state were surveyed.…

  4. Colour Mathematics: With Graphs and Numbers

    ERIC Educational Resources Information Center

    LoPresto, Michael C.

    2009-01-01

    The different combinations involved in additive and subtractive colour mixing can often be difficult for students to remember. Using transmission graphs for filters of the primary colours and a numerical scheme to write out the relationships are good exercises in analytical thinking that can help students recall the combinations rather than just…

  5. Rainbow connection number of rocket graphs

    NASA Astrophysics Data System (ADS)

    Susilawati, Salman, A. N. M.

    2015-09-01

    All graphs in this paper are simple, finite, and undirected. The concept of rainbow coloring was introduced by Chartrand et al2. Let G be a non trivial connected graph. For k ∈ℕ , we define a coloring c :E (G )→{1 ,2 ,…,k } of the edges of G such that the adjacent can be colored the same. A path P in G is a rainbow path if no two edges of P are colored the same. A path connecting two vertices u and u in G is called u-v path. A graph G is said rainbow-connected if for every two vertices u and u of G, there exist a rainbow u-v path. In this case, the coloring c is called the rainbow k-coloring of G. The minimum k such that G has rainbow k-coloring is called the rainbow connection number of G. Clearly that diam(G )≤r c (G ) where diam(G) denotes the diameter of G. In this paper we determine the rainbow connection number of rocket graphs.

  6. Fusion rule algebras from graph theory

    NASA Astrophysics Data System (ADS)

    Caselle, M.; Ponzano, G.

    1989-06-01

    We describe a new class of fusion algebras related to graph theory which bear intriguing connections with group algebras. The structure constants and the matrix S, which diagonalizes the fusion rules, are explicitly computed in terms of SU(2) coupling coefficients.

  7. Reducing Abstraction When Learning Graph Theory

    ERIC Educational Resources Information Center

    Hazzan, Orit; Hadar, Irit

    2005-01-01

    This article presents research on students' understanding of basic concepts in Graph Theory. Students' understanding is analyzed through the lens of the theoretical framework of reducing abstraction (Hazzan, 1999). As it turns out, in spite of the relative simplicity of the concepts that are introduced in the introductory part of a traditional…

  8. Simple scale interpolator facilitates reading of graphs

    NASA Technical Reports Server (NTRS)

    Fazio, A.; Henry, B.; Hood, D.

    1966-01-01

    Set of cards with scale divisions and a scale finder permits accurate reading of the coordinates of points on linear or logarithmic graphs plotted on rectangular grids. The set contains 34 different scales for linear plotting and 28 single cycle scales for log plots.

  9. Communication Graph Generator for Parallel Programs

    2014-04-08

    Graphator is a collection of relatively simple sequential programs that generate communication graphs/matrices for commonly occurring patterns in parallel programs. Currently, there is support for five communication patterns: two-dimensional 4-point stencil, four-dimensional 8-point stencil, all-to-alls over sub-communicators, random near-neighbor communication, and near-neighbor communication.

  10. Horizontal visibility graphs from integer sequences

    NASA Astrophysics Data System (ADS)

    Lacasa, Lucas

    2016-09-01

    The horizontal visibility graph (HVG) is a graph-theoretical representation of a time series and builds a bridge between dynamical systems and graph theory. In recent years this representation has been used to describe and theoretically compare different types of dynamics and has been applied to characterize empirical signals, by extracting topological features from the associated HVGs which have shown to be informative on the class of dynamics. Among some other measures, it has been shown that the degree distribution of these graphs is a very informative feature that encapsulates nontrivial information of the series's generative dynamics. In particular, the HVG associated to a bi-infinite real-valued series of independent and identically distributed random variables is a universal exponential law P(k)=(1/3){(2/3)}k-2, independent of the series marginal distribution. Most of the current applications have however only addressed real-valued time series, as no exact results are known for the topological properties of HVGs associated to integer-valued series. In this paper we explore this latter situation and address univariate time series where each variable can only take a finite number n of consecutive integer values. We are able to construct an explicit formula for the parametric degree distribution {P}n(k), which we prove to converge to the continuous case for large n and deviates otherwise. A few applications are then considered.

  11. A notion of graph likelihood and an infinite monkey theorem

    NASA Astrophysics Data System (ADS)

    Banerji, Christopher R. S.; Mansour, Toufik; Severini, Simone

    2014-01-01

    We play with a graph-theoretic analogue of the folklore infinite monkey theorem. We define a notion of graph likelihood as the probability that a given graph is constructed by a monkey in a number of time steps equal to the number of vertices. We present an algorithm to compute this graph invariant and closed formulas for some infinite classes. We have to leave the computational complexity of the likelihood as an open problem.

  12. GraphPrints: Towards a Graph Analytic Method for Network Anomaly Detection

    SciTech Connect

    Harshaw, Chris R; Bridges, Robert A; Iannacone, Michael D; Reed, Joel W; Goodall, John R

    2016-01-01

    This paper introduces a novel graph-analytic approach for detecting anomalies in network flow data called \\textit{GraphPrints}. Building on foundational network-mining techniques, our method represents time slices of traffic as a graph, then counts graphlets\\textemdash small induced subgraphs that describe local topology. By performing outlier detection on the sequence of graphlet counts, anomalous intervals of traffic are identified, and furthermore, individual IPs experiencing abnormal behavior are singled-out. Initial testing of GraphPrints is performed on real network data with an implanted anomaly. Evaluation shows false positive rates bounded by 2.84\\% at the time-interval level, and 0.05\\% at the IP-level with 100\\% true positive rates at both.

  13. Multigraph: Interactive Data Graphs on the Web

    NASA Astrophysics Data System (ADS)

    Phillips, M. B.

    2010-12-01

    Many aspects of geophysical science involve time dependent data that is often presented in the form of a graph. Considering that the web has become a primary means of communication, there are surprisingly few good tools and techniques available for presenting time-series data on the web. The most common solution is to use a desktop tool such as Excel or Matlab to create a graph which is saved as an image and then included in a web page like any other image. This technique is straightforward, but it limits the user to one particular view of the data, and disconnects the graph from the data in a way that makes updating a graph with new data an often cumbersome manual process. This situation is somewhat analogous to the state of mapping before the advent of GIS. Maps existed only in printed form, and creating a map was a laborious process. In the last several years, however, the world of mapping has experienced a revolution in the form of web-based and other interactive computer technologies, so that it is now commonplace for anyone to easily browse through gigabytes of geographic data. Multigraph seeks to bring a similar ease of access to time series data. Multigraph is a program for displaying interactive time-series data graphs in web pages that includes a simple way of configuring the appearance of the graph and the data to be included. It allows multiple data sources to be combined into a single graph, and allows the user to explore the data interactively. Multigraph lets users explore and visualize "data space" in the same way that interactive mapping applications such as Google Maps facilitate exploring and visualizing geography. Viewing a Multigraph graph is extremely simple and intuitive, and requires no instructions. Creating a new graph for inclusion in a web page involves writing a simple XML configuration file and requires no programming. Multigraph can read data in a variety of formats, and can display data from a web service, allowing users to "surf

  14. Guide to graphing data and taking action.

    PubMed

    1992-01-01

    3 kinds of graphs are presented as instructional examples of how to display data collected on family planning (FP) programs. The first is a trend analysis of new acceptors and requires monthly summaries of new acceptors serviced by the clinic. The objective is to gauge declines or increases over time in new acceptors for each contraceptive method offered. The second graph requires a monthly summary of new acceptors by method mix. The third graph needs data on the reason for attending the particular FP clinic. IEC activities can be enhanced with this information. In the example for graph 1, new acceptors over an 18-month-period are plotted on one axis by monthly units, and the other axis by number of new acceptors. The connection of dots reflects the trend over time. There is a specific example with data from Yena clinic over a 12-month-period; the interpretations and possible actions are indicated. Instructions for presenting a pie chart are also given for new acceptors by method mix; the example is given for data from Yena Clinic and possible interpretations and actions are indicated. A visual presentation of the data worksheet needed for a pie chart is provided. Calculations must be made for the fraction of new acceptors out of total acceptors and the percent of total new acceptors for each method. An explanation is given for constructing a bar chart; again an example is given of a completed bar chart with data and the accompanying data sheet. A checklist identifies important guidelines for developing and using line graphs, bar charts, and pie charts. PMID:12318345

  15. Consensus dynamics on random rectangular graphs

    NASA Astrophysics Data System (ADS)

    Estrada, Ernesto; Sheerin, Matthew

    2016-06-01

    A random rectangular graph (RRG) is a generalization of the random geometric graph (RGG) in which the nodes are embedded into a rectangle with side lengths a and b = 1 / a, instead of on a unit square [ 0 , 1 ] 2. Two nodes are then connected if and only if they are separated at a Euclidean distance smaller than or equal to a certain threshold radius r. When a = 1 the RRG is identical to the RGG. Here we apply the consensus dynamics model to the RRG. Our main result is a lower bound for the time of consensus, i.e., the time at which the network reaches a global consensus state. To prove this result we need first to find an upper bound for the algebraic connectivity of the RRG, i.e., the second smallest eigenvalue of the combinatorial Laplacian of the graph. This bound is based on a tight lower bound found for the graph diameter. Our results prove that as the rectangle in which the nodes are embedded becomes more elongated, the RRG becomes a 'large-world', i.e., the diameter grows to infinity, and a poorly-connected graph, i.e., the algebraic connectivity decays to zero. The main consequence of these findings is the proof that the time of consensus in RRGs grows to infinity as the rectangle becomes more elongated. In closing, consensus dynamics in RRGs strongly depend on the geometric characteristics of the embedding space, and reaching the consensus state becomes more difficult as the rectangle is more elongated.

  16. Learning Financial Reports From Mixed Symbolic-Spatial Graphs

    ERIC Educational Resources Information Center

    Tanlamai, Uthai; Soongswang, Oranuj

    2011-01-01

    Mixed visuals of numbers and graphs are available in various financial reports that demonstrate the financial status and risks of a firm. GWN (graphs with numbers) and TWG (table of numbers with graphs) were used as two alternative visuals derived from the actual data of two large public companies, one from food manufacturing industry (food) and…

  17. 47 CFR 73.184 - Groundwave field strength graphs.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 4 2010-10-01 2010-10-01 false Groundwave field strength graphs. 73.184 Section 73.184 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) BROADCAST RADIO SERVICES RADIO BROADCAST SERVICES AM Broadcast Stations § 73.184 Groundwave field strength graphs. (a) Graphs 1 to 20 show, for each of 20 frequencies,...

  18. Graphing Online Searches with Lotus 1-2-3.

    ERIC Educational Resources Information Center

    Persson, Olle

    1986-01-01

    This article illustrates how Lotus 1-2-3 software can be used to create graphs using downloaded online searches as raw material, notes most commands applied, and outlines three required steps: downloading, importing the downloading file into the worksheet, and making graphs. An example in bibliometrics and sample graphs are included. (EJS)

  19. Deterministic dense coding and faithful teleportation with multipartite graph states

    SciTech Connect

    Huang, C.-Y.; Yu, I-C.; Lin, F.-L.; Hsu, L.-Y.

    2009-05-15

    We propose schemes to perform the deterministic dense coding and faithful teleportation with multipartite graph states. We also find the sufficient and necessary condition of a viable graph state for the proposed schemes. That is, for the associated graph, the reduced adjacency matrix of the Tanner-type subgraph between senders and receivers should be invertible.

  20. Measuring Graph Comprehension, Critique, and Construction in Science

    ERIC Educational Resources Information Center

    Lai, Kevin; Cabrera, Julio; Vitale, Jonathan M.; Madhok, Jacquie; Tinker, Robert; Linn, Marcia C.

    2016-01-01

    Interpreting and creating graphs plays a critical role in scientific practice. The K-12 Next Generation Science Standards call for students to use graphs for scientific modeling, reasoning, and communication. To measure progress on this dimension, we need valid and reliable measures of graph understanding in science. In this research, we designed…

  1. Do Graphs Promote Learning in Principles of Economics?

    ERIC Educational Resources Information Center

    Cohn, Elchanan; Cohn, Sharon; Balch, Donald C.; Bradley, James, Jr.

    2001-01-01

    Tests the effects on student performance when using graphs as part of a University of South Carolina (Columbia) principles of economics lecture. Finds in 1995 that students in the lecture with graphs had significantly lower gain scores than those in the no-graphs lecture. Finds no significant difference in 1997. (RLH)

  2. Hands-on Science: Getting-to-Know-You Graphing.

    ERIC Educational Resources Information Center

    Kepler, Lynne

    1992-01-01

    Elementary teachers can use graphing to introduce students to one another. An eye color graphing activity helps students learn more about each other while experimenting with different ways of organizing and displaying information. For follow up, students can apply their graphing knowledge by collecting and displaying data from their families. (SM)

  3. Students' Cognitive Reasoning of Graphs: Characteristics and Progression

    ERIC Educational Resources Information Center

    Wang, Zu Hao; Wei, Silin; Ding, Wei; Chen, Xiuyun; Wang, Xiaonan; Hu, Kaiyan

    2012-01-01

    Graphs are widely used to present scientific information. Information presented in graphs can be classified into three kinds: explicit information, tacit information, and conclusive information. Reading information from graphs requires not only science content knowledge and understanding but also general logical reasoning. This study examined the…

  4. Can Comparison of Contrastive Examples Facilitate Graph Understanding?

    ERIC Educational Resources Information Center

    Smith, Linsey A.; Gentner, Dedre

    2011-01-01

    The authors explore the role of comparison in improving graph fluency. The ability to use graphs fluently is crucial for STEM achievement, but graphs are challenging to interpret and produce because they often involve integration of multiple variables, continuous change in variables over time, and omission of certain details in order to highlight…

  5. Expert interpretation of bar and line graphs: the role of graphicacy in reducing the effect of graph format

    PubMed Central

    Peebles, David; Ali, Nadia

    2015-01-01

    The distinction between informational and computational equivalence of representations, first articulated by Larkin and Simon (1987) has been a fundamental principle in the analysis of diagrammatic reasoning which has been supported empirically on numerous occasions. We present an experiment that investigates this principle in relation to the performance of expert graph users of 2 × 2 “interaction” bar and line graphs. The study sought to determine whether expert interpretation is affected by graph format in the same way that novice interpretations are. The findings revealed that, unlike novices—and contrary to the assumptions of several graph comprehension models—experts' performance was the same for both graph formats, with their interpretation of bar graphs being no worse than that for line graphs. We discuss the implications of the study for guidelines for presenting such data and for models of expert graph comprehension. PMID:26579052

  6. Representing clusters using a maximum common edge substructure algorithm applied to reduced graphs and molecular graphs.

    PubMed

    Gardiner, Eleanor J; Gillet, Valerie J; Willett, Peter; Cosgrove, David A

    2007-01-01

    Chemical databases are routinely clustered, with the aim of grouping molecules which share similar structural features. Ideally, medicinal chemists are then able to browse a few representatives of the cluster in order to interpret the shared activity of the cluster members. However, when molecules are clustered using fingerprints, it may be difficult to decipher the structural commonalities which are present. Here, we seek to represent a cluster by means of a maximum common substructure based on the shared functionality of the cluster members. Previously, we have used reduced graphs, where each node corresponds to a generalized functional group, as topological molecular descriptors for virtual screening. In this work, we precluster a database using any clustering method. We then represent the molecules in a cluster as reduced graphs. By repeated application of a maximum common edge substructure (MCES) algorithm, we obtain one or more reduced graph cluster representatives. The sparsity of the reduced graphs means that the MCES calculations can be performed in real time. The reduced graph cluster representatives are readily interpretable in terms of functional activity and can be mapped directly back to the molecules to which they correspond, giving the chemist a rapid means of assessing potential activities contained within the cluster. Clusters of interest are then subject to a detailed R-group analysis using the same iterated MCES algorithm applied to the molecular graphs. PMID:17309248

  7. IceCube simulation production and the transition to IceProd2

    NASA Astrophysics Data System (ADS)

    Schultz, David

    2016-04-01

    IceCube's simulation production relies largely on dynamic, heterogeneous resources spread around the world. Datasets consist of many thousands of job workflow subsets running in parallel as directed acyclic graphs (DAGs) and using varying resources. IceProd is a set of Python daemons which process job workflow and maintain configuration and status information on jobs before, during, and after processing. IceProd manages a complex workflow of DAGs to distribute jobs across all computing grids and optimize resource usage. IceProd2 is a new version of IceProd with substantial increases in security, reliability, scalability, and ease of use. It is undergoing testing and will be deployed this fall.

  8. Flexible Acyclic Polyol-Chloride Anion Complexes and Their Characterization by Photoelectron Spectroscopy and Variable Temperature Binding Constant Determinations.

    PubMed

    Shokri, Alireza; Wang, Xue-Bin; Wang, Yanping; O'Doherty, George A; Kass, Steven R

    2016-03-17

    Flexible acyclic alcohols with one to five hydroxyl groups were bound to a chloride anion and these complexes were interrogated by negative ion photoelectron spectroscopy and companion density functional theory computations. The resulting vertical detachment energies are reproduced on average to 0.10 eV by M06-2X/aug-cc-pVTZ predictions and range from 4.45-5.96 eV. These values are 0.84-2.35 eV larger than the adiabatic detachment energy of Cl(-) as a result of the larger hydrogen bond networks in the bigger polyols. Adiabatic detachment energies of the alcohol-Cl(-) clusters are more difficult to determine both experimentally and computationally. This is due to the large geometry changes that occur upon photodetachment and the large bond dissociation energy of H-Cl which enables the resulting chlorine atom to abstract a hydrogen from any of the methylene (CH2) or methine (CH) positions. Both ionic and nonionic hydrogen bonds (i.e., OH···Cl(-) and OH···OH···Cl(-)) form in the larger polyols complexes and are found to be energetically comparable. Subtle structural differences, consequently can lead to the formation of different types of hydrogen bonds, and maximizing the ionic ones is not always preferred. Solution equilibrium binding constants between the alcohols and tetrabutylammonium chloride (TBACl) in acetonitrile at -24.2, +22.0, and +53.6 °C were also determined. The free energies of association are nearly identical for all of the substrates (i.e., ΔG° = -2.8 ± 0.7 kcal mol(-1)). Compensating enthalpy and entropy values reveal, contrary to expectation and the intrinsic gas-phase preferences, that the bigger systems with more hydroxyl groups are entropically favored and enthalpically disfavored relative to the smaller species. This suggests that more solvent molecules are released upon binding TBACl to alcohols with more hydroxyl groups and is consistent with the measured negative heat capacities. These quantities increase with molecular

  9. Induction of ovulation in the acyclic postpartum ewe following continuous, low-dose subcutaneous infusion of GnRH.

    PubMed

    Fray, M D; Lamming, G E; Haresign, W

    1995-04-15

    Pituitary and ovarian responses to subcutaneous infusion of GnRH were investigated in acyclic, lactating Mule ewes during the breeding season. Thirty postpartum ewes were split into 3 equal groups; Group G received GnRH (250 ng/h) for 96 h; Group P + G was primed with progestagen for 10 d then received GnRH (250 ng/h) for 96 h; and Group P received progestagen priming and saline vehicle only. The infusions were delivered via osmotic minipumps inserted 26.6 +/- 0.45 d post partum (Day 0 of the study). Blood samples were collected for LH analysis every 15 min from 12 h before until 8 h after minipump insertion, then every 2 h for a further 112 h. Daily blood samples were collected for progesterone analysis on Days 1 to 10 following minipump insertion, then every third day for a further 25 d. In addition, the reproductive tract was examined by laparoscopy on Day -5 and Day +7 and estrous behavior was monitored between Day -4 and Day +7. Progestagen priming suppressed (P < 0.05) plasma LH levels (0.27 +/- 0.03 vs 0.46 +/- 0.06 ng/ml) during the preinfusion period, but the GnRH-induced LH release was similar for Group G and Group P + G. The LH surge began significantly (P < 0.05) earlier (32.0 +/- 3.0 vs 56.3 +/- 4.1 h) and was of greater magnitude (32.15 +/- 3.56 vs 18.84 +/- 4.13 ng/ml) in the unprimed than the primed ewes. None of the ewes infused with saline produced a preovulatory LH surge. The GnRH infusion induced ovulation in 10/10 unprimed and 7/9 progestagen-primed ewes, with no significant difference in ovulation rate (1.78 +/- 0.15 and 1.33 +/- 0.21, respectively). Ovulation was followed by normal luteal function in 4/10 Group-G ewes, while the remaining 6 ewes had short luteal phases. In contrast, each of the 7 Group-P + G ewes that ovulated secreted progesterone for at least 10 d, although elevated plasma progesterone levels were maintained in 3/7 unmated ewes for >35 d. Throughout the study only 2 ewes (both from Group P + G) displayed estrus. These data

  10. Ovarian acyclicity in zoo African elephants (Loxodonta africana) is associated with high body condition scores and elevated serum insulin and leptin.

    PubMed

    Morfeld, Kari A; Brown, Janine L

    2016-04-01

    The purpose of the present study was to determine whether excessive body fat and altered metabolic hormone concentrations in the circulation were associated with ovarian acyclicity in the world's largest land mammal, the African elephant. We compared body condition, glucose, insulin and leptin concentrations and the glucose-to-insulin ratio (G:I) between cycling (n=23; normal 14-16 week cycles based on serum progestagens for at least 2 years) and non-cycling (n=23; consistent baseline progestagen concentrations for at least 2 years) females. A validated body condition score (BCS) index (five-point scale; 1=thinnest, 5=fattest) was used to assess the degree of fatness of the study elephants. The mean BCS of non-cycling elephants was higher than that of their cycling counterparts. There were differences in concentrations of serum metabolic biomarkers, with non-cycling elephants in the BCS 5 category having higher leptin and insulin concentrations and a lower G:I ratio than cycling BCS 5 females. Using 'non-cycling' as the outcome variable in regression models, high BCS was a strong predictor of a non-cycling status. This study provides the first evidence that ovarian acyclicity in zoo African elephants is associated with body condition indicative of obesity, as well as elevated, perturbed biomarkers of metabolic status. PMID:25375263

  11. Acyclic Cucurbit[n]uril-type Molecular Containers: Influence of Aromatic Walls on their Function as Solubilizing Excipients for Insoluble Drugs

    PubMed Central

    2015-01-01

    We studied the influence of the aromatic sidewalls on the ability of acyclic CB[n]-type molecular containers (1a–1e) to act as solubilizing agents for 19 insoluble drugs including the developmental anticancer agent PBS-1086. All five containers exhibit good water solubility and weak self-association (Ks ≤ 624 M–1). We constructed phase solubility diagrams to extract Krel and Ka values for the container·drug complexes. The acyclic CB[n]-type containers generally display significantly higher Ka values than HP-β-CD toward drugs. Containers 1a–1e bind the steroidal ring system and aromatic moieties of insoluble drugs. Compound 1b displays highest affinity toward most of the drugs studied. Containers 1a and 1b are broadly applicable and can be used to formulate a wider variety of insoluble drugs than was previously possible with cyclodextrin technology. For drugs that are solubilized by both HP-β-CD and 1a–1e, lower concentrations of 1a–1e are required to achieve identical [drug]. PMID:25369565

  12. Advantages of Micro-Based Labs: Electronic Data Acquisition, Computerized Graphing, or Both?

    ERIC Educational Resources Information Center

    Stuessy, Carol L.; Rowland, Paul M.

    1989-01-01

    Discusses a microcomputer-based laboratory (MBL) study (n=75) which uses multiple temperature gathering devices (mercury thermometer, digital thermometer, and computer probe) and graphing methods (hand graphs, delayed computer graphs, and real-time graphs). Reports that MBL real-time graphing provides significant increases in graphing skills. (MVL)

  13. Tight Lower Bound for Percolation Threshold on an Infinite Graph

    NASA Astrophysics Data System (ADS)

    Hamilton, Kathleen E.; Pryadko, Leonid P.

    2014-11-01

    We construct a tight lower bound for the site percolation threshold on an infinite graph, which becomes exact for an infinite tree. The bound is given by the inverse of the maximal eigenvalue of the Hashimoto matrix used to count nonbacktracking walks on the original graph. Our bound always exceeds the inverse spectral radius of the graph's adjacency matrix, and it is also generally tighter than the existing bound in terms of the maximum degree. We give a constructive proof for existence of such an eigenvalue in the case of a connected infinite quasitransitive graph, a graph-theoretic analog of a translationally invariant system.

  14. StreamWorks - A system for Dynamic Graph Search

    SciTech Connect

    Choudhury, Sutanay; Holder, Larry; Chin, George; Ray, Abhik; Beus, Sherman J.; Feo, John T.

    2013-06-11

    Acting on time-critical events by processing ever growing social media, news or cyber data streams is a major technical challenge. Many of these data sources can be modeled as multi-relational graphs. Mining and searching for subgraph patterns in a continuous setting requires an efficient approach to incremental graph search. The goal of our work is to enable real-time search capabilities for graph databases. This demonstration will present a dynamic graph query system that leverages the structural and semantic characteristics of the underlying multi-relational graph.

  15. Modular Environment for Graph Research and Analysis with a Persistent

    2009-11-18

    The MEGRAPHS software package provides a front-end to graphs and vectors residing on special-purpose computing resources. It allows these data objects to be instantiated, destroyed, and manipulated. A variety of primitives needed for typical graph analyses are provided. An example program illustrating how MEGRAPHS can be used to implement a PageRank computation is included in the distribution.The MEGRAPHS software package is targeted towards developers of graph algorithms. Programmers using MEGRAPHS would write graph analysis programsmore » in terms of high-level graph and vector operations. These computations are transparently executed on the Cray XMT compute nodes.« less

  16. A Graph Based Interface for Representing Volume Visualization Results

    NASA Technical Reports Server (NTRS)

    Patten, James M.; Ma, Kwan-Liu

    1998-01-01

    This paper discusses a graph based user interface for representing the results of the volume visualization process. As images are rendered, they are connected to other images in a graph based on their rendering parameters. The user can take advantage of the information in this graph to understand how certain rendering parameter changes affect a dataset, making the visualization process more efficient. Because the graph contains more information than is contained in an unstructured history of images, the image graph is also helpful for collaborative visualization and animation.

  17. Modular Environment for Graph Research and Analysis with a Persistent

    SciTech Connect

    JANSSEN, CURTIS; EVENSKY, DAVID

    2009-11-18

    The MEGRAPHS software package provides a front-end to graphs and vectors residing on special-purpose computing resources. It allows these data objects to be instantiated, destroyed, and manipulated. A variety of primitives needed for typical graph analyses are provided. An example program illustrating how MEGRAPHS can be used to implement a PageRank computation is included in the distribution.The MEGRAPHS software package is targeted towards developers of graph algorithms. Programmers using MEGRAPHS would write graph analysis programs in terms of high-level graph and vector operations. These computations are transparently executed on the Cray XMT compute nodes.

  18. Hyperspectral Data Classification Using Factor Graphs

    NASA Astrophysics Data System (ADS)

    Makarau, A.; Müller, R.; Palubinskas, G.; Reinartz, P.

    2012-07-01

    Accurate classification of hyperspectral data is still a competitive task and new classification methods are developed to achieve desired tasks of hyperspectral data use. The objective of this paper is to develop a new method for hyperspectral data classification ensuring the classification model properties like transferability, generalization, probabilistic interpretation, etc. While factor graphs (undirected graphical models) are unfortunately not widely employed in remote sensing tasks, these models possess important properties such as representation of complex systems to model estimation/decision making tasks. In this paper we present a new method for hyperspectral data classification using factor graphs. Factor graph (a bipartite graph consisting of variables and factor vertices) allows factorization of a more complex function leading to definition of variables (employed to store input data), latent variables (allow to bridge abstract class to data), and factors (defining prior probabilities for spectral features and abstract classes; input data mapping to spectral features mixture and further bridging of the mixture to an abstract class). Latent variables play an important role by defining two-level mapping of the input spectral features to a class. Configuration (learning) on training data of the model allows calculating a parameter set for the model to bridge the input data to a class. The classification algorithm is as follows. Spectral bands are separately pre-processed (unsupervised clustering is used) to be defined on a finite domain (alphabet) leading to a representation of the data on multinomial distribution. The represented hyperspectral data is used as input evidence (evidence vector is selected pixelwise) in a configured factor graph and an inference is run resulting in the posterior probability. Variational inference (Mean field) allows to obtain plausible results with a low calculation time. Calculating the posterior probability for each class

  19. Knowledge Representation Issues in Semantic Graphs for Relationship Detection

    SciTech Connect

    Barthelemy, M; Chow, E; Eliassi-Rad, T

    2005-02-02

    An important task for Homeland Security is the prediction of threat vulnerabilities, such as through the detection of relationships between seemingly disjoint entities. A structure used for this task is a ''semantic graph'', also known as a ''relational data graph'' or an ''attributed relational graph''. These graphs encode relationships as typed links between a pair of typed nodes. Indeed, semantic graphs are very similar to semantic networks used in AI. The node and link types are related through an ontology graph (also known as a schema). Furthermore, each node has a set of attributes associated with it (e.g., ''age'' may be an attribute of a node of type ''person''). Unfortunately, the selection of types and attributes for both nodes and links depends on human expertise and is somewhat subjective and even arbitrary. This subjectiveness introduces biases into any algorithm that operates on semantic graphs. Here, we raise some knowledge representation issues for semantic graphs and provide some possible solutions using recently developed ideas in the field of complex networks. In particular, we use the concept of transitivity to evaluate the relevance of individual links in the semantic graph for detecting relationships. We also propose new statistical measures for semantic graphs and illustrate these semantic measures on graphs constructed from movies and terrorism data.

  20. Frequent Subgraph Discovery in Large Attributed Streaming Graphs

    SciTech Connect

    Ray, Abhik; Holder, Larry; Choudhury, Sutanay

    2014-08-13

    The problem of finding frequent subgraphs in large dynamic graphs has so far only consid- ered a dynamic graph as being represented by a series of static snapshots taken at various points in time. This representation of a dynamic graph does not lend itself well to real time processing of real world graphs like social networks or internet traffic which consist of a stream of nodes and edges. In this paper we propose an algorithm that discovers the frequent subgraphs present in a graph represented by a stream of labeled nodes and edges. Our algorithm is efficient and consists of tunable parameters that can be tuned by the user to get interesting patterns from various kinds of graph data. In our model updates to the graph arrive in the form of batches which contain new nodes and edges. Our algorithm con- tinuously reports the frequent subgraphs that are estimated to be found in the entire graph as each batch arrives. We evaluate our system using 5 large dynamic graph datasets: the Hetrec 2011 challenge data, Twitter, DBLP and two synthetic. We evaluate our approach against two popular large graph miners, i.e., SUBDUE and GERM. Our experimental re- sults show that we can find the same frequent subgraphs as a non-incremental approach applied to snapshot graphs, and in less time.