An algorithm for finding a similar subgraph of all Hamiltonian cycles

NASA Astrophysics Data System (ADS)

Wafdan, R.; Ihsan, M.; Suhaimi, D.

2018-01-01

This paper discusses an algorithm to find a similar subgraph called findSimSubG algorithm. A similar subgraph is a subgraph with a maximum number of edges, contains no isolated vertex and is contained in every Hamiltonian cycle of a Hamiltonian Graph. The algorithm runs only on Hamiltonian graphs with at least two Hamiltonian cycles. The algorithm works by examining whether the initial subgraph of the first Hamiltonian cycle is a subgraph of comparison graphs. If the initial subgraph is not in comparison graphs, the algorithm will remove edges and vertices of the initial subgraph that are not in comparison graphs. There are two main processes in the algorithm, changing Hamiltonian cycle into a cycle graph and removing edges and vertices of the initial subgraph that are not in comparison graphs. The findSimSubG algorithm can find the similar subgraph without using backtracking method. The similar subgraph cannot be found on certain graphs, such as an n-antiprism graph, complete bipartite graph, complete graph, 2n-crossed prism graph, n-crown graph, n-möbius ladder, prism graph, and wheel graph. The complexity of this algorithm is O(m|V|), where m is the number of Hamiltonian cycles and |V| is the number of vertices of a Hamiltonian graph.

Islands and Bridges: Making Sense of Marked Nodes in Large Graphs

DTIC Science & Technology

2012-08-01

time-evolving graphs. References [1] Nouf M. Kh. Alsudairy, Vijay V. Raghavan, Alaaeldin M. Hafez, and Hassan I Mathkour. Connection subgraphs: A survey...Riedy, David A. Bader, Karl Jiang, Pushkar Pande, , and Richa Sharma . Detecting communities from given seeds in social networks. Technical Report GT-CSE

Identification of family-specific residue packing motifs and their use for structure-based protein function prediction: I. Method development.

PubMed

Bandyopadhyay, Deepak; Huan, Jun; Prins, Jan; Snoeyink, Jack; Wang, Wei; Tropsha, Alexander

2009-11-01

Protein function prediction is one of the central problems in computational biology. We present a novel automated protein structure-based function prediction method using libraries of local residue packing patterns that are common to most proteins in a known functional family. Critical to this approach is the representation of a protein structure as a graph where residue vertices (residue name used as a vertex label) are connected by geometrical proximity edges. The approach employs two steps. First, it uses a fast subgraph mining algorithm to find all occurrences of family-specific labeled subgraphs for all well characterized protein structural and functional families. Second, it queries a new structure for occurrences of a set of motifs characteristic of a known family, using a graph index to speed up Ullman's subgraph isomorphism algorithm. The confidence of function inference from structure depends on the number of family-specific motifs found in the query structure compared with their distribution in a large non-redundant database of proteins. This method can assign a new structure to a specific functional family in cases where sequence alignments, sequence patterns, structural superposition and active site templates fail to provide accurate annotation.

Locating overlapping dense subgraphs in gene (protein) association networks and predicting novel protein functional groups among these subgraphs

NASA Astrophysics Data System (ADS)

Palla, Gergely; Derenyi, Imre; Farkas, Illes J.; Vicsek, Tamas

2006-03-01

Most tasks in a cell are performed not by individual proteins, but by functional groups of proteins (either physically interacting with each other or associated in other ways). In gene (protein) association networks these groups show up as sets of densely connected nodes. In the yeast, Saccharomyces cerevisiae, known physically interacting groups of proteins (called protein complexes) strongly overlap: the total number of proteins contained by these complexes by far underestimates the sum of their sizes (2750 vs. 8932). Thus, most functional groups of proteins, both physically interacting and other, are likely to share many of their members with other groups. However, current algorithms searching for dense groups of nodes in networks usually exclude overlaps. With the aim to discover both novel functions of individual proteins and novel protein functional groups we combine in protein association networks (i) a search for overlapping dense subgraphs based on the Clique Percolation Method (CPM) (Palla, G., et.al. Nature 435, 814-818 (2005), http://angel.elte.hu/clustering), which explicitly allows for overlaps among the groups, and (ii) a verification and characterization of the identified groups of nodes (proteins) with the help of standard annotation databases listing known functions.

A simple method for finding the scattering coefficients of quantum graphs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cottrell, Seth S.

2015-09-15

Quantum walks are roughly analogous to classical random walks, and similar to classical walks they have been used to find new (quantum) algorithms. When studying the behavior of large graphs or combinations of graphs, it is useful to find the response of a subgraph to signals of different frequencies. In doing so, we can replace an entire subgraph with a single vertex with variable scattering coefficients. In this paper, a simple technique for quickly finding the scattering coefficients of any discrete-time quantum graph will be presented. These scattering coefficients can be expressed entirely in terms of the characteristic polynomial ofmore » the graph’s time step operator. This is a marked improvement over previous techniques which have traditionally required finding eigenstates for a given eigenvalue, which is far more computationally costly. With the scattering coefficients we can easily derive the “impulse response” which is the key to predicting the response of a graph to any signal. This gives us a powerful set of tools for rapidly understanding the behavior of graphs or for reducing a large graph into its constituent subgraphs regardless of how they are connected.« less

What Causal Forces Shape Internet Connectivity at the AS-level?

DTIC Science & Technology

2003-01-01

business “peering relationship .” By focusing on the AS subgraph ASPC whose links repre- sent provider- customer relationships , we present an empirical... customer relationships may be determined in the actual Internet, we develop a new optimization-driven model for Internet growth at the ASPC level...among ASs. Two ASs are connected in an AS graph by a link only if they have a “peering relationship ” between them, e.g., provider- customer or peer-to

Auditing SNOMED CT hierarchical relations based on lexical features of concepts in non-lattice subgraphs.

PubMed

Cui, Licong; Bodenreider, Olivier; Shi, Jay; Zhang, Guo-Qiang

2018-02-01

We introduce a structural-lexical approach for auditing SNOMED CT using a combination of non-lattice subgraphs of the underlying hierarchical relations and enriched lexical attributes of fully specified concept names. Our goal is to develop a scalable and effective approach that automatically identifies missing hierarchical IS-A relations. Our approach involves 3 stages. In stage 1, all non-lattice subgraphs of SNOMED CT's IS-A hierarchical relations are extracted. In stage 2, lexical attributes of fully-specified concept names in such non-lattice subgraphs are extracted. For each concept in a non-lattice subgraph, we enrich its set of attributes with attributes from its ancestor concepts within the non-lattice subgraph. In stage 3, subset inclusion relations between the lexical attribute sets of each pair of concepts in each non-lattice subgraph are compared to existing IS-A relations in SNOMED CT. For concept pairs within each non-lattice subgraph, if a subset relation is identified but an IS-A relation is not present in SNOMED CT IS-A transitive closure, then a missing IS-A relation is reported. The September 2017 release of SNOMED CT (US edition) was used in this investigation. A total of 14,380 non-lattice subgraphs were extracted, from which we suggested a total of 41,357 missing IS-A relations. For evaluation purposes, 200 non-lattice subgraphs were randomly selected from 996 smaller subgraphs (of size 4, 5, or 6) within the "Clinical Finding" and "Procedure" sub-hierarchies. Two domain experts confirmed 185 (among 223) suggested missing IS-A relations, a precision of 82.96%. Our results demonstrate that analyzing the lexical features of concepts in non-lattice subgraphs is an effective approach for auditing SNOMED CT. Copyright © 2017 Elsevier Inc. All rights reserved.

MISAGA: An Algorithm for Mining Interesting Subgraphs in Attributed Graphs.

PubMed

He, Tiantian; Chan, Keith C C

2018-05-01

An attributed graph contains vertices that are associated with a set of attribute values. Mining clusters or communities, which are interesting subgraphs in the attributed graph is one of the most important tasks of graph analytics. Many problems can be defined as the mining of interesting subgraphs in attributed graphs. Algorithms that discover subgraphs based on predefined topologies cannot be used to tackle these problems. To discover interesting subgraphs in the attributed graph, we propose an algorithm called mining interesting subgraphs in attributed graph algorithm (MISAGA). MISAGA performs its tasks by first using a probabilistic measure to determine whether the strength of association between a pair of attribute values is strong enough to be interesting. Given the interesting pairs of attribute values, then the degree of association is computed for each pair of vertices using an information theoretic measure. Based on the edge structure and degree of association between each pair of vertices, MISAGA identifies interesting subgraphs by formulating it as a constrained optimization problem and solves it by identifying the optimal affiliation of subgraphs for the vertices in the attributed graph. MISAGA has been tested with several large-sized real graphs and is found to be potentially very useful for various applications.

Event-based criteria in GT-STAF information indices: theory, exploratory diversity analysis and QSPR applications.

PubMed

Barigye, S J; Marrero-Ponce, Y; Martínez López, Y; Martínez Santiago, O; Torrens, F; García Domenech, R; Galvez, J

2013-01-01

Versatile event-based approaches for the definition of novel information theory-based indices (IFIs) are presented. An event in this context is the criterion followed in the "discovery" of molecular substructures, which in turn serve as basis for the construction of the generalized incidence and relations frequency matrices, Q and F, respectively. From the resultant F, Shannon's, mutual, conditional and joint entropy-based IFIs are computed. In previous reports, an event named connected subgraphs was presented. The present study is an extension of this notion, in which we introduce other events, namely: terminal paths, vertex path incidence, quantum subgraphs, walks of length k, Sach's subgraphs, MACCs, E-state and substructure fingerprints and, finally, Ghose and Crippen atom-types for hydrophobicity and refractivity. Moreover, we define magnitude-based IFIs, introducing the use of the magnitude criterion in the definition of mutual, conditional and joint entropy-based IFIs. We also discuss the use of information-theoretic parameters as a measure of the dissimilarity of codified structural information of molecules. Finally, a comparison of the statistics for QSPR models obtained with the proposed IFIs and DRAGON's molecular descriptors for two physicochemical properties log P and log K of 34 derivatives of 2-furylethylenes demonstrates similar to better predictive ability than the latter.

Node similarity within subgraphs of protein interaction networks

NASA Astrophysics Data System (ADS)

Penner, Orion; Sood, Vishal; Musso, Gabriel; Baskerville, Kim; Grassberger, Peter; Paczuski, Maya

2008-06-01

We propose a biologically motivated quantity, twinness, to evaluate local similarity between nodes in a network. The twinness of a pair of nodes is the number of connected, labeled subgraphs of size n in which the two nodes possess identical neighbours. The graph animal algorithm is used to estimate twinness for each pair of nodes (for subgraph sizes n=4 to n=12) in four different protein interaction networks (PINs). These include an Escherichia coli PIN and three Saccharomyces cerevisiae PINs - each obtained using state-of-the-art high-throughput methods. In almost all cases, the average twinness of node pairs is vastly higher than that expected from a null model obtained by switching links. For all n, we observe a difference in the ratio of type A twins (which are unlinked pairs) to type B twins (which are linked pairs) distinguishing the prokaryote E. coli from the eukaryote S. cerevisiae. Interaction similarity is expected due to gene duplication, and whole genome duplication paralogues in S. cerevisiae have been reported to co-cluster into the same complexes. Indeed, we find that these paralogous proteins are over-represented as twins compared to pairs chosen at random. These results indicate that twinness can detect ancestral relationships from currently available PIN data.

A Coding Method for Efficient Subgraph Querying on Vertex- and Edge-Labeled Graphs

PubMed Central

Zhu, Lei; Song, Qinbao; Guo, Yuchen; Du, Lei; Zhu, Xiaoyan; Wang, Guangtao

2014-01-01

Labeled graphs are widely used to model complex data in many domains, so subgraph querying has been attracting more and more attention from researchers around the world. Unfortunately, subgraph querying is very time consuming since it involves subgraph isomorphism testing that is known to be an NP-complete problem. In this paper, we propose a novel coding method for subgraph querying that is based on Laplacian spectrum and the number of walks. Our method follows the filtering-and-verification framework and works well on graph databases with frequent updates. We also propose novel two-step filtering conditions that can filter out most false positives and prove that the two-step filtering conditions satisfy the no-false-negative requirement (no dismissal in answers). Extensive experiments on both real and synthetic graphs show that, compared with six existing counterpart methods, our method can effectively improve the efficiency of subgraph querying. PMID:24853266

Sudden emergence of q-regular subgraphs in random graphs

NASA Astrophysics Data System (ADS)

Pretti, M.; Weigt, M.

2006-07-01

We investigate the computationally hard problem whether a random graph of finite average vertex degree has an extensively large q-regular subgraph, i.e., a subgraph with all vertices having degree equal to q. We reformulate this problem as a constraint-satisfaction problem, and solve it using the cavity method of statistical physics at zero temperature. For q = 3, we find that the first large q-regular subgraphs appear discontinuously at an average vertex degree c3 - reg simeq 3.3546 and contain immediately about 24% of all vertices in the graph. This transition is extremely close to (but different from) the well-known 3-core percolation point c3 - core simeq 3.3509. For q > 3, the q-regular subgraph percolation threshold is found to coincide with that of the q-core.

SING: Subgraph search In Non-homogeneous Graphs

PubMed Central

2010-01-01

Background Finding the subgraphs of a graph database that are isomorphic to a given query graph has practical applications in several fields, from cheminformatics to image understanding. Since subgraph isomorphism is a computationally hard problem, indexing techniques have been intensively exploited to speed up the process. Such systems filter out those graphs which cannot contain the query, and apply a subgraph isomorphism algorithm to each residual candidate graph. The applicability of such systems is limited to databases of small graphs, because their filtering power degrades on large graphs. Results In this paper, SING (Subgraph search In Non-homogeneous Graphs), a novel indexing system able to cope with large graphs, is presented. The method uses the notion of feature, which can be a small subgraph, subtree or path. Each graph in the database is annotated with the set of all its features. The key point is to make use of feature locality information. This idea is used to both improve the filtering performance and speed up the subgraph isomorphism task. Conclusions Extensive tests on chemical compounds, biological networks and synthetic graphs show that the proposed system outperforms the most popular systems in query time over databases of medium and large graphs. Other specific tests show that the proposed system is effective for single large graphs. PMID:20170516

RNA Graph Partitioning for the Discovery of RNA Modularity: A Novel Application of Graph Partition Algorithm to Biology

PubMed Central

Elmetwaly, Shereef; Schlick, Tamar

2014-01-01

Graph representations have been widely used to analyze and design various economic, social, military, political, and biological networks. In systems biology, networks of cells and organs are useful for understanding disease and medical treatments and, in structural biology, structures of molecules can be described, including RNA structures. In our RNA-As-Graphs (RAG) framework, we represent RNA structures as tree graphs by translating unpaired regions into vertices and helices into edges. Here we explore the modularity of RNA structures by applying graph partitioning known in graph theory to divide an RNA graph into subgraphs. To our knowledge, this is the first application of graph partitioning to biology, and the results suggest a systematic approach for modular design in general. The graph partitioning algorithms utilize mathematical properties of the Laplacian eigenvector (µ2) corresponding to the second eigenvalues (λ2) associated with the topology matrix defining the graph: λ2 describes the overall topology, and the sum of µ2′s components is zero. The three types of algorithms, termed median, sign, and gap cuts, divide a graph by determining nodes of cut by median, zero, and largest gap of µ2′s components, respectively. We apply these algorithms to 45 graphs corresponding to all solved RNA structures up through 11 vertices (∼220 nucleotides). While we observe that the median cut divides a graph into two similar-sized subgraphs, the sign and gap cuts partition a graph into two topologically-distinct subgraphs. We find that the gap cut produces the best biologically-relevant partitioning for RNA because it divides RNAs at less stable connections while maintaining junctions intact. The iterative gap cuts suggest basic modules and assembly protocols to design large RNA structures. Our graph substructuring thus suggests a systematic approach to explore the modularity of biological networks. In our applications to RNA structures, subgraphs also suggest design strategies for novel RNA motifs. PMID:25188578

Site- and bond-percolation thresholds in K_{n,n}-based lattices: Vulnerability of quantum annealers to random qubit and coupler failures on chimera topologies.

PubMed

Melchert, O; Katzgraber, Helmut G; Novotny, M A

2016-04-01

We estimate the critical thresholds of bond and site percolation on nonplanar, effectively two-dimensional graphs with chimeralike topology. The building blocks of these graphs are complete and symmetric bipartite subgraphs of size 2n, referred to as K_{n,n} graphs. For the numerical simulations we use an efficient union-find-based algorithm and employ a finite-size scaling analysis to obtain the critical properties for both bond and site percolation. We report the respective percolation thresholds for different sizes of the bipartite subgraph and verify that the associated universality class is that of standard two-dimensional percolation. For the canonical chimera graph used in the D-Wave Systems Inc. quantum annealer (n=4), we discuss device failure in terms of network vulnerability, i.e., we determine the critical fraction of qubits and couplers that can be absent due to random failures prior to losing large-scale connectivity throughout the device.

Dense Subgraphs with Restrictions and Applications to Gene Annotation Graphs

NASA Astrophysics Data System (ADS)

Saha, Barna; Hoch, Allison; Khuller, Samir; Raschid, Louiqa; Zhang, Xiao-Ning

In this paper, we focus on finding complex annotation patterns representing novel and interesting hypotheses from gene annotation data. We define a generalization of the densest subgraph problem by adding an additional distance restriction (defined by a separate metric) to the nodes of the subgraph. We show that while this generalization makes the problem NP-hard for arbitrary metrics, when the metric comes from the distance metric of a tree, or an interval graph, the problem can be solved optimally in polynomial time. We also show that the densest subgraph problem with a specified subset of vertices that have to be included in the solution can be solved optimally in polynomial time. In addition, we consider other extensions when not just one solution needs to be found, but we wish to list all subgraphs of almost maximum density as well. We apply this method to a dataset of genes and their annotations obtained from The Arabidopsis Information Resource (TAIR). A user evaluation confirms that the patterns found in the distance restricted densest subgraph for a dataset of photomorphogenesis genes are indeed validated in the literature; a control dataset validates that these are not random patterns. Interestingly, the complex annotation patterns potentially lead to new and as yet unknown hypotheses. We perform experiments to determine the properties of the dense subgraphs, as we vary parameters, including the number of genes and the distance.

Super (a*, d*)-ℋ-antimagic total covering of second order of shackle graphs

NASA Astrophysics Data System (ADS)

Hesti Agustin, Ika; Dafik; Nisviasari, Rosanita; Prihandini, R. M.

2017-12-01

Let H be a simple and connected graph. A shackle of graph H, denoted by G = shack(H, v, n), is a graph G constructed by non-trivial graphs H 1, H 2, …, H n such that, for every 1 ≤ s, t ≤ n, H s and Ht have no a common vertex with |s - t| ≥ 2 and for every 1 ≤ i ≤ n - 1, Hi and H i+1 share exactly one common vertex v, called connecting vertex, and those k - 1 connecting vertices are all distinct. The graph G is said to be an (a*, d*)-H-antimagic total graph of second order if there exist a bijective function f : V(G) ∪ E(G) → {1, 2, …, |V(G)| + |E(G)|} such that for all subgraphs isomorphic to H, the total H-weights W(H)=\\displaystyle {\\sum }v\\in V(H)f(v)+\\displaystyle {\\sum }e\\in E(H)f(e) form an arithmetic sequence of second order of \\{a* ,a* +d* ,a* +3d* ,a* +6d* ,\\ldots ,a* +(\\frac{{n}2-n}{2})d* \\}, where a* and d* are positive integers and n is the number of all subgraphs isomorphic to H. An (a*, d*)-H-antimagic total labeling of second order f is called super if the smallest labels appear in the vertices. In this paper, we study a super (a*, d*)-H antimagic total labeling of second order of G = shack(H, v, n) by using a partition technique of second order.

Quality Assurance of NCI Thesaurus by Mining Structural-Lexical Patterns

PubMed Central

Abeysinghe, Rashmie; Brooks, Michael A.; Talbert, Jeffery; Licong, Cui

2017-01-01

Quality assurance of biomedical terminologies such as the National Cancer Institute (NCI) Thesaurus is an essential part of the terminology management lifecycle. We investigate a structural-lexical approach based on non-lattice subgraphs to automatically identify missing hierarchical relations and missing concepts in the NCI Thesaurus. We mine six structural-lexical patterns exhibiting in non-lattice subgraphs: containment, union, intersection, union-intersection, inference-contradiction, and inference union. Each pattern indicates a potential specific type of error and suggests a potential type of remediation. We found 809 non-lattice subgraphs with these patterns in the NCI Thesaurus (version 16.12d). Domain experts evaluated a random sample of 50 small non-lattice subgraphs, of which 33 were confirmed to contain errors and make correct suggestions (33/50 = 66%). Of the 25 evaluated subgraphs revealing multiple patterns, 22 were verified correct (22/25 = 88%). This shows the effectiveness of our structurallexical-pattern-based approach in detecting errors and suggesting remediations in the NCI Thesaurus. PMID:29854100

Induced subgraph searching for geometric model fitting

NASA Astrophysics Data System (ADS)

Xiao, Fan; Xiao, Guobao; Yan, Yan; Wang, Xing; Wang, Hanzi

2017-11-01

In this paper, we propose a novel model fitting method based on graphs to fit and segment multiple-structure data. In the graph constructed on data, each model instance is represented as an induced subgraph. Following the idea of pursuing the maximum consensus, the multiple geometric model fitting problem is formulated as searching for a set of induced subgraphs including the maximum union set of vertices. After the generation and refinement of the induced subgraphs that represent the model hypotheses, the searching process is conducted on the "qualified" subgraphs. Multiple model instances can be simultaneously estimated by solving a converted problem. Then, we introduce the energy evaluation function to determine the number of model instances in data. The proposed method is able to effectively estimate the number and the parameters of model instances in data severely corrupted by outliers and noises. Experimental results on synthetic data and real images validate the favorable performance of the proposed method compared with several state-of-the-art fitting methods.

A graph lattice approach to maintaining and learning dense collections of subgraphs as image features.

PubMed

Saund, Eric

2013-10-01

Effective object and scene classification and indexing depend on extraction of informative image features. This paper shows how large families of complex image features in the form of subgraphs can be built out of simpler ones through construction of a graph lattice—a hierarchy of related subgraphs linked in a lattice. Robustness is achieved by matching many overlapping and redundant subgraphs, which allows the use of inexpensive exact graph matching, instead of relying on expensive error-tolerant graph matching to a minimal set of ideal model graphs. Efficiency in exact matching is gained by exploitation of the graph lattice data structure. Additionally, the graph lattice enables methods for adaptively growing a feature space of subgraphs tailored to observed data. We develop the approach in the domain of rectilinear line art, specifically for the practical problem of document forms recognition. We are especially interested in methods that require only one or very few labeled training examples per category. We demonstrate two approaches to using the subgraph features for this purpose. Using a bag-of-words feature vector we achieve essentially single-instance learning on a benchmark forms database, following an unsupervised clustering stage. Further performance gains are achieved on a more difficult dataset using a feature voting method and feature selection procedure.

Finding Hierarchical and Overlapping Dense Subgraphs using Nucleus Decompositions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Seshadhri, Comandur; Pinar, Ali; Sariyuce, Ahmet Erdem

Finding dense substructures in a graph is a fundamental graph mining operation, with applications in bioinformatics, social networks, and visualization to name a few. Yet most standard formulations of this problem (like clique, quasiclique, k-densest subgraph) are NP-hard. Furthermore, the goal is rarely to nd the \\true optimum", but to identify many (if not all) dense substructures, understand their distribution in the graph, and ideally determine a hierarchical structure among them. Current dense subgraph nding algorithms usually optimize some objective, and only nd a few such subgraphs without providing any hierarchy. It is also not clear how to account formore » overlaps in dense substructures. We de ne the nucleus decomposition of a graph, which represents the graph as a forest of nuclei. Each nucleus is a subgraph where smaller cliques are present in many larger cliques. The forest of nuclei is a hierarchy by containment, where the edge density increases as we proceed towards leaf nuclei. Sibling nuclei can have limited intersections, which allows for discovery of overlapping dense subgraphs. With the right parameters, the nuclear decomposition generalizes the classic notions of k-cores and k-trusses. We give provable e cient algorithms for nuclear decompositions, and empirically evaluate their behavior in a variety of real graphs. The tree of nuclei consistently gives a global, hierarchical snapshot of dense substructures, and outputs dense subgraphs of higher quality than other state-of-theart solutions. Our algorithm can process graphs with tens of millions of edges in less than an hour.« less

Unsupervised object segmentation with a hybrid graph model (HGM).

PubMed

Liu, Guangcan; Lin, Zhouchen; Yu, Yong; Tang, Xiaoou

2010-05-01

In this work, we address the problem of performing class-specific unsupervised object segmentation, i.e., automatic segmentation without annotated training images. Object segmentation can be regarded as a special data clustering problem where both class-specific information and local texture/color similarities have to be considered. To this end, we propose a hybrid graph model (HGM) that can make effective use of both symmetric and asymmetric relationship among samples. The vertices of a hybrid graph represent the samples and are connected by directed edges and/or undirected ones, which represent the asymmetric and/or symmetric relationship between them, respectively. When applied to object segmentation, vertices are superpixels, the asymmetric relationship is the conditional dependence of occurrence, and the symmetric relationship is the color/texture similarity. By combining the Markov chain formed by the directed subgraph and the minimal cut of the undirected subgraph, the object boundaries can be determined for each image. Using the HGM, we can conveniently achieve simultaneous segmentation and recognition by integrating both top-down and bottom-up information into a unified process. Experiments on 42 object classes (9,415 images in total) show promising results.

The Construction of {P}_{2}\\vartriangleright H-antimagic graph using smaller edge-antimagic vertex labeling

NASA Astrophysics Data System (ADS)

Prihandini, Rafiantika M.; Agustin, I. H.; Dafik

2018-04-01

In this paper we use simple and non trivial graph. If there exist a bijective function g:V(G) \\cup E(G)\\to \\{1,2,\\ldots,|V(G)|+|E(G)|\\}, such that for all subgraphs {P}2\\vartriangleright H of G isomorphic to H, then graph G is called an (a, b)-{P}2\\vartriangleright H-antimagic total graph. Furthermore, we can consider the total {P}2\\vartriangleright H-weights W({P}2\\vartriangleright H)={\\sum }v\\in V({P2\\vartriangleright H)}f(v)+{\\sum }e\\in E({P2\\vartriangleright H)}f(e) which should form an arithmetic sequence {a, a + d, a + 2d, …, a + (n ‑ 1)d}, where a and d are positive integers and n is the number of all subgraphs isomorphic to H. Our paper describes the existence of super (a, b)-{P}2\\vartriangleright H antimagic total labeling for graph operation of comb product namely of G=L\\vartriangleright H, where L is a (b, d*)-edge antimagic vertex labeling graph and H is a connected graph.

Approximation algorithms for the min-power symmetric connectivity problem

NASA Astrophysics Data System (ADS)

Plotnikov, Roman; Erzin, Adil; Mladenovic, Nenad

2016-10-01

We consider the NP-hard problem of synthesis of optimal spanning communication subgraph in a given arbitrary simple edge-weighted graph. This problem occurs in the wireless networks while minimizing the total transmission power consumptions. We propose several new heuristics based on the variable neighborhood search metaheuristic for the approximation solution of the problem. We have performed a numerical experiment where all proposed algorithms have been executed on the randomly generated test samples. For these instances, on average, our algorithms outperform the previously known heuristics.

Discovering interesting molecular substructures for molecular classification.

PubMed

Lam, Winnie W M; Chan, Keith C C

2010-06-01

Given a set of molecular structure data preclassified into a number of classes, the molecular classification problem is concerned with the discovering of interesting structural patterns in the data so that "unseen" molecules not originally in the dataset can be accurately classified. To tackle the problem, interesting molecular substructures have to be discovered and this is done typically by first representing molecular structures in molecular graphs, and then, using graph-mining algorithms to discover frequently occurring subgraphs in them. These subgraphs are then used to characterize different classes for molecular classification. While such an approach can be very effective, it should be noted that a substructure that occurs frequently in one class may also does occur in another. The discovering of frequent subgraphs for molecular classification may, therefore, not always be the most effective. In this paper, we propose a novel technique called mining interesting substructures in molecular data for classification (MISMOC) that can discover interesting frequent subgraphs not just for the characterization of a molecular class but also for the distinguishing of it from the others. Using a test statistic, MISMOC screens each frequent subgraph to determine if they are interesting. For those that are interesting, their degrees of interestingness are determined using an information-theoretic measure. When classifying an unseen molecule, its structure is then matched against the interesting subgraphs in each class and a total interestingness measure for the unseen molecule to be classified into a particular class is determined, which is based on the interestingness of each matched subgraphs. The performance of MISMOC is evaluated using both artificial and real datasets, and the results show that it can be an effective approach for molecular classification.

An novel frequent probability pattern mining algorithm based on circuit simulation method in uncertain biological networks.

PubMed

He, Jieyue; Wang, Chunyan; Qiu, Kunpu; Zhong, Wei

2014-01-01

Motif mining has always been a hot research topic in bioinformatics. Most of current research on biological networks focuses on exact motif mining. However, due to the inevitable experimental error and noisy data, biological network data represented as the probability model could better reflect the authenticity and biological significance, therefore, it is more biological meaningful to discover probability motif in uncertain biological networks. One of the key steps in probability motif mining is frequent pattern discovery which is usually based on the possible world model having a relatively high computational complexity. In this paper, we present a novel method for detecting frequent probability patterns based on circuit simulation in the uncertain biological networks. First, the partition based efficient search is applied to the non-tree like subgraph mining where the probability of occurrence in random networks is small. Then, an algorithm of probability isomorphic based on circuit simulation is proposed. The probability isomorphic combines the analysis of circuit topology structure with related physical properties of voltage in order to evaluate the probability isomorphism between probability subgraphs. The circuit simulation based probability isomorphic can avoid using traditional possible world model. Finally, based on the algorithm of probability subgraph isomorphism, two-step hierarchical clustering method is used to cluster subgraphs, and discover frequent probability patterns from the clusters. The experiment results on data sets of the Protein-Protein Interaction (PPI) networks and the transcriptional regulatory networks of E. coli and S. cerevisiae show that the proposed method can efficiently discover the frequent probability subgraphs. The discovered subgraphs in our study contain all probability motifs reported in the experiments published in other related papers. The algorithm of probability graph isomorphism evaluation based on circuit simulation method excludes most of subgraphs which are not probability isomorphism and reduces the search space of the probability isomorphism subgraphs using the mismatch values in the node voltage set. It is an innovative way to find the frequent probability patterns, which can be efficiently applied to probability motif discovery problems in the further studies.

An novel frequent probability pattern mining algorithm based on circuit simulation method in uncertain biological networks

PubMed Central

2014-01-01

Background Motif mining has always been a hot research topic in bioinformatics. Most of current research on biological networks focuses on exact motif mining. However, due to the inevitable experimental error and noisy data, biological network data represented as the probability model could better reflect the authenticity and biological significance, therefore, it is more biological meaningful to discover probability motif in uncertain biological networks. One of the key steps in probability motif mining is frequent pattern discovery which is usually based on the possible world model having a relatively high computational complexity. Methods In this paper, we present a novel method for detecting frequent probability patterns based on circuit simulation in the uncertain biological networks. First, the partition based efficient search is applied to the non-tree like subgraph mining where the probability of occurrence in random networks is small. Then, an algorithm of probability isomorphic based on circuit simulation is proposed. The probability isomorphic combines the analysis of circuit topology structure with related physical properties of voltage in order to evaluate the probability isomorphism between probability subgraphs. The circuit simulation based probability isomorphic can avoid using traditional possible world model. Finally, based on the algorithm of probability subgraph isomorphism, two-step hierarchical clustering method is used to cluster subgraphs, and discover frequent probability patterns from the clusters. Results The experiment results on data sets of the Protein-Protein Interaction (PPI) networks and the transcriptional regulatory networks of E. coli and S. cerevisiae show that the proposed method can efficiently discover the frequent probability subgraphs. The discovered subgraphs in our study contain all probability motifs reported in the experiments published in other related papers. Conclusions The algorithm of probability graph isomorphism evaluation based on circuit simulation method excludes most of subgraphs which are not probability isomorphism and reduces the search space of the probability isomorphism subgraphs using the mismatch values in the node voltage set. It is an innovative way to find the frequent probability patterns, which can be efficiently applied to probability motif discovery problems in the further studies. PMID:25350277

Separation of ion types in tandem mass spectrometry data interpretation -- a graph-theoretic approach.

PubMed

Yan, Bo; Pan, Chongle; Olman, Victor N; Hettich, Robert L; Xu, Ying

2004-01-01

Mass spectrometry is one of the most popular analytical techniques for identification of individual proteins in a protein mixture, one of the basic problems in proteomics. It identifies a protein through identifying its unique mass spectral pattern. While the problem is theoretically solvable, it remains a challenging problem computationally. One of the key challenges comes from the difficulty in distinguishing the N- and C-terminus ions, mostly b- and y-ions respectively. In this paper, we present a graph algorithm for solving the problem of separating bfrom y-ions in a set of mass spectra. We represent each spectral peak as a node and consider two types of edges: a type-1 edge connects two peaks possibly of the same ion types and a type-2 edge connects two peaks possibly of different ion types, predicted based on local information. The ion-separation problem is then formulated and solved as a graph partition problem, which is to partition the graph into three subgraphs, namely b-, y-ions and others respectively, so to maximize the total weight of type-1 edges while minimizing the total weight of type-2 edges within each subgraph. We have developed a dynamic programming algorithm for rigorously solving this graph partition problem and implemented it as a computer program PRIME. We have tested PRIME on 18 data sets of high accurate FT-ICR tandem mass spectra and found that it achieved ~90% accuracy for separation of b- and y- ions.

Growth and structure of the World Wide Web: Towards realistic modeling

NASA Astrophysics Data System (ADS)

Tadić, Bosiljka

2002-08-01

We simulate evolution of the World Wide Web from the dynamic rules incorporating growth, bias attachment, and rewiring. We show that the emergent double-hierarchical structure with distinct distributions of out- and in-links is comparable with the observed empirical data when the control parameter (average graph flexibility β) is kept in the range β=3-4. We then explore the Web graph by simulating (a) Web crawling to determine size and depth of connected components, and (b) a random walker that discovers the structure of connected subgraphs with dominant attractor and promoter nodes. A random walker that adapts its move strategy to mimic local node linking preferences is shown to have a short access time to "important" nodes on the Web graph.

Limit of a nonpreferential attachment multitype network model

NASA Astrophysics Data System (ADS)

Shang, Yilun

2017-02-01

Here, we deal with a model of multitype network with nonpreferential attachment growth. The connection between two nodes depends asymmetrically on their types, reflecting the implication of time order in temporal networks. Based upon graph limit theory, we analytically determined the limit of the network model characterized by a kernel, in the sense that the number of copies of any fixed subgraph converges when network size tends to infinity. The results are confirmed by extensive simulations. Our work thus provides a theoretical framework for quantitatively understanding grown temporal complex networks as a whole.

High performance genetic algorithm for VLSI circuit partitioning

NASA Astrophysics Data System (ADS)

Dinu, Simona

2016-12-01

Partitioning is one of the biggest challenges in computer-aided design for VLSI circuits (very large-scale integrated circuits). This work address the min-cut balanced circuit partitioning problem- dividing the graph that models the circuit into almost equal sized k sub-graphs while minimizing the number of edges cut i.e. minimizing the number of edges connecting the sub-graphs. The problem may be formulated as a combinatorial optimization problem. Experimental studies in the literature have shown the problem to be NP-hard and thus it is important to design an efficient heuristic algorithm to solve it. The approach proposed in this study is a parallel implementation of a genetic algorithm, namely an island model. The information exchange between the evolving subpopulations is modeled using a fuzzy controller, which determines an optimal balance between exploration and exploitation of the solution space. The results of simulations show that the proposed algorithm outperforms the standard sequential genetic algorithm both in terms of solution quality and convergence speed. As a direction for future study, this research can be further extended to incorporate local search operators which should include problem-specific knowledge. In addition, the adaptive configuration of mutation and crossover rates is another guidance for future research.

An Improved Heuristic Method for Subgraph Isomorphism Problem

NASA Astrophysics Data System (ADS)

Xiang, Yingzhuo; Han, Jiesi; Xu, Haijiang; Guo, Xin

2017-09-01

This paper focus on the subgraph isomorphism (SI) problem. We present an improved genetic algorithm, a heuristic method to search the optimal solution. The contribution of this paper is that we design a dedicated crossover algorithm and a new fitness function to measure the evolution process. Experiments show our improved genetic algorithm performs better than other heuristic methods. For a large graph, such as a subgraph of 40 nodes, our algorithm outperforms the traditional tree search algorithms. We find that the performance of our improved genetic algorithm does not decrease as the number of nodes in prototype graphs.

Aligning Metabolic Pathways Exploiting Binary Relation of Reactions.

PubMed

Huang, Yiran; Zhong, Cheng; Lin, Hai Xiang; Huang, Jing

2016-01-01

Metabolic pathway alignment has been widely used to find one-to-one and/or one-to-many reaction mappings to identify the alternative pathways that have similar functions through different sets of reactions, which has important applications in reconstructing phylogeny and understanding metabolic functions. The existing alignment methods exhaustively search reaction sets, which may become infeasible for large pathways. To address this problem, we present an effective alignment method for accurately extracting reaction mappings between two metabolic pathways. We show that connected relation between reactions can be formalized as binary relation of reactions in metabolic pathways, and the multiplications of zero-one matrices for binary relations of reactions can be accomplished in finite steps. By utilizing the multiplications of zero-one matrices for binary relation of reactions, we efficiently obtain reaction sets in a small number of steps without exhaustive search, and accurately uncover biologically relevant reaction mappings. Furthermore, we introduce a measure of topological similarity of nodes (reactions) by comparing the structural similarity of the k-neighborhood subgraphs of the nodes in aligning metabolic pathways. We employ this similarity metric to improve the accuracy of the alignments. The experimental results on the KEGG database show that when compared with other state-of-the-art methods, in most cases, our method obtains better performance in the node correctness and edge correctness, and the number of the edges of the largest common connected subgraph for one-to-one reaction mappings, and the number of correct one-to-many reaction mappings. Our method is scalable in finding more reaction mappings with better biological relevance in large metabolic pathways.

Scale-free models for the structure of business firm networks.

PubMed

Kitsak, Maksim; Riccaboni, Massimo; Havlin, Shlomo; Pammolli, Fabio; Stanley, H Eugene

2010-03-01

We study firm collaborations in the life sciences and the information and communication technology sectors. We propose an approach to characterize industrial leadership using k -shell decomposition, with top-ranking firms in terms of market value in higher k -shell layers. We find that the life sciences industry network consists of three distinct components: a "nucleus," which is a small well-connected subgraph, "tendrils," which are small subgraphs consisting of small degree nodes connected exclusively to the nucleus, and a "bulk body," which consists of the majority of nodes. Industrial leaders, i.e., the largest companies in terms of market value, are in the highest k -shells of both networks. The nucleus of the life sciences sector is very stable: once a firm enters the nucleus, it is likely to stay there for a long time. At the same time we do not observe the above three components in the information and communication technology sector. We also conduct a systematic study of these three components in random scale-free networks. Our results suggest that the sizes of the nucleus and the tendrils in scale-free networks decrease as the exponent of the power-law degree distribution lambda increases, and disappear for lambda>or=3 . We compare the k -shell structure of random scale-free model networks with two real-world business firm networks in the life sciences and in the information and communication technology sectors. We argue that the observed behavior of the k -shell structure in the two industries is consistent with the coexistence of both preferential and random agreements in the evolution of industrial networks.

Image Analysis and Modeling

DTIC Science & Technology

1975-05-01

place "subgraphs" with more complicated subgraphs. There have beer many re- sults reported which extend string-grammar theorems to web grammar...W. Bacus and E. E. Gose , "Leukocyte Pattern Recognition," IEEE SMC-2. No. 2, pp. 513-536, September 1972. [4] J. K. Hawkins

Faster Mass Spectrometry-based Protein Inference: Junction Trees are More Efficient than Sampling and Marginalization by Enumeration

PubMed Central

Serang, Oliver; Noble, William Stafford

2012-01-01

The problem of identifying the proteins in a complex mixture using tandem mass spectrometry can be framed as an inference problem on a graph that connects peptides to proteins. Several existing protein identification methods make use of statistical inference methods for graphical models, including expectation maximization, Markov chain Monte Carlo, and full marginalization coupled with approximation heuristics. We show that, for this problem, the majority of the cost of inference usually comes from a few highly connected subgraphs. Furthermore, we evaluate three different statistical inference methods using a common graphical model, and we demonstrate that junction tree inference substantially improves rates of convergence compared to existing methods. The python code used for this paper is available at http://noble.gs.washington.edu/proj/fido. PMID:22331862

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.

Key-Node-Separated Graph Clustering and Layouts for Human Relationship Graph Visualization.

PubMed

Itoh, Takayuki; Klein, Karsten

2015-01-01

Many graph-drawing methods apply node-clustering techniques based on the density of edges to find tightly connected subgraphs and then hierarchically visualize the clustered graphs. However, users may want to focus on important nodes and their connections to groups of other nodes for some applications. For this purpose, it is effective to separately visualize the key nodes detected based on adjacency and attributes of the nodes. This article presents a graph visualization technique for attribute-embedded graphs that applies a graph-clustering algorithm that accounts for the combination of connections and attributes. The graph clustering step divides the nodes according to the commonality of connected nodes and similarity of feature value vectors. It then calculates the distances between arbitrary pairs of clusters according to the number of connecting edges and the similarity of feature value vectors and finally places the clusters based on the distances. Consequently, the technique separates important nodes that have connections to multiple large clusters and improves the visibility of such nodes' connections. To test this technique, this article presents examples with human relationship graph datasets, including a coauthorship and Twitter communication network dataset.

A tensorial approach to access cognitive workload related to mental arithmetic from EEG functional connectivity estimates.

PubMed

Dimitriadis, S I; Sun, Yu; Kwok, K; Laskaris, N A; Bezerianos, A

2013-01-01

The association of functional connectivity patterns with particular cognitive tasks has long been a topic of interest in neuroscience, e.g., studies of functional connectivity have demonstrated its potential use for decoding various brain states. However, the high-dimensionality of the pairwise functional connectivity limits its usefulness in some real-time applications. In the present study, the methodology of tensor subspace analysis (TSA) is used to reduce the initial high-dimensionality of the pairwise coupling in the original functional connectivity network to a space of condensed descriptive power, which would significantly decrease the computational cost and facilitate the differentiation of brain states. We assess the feasibility of the proposed method on EEG recordings when the subject was performing mental arithmetic task which differ only in the difficulty level (easy: 1-digit addition v.s. 3-digit additions). Two different cortical connective networks were detected, and by comparing the functional connectivity networks in different work states, it was found that the task-difficulty is best reflected in the connectivity structure of sub-graphs extending over parietooccipital sites. Incorporating this data-driven information within original TSA methodology, we succeeded in predicting the difficulty level from connectivity patterns in an efficient way that can be implemented so as to work in real-time.

Scale-free models for the structure of business firm networks

NASA Astrophysics Data System (ADS)

Kitsak, Maksim; Riccaboni, Massimo; Havlin, Shlomo; Pammolli, Fabio; Stanley, H. Eugene

2010-03-01

We study firm collaborations in the life sciences and the information and communication technology sectors. We propose an approach to characterize industrial leadership using k -shell decomposition, with top-ranking firms in terms of market value in higher k -shell layers. We find that the life sciences industry network consists of three distinct components: a “nucleus,” which is a small well-connected subgraph, “tendrils,” which are small subgraphs consisting of small degree nodes connected exclusively to the nucleus, and a “bulk body,” which consists of the majority of nodes. Industrial leaders, i.e., the largest companies in terms of market value, are in the highest k -shells of both networks. The nucleus of the life sciences sector is very stable: once a firm enters the nucleus, it is likely to stay there for a long time. At the same time we do not observe the above three components in the information and communication technology sector. We also conduct a systematic study of these three components in random scale-free networks. Our results suggest that the sizes of the nucleus and the tendrils in scale-free networks decrease as the exponent of the power-law degree distribution λ increases, and disappear for λ≥3 . We compare the k -shell structure of random scale-free model networks with two real-world business firm networks in the life sciences and in the information and communication technology sectors. We argue that the observed behavior of the k -shell structure in the two industries is consistent with the coexistence of both preferential and random agreements in the evolution of industrial networks.

Super (a, d)-Cycle-Antimagic Total Labeling on Triangular Ladder Graph and Generalized Jahangir Graph

NASA Astrophysics Data System (ADS)

Roswitha, Mania; Amanda, Anna; Sri Martini, Titin; Winarno, Bowo

2017-06-01

Let G(V (G), E(G)) be a finite simple graph with |V (G)| = G and |E(G)| = eG . Let H be a subgraph of G. The graph G is said to be (a, d)-H-antimagic covering if every edge in G belongs to at least one of the subgraphs G isomorphic to H and there is a bijective function ξ : V ∪ E → {1, 2, …,νG + eG } such that all subgraphs H‧ isomorphic to H, the H‧ -weights w(H‧)=∑v∈V(H‧)ξ(v)+∑e∈E(H‧)ξ(e) constitutes an arithmetic progression {a, a + d, a + 2d, …, a + (t - 1)d}, where a and d are positive integers and t is the number of subgraphs G isomorphic to H. Such a labeling is called super if the vertices contain the smallest possible labels. This research provides super (a, d)-C 3-antimagic total labelng on triangular ladder TLn for n ≥ 2 and super (a, d)-C s+2-antimagic total labeling on generalized Jahangir Jk,s for k ≥ 2 and s ≥ 2.

On size-constrained minimum s–t cut problems and size-constrained dense subgraph problems

DOE PAGES

Chen, Wenbin; Samatova, Nagiza F.; Stallmann, Matthias F.; ...

2015-10-30

In some application cases, the solutions of combinatorial optimization problems on graphs should satisfy an additional vertex size constraint. In this paper, we consider size-constrained minimum s–t cut problems and size-constrained dense subgraph problems. We introduce the minimum s–t cut with at-least-k vertices problem, the minimum s–t cut with at-most-k vertices problem, and the minimum s–t cut with exactly k vertices problem. We prove that they are NP-complete. Thus, they are not polynomially solvable unless P = NP. On the other hand, we also study the densest at-least-k-subgraph problem (DalkS) and the densest at-most-k-subgraph problem (DamkS) introduced by Andersen andmore » Chellapilla [1]. We present a polynomial time algorithm for DalkS when k is bounded by some constant c. We also present two approximation algorithms for DamkS. In conclusion, the first approximation algorithm for DamkS has an approximation ratio of n-1/k-1, where n is the number of vertices in the input graph. The second approximation algorithm for DamkS has an approximation ratio of O (n δ), for some δ < 1/3.« less

Symmetry compression method for discovering network motifs.

PubMed

Wang, Jianxin; Huang, Yuannan; Wu, Fang-Xiang; Pan, Yi

2012-01-01

Discovering network motifs could provide a significant insight into systems biology. Interestingly, many biological networks have been found to have a high degree of symmetry (automorphism), which is inherent in biological network topologies. The symmetry due to the large number of basic symmetric subgraphs (BSSs) causes a certain redundant calculation in discovering network motifs. Therefore, we compress all basic symmetric subgraphs before extracting compressed subgraphs and propose an efficient decompression algorithm to decompress all compressed subgraphs without loss of any information. In contrast to previous approaches, the novel Symmetry Compression method for Motif Detection, named as SCMD, eliminates most redundant calculations caused by widespread symmetry of biological networks. We use SCMD to improve three notable exact algorithms and two efficient sampling algorithms. Results of all exact algorithms with SCMD are the same as those of the original algorithms, since SCMD is a lossless method. The sampling results show that the use of SCMD almost does not affect the quality of sampling results. For highly symmetric networks, we find that SCMD used in both exact and sampling algorithms can help get a remarkable speedup. Furthermore, SCMD enables us to find larger motifs in biological networks with notable symmetry than previously possible.

Super (a,d)-H-antimagic covering of möbius ladder graph

NASA Astrophysics Data System (ADS)

Indriyani, Novia; Sri Martini, Titin

2018-04-01

Let G = (V(G), E(G)) be a simple graph. Let H-covering of G is a subgraph H 1, H 2, …, Hj with every edge in G is contained in at least one graph Hi for 1 ≤ i ≤ j. If every Hi is isomorphic, then G admits an H-covering. Furthermore, an (a,d)-H-antimagic covering if there bijective function ξ :V(G)\\cup E(G)\\to \\{1,2,3,\\ldots,|V(G)|+|E(G)|\\}. The H‑-weights for all subgraphs H‑ isomorphic to H ω ({H}^{\\prime })={\\sum }v\\in V({H^{\\prime })}ξ (v)+{\\sum }e\\in E({H^{\\prime })}ξ (e). The weights of subgraphs constitutes an arithmatic progression {a, a + d, …, a + (t ‑ 1)d} where a and d are positive integers and t is the number of subgraphs G isomorphic to H. If ξ (V(G))=\\{1,2,\\ldots,|V(G)|\\} then ξ is called super (a, d)-H-antimagic covering. The research provides super (a, d)-H-antimagic covering with d = {1, 3} of Möbius ladder graph Mn for n > 5 and n is odd.

Continuous-Time Classical and Quantum Random Walk on Direct Product of Cayley Graphs

NASA Astrophysics Data System (ADS)

Salimi, S.; Jafarizadeh, M. A.

2009-06-01

In this paper we define direct product of graphs and give a recipe for obtaining probability of observing particle on vertices in the continuous-time classical and quantum random walk. In the recipe, the probability of observing particle on direct product of graph is obtained by multiplication of probability on the corresponding to sub-graphs, where this method is useful to determining probability of walk on complicated graphs. Using this method, we calculate the probability of continuous-time classical and quantum random walks on many of finite direct product Cayley graphs (complete cycle, complete Kn, charter and n-cube). Also, we inquire that the classical state the stationary uniform distribution is reached as t → ∞ but for quantum state is not always satisfied.

Epidemics in networks: a master equation approach

NASA Astrophysics Data System (ADS)

Cotacallapa, M.; Hase, M. O.

2016-02-01

A problem closely related to epidemiology, where a subgraph of ‘infected’ links is defined inside a larger network, is investigated. This subgraph is generated from the underlying network by a random variable, which decides whether a link is able to propagate a disease/information. The relaxation timescale of this random variable is examined in both annealed and quenched limits, and the effectiveness of propagation of disease/information is analyzed. The dynamics of the model is governed by a master equation and two types of underlying network are considered: one is scale-free and the other has exponential degree distribution. We have shown that the relaxation timescale of the contagion variable has a major influence on the topology of the subgraph of infected links, which determines the efficiency of spreading of disease/information over the network.

Organization of feed-forward loop motifs reveals architectural principles in natural and engineered networks.

PubMed

Gorochowski, Thomas E; Grierson, Claire S; di Bernardo, Mario

2018-03-01

Network motifs are significantly overrepresented subgraphs that have been proposed as building blocks for natural and engineered networks. Detailed functional analysis has been performed for many types of motif in isolation, but less is known about how motifs work together to perform complex tasks. To address this issue, we measure the aggregation of network motifs via methods that extract precisely how these structures are connected. Applying this approach to a broad spectrum of networked systems and focusing on the widespread feed-forward loop motif, we uncover striking differences in motif organization. The types of connection are often highly constrained, differ between domains, and clearly capture architectural principles. We show how this information can be used to effectively predict functionally important nodes in the metabolic network of Escherichia coli . Our findings have implications for understanding how networked systems are constructed from motif parts and elucidate constraints that guide their evolution.

Organization of feed-forward loop motifs reveals architectural principles in natural and engineered networks

PubMed Central

Grierson, Claire S.

2018-01-01

Network motifs are significantly overrepresented subgraphs that have been proposed as building blocks for natural and engineered networks. Detailed functional analysis has been performed for many types of motif in isolation, but less is known about how motifs work together to perform complex tasks. To address this issue, we measure the aggregation of network motifs via methods that extract precisely how these structures are connected. Applying this approach to a broad spectrum of networked systems and focusing on the widespread feed-forward loop motif, we uncover striking differences in motif organization. The types of connection are often highly constrained, differ between domains, and clearly capture architectural principles. We show how this information can be used to effectively predict functionally important nodes in the metabolic network of Escherichia coli. Our findings have implications for understanding how networked systems are constructed from motif parts and elucidate constraints that guide their evolution. PMID:29670941

Biological network motif detection and evaluation

PubMed Central

2011-01-01

Background Molecular level of biological data can be constructed into system level of data as biological networks. Network motifs are defined as over-represented small connected subgraphs in networks and they have been used for many biological applications. Since network motif discovery involves computationally challenging processes, previous algorithms have focused on computational efficiency. However, we believe that the biological quality of network motifs is also very important. Results We define biological network motifs as biologically significant subgraphs and traditional network motifs are differentiated as structural network motifs in this paper. We develop five algorithms, namely, EDGEGO-BNM, EDGEBETWEENNESS-BNM, NMF-BNM, NMFGO-BNM and VOLTAGE-BNM, for efficient detection of biological network motifs, and introduce several evaluation measures including motifs included in complex, motifs included in functional module and GO term clustering score in this paper. Experimental results show that EDGEGO-BNM and EDGEBETWEENNESS-BNM perform better than existing algorithms and all of our algorithms are applicable to find structural network motifs as well. Conclusion We provide new approaches to finding network motifs in biological networks. Our algorithms efficiently detect biological network motifs and further improve existing algorithms to find high quality structural network motifs, which would be impossible using existing algorithms. The performances of the algorithms are compared based on our new evaluation measures in biological contexts. We believe that our work gives some guidelines of network motifs research for the biological networks. PMID:22784624

Matching CCD images to a stellar catalog using locality-sensitive hashing

NASA Astrophysics Data System (ADS)

Liu, Bo; Yu, Jia-Zong; Peng, Qing-Yu

2018-02-01

The usage of a subset of observed stars in a CCD image to find their corresponding matched stars in a stellar catalog is an important issue in astronomical research. Subgraph isomorphic-based algorithms are the most widely used methods in star catalog matching. When more subgraph features are provided, the CCD images are recognized better. However, when the navigation feature database is large, the method requires more time to match the observing model. To solve this problem, this study investigates further and improves subgraph isomorphic matching algorithms. We present an algorithm based on a locality-sensitive hashing technique, which allocates quadrilateral models in the navigation feature database into different hash buckets and reduces the search range to the bucket in which the observed quadrilateral model is located. Experimental results indicate the effectivity of our method.

A nonlinear merging protocol for consensus in multi-agent systems on signed and weighted graphs

NASA Astrophysics Data System (ADS)

Feng, Shasha; Wang, Li; Li, Yijia; Sun, Shiwen; Xia, Chengyi

2018-01-01

In this paper, we investigate the multi-agent consensus for networks with undirected graphs which are not connected, especially for the signed graph in which some edge weights are positive and some edges have negative weights, and the negative-weight graph whose edge weights are negative. We propose a novel nonlinear merging consensus protocol to drive the states of all agents to converge to the same state zero which is not dependent upon the initial states of agents. If the undirected graph whose edge weights are positive is connected, then the states of all agents converge to the same state more quickly when compared to most other protocols. While the undirected graph whose edge weights might be positive or negative is unconnected, the states of all agents can still converge to the same state zero under the premise that the undirected graph can be divided into several connected subgraphs with more than one node. Furthermore, we also discuss the impact of parameter r presented in our protocol. Current results can further deepen the understanding of consensus processes for multi-agent systems.

Simultaneously Discovering and Localizing Common Objects in Wild Images.

PubMed

Wang, Zhenzhen; Yuan, Junsong

2018-09-01

Motivated by the recent success of supervised and weakly supervised common object discovery, in this paper, we move forward one step further to tackle common object discovery in a fully unsupervised way. Generally, object co-localization aims at simultaneously localizing objects of the same class across a group of images. Traditional object localization/detection usually trains specific object detectors which require bounding box annotations of object instances, or at least image-level labels to indicate the presence/absence of objects in an image. Given a collection of images without any annotations, our proposed fully unsupervised method is to simultaneously discover images that contain common objects and also localize common objects in corresponding images. Without requiring to know the total number of common objects, we formulate this unsupervised object discovery as a sub-graph mining problem from a weighted graph of object proposals, where nodes correspond to object proposals, and edges represent the similarities between neighbouring proposals. The positive images and common objects are jointly discovered by finding sub-graphs of strongly connected nodes, with each sub-graph capturing one object pattern. The optimization problem can be efficiently solved by our proposed maximal-flow-based algorithm. Instead of assuming that each image contains only one common object, our proposed solution can better address wild images where each image may contain multiple common objects or even no common object. Moreover, our proposed method can be easily tailored to the task of image retrieval in which the nodes correspond to the similarity between query and reference images. Extensive experiments on PASCAL VOC 2007 and Object Discovery data sets demonstrate that even without any supervision, our approach can discover/localize common objects of various classes in the presence of scale, view point, appearance variation, and partial occlusions. We also conduct broad experiments on image retrieval benchmarks, Holidays and Oxford5k data sets, to show that our proposed method, which considers both the similarity between query and reference images and also similarities among reference images, can help to improve the retrieval results significantly.

Characterization of known protein complexes using k-connectivity and other topological measures

PubMed Central

Gallagher, Suzanne R; Goldberg, Debra S

2015-01-01

Many protein complexes are densely packed, so proteins within complexes often interact with several other proteins in the complex. Steric constraints prevent most proteins from simultaneously binding more than a handful of other proteins, regardless of the number of proteins in the complex. Because of this, as complex size increases, several measures of the complex decrease within protein-protein interaction networks. However, k-connectivity, the number of vertices or edges that need to be removed in order to disconnect a graph, may be consistently high for protein complexes. The property of k-connectivity has been little used previously in the investigation of protein-protein interactions. To understand the discriminative power of k-connectivity and other topological measures for identifying unknown protein complexes, we characterized these properties in known Saccharomyces cerevisiae protein complexes in networks generated both from highly accurate X-ray crystallography experiments which give an accurate model of each complex, and also as the complexes appear in high-throughput yeast 2-hybrid studies in which new complexes may be discovered. We also computed these properties for appropriate random subgraphs.We found that clustering coefficient, mutual clustering coefficient, and k-connectivity are better indicators of known protein complexes than edge density, degree, or betweenness. This suggests new directions for future protein complex-finding algorithms. PMID:26913183

Partial Information Community Detection in a Multilayer Network

DTIC Science & Technology

2016-06-01

Network was taken from the CORE Lab at the Naval Postgraduate School [27]. Facebook dataset We will use a subgraph of the Facebook network to build a...larger synthetic multilayer network. We want to use this Facebook data as a way to introduce a real world example of a network into our synthetic network...This data is provided by the Standford Large Network Dataset Collection [28]. This is a large anonymous subgraph of Facebook . It contains over 4,000

The Development of Novel Chemical Fragment-Based Descriptors Using Frequent Common Subgraph Mining Approach and Their Application in QSAR Modeling.

PubMed

Khashan, Raed; Zheng, Weifan; Tropsha, Alexander

2014-03-01

We present a novel approach to generating fragment-based molecular descriptors. The molecules are represented by labeled undirected chemical graph. Fast Frequent Subgraph Mining (FFSM) is used to find chemical-fragments (subgraphs) that occur in at least a subset of all molecules in a dataset. The collection of frequent subgraphs (FSG) forms a dataset-specific descriptors whose values for each molecule are defined by the number of times each frequent fragment occurs in this molecule. We have employed the FSG descriptors to develop variable selection k Nearest Neighbor (kNN) QSAR models of several datasets with binary target property including Maximum Recommended Therapeutic Dose (MRTD), Salmonella Mutagenicity (Ames Genotoxicity), and P-Glycoprotein (PGP) data. Each dataset was divided into training, test, and validation sets to establish the statistical figures of merit reflecting the model validated predictive power. The classification accuracies of models for both training and test sets for all datasets exceeded 75 %, and the accuracy for the external validation sets exceeded 72 %. The model accuracies were comparable or better than those reported earlier in the literature for the same datasets. Furthermore, the use of fragment-based descriptors affords mechanistic interpretation of validated QSAR models in terms of essential chemical fragments responsible for the compounds' target property. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Searching social networks for subgraph patterns

NASA Astrophysics Data System (ADS)

Ogaard, Kirk; Kase, Sue; Roy, Heather; Nagi, Rakesh; Sambhoos, Kedar; Sudit, Moises

2013-06-01

Software tools for Social Network Analysis (SNA) are being developed which support various types of analysis of social networks extracted from social media websites (e.g., Twitter). Once extracted and stored in a database such social networks are amenable to analysis by SNA software. This data analysis often involves searching for occurrences of various subgraph patterns (i.e., graphical representations of entities and relationships). The authors have developed the Graph Matching Toolkit (GMT) which provides an intuitive Graphical User Interface (GUI) for a heuristic graph matching algorithm called the Truncated Search Tree (TruST) algorithm. GMT is a visual interface for graph matching algorithms processing large social networks. GMT enables an analyst to draw a subgraph pattern by using a mouse to select categories and labels for nodes and links from drop-down menus. GMT then executes the TruST algorithm to find the top five occurrences of the subgraph pattern within the social network stored in the database. GMT was tested using a simulated counter-insurgency dataset consisting of cellular phone communications within a populated area of operations in Iraq. The results indicated GMT (when executing the TruST graph matching algorithm) is a time-efficient approach to searching large social networks. GMT's visual interface to a graph matching algorithm enables intelligence analysts to quickly analyze and summarize the large amounts of data necessary to produce actionable intelligence.

Mining integrated semantic networks for drug repositioning opportunities

PubMed Central

Mullen, Joseph; Tipney, Hannah

2016-01-01

Current research and development approaches to drug discovery have become less fruitful and more costly. One alternative paradigm is that of drug repositioning. Many marketed examples of repositioned drugs have been identified through serendipitous or rational observations, highlighting the need for more systematic methodologies to tackle the problem. Systems level approaches have the potential to enable the development of novel methods to understand the action of therapeutic compounds, but requires an integrative approach to biological data. Integrated networks can facilitate systems level analyses by combining multiple sources of evidence to provide a rich description of drugs, their targets and their interactions. Classically, such networks can be mined manually where a skilled person is able to identify portions of the graph (semantic subgraphs) that are indicative of relationships between drugs and highlight possible repositioning opportunities. However, this approach is not scalable. Automated approaches are required to systematically mine integrated networks for these subgraphs and bring them to the attention of the user. We introduce a formal framework for the definition of integrated networks and their associated semantic subgraphs for drug interaction analysis and describe DReSMin, an algorithm for mining semantically-rich networks for occurrences of a given semantic subgraph. This algorithm allows instances of complex semantic subgraphs that contain data about putative drug repositioning opportunities to be identified in a computationally tractable fashion, scaling close to linearly with network data. We demonstrate the utility of our approach by mining an integrated drug interaction network built from 11 sources. This work identified and ranked 9,643,061 putative drug-target interactions, showing a strong correlation between highly scored associations and those supported by literature. We discuss the 20 top ranked associations in more detail, of which 14 are novel and 6 are supported by the literature. We also show that our approach better prioritizes known drug-target interactions, than other state-of-the art approaches for predicting such interactions. PMID:26844016

Machine-Learning Classifier for Patients with Major Depressive Disorder: Multifeature Approach Based on a High-Order Minimum Spanning Tree Functional Brain Network.

PubMed

Guo, Hao; Qin, Mengna; Chen, Junjie; Xu, Yong; Xiang, Jie

2017-01-01

High-order functional connectivity networks are rich in time information that can reflect dynamic changes in functional connectivity between brain regions. Accordingly, such networks are widely used to classify brain diseases. However, traditional methods for processing high-order functional connectivity networks generally include the clustering method, which reduces data dimensionality. As a result, such networks cannot be effectively interpreted in the context of neurology. Additionally, due to the large scale of high-order functional connectivity networks, it can be computationally very expensive to use complex network or graph theory to calculate certain topological properties. Here, we propose a novel method of generating a high-order minimum spanning tree functional connectivity network. This method increases the neurological significance of the high-order functional connectivity network, reduces network computing consumption, and produces a network scale that is conducive to subsequent network analysis. To ensure the quality of the topological information in the network structure, we used frequent subgraph mining technology to capture the discriminative subnetworks as features and combined this with quantifiable local network features. Then we applied a multikernel learning technique to the corresponding selected features to obtain the final classification results. We evaluated our proposed method using a data set containing 38 patients with major depressive disorder and 28 healthy controls. The experimental results showed a classification accuracy of up to 97.54%.

Machine-Learning Classifier for Patients with Major Depressive Disorder: Multifeature Approach Based on a High-Order Minimum Spanning Tree Functional Brain Network

PubMed Central

Qin, Mengna; Chen, Junjie; Xu, Yong; Xiang, Jie

2017-01-01

High-order functional connectivity networks are rich in time information that can reflect dynamic changes in functional connectivity between brain regions. Accordingly, such networks are widely used to classify brain diseases. However, traditional methods for processing high-order functional connectivity networks generally include the clustering method, which reduces data dimensionality. As a result, such networks cannot be effectively interpreted in the context of neurology. Additionally, due to the large scale of high-order functional connectivity networks, it can be computationally very expensive to use complex network or graph theory to calculate certain topological properties. Here, we propose a novel method of generating a high-order minimum spanning tree functional connectivity network. This method increases the neurological significance of the high-order functional connectivity network, reduces network computing consumption, and produces a network scale that is conducive to subsequent network analysis. To ensure the quality of the topological information in the network structure, we used frequent subgraph mining technology to capture the discriminative subnetworks as features and combined this with quantifiable local network features. Then we applied a multikernel learning technique to the corresponding selected features to obtain the final classification results. We evaluated our proposed method using a data set containing 38 patients with major depressive disorder and 28 healthy controls. The experimental results showed a classification accuracy of up to 97.54%. PMID:29387141

Unapparent Information Revelation: Text Mining for Counterterrorism

NASA Astrophysics Data System (ADS)

Srihari, Rohini K.

Unapparent information revelation (UIR) is a special case of text mining that focuses on detecting possible links between concepts across multiple text documents by generating an evidence trail explaining the connection. A traditional search involving, for example, two or more person names will attempt to find documents mentioning both these individuals. This research focuses on a different interpretation of such a query: what is the best evidence trail across documents that explains a connection between these individuals? For example, all may be good golfers. A generalization of this task involves query terms representing general concepts (e.g. indictment, foreign policy). Previous approaches to this problem have focused on graph mining involving hyperlinked documents, and link analysis exploiting named entities. A new robust framework is presented, based on (i) generating concept chain graphs, a hybrid content representation, (ii) performing graph matching to select candidate subgraphs, and (iii) subsequently using graphical models to validate hypotheses using ranked evidence trails. We adapt the DUC data set for cross-document summarization to evaluate evidence trails generated by this approach

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.

An annealed chaotic maximum neural network for bipartite subgraph problem.

PubMed

Wang, Jiahai; Tang, Zheng; Wang, Ronglong

2004-04-01

In this paper, based on maximum neural network, we propose a new parallel algorithm that can help the maximum neural network escape from local minima by including a transient chaotic neurodynamics for bipartite subgraph problem. The goal of the bipartite subgraph problem, which is an NP- complete problem, is to remove the minimum number of edges in a given graph such that the remaining graph is a bipartite graph. Lee et al. presented a parallel algorithm using the maximum neural model (winner-take-all neuron model) for this NP- complete problem. The maximum neural model always guarantees a valid solution and greatly reduces the search space without a burden on the parameter-tuning. However, the model has a tendency to converge to a local minimum easily because it is based on the steepest descent method. By adding a negative self-feedback to the maximum neural network, we proposed a new parallel algorithm that introduces richer and more flexible chaotic dynamics and can prevent the network from getting stuck at local minima. After the chaotic dynamics vanishes, the proposed algorithm is then fundamentally reined by the gradient descent dynamics and usually converges to a stable equilibrium point. The proposed algorithm has the advantages of both the maximum neural network and the chaotic neurodynamics. A large number of instances have been simulated to verify the proposed algorithm. The simulation results show that our algorithm finds the optimum or near-optimum solution for the bipartite subgraph problem superior to that of the best existing parallel algorithms.

NIBBS-search for fast and accurate prediction of phenotype-biased metabolic systems.

PubMed

Schmidt, Matthew C; Rocha, Andrea M; Padmanabhan, Kanchana; Shpanskaya, Yekaterina; Banfield, Jill; Scott, Kathleen; Mihelcic, James R; Samatova, Nagiza F

2012-01-01

Understanding of genotype-phenotype associations is important not only for furthering our knowledge on internal cellular processes, but also essential for providing the foundation necessary for genetic engineering of microorganisms for industrial use (e.g., production of bioenergy or biofuels). However, genotype-phenotype associations alone do not provide enough information to alter an organism's genome to either suppress or exhibit a phenotype. It is important to look at the phenotype-related genes in the context of the genome-scale network to understand how the genes interact with other genes in the organism. Identification of metabolic subsystems involved in the expression of the phenotype is one way of placing the phenotype-related genes in the context of the entire network. A metabolic system refers to a metabolic network subgraph; nodes are compounds and edges labels are the enzymes that catalyze the reaction. The metabolic subsystem could be part of a single metabolic pathway or span parts of multiple pathways. Arguably, comparative genome-scale metabolic network analysis is a promising strategy to identify these phenotype-related metabolic subsystems. Network Instance-Based Biased Subgraph Search (NIBBS) is a graph-theoretic method for genome-scale metabolic network comparative analysis that can identify metabolic systems that are statistically biased toward phenotype-expressing organismal networks. We set up experiments with target phenotypes like hydrogen production, TCA expression, and acid-tolerance. We show via extensive literature search that some of the resulting metabolic subsystems are indeed phenotype-related and formulate hypotheses for other systems in terms of their role in phenotype expression. NIBBS is also orders of magnitude faster than MULE, one of the most efficient maximal frequent subgraph mining algorithms that could be adjusted for this problem. Also, the set of phenotype-biased metabolic systems output by NIBBS comes very close to the set of phenotype-biased subgraphs output by an exact maximally-biased subgraph enumeration algorithm ( MBS-Enum ). The code (NIBBS and the module to visualize the identified subsystems) is available at http://freescience.org/cs/NIBBS.

NIBBS-Search for Fast and Accurate Prediction of Phenotype-Biased Metabolic Systems

PubMed Central

Padmanabhan, Kanchana; Shpanskaya, Yekaterina; Banfield, Jill; Scott, Kathleen; Mihelcic, James R.; Samatova, Nagiza F.

2012-01-01

Understanding of genotype-phenotype associations is important not only for furthering our knowledge on internal cellular processes, but also essential for providing the foundation necessary for genetic engineering of microorganisms for industrial use (e.g., production of bioenergy or biofuels). However, genotype-phenotype associations alone do not provide enough information to alter an organism's genome to either suppress or exhibit a phenotype. It is important to look at the phenotype-related genes in the context of the genome-scale network to understand how the genes interact with other genes in the organism. Identification of metabolic subsystems involved in the expression of the phenotype is one way of placing the phenotype-related genes in the context of the entire network. A metabolic system refers to a metabolic network subgraph; nodes are compounds and edges labels are the enzymes that catalyze the reaction. The metabolic subsystem could be part of a single metabolic pathway or span parts of multiple pathways. Arguably, comparative genome-scale metabolic network analysis is a promising strategy to identify these phenotype-related metabolic subsystems. Network Instance-Based Biased Subgraph Search (NIBBS) is a graph-theoretic method for genome-scale metabolic network comparative analysis that can identify metabolic systems that are statistically biased toward phenotype-expressing organismal networks. We set up experiments with target phenotypes like hydrogen production, TCA expression, and acid-tolerance. We show via extensive literature search that some of the resulting metabolic subsystems are indeed phenotype-related and formulate hypotheses for other systems in terms of their role in phenotype expression. NIBBS is also orders of magnitude faster than MULE, one of the most efficient maximal frequent subgraph mining algorithms that could be adjusted for this problem. Also, the set of phenotype-biased metabolic systems output by NIBBS comes very close to the set of phenotype-biased subgraphs output by an exact maximally-biased subgraph enumeration algorithm ( MBS-Enum ). The code (NIBBS and the module to visualize the identified subsystems) is available at http://freescience.org/cs/NIBBS. PMID:22589706

Communication efficiency and congestion of signal traffic in large-scale brain networks.

PubMed

Mišić, Bratislav; Sporns, Olaf; McIntosh, Anthony R

2014-01-01

The complex connectivity of the cerebral cortex suggests that inter-regional communication is a primary function. Using computational modeling, we show that anatomical connectivity may be a major determinant for global information flow in brain networks. A macaque brain network was implemented as a communication network in which signal units flowed between grey matter nodes along white matter paths. Compared to degree-matched surrogate networks, information flow on the macaque brain network was characterized by higher loss rates, faster transit times and lower throughput, suggesting that neural connectivity may be optimized for speed rather than fidelity. Much of global communication was mediated by a "rich club" of hub regions: a sub-graph comprised of high-degree nodes that are more densely interconnected with each other than predicted by chance. First, macaque communication patterns most closely resembled those observed for a synthetic rich club network, but were less similar to those seen in a synthetic small world network, suggesting that the former is a more fundamental feature of brain network topology. Second, rich club regions attracted the most signal traffic and likewise, connections between rich club regions carried more traffic than connections between non-rich club regions. Third, a number of rich club regions were significantly under-congested, suggesting that macaque connectivity actively shapes information flow, funneling traffic towards some nodes and away from others. Together, our results indicate a critical role of the rich club of hub nodes in dynamic aspects of global brain communication.

Communication Efficiency and Congestion of Signal Traffic in Large-Scale Brain Networks

PubMed Central

Mišić, Bratislav; Sporns, Olaf; McIntosh, Anthony R.

2014-01-01

The complex connectivity of the cerebral cortex suggests that inter-regional communication is a primary function. Using computational modeling, we show that anatomical connectivity may be a major determinant for global information flow in brain networks. A macaque brain network was implemented as a communication network in which signal units flowed between grey matter nodes along white matter paths. Compared to degree-matched surrogate networks, information flow on the macaque brain network was characterized by higher loss rates, faster transit times and lower throughput, suggesting that neural connectivity may be optimized for speed rather than fidelity. Much of global communication was mediated by a “rich club” of hub regions: a sub-graph comprised of high-degree nodes that are more densely interconnected with each other than predicted by chance. First, macaque communication patterns most closely resembled those observed for a synthetic rich club network, but were less similar to those seen in a synthetic small world network, suggesting that the former is a more fundamental feature of brain network topology. Second, rich club regions attracted the most signal traffic and likewise, connections between rich club regions carried more traffic than connections between non-rich club regions. Third, a number of rich club regions were significantly under-congested, suggesting that macaque connectivity actively shapes information flow, funneling traffic towards some nodes and away from others. Together, our results indicate a critical role of the rich club of hub nodes in dynamic aspects of global brain communication. PMID:24415931

OLSVis: an animated, interactive visual browser for bio-ontologies

PubMed Central

2012-01-01

Background More than one million terms from biomedical ontologies and controlled vocabularies are available through the Ontology Lookup Service (OLS). Although OLS provides ample possibility for querying and browsing terms, the visualization of parts of the ontology graphs is rather limited and inflexible. Results We created the OLSVis web application, a visualiser for browsing all ontologies available in the OLS database. OLSVis shows customisable subgraphs of the OLS ontologies. Subgraphs are animated via a real-time force-based layout algorithm which is fully interactive: each time the user makes a change, e.g. browsing to a new term, hiding, adding, or dragging terms, the algorithm performs smooth and only essential reorganisations of the graph. This assures an optimal viewing experience, because subsequent screen layouts are not grossly altered, and users can easily navigate through the graph. URL: http://ols.wordvis.com Conclusions The OLSVis web application provides a user-friendly tool to visualise ontologies from the OLS repository. It broadens the possibilities to investigate and select ontology subgraphs through a smooth visualisation method. PMID:22646023

Topographic Spreading Analysis of an Empirical Sex Workers' Network

NASA Astrophysics Data System (ADS)

Bjell, Johannes; Canright, Geoffrey; Engø-Monsen, Kenth; Remple, Valencia P.

The problem of epidemic spreading over networks has received considerable attention in recent years, due both to its intrinsic intellectual challenge and to its practical importance. A good recent summary of such work may be found in Newman (8), while (9) gives an outstanding example of a non-trivial prediction which is obtained from explicitly modeling the network in the epidemic spreading. In the language of mathematicians and computer scientists, a network of nodes connected by edges is called a graph. Most work on epidemic spreading over networks focuses on whole-graph properties, such as the percentage of infected nodes at long time. Two of us have, in contrast, focused on understanding the spread of an infection over time and space (the network) (61; 63; 62). This work involves decomposing any given network into subgraphs called regions (61). Regions are precisely defined as disjoint subgraphs which may be viewed as coarse-grained units of infection—in that, once one node in a region is infected, the progress of the infection over the remainder of the region is relatively fast and predictable (63). We note that this approach is based on the ‘Susceptible-Infected’ (SI) model of infection, in which nodes, once infected, are never cured. This model is reasonable for some infections, such as HIV—which is one of the diseases studied here. We also study gonorrhea and chlamydia, for which a more appropriate model is Susceptible-Infected-Susceptible (SIS) (67) (since nodes can be cured); we discuss the limitations of our approach for these cases below.

Enhancing Community Detection By Affinity-based Edge Weighting Scheme

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yoo, Andy; Sanders, Geoffrey; Henson, Van

Community detection refers to an important graph analytics problem of finding a set of densely-connected subgraphs in a graph and has gained a great deal of interest recently. The performance of current community detection algorithms is limited by an inherent constraint of unweighted graphs that offer very little information on their internal community structures. In this paper, we propose a new scheme to address this issue that weights the edges in a given graph based on recently proposed vertex affinity. The vertex affinity quantifies the proximity between two vertices in terms of their clustering strength, and therefore, it is idealmore » for graph analytics applications such as community detection. We also demonstrate that the affinity-based edge weighting scheme can improve the performance of community detection algorithms significantly.« less

Modular biological function is most effectively captured by combining molecular interaction data types.

PubMed

Ames, Ryan M; Macpherson, Jamie I; Pinney, John W; Lovell, Simon C; Robertson, David L

2013-01-01

Large-scale molecular interaction data sets have the potential to provide a comprehensive, system-wide understanding of biological function. Although individual molecules can be promiscuous in terms of their contribution to function, molecular functions emerge from the specific interactions of molecules giving rise to modular organisation. As functions often derive from a range of mechanisms, we demonstrate that they are best studied using networks derived from different sources. Implementing a graph partitioning algorithm we identify subnetworks in yeast protein-protein interaction (PPI), genetic interaction and gene co-regulation networks. Among these subnetworks we identify cohesive subgraphs that we expect to represent functional modules in the different data types. We demonstrate significant overlap between the subgraphs generated from the different data types and show these overlaps can represent related functions as represented by the Gene Ontology (GO). Next, we investigate the correspondence between our subgraphs and the Gene Ontology. This revealed varying degrees of coverage of the biological process, molecular function and cellular component ontologies, dependent on the data type. For example, subgraphs from the PPI show enrichment for 84%, 58% and 93% of annotated GO terms, respectively. Integrating the interaction data into a combined network increases the coverage of GO. Furthermore, the different annotation types of GO are not predominantly associated with one of the interaction data types. Collectively our results demonstrate that successful capture of functional relationships by network data depends on both the specific biological function being characterised and the type of network data being used. We identify functions that require integrated information to be accurately represented, demonstrating the limitations of individual data types. Combining interaction subnetworks across data types is therefore essential for fully understanding the complex and emergent nature of biological function.

The median problems on linear multichromosomal genomes: graph representation and fast exact solutions.

PubMed

Xu, Andrew Wei

2010-09-01

In genome rearrangement, given a set of genomes G and a distance measure d, the median problem asks for another genome q that minimizes the total distance [Formula: see text]. This is a key problem in genome rearrangement based phylogenetic analysis. Although this problem is known to be NP-hard, we have shown in a previous article, on circular genomes and under the DCJ distance measure, that a family of patterns in the given genomes--represented by adequate subgraphs--allow us to rapidly find exact solutions to the median problem in a decomposition approach. In this article, we extend this result to the case of linear multichromosomal genomes, in order to solve more interesting problems on eukaryotic nuclear genomes. A multi-way capping problem in the linear multichromosomal case imposes an extra computational challenge on top of the difficulty in the circular case, and this difficulty has been underestimated in our previous study and is addressed in this article. We represent the median problem by the capped multiple breakpoint graph, extend the adequate subgraphs into the capped adequate subgraphs, and prove optimality-preserving decomposition theorems, which give us the tools to solve the median problem and the multi-way capping optimization problem together. We also develop an exact algorithm ASMedian-linear, which iteratively detects instances of (capped) adequate subgraphs and decomposes problems into subproblems. Tested on simulated data, ASMedian-linear can rapidly solve most problems with up to several thousand genes, and it also can provide optimal or near-optimal solutions to the median problem under the reversal/HP distance measures. ASMedian-linear is available at http://sites.google.com/site/andrewweixu .

Machine Learning Classification Combining Multiple Features of A Hyper-Network of fMRI Data in Alzheimer's Disease

PubMed Central

Guo, Hao; Zhang, Fan; Chen, Junjie; Xu, Yong; Xiang, Jie

2017-01-01

Exploring functional interactions among various brain regions is helpful for understanding the pathological underpinnings of neurological disorders. Brain networks provide an important representation of those functional interactions, and thus are widely applied in the diagnosis and classification of neurodegenerative diseases. Many mental disorders involve a sharp decline in cognitive ability as a major symptom, which can be caused by abnormal connectivity patterns among several brain regions. However, conventional functional connectivity networks are usually constructed based on pairwise correlations among different brain regions. This approach ignores higher-order relationships, and cannot effectively characterize the high-order interactions of many brain regions working together. Recent neuroscience research suggests that higher-order relationships between brain regions are important for brain network analysis. Hyper-networks have been proposed that can effectively represent the interactions among brain regions. However, this method extracts the local properties of brain regions as features, but ignores the global topology information, which affects the evaluation of network topology and reduces the performance of the classifier. This problem can be compensated by a subgraph feature-based method, but it is not sensitive to change in a single brain region. Considering that both of these feature extraction methods result in the loss of information, we propose a novel machine learning classification method that combines multiple features of a hyper-network based on functional magnetic resonance imaging in Alzheimer's disease. The method combines the brain region features and subgraph features, and then uses a multi-kernel SVM for classification. This retains not only the global topological information, but also the sensitivity to change in a single brain region. To certify the proposed method, 28 normal control subjects and 38 Alzheimer's disease patients were selected to participate in an experiment. The proposed method achieved satisfactory classification accuracy, with an average of 91.60%. The abnormal brain regions included the bilateral precuneus, right parahippocampal gyrus\\hippocampus, right posterior cingulate gyrus, and other regions that are known to be important in Alzheimer's disease. Machine learning classification combining multiple features of a hyper-network of functional magnetic resonance imaging data in Alzheimer's disease obtains better classification performance. PMID:29209156

Coordination of networked systems on digraphs with multiple leaders via pinning control

NASA Astrophysics Data System (ADS)

Chen, Gang; Lewis, Frank L.

2012-02-01

It is well known that achieving consensus among a group of multi-vehicle systems by local distributed control is feasible if and only if all nodes in the communication digraph are reachable from a single (root) node. In this article, we take into account a more general case that the communication digraph of the networked multi-vehicle systems is weakly connected and has two or more zero-in-degree and strongly connected subgraphs, i.e. there are two or more leader groups. Based on the pinning control strategy, the feasibility problem of achieving second-order controlled consensus is studied. At first, a necessary and sufficient condition is given when the topology is fixed. Then the method to design the controller and the rule to choose the pinned vehicles are discussed. The proposed approach allows us to extend several existing results for undirected graphs to directed balanced graphs. A sufficient condition is proposed in the case where the coupling topology is variable. As an illustrative example, a second-order controlled consensus scheme is applied to coordinate the movement of networked multiple mobile robots.

A novel information cascade model in online social networks

NASA Astrophysics Data System (ADS)

Tong, Chao; He, Wenbo; Niu, Jianwei; Xie, Zhongyu

2016-02-01

The spread and diffusion of information has become one of the hot issues in today's social network analysis. To analyze the spread of online social network information and the attribute of cascade, in this paper, we discuss the spread of two kinds of users' decisions for city-wide activities, namely the "want to take part in the activity" and "be interested in the activity", based on the users' attention in "DouBan" and the data of the city-wide activities. We analyze the characteristics of the activity-decision's spread in these aspects: the scale and scope of the cascade subgraph, the structure characteristic of the cascade subgraph, the topological attribute of spread tree, and the occurrence frequency of cascade subgraph. On this basis, we propose a new information spread model. Based on the classical independent diffusion model, we introduce three mechanisms, equal probability, similarity of nodes, and popularity of nodes, which can generate and affect the spread of information. Besides, by conducting the experiments in six different kinds of network data set, we compare the effects of three mechanisms above mentioned, totally six specific factors, on the spread of information, and put forward that the node's popularity plays an important role in the information spread.

Percolation critical polynomial as a graph invariant

DOE PAGES

Scullard, Christian R.

2012-10-18

Every lattice for which the bond percolation critical probability can be found exactly possesses a critical polynomial, with the root in [0; 1] providing the threshold. Recent work has demonstrated that this polynomial may be generalized through a definition that can be applied on any periodic lattice. The polynomial depends on the lattice and on its decomposition into identical finite subgraphs, but once these are specified, the polynomial is essentially unique. On lattices for which the exact percolation threshold is unknown, the polynomials provide approximations for the critical probability with the estimates appearing to converge to the exact answer withmore » increasing subgraph size. In this paper, I show how the critical polynomial can be viewed as a graph invariant like the Tutte polynomial. In particular, the critical polynomial is computed on a finite graph and may be found using the deletion-contraction algorithm. This allows calculation on a computer, and I present such results for the kagome lattice using subgraphs of up to 36 bonds. For one of these, I find the prediction p c = 0:52440572:::, which differs from the numerical value, p c = 0:52440503(5), by only 6:9 X 10 -7.« less

[A retrieval method of drug molecules based on graph collapsing].

PubMed

Qu, J W; Lv, X Q; Liu, Z M; Liao, Y; Sun, P H; Wang, B; Tang, Z

2018-04-18

To establish a compact and efficient hypergraph representation and a graph-similarity-based retrieval method of molecules to achieve effective and efficient medicine information retrieval. Chemical structural formula (CSF) was a primary search target as a unique and precise identifier for each compound at the molecular level in the research field of medicine information retrieval. To retrieve medicine information effectively and efficiently, a complete workflow of the graph-based CSF retrieval system was introduced. This system accepted the photos taken from smartphones and the sketches drawn on tablet personal computers as CSF inputs, and formalized the CSFs with the corresponding graphs. Then this paper proposed a compact and efficient hypergraph representation for molecules on the basis of analyzing factors that directly affected the efficiency of graph matching. According to the characteristics of CSFs, a hierarchical collapsing method combining graph isomorphism and frequent subgraph mining was adopted. There was yet a fundamental challenge, subgraph overlapping during the collapsing procedure, which hindered the method from establishing the correct compact hypergraph of an original CSF graph. Therefore, a graph-isomorphism-based algorithm was proposed to select dominant acyclic subgraphs on the basis of overlapping analysis. Finally, the spatial similarity among graphical CSFs was evaluated by multi-dimensional measures of similarity. To evaluate the performance of the proposed method, the proposed system was firstly compared with Wikipedia Chemical Structure Explorer (WCSE), the state-of-the-art system that allowed CSF similarity searching within Wikipedia molecules dataset, on retrieval accuracy. The system achieved higher values on mean average precision, discounted cumulative gain, rank-biased precision, and expected reciprocal rank than WCSE from the top-2 to the top-10 retrieved results. Specifically, the system achieved 10%, 1.41, 6.42%, and 1.32% higher than WCSE on these metrics for top-10 retrieval results, respectively. Moreover, several retrieval cases were presented to intuitively compare with WCSE. The results of the above comparative study demonstrated that the proposed method outperformed the existing method with regard to accuracy and effectiveness. This paper proposes a graph-similarity-based retrieval approach for medicine information. To obtain satisfactory retrieval results, an isomorphism-based algorithm is proposed for dominant subgraph selection based on the subgraph overlapping analysis, as well as an effective and efficient hypergraph representation of molecules. Experiment results demonstrate the effectiveness of the proposed approach.

Assortativity and leadership emerge from anti-preferential attachment in heterogeneous networks.

PubMed

Sendiña-Nadal, I; Danziger, M M; Wang, Z; Havlin, S; Boccaletti, S

2016-02-18

Real-world networks have distinct topologies, with marked deviations from purely random networks. Many of them exhibit degree-assortativity, with nodes of similar degree more likely to link to one another. Though microscopic mechanisms have been suggested for the emergence of other topological features, assortativity has proven elusive. Assortativity can be artificially implanted in a network via degree-preserving link permutations, however this destroys the graph's hierarchical clustering and does not correspond to any microscopic mechanism. Here, we propose the first generative model which creates heterogeneous networks with scale-free-like properties in degree and clustering distributions and tunable realistic assortativity. Two distinct populations of nodes are incrementally added to an initial network by selecting a subgraph to connect to at random. One population (the followers) follows preferential attachment, while the other population (the potential leaders) connects via anti-preferential attachment: they link to lower degree nodes when added to the network. By selecting the lower degree nodes, the potential leader nodes maintain high visibility during the growth process, eventually growing into hubs. The evolution of links in Facebook empirically validates the connection between the initial anti-preferential attachment and long term high degree. In this way, our work sheds new light on the structure and evolution of social networks.

Assortativity and leadership emerge from anti-preferential attachment in heterogeneous networks

NASA Astrophysics Data System (ADS)

Sendiña-Nadal, I.; Danziger, M. M.; Wang, Z.; Havlin, S.; Boccaletti, S.

2016-02-01

Real-world networks have distinct topologies, with marked deviations from purely random networks. Many of them exhibit degree-assortativity, with nodes of similar degree more likely to link to one another. Though microscopic mechanisms have been suggested for the emergence of other topological features, assortativity has proven elusive. Assortativity can be artificially implanted in a network via degree-preserving link permutations, however this destroys the graph’s hierarchical clustering and does not correspond to any microscopic mechanism. Here, we propose the first generative model which creates heterogeneous networks with scale-free-like properties in degree and clustering distributions and tunable realistic assortativity. Two distinct populations of nodes are incrementally added to an initial network by selecting a subgraph to connect to at random. One population (the followers) follows preferential attachment, while the other population (the potential leaders) connects via anti-preferential attachment: they link to lower degree nodes when added to the network. By selecting the lower degree nodes, the potential leader nodes maintain high visibility during the growth process, eventually growing into hubs. The evolution of links in Facebook empirically validates the connection between the initial anti-preferential attachment and long term high degree. In this way, our work sheds new light on the structure and evolution of social networks.

Pre-configured polyhedron based protection against multi-link failures in optical mesh networks.

PubMed

Huang, Shanguo; Guo, Bingli; Li, Xin; Zhang, Jie; Zhao, Yongli; Gu, Wanyi

2014-02-10

This paper focuses on random multi-link failures protection in optical mesh networks, instead of single, the dual or sequential failures of previous studies. Spare resource efficiency and failure robustness are major concerns in link protection strategy designing and a k-regular and k-edge connected structure is proved to be one of the optimal solutions for link protection network. Based on this, a novel pre-configured polyhedron based protection structure is proposed, and it could provide protection for both simultaneous and sequential random link failures with improved spare resource efficiency. Its performance is evaluated in terms of spare resource consumption, recovery rate and average recovery path length, as well as compared with ring based and subgraph protection under probabilistic link failure scenarios. Results show the proposed novel link protection approach has better performance than previous works.

Path scanning for the detection of anomalous subgraphs and use of DNS requests and host agents for anomaly/change detection and network situational awareness

DOE Office of Scientific and Technical Information (OSTI.GOV)

Neil, Joshua Charles; Fisk, Michael Edward; Brugh, Alexander William

A system, apparatus, computer-readable medium, and computer-implemented method are provided for detecting anomalous behavior in a network. Historical parameters of the network are determined in order to determine normal activity levels. A plurality of paths in the network are enumerated as part of a graph representing the network, where each computing system in the network may be a node in the graph and the sequence of connections between two computing systems may be a directed edge in the graph. A statistical model is applied to the plurality of paths in the graph on a sliding window basis to detect anomalousmore » behavior. Data collected by a Unified Host Collection Agent ("UHCA") may also be used to detect anomalous behavior.« less

Directed random walks and constraint programming reveal active pathways in hepatocyte growth factor signaling.

PubMed

Kittas, Aristotelis; Delobelle, Aurélien; Schmitt, Sabrina; Breuhahn, Kai; Guziolowski, Carito; Grabe, Niels

2016-01-01

An effective means to analyze mRNA expression data is to take advantage of established knowledge from pathway databases, using methods such as pathway-enrichment analyses. However, pathway databases are not case-specific and expression data could be used to infer gene-regulation patterns in the context of specific pathways. In addition, canonical pathways may not always describe the signaling mechanisms properly, because interactions can frequently occur between genes in different pathways. Relatively few methods have been proposed to date for generating and analyzing such networks, preserving the causality between gene interactions and reasoning over the qualitative logic of regulatory effects. We present an algorithm (MCWalk) integrated with a logic programming approach, to discover subgraphs in large-scale signaling networks by random walks in a fully automated pipeline. As an exemplary application, we uncover the signal transduction mechanisms in a gene interaction network describing hepatocyte growth factor-stimulated cell migration and proliferation from gene-expression measured with microarray and RT-qPCR using in-house perturbation experiments in a keratinocyte-fibroblast co-culture. The resulting subgraphs illustrate possible associations of hepatocyte growth factor receptor c-Met nodes, differentially expressed genes and cellular states. Using perturbation experiments and Answer Set programming, we are able to select those which are more consistent with the experimental data. We discover key regulator nodes by measuring the frequency with which they are traversed when connecting signaling between receptors and significantly regulated genes and predict their expression-shift consistently with the measured data. The Java implementation of MCWalk is publicly available under the MIT license at: https://bitbucket.org/akittas/biosubg. © 2015 FEBS.

Eigenvector synchronization, graph rigidity and the molecule problemR

PubMed Central

Cucuringu, Mihai; Singer, Amit; Cowburn, David

2013-01-01

The graph realization problem has received a great deal of attention in recent years, due to its importance in applications such as wireless sensor networks and structural biology. In this paper, we extend the previous work and propose the 3D-As-Synchronized-As-Possible (3D-ASAP) algorithm, for the graph realization problem in ℝ3, given a sparse and noisy set of distance measurements. 3D-ASAP is a divide and conquer, non-incremental and non-iterative algorithm, which integrates local distance information into a global structure determination. Our approach starts with identifying, for every node, a subgraph of its 1-hop neighborhood graph, which can be accurately embedded in its own coordinate system. In the noise-free case, the computed coordinates of the sensors in each patch must agree with their global positioning up to some unknown rigid motion, that is, up to translation, rotation and possibly reflection. In other words, to every patch, there corresponds an element of the Euclidean group, Euc(3), of rigid transformations in ℝ3, and the goal was to estimate the group elements that will properly align all the patches in a globally consistent way. Furthermore, 3D-ASAP successfully incorporates information specific to the molecule problem in structural biology, in particular information on known substructures and their orientation. In addition, we also propose 3D-spectral-partitioning (SP)-ASAP, a faster version of 3D-ASAP, which uses a spectral partitioning algorithm as a pre-processing step for dividing the initial graph into smaller subgraphs. Our extensive numerical simulations show that 3D-ASAP and 3D-SP-ASAP are very robust to high levels of noise in the measured distances and to sparse connectivity in the measurement graph, and compare favorably with similar state-of-the-art localization algorithms. PMID:24432187

Synchronization of Coupled Dynamical Systems: Tolerance to Weak Connectivity and Arbitrarily Bounded Time-Varying Delays

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meng, Ziyang; Yang, Tao; Li, Guoqi

Here, we study synchronization of coupled linear systems over networks with weak connectivity and nonuniform time-varying delays. We focus on the case where the internal dynamics are time-varying but non-expansive (stable dynamics with a quadratic Lyapunov function). Both uniformly jointly connected and infinitely jointly connected communication topologies are considered. A new concept of quadratic synchronization is introduced. We first show that global asymptotic quadratic synchronization can be achieved over directed networks with uniform joint connectivity and arbitrarily bounded delays. We then study the case of infinitely jointly connected communication topology. In particular, for the undirected communication topologies, it turns outmore » that the existence of a uniform time interval for the jointly connected communication topology is not necessary and quadratic synchronization can be achieved when the time-varying nonuniform delays are arbitrarily bounded. Finally, simulation results are provided to validate the theoretical results.« less

Synchronization of Coupled Dynamical Systems: Tolerance to Weak Connectivity and Arbitrarily Bounded Time-Varying Delays

DOE PAGES

Meng, Ziyang; Yang, Tao; Li, Guoqi; ...

2017-09-18

Here, we study synchronization of coupled linear systems over networks with weak connectivity and nonuniform time-varying delays. We focus on the case where the internal dynamics are time-varying but non-expansive (stable dynamics with a quadratic Lyapunov function). Both uniformly jointly connected and infinitely jointly connected communication topologies are considered. A new concept of quadratic synchronization is introduced. We first show that global asymptotic quadratic synchronization can be achieved over directed networks with uniform joint connectivity and arbitrarily bounded delays. We then study the case of infinitely jointly connected communication topology. In particular, for the undirected communication topologies, it turns outmore » that the existence of a uniform time interval for the jointly connected communication topology is not necessary and quadratic synchronization can be achieved when the time-varying nonuniform delays are arbitrarily bounded. Finally, simulation results are provided to validate the theoretical results.« less

Synchronization of Coupled Dynamical Systems: Tolerance to Weak Connectivity and Arbitrarily Bounded Time-Varying Delays

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meng, Ziyang; Yang, Tao; Li, Guoqi

We study synchronization of coupled linear systems over networks with weak connectivity and time-varying delays. We focus on the case that the internal dynamics are time-varying but non-expansive. Both uniformly connected and infinitely connected communication topologies are considered. A new concept of P-synchronization is introduced and we first show that global asymptotic P-synchronization can be achieved over directed networks with uniform joint connectivity and arbitrarily bounded delays. We then study the case of the infinitely jointly connected communication topology. In particular, for the undirected communication topologies, it turns out that the existence of a uniform time interval for the communicationmore » topology is not necessary and P-synchronization can be achieved when the time varying delays are arbitrarily bounded. Simulations are given to validate the theoretical results.« less

Theoretic derivation of directed acyclic subgraph algorithm and comparisons with message passing algorithm

NASA Astrophysics Data System (ADS)

Ha, Jeongmok; Jeong, Hong

2016-07-01

This study investigates the directed acyclic subgraph (DAS) algorithm, which is used to solve discrete labeling problems much more rapidly than other Markov-random-field-based inference methods but at a competitive accuracy. However, the mechanism by which the DAS algorithm simultaneously achieves competitive accuracy and fast execution speed, has not been elucidated by a theoretical derivation. We analyze the DAS algorithm by comparing it with a message passing algorithm. Graphical models, inference methods, and energy-minimization frameworks are compared between DAS and message passing algorithms. Moreover, the performances of DAS and other message passing methods [sum-product belief propagation (BP), max-product BP, and tree-reweighted message passing] are experimentally compared.

A Selectivity based approach to Continuous Pattern Detection in Streaming Graphs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Choudhury, Sutanay; Holder, Larry; Chin, George

2015-02-02

Cyber security is one of the most significant technical challenges in current times. Detecting adversarial activities, prevention of theft of intellectual properties and customer data is a high priority for corporations and government agencies around the world. Cyber defenders need to analyze massive-scale, high-resolution network flows to identify, categorize, and mitigate attacks involving net- works spanning institutional and national boundaries. Many of the cyber attacks can be described as subgraph patterns, with promi- nent examples being insider infiltrations (path queries), denial of service (parallel paths) and malicious spreads (tree queries). This motivates us to explore subgraph matching on streaming graphsmore » in a continuous setting. The novelty of our work lies in using the subgraph distributional statistics collected from the streaming graph to determine the query processing strategy. We introduce a “Lazy Search" algorithm where the search strategy is decided on a vertex-to-vertex basis depending on the likelihood of a match in the vertex neighborhood. We also propose a metric named “Relative Selectivity" that is used to se- lect between different query processing strategies. Our experiments performed on real online news, network traffic stream and a syn- thetic social network benchmark demonstrate 10-100x speedups over selectivity agnostic approaches.« less

A Selectivity based approach to Continuous Pattern Detection in Streaming Graphs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Choudhury, Sutanay; Holder, Larry; Chin, George

2015-05-27

Cyber security is one of the most significant technical challenges in current times. Detecting adversarial activities, prevention of theft of intellectual properties and customer data is a high priority for corporations and government agencies around the world. Cyber defenders need to analyze massive-scale, high-resolution network flows to identify, categorize, and mitigate attacks involving networks spanning institutional and national boundaries. Many of the cyber attacks can be described as subgraph patterns, with prominent examples being insider infiltrations (path queries), denial of service (parallel paths) and malicious spreads (tree queries). This motivates us to explore subgraph matching on streaming graphs in amore » continuous setting. The novelty of our work lies in using the subgraph distributional statistics collected from the streaming graph to determine the query processing strategy. We introduce a ``Lazy Search" algorithm where the search strategy is decided on a vertex-to-vertex basis depending on the likelihood of a match in the vertex neighborhood. We also propose a metric named ``Relative Selectivity" that is used to select between different query processing strategies. Our experiments performed on real online news, network traffic stream and a synthetic social network benchmark demonstrate 10-100x speedups over non-incremental, selectivity agnostic approaches.« less

Optimizing graph-based patterns to extract biomedical events from the literature

PubMed Central

2015-01-01

In BioNLP-ST 2013 We participated in the BioNLP 2013 shared tasks on event extraction. Our extraction method is based on the search for an approximate subgraph isomorphism between key context dependencies of events and graphs of input sentences. Our system was able to address both the GENIA (GE) task focusing on 13 molecular biology related event types and the Cancer Genetics (CG) task targeting a challenging group of 40 cancer biology related event types with varying arguments concerning 18 kinds of biological entities. In addition to adapting our system to the two tasks, we also attempted to integrate semantics into the graph matching scheme using a distributional similarity model for more events, and evaluated the event extraction impact of using paths of all possible lengths as key context dependencies beyond using only the shortest paths in our system. We achieved a 46.38% F-score in the CG task (ranking 3rd) and a 48.93% F-score in the GE task (ranking 4th). After BioNLP-ST 2013 We explored three ways to further extend our event extraction system in our previously published work: (1) We allow non-essential nodes to be skipped, and incorporated a node skipping penalty into the subgraph distance function of our approximate subgraph matching algorithm. (2) Instead of assigning a unified subgraph distance threshold to all patterns of an event type, we learned a customized threshold for each pattern. (3) We implemented the well-known Empirical Risk Minimization (ERM) principle to optimize the event pattern set by balancing prediction errors on training data against regularization. When evaluated on the official GE task test data, these extensions help to improve the extraction precision from 62% to 65%. However, the overall F-score stays equivalent to the previous performance due to a 1% drop in recall. PMID:26551594

Relating Topological Determinants of Complex Networks to Their Spectral Properties: Structural and Dynamical Effects

NASA Astrophysics Data System (ADS)

Castellano, Claudio; Pastor-Satorras, Romualdo

2017-10-01

The largest eigenvalue of a network's adjacency matrix and its associated principal eigenvector are key elements for determining the topological structure and the properties of dynamical processes mediated by it. We present a physically grounded expression relating the value of the largest eigenvalue of a given network to the largest eigenvalue of two network subgraphs, considered as isolated: the hub with its immediate neighbors and the densely connected set of nodes with maximum K -core index. We validate this formula by showing that it predicts, with good accuracy, the largest eigenvalue of a large set of synthetic and real-world topologies. We also present evidence of the consequences of these findings for broad classes of dynamics taking place on the networks. As a by-product, we reveal that the spectral properties of heterogeneous networks built according to the linear preferential attachment model are qualitatively different from those of their static counterparts.

A complex systems analysis of stick-slip dynamics of a laboratory fault

DOE Office of Scientific and Technical Information (OSTI.GOV)

Walker, David M.; Tordesillas, Antoinette, E-mail: atordesi@unimelb.edu.au; Small, Michael

2014-03-15

We study the stick-slip behavior of a granular bed of photoelastic disks sheared by a rough slider pulled along the surface. Time series of a proxy for granular friction are examined using complex systems methods to characterize the observed stick-slip dynamics of this laboratory fault. Nonlinear surrogate time series methods show that the stick-slip behavior appears more complex than a periodic dynamics description. Phase space embedding methods show that the dynamics can be locally captured within a four to six dimensional subspace. These slider time series also provide an experimental test for recent complex network methods. Phase space networks, constructedmore » by connecting nearby phase space points, proved useful in capturing the key features of the dynamics. In particular, network communities could be associated to slip events and the ranking of small network subgraphs exhibited a heretofore unreported ordering.« less

Probabilistic graphlet transfer for photo cropping.

PubMed

Zhang, Luming; Song, Mingli; Zhao, Qi; Liu, Xiao; Bu, Jiajun; Chen, Chun

2013-02-01

As one of the most basic photo manipulation processes, photo cropping is widely used in the printing, graphic design, and photography industries. In this paper, we introduce graphlets (i.e., small connected subgraphs) to represent a photo's aesthetic features, and propose a probabilistic model to transfer aesthetic features from the training photo onto the cropped photo. In particular, by segmenting each photo into a set of regions, we construct a region adjacency graph (RAG) to represent the global aesthetic feature of each photo. Graphlets are then extracted from the RAGs, and these graphlets capture the local aesthetic features of the photos. Finally, we cast photo cropping as a candidate-searching procedure on the basis of a probabilistic model, and infer the parameters of the cropped photos using Gibbs sampling. The proposed method is fully automatic. Subjective evaluations have shown that it is preferred over a number of existing approaches.

Non-isolated Resolving Sets of certain Graphs Cartesian Product with a Path

NASA Astrophysics Data System (ADS)

Hasibuan, I. M.; Salman, A. N. M.; Saputro, S. W.

2018-04-01

Let G be a connected, simple, and finite graph. For an ordered subset W = {w 1 , w 2 , · · ·, wk } of vertices in a graph G and a vertex v of G, the metric representation of v with respect to W is the k-vector r(v|W ) = (d(v, w 1), d(v, w 2), · · ·, d(v, wk )). The set W is called a resolving set for G if every vertex of G has a distinct representation. The minimum cardinality of W is called the metric dimension of G, denoted by dim(G). If the induced subgraph < W> has no isolated vertices, then W is called a non-isolated resolving set. The minimum cardinality of non-isolated resolving set of G is called the non-isolated resolving number of G, denoted by nr(G). In this paper, we consider H\\square {P}n that is a graph obtained from Cartesian product between a connected graph H and a path Pn . We determine nr(H\\square {P}n), for some classes of H, including cycles, complete graphs, complete bipartite graphs, and friendship graphs.

CombiMotif: A new algorithm for network motifs discovery in protein-protein interaction networks

NASA Astrophysics Data System (ADS)

Luo, Jiawei; Li, Guanghui; Song, Dan; Liang, Cheng

2014-12-01

Discovering motifs in protein-protein interaction networks is becoming a current major challenge in computational biology, since the distribution of the number of network motifs can reveal significant systemic differences among species. However, this task can be computationally expensive because of the involvement of graph isomorphic detection. In this paper, we present a new algorithm (CombiMotif) that incorporates combinatorial techniques to count non-induced occurrences of subgraph topologies in the form of trees. The efficiency of our algorithm is demonstrated by comparing the obtained results with the current state-of-the art subgraph counting algorithms. We also show major differences between unicellular and multicellular organisms. The datasets and source code of CombiMotif are freely available upon request.

Graph-theoretic approach to quantum correlations.

PubMed

Cabello, Adán; Severini, Simone; Winter, Andreas

2014-01-31

Correlations in Bell and noncontextuality inequalities can be expressed as a positive linear combination of probabilities of events. Exclusive events can be represented as adjacent vertices of a graph, so correlations can be associated to a subgraph. We show that the maximum value of the correlations for classical, quantum, and more general theories is the independence number, the Lovász number, and the fractional packing number of this subgraph, respectively. We also show that, for any graph, there is always a correlation experiment such that the set of quantum probabilities is exactly the Grötschel-Lovász-Schrijver theta body. This identifies these combinatorial notions as fundamental physical objects and provides a method for singling out experiments with quantum correlations on demand.

Multi-Level Anomaly Detection on Time-Varying Graph Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bridges, Robert A; Collins, John P; Ferragut, Erik M

This work presents a novel modeling and analysis framework for graph sequences which addresses the challenge of detecting and contextualizing anomalies in labelled, streaming graph data. We introduce a generalization of the BTER model of Seshadhri et al. by adding flexibility to community structure, and use this model to perform multi-scale graph anomaly detection. Specifically, probability models describing coarse subgraphs are built by aggregating probabilities at finer levels, and these closely related hierarchical models simultaneously detect deviations from expectation. This technique provides insight into a graph's structure and internal context that may shed light on a detected event. Additionally, thismore » multi-scale analysis facilitates intuitive visualizations by allowing users to narrow focus from an anomalous graph to particular subgraphs or nodes causing the anomaly. For evaluation, two hierarchical anomaly detectors are tested against a baseline Gaussian method on a series of sampled graphs. We demonstrate that our graph statistics-based approach outperforms both a distribution-based detector and the baseline in a labeled setting with community structure, and it accurately detects anomalies in synthetic and real-world datasets at the node, subgraph, and graph levels. To illustrate the accessibility of information made possible via this technique, the anomaly detector and an associated interactive visualization tool are tested on NCAA football data, where teams and conferences that moved within the league are identified with perfect recall, and precision greater than 0.786.« less

Counting Triangles to Sum Squares

ERIC Educational Resources Information Center

DeMaio, Joe

2012-01-01

Counting complete subgraphs of three vertices in complete graphs, yields combinatorial arguments for identities for sums of squares of integers, odd integers, even integers and sums of the triangular numbers.

Reproducibility of graph metrics of human brain structural networks.

PubMed

Duda, Jeffrey T; Cook, Philip A; Gee, James C

2014-01-01

Recent interest in human brain connectivity has led to the application of graph theoretical analysis to human brain structural networks, in particular white matter connectivity inferred from diffusion imaging and fiber tractography. While these methods have been used to study a variety of patient populations, there has been less examination of the reproducibility of these methods. A number of tractography algorithms exist and many of these are known to be sensitive to user-selected parameters. The methods used to derive a connectivity matrix from fiber tractography output may also influence the resulting graph metrics. Here we examine how these algorithm and parameter choices influence the reproducibility of proposed graph metrics on a publicly available test-retest dataset consisting of 21 healthy adults. The dice coefficient is used to examine topological similarity of constant density subgraphs both within and between subjects. Seven graph metrics are examined here: mean clustering coefficient, characteristic path length, largest connected component size, assortativity, global efficiency, local efficiency, and rich club coefficient. The reproducibility of these network summary measures is examined using the intraclass correlation coefficient (ICC). Graph curves are created by treating the graph metrics as functions of a parameter such as graph density. Functional data analysis techniques are used to examine differences in graph measures that result from the choice of fiber tracking algorithm. The graph metrics consistently showed good levels of reproducibility as measured with ICC, with the exception of some instability at low graph density levels. The global and local efficiency measures were the most robust to the choice of fiber tracking algorithm.

A Graph Analytic Metric for Mitigating Advanced Persistent Threat

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnson, John R.; Hogan, Emilie A.

2013-06-04

This paper introduces a novel graph analytic metric that can be used to measure the potential vulnerability of a cyber network to specific types of attacks that use lateral movement and privilege escalation such as the well known Pass The Hash, (PTH). The metric is computed from an oriented subgraph of the underlying cyber network induced by selecting only those edges for which a given property holds between the two vertices of the edge. The metric with respect to a select node on the subgraph is defined as the likelihood that the select node is reachable from another arbitrary nodemore » in the graph. This metric can be calculated dynamically from the authorization and auditing layers during the network security authorization phase and will potentially enable predictive deterrence against attacks such as PTH.« less

On P2 ⋄ Pn -supermagic labeling of edge corona product of cycle and path graph

NASA Astrophysics Data System (ADS)

Yulianto, R.; Martini, Titin S.

2018-04-01

A simple graph G = (V, E) admits a H-covering, where H is subgraph of G, if every edge in E belongs to a subgraph of G isomorphic to H. Graph G is H-magic if there is a total labeling f:V(G)\\cup E(G)\\to 1,2,\\ldots,|V(G)|+|E(G)|, such that each subgraph {H}{\\prime }=({V}{\\prime },{E}{\\prime }) of G isomorphic to H and satisfying f{({H}{\\prime })}=def{\\sum }\\upsilon \\in {V{\\prime }}f(\\upsilon )+{\\sum }e\\in {E{\\prime }}f(e)=m(f) where m(f) is a constant magic sum. Additionaly, G admits H-supermagic if f(V)=1,2,\\ldots,|V|. The edge corona {C}n \\diamond {P}n of Cn and Pn is defined as the graph obtained by taking one copy of Cn and n copies of Pn , and then joining two end-vertices of the i-th edge of Cn to every vertex in the i-th copy of Pn . This research aim is to find H-supermagic covering on an edge corona product of cycle and path graph {C}n \\diamond {P}n where H is {P}2 \\diamond {P}n. We use k-balanced multiset to solve our reserarch. Here, we find that an edge corona product of cycle and path graph {C}n \\diamond {P}n is {P}2 \\diamond {P}n supermagic for n > 3.

A multi-level anomaly detection algorithm for time-varying graph data with interactive visualization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bridges, Robert A.; Collins, John P.; Ferragut, Erik M.

This work presents a novel modeling and analysis framework for graph sequences which addresses the challenge of detecting and contextualizing anomalies in labelled, streaming graph data. We introduce a generalization of the BTER model of Seshadhri et al. by adding flexibility to community structure, and use this model to perform multi-scale graph anomaly detection. Specifically, probability models describing coarse subgraphs are built by aggregating node probabilities, and these related hierarchical models simultaneously detect deviations from expectation. This technique provides insight into a graph's structure and internal context that may shed light on a detected event. Additionally, this multi-scale analysis facilitatesmore » intuitive visualizations by allowing users to narrow focus from an anomalous graph to particular subgraphs or nodes causing the anomaly. For evaluation, two hierarchical anomaly detectors are tested against a baseline Gaussian method on a series of sampled graphs. We demonstrate that our graph statistics-based approach outperforms both a distribution-based detector and the baseline in a labeled setting with community structure, and it accurately detects anomalies in synthetic and real-world datasets at the node, subgraph, and graph levels. Furthermore, to illustrate the accessibility of information made possible via this technique, the anomaly detector and an associated interactive visualization tool are tested on NCAA football data, where teams and conferences that moved within the league are identified with perfect recall, and precision greater than 0.786.« less

VIGOR: Interactive Visual Exploration of Graph Query Results.

PubMed

Pienta, Robert; Hohman, Fred; Endert, Alex; Tamersoy, Acar; Roundy, Kevin; Gates, Chris; Navathe, Shamkant; Chau, Duen Horng

2018-01-01

Finding patterns in graphs has become a vital challenge in many domains from biological systems, network security, to finance (e.g., finding money laundering rings of bankers and business owners). While there is significant interest in graph databases and querying techniques, less research has focused on helping analysts make sense of underlying patterns within a group of subgraph results. Visualizing graph query results is challenging, requiring effective summarization of a large number of subgraphs, each having potentially shared node-values, rich node features, and flexible structure across queries. We present VIGOR, a novel interactive visual analytics system, for exploring and making sense of query results. VIGOR uses multiple coordinated views, leveraging different data representations and organizations to streamline analysts sensemaking process. VIGOR contributes: (1) an exemplar-based interaction technique, where an analyst starts with a specific result and relaxes constraints to find other similar results or starts with only the structure (i.e., without node value constraints), and adds constraints to narrow in on specific results; and (2) a novel feature-aware subgraph result summarization. Through a collaboration with Symantec, we demonstrate how VIGOR helps tackle real-world problems through the discovery of security blindspots in a cybersecurity dataset with over 11,000 incidents. We also evaluate VIGOR with a within-subjects study, demonstrating VIGOR's ease of use over a leading graph database management system, and its ability to help analysts understand their results at higher speed and make fewer errors.

A multi-level anomaly detection algorithm for time-varying graph data with interactive visualization

DOE PAGES

Bridges, Robert A.; Collins, John P.; Ferragut, Erik M.; ...

2016-01-01

This work presents a novel modeling and analysis framework for graph sequences which addresses the challenge of detecting and contextualizing anomalies in labelled, streaming graph data. We introduce a generalization of the BTER model of Seshadhri et al. by adding flexibility to community structure, and use this model to perform multi-scale graph anomaly detection. Specifically, probability models describing coarse subgraphs are built by aggregating node probabilities, and these related hierarchical models simultaneously detect deviations from expectation. This technique provides insight into a graph's structure and internal context that may shed light on a detected event. Additionally, this multi-scale analysis facilitatesmore » intuitive visualizations by allowing users to narrow focus from an anomalous graph to particular subgraphs or nodes causing the anomaly. For evaluation, two hierarchical anomaly detectors are tested against a baseline Gaussian method on a series of sampled graphs. We demonstrate that our graph statistics-based approach outperforms both a distribution-based detector and the baseline in a labeled setting with community structure, and it accurately detects anomalies in synthetic and real-world datasets at the node, subgraph, and graph levels. Furthermore, to illustrate the accessibility of information made possible via this technique, the anomaly detector and an associated interactive visualization tool are tested on NCAA football data, where teams and conferences that moved within the league are identified with perfect recall, and precision greater than 0.786.« less

Trapped surfaces and emergent curved space in the Bose-Hubbard model

NASA Astrophysics Data System (ADS)

Caravelli, Francesco; Hamma, Alioscia; Markopoulou, Fotini; Riera, Arnau

2012-02-01

A Bose-Hubbard model on a dynamical lattice was introduced in previous work as a spin system analogue of emergent geometry and gravity. Graphs with regions of high connectivity in the lattice were identified as candidate analogues of spacetime geometries that contain trapped surfaces. We carry out a detailed study of these systems and show explicitly that the highly connected subgraphs trap matter. We do this by solving the model in the limit of no back-reaction of the matter on the lattice, and for states with certain symmetries that are natural for our problem. We find that in this case the problem reduces to a one-dimensional Hubbard model on a lattice with variable vertex degree and multiple edges between the same two vertices. In addition, we obtain a (discrete) differential equation for the evolution of the probability density of particles which is closed in the classical regime. This is a wave equation in which the vertex degree is related to the local speed of propagation of probability. This allows an interpretation of the probability density of particles similar to that in analogue gravity systems: matter inside this analogue system sees a curved spacetime. We verify our analytic results by numerical simulations. Finally, we analyze the dependence of localization on a gradual, rather than abrupt, falloff of the vertex degree on the boundary of the highly connected region and find that matter is localized in and around that region.

Improved visibility of character conflicts in quasi-median networks with the EMPOP NETWORK software

PubMed Central

Zimmermann, Bettina; Röck, Alexander W.; Dür, Arne; Parson, Walther

2014-01-01

Aim To provide a valuable tool for graphical representation of mitochondrial DNA (mtDNA) data that enables visual emphasis on complex substructures within the network to highlight possible ambiguities and errors. Method We applied the new NETWORK graphical user interface, available via EMPOP (European DNA Profiling Group Mitochondrial DNA Population Database; www.empop.org) by means of two mtDNA data sets that were submitted for quality control. Results The quasi-median network torsi of the two data sets resulted in complex reticulations, suggesting ambiguous data. To check the corresponding raw data, accountable nodes and connecting branches of the network could be identified by highlighting induced subgraphs with concurrent dimming of their complements. This is achieved by accentuating the relevant substructures in the network: mouse clicking on a node displays a list of all mtDNA haplotypes included in that node; the selection of a branch specifies the mutation(s) connecting two nodes. It is indicated to evaluate these mutations by means of the raw data. Conclusion Inspection of the raw data confirmed the presence of phantom mutations due to suboptimal electrophoresis conditions and data misinterpretation. The network software proved to be a powerful tool to highlight problematic data and guide quality control of mtDNA data tables. PMID:24778097

Clique-based data mining for related genes in a biomedical database.

PubMed

Matsunaga, Tsutomu; Yonemori, Chikara; Tomita, Etsuji; Muramatsu, Masaaki

2009-07-01

Progress in the life sciences cannot be made without integrating biomedical knowledge on numerous genes in order to help formulate hypotheses on the genetic mechanisms behind various biological phenomena, including diseases. There is thus a strong need for a way to automatically and comprehensively search from biomedical databases for related genes, such as genes in the same families and genes encoding components of the same pathways. Here we address the extraction of related genes by searching for densely-connected subgraphs, which are modeled as cliques, in a biomedical relational graph. We constructed a graph whose nodes were gene or disease pages, and edges were the hyperlink connections between those pages in the Online Mendelian Inheritance in Man (OMIM) database. We obtained over 20,000 sets of related genes (called 'gene modules') by enumerating cliques computationally. The modules included genes in the same family, genes for proteins that form a complex, and genes for components of the same signaling pathway. The results of experiments using 'metabolic syndrome'-related gene modules show that the gene modules can be used to get a coherent holistic picture helpful for interpreting relations among genes. We presented a data mining approach extracting related genes by enumerating cliques. The extracted gene sets provide a holistic picture useful for comprehending complex disease mechanisms.

Identifying the minor set cover of dense connected bipartite graphs via random matching edge sets

NASA Astrophysics Data System (ADS)

Hamilton, Kathleen E.; Humble, Travis S.

2017-04-01

Using quantum annealing to solve an optimization problem requires minor embedding a logic graph into a known hardware graph. In an effort to reduce the complexity of the minor embedding problem, we introduce the minor set cover (MSC) of a known graph G: a subset of graph minors which contain any remaining minor of the graph as a subgraph. Any graph that can be embedded into G will be embeddable into a member of the MSC. Focusing on embedding into the hardware graph of commercially available quantum annealers, we establish the MSC for a particular known virtual hardware, which is a complete bipartite graph. We show that the complete bipartite graph K_{N,N} has a MSC of N minors, from which K_{N+1} is identified as the largest clique minor of K_{N,N}. The case of determining the largest clique minor of hardware with faults is briefly discussed but remains an open question.

Identifying the minor set cover of dense connected bipartite graphs via random matching edge sets

DOE PAGES

Hamilton, Kathleen E.; Humble, Travis S.

2017-02-23

Using quantum annealing to solve an optimization problem requires minor embedding a logic graph into a known hardware graph. We introduce the minor set cover (MSC) of a known graph GG : a subset of graph minors which contain any remaining minor of the graph as a subgraph, in an effort to reduce the complexity of the minor embedding problem. Any graph that can be embedded into GG will be embeddable into a member of the MSC. Focusing on embedding into the hardware graph of commercially available quantum annealers, we establish the MSC for a particular known virtual hardware, whichmore » is a complete bipartite graph. Furthermore, we show that the complete bipartite graph K N,N has a MSC of N minors, from which K N+1 is identified as the largest clique minor of K N,N. In the case of determining the largest clique minor of hardware with faults we briefly discussed this open question.« less

Spectrum of walk matrix for Koch network and its application

NASA Astrophysics Data System (ADS)

Xie, Pinchen; Lin, Yuan; Zhang, Zhongzhi

2015-06-01

Various structural and dynamical properties of a network are encoded in the eigenvalues of walk matrix describing random walks on the network. In this paper, we study the spectra of walk matrix of the Koch network, which displays the prominent scale-free and small-world features. Utilizing the particular architecture of the network, we obtain all the eigenvalues and their corresponding multiplicities. Based on the link between the eigenvalues of walk matrix and random target access time defined as the expected time for a walker going from an arbitrary node to another one selected randomly according to the steady-state distribution, we then derive an explicit solution to the random target access time for random walks on the Koch network. Finally, we corroborate our computation for the eigenvalues by enumerating spanning trees in the Koch network, using the connection governing eigenvalues and spanning trees, where a spanning tree of a network is a subgraph of the network, that is, a tree containing all the nodes.

Spatial fingerprints of community structure in human interaction network for an extensive set of large-scale regions.

PubMed

Kallus, Zsófia; Barankai, Norbert; Szüle, János; Vattay, Gábor

2015-01-01

Human interaction networks inferred from country-wide telephone activity recordings were recently used to redraw political maps by projecting their topological partitions into geographical space. The results showed remarkable spatial cohesiveness of the network communities and a significant overlap between the redrawn and the administrative borders. Here we present a similar analysis based on one of the most popular online social networks represented by the ties between more than 5.8 million of its geo-located users. The worldwide coverage of their measured activity allowed us to analyze the large-scale regional subgraphs of entire continents and an extensive set of examples for single countries. We present results for North and South America, Europe and Asia. In our analysis we used the well-established method of modularity clustering after an aggregation of the individual links into a weighted graph connecting equal-area geographical pixels. Our results show fingerprints of both of the opposing forces of dividing local conflicts and of uniting cross-cultural trends of globalization.

Augmenting computer networks

NASA Technical Reports Server (NTRS)

Bokhari, S. H.; Raza, A. D.

1984-01-01

Three methods of augmenting computer networks by adding at most one link per processor are discussed: (1) A tree of N nodes may be augmented such that the resulting graph has diameter no greater than 4log sub 2((N+2)/3)-2. Thi O(N(3)) algorithm can be applied to any spanning tree of a connected graph to reduce the diameter of that graph to O(log N); (2) Given a binary tree T and a chain C of N nodes each, C may be augmented to produce C so that T is a subgraph of C. This algorithm is O(N) and may be used to produce augmented chains or rings that have diameter no greater than 2log sub 2((N+2)/3) and are planar; (3) Any rectangular two-dimensional 4 (8) nearest neighbor array of size N = 2(k) may be augmented so that it can emulate a single step shuffle-exchange network of size N/2 in 3(t) time steps.

Applied Graph-Mining Algorithms to Study Biomolecular Interaction Networks

PubMed Central

2014-01-01

Protein-protein interaction (PPI) networks carry vital information on the organization of molecular interactions in cellular systems. The identification of functionally relevant modules in PPI networks is one of the most important applications of biological network analysis. Computational analysis is becoming an indispensable tool to understand large-scale biomolecular interaction networks. Several types of computational methods have been developed and employed for the analysis of PPI networks. Of these computational methods, graph comparison and module detection are the two most commonly used strategies. This review summarizes current literature on graph kernel and graph alignment methods for graph comparison strategies, as well as module detection approaches including seed-and-extend, hierarchical clustering, optimization-based, probabilistic, and frequent subgraph methods. Herein, we provide a comprehensive review of the major algorithms employed under each theme, including our recently published frequent subgraph method, for detecting functional modules commonly shared across multiple cancer PPI networks. PMID:24800226

Predictions of first passage times in sparse discrete fracture networks using graph-based reductions

NASA Astrophysics Data System (ADS)

Hyman, J.; Hagberg, A.; Srinivasan, G.; Mohd-Yusof, J.; Viswanathan, H. S.

2017-12-01

We present a graph-based methodology to reduce the computational cost of obtaining first passage times through sparse fracture networks. We derive graph representations of generic three-dimensional discrete fracture networks (DFNs) using the DFN topology and flow boundary conditions. Subgraphs corresponding to the union of the k shortest paths between the inflow and outflow boundaries are identified and transport on their equivalent subnetworks is compared to transport through the full network. The number of paths included in the subgraphs is based on the scaling behavior of the number of edges in the graph with the number of shortest paths. First passage times through the subnetworks are in good agreement with those obtained in the full network, both for individual realizations and in distribution. Accurate estimates of first passage times are obtained with an order of magnitude reduction of CPU time and mesh size using the proposed method.

Predictions of first passage times in sparse discrete fracture networks using graph-based reductions

NASA Astrophysics Data System (ADS)

Hyman, Jeffrey D.; Hagberg, Aric; Srinivasan, Gowri; Mohd-Yusof, Jamaludin; Viswanathan, Hari

2017-07-01

We present a graph-based methodology to reduce the computational cost of obtaining first passage times through sparse fracture networks. We derive graph representations of generic three-dimensional discrete fracture networks (DFNs) using the DFN topology and flow boundary conditions. Subgraphs corresponding to the union of the k shortest paths between the inflow and outflow boundaries are identified and transport on their equivalent subnetworks is compared to transport through the full network. The number of paths included in the subgraphs is based on the scaling behavior of the number of edges in the graph with the number of shortest paths. First passage times through the subnetworks are in good agreement with those obtained in the full network, both for individual realizations and in distribution. Accurate estimates of first passage times are obtained with an order of magnitude reduction of CPU time and mesh size using the proposed method.

Prediction of missing common genes for disease pairs using network based module separation on incomplete human interactome.

PubMed

Akram, Pakeeza; Liao, Li

2017-12-06

Identification of common genes associated with comorbid diseases can be critical in understanding their pathobiological mechanism. This work presents a novel method to predict missing common genes associated with a disease pair. Searching for missing common genes is formulated as an optimization problem to minimize network based module separation from two subgraphs produced by mapping genes associated with disease onto the interactome. Using cross validation on more than 600 disease pairs, our method achieves significantly higher average receiver operating characteristic ROC Score of 0.95 compared to a baseline ROC score 0.60 using randomized data. Missing common genes prediction is aimed to complete gene set associated with comorbid disease for better understanding of biological intervention. It will also be useful for gene targeted therapeutics related to comorbid diseases. This method can be further considered for prediction of missing edges to complete the subgraph associated with disease pair.

Locating influential nodes in complex networks

PubMed Central

Malliaros, Fragkiskos D.; Rossi, Maria-Evgenia G.; Vazirgiannis, Michalis

2016-01-01

Understanding and controlling spreading processes in networks is an important topic with many diverse applications, including information dissemination, disease propagation and viral marketing. It is of crucial importance to identify which entities act as influential spreaders that can propagate information to a large portion of the network, in order to ensure efficient information diffusion, optimize available resources or even control the spreading. In this work, we capitalize on the properties of the K-truss decomposition, a triangle-based extension of the core decomposition of graphs, to locate individual influential nodes. Our analysis on real networks indicates that the nodes belonging to the maximal K-truss subgraph show better spreading behavior compared to previously used importance criteria, including node degree and k-core index, leading to faster and wider epidemic spreading. We further show that nodes belonging to such dense subgraphs, dominate the small set of nodes that achieve the optimal spreading in the network. PMID:26776455

Using new edges for anomaly detection in computer networks

DOEpatents

Neil, Joshua Charles

2017-07-04

Creation of new edges in a network may be used as an indication of a potential attack on the network. Historical data of a frequency with which nodes in a network create and receive new edges may be analyzed. Baseline models of behavior among the edges in the network may be established based on the analysis of the historical data. A new edge that deviates from a respective baseline model by more than a predetermined threshold during a time window may be detected. The new edge may be flagged as potentially anomalous when the deviation from the respective baseline model is detected. Probabilities for both new and existing edges may be obtained for all edges in a path or other subgraph. The probabilities may then be combined to obtain a score for the path or other subgraph. A threshold may be obtained by calculating an empirical distribution of the scores under historical conditions.

Generalized monogamy of contextual inequalities from the no-disturbance principle.

PubMed

Ramanathan, Ravishankar; Soeda, Akihito; Kurzyński, Paweł; Kaszlikowski, Dagomir

2012-08-03

In this Letter, we demonstrate that the property of monogamy of Bell violations seen for no-signaling correlations in composite systems can be generalized to the monogamy of contextuality in single systems obeying the Gleason property of no disturbance. We show how one can construct monogamies for contextual inequalities by using the graph-theoretic technique of vertex decomposition of a graph representing a set of measurements into subgraphs of suitable independence numbers that themselves admit a joint probability distribution. After establishing that all the subgraphs that are chordal graphs admit a joint probability distribution, we formulate a precise graph-theoretic condition that gives rise to the monogamy of contextuality. We also show how such monogamies arise within quantum theory for a single four-dimensional system and interpret violation of these relations in terms of a violation of causality. These monogamies can be tested with current experimental techniques.

Using new edges for anomaly detection in computer networks

DOEpatents

Neil, Joshua Charles

2015-05-19

Creation of new edges in a network may be used as an indication of a potential attack on the network. Historical data of a frequency with which nodes in a network create and receive new edges may be analyzed. Baseline models of behavior among the edges in the network may be established based on the analysis of the historical data. A new edge that deviates from a respective baseline model by more than a predetermined threshold during a time window may be detected. The new edge may be flagged as potentially anomalous when the deviation from the respective baseline model is detected. Probabilities for both new and existing edges may be obtained for all edges in a path or other subgraph. The probabilities may then be combined to obtain a score for the path or other subgraph. A threshold may be obtained by calculating an empirical distribution of the scores under historical conditions.

CUDA Enabled Graph Subset Examiner

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnston, Jeremy T.

2016-12-22

Finding Godsil-McKay switching sets in graphs is one way to demonstrate that a specific graph is not determined by its spectrum--the eigenvalues of its adjacency matrix. An important area of active research in pure mathematics is determining which graphs are determined by their spectra, i.e. when the spectrum of the adjacency matrix uniquely determines the underlying graph. We are interested in exploring the spectra of graphs in the Johnson scheme and specifically seek to determine which of these graphs are determined by their spectra. Given a graph G, a Godsil-McKay switching set is an induced subgraph H on 2k verticesmore » with the following properties: I) H is regular, ii) every vertex in G/H is adjacent to either 0, k, or 2k vertices of H, and iii) at least one vertex in G/H is adjacent to k vertices in H. The software package examines each subset of a user specified size to determine whether or not it satisfies those 3 conditions. The software makes use of the massive parallel processing power of CUDA enabled GPUs. It also exploits the vertex transitivity of graphs in the Johnson scheme by reasoning that if G has a Godsil-McKay switching set, then it has a switching set which includes vertex 1. While the code (in its current state) is tuned to this specific problem, the method of examining each induced subgraph of G can be easily re-written to check for any user specified conditions on the subgraphs and can therefore be used much more broadly.« less

Electrode structure for uniform corona discharge

NASA Technical Reports Server (NTRS)

Gange, R. A.; Steinmetz, C. C.

1976-01-01

Single corona-discharge needle is used to apply uniform charge to thermoplastic medium in holograph-storage system. Needle is connected to flat transparent electrode that is parallel to thermoplastic.

Derivatives in discrete mathematics: a novel graph-theoretical invariant for generating new 2/3D molecular descriptors. I. Theory and QSPR application.

PubMed

Marrero-Ponce, Yovani; Santiago, Oscar Martínez; López, Yoan Martínez; Barigye, Stephen J; Torrens, Francisco

2012-11-01

In this report, we present a new mathematical approach for describing chemical structures of organic molecules at atomic-molecular level, proposing for the first time the use of the concept of the derivative ([Formula: see text]) of a molecular graph (MG) with respect to a given event (E), to obtain a new family of molecular descriptors (MDs). With this purpose, a new matrix representation of the MG, which generalizes graph's theory's traditional incidence matrix, is introduced. This matrix, denominated the generalized incidence matrix, Q, arises from the Boolean representation of molecular sub-graphs that participate in the formation of the graph molecular skeleton MG and could be complete (representing all possible connected sub-graphs) or constitute sub-graphs of determined orders or types as well as a combination of these. The Q matrix is a non-quadratic and unsymmetrical in nature, its columns (n) and rows (m) are conditions (letters) and collection of conditions (words) with which the event occurs. This non-quadratic and unsymmetrical matrix is transformed, by algebraic manipulation, to a quadratic and symmetric matrix known as relations frequency matrix, F, which characterizes the participation intensity of the conditions (letters) in the events (words). With F, we calculate the derivative over a pair of atomic nuclei. The local index for the atomic nuclei i, Δ(i), can therefore be obtained as a linear combination of all the pair derivatives of the atomic nuclei i with all the rest of the j's atomic nuclei. Here, we also define new strategies that generalize the present form of obtaining global or local (group or atom-type) invariants from atomic contributions (local vertex invariants, LOVIs). In respect to this, metric (norms), means and statistical invariants are introduced. These invariants are applied to a vector whose components are the values Δ(i) for the atomic nuclei of the molecule or its fragments. Moreover, with the purpose of differentiating among different atoms, an atomic weighting scheme (atom-type labels) is used in the formation of the matrix Q or in LOVIs state. The obtained indices were utilized to describe the partition coefficient (Log P) and the reactivity index (Log K) of the 34 derivatives of 2-furylethylenes. In all the cases, our MDs showed better statistical results than those previously obtained using some of the most used families of MDs in chemometric practice. Therefore, it has been demonstrated to that the proposed MDs are useful in molecular design and permit obtaining easier and robust mathematical models than the majority of those reported in the literature. All this range of mentioned possibilities open "the doors" to the creation of a new family of MDs, using the graph derivative, and avail a new tool for QSAR/QSPR and molecular diversity/similarity studies.

Impact of Beamforming on the Path Connectivity in Cognitive Radio Ad Hoc Networks

PubMed Central

Dung, Le The; Hieu, Tran Dinh; Choi, Seong-Gon; Kim, Byung-Seo; An, Beongku

2017-01-01

This paper investigates the impact of using directional antennas and beamforming schemes on the connectivity of cognitive radio ad hoc networks (CRAHNs). Specifically, considering that secondary users use two kinds of directional antennas, i.e., uniform linear array (ULA) and uniform circular array (UCA) antennas, and two different beamforming schemes, i.e., randomized beamforming and center-directed to communicate with each other, we study the connectivity of all combination pairs of directional antennas and beamforming schemes and compare their performances to those of omnidirectional antennas. The results obtained in this paper show that, compared with omnidirectional transmission, beamforming transmission only benefits the connectivity when the density of secondary user is moderate. Moreover, the combination of UCA and randomized beamforming scheme gives the highest path connectivity in all evaluating scenarios. Finally, the number of antenna elements and degree of path loss greatly affect path connectivity in CRAHNs. PMID:28346377

RAG-3D: A search tool for RNA 3D substructures

DOE PAGES

Zahran, Mai; Sevim Bayrak, Cigdem; Elmetwaly, Shereef; ...

2015-08-24

In this study, to address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D—a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool—designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally describedmore » in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding.« less

RAG-3D: a search tool for RNA 3D substructures

PubMed Central

Zahran, Mai; Sevim Bayrak, Cigdem; Elmetwaly, Shereef; Schlick, Tamar

2015-01-01

To address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D—a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool—designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally described in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding. PMID:26304547

RAG-3D: A search tool for RNA 3D substructures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zahran, Mai; Sevim Bayrak, Cigdem; Elmetwaly, Shereef

In this study, to address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D—a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool—designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally describedmore » in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding.« less

Effect of Cooling Units on the Performance of an Automotive Exhaust-Based Thermoelectric Generator

NASA Astrophysics Data System (ADS)

Su, C. Q.; Zhu, D. C.; Deng, Y. D.; Wang, Y. P.; Liu, X.

2017-05-01

Currently, automotive exhaust-based thermoelectric generators (AETEGs) are a hot topic in energy recovery. In order to investigate the influence of coolant flow rate, coolant flow direction and cooling unit arrangement in the AETEG, a thermoelectric generator (TEG) model and a related test bench are constructed. Water cooling is adopted in this study. Due to the non-uniformity of the surface temperature of the heat source, the coolant flow direction would affect the output performance of the TEG. Changing the volumetric flow rate of coolant can increase the output power of multi-modules connected in series or/and parallel as it can improve the temperature uniformity of the cooling unit. Since the temperature uniformity of the cooling unit has a strong influence on the output power, two cooling units are connected in series or parallel to research the effect of cooling unit arrangements on the maximum output power of the TEG. Experimental and theoretical analyses reveal that the net output power is generally higher with cooling units connected in parallel than cooling units connected in series in the cooling system with two cooling units.

Subgraph augmented non-negative tensor factorization (SANTF) for modeling clinical narrative text

PubMed Central

Xin, Yu; Hochberg, Ephraim; Joshi, Rohit; Uzuner, Ozlem; Szolovits, Peter

2015-01-01

Objective Extracting medical knowledge from electronic medical records requires automated approaches to combat scalability limitations and selection biases. However, existing machine learning approaches are often regarded by clinicians as black boxes. Moreover, training data for these automated approaches at often sparsely annotated at best. The authors target unsupervised learning for modeling clinical narrative text, aiming at improving both accuracy and interpretability. Methods The authors introduce a novel framework named subgraph augmented non-negative tensor factorization (SANTF). In addition to relying on atomic features (e.g., words in clinical narrative text), SANTF automatically mines higher-order features (e.g., relations of lymphoid cells expressing antigens) from clinical narrative text by converting sentences into a graph representation and identifying important subgraphs. The authors compose a tensor using patients, higher-order features, and atomic features as its respective modes. We then apply non-negative tensor factorization to cluster patients, and simultaneously identify latent groups of higher-order features that link to patient clusters, as in clinical guidelines where a panel of immunophenotypic features and laboratory results are used to specify diagnostic criteria. Results and Conclusion SANTF demonstrated over 10% improvement in averaged F-measure on patient clustering compared to widely used non-negative matrix factorization (NMF) and k-means clustering methods. Multiple baselines were established by modeling patient data using patient-by-features matrices with different feature configurations and then performing NMF or k-means to cluster patients. Feature analysis identified latent groups of higher-order features that lead to medical insights. We also found that the latent groups of atomic features help to better correlate the latent groups of higher-order features. PMID:25862765

Constraints on signaling network logic reveal functional subgraphs on Multiple Myeloma OMIC data.

PubMed

Miannay, Bertrand; Minvielle, Stéphane; Magrangeas, Florence; Guziolowski, Carito

2018-03-21

The integration of gene expression profiles (GEPs) and large-scale biological networks derived from pathways databases is a subject which is being widely explored. Existing methods are based on network distance measures among significantly measured species. Only a small number of them include the directionality and underlying logic existing in biological networks. In this study we approach the GEP-networks integration problem by considering the network logic, however our approach does not require a prior species selection according to their gene expression level. We start by modeling the biological network representing its underlying logic using Logic Programming. This model points to reachable network discrete states that maximize a notion of harmony between the molecular species active or inactive possible states and the directionality of the pathways reactions according to their activator or inhibitor control role. Only then, we confront these network states with the GEP. From this confrontation independent graph components are derived, each of them related to a fixed and optimal assignment of active or inactive states. These components allow us to decompose a large-scale network into subgraphs and their molecular species state assignments have different degrees of similarity when compared to the same GEP. We apply our method to study the set of possible states derived from a subgraph from the NCI-PID Pathway Interaction Database. This graph links Multiple Myeloma (MM) genes to known receptors for this blood cancer. We discover that the NCI-PID MM graph had 15 independent components, and when confronted to 611 MM GEPs, we find 1 component as being more specific to represent the difference between cancer and healthy profiles.

Exploring the structure and function of temporal networks with dynamic graphlets

PubMed Central

Hulovatyy, Y.; Chen, H.; Milenković, T.

2015-01-01

Motivation: With increasing availability of temporal real-world networks, how to efficiently study these data? One can model a temporal network as a single aggregate static network, or as a series of time-specific snapshots, each being an aggregate static network over the corresponding time window. Then, one can use established methods for static analysis on the resulting aggregate network(s), but losing in the process valuable temporal information either completely, or at the interface between different snapshots, respectively. Here, we develop a novel approach for studying a temporal network more explicitly, by capturing inter-snapshot relationships. Results: We base our methodology on well-established graphlets (subgraphs), which have been proven in numerous contexts in static network research. We develop new theory to allow for graphlet-based analyses of temporal networks. Our new notion of dynamic graphlets is different from existing dynamic network approaches that are based on temporal motifs (statistically significant subgraphs). The latter have limitations: their results depend on the choice of a null network model that is required to evaluate the significance of a subgraph, and choosing a good null model is non-trivial. Our dynamic graphlets overcome the limitations of the temporal motifs. Also, when we aim to characterize the structure and function of an entire temporal network or of individual nodes, our dynamic graphlets outperform the static graphlets. Clearly, accounting for temporal information helps. We apply dynamic graphlets to temporal age-specific molecular network data to deepen our limited knowledge about human aging. Availability and implementation: http://www.nd.edu/∼cone/DG. Contact: tmilenko@nd.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26072480

Predictions of first passage times in sparse discrete fracture networks using graph-based reductions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hyman, Jeffrey De'Haven; Hagberg, Aric Arild; Mohd-Yusof, Jamaludin

Here, we present a graph-based methodology to reduce the computational cost of obtaining first passage times through sparse fracture networks. We also derive graph representations of generic three-dimensional discrete fracture networks (DFNs) using the DFN topology and flow boundary conditions. Subgraphs corresponding to the union of the k shortest paths between the inflow and outflow boundaries are identified and transport on their equivalent subnetworks is compared to transport through the full network. The number of paths included in the subgraphs is based on the scaling behavior of the number of edges in the graph with the number of shortest paths.more » First passage times through the subnetworks are in good agreement with those obtained in the full network, both for individual realizations and in distribution. We obtain accurate estimates of first passage times with an order of magnitude reduction of CPU time and mesh size using the proposed method.« less

Predictions of first passage times in sparse discrete fracture networks using graph-based reductions

DOE PAGES

Hyman, Jeffrey De'Haven; Hagberg, Aric Arild; Mohd-Yusof, Jamaludin; ...

2017-07-10

Here, we present a graph-based methodology to reduce the computational cost of obtaining first passage times through sparse fracture networks. We also derive graph representations of generic three-dimensional discrete fracture networks (DFNs) using the DFN topology and flow boundary conditions. Subgraphs corresponding to the union of the k shortest paths between the inflow and outflow boundaries are identified and transport on their equivalent subnetworks is compared to transport through the full network. The number of paths included in the subgraphs is based on the scaling behavior of the number of edges in the graph with the number of shortest paths.more » First passage times through the subnetworks are in good agreement with those obtained in the full network, both for individual realizations and in distribution. We obtain accurate estimates of first passage times with an order of magnitude reduction of CPU time and mesh size using the proposed method.« less

Isolation and Connectivity in Random Geometric Graphs with Self-similar Intensity Measures

NASA Astrophysics Data System (ADS)

Dettmann, Carl P.

2018-05-01

Random geometric graphs consist of randomly distributed nodes (points), with pairs of nodes within a given mutual distance linked. In the usual model the distribution of nodes is uniform on a square, and in the limit of infinitely many nodes and shrinking linking range, the number of isolated nodes is Poisson distributed, and the probability of no isolated nodes is equal to the probability the whole graph is connected. Here we examine these properties for several self-similar node distributions, including smooth and fractal, uniform and nonuniform, and finitely ramified or otherwise. We show that nonuniformity can break the Poisson distribution property, but it strengthens the link between isolation and connectivity. It also stretches out the connectivity transition. Finite ramification is another mechanism for lack of connectivity. The same considerations apply to fractal distributions as smooth, with some technical differences in evaluation of the integrals and analytical arguments.

Results on Vertex Degree and K-Connectivity in Uniform S-Intersection Graphs

DTIC Science & Technology

2014-01-01

distribution. A uniform s-intersection graph models the topology of a secure wireless sensor network employing the widely used s-composite key predistribution scheme. Our theoretical findings is also confirmed by numerical results.

Research on Creep Relaxation Non-uniformity and Effect on Performance of Combined Rotor

NASA Astrophysics Data System (ADS)

Liu, Qingya; He, Jingfei; Zhao, Lijia

2017-11-01

The combined rotor of gas turbine is connected by a certain number of rod bolts. It works in the high temperature environment for a long time, and the rod bolts will creep and relax. Under the influence of elastic interaction, the loss of pretightening force of rod bolts at different positions is non-uniform, which will cause the connection of the combined rotor to be out of tune. In this paper, the creep relaxation non-uniformity model for a class F heavy duty gas turbine is established. On the basis of this, the performance degradation and structural strength change of combined rotor resulting from creep relaxation non-uniformity of rod bolts are studied. The results show that the ratio of preload mistuning increases with time and then converges, and there is a threshold inflection point in about seven thousand hours.

Finding undetected protein associations in cell signaling by belief propagation.

PubMed

Bailly-Bechet, M; Borgs, C; Braunstein, A; Chayes, J; Dagkessamanskaia, A; François, J-M; Zecchina, R

2011-01-11

External information propagates in the cell mainly through signaling cascades and transcriptional activation, allowing it to react to a wide spectrum of environmental changes. High-throughput experiments identify numerous molecular components of such cascades that may, however, interact through unknown partners. Some of them may be detected using data coming from the integration of a protein-protein interaction network and mRNA expression profiles. This inference problem can be mapped onto the problem of finding appropriate optimal connected subgraphs of a network defined by these datasets. The optimization procedure turns out to be computationally intractable in general. Here we present a new distributed algorithm for this task, inspired from statistical physics, and apply this scheme to alpha factor and drug perturbations data in yeast. We identify the role of the COS8 protein, a member of a gene family of previously unknown function, and validate the results by genetic experiments. The algorithm we present is specially suited for very large datasets, can run in parallel, and can be adapted to other problems in systems biology. On renowned benchmarks it outperforms other algorithms in the field.

Network Reliability: The effect of local network structure on diffusive processes

PubMed Central

Youssef, Mina; Khorramzadeh, Yasamin; Eubank, Stephen

2014-01-01

This paper re-introduces the network reliability polynomial – introduced by Moore and Shannon in 1956 – for studying the effect of network structure on the spread of diseases. We exhibit a representation of the polynomial that is well-suited for estimation by distributed simulation. We describe a collection of graphs derived from Erdős-Rényi and scale-free-like random graphs in which we have manipulated assortativity-by-degree and the number of triangles. We evaluate the network reliability for all these graphs under a reliability rule that is related to the expected size of a connected component. Through these extensive simulations, we show that for positively or neutrally assortative graphs, swapping edges to increase the number of triangles does not increase the network reliability. Also, positively assortative graphs are more reliable than neutral or disassortative graphs with the same number of edges. Moreover, we show the combined effect of both assortativity-by-degree and the presence of triangles on the critical point and the size of the smallest subgraph that is reliable. PMID:24329321

Research on Some Bus Transport Networks with Random Overlapping Clique Structure

NASA Astrophysics Data System (ADS)

Yang, Xu-Hua; Wang, Bo; Wang, Wan-Liang; Sun, You-Xian

2008-11-01

On the basis of investigating the statistical data of bus transport networks of three big cities in China, we propose that each bus route is a clique (maximal complete subgraph) and a bus transport network (BTN) consists of a lot of cliques, which intensively connect and overlap with each other. We study the network properties, which include the degree distribution, multiple edges' overlapping time distribution, distribution of the overlap size between any two overlapping cliques, distribution of the number of cliques that a node belongs to. Naturally, the cliques also constitute a network, with the overlapping nodes being their multiple links. We also research its network properties such as degree distribution, clustering, average path length, and so on. We propose that a BTN has the properties of random clique increment and random overlapping clique, at the same time, a BTN is a small-world network with highly clique-clustered and highly clique-overlapped. Finally, we introduce a BTN evolution model, whose simulation results agree well with the statistical laws that emerge in real BTNs.

Convergence analysis of directed signed networks via an M-matrix approach

NASA Astrophysics Data System (ADS)

Meng, Deyuan

2018-04-01

This paper aims at solving convergence problems on directed signed networks with multiple nodes, where interactions among nodes are described by signed digraphs. The convergence analysis is achieved by matrix-theoretic and graph-theoretic tools, in which M-matrices play a central role. The fundamental digon sign-symmetry assumption upon signed digraphs can be removed with the proposed analysis approach. Furthermore, necessary and sufficient conditions are established for semi-positive and positive stabilities of Laplacian matrices of signed digraphs, respectively. A benefit of this result is that given strong connectivity, a directed signed network can achieve bipartite consensus (or state stability) if and only if the signed digraph associated with it is structurally balanced (or unbalanced). If the interactions between nodes are described by a signed digraph only with spanning trees, a directed signed network can achieve interval bipartite consensus (or state stability) if and only if the signed digraph contains a structurally balanced (or unbalanced) rooted subgraph. Simulations are given to illustrate the developed results by considering signed networks associated with digon sign-unsymmetric signed digraphs.

Spatial Fingerprints of Community Structure in Human Interaction Network for an Extensive Set of Large-Scale Regions

PubMed Central

Kallus, Zsófia; Barankai, Norbert; Szüle, János; Vattay, Gábor

2015-01-01

Human interaction networks inferred from country-wide telephone activity recordings were recently used to redraw political maps by projecting their topological partitions into geographical space. The results showed remarkable spatial cohesiveness of the network communities and a significant overlap between the redrawn and the administrative borders. Here we present a similar analysis based on one of the most popular online social networks represented by the ties between more than 5.8 million of its geo-located users. The worldwide coverage of their measured activity allowed us to analyze the large-scale regional subgraphs of entire continents and an extensive set of examples for single countries. We present results for North and South America, Europe and Asia. In our analysis we used the well-established method of modularity clustering after an aggregation of the individual links into a weighted graph connecting equal-area geographical pixels. Our results show fingerprints of both of the opposing forces of dividing local conflicts and of uniting cross-cultural trends of globalization. PMID:25993329

Motif formation and industry specific topologies in the Japanese business firm network

NASA Astrophysics Data System (ADS)

Maluck, Julian; Donner, Reik V.; Takayasu, Hideki; Takayasu, Misako

2017-05-01

Motifs and roles are basic quantities for the characterization of interactions among 3-node subsets in complex networks. In this work, we investigate how the distribution of 3-node motifs can be influenced by modifying the rules of an evolving network model while keeping the statistics of simpler network characteristics, such as the link density and the degree distribution, invariant. We exemplify this problem for the special case of the Japanese Business Firm Network, where a well-studied and relatively simple yet realistic evolving network model is available, and compare the resulting motif distribution in the real-world and simulated networks. To better approximate the motif distribution of the real-world network in the model, we introduce both subgraph dependent and global additional rules. We find that a specific rule that allows only for the merging process between nodes with similar link directionality patterns reduces the observed excess of densely connected motifs with bidirectional links. Our study improves the mechanistic understanding of motif formation in evolving network models to better describe the characteristic features of real-world networks with a scale-free topology.

Top-K Interesting Subgraph Discovery in Information Networks

DTIC Science & Technology

2014-03-03

Integrative Biomarker Discovery for Breast Cancer Metastasis from Gene Expression and Protein Interaction Data Using Error-tolerant Pattern Mining” at...Jiawei Han¶ ∗Microsoft, India . Email: gmanish@microsoft.com †State University of New York at Buffalo. Email: jing@buffalo.edu ‡University of California

10 CFR Appendix H to Subpart B of... - Uniform Test Method for Measuring the Power Consumption of Television Sets

Code of Federal Regulations, 2014 CFR

2014-01-01

... connections (e.g., Wi-Fi and Ethernet), the TV shall be configured and connected to a single network source in... Hierarchy Priority Network connection type 1 Wi-Fi (Institution of Electrical and Electronics Engineers—IEEE...

10 CFR Appendix A to Subpart K of... - Uniform Test Method for Measuring the Energy Consumption of Distribution Transformers

Code of Federal Regulations, 2014 CFR

2014-01-01

... Uniform Test Method is used to test more than one unit of a basic model to determine the efficiency of... one ampere and the test current is limited to 15 percent of the winding current. Connect the... 10 Energy 3 2014-01-01 2014-01-01 false Uniform Test Method for Measuring the Energy Consumption...

A Smart Cage With Uniform Wireless Power Distribution in 3D for Enabling Long-Term Experiments With Freely Moving Animals.

PubMed

Mirbozorgi, S Abdollah; Bahrami, Hadi; Sawan, Mohamad; Gosselin, Benoit

2016-04-01

This paper presents a novel experimental chamber with uniform wireless power distribution in 3D for enabling long-term biomedical experiments with small freely moving animal subjects. The implemented power transmission chamber prototype is based on arrays of parallel resonators and multicoil inductive links, to form a novel and highly efficient wireless power transmission system. The power transmitter unit includes several identical resonators enclosed in a scalable array of overlapping square coils which are connected in parallel to provide uniform power distribution along x and y. Moreover, the proposed chamber uses two arrays of primary resonators, facing each other, and connected in parallel to achieve uniform power distribution along the z axis. Each surface includes 9 overlapped coils connected in parallel and implemented into two layers of FR4 printed circuit board. The chamber features a natural power localization mechanism, which simplifies its implementation and ease its operation by avoiding the need for active detection and control mechanisms. A single power surface based on the proposed approach can provide a power transfer efficiency (PTE) of 69% and a power delivered to the load (PDL) of 120 mW, for a separation distance of 4 cm, whereas the complete chamber prototype provides a uniform PTE of 59% and a PDL of 100 mW in 3D, everywhere inside the chamber with a size of 27×27×16 cm(3).

Latent geometry of bipartite networks

NASA Astrophysics Data System (ADS)

Kitsak, Maksim; Papadopoulos, Fragkiskos; Krioukov, Dmitri

2017-03-01

Despite the abundance of bipartite networked systems, their organizing principles are less studied compared to unipartite networks. Bipartite networks are often analyzed after projecting them onto one of the two sets of nodes. As a result of the projection, nodes of the same set are linked together if they have at least one neighbor in common in the bipartite network. Even though these projections allow one to study bipartite networks using tools developed for unipartite networks, one-mode projections lead to significant loss of information and artificial inflation of the projected network with fully connected subgraphs. Here we pursue a different approach for analyzing bipartite systems that is based on the observation that such systems have a latent metric structure: network nodes are points in a latent metric space, while connections are more likely to form between nodes separated by shorter distances. This approach has been developed for unipartite networks, and relatively little is known about its applicability to bipartite systems. Here, we fully analyze a simple latent-geometric model of bipartite networks and show that this model explains the peculiar structural properties of many real bipartite systems, including the distributions of common neighbors and bipartite clustering. We also analyze the geometric information loss in one-mode projections in this model and propose an efficient method to infer the latent pairwise distances between nodes. Uncovering the latent geometry underlying real bipartite networks can find applications in diverse domains, ranging from constructing efficient recommender systems to understanding cell metabolism.

New nut and sleeve improve flared connections

NASA Technical Reports Server (NTRS)

Garrard, J. S.

1965-01-01

Improved nut and sleeve of standard stainless steel flared tube connection allows forces on the mating surfaces to be uniformly applied. This can be applied to pressurized fluid systems such as refrigeration, air conditioning, and hydraulic systems.

Layer-by-layer growth of vertex graph of Penrose tiling

NASA Astrophysics Data System (ADS)

Shutov, A. V.; Maleev, A. V.

2017-09-01

The growth form for the vertex graph of Penrose tiling is found to be a regular decagon. The lower and upper bounds for this form, coinciding with it, are strictly proven. A fractal character of layer-by-layer growth is revealed for some subgraphs of the vertex graph of Penrose tiling.

Approximate Subgraph Isomorphism for Image Localization (Author’s Manuscript)

DTIC Science & Technology

2016-02-18

a working database for feature matching methods is nearly impossible to generate. In a proof of feasibility, Bansal et. al. [2] claim that overhead...of images in mountainous terrain. In Computer Vision–ECCV 2012, pages 517–530. Springer, 2012. 1 [2] M. Bansal , H. S. Sawhney, H. Cheng, and K

Mean Field Analysis of Stochastic Neural Network Models with Synaptic Depression

NASA Astrophysics Data System (ADS)

Yasuhiko Igarashi,; Masafumi Oizumi,; Masato Okada,

2010-08-01

We investigated the effects of synaptic depression on the macroscopic behavior of stochastic neural networks. Dynamical mean field equations were derived for such networks by taking the average of two stochastic variables: a firing-state variable and a synaptic variable. In these equations, the average product of thesevariables is decoupled as the product of their averages because the two stochastic variables are independent. We proved the independence of these two stochastic variables assuming that the synaptic weight Jij is of the order of 1/N with respect to the number of neurons N. Using these equations, we derived macroscopic steady-state equations for a network with uniform connections and for a ring attractor network with Mexican hat type connectivity and investigated the stability of the steady-state solutions. An oscillatory uniform state was observed in the network with uniform connections owing to a Hopf instability. For the ring network, high-frequency perturbations were shown not to affect system stability. Two mechanisms destabilize the inhomogeneous steady state, leading to two oscillatory states. A Turing instability leads to a rotating bump state, while a Hopf instability leads to an oscillatory bump state, which was previously unreported. Various oscillatory states take place in a network with synaptic depression depending on the strength of the interneuron connections.

Residuals-Based Subgraph Detection with Cue Vertices

DTIC Science & Technology

2015-11-30

Workshop, 2012, pp. 129–132. [5] M. E. J. Newman , “Finding community structure in networks using the eigenvectors of matrices,” Phys. Rev. E, vol. 74, no...from Data, vol. 1, no. 1, 2007. [7] M. W. Mahoney , L. Orecchia, and N. K. Vishnoi, “A spectral algorithm for improving graph partitions,” CoRR, vol. abs

Network Approach to Disease Diagnosis

NASA Astrophysics Data System (ADS)

Sharma, Amitabh; Bashan, Amir; Barabasi, Alber-Laszlo

2014-03-01

Human diseases could be viewed as perturbations of the underlying biological system. A thorough understanding of the topological and dynamical properties of the biological system is crucial to explain the mechanisms of many complex diseases. Recently network-based approaches have provided a framework for integrating multi-dimensional biological data that results in a better understanding of the pathophysiological state of complex diseases. Here we provide a network-based framework to improve the diagnosis of complex diseases. This framework is based on the integration of transcriptomics and the interactome. We analyze the overlap between the differentially expressed (DE) genes and disease genes (DGs) based on their locations in the molecular interaction network (''interactome''). Disease genes and their protein products tend to be much more highly connected than random, hence defining a disease sub-graph (called disease module) in the interactome. DE genes, even though different from the known set of DGs, may be significantly associated with the disease when considering their closeness to the disease module in the interactome. This new network approach holds the promise to improve the diagnosis of patients who cannot be diagnosed using conventional tools. Support was provided by HL066289 and HL105339 grants from the U.S. National Institutes of Health.

PLACNETw: a web-based tool for plasmid reconstruction from bacterial genomes.

PubMed

Vielva, Luis; de Toro, María; Lanza, Val F; de la Cruz, Fernando

2017-12-01

PLACNET is a graph-based tool for reconstruction of plasmids from next generation sequence pair-end datasets. PLACNET graphs contain two types of nodes (assembled contigs and reference genomes) and two types of edges (scaffold links and homology to references). Manual pruning of the graphs is a necessary requirement in PLACNET, but this is difficult for users without solid bioinformatic background. PLACNETw, a webtool based on PLACNET, provides an interactive graphic interface, automates BLAST searches, and extracts the relevant information for decision making. It allows a user with domain expertise to visualize the scaffold graphs and related information of contigs as well as reference sequences, so that the pruning operations can be done interactively from a personal computer without the need for additional tools. After successful pruning, each plasmid becomes a separate connected component subgraph. The resulting data are automatically downloaded by the user. PLACNETw is freely available at https://castillo.dicom.unican.es/upload/. delacruz@unican.es. A tutorial video and several solved examples are available at https://castillo.dicom.unican.es/placnetw_video/ and https://castillo.dicom.unican.es/examples/. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Streaming data analytics via message passing with application to graph algorithms

DOE PAGES

Plimpton, Steven J.; Shead, Tim

2014-05-06

The need to process streaming data, which arrives continuously at high-volume in real-time, arises in a variety of contexts including data produced by experiments, collections of environmental or network sensors, and running simulations. Streaming data can also be formulated as queries or transactions which operate on a large dynamic data store, e.g. a distributed database. We describe a lightweight, portable framework named PHISH which enables a set of independent processes to compute on a stream of data in a distributed-memory parallel manner. Datums are routed between processes in patterns defined by the application. PHISH can run on top of eithermore » message-passing via MPI or sockets via ZMQ. The former means streaming computations can be run on any parallel machine which supports MPI; the latter allows them to run on a heterogeneous, geographically dispersed network of machines. We illustrate how PHISH can support streaming MapReduce operations, and describe streaming versions of three algorithms for large, sparse graph analytics: triangle enumeration, subgraph isomorphism matching, and connected component finding. Lastly, we also provide benchmark timings for MPI versus socket performance of several kernel operations useful in streaming algorithms.« less

Crystalline cellulose elastic modulus predicted by atomistic models of uniform deformation and nanoscale indentation

Treesearch

Xiawa Wu; Robert J. Moon; Ashlie Martini

2013-01-01

The elastic modulus of cellulose Iß in the axial and transverse directions was obtained from atomistic simulations using both the standard uniform deformation approach and a complementary approach based on nanoscale indentation. This allowed comparisons between the methods and closer connectivity to experimental measurement techniques. A reactive...

Optimization of the Hot Forging Processing Parameters for Powder Metallurgy Fe-Cu-C Connecting Rods Based on Finite Element Simulation

NASA Astrophysics Data System (ADS)

Li, Fengxian; Yi, Jianhong; Eckert, Jürgen

2017-12-01

Powder forged connecting rods have the problem of non-uniform density distributions because of their complex geometric shape. The densification behaviors of powder metallurgy (PM) connecting rod preforms during hot forging processes play a significant role in optimizing the connecting rod quality. The deformation behaviors of a connecting rod preform, a Fe-3Cu-0.5C (wt pct) alloy compacted and sintered by the powder metallurgy route (PM Fe-Cu-C), were investigated using the finite element method, while damage and friction behaviors of the material were considered in the complicated forging process. The calculated results agree well with the experimental results. The relationship between the processing parameters of hot forging and the relative density of the connecting rod was revealed. The results showed that the relative density of the hot forged connecting rod at the central shank changed significantly compared with the relative density at the big end and at the small end. Moreover, the relative density of the connecting rod was sensitive to the processing parameters such as the forging velocity and the initial density of the preform. The optimum forging processing parameters were determined and presented by using an orthogonal design method. This work suggests that the processing parameters can be optimized to prepare a connecting rod with uniform density distribution and can help to better meet the requirements of the connecting rod industry.

UNIFORMLY MOST POWERFUL BAYESIAN TESTS

PubMed Central

Johnson, Valen E.

2014-01-01

Uniformly most powerful tests are statistical hypothesis tests that provide the greatest power against a fixed null hypothesis among all tests of a given size. In this article, the notion of uniformly most powerful tests is extended to the Bayesian setting by defining uniformly most powerful Bayesian tests to be tests that maximize the probability that the Bayes factor, in favor of the alternative hypothesis, exceeds a specified threshold. Like their classical counterpart, uniformly most powerful Bayesian tests are most easily defined in one-parameter exponential family models, although extensions outside of this class are possible. The connection between uniformly most powerful tests and uniformly most powerful Bayesian tests can be used to provide an approximate calibration between p-values and Bayes factors. Finally, issues regarding the strong dependence of resulting Bayes factors and p-values on sample size are discussed. PMID:24659829

Betweenness centrality in a weighted network

NASA Astrophysics Data System (ADS)

Wang, Huijuan; Hernandez, Javier Martin; van Mieghem, Piet

2008-04-01

When transport in networks follows the shortest paths, the union of all shortest path trees G∪SPT can be regarded as the “transport overlay network.” Overlay networks such as peer-to-peer networks or virtual private networks can be considered as a subgraph of G∪SPT . The traffic through the network is examined by the betweenness Bl of links in the overlay G∪SPT . The strength of disorder can be controlled by, e.g., tuning the extreme value index α of the independent and identically distributed polynomial link weights. In the strong disorder limit (α→0) , all transport flows over a critical backbone, the minimum spanning tree (MST). We investigate the betweenness distributions of wide classes of trees, such as the MST of those well-known network models and of various real-world complex networks. All these trees with different degree distributions (e.g., uniform, exponential, or power law) are found to possess a power law betweenness distribution Pr[Bl=j]˜j-c . The exponent c seems to be positively correlated with the degree variance of the tree and to be insensitive of the size N of a network. In the weak disorder regime, transport in the network traverses many links. We show that a link with smaller link weight tends to carry more traffic. This negative correlation between link weight and betweenness depends on α and the structure of the underlying topology.

10 CFR Appendix Z to Subpart B of... - Uniform Test Method for Measuring the Energy Consumption of External Power Supplies

Code of Federal Regulations, 2012 CFR

2012-01-01

... operation when the external power supply is connected to the main electricity supply and the output is (or... external power supply is connected to the main electricity supply and the output is (or “all outputs are... switches, in which the external power supply is (1) connected to the main electricity supply; (2) the...

10 CFR Appendix Z to Subpart B of... - Uniform Test Method for Measuring the Energy Consumption of External Power Supplies

Code of Federal Regulations, 2013 CFR

2013-01-01

... operation when the external power supply is connected to the main electricity supply and the output is (or... external power supply is connected to the main electricity supply and the output is (or “all outputs are... switches, in which the external power supply is (1) connected to the main electricity supply; (2) the...

10 CFR Appendix Z to Subpart B of... - Uniform Test Method for Measuring the Energy Consumption of External Power Supplies

Code of Federal Regulations, 2014 CFR

2014-01-01

... operation when the external power supply is connected to the main electricity supply and the output is (or... external power supply is connected to the main electricity supply and the output is (or “all outputs are... switches, in which the external power supply is (1) connected to the main electricity supply; (2) the...

Protein-protein interaction network-based detection of functionally similar proteins within species.

PubMed

Song, Baoxing; Wang, Fen; Guo, Yang; Sang, Qing; Liu, Min; Li, Dengyun; Fang, Wei; Zhang, Deli

2012-07-01

Although functionally similar proteins across species have been widely studied, functionally similar proteins within species showing low sequence similarity have not been examined in detail. Identification of these proteins is of significant importance for understanding biological functions, evolution of protein families, progression of co-evolution, and convergent evolution and others which cannot be obtained by detection of functionally similar proteins across species. Here, we explored a method of detecting functionally similar proteins within species based on graph theory. After denoting protein-protein interaction networks using graphs, we split the graphs into subgraphs using the 1-hop method. Proteins with functional similarities in a species were detected using a method of modified shortest path to compare these subgraphs and to find the eligible optimal results. Using seven protein-protein interaction networks and this method, some functionally similar proteins with low sequence similarity that cannot detected by sequence alignment were identified. By analyzing the results, we found that, sometimes, it is difficult to separate homologous from convergent evolution. Evaluation of the performance of our method by gene ontology term overlap showed that the precision of our method was excellent. Copyright © 2012 Wiley Periodicals, Inc.

Towards comprehensive structural motif mining for better fold annotation in the "twilight zone" of sequence dissimilarity

PubMed Central

Jia, Yi; Huan, Jun; Buhr, Vincent; Zhang, Jintao; Carayannopoulos, Leonidas N

2009-01-01

Background Automatic identification of structure fingerprints from a group of diverse protein structures is challenging, especially for proteins whose divergent amino acid sequences may fall into the "twilight-" or "midnight-" zones where pair-wise sequence identities to known sequences fall below 25% and sequence-based functional annotations often fail. Results Here we report a novel graph database mining method and demonstrate its application to protein structure pattern identification and structure classification. The biologic motivation of our study is to recognize common structure patterns in "immunoevasins", proteins mediating virus evasion of host immune defense. Our experimental study, using both viral and non-viral proteins, demonstrates the efficiency and efficacy of the proposed method. Conclusion We present a theoretic framework, offer a practical software implementation for incorporating prior domain knowledge, such as substitution matrices as studied here, and devise an efficient algorithm to identify approximate matched frequent subgraphs. By doing so, we significantly expanded the analytical power of sophisticated data mining algorithms in dealing with large volume of complicated and noisy protein structure data. And without loss of generality, choice of appropriate compatibility matrices allows our method to be easily employed in domains where subgraph labels have some uncertainty. PMID:19208148

Aligning Biomolecular Networks Using Modular Graph Kernels

NASA Astrophysics Data System (ADS)

Towfic, Fadi; Greenlee, M. Heather West; Honavar, Vasant

Comparative analysis of biomolecular networks constructed using measurements from different conditions, tissues, and organisms offer a powerful approach to understanding the structure, function, dynamics, and evolution of complex biological systems. We explore a class of algorithms for aligning large biomolecular networks by breaking down such networks into subgraphs and computing the alignment of the networks based on the alignment of their subgraphs. The resulting subnetworks are compared using graph kernels as scoring functions. We provide implementations of the resulting algorithms as part of BiNA, an open source biomolecular network alignment toolkit. Our experiments using Drosophila melanogaster, Saccharomyces cerevisiae, Mus musculus and Homo sapiens protein-protein interaction networks extracted from the DIP repository of protein-protein interaction data demonstrate that the performance of the proposed algorithms (as measured by % GO term enrichment of subnetworks identified by the alignment) is competitive with some of the state-of-the-art algorithms for pair-wise alignment of large protein-protein interaction networks. Our results also show that the inter-species similarity scores computed based on graph kernels can be used to cluster the species into a species tree that is consistent with the known phylogenetic relationships among the species.

Finite Correlation Length Implies Efficient Preparation of Quantum Thermal States

NASA Astrophysics Data System (ADS)

Brandão, Fernando G. S. L.; Kastoryano, Michael J.

2018-05-01

Preparing quantum thermal states on a quantum computer is in general a difficult task. We provide a procedure to prepare a thermal state on a quantum computer with a logarithmic depth circuit of local quantum channels assuming that the thermal state correlations satisfy the following two properties: (i) the correlations between two regions are exponentially decaying in the distance between the regions, and (ii) the thermal state is an approximate Markov state for shielded regions. We require both properties to hold for the thermal state of the Hamiltonian on any induced subgraph of the original lattice. Assumption (ii) is satisfied for all commuting Gibbs states, while assumption (i) is satisfied for every model above a critical temperature. Both assumptions are satisfied in one spatial dimension. Moreover, both assumptions are expected to hold above the thermal phase transition for models without any topological order at finite temperature. As a building block, we show that exponential decay of correlation (for thermal states of Hamiltonians on all induced subgraphs) is sufficient to efficiently estimate the expectation value of a local observable. Our proof uses quantum belief propagation, a recent strengthening of strong sub-additivity, and naturally breaks down for states with topological order.

Synaptic convergence regulates synchronization-dependent spike transfer in feedforward neural networks.

PubMed

Sailamul, Pachaya; Jang, Jaeson; Paik, Se-Bum

2017-12-01

Correlated neural activities such as synchronizations can significantly alter the characteristics of spike transfer between neural layers. However, it is not clear how this synchronization-dependent spike transfer can be affected by the structure of convergent feedforward wiring. To address this question, we implemented computer simulations of model neural networks: a source and a target layer connected with different types of convergent wiring rules. In the Gaussian-Gaussian (GG) model, both the connection probability and the strength are given as Gaussian distribution as a function of spatial distance. In the Uniform-Constant (UC) and Uniform-Exponential (UE) models, the connection probability density is a uniform constant within a certain range, but the connection strength is set as a constant value or an exponentially decaying function, respectively. Then we examined how the spike transfer function is modulated under these conditions, while static or synchronized input patterns were introduced to simulate different levels of feedforward spike synchronization. We observed that the synchronization-dependent modulation of the transfer function appeared noticeably different for each convergence condition. The modulation of the spike transfer function was largest in the UC model, and smallest in the UE model. Our analysis showed that this difference was induced by the different spike weight distributions that was generated from convergent synapses in each model. Our results suggest that, the structure of the feedforward convergence is a crucial factor for correlation-dependent spike control, thus must be considered important to understand the mechanism of information transfer in the brain.

Vegetation Patchiness Enhances Hydrological Connectivity in River Deltas Below the Percolation Threshold

NASA Astrophysics Data System (ADS)

Wright, K. A.; Hiatt, M. R.; Passalacqua, P.

2017-12-01

The humanitarian and ecological importance of coastal deltas has led many to research the factors influencing their ecogeomorphic evolution, in hopes of predicting the response of these regions to the growing number of natural and anthropogenic threats they face. One area of this effort, in which many unresolved questions remain, concerns the hydrological connectivity between the distributary channels and interdistributary islands, which field observations and numerical modeling have shown to be significant. Island vegetation is known to affect the degree of connectivity, but the effect of the spatial distribution of vegetation on connectivity remains an important question. This research aims to determine to what extent vegetation percent cover, patch size, and plant density affect connectivity in an idealized deltaic system. A 2D hydrodynamic model was used to numerically solve the shallow water equations in an idealized channel-island complex, modeled after Wax Lake Delta in Louisiana. For each model run, vegetation patches were distributed randomly throughout the islands according to a specified percent cover and patch size. Vegetation was modeled as a modified bed roughness, which was varied to represent a range of sparse-to-dense vegetation. To determine the effect of heterogeneity, the results of each patchy scenario were compared to results from a uniform run with the same spatially-averaged roughness. It was found that, while all patchy model runs demonstrated more channel-island connectivity than comparable uniform runs, this was particularly true when vegetation patches were dense and covered <50% of the island domain. Below this threshold, high-velocity pathways form in-between patches, greatly enhancing connectivity and transport capabilities. Above this threshold, however, little discrepancy is seen between patchy and uniform model runs. This threshold sits within the range of percent cover values observed in natural systems, and calculations show that these pathways affect shear stresses and residence time distributions in the deltaic islands, which can have implications for the fate and transport of sediment/nutrients. These results indicate that the spatial distribution of vegetation can have a notable impact on our ability to model connectivity in deltaic systems.

Effect on Non-Uniform Heat Generation on Thermionic Reactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schock, Alfred

The penalty resulting from non-uniform heat generation in a thermionic reactor is examined. Operation at sub-optimum cesium pressure is shown to reduce this penalty, but at the risk of a condition analogous to burnout. For high pressure diodes, a simple empirical correlation between current, voltage and heat flux is developed and used to analyze the performance penalty associated with two different heat flux profiles, for series-and parallel-connected converters. The results demonstrate that series-connected converters require much finer power flattening than parallel converters. For example, a ±10% variation in heat generation across a series array can result in a 25 tomore » 50% power penalty.« less

Generalizing Experimental Findings

DTIC Science & Technology

2015-06-01

ity.” In graphical terms, these assumptions may require several d-separation tests on several sub-graphs. It is utterly unimaginable therefore that...Education) (a) (Salary)(Education) (Skill) (b) S ( Test ) YX ZZ YX Figure 1: (a) A transportability model in which a post-treatment variable Z is S-admissible...observational studies to estimate population treatment ef- fects. Journal Royal Statistical Society: Series A (Statistics in Society) Forthcoming, doi

Dynamic mobility application policy analysis : policy and institutional issues for Response, Emergency Staging and Communications, Uniform Management, and Evacuation (R.E.S.C.U.M.E).

DOT National Transportation Integrated Search

2015-07-01

This report documents policy considerations for Response, Emergency Staging and Communications, Uniform Management, and Evacuation (R.E.S.C.U.M.E). R.E.S.C.U.M.E. comprises a "bundle" of mobility applications that use existing and new connected vehic...

Low-cost fabrication and polar-dependent switching uniformity of memory devices using alumina interfacial layer and Ag nanoparticle monolayer

NASA Astrophysics Data System (ADS)

Xia, Peng; Li, Luman; Wang, Pengfei; Gan, Ying; Xu, Wei

2017-11-01

A facile and low-cost process was developed for fabricating write-once-read-many-times (WORM) Cu/Ag NPs/Alumina/Al memory devices, where the alumina passivation layer formed naturally in air at room temperature, whereas the Ag nanoparticle monolayer was in situ prepared through thermal annealing of a 4.5 nm Ag film in air at 150°C. The devices exhibit irreversible transition from initial high resistance (OFF) state to low resistance (ON) state, with ON/OFF ratio of 107, indicating the introduction of Ag nanoparticle monolayer greatly improves ON/OFF ratio by four orders of magnitude. The uniformity of threshold voltages exhibits a polar-dependent behavior, and a narrow range of threshold voltages of 0.40 V among individual devices was achieved upon the forward voltage. The memory device can be regarded as two switching units connected in series. The uniform alumina interfacial layer and the non-uniform distribution of local electric fields originated from Ag nanoparticles might be responsible for excellent switching uniformity. Since silver ions in active layer can act as fast ion conductor, a plausible mechanism relating to the formation of filaments sequentially among the two switching units connected in series is suggested for the polar-dependent switching behavior. Furthermore, we demonstrate both alumina layer and Ag NPs monolayer play essential roles in improving switching parameters based on comparative experiments.

10 CFR Appendix A to Subpart K of... - Uniform Test Method for Measuring the Energy Consumption of Distribution Transformers

Code of Federal Regulations, 2013 CFR

2013-01-01

... test more than one unit of a basic model to determine the efficiency of that basic model, the... one ampere and the test current is limited to 15 percent of the winding current. Connect the... 10 Energy 3 2013-01-01 2013-01-01 false Uniform Test Method for Measuring the Energy Consumption...

10 CFR Appendix A to Subpart K of... - Uniform Test Method for Measuring the Energy Consumption of Distribution Transformers

Code of Federal Regulations, 2012 CFR

2012-01-01

... test more than one unit of a basic model to determine the efficiency of that basic model, the... one ampere and the test current is limited to 15 percent of the winding current. Connect the... 10 Energy 3 2012-01-01 2012-01-01 false Uniform Test Method for Measuring the Energy Consumption...

10 CFR Appendix A to Subpart K of... - Uniform Test Method for Measuring the Energy Consumption of Distribution Transformers

Code of Federal Regulations, 2010 CFR

2010-01-01

... test more than one unit of a basic model to determine the efficiency of that basic model, the... one ampere and the test current is limited to 15 percent of the winding current. Connect the... 10 Energy 3 2010-01-01 2010-01-01 false Uniform Test Method for Measuring the Energy Consumption...

10 CFR Appendix A to Subpart K of... - Uniform Test Method for Measuring the Energy Consumption of Distribution Transformers

Code of Federal Regulations, 2011 CFR

2011-01-01

... test more than one unit of a basic model to determine the efficiency of that basic model, the... one ampere and the test current is limited to 15 percent of the winding current. Connect the... 10 Energy 3 2011-01-01 2011-01-01 false Uniform Test Method for Measuring the Energy Consumption...

The finite body triangulation: algorithms, subgraphs, homogeneity estimation and application.

PubMed

Carson, Cantwell G; Levine, Jonathan S

2016-09-01

The concept of a finite body Dirichlet tessellation has been extended to that of a finite body Delaunay 'triangulation' to provide a more meaningful description of the spatial distribution of nonspherical secondary phase bodies in 2- and 3-dimensional images. A finite body triangulation (FBT) consists of a network of minimum edge-to-edge distances between adjacent objects in a microstructure. From this is also obtained the characteristic object chords formed by the intersection of the object boundary with the finite body tessellation. These two sets of distances form the basis of a parsimonious homogeneity estimation. The characteristics of the spatial distribution are then evaluated with respect to the distances between objects and the distances within them. Quantitative analysis shows that more physically representative distributions can be obtained by selecting subgraphs, such as the relative neighbourhood graph and the minimum spanning tree, from the finite body tessellation. To demonstrate their potential, we apply these methods to 3-dimensional X-ray computed tomographic images of foamed cement and their 2-dimensional cross sections. The Python computer code used to estimate the FBT is made available. Other applications for the algorithm - such as porous media transport and crack-tip propagation - are also discussed. © 2016 The Authors Journal of Microscopy © 2016 Royal Microscopical Society.

Origin of hyperbolicity in brain-to-brain coordination networks

NASA Astrophysics Data System (ADS)

Tadić, Bosiljka; Andjelković, Miroslav; Šuvakov, Milovan

2018-02-01

Hyperbolicity or negative curvature of complex networks is the intrinsic geometric proximity of nodes in the graph metric space, which implies an improved network function. Here, we investigate hidden combinatorial geometries in brain-to-brain coordination networks arising through social communications. The networks originate from correlations among EEG signals previously recorded during spoken communications comprising of 14 individuals with 24 speaker-listener pairs. We find that the corresponding networks are delta-hyperbolic with delta_max=1 and the graph diameter D=3 in each brain. While the emergent hyperbolicity in the two-brain networks satisfies delta_max/D/2 < 1 and can be attributed to the topology of the subgraph formed around the cross-brains linking channels. We identify these subgraphs in each studied two-brain network and decompose their structure into simple geometric descriptors (triangles, tetrahedra and cliques of higher orders) that contribute to hyperbolicity. Considering topologies that exceed two separate brain networks as a measure of coordination synergy between the brains, we identify different neuronal correlation patterns ranging from weak coordination to super-brain structure. These topology features are in qualitative agreement with the listener’s self-reported ratings of own experience and quality of the speaker, suggesting that studies of the cross-brain connector networks can reveal new insight into the neural mechanisms underlying human social behavior.

Robust cell tracking in epithelial tissues through identification of maximum common subgraphs.

PubMed

Kursawe, Jochen; Bardenet, Rémi; Zartman, Jeremiah J; Baker, Ruth E; Fletcher, Alexander G

2016-11-01

Tracking of cells in live-imaging microscopy videos of epithelial sheets is a powerful tool for investigating fundamental processes in embryonic development. Characterizing cell growth, proliferation, intercalation and apoptosis in epithelia helps us to understand how morphogenetic processes such as tissue invagination and extension are locally regulated and controlled. Accurate cell tracking requires correctly resolving cells entering or leaving the field of view between frames, cell neighbour exchanges, cell removals and cell divisions. However, current tracking methods for epithelial sheets are not robust to large morphogenetic deformations and require significant manual interventions. Here, we present a novel algorithm for epithelial cell tracking, exploiting the graph-theoretic concept of a 'maximum common subgraph' to track cells between frames of a video. Our algorithm does not require the adjustment of tissue-specific parameters, and scales in sub-quadratic time with tissue size. It does not rely on precise positional information, permitting large cell movements between frames and enabling tracking in datasets acquired at low temporal resolution due to experimental constraints such as phototoxicity. To demonstrate the method, we perform tracking on the Drosophila embryonic epidermis and compare cell-cell rearrangements to previous studies in other tissues. Our implementation is open source and generally applicable to epithelial tissues. © 2016 The Authors.

High-performance analysis of filtered semantic graphs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Buluc, Aydin; Fox, Armando; Gilbert, John R.

2012-01-01

High performance is a crucial consideration when executing a complex analytic query on a massive semantic graph. In a semantic graph, vertices and edges carry "attributes" of various types. Analytic queries on semantic graphs typically depend on the values of these attributes; thus, the computation must either view the graph through a filter that passes only those individual vertices and edges of interest, or else must first materialize a subgraph or subgraphs consisting of only the vertices and edges of interest. The filtered approach is superior due to its generality, ease of use, and memory efficiency, but may carry amore » performance cost. In the Knowledge Discovery Toolbox (KDT), a Python library for parallel graph computations, the user writes filters in a high-level language, but those filters result in relatively low performance due to the bottleneck of having to call into the Python interpreter for each edge. In this work, we use the Selective Embedded JIT Specialization (SEJITS) approach to automatically translate filters defined by programmers into a lower-level efficiency language, bypassing the upcall into Python. We evaluate our approach by comparing it with the high-performance C++ /MPI Combinatorial BLAS engine, and show that the productivity gained by using a high-level filtering language comes without sacrificing performance.« less

Multiscale weighted colored graphs for protein flexibility and rigidity analysis

NASA Astrophysics Data System (ADS)

Bramer, David; Wei, Guo-Wei

2018-02-01

Protein structural fluctuation, measured by Debye-Waller factors or B-factors, is known to correlate to protein flexibility and function. A variety of methods has been developed for protein Debye-Waller factor prediction and related applications to domain separation, docking pose ranking, entropy calculation, hinge detection, stability analysis, etc. Nevertheless, none of the current methodologies are able to deliver an accuracy of 0.7 in terms of the Pearson correlation coefficients averaged over a large set of proteins. In this work, we introduce a paradigm-shifting geometric graph model, multiscale weighted colored graph (MWCG), to provide a new generation of computational algorithms to significantly change the current status of protein structural fluctuation analysis. Our MWCG model divides a protein graph into multiple subgraphs based on interaction types between graph nodes and represents the protein rigidity by generalized centralities of subgraphs. MWCGs not only predict the B-factors of protein residues but also accurately analyze the flexibility of all atoms in a protein. The MWCG model is validated over a number of protein test sets and compared with many standard methods. An extensive numerical study indicates that the proposed MWCG offers an accuracy of over 0.8 and thus provides perhaps the first reliable method for estimating protein flexibility and B-factors. It also simultaneously predicts all-atom flexibility in a molecule.

Concerted Perturbation Observed in a Hub Network in Alzheimer’s Disease

PubMed Central

Liang, Dapeng; Han, Guangchun; Feng, Xuemei; Sun, Jiya; Duan, Yong; Lei, Hongxing

2012-01-01

Alzheimer’s disease (AD) is a progressive neurodegenerative disease involving the alteration of gene expression at the whole genome level. Genome-wide transcriptional profiling of AD has been conducted by many groups on several relevant brain regions. However, identifying the most critical dys-regulated genes has been challenging. In this work, we addressed this issue by deriving critical genes from perturbed subnetworks. Using a recent microarray dataset on six brain regions, we applied a heaviest induced subgraph algorithm with a modular scoring function to reveal the significantly perturbed subnetwork in each brain region. These perturbed subnetworks were found to be significantly overlapped with each other. Furthermore, the hub genes from these perturbed subnetworks formed a connected hub network consisting of 136 genes. Comparison between AD and several related diseases demonstrated that the hub network was robustly and specifically perturbed in AD. In addition, strong correlation between the expression level of these hub genes and indicators of AD severity suggested that this hub network can partially reflect AD progression. More importantly, this hub network reflected the adaptation of neurons to the AD-specific microenvironment through a variety of adjustments, including reduction of neuronal and synaptic activities and alteration of survival signaling. Therefore, it is potentially useful for the development of biomarkers and network medicine for AD. PMID:22815752

Improving the Efficiency and Effectiveness of Community Detection via Prior-Induced Equivalent Super-Network.

PubMed

Yang, Liang; Jin, Di; He, Dongxiao; Fu, Huazhu; Cao, Xiaochun; Fogelman-Soulie, Francoise

2017-03-29

Due to the importance of community structure in understanding network and a surge of interest aroused on community detectability, how to improve the community identification performance with pairwise prior information becomes a hot topic. However, most existing semi-supervised community detection algorithms only focus on improving the accuracy but ignore the impacts of priors on speeding detection. Besides, they always require to tune additional parameters and cannot guarantee pairwise constraints. To address these drawbacks, we propose a general, high-speed, effective and parameter-free semi-supervised community detection framework. By constructing the indivisible super-nodes according to the connected subgraph of the must-link constraints and by forming the weighted super-edge based on network topology and cannot-link constraints, our new framework transforms the original network into an equivalent but much smaller Super-Network. Super-Network perfectly ensures the must-link constraints and effectively encodes cannot-link constraints. Furthermore, the time complexity of super-network construction process is linear in the original network size, which makes it efficient. Meanwhile, since the constructed super-network is much smaller than the original one, any existing community detection algorithm is much faster when using our framework. Besides, the overall process will not introduce any additional parameters, making it more practical.

New publicly available chemical query language, CSRML, to support chemotype representations for application to data mining and modeling.

PubMed

Yang, Chihae; Tarkhov, Aleksey; Marusczyk, Jörg; Bienfait, Bruno; Gasteiger, Johann; Kleinoeder, Thomas; Magdziarz, Tomasz; Sacher, Oliver; Schwab, Christof H; Schwoebel, Johannes; Terfloth, Lothar; Arvidson, Kirk; Richard, Ann; Worth, Andrew; Rathman, James

2015-03-23

Chemotypes are a new approach for representing molecules, chemical substructures and patterns, reaction rules, and reactions. Chemotypes are capable of integrating types of information beyond what is possible using current representation methods (e.g., SMARTS patterns) or reaction transformations (e.g., SMIRKS, reaction SMILES). Chemotypes are expressed in the XML-based Chemical Subgraphs and Reactions Markup Language (CSRML), and can be encoded not only with connectivity and topology but also with properties of atoms, bonds, electronic systems, or molecules. CSRML has been developed in parallel with a public set of chemotypes, i.e., the ToxPrint chemotypes, which are designed to provide excellent coverage of environmental, regulatory, and commercial-use chemical space, as well as to represent chemical patterns and properties especially relevant to various toxicity concerns. A software application, ChemoTyper has also been developed and made publicly available in order to enable chemotype searching and fingerprinting against a target structure set. The public ChemoTyper houses the ToxPrint chemotype CSRML dictionary, as well as reference implementation so that the query specifications may be adopted by other chemical structure knowledge systems. The full specifications of the XML-based CSRML standard used to express chemotypes are publicly available to facilitate and encourage the exchange of structural knowledge.

Complexity and approximability for a problem of intersecting of proximity graphs with minimum number of equal disks

NASA Astrophysics Data System (ADS)

Kobylkin, Konstantin

2016-10-01

Computational complexity and approximability are studied for the problem of intersecting of a set of straight line segments with the smallest cardinality set of disks of fixed radii r > 0 where the set of segments forms straight line embedding of possibly non-planar geometric graph. This problem arises in physical network security analysis for telecommunication, wireless and road networks represented by specific geometric graphs defined by Euclidean distances between their vertices (proximity graphs). It can be formulated in a form of known Hitting Set problem over a set of Euclidean r-neighbourhoods of segments. Being of interest computational complexity and approximability of Hitting Set over so structured sets of geometric objects did not get much focus in the literature. Strong NP-hardness of the problem is reported over special classes of proximity graphs namely of Delaunay triangulations, some of their connected subgraphs, half-θ6 graphs and non-planar unit disk graphs as well as APX-hardness is given for non-planar geometric graphs at different scales of r with respect to the longest graph edge length. Simple constant factor approximation algorithm is presented for the case where r is at the same scale as the longest edge length.

Discrete geometric analysis of message passing algorithm on graphs

NASA Astrophysics Data System (ADS)

Watanabe, Yusuke

2010-04-01

We often encounter probability distributions given as unnormalized products of non-negative functions. The factorization structures are represented by hypergraphs called factor graphs. Such distributions appear in various fields, including statistics, artificial intelligence, statistical physics, error correcting codes, etc. Given such a distribution, computations of marginal distributions and the normalization constant are often required. However, they are computationally intractable because of their computational costs. One successful approximation method is Loopy Belief Propagation (LBP) algorithm. The focus of this thesis is an analysis of the LBP algorithm. If the factor graph is a tree, i.e. having no cycle, the algorithm gives the exact quantities. If the factor graph has cycles, however, the LBP algorithm does not give exact results and possibly exhibits oscillatory and non-convergent behaviors. The thematic question of this thesis is "How the behaviors of the LBP algorithm are affected by the discrete geometry of the factor graph?" The primary contribution of this thesis is the discovery of a formula that establishes the relation between the LBP, the Bethe free energy and the graph zeta function. This formula provides new techniques for analysis of the LBP algorithm, connecting properties of the graph and of the LBP and the Bethe free energy. We demonstrate applications of the techniques to several problems including (non) convexity of the Bethe free energy, the uniqueness and stability of the LBP fixed point. We also discuss the loop series initiated by Chertkov and Chernyak. The loop series is a subgraph expansion of the normalization constant, or partition function, and reflects the graph geometry. We investigate theoretical natures of the series. Moreover, we show a partial connection between the loop series and the graph zeta function.

Ground States of Random Spanning Trees on a D-Wave 2X

NASA Astrophysics Data System (ADS)

Hall, J. S.; Hobl, L.; Novotny, M. A.; Michielsen, Kristel

The performances of two D-Wave 2 machines (476 and 496 qubits) and of a 1097-qubit D-Wave 2X were investigated. Each chip has a Chimera interaction graph calG . Problem input consists of values for the fields hj and for the two-qubit interactions Ji , j of an Ising spin-glass problem formulated on calG . Output is returned in terms of a spin configuration {sj } , with sj = +/- 1 . We generated random spanning trees (RSTs) uniformly distributed over all spanning trees of calG . On the 476-qubit D-Wave 2, RSTs were generated on the full chip with Ji , j = - 1 and hj = 0 and solved one thousand times. The distribution of solution energies and the average magnetization of each qubit were determined. On both the 476- and 1097-qubit machines, four identical spanning trees were generated on each quadrant of the chip. The statistical independence of these regions was investigated. In another study, on the D-Wave 2X, one hundred RSTs with random Ji , j ∈ { - 1 , 1 } and hj = 0 were generated on the full chip. Each RST problem was solved one hundred times and the number of times the ground state energy was found was recorded. This procedure was repeated for square subgraphs, with dimensions ranging from 7 ×7 to 11 ×11. Supported in part by NSF Grants DGE-0947419 and DMR-1206233. D-Wave time provided by D-Wave Systems and by the USRA Quantum Artificial Intelligence Laboratory Research Opportunity.

Temporal ventriloquism along the path of apparent motion: speed perception under different spatial grouping principles.

PubMed

Ogulmus, Cansu; Karacaoglu, Merve; Kafaligonul, Hulusi

2018-03-01

The coordination of intramodal perceptual grouping and crossmodal interactions plays a critical role in constructing coherent multisensory percepts. However, the basic principles underlying such coordinating mechanisms still remain unclear. By taking advantage of an illusion called temporal ventriloquism and its influences on perceived speed, we investigated how audiovisual interactions in time are modulated by the spatial grouping principles of vision. In our experiments, we manipulated the spatial grouping principles of proximity, uniform connectedness, and similarity/common fate in apparent motion displays. Observers compared the speed of apparent motions across different sound timing conditions. Our results revealed that the effects of sound timing (i.e., temporal ventriloquism effects) on perceived speed also existed in visual displays containing more than one object and were modulated by different spatial grouping principles. In particular, uniform connectedness was found to modulate these audiovisual interactions in time. The effect of sound timing on perceived speed was smaller when horizontal connecting bars were introduced along the path of apparent motion. When the objects in each apparent motion frame were not connected or connected with vertical bars, the sound timing was more influential compared to the horizontal bar conditions. Overall, our findings here suggest that the effects of sound timing on perceived speed exist in different spatial configurations and can be modulated by certain intramodal spatial grouping principles such as uniform connectedness.

Synergistic Approach Integrating Joint Capabilities for USSOCOM Contingency Contracting: Construction Management Module

DTIC Science & Technology

2010-12-01

59 a. The Joint Uniform Lessons Learned System (JULLS) .........59 b. Acquisition Community Connection (ACC) ..........................59 c...Report ACC Acquisition Community Connection ADDIE Analyze, Design, Develop, Implement, Evaluate AFFARS Air Force Federal Acquisition Regulation...Operations J4 Logistics J5 Plans J6 Communications J8 Programming and Comptroller J&A Justification and Approval JARB Joint Acquisition

Maximizing algebraic connectivity in interconnected networks.

PubMed

Shakeri, Heman; Albin, Nathan; Darabi Sahneh, Faryad; Poggi-Corradini, Pietro; Scoglio, Caterina

2016-03-01

Algebraic connectivity, the second eigenvalue of the Laplacian matrix, is a measure of node and link connectivity on networks. When studying interconnected networks it is useful to consider a multiplex model, where the component networks operate together with interlayer links among them. In order to have a well-connected multilayer structure, it is necessary to optimally design these interlayer links considering realistic constraints. In this work, we solve the problem of finding an optimal weight distribution for one-to-one interlayer links under budget constraint. We show that for the special multiplex configurations with identical layers, the uniform weight distribution is always optimal. On the other hand, when the two layers are arbitrary, increasing the budget reveals the existence of two different regimes. Up to a certain threshold budget, the second eigenvalue of the supra-Laplacian is simple, the optimal weight distribution is uniform, and the Fiedler vector is constant on each layer. Increasing the budget past the threshold, the optimal weight distribution can be nonuniform. The interesting consequence of this result is that there is no need to solve the optimization problem when the available budget is less than the threshold, which can be easily found analytically.

Distributed Sensing and Processing Adaptive Collaboration Environment (D-SPACE)

DTIC Science & Technology

2014-07-01

to the query graph, or subgraph permutations with the same mismatch cost (often the case for homogeneous and/or symmetrical data/query). To avoid...decisions are generated in a bottom-up manner using the metric of entropy at the cluster level (Figure 9c). Using the definition of belief messages...for a cluster and a set of data nodes in this cluster , we compute the entropy for forward and backward messages as (,) = −∑ (

A non-uniformly sampled 4D HCC(CO)NH-TOCSY experiment processed using maximum entropy for rapid protein sidechain assignment

PubMed Central

Mobli, Mehdi; Stern, Alan S.; Bermel, Wolfgang; King, Glenn F.; Hoch, Jeffrey C.

2010-01-01

One of the stiffest challenges in structural studies of proteins using NMR is the assignment of sidechain resonances. Typically, a panel of lengthy 3D experiments are acquired in order to establish connectivities and resolve ambiguities due to overlap. We demonstrate that these experiments can be replaced by a single 4D experiment that is time-efficient, yields excellent resolution, and captures unique carbon-proton connectivity information. The approach is made practical by the use of non-uniform sampling in the three indirect time dimensions and maximum entropy reconstruction of the corresponding 3D frequency spectrum. This 4D method will facilitate automated resonance assignment procedures and it should be particularly beneficial for increasing throughput in NMR-based structural genomics initiatives. PMID:20299257

Investigations of Novel Surface Modification Techniques for Wear Resistant Al and Mg Based Materials

DTIC Science & Technology

1994-01-01

microhardness to resist the abrasive wear. Moreover it is required to form dense or fine-porous uniform layers to provide the antifriction characteristics...technological regimes for production of OCC having maximum of thickness, microhardness and uniformity is expediently to carry on using the silicate-alkali...includes at the same time both the index of the process effectiveness and the strength and geometrical characteristics of the product . In connection

Leveraging the Cloud for Integrated Network Experimentation

DTIC Science & Technology

2014-03-01

kernel settings, or any of the low-level subcomponents. 3. Scalable Solutions: Businesses can build scalable solutions for their clients , ranging from...values. These values 13 can assume several distributions that include normal, Pareto , uniform, exponential and Poisson, among others [21]. Additionally, D...communication, the web client establishes a connection to the server before traffic begins to flow. Web servers do not initiate connections to clients in

The Challenge of Characterizing Branching in Molecular Species.

DTIC Science & Technology

1986-07-16

representing respectively paths of lengths two and three. Strictly speaking, a septuple rather than a pair should have been used to account for all the paths...same counts, are of fundmental importance in the study of isospectral graphs. These facts were exploited by the latter workers to establish a 1-1...case of the Hosoya index, Z(G), a composition principle was given [38] from which it was apparent that Z(G) depends on certain subgraphs of C for

Sequential Monte Carlo for Maximum Weight Subgraphs with Application to Solving Image Jigsaw Puzzles.

PubMed

Adluru, Nagesh; Yang, Xingwei; Latecki, Longin Jan

2015-05-01

We consider a problem of finding maximum weight subgraphs (MWS) that satisfy hard constraints in a weighted graph. The constraints specify the graph nodes that must belong to the solution as well as mutual exclusions of graph nodes, i.e., pairs of nodes that cannot belong to the same solution. Our main contribution is a novel inference approach for solving this problem in a sequential monte carlo (SMC) sampling framework. Usually in an SMC framework there is a natural ordering of the states of the samples. The order typically depends on observations about the states or on the annealing setup used. In many applications (e.g., image jigsaw puzzle problems), all observations (e.g., puzzle pieces) are given at once and it is hard to define a natural ordering. Therefore, we relax the assumption of having ordered observations about states and propose a novel SMC algorithm for obtaining maximum a posteriori estimate of a high-dimensional posterior distribution. This is achieved by exploring different orders of states and selecting the most informative permutations in each step of the sampling. Our experimental results demonstrate that the proposed inference framework significantly outperforms loopy belief propagation in solving the image jigsaw puzzle problem. In particular, our inference quadruples the accuracy of the puzzle assembly compared to that of loopy belief propagation.

Optimal Co-segmentation of Tumor in PET-CT Images with Context Information

PubMed Central

Song, Qi; Bai, Junjie; Han, Dongfeng; Bhatia, Sudershan; Sun, Wenqing; Rockey, William; Bayouth, John E.; Buatti, John M.

2014-01-01

PET-CT images have been widely used in clinical practice for radiotherapy treatment planning of the radiotherapy. Many existing segmentation approaches only work for a single imaging modality, which suffer from the low spatial resolution in PET or low contrast in CT. In this work we propose a novel method for the co-segmentation of the tumor in both PET and CT images, which makes use of advantages from each modality: the functionality information from PET and the anatomical structure information from CT. The approach formulates the segmentation problem as a minimization problem of a Markov Random Field (MRF) model, which encodes the information from both modalities. The optimization is solved using a graph-cut based method. Two sub-graphs are constructed for the segmentation of the PET and the CT images, respectively. To achieve consistent results in two modalities, an adaptive context cost is enforced by adding context arcs between the two subgraphs. An optimal solution can be obtained by solving a single maximum flow problem, which leads to simultaneous segmentation of the tumor volumes in both modalities. The proposed algorithm was validated in robust delineation of lung tumors on 23 PET-CT datasets and two head-and-neck cancer subjects. Both qualitative and quantitative results show significant improvement compared to the graph cut methods solely using PET or CT. PMID:23693127

Sequential Monte Carlo for Maximum Weight Subgraphs with Application to Solving Image Jigsaw Puzzles

PubMed Central

Adluru, Nagesh; Yang, Xingwei; Latecki, Longin Jan

2015-01-01

We consider a problem of finding maximum weight subgraphs (MWS) that satisfy hard constraints in a weighted graph. The constraints specify the graph nodes that must belong to the solution as well as mutual exclusions of graph nodes, i.e., pairs of nodes that cannot belong to the same solution. Our main contribution is a novel inference approach for solving this problem in a sequential monte carlo (SMC) sampling framework. Usually in an SMC framework there is a natural ordering of the states of the samples. The order typically depends on observations about the states or on the annealing setup used. In many applications (e.g., image jigsaw puzzle problems), all observations (e.g., puzzle pieces) are given at once and it is hard to define a natural ordering. Therefore, we relax the assumption of having ordered observations about states and propose a novel SMC algorithm for obtaining maximum a posteriori estimate of a high-dimensional posterior distribution. This is achieved by exploring different orders of states and selecting the most informative permutations in each step of the sampling. Our experimental results demonstrate that the proposed inference framework significantly outperforms loopy belief propagation in solving the image jigsaw puzzle problem. In particular, our inference quadruples the accuracy of the puzzle assembly compared to that of loopy belief propagation. PMID:26052182

Interactions of information transfer along separable causal paths

NASA Astrophysics Data System (ADS)

Jiang, Peishi; Kumar, Praveen

2018-04-01

Complex systems arise as a result of interdependences between multiple variables, whose causal interactions can be visualized in a time-series graph. Transfer entropy and information partitioning approaches have been used to characterize such dependences. However, these approaches capture net information transfer occurring through a multitude of pathways involved in the interaction and as a result mask our ability to discern the causal interaction within a subgraph of interest through specific pathways. We build on recent developments of momentary information transfer along causal paths proposed by Runge [Phys. Rev. E 92, 062829 (2015), 10.1103/PhysRevE.92.062829] to develop a framework for quantifying information partitioning along separable causal paths. Momentary information transfer along causal paths captures the amount of information transfer between any two variables lagged at two specific points in time. Our approach expands this concept to characterize the causal interaction in terms of synergistic, unique, and redundant information transfer through separable causal paths. Through a graphical model, we analyze the impact of the separable and nonseparable causal paths and the causality structure embedded in the graph as well as the noise effect on information partitioning by using synthetic data generated from two coupled logistic equation models. Our approach can provide a valuable reference for an autonomous information partitioning along separable causal paths which form a causal subgraph influencing a target.

An analysis of multi-type relational interactions in FMA using graph motifs with disjointness constraints.

PubMed

Zhang, Guo-Qiang; Luo, Lingyun; Ogbuji, Chime; Joslyn, Cliff; Mejino, Jose; Sahoo, Satya S

2012-01-01

The interaction of multiple types of relationships among anatomical classes in the Foundational Model of Anatomy (FMA) can provide inferred information valuable for quality assurance. This paper introduces a method called Motif Checking (MOCH) to study the effects of such multi-relation type interactions for detecting logical inconsistencies as well as other anomalies represented by the motifs. MOCH represents patterns of multi-type interaction as small labeled (with multiple types of edges) sub-graph motifs, whose nodes represent class variables, and labeled edges represent relational types. By representing FMA as an RDF graph and motifs as SPARQL queries, fragments of FMA are automatically obtained as auditing candidates. Leveraging the scalability and reconfigurability of Semantic Web Technology, we performed exhaustive analyses of a variety of labeled sub-graph motifs. The quality assurance feature of MOCH comes from the distinct use of a subset of the edges of the graph motifs as constraints for disjointness, whereby bringing in rule-based flavor to the approach as well. With possible disjointness implied by antonyms, we performed manual inspection of the resulting FMA fragments and tracked down sources of abnormal inferred conclusions (logical inconsistencies), which are amendable for programmatic revision of the FMA. Our results demonstrate that MOCH provides a unique source of valuable information for quality assurance. Since our approach is general, it is applicable to any ontological system with an OWL representation.

Dynamic Visualization of Co-expression in Systems Genetics Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

New, Joshua Ryan; Huang, Jian; Chesler, Elissa J

2008-01-01

Biologists hope to address grand scientific challenges by exploring the abundance of data made available through modern microarray technology and other high-throughput techniques. The impact of this data, however, is limited unless researchers can effectively assimilate such complex information and integrate it into their daily research; interactive visualization tools are called for to support the effort. Specifically, typical studies of gene co-expression require novel visualization tools that enable the dynamic formulation and fine-tuning of hypotheses to aid the process of evaluating sensitivity of key parameters. These tools should allow biologists to develop an intuitive understanding of the structure of biologicalmore » networks and discover genes which reside in critical positions in networks and pathways. By using a graph as a universal data representation of correlation in gene expression data, our novel visualization tool employs several techniques that when used in an integrated manner provide innovative analytical capabilities. Our tool for interacting with gene co-expression data integrates techniques such as: graph layout, qualitative subgraph extraction through a novel 2D user interface, quantitative subgraph extraction using graph-theoretic algorithms or by querying an optimized b-tree, dynamic level-of-detail graph abstraction, and template-based fuzzy classification using neural networks. We demonstrate our system using a real-world workflow from a large-scale, systems genetics study of mammalian gene co-expression.« less

An Analysis of Multi-type Relational Interactions in FMA Using Graph Motifs with Disjointness Constraints

PubMed Central

Zhang, Guo-Qiang; Luo, Lingyun; Ogbuji, Chime; Joslyn, Cliff; Mejino, Jose; Sahoo, Satya S

2012-01-01

The interaction of multiple types of relationships among anatomical classes in the Foundational Model of Anatomy (FMA) can provide inferred information valuable for quality assurance. This paper introduces a method called Motif Checking (MOCH) to study the effects of such multi-relation type interactions for detecting logical inconsistencies as well as other anomalies represented by the motifs. MOCH represents patterns of multi-type interaction as small labeled (with multiple types of edges) sub-graph motifs, whose nodes represent class variables, and labeled edges represent relational types. By representing FMA as an RDF graph and motifs as SPARQL queries, fragments of FMA are automatically obtained as auditing candidates. Leveraging the scalability and reconfigurability of Semantic Web Technology, we performed exhaustive analyses of a variety of labeled sub-graph motifs. The quality assurance feature of MOCH comes from the distinct use of a subset of the edges of the graph motifs as constraints for disjointness, whereby bringing in rule-based flavor to the approach as well. With possible disjointness implied by antonyms, we performed manual inspection of the resulting FMA fragments and tracked down sources of abnormal inferred conclusions (logical inconsistencies), which are amendable for programmatic revision of the FMA. Our results demonstrate that MOCH provides a unique source of valuable information for quality assurance. Since our approach is general, it is applicable to any ontological system with an OWL representation. PMID:23304382

Motif structure and cooperation in real-world complex networks

NASA Astrophysics Data System (ADS)

Salehi, Mostafa; Rabiee, Hamid R.; Jalili, Mahdi

2010-12-01

Networks of dynamical nodes serve as generic models for real-world systems in many branches of science ranging from mathematics to physics, technology, sociology and biology. Collective behavior of agents interacting over complex networks is important in many applications. The cooperation between selfish individuals is one of the most interesting collective phenomena. In this paper we address the interplay between the motifs’ cooperation properties and their abundance in a number of real-world networks including yeast protein-protein interaction, human brain, protein structure, email communication, dolphins’ social interaction, Zachary karate club and Net-science coauthorship networks. First, the amount of cooperativity for all possible undirected subgraphs with three to six nodes is calculated. To this end, the evolutionary dynamics of the Prisoner’s Dilemma game is considered and the cooperativity of each subgraph is calculated as the percentage of cooperating agents at the end of the simulation time. Then, the three- to six-node motifs are extracted for each network. The significance of the abundance of a motif, represented by a Z-value, is obtained by comparing them with some properly randomized versions of the original network. We found that there is always a group of motifs showing a significant inverse correlation between their cooperativity amount and Z-value, i.e. the more the Z-value the less the amount of cooperativity. This suggests that networks composed of well-structured units do not have good cooperativity properties.

Some cycle-supermagic labelings of the calendula graphs

NASA Astrophysics Data System (ADS)

Pradipta, T. R.; Salman, A. N. M.

2018-01-01

In this paper, we introduce a calendula graph, denoted by Clm,n . It is a graph constructed from a cycle on m vertices Cm and m copies of Cn which are Cn1 , Cn2 , ⋯, Cnm and grafting the i-th edge of Cm to an edge of in Cni for each i ∈ {1,2,⋯,m}. A graph G = (V, E) admits a Cn -covering, if every edge e ∈ E(G) belongs to a subgraph of G isomorphic to Cn . The graph G is called cycle-magic, if there exists a total labeling ϕ: V ∪ E → {1,2,…,|V|+|E|} such that for every subgraph Cn ‧ = (V‧,E‧) of G isomorphic to Cn has the same weight. In this case, the weight of Cn , denoted by ϕ(Cn ’), is defined as ∑ v∈V(C’n ) ϕ(v) + ∑ e∈E(C’n ) ϕ(e). Furthermore, G is called cycle-supermagic, if ϕ:V→{1,2,…,|V|}. In this paper, we provide some cycle-supermagic labelings of calendula graphs. In order to prove it, we develop a technique, to make a partition of a multiset into m sub-multisets with the same cardinality such that the sum of all elements of each sub-multiset is same. The technique is called an m-balanced multiset.

On automating domain connectivity for overset grids

NASA Technical Reports Server (NTRS)

Chiu, Ing-Tsau

1994-01-01

An alternative method for domain connectivity among systems of overset grids is presented. Reference uniform Cartesian systems of points are used to achieve highly efficient domain connectivity, and form the basis for a future fully automated system. The Cartesian systems are used to approximated body surfaces and to map the computational space of component grids. By exploiting the characteristics of Cartesian Systems, Chimera type hole-cutting and identification of donor elements for intergrid boundary points can be carried out very efficiently. The method is tested for a range of geometrically complex multiple-body overset grid systems.

50 CFR 11.1 - Purpose of regulations.

Code of Federal Regulations, 2010 CFR

2010-10-01

... PROCEDURES Introduction § 11.1 Purpose of regulations. The regulations contained in this part provide uniform rules and procedures for the assessment of civil penalties in connection with violations of certain laws...

On the ground state of Yang-Mills theory

NASA Astrophysics Data System (ADS)

Bakry, Ahmed S.; Leinweber, Derek B.; Williams, Anthony G.

2011-08-01

We investigate the overlap of the ground state meson potential with sets of mesonic-trial wave functions corresponding to different gluonic distributions. We probe the transverse structure of the flux tube through the creation of non-uniform smearing profiles for the string of glue connecting two color sources in Wilson loop operator. The non-uniformly UV-regulated flux-tube operators are found to optimize the overlap with the ground state and display interesting features in the ground state overlap.

Distortions and disconnections: disrupted brain connectivity in autism.

PubMed

Wass, Sam

2011-02-01

The past few years have seen considerable interest in findings of abnormal brain connectivity in the autism spectrum disorders (ASD). We review recent work from neuroimaging and other sources, and argue that there is considerable convergent evidence suggesting that connectivity is disrupted in ASD. We point to evidence both of local over-connectivity and of long-distance under-connectivity, and describe some non-uniformities in this picture, most notably that disruptions appear more severe in later-developing cortical regions. We conclude by discussing a number of extant questions. Firstly, we consider whether aberrant connectivity should be seen as part of the primary pathogenesis of autism, or whether disrupted connectivity in ASD emerges over time. Secondly, we consider how the patterns of disrupted connectivity found in ASD might relate to those being found in a range of other disorders. Copyright © 2010 Elsevier Inc. All rights reserved.

Topological image texture analysis for quality assessment

NASA Astrophysics Data System (ADS)

Asaad, Aras T.; Rashid, Rasber Dh.; Jassim, Sabah A.

2017-05-01

Image quality is a major factor influencing pattern recognition accuracy and help detect image tampering for forensics. We are concerned with investigating topological image texture analysis techniques to assess different type of degradation. We use Local Binary Pattern (LBP) as a texture feature descriptor. For any image construct simplicial complexes for selected groups of uniform LBP bins and calculate persistent homology invariants (e.g. number of connected components). We investigated image quality discriminating characteristics of these simplicial complexes by computing these models for a large dataset of face images that are affected by the presence of shadows as a result of variation in illumination conditions. Our tests demonstrate that for specific uniform LBP patterns, the number of connected component not only distinguish between different levels of shadow effects but also help detect the infected regions as well.

Measuring Symmetry, Asymmetry and Randomness in Neural Network Connectivity

PubMed Central

Esposito, Umberto; Giugliano, Michele; van Rossum, Mark; Vasilaki, Eleni

2014-01-01

Cognitive functions are stored in the connectome, the wiring diagram of the brain, which exhibits non-random features, so-called motifs. In this work, we focus on bidirectional, symmetric motifs, i.e. two neurons that project to each other via connections of equal strength, and unidirectional, non-symmetric motifs, i.e. within a pair of neurons only one neuron projects to the other. We hypothesise that such motifs have been shaped via activity dependent synaptic plasticity processes. As a consequence, learning moves the distribution of the synaptic connections away from randomness. Our aim is to provide a global, macroscopic, single parameter characterisation of the statistical occurrence of bidirectional and unidirectional motifs. To this end we define a symmetry measure that does not require any a priori thresholding of the weights or knowledge of their maximal value. We calculate its mean and variance for random uniform or Gaussian distributions, which allows us to introduce a confidence measure of how significantly symmetric or asymmetric a specific configuration is, i.e. how likely it is that the configuration is the result of chance. We demonstrate the discriminatory power of our symmetry measure by inspecting the eigenvalues of different types of connectivity matrices. We show that a Gaussian weight distribution biases the connectivity motifs to more symmetric configurations than a uniform distribution and that introducing a random synaptic pruning, mimicking developmental regulation in synaptogenesis, biases the connectivity motifs to more asymmetric configurations, regardless of the distribution. We expect that our work will benefit the computational modelling community, by providing a systematic way to characterise symmetry and asymmetry in network structures. Further, our symmetry measure will be of use to electrophysiologists that investigate symmetry of network connectivity. PMID:25006663

Measuring symmetry, asymmetry and randomness in neural network connectivity.

PubMed

Esposito, Umberto; Giugliano, Michele; van Rossum, Mark; Vasilaki, Eleni

2014-01-01

Cognitive functions are stored in the connectome, the wiring diagram of the brain, which exhibits non-random features, so-called motifs. In this work, we focus on bidirectional, symmetric motifs, i.e. two neurons that project to each other via connections of equal strength, and unidirectional, non-symmetric motifs, i.e. within a pair of neurons only one neuron projects to the other. We hypothesise that such motifs have been shaped via activity dependent synaptic plasticity processes. As a consequence, learning moves the distribution of the synaptic connections away from randomness. Our aim is to provide a global, macroscopic, single parameter characterisation of the statistical occurrence of bidirectional and unidirectional motifs. To this end we define a symmetry measure that does not require any a priori thresholding of the weights or knowledge of their maximal value. We calculate its mean and variance for random uniform or Gaussian distributions, which allows us to introduce a confidence measure of how significantly symmetric or asymmetric a specific configuration is, i.e. how likely it is that the configuration is the result of chance. We demonstrate the discriminatory power of our symmetry measure by inspecting the eigenvalues of different types of connectivity matrices. We show that a Gaussian weight distribution biases the connectivity motifs to more symmetric configurations than a uniform distribution and that introducing a random synaptic pruning, mimicking developmental regulation in synaptogenesis, biases the connectivity motifs to more asymmetric configurations, regardless of the distribution. We expect that our work will benefit the computational modelling community, by providing a systematic way to characterise symmetry and asymmetry in network structures. Further, our symmetry measure will be of use to electrophysiologists that investigate symmetry of network connectivity.

Flexural torsional buckling of uniformly compressed beam-like structures

NASA Astrophysics Data System (ADS)

Ferretti, M.

2018-02-01

A Timoshenko beam model embedded in a 3D space is introduced for buckling analysis of multi-store buildings, made by rigid floors connected by elastic columns. The beam model is developed via a direct approach, and the constitutive law, accounting for prestress forces, is deduced via a suitable homogenization procedure. The bifurcation analysis for the case of uniformly compressed buildings is then addressed, and numerical results concerning the Timoshenko model are compared with 3D finite element analyses. Finally, some conclusions and perspectives are drawn.

Matching and Vertex Packing: How Hard Are They?

DTIC Science & Technology

1991-01-01

Theory, 29, Ann. Discrete Math ., North-Holland, Amsterdam, 1986. [2] M.D. Plummer, Matching theory - a sampler: from D~nes K~nig to the present...Ser. B, 28, 1980, 284-304. [20i N. Sbihi, Algorithme de recherche d’un stable de cardinalit6 maximum dans un graphe sans 6toile, Discrete Math ., 29...cliques and by finite families of graphs, Discrete Math ., 49, 1984, 45-59. [92] G. Cornu~jols, D. Hartvigsen and W.R. Pulleyblank, Packing subgraphs in

On k-ary n-cubes: Theory and applications

NASA Technical Reports Server (NTRS)

Mao, Weizhen; Nicol, David M.

1994-01-01

Many parallel processing networks can be viewed as graphs called k-ary n-cubes, whose special cases include rings, hypercubes and toruses. In this paper, combinatorial properties of k-ary n-cubes are explored. In particular, the problem of characterizing the subgraph of a given number of nodes with the maximum edge count is studied. These theoretical results are then used to compute a lower bounding function in branch-and-bound partitioning algorithms and to establish the optimality of some irregular partitions.

Tracing Actual Causes

DTIC Science & Technology

2016-08-08

actual values for variables in the SEM ), and an event e with M ,~u |= e, our definition answers the question : Which paths of the causal network G( M ...for each variable and a directed edge from vari- able X to Y if the equation for computing X uses Y . Given an SEM M , a context ~u (that supplies the...caused the event e1? Our definition answers this question as a set of causal slices, where each causal slice is a subgraph of G( M ). All paths in each

Identification of informative subgraphs in brain networks

NASA Astrophysics Data System (ADS)

Marinazzo, D.; Wu, G.; Pellicoro, M.; Stramaglia, S.

2013-01-01

Measuring directed interactions in the brain in terms of information flow is a promising approach, mathematically treatable and amenable to encompass several methods. Here we present a formal expansion of the transfer entropy to put in evidence irreducible sets of variables which provide information for the future state of each assigned target. Multiplets characterized by a large contribution to the expansion are associated to informational circuits present in the system, with an informational character (synergetic or redundant) which can be inferred from the sign of the contribution.

Using Graph Components Derived from an Associative Concept Dictionary to Predict fMRI Neural Activation Patterns that Represent the Meaning of Nouns.

PubMed

Akama, Hiroyuki; Miyake, Maki; Jung, Jaeyoung; Murphy, Brian

2015-01-01

In this study, we introduce an original distance definition for graphs, called the Markov-inverse-F measure (MiF). This measure enables the integration of classical graph theory indices with new knowledge pertaining to structural feature extraction from semantic networks. MiF improves the conventional Jaccard and/or Simpson indices, and reconciles both the geodesic information (random walk) and co-occurrence adjustment (degree balance and distribution). We measure the effectiveness of graph-based coefficients through the application of linguistic graph information for a neural activity recorded during conceptual processing in the human brain. Specifically, the MiF distance is computed between each of the nouns used in a previous neural experiment and each of the in-between words in a subgraph derived from the Edinburgh Word Association Thesaurus of English. From the MiF-based information matrix, a machine learning model can accurately obtain a scalar parameter that specifies the degree to which each voxel in (the MRI image of) the brain is activated by each word or each principal component of the intermediate semantic features. Furthermore, correlating the voxel information with the MiF-based principal components, a new computational neurolinguistics model with a network connectivity paradigm is created. This allows two dimensions of context space to be incorporated with both semantic and neural distributional representations.

Unified Photo Enhancement by Discovering Aesthetic Communities From Flickr.

PubMed

Hong, Richang; Zhang, Luming; Tao, Dacheng

2016-03-01

Photo enhancement refers to the process of increasing the aesthetic appeal of a photo, such as changing the photo aspect ratio and spatial recomposition. It is a widely used technique in the printing industry, graphic design, and cinematography. In this paper, we propose a unified and socially aware photo enhancement framework which can leverage the experience of photographers with various aesthetic topics (e.g., portrait and landscape). We focus on photos from the image hosting site Flickr, which has 87 million users and to which more than 3.5 million photos are uploaded daily. First, a tagwise regularized topic model is proposed to describe the aesthetic topic of each Flickr user, and coherent and interpretable topics are discovered by leveraging both the visual features and tags of photos. Next, a graph is constructed to describe the similarities in aesthetic topics between the users. Noticeably, densely connected users have similar aesthetic topics, which are categorized into different communities by a dense subgraph mining algorithm. Finally, a probabilistic model is exploited to enhance the aesthetic attractiveness of a test photo by leveraging the photographic experiences of Flickr users from the corresponding communities of that photo. Paired-comparison-based user studies show that our method performs competitively on photo retargeting and recomposition. Moreover, our approach accurately detects aesthetic communities in a photo set crawled from nearly 100000 Flickr users.

Evaluation of dripper clogging using magnetic water in drip irrigation

NASA Astrophysics Data System (ADS)

Khoshravesh, Mojtaba; Mirzaei, Sayyed Mohammad Javad; Shirazi, Pooya; Valashedi, Reza Norooz

2018-06-01

This study was performed to investigate the uniformity of distribution of water and discharge variations in drip irrigation using magnetic water. Magnetic water was achieved by transition of water using a robust permanent magnet connected to a feed pipeline. Two main factors including magnetic and non-magnetic water and three sub-factor of salt concentration including well water, addition of 150 and 300 mg L-1 calcium carbonate to irrigation water with three replications were applied. The result of magnetic water on average dripper discharge was significant at ( P ≤ 0.05). At the final irrigation, the average dripper discharge and distribution uniformity were higher for the magnetic water compared to the non-magnetic water. The magnetic water showed a significant effect ( P ≤ 0.01) on distribution uniformity of drippers. At the first irrigation, the water distribution uniformity was almost the same for both the magnetic water and the non-magnetic water. The use of magnetic water for drip irrigation is recommended to achieve higher uniformity.

Optimal degrees of synaptic connectivity

PubMed Central

Litwin-Kumar, Ashok; Harris, Kameron Decker; Axel, Richard; Sompolinsky, Haim; Abbott, L. F.

2017-01-01

Summary Synaptic connectivity varies widely across neuronal types. Cerebellar granule cells receive five orders of magnitude fewer inputs than the Purkinje cells they innervate, and cerebellum-like circuits including the insect mushroom body also exhibit large divergences in connectivity. In contrast, the number of inputs per neuron in cerebral cortex is more uniform and large. We investigate how the dimension of a representation formed by a population of neurons depends on how many inputs they each receive and what this implies for learning associations. Our theory predicts that the dimensions of the cerebellar granule-cell and Drosophila Kenyon-cell representations are maximized at degrees of synaptic connectivity that match those observed anatomically, showing that sparse connectivity is sometimes superior to dense connectivity. When input synapses are subject to supervised plasticity, however, dense wiring becomes advantageous, suggesting that the type of plasticity exhibited by a set of synapses is a major determinant of connection density. PMID:28215558

Flexible sampling large-scale social networks by self-adjustable random walk

NASA Astrophysics Data System (ADS)

Xu, Xiao-Ke; Zhu, Jonathan J. H.

2016-12-01

Online social networks (OSNs) have become an increasingly attractive gold mine for academic and commercial researchers. However, research on OSNs faces a number of difficult challenges. One bottleneck lies in the massive quantity and often unavailability of OSN population data. Sampling perhaps becomes the only feasible solution to the problems. How to draw samples that can represent the underlying OSNs has remained a formidable task because of a number of conceptual and methodological reasons. Especially, most of the empirically-driven studies on network sampling are confined to simulated data or sub-graph data, which are fundamentally different from real and complete-graph OSNs. In the current study, we propose a flexible sampling method, called Self-Adjustable Random Walk (SARW), and test it against with the population data of a real large-scale OSN. We evaluate the strengths of the sampling method in comparison with four prevailing methods, including uniform, breadth-first search (BFS), random walk (RW), and revised RW (i.e., MHRW) sampling. We try to mix both induced-edge and external-edge information of sampled nodes together in the same sampling process. Our results show that the SARW sampling method has been able to generate unbiased samples of OSNs with maximal precision and minimal cost. The study is helpful for the practice of OSN research by providing a highly needed sampling tools, for the methodological development of large-scale network sampling by comparative evaluations of existing sampling methods, and for the theoretical understanding of human networks by highlighting discrepancies and contradictions between existing knowledge/assumptions of large-scale real OSN data.

On automating domain connectivity for overset grids

NASA Technical Reports Server (NTRS)

Chiu, Ing-Tsau; Meakin, Robert L.

1995-01-01

An alternative method for domain connectivity among systems of overset grids is presented. Reference uniform Cartesian systems of points are used to achieve highly efficient domain connectivity, and form the basis for a future fully automated system. The Cartesian systems are used to approximate body surfaces and to map the computational space of component grids. By exploiting the characteristics of Cartesian systems, Chimera type hole-cutting and identification of donor elements for intergrid boundary points can be carried out very efficiently. The method is tested for a range of geometrically complex multiple-body overset grid systems. A dynamic hole expansion/contraction algorithm is also implemented to obtain optimum domain connectivity; however, it is tested only for geometry of generic shapes.

Network for minimizing current imbalances in a faradaic battery

DOEpatents

Wozniak, Walter; Haskins, Harold J.

1994-01-01

A circuit for connecting a faradaic battery with circuitry for monitoring the condition of the battery includes a plurality of voltage divider networks providing battery voltage monitoring nodes and includes compensating resistors connected with the networks to maintain uniform discharge currents through the cells of the battery. The circuit also provides a reduced common mode voltage requirement for the monitoring circuitry by referencing the divider networks to one-half the battery voltage.

Eb&D: A new clustering approach for signed social networks based on both edge-betweenness centrality and density of subgraphs

NASA Astrophysics Data System (ADS)

Qi, Xingqin; Song, Huimin; Wu, Jianliang; Fuller, Edgar; Luo, Rong; Zhang, Cun-Quan

2017-09-01

Clustering algorithms for unsigned social networks which have only positive edges have been studied intensively. However, when a network has like/dislike, love/hate, respect/disrespect, or trust/distrust relationships, unsigned social networks with only positive edges are inadequate. Thus we model such kind of networks as signed networks which can have both negative and positive edges. Detecting the cluster structures of signed networks is much harder than for unsigned networks, because it not only requires that positive edges within clusters are as many as possible, but also requires that negative edges between clusters are as many as possible. Currently, we have few clustering algorithms for signed networks, and most of them requires the number of final clusters as an input while it is actually hard to predict beforehand. In this paper, we will propose a novel clustering algorithm called Eb &D for signed networks, where both the betweenness of edges and the density of subgraphs are used to detect cluster structures. A hierarchically nested system will be constructed to illustrate the inclusion relationships of clusters. To show the validity and efficiency of Eb &D, we test it on several classical social networks and also hundreds of synthetic data sets, and all obtain better results compared with other methods. The biggest advantage of Eb &D compared with other methods is that the number of clusters do not need to be known prior.

HEAT TRANSFER MEANS

DOEpatents

Fraas, A.P.; Wislicenus, G.F.

1961-07-11

A heat exchanger is adapted to unifomly cool a spherical surface. Equations for the design of a spherical heat exchanger hav~g tubes with a uniform center-to-center spining are given. The heat exchanger is illustrated in connection with a liquid-fueled reactor.

Covariant Formulation of Hooke's Law.

ERIC Educational Resources Information Center

Gron, O.

1981-01-01

Introducing a four-vector strain and a four-force stress, Hooke's law is written as a four-vector equation. This formulation is shown to clarify seemingly paradoxical results in connection with uniformly accelerated motion, and rotational motion with angular acceleration. (Author/JN)

Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads.

PubMed

Lima, Leandro; Sinaimeri, Blerina; Sacomoto, Gustavo; Lopez-Maestre, Helene; Marchet, Camille; Miele, Vincent; Sagot, Marie-France; Lacroix, Vincent

2017-01-01

The main challenge in de novo genome assembly of DNA-seq data is certainly to deal with repeats that are longer than the reads. In de novo transcriptome assembly of RNA-seq reads, on the other hand, this problem has been underestimated so far. Even though we have fewer and shorter repeated sequences in transcriptomics, they do create ambiguities and confuse assemblers if not addressed properly. Most transcriptome assemblers of short reads are based on de Bruijn graphs (DBG) and have no clear and explicit model for repeats in RNA-seq data, relying instead on heuristics to deal with them. The results of this work are threefold. First, we introduce a formal model for representing high copy-number and low-divergence repeats in RNA-seq data and exploit its properties to infer a combinatorial characteristic of repeat-associated subgraphs. We show that the problem of identifying such subgraphs in a DBG is NP-complete. Second, we show that in the specific case of local assembly of alternative splicing (AS) events, we can implicitly avoid such subgraphs, and we present an efficient algorithm to enumerate AS events that are not included in repeats. Using simulated data, we show that this strategy is significantly more sensitive and precise than the previous version of KisSplice (Sacomoto et al. in WABI, pp 99-111, 1), Trinity (Grabherr et al. in Nat Biotechnol 29(7):644-652, 2), and Oases (Schulz et al. in Bioinformatics 28(8):1086-1092, 3), for the specific task of calling AS events. Third, we turn our focus to full-length transcriptome assembly, and we show that exploring the topology of DBGs can improve de novo transcriptome evaluation methods. Based on the observation that repeats create complicated regions in a DBG, and when assemblers try to traverse these regions, they can infer erroneous transcripts, we propose a measure to flag transcripts traversing such troublesome regions, thereby giving a confidence level for each transcript. The originality of our work when compared to other transcriptome evaluation methods is that we use only the topology of the DBG, and not read nor coverage information. We show that our simple method gives better results than Rsem-Eval (Li et al. in Genome Biol 15(12):553, 4) and TransRate (Smith-Unna et al. in Genome Res 26(8):1134-1144, 5) on both real and simulated datasets for detecting chimeras, and therefore is able to capture assembly errors missed by these methods.

Superconducting matrix fault current limiter with current-driven trigger mechanism

DOEpatents

Yuan; Xing

2008-04-15

A modular and scalable Matrix-type Fault Current Limiter (MFCL) that functions as a "variable impedance" device in an electric power network, using components made of superconducting and non-superconducting electrically conductive materials. An inductor is connected in series with the trigger superconductor in the trigger matrix and physically surrounds the superconductor. The current surge during a fault will generate a trigger magnetic field in the series inductor to cause fast and uniform quenching of the trigger superconductor to significantly reduce burnout risk due to superconductor material non-uniformity.

Slow opening valve. [valve design for shuttle portable oxygen system

NASA Technical Reports Server (NTRS)

Drapeau, D. F. (Inventor)

1984-01-01

A valve control is described having a valve body with an actuator stem and a rotating handle connected to the actuator stem by a differential drive mechanism which, during uniform movement of the handle in one direction, initially opens the valve at a relatively slow rate and, thereafter, complete the valve movement at a substantially faster rate. A series of stop rings are received about the body in frictional abutting relationship and serially rotated by the handle to uniformly resist handle movement independently of the extent of handle movement.

Immunization of complex networks

NASA Astrophysics Data System (ADS)

Pastor-Satorras, Romualdo; Vespignani, Alessandro

2002-03-01

Complex networks such as the sexual partnership web or the Internet often show a high degree of redundancy and heterogeneity in their connectivity properties. This peculiar connectivity provides an ideal environment for the spreading of infective agents. Here we show that the random uniform immunization of individuals does not lead to the eradication of infections in all complex networks. Namely, networks with scale-free properties do not acquire global immunity from major epidemic outbreaks even in the presence of unrealistically high densities of randomly immunized individuals. The absence of any critical immunization threshold is due to the unbounded connectivity fluctuations of scale-free networks. Successful immunization strategies can be developed only by taking into account the inhomogeneous connectivity properties of scale-free networks. In particular, targeted immunization schemes, based on the nodes' connectivity hierarchy, sharply lower the network's vulnerability to epidemic attacks.

Binary synaptic connections based on memory switching in a-Si:H for artificial neural networks

NASA Technical Reports Server (NTRS)

Thakoor, A. P.; Lamb, J. L.; Moopenn, A.; Khanna, S. K.

1987-01-01

A scheme for nonvolatile associative electronic memory storage with high information storage density is proposed which is based on neural network models and which uses a matrix of two-terminal passive interconnections (synapses). It is noted that the massive parallelism in the architecture would require the ON state of a synaptic connection to be unusually weak (highly resistive). Memory switching using a-Si:H along with ballast resistors patterned from amorphous Ge-metal alloys is investigated for a binary programmable read only memory matrix. The fabrication of a 1600 synapse test array of uniform connection strengths and a-Si:H switching elements is discussed.

One-Time URL: A Proximity Security Mechanism between Internet of Things and Mobile Devices.

PubMed

Solano, Antonio; Dormido, Raquel; Duro, Natividad; González, Víctor

2016-10-13

The aim of this paper is to determine the physical proximity of connected things when they are accessed from a smartphone. Links between connected things and mobile communication devices are temporarily created by means of dynamic URLs (uniform resource locators) which may be easily discovered with pervasive short-range radio frequency technologies available on smartphones. In addition, a multi cross domain silent logging mechanism to allow people to interact with their surrounding connected things from their mobile communication devices is presented. The proposed mechanisms are based in web standards technologies, evolving our social network of Internet of Things towards the so-called Web of Things.

Internally supported flexible duct joint. [device for conducting fluids in high pressure systems

NASA Technical Reports Server (NTRS)

Kuhn, R. F., Jr. (Inventor)

1975-01-01

An internally supported, flexible duct joint for use in conducting fluids under relatively high pressures in systems where relatively large deflection angles must be accommodated is presented. The joint includes a flexible tubular bellows and an elongated base disposed within the bellows. The base is connected through radiating struts to the bellows near mid-portion and to each of the opposite end portions of the bellows through a pivotal connecting body. A motion-controlling linkage is provided for linking the connecting bodies, whereby angular displacement of the joint is controlled and uniformity in the instantaneous bend radius of the duct is achieved as deflection is imposed.

Self-consistent molecular dynamics formulation for electric-field-mediated electrolyte transport through nanochannels

NASA Astrophysics Data System (ADS)

Raghunathan, A. V.; Aluru, N. R.

2007-07-01

A self-consistent molecular dynamics (SCMD) formulation is presented for electric-field-mediated transport of water and ions through a nanochannel connected to reservoirs or baths. The SCMD formulation is compared with a uniform field MD approach, where the applied electric field is assumed to be uniform, for 2nm and 3.5nm wide nanochannels immersed in a 0.5M KCl solution. Reservoir ionic concentrations are maintained using the dual-control-volume grand canonical molecular dynamics technique. Simulation results with varying channel height indicate that the SCMD approach calculates the electrostatic potential in the simulation domain more accurately compared to the uniform field approach, with the deviation in results increasing with the channel height. The translocation times and ionic fluxes predicted by uniform field MD can be substantially different from those predicted by the SCMD approach. Our results also indicate that during a 2ns simulation time K+ ions can permeate through a 1nm channel when the applied electric field is computed self-consistently, while the permeation is not observed when the electric field is assumed to be uniform.

BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks.

PubMed

Maere, Steven; Heymans, Karel; Kuiper, Martin

2005-08-15

The Biological Networks Gene Ontology tool (BiNGO) is an open-source Java tool to determine which Gene Ontology (GO) terms are significantly overrepresented in a set of genes. BiNGO can be used either on a list of genes, pasted as text, or interactively on subgraphs of biological networks visualized in Cytoscape. BiNGO maps the predominant functional themes of the tested gene set on the GO hierarchy, and takes advantage of Cytoscape's versatile visualization environment to produce an intuitive and customizable visual representation of the results.

Discovering protein complexes in protein interaction networks via exploring the weak ties effect

PubMed Central

2012-01-01

Background Studying protein complexes is very important in biological processes since it helps reveal the structure-functionality relationships in biological networks and much attention has been paid to accurately predict protein complexes from the increasing amount of protein-protein interaction (PPI) data. Most of the available algorithms are based on the assumption that dense subgraphs correspond to complexes, failing to take into account the inherence organization within protein complex and the roles of edges. Thus, there is a critical need to investigate the possibility of discovering protein complexes using the topological information hidden in edges. Results To provide an investigation of the roles of edges in PPI networks, we show that the edges connecting less similar vertices in topology are more significant in maintaining the global connectivity, indicating the weak ties phenomenon in PPI networks. We further demonstrate that there is a negative relation between the weak tie strength and the topological similarity. By using the bridges, a reliable virtual network is constructed, in which each maximal clique corresponds to the core of a complex. By this notion, the detection of the protein complexes is transformed into a classic all-clique problem. A novel core-attachment based method is developed, which detects the cores and attachments, respectively. A comprehensive comparison among the existing algorithms and our algorithm has been made by comparing the predicted complexes against benchmark complexes. Conclusions We proved that the weak tie effect exists in the PPI network and demonstrated that the density is insufficient to characterize the topological structure of protein complexes. Furthermore, the experimental results on the yeast PPI network show that the proposed method outperforms the state-of-the-art algorithms. The analysis of detected modules by the present algorithm suggests that most of these modules have well biological significance in context of complexes, suggesting that the roles of edges are critical in discovering protein complexes. PMID:23046740

Efficient and accurate Greedy Search Methods for mining functional modules in protein interaction networks.

PubMed

He, Jieyue; Li, Chaojun; Ye, Baoliu; Zhong, Wei

2012-06-25

Most computational algorithms mainly focus on detecting highly connected subgraphs in PPI networks as protein complexes but ignore their inherent organization. Furthermore, many of these algorithms are computationally expensive. However, recent analysis indicates that experimentally detected protein complexes generally contain Core/attachment structures. In this paper, a Greedy Search Method based on Core-Attachment structure (GSM-CA) is proposed. The GSM-CA method detects densely connected regions in large protein-protein interaction networks based on the edge weight and two criteria for determining core nodes and attachment nodes. The GSM-CA method improves the prediction accuracy compared to other similar module detection approaches, however it is computationally expensive. Many module detection approaches are based on the traditional hierarchical methods, which is also computationally inefficient because the hierarchical tree structure produced by these approaches cannot provide adequate information to identify whether a network belongs to a module structure or not. In order to speed up the computational process, the Greedy Search Method based on Fast Clustering (GSM-FC) is proposed in this work. The edge weight based GSM-FC method uses a greedy procedure to traverse all edges just once to separate the network into the suitable set of modules. The proposed methods are applied to the protein interaction network of S. cerevisiae. Experimental results indicate that many significant functional modules are detected, most of which match the known complexes. Results also demonstrate that the GSM-FC algorithm is faster and more accurate as compared to other competing algorithms. Based on the new edge weight definition, the proposed algorithm takes advantages of the greedy search procedure to separate the network into the suitable set of modules. Experimental analysis shows that the identified modules are statistically significant. The algorithm can reduce the computational time significantly while keeping high prediction accuracy.

18 CFR 367.9310 - Account 931, Rents.

Code of Federal Regulations, 2010 CFR

2010-04-01

... NATURAL GAS ACT UNIFORM SYSTEM OF ACCOUNTS FOR CENTRALIZED SERVICE COMPANIES SUBJECT TO THE PROVISIONS OF..., including taxes, paid for the property of others used, occupied or operated in connection with service... structure, office furniture, fixtures, computers, data processing equipment, microwave and telecommunication...

18 CFR 367.9310 - Account 931, Rents.

Code of Federal Regulations, 2011 CFR

2011-04-01

... NATURAL GAS ACT UNIFORM SYSTEM OF ACCOUNTS FOR CENTRALIZED SERVICE COMPANIES SUBJECT TO THE PROVISIONS OF..., including taxes, paid for the property of others used, occupied or operated in connection with service... structure, office furniture, fixtures, computers, data processing equipment, microwave and telecommunication...

18 CFR 367.9310 - Account 931, Rents.

Code of Federal Regulations, 2012 CFR

2012-04-01

... NATURAL GAS ACT UNIFORM SYSTEM OF ACCOUNTS FOR CENTRALIZED SERVICE COMPANIES SUBJECT TO THE PROVISIONS OF..., including taxes, paid for the property of others used, occupied or operated in connection with service... structure, office furniture, fixtures, computers, data processing equipment, microwave and telecommunication...

18 CFR 367.9310 - Account 931, Rents.

Code of Federal Regulations, 2014 CFR

2014-04-01

... NATURAL GAS ACT UNIFORM SYSTEM OF ACCOUNTS FOR CENTRALIZED SERVICE COMPANIES SUBJECT TO THE PROVISIONS OF..., including taxes, paid for the property of others used, occupied or operated in connection with service... structure, office furniture, fixtures, computers, data processing equipment, microwave and telecommunication...

18 CFR 367.9310 - Account 931, Rents.

Code of Federal Regulations, 2013 CFR

2013-04-01

... NATURAL GAS ACT UNIFORM SYSTEM OF ACCOUNTS FOR CENTRALIZED SERVICE COMPANIES SUBJECT TO THE PROVISIONS OF..., including taxes, paid for the property of others used, occupied or operated in connection with service... structure, office furniture, fixtures, computers, data processing equipment, microwave and telecommunication...

Electrical contact structures for solid oxide electrolyte fuel cell

DOEpatents

Isenberg, Arnold O.

1984-01-01

An improved electrical output connection means is provided for a high temperature solid oxide electrolyte type fuel cell generator. The electrical connection of the fuel cell electrodes to the electrical output bus, which is brought through the generator housing to be connected to an electrical load line maintains a highly uniform temperature distribution. The electrical connection means includes an electrode bus which is spaced parallel to the output bus with a plurality of symmetrically spaced transversely extending conductors extending between the electrode bus and the output bus, with thermal insulation means provided about the transverse conductors between the spaced apart buses. Single or plural stages of the insulated transversely extending conductors can be provided within the high temperatures regions of the fuel cell generator to provide highly homogeneous temperature distribution over the contacting surfaces.

50 CFR 11.1 - Purpose of regulations.

Code of Federal Regulations, 2011 CFR

2011-10-01

..., POSSESSION, TRANSPORTATION, SALE, PURCHASE, BARTER, EXPORTATION, AND IMPORTATION OF WILDLIFE AND PLANTS CIVIL PROCEDURES Introduction § 11.1 Purpose of regulations. The regulations contained in this part provide uniform rules and procedures for the assessment of civil penalties in connection with violations of certain laws...

Flexible single-layer ionic organic-inorganic frameworks towards precise nano-size separation

NASA Astrophysics Data System (ADS)

Yue, Liang; Wang, Shan; Zhou, Ding; Zhang, Hao; Li, Bao; Wu, Lixin

2016-02-01

Consecutive two-dimensional frameworks comprised of molecular or cluster building blocks in large area represent ideal candidates for membranes sieving molecules and nano-objects, but challenges still remain in methodology and practical preparation. Here we exploit a new strategy to build soft single-layer ionic organic-inorganic frameworks via electrostatic interaction without preferential binding direction in water. Upon consideration of steric effect and additional interaction, polyanionic clusters as connection nodes and cationic pseudorotaxanes acting as bridging monomers connect with each other to form a single-layer ionic self-assembled framework with 1.4 nm layer thickness. Such soft supramolecular polymer frameworks possess uniform and adjustable ortho-tetragonal nanoporous structure in pore size of 3.4-4.1 nm and exhibit greatly convenient solution processability. The stable membranes maintaining uniform porous structure demonstrate precisely size-selective separation of semiconductor quantum dots within 0.1 nm of accuracy and may hold promise for practical applications in selective transport, molecular separation and dialysis systems.

Equation of state of an ideal gas with nonergodic behavior in two connected vessels.

PubMed

Naplekov, D M; Semynozhenko, V P; Yanovsky, V V

2014-01-01

We consider a two-dimensional collisionless ideal gas in the two vessels connected through a small hole. One of them is a well-behaved chaotic billiard, another one is known to be nonergodic. A significant part of the second vessel's phase space is occupied by an island of stability. In the works of Zaslavsky and coauthors, distribution of Poincaré recurrence times in similar systems was considered. We study the gas pressure in the vessels; it is uniform in the first vessel and not uniform in second one. An equation of the gas state in the first vessel is obtained. Despite the very different phase-space structure, behavior of the second vessel is found to be very close to the behavior of a good ergodic billiard but of different volume. The equation of state differs from the ordinary equation of ideal gas state by an amendment to the vessel's volume. Correlation of this amendment with a share of the phase space under remaining intact islands of stability is shown.

Uniformity of nucleosome preservation pattern in Mammalian sperm and its connection to repetitive DNA elements.

PubMed

Samans, Birgit; Yang, Yang; Krebs, Stefan; Sarode, Gaurav Vilas; Blum, Helmut; Reichenbach, Myriam; Wolf, Eckhard; Steger, Klaus; Dansranjavin, Temuujin; Schagdarsurengin, Undraga

2014-07-14

Nucleosome-to-protamine exchange during mammalian spermiogenesis is essential for compaction and protection of paternal DNA. It is interesting that, depending on the species, 1% to 15% of nucleosomes are retained, but the generalizability and biological function of this retention are unknown. Here, we show concordantly in human and bovine that nucleosomes remained in sperm chromatin predominantly within distal intergenic regions and introns and associated with centromere repeats and retrotransposons (LINE1 and SINEs). In contrast, nucleosome depletion concerned particularly exons, 5'-UTR, 3'-UTR, TSS, and TTS and was associated with simple and low-complexity repeats. Overlap of human and bovine genes exhibiting nucleosome preservation in the promoter and gene body revealed a significant enrichment of signal transduction and RNA- and protein-processing factors. Our study demonstrates the genome-wide uniformity of the nucleosome preservation pattern in mammalian sperm and its connection to repetitive DNA elements and suggests a function in preimplantation processes for paternally derived nucleosomes. Copyright © 2014 Elsevier Inc. All rights reserved.

Being around and knowing the players: networks of influence in health policy.

PubMed

Lewis, Jenny M

2006-05-01

The accumulation and use of power is crucial to the health policy process. This paper examines the power of the medical profession in the health policy arena, by analysing which actors are perceived as influential, and how influence is structured in health policy. It combines an analysis of policy networks and social networks, to examine positional and personal influence in health policy in the state of Victoria, Australia. In the sub-graph of the influence network examined here, those most widely regarded as influential are academics, medically qualified and male. Positional actors (the top politician, political advisor and bureaucrat in health and the top nursing official) form part of a core group within this network structure. A second central group consists of medical influentials working in academia, research institutes and health-related NGOs. In this network locale overall, medical academics appear to combine positional and personal influence, and play significant intermediary roles across the network. While many claim that the medical profession has lost power in health policy and politics, this analysis yields few signs that the power of medicine to shape the health policy process has been greatly diminished in Victoria. Medical expertise is a potent embedded resource connecting actors through ties of association, making it difficult for actors with other resources and different knowledge to be considered influential. The network concepts and analytical techniques used here provide a novel means for uncovering different types of influence in health policy.

Lost in the city: revisiting Milgram's experiment in the age of social networks.

PubMed

Szüle, János; Kondor, Dániel; Dobos, László; Csabai, István; Vattay, Gábor

2014-01-01

As more and more users access social network services from smart devices with GPS receivers, the available amount of geo-tagged information makes repeating classical experiments possible on global scales and with unprecedented precision. Inspired by the original experiments of Milgram, we simulated message routing within a representative sub-graph of the network of Twitter users with about 6 million geo-located nodes and 122 million edges. We picked pairs of users from two distant metropolitan areas and tried to find a route between them using local geographic information only; our method was to forward messages to a friend living closest to the target. We found that the examined network is navigable on large scales, but navigability breaks down at the city scale and the network becomes unnavigable on intra-city distances. This means that messages usually arrived to the close proximity of the target in only 3-6 steps, but only in about 20% of the cases was it possible to find a route all the way to the recipient, in spite of the network being connected. This phenomenon is supported by the distribution of link lengths; on larger scales the distribution behaves approximately as P(d) ≈ 1/d, which was found earlier by Kleinberg to allow efficient navigation, while on smaller scales, a fractal structure becomes apparent. The intra-city correlation dimension of the network was found to be D2 = 1.25, less than the dimension D2 = 1.78 of the distribution of the population.

Predicting and Detecting Emerging Cyberattack Patterns Using StreamWorks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chin, George; Choudhury, Sutanay; Feo, John T.

2014-06-30

The number and sophistication of cyberattacks on industries and governments have dramatically grown in recent years. To counter this movement, new advanced tools and techniques are needed to detect cyberattacks in their early stages such that defensive actions may be taken to avert or mitigate potential damage. From a cybersecurity analysis perspective, detecting cyberattacks may be cast as a problem of identifying patterns in computer network traffic. Logically and intuitively, these patterns may take on the form of a directed graph that conveys how an attack or intrusion propagates through the computers of a network. Such cyberattack graphs could providemore » cybersecurity analysts with powerful conceptual representations that are natural to express and analyze. We have been researching and developing graph-centric approaches and algorithms for dynamic cyberattack detection. The advanced dynamic graph algorithms we are developing will be packaged into a streaming network analysis framework known as StreamWorks. With StreamWorks, a scientist or analyst may detect and identify precursor events and patterns as they emerge in complex networks. This analysis framework is intended to be used in a dynamic environment where network data is streamed in and is appended to a large-scale dynamic graph. Specific graphical query patterns are decomposed and collected into a graph query library. The individual decomposed subpatterns in the library are continuously and efficiently matched against the dynamic graph as it evolves to identify and detect early, partial subgraph patterns. The scalable emerging subgraph pattern algorithms will match on both structural and semantic network properties.« less

An efficient, large-scale, non-lattice-detection algorithm for exhaustive structural auditing of biomedical ontologies.

PubMed

Zhang, Guo-Qiang; Xing, Guangming; Cui, Licong

2018-04-01

One of the basic challenges in developing structural methods for systematic audition on the quality of biomedical ontologies is the computational cost usually involved in exhaustive sub-graph analysis. We introduce ANT-LCA, a new algorithm for computing all non-trivial lowest common ancestors (LCA) of each pair of concepts in the hierarchical order induced by an ontology. The computation of LCA is a fundamental step for non-lattice approach for ontology quality assurance. Distinct from existing approaches, ANT-LCA only computes LCAs for non-trivial pairs, those having at least one common ancestor. To skip all trivial pairs that may be of no practical interest, ANT-LCA employs a simple but innovative algorithmic strategy combining topological order and dynamic programming to keep track of non-trivial pairs. We provide correctness proofs and demonstrate a substantial reduction in computational time for two largest biomedical ontologies: SNOMED CT and Gene Ontology (GO). ANT-LCA achieved an average computation time of 30 and 3 sec per version for SNOMED CT and GO, respectively, about 2 orders of magnitude faster than the best known approaches. Our algorithm overcomes a fundamental computational barrier in sub-graph based structural analysis of large ontological systems. It enables the implementation of a new breed of structural auditing methods that not only identifies potential problematic areas, but also automatically suggests changes to fix the issues. Such structural auditing methods can lead to more effective tools supporting ontology quality assurance work. Copyright © 2018 Elsevier Inc. All rights reserved.

A Simulation Study Comparing Epidemic Dynamics on Exponential Random Graph and Edge-Triangle Configuration Type Contact Network Models

PubMed Central

Rolls, David A.; Wang, Peng; McBryde, Emma; Pattison, Philippa; Robins, Garry

2015-01-01

We compare two broad types of empirically grounded random network models in terms of their abilities to capture both network features and simulated Susceptible-Infected-Recovered (SIR) epidemic dynamics. The types of network models are exponential random graph models (ERGMs) and extensions of the configuration model. We use three kinds of empirical contact networks, chosen to provide both variety and realistic patterns of human contact: a highly clustered network, a bipartite network and a snowball sampled network of a “hidden population”. In the case of the snowball sampled network we present a novel method for fitting an edge-triangle model. In our results, ERGMs consistently capture clustering as well or better than configuration-type models, but the latter models better capture the node degree distribution. Despite the additional computational requirements to fit ERGMs to empirical networks, the use of ERGMs provides only a slight improvement in the ability of the models to recreate epidemic features of the empirical network in simulated SIR epidemics. Generally, SIR epidemic results from using configuration-type models fall between those from a random network model (i.e., an Erdős-Rényi model) and an ERGM. The addition of subgraphs of size four to edge-triangle type models does improve agreement with the empirical network for smaller densities in clustered networks. Additional subgraphs do not make a noticeable difference in our example, although we would expect the ability to model cliques to be helpful for contact networks exhibiting household structure. PMID:26555701

Fault tolerance in protein interaction networks: stable bipartite subgraphs and redundant pathways.

PubMed

Brady, Arthur; Maxwell, Kyle; Daniels, Noah; Cowen, Lenore J

2009-01-01

As increasing amounts of high-throughput data for the yeast interactome become available, more system-wide properties are uncovered. One interesting question concerns the fault tolerance of protein interaction networks: whether there exist alternative pathways that can perform some required function if a gene essential to the main mechanism is defective, absent or suppressed. A signature pattern for redundant pathways is the BPM (between-pathway model) motif, introduced by Kelley and Ideker. Past methods proposed to search the yeast interactome for BPM motifs have had several important limitations. First, they have been driven heuristically by local greedy searches, which can lead to the inclusion of extra genes that may not belong in the motif; second, they have been validated solely by functional coherence of the putative pathways using GO enrichment, making it difficult to evaluate putative BPMs in the absence of already known biological annotation. We introduce stable bipartite subgraphs, and show they form a clean and efficient way of generating meaningful BPMs which naturally discard extra genes included by local greedy methods. We show by GO enrichment measures that our BPM set outperforms previous work, covering more known complexes and functional pathways. Perhaps most importantly, since our BPMs are initially generated by examining the genetic-interaction network only, the location of edges in the protein-protein physical interaction network can then be used to statistically validate each candidate BPM, even with sparse GO annotation (or none at all). We uncover some interesting biological examples of previously unknown putative redundant pathways in such areas as vesicle-mediated transport and DNA repair.

Fault Tolerance in Protein Interaction Networks: Stable Bipartite Subgraphs and Redundant Pathways

PubMed Central

Brady, Arthur; Maxwell, Kyle; Daniels, Noah; Cowen, Lenore J.

2009-01-01

As increasing amounts of high-throughput data for the yeast interactome become available, more system-wide properties are uncovered. One interesting question concerns the fault tolerance of protein interaction networks: whether there exist alternative pathways that can perform some required function if a gene essential to the main mechanism is defective, absent or suppressed. A signature pattern for redundant pathways is the BPM (between-pathway model) motif, introduced by Kelley and Ideker. Past methods proposed to search the yeast interactome for BPM motifs have had several important limitations. First, they have been driven heuristically by local greedy searches, which can lead to the inclusion of extra genes that may not belong in the motif; second, they have been validated solely by functional coherence of the putative pathways using GO enrichment, making it difficult to evaluate putative BPMs in the absence of already known biological annotation. We introduce stable bipartite subgraphs, and show they form a clean and efficient way of generating meaningful BPMs which naturally discard extra genes included by local greedy methods. We show by GO enrichment measures that our BPM set outperforms previous work, covering more known complexes and functional pathways. Perhaps most importantly, since our BPMs are initially generated by examining the genetic-interaction network only, the location of edges in the protein-protein physical interaction network can then be used to statistically validate each candidate BPM, even with sparse GO annotation (or none at all). We uncover some interesting biological examples of previously unknown putative redundant pathways in such areas as vesicle-mediated transport and DNA repair. PMID:19399174

On Bernstein type inequalities and a weighted Chebyshev approximation problem on ellipses

NASA Technical Reports Server (NTRS)

Freund, Roland

1989-01-01

A classical inequality due to Bernstein which estimates the norm of polynomials on any given ellipse in terms of their norm on any smaller ellipse with the same foci is examined. For the uniform and a certain weighted uniform norm, and for the case that the two ellipses are not too close, sharp estimates of this type were derived and the corresponding extremal polynomials were determined. These Bernstein type inequalities are closely connected with certain constrained Chebyshev approximation problems on ellipses. Some new results were also presented for a weighted approximation problem of this type.

CD uniformity control for thick resist process

NASA Astrophysics Data System (ADS)

Huang, Chi-hao; Liu, Yu-Lin; Wang, Weihung; Yang, Mars; Yang, Elvis; Yang, T. H.; Chen, K. C.

2017-03-01

In order to meet the increasing storage capacity demand and reduce bit cost of NAND flash memories, 3D stacked flash cell array has been proposed. In constructing 3D NAND flash memories, the higher bit number per area is achieved by increasing the number of stacked layers. Thus the so-called "staircase" patterning to form electrical connection between memory cells and word lines has become one of the primarily critical processes in 3D memory manufacture. To provide controllable critical dimension (CD) with good uniformity involving thick photo-resist has also been of particular concern for staircase patterning. The CD uniformity control has been widely investigated with relatively thinner resist associated with resolution limit dimension but thick resist coupling with wider dimension. This study explores CD uniformity control associated with thick photo-resist processing. Several critical parameters including exposure focus, exposure dose, baking condition, pattern size and development recipe, were found to strongly correlate with the thick photo-resist profile accordingly affecting the CD uniformity control. To minimize the within-wafer CD variation, the slightly tapered resist profile is proposed through well tailoring the exposure focus and dose together with optimal development recipe. Great improvements on DCD (ADI CD) and ECD (AEI CD) uniformity as well as line edge roughness were achieved through the optimization of photo resist profile.

Robustness of crossover trials against subject drop-out - Examples of perpetually connected designs.

PubMed

Godolphin, P J; Godolphin, E J

2017-01-01

When performing a repeated measures experiment, such as a clinical trial, there is a risk of subject drop-out during the experiment. If one or more subjects leave the study prematurely, a situation could arise where the eventual design is disconnected, implying that very few treatment contrasts for both direct effects and carryover effects are estimable. This paper aims to identify experimental conditions where this problem with the eventual design can be avoided. It is shown that in the class of uniformly balanced repeated measurement designs consisting of two or more Latin squares, there are planned designs with the following useful property. Provided that all subjects have completed the first two periods of study, such a design will not be replaced by a disconnected eventual design due to drop-out, irrespective of the type of drop-out behaviour that may occur. Designs with this property are referred to as perpetually connected. These experimental conditions are identified and examined in the paper and an example of at least one perpetually connected uniformly balanced repeated measurement design is given in each case. The results improve upon previous contributions in the literature that have been confined largely to cases in which drop-out occurs only in the final periods of study.

One-Time URL: A Proximity Security Mechanism between Internet of Things and Mobile Devices

PubMed Central

Solano, Antonio; Dormido, Raquel; Duro, Natividad; González, Víctor

2016-01-01

The aim of this paper is to determine the physical proximity of connected things when they are accessed from a smartphone. Links between connected things and mobile communication devices are temporarily created by means of dynamic URLs (uniform resource locators) which may be easily discovered with pervasive short-range radio frequency technologies available on smartphones. In addition, a multi cross domain silent logging mechanism to allow people to interact with their surrounding connected things from their mobile communication devices is presented. The proposed mechanisms are based in web standards technologies, evolving our social network of Internet of Things towards the so-called Web of Things. PMID:27754378

45 CFR 74.45 - Cost and price analysis.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 45 Public Welfare 1 2011-10-01 2011-10-01 false Cost and price analysis. 74.45 Section 74.45 Public Welfare DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL ADMINISTRATION UNIFORM ADMINISTRATIVE... connection with every procurement action. Price analysis may be accomplished in various ways, including the...

45 CFR 74.45 - Cost and price analysis.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 45 Public Welfare 1 2010-10-01 2010-10-01 false Cost and price analysis. 74.45 Section 74.45 Public Welfare DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL ADMINISTRATION UNIFORM ADMINISTRATIVE... connection with every procurement action. Price analysis may be accomplished in various ways, including the...

46 CFR 168.01-1 - Purpose of regulations.

Code of Federal Regulations, 2011 CFR

2011-10-01

... Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) NAUTICAL SCHOOLS CIVILIAN NAUTICAL SCHOOL... this part is to set forth uniform minimum requirements for vessels, whether being navigated or not, which are used by or in connection with any civilian nautical school, except vessels of the Navy or...

46 CFR 168.01-1 - Purpose of regulations.

Code of Federal Regulations, 2014 CFR

2014-10-01

... Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) NAUTICAL SCHOOLS CIVILIAN NAUTICAL SCHOOL... this part is to set forth uniform minimum requirements for vessels, whether being navigated or not, which are used by or in connection with any civilian nautical school, except vessels of the Navy or...

46 CFR 168.01-1 - Purpose of regulations.

Code of Federal Regulations, 2010 CFR

2010-10-01

... Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) NAUTICAL SCHOOLS CIVILIAN NAUTICAL SCHOOL... this part is to set forth uniform minimum requirements for vessels, whether being navigated or not, which are used by or in connection with any civilian nautical school, except vessels of the Navy or...

46 CFR 168.01-1 - Purpose of regulations.

Code of Federal Regulations, 2013 CFR

2013-10-01

... Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) NAUTICAL SCHOOLS CIVILIAN NAUTICAL SCHOOL... this part is to set forth uniform minimum requirements for vessels, whether being navigated or not, which are used by or in connection with any civilian nautical school, except vessels of the Navy or...

46 CFR 168.01-1 - Purpose of regulations.

Code of Federal Regulations, 2012 CFR

2012-10-01

... Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) NAUTICAL SCHOOLS CIVILIAN NAUTICAL SCHOOL... this part is to set forth uniform minimum requirements for vessels, whether being navigated or not, which are used by or in connection with any civilian nautical school, except vessels of the Navy or...

32 CFR 518.19 - General provisions.

Code of Federal Regulations, 2012 CFR

2012-07-01

... PUBLIC RELATIONS THE FREEDOM OF INFORMATION ACT PROGRAM Fee Schedule § 518.19 General provisions. (a... requests, and conform to the Office of Management and Budget Uniform Freedom of Information Act Fee... to imply that fees must be charged in connection with providing information to the public in the...

32 CFR 518.19 - General provisions.

Code of Federal Regulations, 2014 CFR

2014-07-01

... PUBLIC RELATIONS THE FREEDOM OF INFORMATION ACT PROGRAM Fee Schedule § 518.19 General provisions. (a... requests, and conform to the Office of Management and Budget Uniform Freedom of Information Act Fee... to imply that fees must be charged in connection with providing information to the public in the...

32 CFR 518.19 - General provisions.

Code of Federal Regulations, 2013 CFR

2013-07-01

... PUBLIC RELATIONS THE FREEDOM OF INFORMATION ACT PROGRAM Fee Schedule § 518.19 General provisions. (a... requests, and conform to the Office of Management and Budget Uniform Freedom of Information Act Fee... to imply that fees must be charged in connection with providing information to the public in the...

Characteristic distribution: An application to material bodies

NASA Astrophysics Data System (ADS)

Jiménez, Víctor Manuel; de León, Manuel; Epstein, Marcelo

2018-04-01

Associated to each material body B there exists a groupoid Ω(B) consisting of all the material isomorphisms connecting the points of B. The uniformity character of B is reflected in the properties of Ω(B): B is uniform if, and only if, Ω(B) is transitive. Smooth uniformity corresponds to a Lie groupoid and, specifically, to a Lie subgroupoid of the groupoid Π1(B , B) of 1-jets of B. We consider a general situation when Ω(B) is only an algebraic subgroupoid. Even in this case, we can cover B by a material foliation whose leaves are transitive. The same happens with Ω(B) and the corresponding leaves generate transitive Lie groupoids (roughly speaking, the leaves covering B). This result opens the possibility to study the homogeneity of general material bodies using geometric instruments.

Covariant Uniform Acceleration

NASA Astrophysics Data System (ADS)

Friedman, Yaakov; Scarr, Tzvi

2013-04-01

We derive a 4D covariant Relativistic Dynamics Equation. This equation canonically extends the 3D relativistic dynamics equation , where F is the 3D force and p = m0γv is the 3D relativistic momentum. The standard 4D equation is only partially covariant. To achieve full Lorentz covariance, we replace the four-force F by a rank 2 antisymmetric tensor acting on the four-velocity. By taking this tensor to be constant, we obtain a covariant definition of uniformly accelerated motion. This solves a problem of Einstein and Planck. We compute explicit solutions for uniformly accelerated motion. The solutions are divided into four Lorentz-invariant types: null, linear, rotational, and general. For null acceleration, the worldline is cubic in the time. Linear acceleration covariantly extends 1D hyperbolic motion, while rotational acceleration covariantly extends pure rotational motion. We use Generalized Fermi-Walker transport to construct a uniformly accelerated family of inertial frames which are instantaneously comoving to a uniformly accelerated observer. We explain the connection between our approach and that of Mashhoon. We show that our solutions of uniformly accelerated motion have constant acceleration in the comoving frame. Assuming the Weak Hypothesis of Locality, we obtain local spacetime transformations from a uniformly accelerated frame K' to an inertial frame K. The spacetime transformations between two uniformly accelerated frames with the same acceleration are Lorentz. We compute the metric at an arbitrary point of a uniformly accelerated frame. We obtain velocity and acceleration transformations from a uniformly accelerated system K' to an inertial frame K. We introduce the 4D velocity, an adaptation of Horwitz and Piron s notion of "off-shell." We derive the general formula for the time dilation between accelerated clocks. We obtain a formula for the angular velocity of a uniformly accelerated object. Every rest point of K' is uniformly accelerated, and its acceleration is a function of the observer's acceleration and its position. We obtain an interpretation of the Lorentz-Abraham-Dirac equation as an acceleration transformation from K' to K.

Connection formulas for thermal density functional theory

DOE PAGES

Pribram-Jones, A.; Burke, K.

2016-05-23

We show that the adiabatic connection formula of ground-state density functional theory relates the correlation energy to a coupling-constant integral over a purely potential contribution, and is widely used to understand and improve approximations. The corresponding formula for thermal density functional theory is cast as an integral over temperatures instead, ranging upward from the system's physical temperature. We also show how to relate different correlation components to each other, either in terms of temperature or coupling-constant integrations. Lastly, we illustrate our results on the uniform electron gas.

Understanding spatial connectivity of individuals with non-uniform population density.

PubMed

Wang, Pu; González, Marta C

2009-08-28

We construct a two-dimensional geometric graph connecting individuals placed in space within a given contact distance. The individuals are distributed using a measured country's density of population. We observe that while large clusters (group of individuals connected) emerge within some regions, they are trapped in detached urban areas owing to the low population density of the regions bordering them. To understand the emergence of a giant cluster that connects the entire population, we compare the empirical geometric graph with the one generated by placing the same number of individuals randomly in space. We find that, for small contact distances, the empirical distribution of population dominates the growth of connected components, but no critical percolation transition is observed in contrast to the graph generated by a random distribution of population. Our results show that contact distances from real-world situations as for WIFI and Bluetooth connections drop in a zone where a fully connected cluster is not observed, hinting that human mobility must play a crucial role in contact-based diseases and wireless viruses' large-scale spreading.

Emergence of small-world structure in networks of spiking neurons through STDP plasticity.

PubMed

Basalyga, Gleb; Gleiser, Pablo M; Wennekers, Thomas

2011-01-01

In this work, we use a complex network approach to investigate how a neural network structure changes under synaptic plasticity. In particular, we consider a network of conductance-based, single-compartment integrate-and-fire excitatory and inhibitory neurons. Initially the neurons are connected randomly with uniformly distributed synaptic weights. The weights of excitatory connections can be strengthened or weakened during spiking activity by the mechanism known as spike-timing-dependent plasticity (STDP). We extract a binary directed connection matrix by thresholding the weights of the excitatory connections at every simulation step and calculate its major topological characteristics such as the network clustering coefficient, characteristic path length and small-world index. We numerically demonstrate that, under certain conditions, a nontrivial small-world structure can emerge from a random initial network subject to STDP learning.

Rhythmogenic neuronal networks, emergent leaders, and k-cores.

PubMed

Schwab, David J; Bruinsma, Robijn F; Feldman, Jack L; Levine, Alex J

2010-11-01

Neuronal network behavior results from a combination of the dynamics of individual neurons and the connectivity of the network that links them together. We study a simplified model, based on the proposal of Feldman and Del Negro (FDN) [Nat. Rev. Neurosci. 7, 232 (2006)], of the preBötzinger Complex, a small neuronal network that participates in the control of the mammalian breathing rhythm through periodic firing bursts. The dynamics of this randomly connected network of identical excitatory neurons differ from those of a uniformly connected one. Specifically, network connectivity determines the identity of emergent leader neurons that trigger the firing bursts. When neuronal desensitization is controlled by the number of input signals to the neurons (as proposed by FDN), the network's collective desensitization--required for successful burst termination--is mediated by k-core clusters of neurons.

[Total cavopulmonary connection using a knitted dacron prosthesis impregnated with gelatin (GELSEAL) as an intracardiac conduit].

PubMed

Iwaya, F; Tanji, M; Ono, T; Tsuda, A; Hoshino, S

1996-05-01

It is important to find a suitable vascular prosthesis as an intracardiac conduit for a total cavopulmonary connection because of the need for long-term patency. A 7-year-old girl with a double outlet of right ventricle, hypoplastic left ventricle, pulmonary atresia and single atrium with azygos connection underwent a total cavopulmonary connection using a knitted dacron prosthesis impregnated with gelatin (GELSEAL) as an intracardiac conduit. Her postoperative course was uneventful. GELSEAL is soft, easy to hand and effective at preventing blood loss. The conduit is also expected to have long-term patency because of good healing with thin and uniform pseudointimal formation. However, long-term patency especially in the right side of the heart is still unknown. She should be followed with close anticoagulant therapy and careful observation.

Plumbing and Piping: Construction, Supervision, and Inspection. Course of Study.

ERIC Educational Resources Information Center

O'Meara, Lester; Turley, John

This course of study on plumbing and piping is part of a construction, supervision, and inspection series, which provides instructional materials for community or junior college technical courses in the inspection program. Material covered in this volume pertains to: uniform plumbing code; pipes, fittings, supports, and connections; sewer and…

Circuits in the Sun: Solar Panel Physics

ERIC Educational Resources Information Center

Gfroerer, Tim

2013-01-01

Typical commercial solar panels consist of approximately 60 individual photovoltaic cells connected in series. Since the usual Kirchhoff rules apply, the current is uniform throughout the circuit, while the electric potential of the individual devices is cumulative. Hence, a solar panel is a good analog of a simple resistive series circuit, except…

Avian inhalation exposure chamber

DOEpatents

Briant, James K.; Driver, Crystal J.

1992-01-01

An exposure system for delivering gaseous material ranging in particle size from 0.4 micrometers to 20.0 micrometers uniformly to the heads of experimental animals, primarily birds. The system includes a vertical outer cylinder and a central chimney with animal holding bottles connected to exposure ports on the vertical outer cylinder.

Uncovering the overlapping community structure of complex networks by maximal cliques

NASA Astrophysics Data System (ADS)

Li, Junqiu; Wang, Xingyuan; Cui, Yaozu

2014-12-01

In this paper, a unique algorithm is proposed to detect overlapping communities in the un-weighted and weighted networks with considerable accuracy. The maximal cliques, overlapping vertex, bridge vertex and isolated vertex are introduced. First, all the maximal cliques are extracted by the algorithm based on the deep and bread searching. Then two maximal cliques can be merged into a larger sub-graph by some given rules. In addition, the proposed algorithm successfully finds overlapping vertices and bridge vertices between communities. Experimental results using some real-world networks data show that the performance of the proposed algorithm is satisfactory.

The Communications and Networks Collaborative Technology Alliance Publication Network: A Case Study on Graph and Simplicial Complex Analysis

DTIC Science & Technology

2015-05-01

Amer 26 19 Adarshpal S Sethi 24 20 Sunil Samtani 22 21 Alenka G Zajic 22 7 We study 2 important types of subgraphs on the C&N CTA network: 1) the...Maria Striki 0.0841 20 Sunil Samtani at least 4 times the end-of-program mean degree (4.8185). These authors also have at least 7 times the end-of...Lee Tarek N Saadawi 19 2 Mariusz A Fecko Sunil Samtani 18 3 Maitreya Natu Adarshpal S Sethi 17 3 Anthony J McAuley Raquel Morera 17 5 Richard Gopaul

Exhibition of Monogamy Relations between Entropic Non-contextuality Inequalities

NASA Astrophysics Data System (ADS)

Zhu, Feng; Zhang, Wei; Huang, Yi-Dong

2017-06-01

We exhibit the monogamy relation between two entropic non-contextuality inequalities in the scenario where compatible projectors are orthogonal. We show the monogamy relation can be exhibited by decomposing the orthogonality graph into perfect induced subgraphs. Then we find two entropic non-contextuality inequalities are monogamous while the KCBS-type non-contextuality inequalities are not if the orthogonality graphs of the observable sets are two odd cycles with two shared vertices. Supported by 973 Programs of China under Grant Nos. 2011CBA00303 and 2013CB328700, Basic Research Foundation of Tsinghua National Laboratory for Information Science and Technology (TNList)

FINAL REPORT (MILESTONE DATE 9/30/11) FOR SUBCONTRACT NO. B594099 NUMERICAL METHODS FOR LARGE-SCALE DATA FACTORIZATION

DOE Office of Scientific and Technical Information (OSTI.GOV)

De Sterck, H

2011-10-18

The following work has been performed by PI Hans De Sterck and graduate student Manda Winlaw for the required tasks 1-5 (as listed in the Statement of Work). Graduate student Manda Winlaw has visited LLNL January 31-March 11, 2011 and May 23-August 19, 2010, working with Van Henson and Mike O'Hara on non-negative matrix factorizations (NMF). She has investigated the dense subgraph clustering algorithm from 'Finding Dense Subgraphs for Sparse Undirected, Directed, and Bipartite Graphs' by Chen and Saad, testing this method on several term-document matrices and adapting it to cluster based on the rank of the subgraphs instead ofmore » the density. Manda Winlaw was awarded a first prize in the annual LLNL summer student poster competition for a poster on her NMF research. PI Hans De Sterck has developed a new adaptive algebraic multigrid algorithm for computing a few dominant or minimal singular triplets of sparse rectangular matrices. This work builds on adaptive algebraic multigrid methods that were further developed by the PI and collaborators (including Sanders and Henson) for Markov chains. The method also combines and extends existing multigrid algorithms for the symmetric eigenproblem. The PI has visited LLNL February 22-25, 2011, and has given a CASC seminar 'Algebraic Multigrid for the Singular Value Problem' on this work on February 23, 2011. During his visit, he has discussed this work and related topics with Van Henson, Geoffrey Sanders, Panayot Vassilevski, and others. He has tested the algorithm on PDE matrices and on a term-document matrix, with promising initial results. Manda Winlaw has also started to work, with O'Hara, on estimating probability distributions over undirected graph edges. The goal is to estimate probabilistic models from sets of undirected graph edges for the purpose of prediction, anomaly detection and support to supervised learning. Graduate student Manda Winlaw is writing a paper on the results obtained with O'Hara which will be submitted some time later in 2011 to a data mining conference. PI Hans De Sterck has developed a new optimization algorithm for canonical tensor approximation, formulating an extension of the nonlinear GMRES method to optimization problems. Numerical results for tensors with up to 8 modes show that this new method is efficient for sparse and dense tensors. He has written a paper on this which has been submitted to the SIAM Journal on Scientific Computing. PI Hans De Sterck has further developed his new optimization algorithm for canonical tensor approximation, formulating an extension in terms of steepest-descent preconditioning, which makes the approach generally applicable for nonlinear optimization. He has written a paper on this extension which has been submitted to Numerical Linear Algebra with Applications.« less

Topographical maps as complex networks

NASA Astrophysics Data System (ADS)

da Fontoura Costa, Luciano; Diambra, Luis

2005-02-01

The neuronal networks in the mammalian cortex are characterized by the coexistence of hierarchy, modularity, short and long range interactions, spatial correlations, and topographical connections. Particularly interesting, the latter type of organization implies special demands on developing systems in order to achieve precise maps preserving spatial adjacencies, even at the expense of isometry. Although the object of intensive biological research, the elucidation of the main anatomic-functional purposes of the ubiquitous topographical connections in the mammalian brain remains an elusive issue. The present work reports on how recent results from complex network formalism can be used to quantify and model the effect of topographical connections between neuronal cells over the connectivity of the network. While the topographical mapping between two cortical modules is achieved by connecting nearest cells from each module, four kinds of network models are adopted for implementing intramodular connections, including random, preferential-attachment, short-range, and long-range networks. It is shown that, though spatially uniform and simple, topographical connections between modules can lead to major changes in the network properties in some specific cases, depending on intramodular connections schemes, fostering more effective intercommunication between the involved neuronal cells and modules. The possible implications of such effects on cortical operation are discussed.

DIMENSION MEASURING OPTICAL SIGHTING DEVICE

DOEpatents

Kerr, G.E.

1959-08-01

A sighting device to check the uniformity of thickness of a lining applied to a container is presented. The sighting devlce comprises two tubular members having their ends in threaded connection with one another and a lens lying within the outer end of one of the tubular members. A ground glass inscribed with two concentric circles is located at the outer end of the other tubular section so that the image of the circular junctures, with and without the lining at the closed end of the container, can be focused on the proper circle inscribed in the ground glass so as to determine whether the lining has uniformity and whether there are thin spots.

Derivatives in discrete mathematics: a novel graph-theoretical invariant for generating new 2/3D molecular descriptors. I. Theory and QSPR application

NASA Astrophysics Data System (ADS)

Marrero-Ponce, Yovani; Santiago, Oscar Martínez; López, Yoan Martínez; Barigye, Stephen J.; Torrens, Francisco

2012-11-01

In this report, we present a new mathematical approach for describing chemical structures of organic molecules at atomic-molecular level, proposing for the first time the use of the concept of the derivative ( partial ) of a molecular graph (MG) with respect to a given event ( E), to obtain a new family of molecular descriptors (MDs). With this purpose, a new matrix representation of the MG, which generalizes graph's theory's traditional incidence matrix, is introduced. This matrix, denominated the generalized incidence matrix, Q, arises from the Boolean representation of molecular sub- graphs that participate in the formation of the graph molecular skeleton MG and could be complete (representing all possible connected sub-graphs) or constitute sub-graphs of determined orders or types as well as a combination of these. The Q matrix is a non-quadratic and unsymmetrical in nature, its columns ( n) and rows ( m) are conditions (letters) and collection of conditions (words) with which the event occurs. This non-quadratic and unsymmetrical matrix is transformed, by algebraic manipulation, to a quadratic and symmetric matrix known as relations frequency matrix, F, which characterizes the participation intensity of the conditions (letters) in the events (words). With F, we calculate the derivative over a pair of atomic nuclei. The local index for the atomic nuclei i, Δ i , can therefore be obtained as a linear combination of all the pair derivatives of the atomic nuclei i with all the rest of the j's atomic nuclei. Here, we also define new strategies that generalize the present form of obtaining global or local (group or atom-type) invariants from atomic contributions (local vertex invariants, LOVIs). In respect to this, metric (norms), means and statistical invariants are introduced. These invariants are applied to a vector whose components are the values Δ i for the atomic nuclei of the molecule or its fragments. Moreover, with the purpose of differentiating among different atoms, an atomic weighting scheme (atom-type labels) is used in the formation of the matrix Q or in LOVIs state. The obtained indices were utilized to describe the partition coefficient (Log P) and the reactivity index (Log K) of the 34 derivatives of 2-furylethylenes. In all the cases, our MDs showed better statistical results than those previously obtained using some of the most used families of MDs in chemometric practice. Therefore, it has been demonstrated to that the proposed MDs are useful in molecular design and permit obtaining easier and robust mathematical models than the majority of those reported in the literature. All this range of mentioned possibilities open "the doors" to the creation of a new family of MDs, using the graph derivative, and avail a new tool for QSAR/QSPR and molecular diversity/similarity studies.

Longitudinal gradient coils with enhanced radial uniformity in restricted diameter: Single-current and multiple-current approaches.

PubMed

Romero, Javier A; Domínguez, Gabriela A; Anoardo, Esteban

2017-03-01

An important requirement for a gradient coil is that the uniformity of the generated magnetic field gradient should be maximal within the active volume of the coil. For a cylindrical geometry, the radial uniformity of the gradient turns critic, particularly in cases where the gradient-unit has to be designed to fit into the inner bore of a compact magnet of reduced dimensions, like those typically used in fast-field-cycling NMR. In this paper we present two practical solutions aimed to fulfill this requirement. We propose a matrix-inversion optimization algorithm based on the Biot-Savart law, that using a proper cost function, allows maximizing the uniformity of the gradient and power efficiency. The used methodology and the simulation code were validated in a single-current design, by comparing the computer simulated field map with the experimental data measured in a real prototype. After comparing the obtained results with the target field approach, a multiple-element coil driven by independent current sources is discussed, and a real prototype evaluated. Opposed equispaced independent windings are connected in pairs conforming an arrangement of independent anti-Helmholtz units. This last coil seizes 80% of its radial dimension with a gradient uniformity better than 5%. The design also provides an adaptable region of uniformity along with adjustable coil efficiency. Copyright © 2017 Elsevier Inc. All rights reserved.

Uniform, stable supply of medium for in vitro cell culture using a robust chamber

NASA Astrophysics Data System (ADS)

Wei, Juan; Liu, Chong; Jiang, Yang; Liu, Tao; Chen, Li; Liu, Bo; Li, Jingmin

2018-06-01

A uniform, stable supply of medium is important for in vitro cell culture. In this paper, a microfluidic device is presented for culturing cells inside a robust chamber with continuous perfusion of medium. The device consists of a main channel, two bifurcated channels and a culture chamber. The culture chamber connects to the bifurcated channels via multiple paths, and distributes symmetrically on the main channel, to improve the efficiency of medium exchange. Furthermore, regular polygonal chambers with various numbers of edges have been designed, to study the effects of chamber shape on flow fields. The finite element method has been employed to predict the effects of multiple paths on the uniformity and stability of flow fields in the culture chamber. Particle tracking technology has been used to evaluate the flow fields in the chambers, and PC-12 cells have been cultured using the microfluidic device, to test its validity. The results of simulation and experiment indicate that the microfluidic design could provide a continuous interstitial-like flow microenvironment, with a relatively stable and uniform supply of medium.

Functional Module Analysis for Gene Coexpression Networks with Network Integration.

PubMed

Zhang, Shuqin; Zhao, Hongyu; Ng, Michael K

2015-01-01

Network has been a general tool for studying the complex interactions between different genes, proteins, and other small molecules. Module as a fundamental property of many biological networks has been widely studied and many computational methods have been proposed to identify the modules in an individual network. However, in many cases, a single network is insufficient for module analysis due to the noise in the data or the tuning of parameters when building the biological network. The availability of a large amount of biological networks makes network integration study possible. By integrating such networks, more informative modules for some specific disease can be derived from the networks constructed from different tissues, and consistent factors for different diseases can be inferred. In this paper, we have developed an effective method for module identification from multiple networks under different conditions. The problem is formulated as an optimization model, which combines the module identification in each individual network and alignment of the modules from different networks together. An approximation algorithm based on eigenvector computation is proposed. Our method outperforms the existing methods, especially when the underlying modules in multiple networks are different in simulation studies. We also applied our method to two groups of gene coexpression networks for humans, which include one for three different cancers, and one for three tissues from the morbidly obese patients. We identified 13 modules with three complete subgraphs, and 11 modules with two complete subgraphs, respectively. The modules were validated through Gene Ontology enrichment and KEGG pathway enrichment analysis. We also showed that the main functions of most modules for the corresponding disease have been addressed by other researchers, which may provide the theoretical basis for further studying the modules experimentally.

GenoLink: a graph-based querying and browsing system for investigating the function of genes and proteins.

PubMed

Durand, Patrick; Labarre, Laurent; Meil, Alain; Divo, Jean-Louis; Vandenbrouck, Yves; Viari, Alain; Wojcik, Jérôme

2006-01-17

A large variety of biological data can be represented by graphs. These graphs can be constructed from heterogeneous data coming from genomic and post-genomic technologies, but there is still need for tools aiming at exploring and analysing such graphs. This paper describes GenoLink, a software platform for the graphical querying and exploration of graphs. GenoLink provides a generic framework for representing and querying data graphs. This framework provides a graph data structure, a graph query engine, allowing to retrieve sub-graphs from the entire data graph, and several graphical interfaces to express such queries and to further explore their results. A query consists in a graph pattern with constraints attached to the vertices and edges. A query result is the set of all sub-graphs of the entire data graph that are isomorphic to the pattern and satisfy the constraints. The graph data structure does not rely upon any particular data model but can dynamically accommodate for any user-supplied data model. However, for genomic and post-genomic applications, we provide a default data model and several parsers for the most popular data sources. GenoLink does not require any programming skill since all operations on graphs and the analysis of the results can be carried out graphically through several dedicated graphical interfaces. GenoLink is a generic and interactive tool allowing biologists to graphically explore various sources of information. GenoLink is distributed either as a standalone application or as a component of the Genostar/Iogma platform. Both distributions are free for academic research and teaching purposes and can be requested at academy@genostar.com. A commercial licence form can be obtained for profit company at info@genostar.com. See also http://www.genostar.org.

L-GRAAL: Lagrangian graphlet-based network aligner.

PubMed

Malod-Dognin, Noël; Pržulj, Nataša

2015-07-01

Discovering and understanding patterns in networks of protein-protein interactions (PPIs) is a central problem in systems biology. Alignments between these networks aid functional understanding as they uncover important information, such as evolutionary conserved pathways, protein complexes and functional orthologs. A few methods have been proposed for global PPI network alignments, but because of NP-completeness of underlying sub-graph isomorphism problem, producing topologically and biologically accurate alignments remains a challenge. We introduce a novel global network alignment tool, Lagrangian GRAphlet-based ALigner (L-GRAAL), which directly optimizes both the protein and the interaction functional conservations, using a novel alignment search heuristic based on integer programming and Lagrangian relaxation. We compare L-GRAAL with the state-of-the-art network aligners on the largest available PPI networks from BioGRID and observe that L-GRAAL uncovers the largest common sub-graphs between the networks, as measured by edge-correctness and symmetric sub-structures scores, which allow transferring more functional information across networks. We assess the biological quality of the protein mappings using the semantic similarity of their Gene Ontology annotations and observe that L-GRAAL best uncovers functionally conserved proteins. Furthermore, we introduce for the first time a measure of the semantic similarity of the mapped interactions and show that L-GRAAL also uncovers best functionally conserved interactions. In addition, we illustrate on the PPI networks of baker's yeast and human the ability of L-GRAAL to predict new PPIs. Finally, L-GRAAL's results are the first to show that topological information is more important than sequence information for uncovering functionally conserved interactions. L-GRAAL is coded in C++. Software is available at: http://bio-nets.doc.ic.ac.uk/L-GRAAL/. n.malod-dognin@imperial.ac.uk Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

GenoLink: a graph-based querying and browsing system for investigating the function of genes and proteins

PubMed Central

Durand, Patrick; Labarre, Laurent; Meil, Alain; Divo1, Jean-Louis; Vandenbrouck, Yves; Viari, Alain; Wojcik, Jérôme

2006-01-01

Background A large variety of biological data can be represented by graphs. These graphs can be constructed from heterogeneous data coming from genomic and post-genomic technologies, but there is still need for tools aiming at exploring and analysing such graphs. This paper describes GenoLink, a software platform for the graphical querying and exploration of graphs. Results GenoLink provides a generic framework for representing and querying data graphs. This framework provides a graph data structure, a graph query engine, allowing to retrieve sub-graphs from the entire data graph, and several graphical interfaces to express such queries and to further explore their results. A query consists in a graph pattern with constraints attached to the vertices and edges. A query result is the set of all sub-graphs of the entire data graph that are isomorphic to the pattern and satisfy the constraints. The graph data structure does not rely upon any particular data model but can dynamically accommodate for any user-supplied data model. However, for genomic and post-genomic applications, we provide a default data model and several parsers for the most popular data sources. GenoLink does not require any programming skill since all operations on graphs and the analysis of the results can be carried out graphically through several dedicated graphical interfaces. Conclusion GenoLink is a generic and interactive tool allowing biologists to graphically explore various sources of information. GenoLink is distributed either as a standalone application or as a component of the Genostar/Iogma platform. Both distributions are free for academic research and teaching purposes and can be requested at academy@genostar.com. A commercial licence form can be obtained for profit company at info@genostar.com. See also . PMID:16417636

Symmetries and synchronization in multilayer random networks

NASA Astrophysics Data System (ADS)

Saa, Alberto

2018-04-01

In the light of the recently proposed scenario of asymmetry-induced synchronization (AISync), in which dynamical uniformity and consensus in a distributed system would demand certain asymmetries in the underlying network, we investigate here the influence of some regularities in the interlayer connection patterns on the synchronization properties of multilayer random networks. More specifically, by considering a Stuart-Landau model of complex oscillators with random frequencies, we report for multilayer networks a dynamical behavior that could be also classified as a manifestation of AISync. We show, namely, that the presence of certain symmetries in the interlayer connection pattern tends to diminish the synchronization capability of the whole network or, in other words, asymmetries in the interlayer connections would enhance synchronization in such structured networks. Our results might help the understanding not only of the AISync mechanism itself but also its possible role in the determination of the interlayer connection pattern of multilayer and other structured networks with optimal synchronization properties.

The Electrostatic Potential of a Uniformly Charged Ring

ERIC Educational Resources Information Center

Ciftja, Orion; Babineaux, Arica; Hafeez, Nadia

2009-01-01

When faced with mathematical methods, undergraduate students have difficulty in grasping the reality of various approaches and special functions. It is only when they take a more specialized course such as classical electromagnetism that they finally see the connection. A problem that we believe illustrates very well the depth and variety of…

Avian inhalation exposure chamber

DOEpatents

Briant, J.K.; Driver, C.J.

1992-05-05

An exposure system is designed for delivering gaseous material ranging in particle size from 0.4 micrometers to 20.0 micrometers uniformly to the heads of experimental animals, primarily birds. The system includes a vertical outer cylinder and a central chimney with animal holding bottles connected to exposure ports on the vertical outer cylinder. 2 figs.

23 CFR 470.107 - Federal-aid highway systems.

Code of Federal Regulations, 2011 CFR

2011-04-01

... permitted under the provisions of 23 U.S.C. 103(c)(4) and section 1105(e)(5)(A) of the Intermodal Surface... highest importance to the Nation, built to the uniform geometric and construction standards of 23 U.S.C. 109(h), which connect, as directly as practicable, the principal metropolitan areas, cities, and...

Possible Connection of Geological Composition With Geomagnetic Field Change In Kopaonik Thrust Region

NASA Astrophysics Data System (ADS)

Popeskov, Mirjana; Cukavac, Milena; Lazovic, Caslav

This paper should consider interpretation of geomagnetic field changes on the basis of possible connection with geological composition of deformation zone. Analysis of total magnetic field intensity data from 38 surveys, carried out in the period may 1980 ­ november 2001 in Kopaonik thrust region, central Serbia, reveals anomalous behaviour of local field changes in particular time intervals. These data give us possibility to observe geomagnetic changes in long period of time. This paper shall consider if and how different magnetizations of geological composition of array are in connection with anomalous geomagnetic field change. We shall consider how non-uniform geological structure or rocks with different magnetizations can effect geomagnetic observations and weather sharp contrast in rock magnetization between neighbour layers can give rise to larger changes in the geomagnetic total intensity than those for a uniform layer. For that purpose we are going to consider geological and tectonical map of Kopaonik region. We shall also consider map of vertical component of geomagnetic field because Kopaonik belongs to high magnetic anomaly zone. Corelation of geomagnetic and geological data is supposed to give us some answers to the question of origine of some anomalious geomagnetic changes in total intensity of geomagnetic field. It can also represent first step in corelationof geomagnetic field changes to other geophysical, seismological or geological data that can be couse of geomagnetic field change.

Probabilistic pathway construction.

PubMed

Yousofshahi, Mona; Lee, Kyongbum; Hassoun, Soha

2011-07-01

Expression of novel synthesis pathways in host organisms amenable to genetic manipulations has emerged as an attractive metabolic engineering strategy to overproduce natural products, biofuels, biopolymers and other commercially useful metabolites. We present a pathway construction algorithm for identifying viable synthesis pathways compatible with balanced cell growth. Rather than exhaustive exploration, we investigate probabilistic selection of reactions to construct the pathways. Three different selection schemes are investigated for the selection of reactions: high metabolite connectivity, low connectivity and uniformly random. For all case studies, which involved a diverse set of target metabolites, the uniformly random selection scheme resulted in the highest average maximum yield. When compared to an exhaustive search enumerating all possible reaction routes, our probabilistic algorithm returned nearly identical distributions of yields, while requiring far less computing time (minutes vs. years). The pathways identified by our algorithm have previously been confirmed in the literature as viable, high-yield synthesis routes. Prospectively, our algorithm could facilitate the design of novel, non-native synthesis routes by efficiently exploring the diversity of biochemical transformations in nature. Copyright © 2011 Elsevier Inc. All rights reserved.

Characterization, scaling, and partial representation of diffuse and discrete input junctions to CA3 hippocampus.

PubMed

Ascarrunz, F G; Kisley, M A; Flach, K A; Hamilton, R W; MacGregor, R J

1995-07-01

This paper applies a general mathematical system for characterizing and scaling functional connectivity and information flow across the diffuse (EC) and discrete (DG) input junctions to the CA3 hippocampus. Both gross connectivity and coordinated multiunit informational firing patterns are quantitatively characterized in terms of 32 defining parameters interrelated by 17 equations, and then scaled down according to rules for uniformly proportional scaling and for partial representation. The diffuse EC-CA3 junction is shown to be uniformly scalable with realistic representation of both essential spatiotemporal cooperativity and coordinated firing patterns down to populations of a few hundred neurons. Scaling of the discrete DG-CA3 junction can be effected with a two-step process, which necessarily deviates from uniform proportionality but nonetheless produces a valuable and readily interpretable reduced model, also utilizing a few hundred neurons in the receiving population. Partial representation produces a reduced model of only a portion of the full network where each model neuron corresponds directly to a biological neuron. The mathematical analysis illustrated here shows that although omissions and distortions are inescapable in such an application, satisfactorily complete and accurate models the size of pattern modules are possible. Finally, the mathematical characterization of these junctions generates a theory which sees the DG as a definer of the fine structure of embedded traces in the hippocampus and entire coordinated patterns of sequences of 14-cell links in CA3 as triggered by the firing of sequences of individual neurons in DG.

Adaptive random walks on the class of Web graphs

NASA Astrophysics Data System (ADS)

Tadić, B.

2001-09-01

We study random walk with adaptive move strategies on a class of directed graphs with variable wiring diagram. The graphs are grown from the evolution rules compatible with the dynamics of the world-wide Web [B. Tadić, Physica A 293, 273 (2001)], and are characterized by a pair of power-law distributions of out- and in-degree for each value of the parameter β, which measures the degree of rewiring in the graph. The walker adapts its move strategy according to locally available information both on out-degree of the visited node and in-degree of target node. A standard random walk, on the other hand, uses the out-degree only. We compute the distribution of connected subgraphs visited by an ensemble of walkers, the average access time and survival probability of the walks. We discuss these properties of the walk dynamics relative to the changes in the global graph structure when the control parameter β is varied. For β≥ 3, corresponding to the world-wide Web, the access time of the walk to a given level of hierarchy on the graph is much shorter compared to the standard random walk on the same graph. By reducing the amount of rewiring towards rigidity limit β↦βc≲ 0.1, corresponding to the range of naturally occurring biochemical networks, the survival probability of adaptive and standard random walk become increasingly similar. The adaptive random walk can be used as an efficient message-passing algorithm on this class of graphs for large degree of rewiring.

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.

On the star partition dimension of comb product of cycle and path

NASA Astrophysics Data System (ADS)

Alfarisi, Ridho; Darmaji

2017-08-01

Let G = (V, E) be a connected graphs with vertex set V(G), edge set E(G) and S ⊆ V(G). Given an ordered partition Π = {S1, S2, S3, …, Sk} of the vertex set V of G, the representation of a vertex v ∈ V with respect to Π is the vector r(v|Π) = (d(v, S1), d(v, S2), …, d(v, Sk)), where d(v, Sk) represents the distance between the vertex v and the set Sk and d(v, Sk) = min{d(v, x)|x ∈ Sk }. A partition Π of V(G) is a resolving partition if different vertices of G have distinct representations, i.e., for every pair of vertices u, v ∈ V(G), r(u|Π) ≠ r(v|Π). The minimum k of Π resolving partition is a partition dimension of G, denoted by pd(G). The resolving partition Π = {S1, S2, S3, …, Sk } is called a star resolving partition for G if it is a resolving partition and each subgraph induced by Si, 1 ≤ i ≤ k, is a star. The minimum k for which there exists a star resolving partition of V(G) is the star partition dimension of G, denoted by spd(G). Finding the star partition dimension of G is classified to be a NP-Hard problem. In this paper, we will show that the partition dimension of comb product of cycle and path namely Cm⊳Pn and Pn⊳Cm for n ≥ 2 and m ≥ 3.

Apparatus for gas sorption measurement with integrated gas composition measurement device and gas mixing

DOEpatents

Micklash. II, Kenneth James; Dutton, Justin James; Kaye, Steven

2014-06-03

An apparatus for testing of multiple material samples includes a gas delivery control system operatively connectable to the multiple material samples and configured to provide gas to the multiple material samples. Both a gas composition measurement device and pressure measurement devices are included in the apparatus. The apparatus includes multiple selectively openable and closable valves and a series of conduits configured to selectively connect the multiple material samples individually to the gas composition device and the pressure measurement devices by operation of the valves. A mixing system is selectively connectable to the series of conduits and is operable to cause forced mixing of the gas within the series of conduits to achieve a predetermined uniformity of gas composition within the series of conduits and passages.

Graph Kernels for Molecular Similarity.

PubMed

Rupp, Matthias; Schneider, Gisbert

2010-04-12

Molecular similarity measures are important for many cheminformatics applications like ligand-based virtual screening and quantitative structure-property relationships. Graph kernels are formal similarity measures defined directly on graphs, such as the (annotated) molecular structure graph. Graph kernels are positive semi-definite functions, i.e., they correspond to inner products. This property makes them suitable for use with kernel-based machine learning algorithms such as support vector machines and Gaussian processes. We review the major types of kernels between graphs (based on random walks, subgraphs, and optimal assignments, respectively), and discuss their advantages, limitations, and successful applications in cheminformatics. Copyright © 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Meraculous2

DOE Office of Scientific and Technical Information (OSTI.GOV)

2014-06-01

meraculous2 is a whole genome shotgun assembler for short-reads that is capable of assembling large, polymorphic genomes with modest computational requirements. Meraculous relies on an efficient and conservative traversal of the subgraph of the k-mer (deBruijn) graph of oligonucleotides with unique high quality extensions in the dataset, avoiding an explicit error correction step as used in other short-read assemblers. Additional features include (1) handling of allelic variation using "bubble" structures within the deBruijn graph, (2) gap closing of repetitive and low quality regions using localized assemblies, and (3) an improved scaffolding algorithm that produces more complete assemblies without compromising onmore » scaffolding accuracy« less

Subtractive procedure for calculating the anomalous electron magnetic moment in QED and its application for numerical calculation at the three-loop level

DOE Office of Scientific and Technical Information (OSTI.GOV)

Volkov, S. A., E-mail: volkoff-sergey@mail.ru

2016-06-15

A new subtractive procedure for canceling ultraviolet and infrared divergences in the Feynman integrals described here is developed for calculating QED corrections to the electron anomalous magnetic moment. The procedure formulated in the form of a forest expression with linear operators applied to Feynman amplitudes of UV-diverging subgraphs makes it possible to represent the contribution of each Feynman graph containing only electron and photon propagators in the form of a converging integral with respect to Feynman parameters. The application of the developed method for numerical calculation of two- and threeloop contributions is described.

An Efficient Means of Adaptive Refinement Within Systems of Overset Grids

NASA Technical Reports Server (NTRS)

Meakin, Robert L.

1996-01-01

An efficient means of adaptive refinement within systems of overset grids is presented. Problem domains are segregated into near-body and off-body fields. Near-body fields are discretized via overlapping body-fitted grids that extend only a short distance from body surfaces. Off-body fields are discretized via systems of overlapping uniform Cartesian grids of varying levels of refinement. a novel off-body grid generation and management scheme provides the mechanism for carrying out adaptive refinement of off-body flow dynamics and solid body motion. The scheme allows for very efficient use of memory resources, and flow solvers and domain connectivity routines that can exploit the structure inherent to uniform Cartesian grids.

Synchronization in a non-uniform network of excitatory spiking neurons

NASA Astrophysics Data System (ADS)

Echeveste, Rodrigo; Gros, Claudius

Spontaneous synchronization of pulse coupled elements is ubiquitous in nature and seems to be of vital importance for life. Networks of pacemaker cells in the heart, extended populations of southeast asian fireflies, and neuronal oscillations in cortical networks, are examples of this. In the present work, a rich repertoire of dynamical states with different degrees of synchronization are found in a network of excitatory-only spiking neurons connected in a non-uniform fashion. In particular, uncorrelated and partially correlated states are found without the need for inhibitory neurons or external currents. The phase transitions between these states, as well the robustness, stability, and response of the network to external stimulus are studied.

Is Object-Based Attention Mandatory? Strategic Control over Mode of Attention

ERIC Educational Resources Information Center

Yeari, Menahem; Goldsmith, Morris

2010-01-01

Is object-based attention mandatory or under strategic control? In an adapted spatial cuing paradigm, participants focused initially on a central arrow cue that was part of a perceptual group (Experiment 1) or a uniformly connected object (Experiment 2), encompassing one of the potential target locations. The cue always pointed to an opposite,…

Deployment-based lifetime optimization model for homogeneous Wireless Sensor Network under retransmission.

PubMed

Li, Ruiying; Liu, Xiaoxi; Xie, Wei; Huang, Ning

2014-12-10

Sensor-deployment-based lifetime optimization is one of the most effective methods used to prolong the lifetime of Wireless Sensor Network (WSN) by reducing the distance-sensitive energy consumption. In this paper, data retransmission, a major consumption factor that is usually neglected in the previous work, is considered. For a homogeneous WSN, monitoring a circular target area with a centered base station, a sensor deployment model based on regular hexagonal grids is analyzed. To maximize the WSN lifetime, optimization models for both uniform and non-uniform deployment schemes are proposed by constraining on coverage, connectivity and success transmission rate. Based on the data transmission analysis in a data gathering cycle, the WSN lifetime in the model can be obtained through quantifying the energy consumption at each sensor location. The results of case studies show that it is meaningful to consider data retransmission in the lifetime optimization. In particular, our investigations indicate that, with the same lifetime requirement, the number of sensors needed in a non-uniform topology is much less than that in a uniform one. Finally, compared with a random scheme, simulation results further verify the advantage of our deployment model.

Distribution of Orientation Selectivity in Recurrent Networks of Spiking Neurons with Different Random Topologies

PubMed Central

Sadeh, Sadra; Rotter, Stefan

2014-01-01

Neurons in the primary visual cortex are more or less selective for the orientation of a light bar used for stimulation. A broad distribution of individual grades of orientation selectivity has in fact been reported in all species. A possible reason for emergence of broad distributions is the recurrent network within which the stimulus is being processed. Here we compute the distribution of orientation selectivity in randomly connected model networks that are equipped with different spatial patterns of connectivity. We show that, for a wide variety of connectivity patterns, a linear theory based on firing rates accurately approximates the outcome of direct numerical simulations of networks of spiking neurons. Distance dependent connectivity in networks with a more biologically realistic structure does not compromise our linear analysis, as long as the linearized dynamics, and hence the uniform asynchronous irregular activity state, remain stable. We conclude that linear mechanisms of stimulus processing are indeed responsible for the emergence of orientation selectivity and its distribution in recurrent networks with functionally heterogeneous synaptic connectivity. PMID:25469704

Acoustic theory of axisymmetric multisectioned ducts. [reduction of turbofan engine noise

NASA Technical Reports Server (NTRS)

Zorumski, W. E.

1974-01-01

Equations are developed for the acoustic field in a duct system which is made up of a number of connected circular and annular ducts. These equations are suitable for finding the acoustic field inside of and radiated from an aircraft turbofan engine. Acoustic modes are used as generalized coordinates in order to develop a set of matrix equations for the acoustic field. Equations for these modes are given for circular and annular ducts with uniform flow. Modal source equations are derived for point acoustic sources. General equations for mode transmission and reflection are developed and detailed equations are derived for ducts with multiple sections of acoustic treatment and for ducts with circumferential splitter rings. The general theory is applied to the special case of a uniform area circular duct with multisection liners and it is shown that the mode reflection effects are proportional to differences of the acoustic admittances of adjacent liners. A numerical example is given which shows that multisection liners may provide greater noise suppression than uniform liners.

In Vitro Mineralization by Preosteoblasts in Poly(D, L-lactide-co-glycolide) Inverse Opal Scaffolds Reinforced with Hydroxyapatite Nanoparticles

PubMed Central

Choi, Sung-Wook; Zhang, Yu; Thomopoulos, Stavros; Xia, Younan

2010-01-01

Inverse opal scaffolds made of poly(D, L-lactide-co-glycolide) (PLGA) and hydroxyapatite (HAp) were fabricated using cubic-closed packed (ccp) lattices of uniform gelatin microspheres as templates and evaluated for bone tissue engineering. The scaffolds exhibited a uniform pore size (213 ± 4.4 μm), a porosity of ∼75%, and an excellent connectivity in three dimensions. Three different formulations were examined: pure PLGA, HAp-impregnated PLGA (PLGA/HAp), and apatite (Ap)-coated PLGA/HAp. After seeding with preosteoblasts (MC3T3-E1), the samples were cultured for different periods of time and then characterized by X-ray microcomputed tomography (micro-CT) and scanning electron microscopy to evaluate osteoinductivity in terms of the amount and spatial distribution of mineral secreted from the differentiated preosteoblasts. Our results indicate that preosteoblasts cultured in the Ap-coated PLGA/HAp scaffolds secreted the largest amount of mineral, which was also homogeneously distributed throughout the scaffolds. In contrast, the cells in the pure PLGA scaffolds secreted very little mineral, which was mainly deposited around the perimeter of the scaffolds. These results suggest that the uniform pore structure and favorable surface properties could facilitate the uniform secretion of extracellular matrix from cells throughout the scaffold. The Ap-coated PLGA/HAp scaffold with uniform pore structure could be a promising material for bone tissue engineering. PMID:20450216

Pupil Selection Segments Urban Comprehensive Schooling in Finland: Composition of School Classes in Pupils' School Performance, Gender, and Ethnicity

ERIC Educational Resources Information Center

Berisha, Anna-Kaisa; Seppänen, Piia

2017-01-01

The Finnish comprehensive school system is regularly referred to as a uniform and "no-tracking". In this article, we show with novel urban case data in Finland that school performance differed significantly between schools, most strikingly between school classes, and was connected to the school's selectiveness in pupil admission. A…

Using a Computer Microphone Port to Study Circular Motion: Proposal of a Secondary School Experiment

ERIC Educational Resources Information Center

Soares, A. A.; Borcsik, F. S.

2016-01-01

In this work we present an inexpensive experiment proposal to study the kinematics of uniform circular motion in a secondary school. We used a PC sound card to connect a homemade simple sensor to a computer and used the free sound analysis software "Audacity" to record experimental data. We obtained quite good results even in comparison…

10 CFR 431.324 - Uniform test method for the measurement of energy efficiency and standby mode energy consumption...

Code of Federal Regulations, 2014 CFR

2014-01-01

... extinguishing the lamp is impossible or for low-frequency electronic ballasts, the following alternative... (V), and current, using an ammeter (A) connected to the ballast in accordance with the circuit shown... ballast in accordance with the circuit shown in Figure 2. ER09MR10.006 (iii) Power Line Carrier (PLC...

10 CFR 431.324 - Uniform test method for the measurement of energy efficiency and standby mode energy consumption...

Code of Federal Regulations, 2013 CFR

2013-01-01

... extinguishing the lamp is impossible or for low-frequency electronic ballasts, the following alternative... (V), and current, using an ammeter (A) connected to the ballast in accordance with the circuit shown... ballast in accordance with the circuit shown in Figure 2. ER09MR10.006 (iii) Power Line Carrier (PLC...

10 CFR 431.324 - Uniform test method for the measurement of energy efficiency and standby mode energy consumption...

Code of Federal Regulations, 2012 CFR

2012-01-01

... extinguishing the lamp is impossible or for low-frequency electronic ballasts, the following alternative... (V), and current, using an ammeter (A) connected to the ballast in accordance with the circuit shown... ballast in accordance with the circuit shown in Figure 2. ER09MR10.006 (iii) Power Line Carrier (PLC...

Partial Agenesis and Hypoplasia of the Corpus Callosum in Idiopathic Autism

PubMed Central

Wegiel, Jarek; Flory, Michael; Kaczmarski, Wojciech; Brown, W. Ted; Chadman, Kathryn; Wisniewski, Thomas; Nowicki, Krzysztof; Kuchna, Izabela; Ma, Shuang Yong; Wegiel, Jerzy

2017-01-01

Abstract To test the hypothesis that developmental anomalies of the corpus callosum (CC), contribute to the pathogenesis of autism, we characterized the type, topography, and severity of CC pathology corresponding to reduced CC areas that are detected by magnetic resonance imaging in the brains of 11 individuals with autism and 11 controls. In the brains of 3 autistic subjects, partial CC agenesis resulted in complete or partial lack of interhemispheric axonal connections in CC segments III–V. In these cases, a combination of focal agenesis and uniform axonal deficit caused reduction of CC areas by 37%, of axon numbers by 62%, and of the numerical density of axons by 39%. In the CC of 8 autistic subjects without agenesis, there was an 18% deficit of the midsagittal CC area, 48.4% deficit of axon numbers, and 37% reduction of the numerical density of axons. The significantly thinner CC, reduced CC area, and uniform axonal deficit in all autistic subjects were classified as CC hypoplasia. Thus, the byproduct of partial CC agenesis and hypoplasia is reduction of axonal connections between cortical areas known to be involved in behavioral alterations observed in people with autism. PMID:28395085

Empirical study on a directed and weighted bus transport network in China

NASA Astrophysics Data System (ADS)

Feng, Shumin; Hu, Baoyu; Nie, Cen; Shen, Xianghao

2016-01-01

Bus transport networks are directed complex networks that consist of routes, stations, and passenger flow. In this study, the concept of duplication factor is introduced to analyze the differences between uplinks and downlinks for the bus transport network of Harbin (BTN-H). Further, a new representation model for BTNs is proposed, named as directed-space P. Two empirical characteristics of BTN-H are reported in this paper. First, the cumulative distributions of weighted degree, degree, number of routes that connect to each station, and node weight (peak-hour trips at a station) uniformly follow the exponential law. Meanwhile, the node weight shows positive correlations with the corresponding weighted degree, degree, and number of routes that connect to a station. Second, a new richness parameter of a node is explored by its node weight and the connectivity, weighted connectivity, average shortest path length and efficiency between rich nodes can be fitted by composite exponential functions to demonstrate the rich-club phenomenon.

Maturational trajectories of local and long-range functional connectivity in autism during face processing.

PubMed

Mamashli, Fahimeh; Khan, Sheraz; Bharadwaj, Hari; Losh, Ainsley; Pawlyszyn, Stephanie M; Hämäläinen, Matti S; Kenet, Tal

2018-06-26

Autism spectrum disorder (ASD) is characterized neurophysiologically by, among other things, functional connectivity abnormalities in the brain. Recent evidence suggests that the nature of these functional connectivity abnormalities might not be uniform throughout maturation. Comparing between adolescents and young adults (ages 14-21) with ASD and age- and IQ-matched typically developing (TD) individuals, we previously documented, using magnetoencephalography (MEG) data, that local functional connectivity in the fusiform face areas (FFA) and long-range functional connectivity between FFA and three higher order cortical areas were all reduced in ASD. Given the findings on abnormal maturation trajectories in ASD, we tested whether these results extend to preadolescent children (ages 7-13). We found that both local and long-range functional connectivity were in fact normal in this younger age group in ASD. Combining the two age groups, we found that local and long-range functional connectivity measures were positively correlated with age in TD, but negatively correlated with age in ASD. Last, we showed that local functional connectivity was the primary feature in predicting age in ASD group, but not in the TD group. Furthermore, local functional connectivity was only correlated with ASD severity in the older group. These results suggest that the direction of maturation of functional connectivity for processing of faces from childhood to young adulthood is itself abnormal in ASD, and that during the processing of faces, these trajectory abnormalities are more pronounced for local functional connectivity measures than they are for long-range functional connectivity measures. © 2018 Wiley Periodicals, Inc.

Spherical Pendulum Small Oscillations for Slewing Crane Motion

PubMed Central

Perig, Alexander V.; Stadnik, Alexander N.; Deriglazov, Alexander I.

2014-01-01

The present paper focuses on the Lagrange mechanics-based description of small oscillations of a spherical pendulum with a uniformly rotating suspension center. The analytical solution of the natural frequencies' problem has been derived for the case of uniform rotation of a crane boom. The payload paths have been found in the inertial reference frame fixed on earth and in the noninertial reference frame, which is connected with the rotating crane boom. The numerical amplitude-frequency characteristics of the relative payload motion have been found. The mechanical interpretation of the terms in Lagrange equations has been outlined. The analytical expression and numerical estimation for cable tension force have been proposed. The numerical computational results, which correlate very accurately with the experimental observations, have been shown. PMID:24526891

Reappraisal of criticality for two-layer flows and its role in the generation of internal solitary waves

NASA Astrophysics Data System (ADS)

Bridges, Thomas J.; Donaldson, Neil M.

2007-07-01

A geometric view of criticality for two-layer flows is presented. Uniform flows are classified by diagrams in the momentum-massflux space for fixed Bernoulli energy, and cuspoidal curves on these diagrams correspond to critical uniform flows. Restriction of these surfaces to critical flow leads to new subsurfaces in energy-massflux space. While the connection between criticality and the generation of solitary waves is well known, we find that the nonlinear properties of these bifurcating solitary waves are also determined by the properties of the criticality surfaces. To be specific, the case of two layers with a rigid lid is considered, and application of the theory to other multilayer flows is sketched.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bradonjic, Milan; Elsasser, Robert; Friedrich, Tobias

A Randon Geometric Graph (RGG) is constructed by distributing n nodes uniformly at random in the unit square and connecting two nodes if their Euclidean distance is at most r, for some prescribed r. They analyze the following randomized broadcast algorithm on RGGs. At the beginning, there is only one informed node. Then in each round, each informed node chooses a neighbor uniformly at random and informs it. They prove that this algorithm informs every node in the largest component of a RGG in {Omicron}({radical}n/r) rounds with high probability. This holds for any value of r larger than the criticalmore » value for the emergence of a giant component. In particular, the result implies that the diameter of the giant component is {Theta}({radical}n/r).« less

Bayesian Community Detection in the Space of Group-Level Functional Differences

PubMed Central

Venkataraman, Archana; Yang, Daniel Y.-J.; Pelphrey, Kevin A.; Duncan, James S.

2017-01-01

We propose a unified Bayesian framework to detect both hyper- and hypo-active communities within whole-brain fMRI data. Specifically, our model identifies dense subgraphs that exhibit population-level differences in functional synchrony between a control and clinical group. We derive a variational EM algorithm to solve for the latent posterior distributions and parameter estimates, which subsequently inform us about the afflicted network topology. We demonstrate that our method provides valuable insights into the neural mechanisms underlying social dysfunction in autism, as verified by the Neurosynth meta-analytic database. In contrast, both univariate testing and community detection via recursive edge elimination fail to identify stable functional communities associated with the disorder. PMID:26955022

Bayesian Community Detection in the Space of Group-Level Functional Differences.

PubMed

Venkataraman, Archana; Yang, Daniel Y-J; Pelphrey, Kevin A; Duncan, James S

2016-08-01

We propose a unified Bayesian framework to detect both hyper- and hypo-active communities within whole-brain fMRI data. Specifically, our model identifies dense subgraphs that exhibit population-level differences in functional synchrony between a control and clinical group. We derive a variational EM algorithm to solve for the latent posterior distributions and parameter estimates, which subsequently inform us about the afflicted network topology. We demonstrate that our method provides valuable insights into the neural mechanisms underlying social dysfunction in autism, as verified by the Neurosynth meta-analytic database. In contrast, both univariate testing and community detection via recursive edge elimination fail to identify stable functional communities associated with the disorder.

Constraint Embedding for Multibody System Dynamics

NASA Technical Reports Server (NTRS)

Jain, Abhinandan

2009-01-01

This paper describes a constraint embedding approach for the handling of local closure constraints in multibody system dynamics. The approach uses spatial operator techniques to eliminate local-loop constraints from the system and effectively convert the system into tree-topology systems. This approach allows the direct derivation of recursive O(N) techniques for solving the system dynamics and avoiding the expensive steps that would otherwise be required for handling the closedchain dynamics. The approach is very effective for systems where the constraints are confined to small-subgraphs within the system topology. The paper provides background on the spatial operator O(N) algorithms, the extensions for handling embedded constraints, and concludes with some examples of such constraints.

Optimization of the Conical Angle Design in Conical Implant-Abutment Connections: A Pilot Study Based on the Finite Element Method.

PubMed

Yao, Kuang-Ta; Chen, Chen-Sheng; Cheng, Cheng-Kung; Fang, Hsu-Wei; Huang, Chang-Hung; Kao, Hung-Chan; Hsu, Ming-Lun

2018-02-01

Conical implant-abutment connections are popular for their excellent connection stability, which is attributable to frictional resistance in the connection. However, conical angles, the inherent design parameter of conical connections, exert opposing effects on 2 influencing factors of the connection stability: frictional resistance and abutment rigidity. This pilot study employed an optimization approach through the finite element method to obtain an optimal conical angle for the highest connection stability in an Ankylos-based conical connection system. A nonlinear 3-dimensional finite element parametric model was developed according to the geometry of the Ankylos system (conical half angle = 5.7°) by using the ANSYS 11.0 software. Optimization algorithms were conducted to obtain the optimal conical half angle and achieve the minimal value of maximum von Mises stress in the abutment, which represents the highest connection stability. The optimal conical half angle obtained was 10.1°. Compared with the original design (5.7°), the optimal design demonstrated an increased rigidity of abutment (36.4%) and implant (25.5%), a decreased microgap at the implant-abutment interface (62.3%), a decreased contact pressure (37.9%) with a more uniform stress distribution in the connection, and a decreased stress in the cortical bone (4.5%). In conclusion, the methodology of design optimization to determine the optimal conical angle of the Ankylos-based system is feasible. Because of the heterogeneity of different systems, more studies should be conducted to define the optimal conical angle in various conical connection designs.

Postsynaptic FMRP Promotes the Pruning of Cell-to-Cell Connections among Pyramidal Neurons in the L5A Neocortical Network

PubMed Central

Patel, Ankur B.; Loerwald, Kristofer W.; Huber, Kimberly M.

2014-01-01

Pruning of structural synapses occurs with development and learning. A deficit in pruning of cortical excitatory synapses and the resulting hyperconnectivity is hypothesized to underlie the etiology of fragile X syndrome (FXS) and related autistic disorders. However, clear evidence for pruning in neocortex and its impairment in FXS remains elusive. Using simultaneous recordings of pyramidal neurons in the layer 5A neocortical network of the wild-type (WT) mouse to observe cell-to-cell connections in isolation, we demonstrate here a specific form of “connection pruning.” Connection frequency among pyramidal neurons decreases between the third and fifth postnatal weeks, indicating a period of connection pruning. Over the same interval in the FXS model mouse, the Fmr1 knock-out (KO), connection frequency does not decrease. Therefore, connection frequency in the fifth week is higher in the Fmr1 KO compared with WT, indicating a state of hyperconnectivity. These alterations are due to postsynaptic deletion of Fmr1. At early ages (2 weeks), postsynaptic Fmr1 promoted the maturation of cell-to-cell connections, but not their number. These findings indicate that impaired connection pruning at later ages, and not an excess of connection formation, underlies the hyperconnectivity in the Fmr1 KO mouse. FMRP did not appear to regulate synapses individually, but instead regulated cell-to-cell connectivity in which groups of synapses mediating a single cell-to-cell connection are uniformly removed, retained, and matured. Although we do not link connection pruning directly to the pruning of structurally defined synapses, this study nevertheless provides an important model system for studying altered pruning in FXS. PMID:24573297

Postsynaptic FMRP promotes the pruning of cell-to-cell connections among pyramidal neurons in the L5A neocortical network.

PubMed

Patel, Ankur B; Loerwald, Kristofer W; Huber, Kimberly M; Gibson, Jay R

2014-02-26

Pruning of structural synapses occurs with development and learning. A deficit in pruning of cortical excitatory synapses and the resulting hyperconnectivity is hypothesized to underlie the etiology of fragile X syndrome (FXS) and related autistic disorders. However, clear evidence for pruning in neocortex and its impairment in FXS remains elusive. Using simultaneous recordings of pyramidal neurons in the layer 5A neocortical network of the wild-type (WT) mouse to observe cell-to-cell connections in isolation, we demonstrate here a specific form of "connection pruning." Connection frequency among pyramidal neurons decreases between the third and fifth postnatal weeks, indicating a period of connection pruning. Over the same interval in the FXS model mouse, the Fmr1 knock-out (KO), connection frequency does not decrease. Therefore, connection frequency in the fifth week is higher in the Fmr1 KO compared with WT, indicating a state of hyperconnectivity. These alterations are due to postsynaptic deletion of Fmr1. At early ages (2 weeks), postsynaptic Fmr1 promoted the maturation of cell-to-cell connections, but not their number. These findings indicate that impaired connection pruning at later ages, and not an excess of connection formation, underlies the hyperconnectivity in the Fmr1 KO mouse. FMRP did not appear to regulate synapses individually, but instead regulated cell-to-cell connectivity in which groups of synapses mediating a single cell-to-cell connection are uniformly removed, retained, and matured. Although we do not link connection pruning directly to the pruning of structurally defined synapses, this study nevertheless provides an important model system for studying altered pruning in FXS.

Equilibrium statistical mechanics on correlated random graphs

NASA Astrophysics Data System (ADS)

Barra, Adriano; Agliari, Elena

2011-02-01

Biological and social networks have recently attracted great attention from physicists. Among several aspects, two main ones may be stressed: a non-trivial topology of the graph describing the mutual interactions between agents and, typically, imitative, weighted, interactions. Despite such aspects being widely accepted and empirically confirmed, the schemes currently exploited in order to generate the expected topology are based on a priori assumptions and, in most cases, implement constant intensities for links. Here we propose a simple shift [-1,+1]\\to [0,+1] in the definition of patterns in a Hopfield model: a straightforward effect is the conversion of frustration into dilution. In fact, we show that by varying the bias of pattern distribution, the network topology (generated by the reciprocal affinities among agents, i.e. the Hebbian rule) crosses various well-known regimes, ranging from fully connected, to an extreme dilution scenario, then to completely disconnected. These features, as well as small-world properties, are, in this context, emergent and no longer imposed a priori. The model is throughout investigated also from a thermodynamics perspective: the Ising model defined on the resulting graph is analytically solved (at a replica symmetric level) by extending the double stochastic stability technique, and presented together with its fluctuation theory for a picture of criticality. Overall, our findings show that, at least at equilibrium, dilution (of whatever kind) simply decreases the strength of the coupling felt by the spins, but leaves the paramagnetic/ferromagnetic flavors unchanged. The main difference with respect to previous investigations is that, within our approach, replicas do not appear: instead of (multi)-overlaps as order parameters, we introduce a class of magnetizations on all the possible subgraphs belonging to the main one investigated: as a consequence, for these objects a closure for a self-consistent relation is achieved.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Sangkeun; Sukumar, Sreenivas R; Hong, Seokyong

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

Human Rights Event Detection from Heterogeneous Social Media Graphs.

PubMed

Chen, Feng; Neill, Daniel B

2015-03-01

Human rights organizations are increasingly monitoring social media for identification, verification, and documentation of human rights violations. Since manual extraction of events from the massive amount of online social network data is difficult and time-consuming, we propose an approach for automated, large-scale discovery and analysis of human rights-related events. We apply our recently developed Non-Parametric Heterogeneous Graph Scan (NPHGS), which models social media data such as Twitter as a heterogeneous network (with multiple different node types, features, and relationships) and detects emerging patterns in the network, to identify and characterize human rights events. NPHGS efficiently maximizes a nonparametric scan statistic (an aggregate measure of anomalousness) over connected subgraphs of the heterogeneous network to identify the most anomalous network clusters. It summarizes each event with information such as type of event, geographical locations, time, and participants, and provides documentation such as links to videos and news reports. Building on our previous work that demonstrates the utility of NPHGS for civil unrest prediction and rare disease outbreak detection, we present an analysis of human rights events detected by NPHGS using two years of Twitter data from Mexico. NPHGS was able to accurately detect relevant clusters of human rights-related tweets prior to international news sources, and in some cases, prior to local news reports. Analysis of social media using NPHGS could enhance the information-gathering missions of human rights organizations by pinpointing specific abuses, revealing events and details that may be blocked from traditional media sources, and providing evidence of emerging patterns of human rights violations. This could lead to more timely, targeted, and effective advocacy, as well as other potential interventions.

Semi-Metric Topology of the Human Connectome: Sensitivity and Specificity to Autism and Major Depressive Disorder.

PubMed

Simas, Tiago; Chattopadhyay, Shayanti; Hagan, Cindy; Kundu, Prantik; Patel, Ameera; Holt, Rosemary; Floris, Dorothea; Graham, Julia; Ooi, Cinly; Tait, Roger; Spencer, Michael; Baron-Cohen, Simon; Sahakian, Barbara; Bullmore, Ed; Goodyer, Ian; Suckling, John

2015-01-01

The human functional connectome is a graphical representation, consisting of nodes connected by edges, of the inter-relationships of blood oxygenation-level dependent (BOLD) time-series measured by MRI from regions encompassing the cerebral cortices and, often, the cerebellum. Semi-metric analysis of the weighted, undirected connectome distinguishes an edge as either direct (metric), such that there is no alternative path that is accumulatively stronger, or indirect (semi-metric), where one or more alternative paths exist that have greater strength than the direct edge. The sensitivity and specificity of this method of analysis is illustrated by two case-control analyses with independent, matched groups of adolescents with autism spectrum conditions (ASC) and major depressive disorder (MDD). Significance differences in the global percentage of semi-metric edges was observed in both groups, with increases in ASC and decreases in MDD relative to controls. Furthermore, MDD was associated with regional differences in left frontal and temporal lobes, the right limbic system and cerebellum. In contrast, ASC had a broadly increased percentage of semi-metric edges with a more generalised distribution of effects and some areas of reduction. In summary, MDD was characterised by localised, large reductions in the percentage of semi-metric edges, whilst ASC is characterised by more generalised, subtle increases. These differences were corroborated in greater detail by inspection of the semi-metric backbone for each group; that is, the sub-graph of semi-metric edges present in >90% of participants, and by nodal degree differences in the semi-metric connectome. These encouraging results, in what we believe is the first application of semi-metric analysis to neuroimaging data, raise confidence in the methodology as potentially capable of detection and characterisation of a range of neurodevelopmental and psychiatric disorders.

Semi-Metric Topology of the Human Connectome: Sensitivity and Specificity to Autism and Major Depressive Disorder

PubMed Central

Simas, Tiago; Chattopadhyay, Shayanti; Hagan, Cindy; Kundu, Prantik; Patel, Ameera; Holt, Rosemary; Floris, Dorothea; Graham, Julia; Ooi, Cinly; Tait, Roger; Spencer, Michael; Baron-Cohen, Simon; Sahakian, Barbara; Bullmore, Ed; Goodyer, Ian; Suckling, John

2015-01-01

Introduction The human functional connectome is a graphical representation, consisting of nodes connected by edges, of the inter-relationships of blood oxygenation-level dependent (BOLD) time-series measured by MRI from regions encompassing the cerebral cortices and, often, the cerebellum. Semi-metric analysis of the weighted, undirected connectome distinguishes an edge as either direct (metric), such that there is no alternative path that is accumulatively stronger, or indirect (semi-metric), where one or more alternative paths exist that have greater strength than the direct edge. The sensitivity and specificity of this method of analysis is illustrated by two case-control analyses with independent, matched groups of adolescents with autism spectrum conditions (ASC) and major depressive disorder (MDD). Results Significance differences in the global percentage of semi-metric edges was observed in both groups, with increases in ASC and decreases in MDD relative to controls. Furthermore, MDD was associated with regional differences in left frontal and temporal lobes, the right limbic system and cerebellum. In contrast, ASC had a broadly increased percentage of semi-metric edges with a more generalised distribution of effects and some areas of reduction. In summary, MDD was characterised by localised, large reductions in the percentage of semi-metric edges, whilst ASC is characterised by more generalised, subtle increases. These differences were corroborated in greater detail by inspection of the semi-metric backbone for each group; that is, the sub-graph of semi-metric edges present in >90% of participants, and by nodal degree differences in the semi-metric connectome. Conclusion These encouraging results, in what we believe is the first application of semi-metric analysis to neuroimaging data, raise confidence in the methodology as potentially capable of detection and characterisation of a range of neurodevelopmental and psychiatric disorders. PMID:26308854

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

DOE PAGES

Lee, Sangkeun; Sukumar, Sreenivas R; Hong, Seokyong; ...

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

A scheme for synchronizing clocks connected by a packet communication network

NASA Astrophysics Data System (ADS)

dos Santos, R. V.; Monteiro, L. H. A.

2012-07-01

Consider a communication system in which a transmitter equipment sends fixed-size packets of data at a uniform rate to a receiver equipment. Consider also that these equipments are connected by a packet-switched network, which introduces a random delay to each packet. Here we propose an adaptive clock recovery scheme able of synchronizing the frequencies and the phases of these devices, within specified limits of precision. This scheme for achieving frequency and phase synchronization is based on measurements of the packet arrival times at the receiver, which are used to control the dynamics of a digital phase-locked loop. The scheme performance is evaluated via numerical simulations performed by using realistic parameter values.

Improving the image discontinuous problem by using color temperature mapping method

NASA Astrophysics Data System (ADS)

Jeng, Wei-De; Mang, Ou-Yang; Lai, Chien-Cheng; Wu, Hsien-Ming

2011-09-01

This article mainly focuses on image processing of radial imaging capsule endoscope (RICE). First, it used the radial imaging capsule endoscope (RICE) to take the images, the experimental used a piggy to get the intestines and captured the images, but the images captured by RICE were blurred due to the RICE has aberration problems in the image center and lower light uniformity affect the image quality. To solve the problems, image processing can use to improve it. Therefore, the images captured by different time can use Person correlation coefficient algorithm to connect all the images, and using the color temperature mapping way to improve the discontinuous problem in the connection region.

Linking a one-dimensional pesticide fate model to a three-dimensional groundwater model to simulate pollution risks of shallow and deep groundwater underlying fractured till.

PubMed

Stenemo, Fredrik; Jørgensen, Peter R; Jarvis, Nicholas

2005-09-01

The one-dimensional pesticide fate model MACRO was loose-linked to the three-dimensional discrete fracture/matrix diffusion model FRAC3DVS to describe transport of the pesticide mecoprop in a fractured moraine till and local sand aquifer (5-5.5 m depth) overlying a regional limestone aquifer (16 m depth) at Havdrup, Denmark. Alternative approaches to describe the upper boundary in the groundwater model were examined. Field-scale simulations were run to compare a uniform upper boundary condition with a spatially variable upper boundary derived from Monte-Carlo simulations with MACRO. Plot-scale simulations were run to investigate the influence of the temporal resolution of the upper boundary conditions for fluxes in the groundwater model and the effects of different assumptions concerning the macropore/fracture connectivity between the two models. The influence of within-field variability of leaching on simulated mecoprop concentrations in the local aquifer was relatively small. A fully transient simulation with FRAC3DVS gave 20 times larger leaching to the regional aquifer compared to the case with steady-state water flow, assuming full connectivity with respect to macropores/fractures across the boundary between the two models. For fully transient simulations 'disconnecting' the macropores/fractures at the interface between the two models reduced leaching by a factor 24. A fully connected, transient simulation with FRAC3DVS, with spatially uniform upper boundary fluxes derived from a MACRO simulation with 'effective' parameters is therefore recommended for assessing leaching risks to the regional aquifer, at this, and similar sites.

An impatient evolutionary algorithm with probabilistic tabu search for unified solution of some NP-hard problems in graph and set theory via clique finding.

PubMed

Guturu, Parthasarathy; Dantu, Ram

2008-06-01

Many graph- and set-theoretic problems, because of their tremendous application potential and theoretical appeal, have been well investigated by the researchers in complexity theory and were found to be NP-hard. Since the combinatorial complexity of these problems does not permit exhaustive searches for optimal solutions, only near-optimal solutions can be explored using either various problem-specific heuristic strategies or metaheuristic global-optimization methods, such as simulated annealing, genetic algorithms, etc. In this paper, we propose a unified evolutionary algorithm (EA) to the problems of maximum clique finding, maximum independent set, minimum vertex cover, subgraph and double subgraph isomorphism, set packing, set partitioning, and set cover. In the proposed approach, we first map these problems onto the maximum clique-finding problem (MCP), which is later solved using an evolutionary strategy. The proposed impatient EA with probabilistic tabu search (IEA-PTS) for the MCP integrates the best features of earlier successful approaches with a number of new heuristics that we developed to yield a performance that advances the state of the art in EAs for the exploration of the maximum cliques in a graph. Results of experimentation with the 37 DIMACS benchmark graphs and comparative analyses with six state-of-the-art algorithms, including two from the smaller EA community and four from the larger metaheuristics community, indicate that the IEA-PTS outperforms the EAs with respect to a Pareto-lexicographic ranking criterion and offers competitive performance on some graph instances when individually compared to the other heuristic algorithms. It has also successfully set a new benchmark on one graph instance. On another benchmark suite called Benchmarks with Hidden Optimal Solutions, IEA-PTS ranks second, after a very recent algorithm called COVER, among its peers that have experimented with this suite.

A Network of Networks Perspective on Global Trade.

PubMed

Maluck, Julian; Donner, Reik V

2015-01-01

Mutually intertwined supply chains in contemporary economy result in a complex network of trade relationships with a highly non-trivial topology that varies with time. In order to understand the complex interrelationships among different countries and economic sectors, as well as their dynamics, a holistic view on the underlying structural properties of this network is necessary. This study employs multi-regional input-output data to decompose 186 national economies into 26 industry sectors and utilizes the approach of interdependent networks to analyze the substructure of the resulting international trade network for the years 1990-2011. The partition of the network into national economies is observed to be compatible with the notion of communities in the sense of complex network theory. By studying internal versus cross-subgraph contributions to established complex network metrics, new insights into the architecture of global trade are obtained, which allow to identify key elements of global economy. Specifically, financial services and business activities dominate domestic trade whereas electrical and machinery industries dominate foreign trade. In order to further specify each national sector's role individually, (cross-)clustering coefficients and cross-betweenness are obtained for different pairs of subgraphs. The corresponding analysis reveals that specific industrial sectors tend to favor distinct directionality patterns and that the cross-clustering coefficient for geographically close country pairs is remarkably high, indicating that spatial factors are still of paramount importance for the organization of trade patterns in modern economy. Regarding the evolution of the trade network's substructure, globalization is well-expressed by trends of several structural characteristics (e.g., link density and node strength) in the interacting network framework. Extreme events, such as the financial crisis 2008/2009, are manifested as anomalies superimposed to these trends. The marked reorganization of trade patterns, associated with this economic crisis in comparison to "normal" annual fluctuations in the network structure is traced and quantified by a new widely applicable generalization of the Hamming distance to weighted networks.

A Network of Networks Perspective on Global Trade

PubMed Central

Maluck, Julian; Donner, Reik V.

2015-01-01

Mutually intertwined supply chains in contemporary economy result in a complex network of trade relationships with a highly non-trivial topology that varies with time. In order to understand the complex interrelationships among different countries and economic sectors, as well as their dynamics, a holistic view on the underlying structural properties of this network is necessary. This study employs multi-regional input-output data to decompose 186 national economies into 26 industry sectors and utilizes the approach of interdependent networks to analyze the substructure of the resulting international trade network for the years 1990–2011. The partition of the network into national economies is observed to be compatible with the notion of communities in the sense of complex network theory. By studying internal versus cross-subgraph contributions to established complex network metrics, new insights into the architecture of global trade are obtained, which allow to identify key elements of global economy. Specifically, financial services and business activities dominate domestic trade whereas electrical and machinery industries dominate foreign trade. In order to further specify each national sector’s role individually, (cross-)clustering coefficients and cross-betweenness are obtained for different pairs of subgraphs. The corresponding analysis reveals that specific industrial sectors tend to favor distinct directionality patterns and that the cross-clustering coefficient for geographically close country pairs is remarkably high, indicating that spatial factors are still of paramount importance for the organization of trade patterns in modern economy. Regarding the evolution of the trade network’s substructure, globalization is well-expressed by trends of several structural characteristics (e.g., link density and node strength) in the interacting network framework. Extreme events, such as the financial crisis 2008/2009, are manifested as anomalies superimposed to these trends. The marked reorganization of trade patterns, associated with this economic crisis in comparison to “normal” annual fluctuations in the network structure is traced and quantified by a new widely applicable generalization of the Hamming distance to weighted networks. PMID:26197439

Enhancing sedimentation by improving flow conditions using parallel retrofit baffles.

PubMed

He, Cheng; Scott, Eric; Rochfort, Quintin

2015-09-01

In this study, placing parallel-connected baffles in the vicinity of the inlet was proposed to improve hydraulic conditions for enhancing TSS (total suspended solids) removal. The purpose of the retrofit baffle design is to divide the large and fast inflow into smaller and slower flows to increase flow uniformity. This avoids short-circuiting and increases residence time in the sedimentation basin. The newly proposed parallel-connected baffle configuration was assessed in the laboratory by comparing its TSS removal performance and the optimal flow residence time with those from the widely used series-connected baffles. The experimental results showed that the parallel-connected baffles outperformed the series-connected baffles because it could disperse flow faster and in less space by splitting the large inflow into many small branches instead of solely depending on flow internal friction over a longer flow path, as was the case under the series-connected baffles. Being able to dampen faster flow before entering the sedimentation basin is critical to reducing the possibility of disturbing any settled particles, especially under high inflow conditions. Also, for a large sedimentation basin, it may be more economically feasible to deploy the proposed parallel retrofit baffle in the vicinity of the inlet than series-connected baffles throughout the entire settling basin. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

Identified Serotonergic Modulatory Neurons Have Heterogeneous Synaptic Connectivity within the Olfactory System of Drosophila.

PubMed

Coates, Kaylynn E; Majot, Adam T; Zhang, Xiaonan; Michael, Cole T; Spitzer, Stacy L; Gaudry, Quentin; Dacks, Andrew M

2017-08-02

Modulatory neurons project widely throughout the brain, dynamically altering network processing based on an animal's physiological state. The connectivity of individual modulatory neurons can be complex, as they often receive input from a variety of sources and are diverse in their physiology, structure, and gene expression profiles. To establish basic principles about the connectivity of individual modulatory neurons, we examined a pair of identified neurons, the "contralaterally projecting, serotonin-immunoreactive deutocerebral neurons" (CSDns), within the olfactory system of Drosophila Specifically, we determined the neuronal classes providing synaptic input to the CSDns within the antennal lobe (AL), an olfactory network targeted by the CSDns, and the degree to which CSDn active zones are uniformly distributed across the AL. Using anatomical techniques, we found that the CSDns received glomerulus-specific input from olfactory receptor neurons (ORNs) and projection neurons (PNs), and networkwide input from local interneurons (LNs). Furthermore, we quantified the number of CSDn active zones in each glomerulus and found that CSDn output is not uniform, but rather heterogeneous, across glomeruli and stereotyped from animal to animal. Finally, we demonstrate that the CSDns synapse broadly onto LNs and PNs throughout the AL but do not synapse upon ORNs. Our results demonstrate that modulatory neurons do not necessarily provide purely top-down input but rather receive neuron class-specific input from the networks that they target, and that even a two cell modulatory network has highly heterogeneous, yet stereotyped, pattern of connectivity. SIGNIFICANCE STATEMENT Modulatory neurons often project broadly throughout the brain to alter processing based on physiological state. However, the connectivity of individual modulatory neurons to their target networks is not well understood, as modulatory neuron populations are heterogeneous in their physiology, morphology, and gene expression. In this study, we use a pair of identified serotonergic neurons within the Drosophila olfactory system as a model to establish a framework for modulatory neuron connectivity. We demonstrate that individual modulatory neurons can integrate neuron class-specific input from their target network, which is often nonreciprocal. Additionally, modulatory neuron output can be stereotyped, yet nonuniform, across network regions. Our results provide new insight into the synaptic relationships that underlie network function of modulatory neurons. Copyright © 2017 the authors 0270-6474/17/377318-14$15.00/0.

Towards spatially constrained gust models

NASA Astrophysics Data System (ADS)

Bos, René; Bierbooms, Wim; van Bussel, Gerard

2014-06-01

With the trend of moving towards 10-20 MW turbines, rotor diameters are growing beyond the size of the largest turbulent structures in the atmospheric boundary layer. As a consequence, the fully uniform transients that are commonly used to predict extreme gust loads are losing their connection to reality and may lead to gross overdimensioning. More suiting would be to represent gusts by advecting air parcels and posing certain physical constraints on size and position. However, this would introduce several new degrees of freedom that significantly increase the computational burden of extreme load prediction. In an attempt to elaborate on the costs and benefits of such an approach, load calculations were done on the DTU 10 MW reference turbine where a single uniform gust shape was given various spatial dimensions with the transverse wavelength ranging up to twice the rotor diameter (357 m). The resulting loads displayed a very high spread, but remained well under the level of a uniform gust. Moving towards spatially constrained gust models would therefore yield far less conservative, though more realistic predictions at the cost of higher computation time.

Synchronization of Lienard-Type Oscillators in Uniform Electrical Networks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sinha, Mohit; Dorfler, Florian; Johnson, Brian B.

2016-08-01

This paper presents a condition for global asymptotic synchronization of Lienard-type nonlinear oscillators in uniform LTI electrical networks with series R-L circuits modeling interconnections. By uniform electrical networks, we mean that the per-unit-length impedances are identical for the interconnecting lines. We derive conditions for global asymptotic synchronization for a particular feedback architecture where the derivative of the oscillator output current supplements the innate current feedback induced by simply interconnecting the oscillator to the network. Our proof leverages a coordinate transformation to a set of differential coordinates that emphasizes signal differences and the particular form of feedback permits the formulation ofmore » a quadratic Lyapunov function for this class of networks. This approach is particularly interesting since synchronization conditions are difficult to obtain by means of quadratic Lyapunov functions when only current feedback is used and for networks composed of series R-L circuits. Our synchronization condition depends on the algebraic connectivity of the underlying network, and reiterates the conventional wisdom from Lyapunov- and passivity-based arguments that strong coupling is required to ensure synchronization.« less

Maternally expressed PGK-Cre transgene as a tool for early and uniform activation of the Cre site-specific recombinase.

PubMed

Lallemand, Y; Luria, V; Haffner-Krausz, R; Lonai, P

1998-03-01

A transgenic mouse strain with early and uniform expression of the Cre site-specific recombinase is described. In this strain, PGK-Crem, Cre is driven by the early acting PGK-1 promoter, but, probably due to cis effects at the integration site, the recombinase is under dominant maternal control. When Cre is transmitted by PGK-Crem females mated to males that carry a reporter transgene flanked by loxP sites, even offspring that do not inherit PGK-Cre delete the target gene. It follows that in the PGK-Crem female Cre activity commences in the diploid phase of oogenesis. In PGK-Crem crosses complete recombination was observed in all organs, including testis and ovary. We prepared a mouse stock that is homozygous for PGK-Crem and at the albino (c) locus. This strain will be useful for the early and uniform induction of ectopic and dominant negative mutations, for the in vivo removal of selective elements from targeted mutations and in connection with the manipulation of targeted loci in 'knock in' and related technologies.

On the evolution of a retracting straight liquid sheet edge: experimental study

NASA Astrophysics Data System (ADS)

Krechetnikov, Rouslan; Mayer, Hans C.

2011-11-01

The evolution of the initially straight edge of a retracting liquid sheet is still a subject of debate. Theoretical and numerical studies have provided conflicting results, and experimental efforts have, to our knowledge, never been attempted owing to the difficulty in achieving a uniform edge. However, recent advances in experimental techniques, specifically those presented in detail in Poster #72 of APS-DFD 2010 (H.C. Mayer and R. Krechetnikov), have allowed us to uniformly detach a soap film from a straight edge using an impulsively heated wire frame. The detachment, retraction, and breakup of soap films (h ~ 10 μm) is analyzed using high speed photography. Owing to the Plateau border that connects the uniform film to the wire frames (wire diameter 25-250 μm) - a feature not present when rupturing films from a point - the early stages of retraction are dominated by a relatively large rim mass. We explore the phenomena at very early times (t < 100 μs) associated with the birth of these detached films which may add complexity to the problem of determining what instability mechanism(s) are responsible for their breakup.

Hague Convention on the Civil Aspects of International Child Abduction. Report from the Committee on Foreign Relations (To Accompany Treaty Doc. 99-11). 99th Congress, 2d Session.

ERIC Educational Resources Information Center

Congress of the U.S., Washington, DC. Senate Committee on Foreign Relations.

The Hague Convention on the Civil Aspects of International Child Abduction, an international law whose purpose is to establish uniform rules to be applied in cases of international child abduction, is described. The Hague Convention requires that children wrongfully removed or retained abroad in connection with parental custody disputes be…

Germanium Resistance Thermometer For Subkelvin Temperatures

NASA Technical Reports Server (NTRS)

Castles, Stephen H.

1993-01-01

Improved germanium resistance thermometer measures temperatures as small as 0.01 K accurately. Design provides large area for electrical connections (to reduce electrical gradients and increase sensitivity to changes in temperatures) and large heat sink (to minimize resistance heating). Gold pads on top and bottom of germanium crystal distribute electrical current and flow of heat nearly uniformly across crystal. Less expensive than magnetic thermometers or superconducting quantum interference devices (SQUID's) otherwise used.

10 CFR Appendix Y to Subpart B of... - Uniform Test Method for Measuring the Energy Consumption of Battery Chargers

Code of Federal Regulations, 2012 CFR

2012-01-01

..., the test shall be run for the longest estimated charge time plus 5 hours. (3) If there is no indicator...-detachable AC power cord or plug blades, then no part of the system will remain connected to mains, and... conversion and charging circuitry but is powered through a non-detachable AC power cord or plug blades, then...

10 CFR Appendix Y to Subpart B of... - Uniform Test Method for Measuring the Energy Consumption of Battery Chargers

Code of Federal Regulations, 2014 CFR

2014-01-01

..., the test shall be run for the longest estimated charge time plus 5 hours. (3) If there is no indicator...-detachable AC power cord or plug blades, then no part of the system will remain connected to mains, and... conversion and charging circuitry but is powered through a non-detachable AC power cord or plug blades, then...

10 CFR Appendix Y to Subpart B of... - Uniform Test Method for Measuring the Energy Consumption of Battery Chargers

Code of Federal Regulations, 2013 CFR

2013-01-01

..., the test shall be run for the longest estimated charge time plus 5 hours. (3) If there is no indicator...-detachable AC power cord or plug blades, then no part of the system will remain connected to mains, and... conversion and charging circuitry but is powered through a non-detachable AC power cord or plug blades, then...

Buckling Tests with a Spar-rib Grill

NASA Technical Reports Server (NTRS)

Weinhold, Josef

1940-01-01

The present report deals with a comparison of mathematically and experimentally defined buckling loads of a spar-rib grill, on the assumption of constant spar section, and infinitely closely spaced ribs with rigidity symmetrical to the grill center. The loads are applied as equal bending moments at both spar ends, as compression in the line connecting the joints, and in the spar center line as the assumedly uniformly distributed spar weight.

Rigorous Results for the Distribution of Money on Connected Graphs

NASA Astrophysics Data System (ADS)

Lanchier, Nicolas; Reed, Stephanie

2018-05-01

This paper is concerned with general spatially explicit versions of three stochastic models for the dynamics of money that have been introduced and studied numerically by statistical physicists: the uniform reshuffling model, the immediate exchange model and the model with saving propensity. All three models consist of systems of economical agents that consecutively engage in pairwise monetary transactions. Computer simulations performed in the physics literature suggest that, when the number of agents and the average amount of money per agent are large, the limiting distribution of money as time goes to infinity approaches the exponential distribution for the first model, the gamma distribution with shape parameter two for the second model and a distribution similar but not exactly equal to a gamma distribution whose shape parameter depends on the saving propensity for the third model. The main objective of this paper is to give rigorous proofs of these conjectures and also extend these conjectures to generalizations of the first two models and a variant of the third model that include local rather than global interactions, i.e., instead of choosing the two interacting agents uniformly at random from the system, the agents are located on the vertex set of a general connected graph and can only interact with their neighbors.

The contribution of reserves and anthropogenic habitat for functional connectivity and resilience of ephemeral wetland networks

NASA Astrophysics Data System (ADS)

Allen, C. R.; Uden, D.; Angeler, D.; Hellman, M.

2015-12-01

Functional connectivity of reserves and other suitable habitat patches is crucial for persistence of spatially structured populations, and therefore for resilience. To maintain or increase connectivity at spatial scales larger than individual patches, conservation actions may focus on creating and maintaining reserves or influencing management actions taken on non-reserves. We assess functional connectivity of isolated wetlands within an intensively managed agricultural matrix. Using a graph-theoretic approach, we assessed the functional connectivity and spatial distribution of wetlands in the Rainwater Basins, Nebraska, U.S.A. at four assumed anuran dispersal distances. We compare the contemporary wetlands landscape to the historical landscape and putative future landscapes and evaluate the importance of individual and aggregated reserve and non-reserve wetlands for maintaining connectivity. Connectivity was greatest in the historical landscape, where wetlands were also the most densely distributed. The construction of irrigation reuse pits for water storage has substantially increased connectivity in the current landscape, but because their distribution is more uniform than historical wetlands, larger and longer-dispersing species may be favored over smaller, shorter-dispersing species. Because of their relatively low number, wetland reserves did not affect connectivity as greatly as non-reserve wetlands or irrigation reuse pits; however, they provide the highest-quality anuran habitat. Future levels of connectivity in the region will be directly impacted by the planned removal of irrigation reuse pits, and on non-reserve wetlands. Multi-scale spatial and temporal assessments of the effects of landuse change and conservation actions on landscape connectivity may be used to direct and prioritize conservation actions, and should also be useful for reserve network and landscape resilience assessments.

Renal cortex segmentation using optimal surface search with novel graph construction.

PubMed

Li, Xiuli; Chen, Xinjian; Yao, Jianhua; Zhang, Xing; Tian, Jie

2011-01-01

In this paper, we propose a novel approach to solve the renal cortex segmentation problem, which has rarely been studied. In this study, the renal cortex segmentation problem is handled as a multiple-surfaces extraction problem, which is solved using the optimal surface search method. We propose a novel graph construction scheme in the optimal surface search to better accommodate multiple surfaces. Different surface sub-graphs are constructed according to their properties, and inter-surface relationships are also modeled in the graph. The proposed method was tested on 17 clinical CT datasets. The true positive volume fraction (TPVF) and false positive volume fraction (FPVF) are 74.10% and 0.08%, respectively. The experimental results demonstrate the effectiveness of the proposed method.

Efficient reordering of PROLOG programs

NASA Technical Reports Server (NTRS)

Gooley, Markian M.; Wah, Benjamin W.

1989-01-01

PROLOG programs are often inefficient: execution corresponds to a depth-first traversal of an AND/OR graph; traversing subgraphs in another order can be less expensive. It is shown how the reordering of clauses within PROLOG predicates, and especially of goals within clauses, can prevent unnecessary search. The characterization and detection of restrictions on reordering is discussed. A system of calling modes for PROLOG, geared to reordering, is proposed, and ways to infer them automatically are discussed. The information needed for safe reordering is summarized, and which types can be inferred automatically and which must be provided by the user are considered. An improved method for determining a good order for the goals of PROLOG clauses is presented and used as the basis for a reordering system.

Motif-based success scores in coauthorship networks are highly sensitive to author name disambiguation

NASA Astrophysics Data System (ADS)

Klosik, David F.; Bornholdt, Stefan; Hütt, Marc-Thorsten

2014-09-01

Following the work of Krumov et al. [Eur. Phys. J. B 84, 535 (2011), 10.1140/epjb/e2011-10746-5] we revisit the question whether the usage of large citation datasets allows for the quantitative assessment of social (by means of coauthorship of publications) influence on the progression of science. Applying a more comprehensive and well-curated dataset containing the publications in the journals of the American Physical Society during the whole 20th century we find that the measure chosen in the original study, a score based on small induced subgraphs, has to be used with caution, since the obtained results are highly sensitive to the exact implementation of the author disambiguation task.

A tool for filtering information in complex systems

PubMed Central

Tumminello, M.; Aste, T.; Di Matteo, T.; Mantegna, R. N.

2005-01-01

We introduce a technique to filter out complex data sets by extracting a subgraph of representative links. Such a filtering can be tuned up to any desired level by controlling the genus of the resulting graph. We show that this technique is especially suitable for correlation-based graphs, giving filtered graphs that preserve the hierarchical organization of the minimum spanning tree but containing a larger amount of information in their internal structure. In particular in the case of planar filtered graphs (genus equal to 0), triangular loops and four-element cliques are formed. The application of this filtering procedure to 100 stocks in the U.S. equity markets shows that such loops and cliques have important and significant relationships with the market structure and properties. PMID:16027373

A tool for filtering information in complex systems.

PubMed

Tumminello, M; Aste, T; Di Matteo, T; Mantegna, R N

2005-07-26

We introduce a technique to filter out complex data sets by extracting a subgraph of representative links. Such a filtering can be tuned up to any desired level by controlling the genus of the resulting graph. We show that this technique is especially suitable for correlation-based graphs, giving filtered graphs that preserve the hierarchical organization of the minimum spanning tree but containing a larger amount of information in their internal structure. In particular in the case of planar filtered graphs (genus equal to 0), triangular loops and four-element cliques are formed. The application of this filtering procedure to 100 stocks in the U.S. equity markets shows that such loops and cliques have important and significant relationships with the market structure and properties.

GraphPrints: Towards a Graph Analytic Method for Network Anomaly Detection

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harshaw, Chris R; Bridges, Robert A; Iannacone, Michael D

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\\% truemore » positive rates at both.« less

A novel sub-shot segmentation method for user-generated video

NASA Astrophysics Data System (ADS)

Lei, Zhuo; Zhang, Qian; Zheng, Chi; Qiu, Guoping

2018-04-01

With the proliferation of the user-generated videos, temporal segmentation is becoming a challengeable problem. Traditional video temporal segmentation methods like shot detection are not able to work on unedited user-generated videos, since they often only contain one single long shot. We propose a novel temporal segmentation framework for user-generated video. It finds similar frames with a tree partitioning min-Hash technique, constructs sparse temporal constrained affinity sub-graphs, and finally divides the video into sub-shot-level segments with a dense-neighbor-based clustering method. Experimental results show that our approach outperforms all the other related works. Furthermore, it is indicated that the proposed approach is able to segment user-generated videos at an average human level.

Posttraumatic stress disorder symptom severity is associated with reduced default mode network connectivity in individuals with elevated genetic risk for psychopathology.

PubMed

Miller, Danielle R; Logue, Mark W; Wolf, Erika J; Maniates, Hannah; Robinson, Meghan E; Hayes, Jasmeet P; Stone, Annjanette; Schichman, Steven; McGlinchey, Regina E; Milberg, William P; Miller, Mark W

2017-07-01

Accumulating evidence suggests that posttraumatic stress disorder (PTSD) is associated with disrupted default mode network (DMN) connectivity, but findings across studies have not been uniform. Individual differences in relevant genes may account for some of the reported variability in the relationship between DMN connectivity and PTSD. In this study, we investigated this possibility using genome-wide association study (GWAS) derived polygenic risk scores (PRSs) for relevant psychiatric traits. We hypothesized that the association between PTSD and DMN connectivity would be moderated by genetic risk for one or more psychiatric traits such that individuals with elevated polygenic risk for psychopathology and severe PTSD would exhibit disrupted DMN connectivity. Participants were 156 white, non-Hispanic veterans of the wars in Iraq and Afghanistan who were genotyped and underwent resting state functional magnetic resonance imaging and clinical assessment. PRSs for neuroticism, anxiety, major depressive disorder, and cross-disorder risk (based on five psychiatric disorders) were calculated using summary statistics from published large-scale consortia-based GWASs. Cross-disorder polygenic risk influenced the relationship between DMN connectivity and PTSD symptom severity such that individuals at greater genetic risk showed a significant negative association between PTSD symptom severity and connectivity between the posterior cingulate cortex and right middle temporal gyrus. Polygenic risk for neuroticism, anxiety, and major depressive disorder did not influence DMN connectivity directly or through an interaction with PTSD. Findings illustrate the potential power of genome-wide PRSs to advance understanding of the relationship between PTSD and DMN connectivity, a putative neural endophenotype of the disorder. © 2017 Wiley Periodicals, Inc.

Connective tissue growth factor (CTGF) and cancer progression.

PubMed

Chu, Chia-Yu; Chang, Cheng-Chi; Prakash, Ekambaranellore; Kuo, Min-Liang

2008-11-01

Connective tissue growth factor (CTGF) is a member of the CCN family of secreted, matrix-associated proteins encoded by immediate early genes that play various roles in angiogenesis and tumor growth. CCN family proteins share uniform modular structure which mediates various cellular functions such as regulation of cell division, chemotaxis, apoptosis, adhesion, motility, angiogenesis, neoplastic transformation, and ion transport. Recently, CTGF expression has been shown to be associated with tumor development and progression. There is growing body of evidence that CTGF may regulate cancer cell migration, invasion, angiogenesis, and anoikis. In this review, we will highlight the influence of CTGF expression on the biological behavior and progression of various cancer cells, as well as its regulation on various types of protein signals and their mechanisms.

Cooperative Optimal Coordination for Distributed Energy Resources

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Tao; Wu, Di; Ren, Wei

In this paper, we consider the optimal coordination problem for distributed energy resources (DERs) including distributed generators and energy storage devices. We propose an algorithm based on the push-sum and gradient method to optimally coordinate storage devices and distributed generators in a distributed manner. In the proposed algorithm, each DER only maintains a set of variables and updates them through information exchange with a few neighbors over a time-varying directed communication network. We show that the proposed distributed algorithm solves the optimal DER coordination problem if the time-varying directed communication network is uniformly jointly strongly connected, which is a mildmore » condition on the connectivity of communication topologies. The proposed distributed algorithm is illustrated and validated by numerical simulations.« less

Local self-uniformity in photonic networks.

PubMed

Sellers, Steven R; Man, Weining; Sahba, Shervin; Florescu, Marian

2017-02-17

The interaction of a material with light is intimately related to its wavelength-scale structure. Simple connections between structure and optical response empower us with essential intuition to engineer complex optical functionalities. Here we develop local self-uniformity (LSU) as a measure of a random network's internal structural similarity, ranking networks on a continuous scale from crystalline, through glassy intermediate states, to chaotic configurations. We demonstrate that complete photonic bandgap structures possess substantial LSU and validate LSU's importance in gap formation through design of amorphous gyroid structures. Amorphous gyroid samples are fabricated via three-dimensional ceramic printing and the bandgaps experimentally verified. We explore also the wing-scale structuring in the butterfly Pseudolycaena marsyas and show that it possesses substantial amorphous gyroid character, demonstrating the subtle order achieved by evolutionary optimization and the possibility of an amorphous gyroid's self-assembly.

Local self-uniformity in photonic networks

NASA Astrophysics Data System (ADS)

Sellers, Steven R.; Man, Weining; Sahba, Shervin; Florescu, Marian

2017-02-01

The interaction of a material with light is intimately related to its wavelength-scale structure. Simple connections between structure and optical response empower us with essential intuition to engineer complex optical functionalities. Here we develop local self-uniformity (LSU) as a measure of a random network's internal structural similarity, ranking networks on a continuous scale from crystalline, through glassy intermediate states, to chaotic configurations. We demonstrate that complete photonic bandgap structures possess substantial LSU and validate LSU's importance in gap formation through design of amorphous gyroid structures. Amorphous gyroid samples are fabricated via three-dimensional ceramic printing and the bandgaps experimentally verified. We explore also the wing-scale structuring in the butterfly Pseudolycaena marsyas and show that it possesses substantial amorphous gyroid character, demonstrating the subtle order achieved by evolutionary optimization and the possibility of an amorphous gyroid's self-assembly.

Investigation of the effect of a power feed vacuum gap in solid liner experiments at 1 MA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bott-Suzuki, S. C., E-mail: sbottsuzuki@ucsd.edu, E-mail: sbottsuzuki@p3ucsd.com; Cordaro, S. W.; Caballero Bendixsen, L. S.

We present an experimental study of plasma initiation of a solid metal liner at the 1 MA level. In contrast to previous work, we introduce a vacuum gap at one of the liner connections to the power feed to investigate how this affects plasma initiation and to infer how this may affect the symmetry of the liner in compression experiments. We observed that the vacuum gap causes non-uniform plasma initiation both azimuthally and axially in liners, diagnosed by gated optical imaging. Using magnetic field probes external to the liner, we also determined that the optical emission is strongly linked to themore » current distribution in the liner. The apparent persistent of azimuthal non-uniformities may have implications for fusion-scale liner experiments.« less

Neurophysiological Study of Vector Responses to Repellents.

DTIC Science & Technology

1980-08-01

vector organisms and of the relationship between the physiologic condition of the organisms and the generation and trans- mission of sensory... hemolymph space at the tip of the antenna and connected to ground. A similar recording electrode was inserted through the cuticle at the base of a...pieces of filter paper of uniform size and placed them in glass tubes, through which the airstream was passed, rather than in the gas bubbler flask

Uncovering the Physical Basis Connecting Environment and Tribological Performance of Ultrananocrystalline Diamond

DTIC Science & Technology

2014-04-17

measured with an infrared pyrometer (550-3200°C). The substrates were coated with diamond nanoparticles (ITC Inc.) which serve as nucleation sites...wafers were seeded with nano-diamond particles prior to film growth to provide nucleation sites for diamond growth. To study the effect of surface...wafers are appropriate to generate uniform seeding. AFM tips were seeded with nano-diamond particles prior to coating with NCD to provide nucleation

The terminal crest: morphological features relevant to electrophysiology

PubMed Central

Sánchez-Quintana, D; Anderson, R H; Cabrera, J A; Climent, V; Martin, R; Farré, J; Ho, S Y

2002-01-01

Objective: To investigate the detailed anatomy of the terminal crest (crista terminalis) and its junctional regions with the pectinate muscles and intercaval area to provide the yardstick for structural normality. Design: 97 human necropsy hearts were studied from patients who were not known to have medical histories of atrial arrhythmias. The dimensions of the terminal crest were measured in width and thickness from epicardium to endocardium, at the four points known to be chosen as sites of ablation. Results: The pectinate muscles originating from the crest and extending along the wall of the appendage towards the vestibule of the tricuspid valve had a non-uniform trabecular pattern in 80% of hearts. Fine structure of the terminal crest studied using light and scanning electron microscopy consisted of much thicker and more numerous fibrous sheaths of endomysium with increasing age of the patient. 36 specimens of 45 (80%) specimens studied by electron microscopy had a predominantly uniform longitudinal arrangement of myocardial fibres within the terminal crest. In contrast, in all specimens, the junctional areas of the terminal crest with the pectinate muscles and with the intercaval area had crossing and non-uniform architecture of myofibres. Conclusions: The normal anatomy of the muscle fibres and connective tissue in the junctional area of the terminal crest/pectinate muscles and terminal crest/intercaval bundle favours non-uniform anisotropic properties. PMID:12231604

Cross-population myelination covariance of human cerebral cortex.

PubMed

Ma, Zhiwei; Zhang, Nanyin

2017-09-01

Cross-population covariance of brain morphometric quantities provides a measure of interareal connectivity, as it is believed to be determined by the coordinated neurodevelopment of connected brain regions. Although useful, structural covariance analysis predominantly employed bulky morphological measures with mixed compartments, whereas studies of the structural covariance of any specific subdivisions such as myelin are rare. Characterizing myelination covariance is of interest, as it will reveal connectivity patterns determined by coordinated development of myeloarchitecture between brain regions. Using myelin content MRI maps from the Human Connectome Project, here we showed that the cortical myelination covariance was highly reproducible, and exhibited a brain organization similar to that previously revealed by other connectivity measures. Additionally, the myelination covariance network shared common topological features of human brain networks such as small-worldness. Furthermore, we found that the correlation between myelination covariance and resting-state functional connectivity (RSFC) was uniform within each resting-state network (RSN), but could considerably vary across RSNs. Interestingly, this myelination covariance-RSFC correlation was appreciably stronger in sensory and motor networks than cognitive and polymodal association networks, possibly due to their different circuitry structures. This study has established a new brain connectivity measure specifically related to axons, and this measure can be valuable to investigating coordinated myeloarchitecture development. Hum Brain Mapp 38:4730-4743, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Discovering functional interdependence relationship in PPI networks for protein complex identification.

PubMed

Lam, Winnie W M; Chan, Keith C C

2012-04-01

Protein molecules interact with each other in protein complexes to perform many vital functions, and different computational techniques have been developed to identify protein complexes in protein-protein interaction (PPI) networks. These techniques are developed to search for subgraphs of high connectivity in PPI networks under the assumption that the proteins in a protein complex are highly interconnected. While these techniques have been shown to be quite effective, it is also possible that the matching rate between the protein complexes they discover and those that are previously determined experimentally be relatively low and the "false-alarm" rate can be relatively high. This is especially the case when the assumption of proteins in protein complexes being more highly interconnected be relatively invalid. To increase the matching rate and reduce the false-alarm rate, we have developed a technique that can work effectively without having to make this assumption. The name of the technique called protein complex identification by discovering functional interdependence (PCIFI) searches for protein complexes in PPI networks by taking into consideration both the functional interdependence relationship between protein molecules and the network topology of the network. The PCIFI works in several steps. The first step is to construct a multiple-function protein network graph by labeling each vertex with one or more of the molecular functions it performs. The second step is to filter out protein interactions between protein pairs that are not functionally interdependent of each other in the statistical sense. The third step is to make use of an information-theoretic measure to determine the strength of the functional interdependence between all remaining interacting protein pairs. Finally, the last step is to try to form protein complexes based on the measure of the strength of functional interdependence and the connectivity between proteins. For performance evaluation, PCIFI was used to identify protein complexes in real PPI network data and the protein complexes it found were matched against those that were previously known in MIPS. The results show that PCIFI can be an effective technique for the identification of protein complexes. The protein complexes it found can match more known protein complexes with a smaller false-alarm rate and can provide useful insights into the understanding of the functional interdependence relationships between proteins in protein complexes.

Functional Brain Networks: Does the Choice of Dependency Estimator and Binarization Method Matter?

NASA Astrophysics Data System (ADS)

Jalili, Mahdi

2016-07-01

The human brain can be modelled as a complex networked structure with brain regions as individual nodes and their anatomical/functional links as edges. Functional brain networks are constructed by first extracting weighted connectivity matrices, and then binarizing them to minimize the noise level. Different methods have been used to estimate the dependency values between the nodes and to obtain a binary network from a weighted connectivity matrix. In this work we study topological properties of EEG-based functional networks in Alzheimer’s Disease (AD). To estimate the connectivity strength between two time series, we use Pearson correlation, coherence, phase order parameter and synchronization likelihood. In order to binarize the weighted connectivity matrices, we use Minimum Spanning Tree (MST), Minimum Connected Component (MCC), uniform threshold and density-preserving methods. We find that the detected AD-related abnormalities highly depend on the methods used for dependency estimation and binarization. Topological properties of networks constructed using coherence method and MCC binarization show more significant differences between AD and healthy subjects than the other methods. These results might explain contradictory results reported in the literature for network properties specific to AD symptoms. The analysis method should be seriously taken into account in the interpretation of network-based analysis of brain signals.

Efficient Skeletonization of Volumetric Objects.

PubMed

Zhou, Yong; Toga, Arthur W

1999-07-01

Skeletonization promises to become a powerful tool for compact shape description, path planning, and other applications. However, current techniques can seldom efficiently process real, complicated 3D data sets, such as MRI and CT data of human organs. In this paper, we present an efficient voxel-coding based algorithm for Skeletonization of 3D voxelized objects. The skeletons are interpreted as connected centerlines. consisting of sequences of medial points of consecutive clusters. These centerlines are initially extracted as paths of voxels, followed by medial point replacement, refinement, smoothness, and connection operations. The voxel-coding techniques have been proposed for each of these operations in a uniform and systematic fashion. In addition to preserving basic connectivity and centeredness, the algorithm is characterized by straightforward computation, no sensitivity to object boundary complexity, explicit extraction of ready-to-parameterize and branch-controlled skeletons, and efficient object hole detection. These issues are rarely discussed in traditional methods. A range of 3D medical MRI and CT data sets were used for testing the algorithm, demonstrating its utility.

Computational representation of the aponeuroses as NURBS surfaces in 3D musculoskeletal models.

PubMed

Wu, Florence T H; Ng-Thow-Hing, Victor; Singh, Karan; Agur, Anne M; McKee, Nancy H

2007-11-01

Computational musculoskeletal (MSK) models - 3D graphics-based models that accurately simulate the anatomical architecture and/or the biomechanical behaviour of organ systems consisting of skeletal muscles, tendons, ligaments, cartilage and bones - are valued biomedical tools, with applications ranging from pathological diagnosis to surgical planning. However, current MSK models are often limited by their oversimplifications in anatomical geometries, sometimes lacking discrete representations of connective tissue components entirely, which ultimately affect their accuracy in biomechanical simulation. In particular, the aponeuroses - the flattened fibrous connective sheets connecting muscle fibres to tendons - have never been geometrically modeled. The initiative was thus to extend Anatomy3D - a previously developed software bundle for reconstructing muscle fibre architecture - to incorporate aponeurosis-modeling capacity. Two different algorithms for aponeurosis reconstruction were written in the MEL scripting language of the animation software Maya 6.0, using its NURBS (non-uniform rational B-splines) modeling functionality for aponeurosis surface representation. Both algorithms were validated qualitatively against anatomical and functional criteria.

FDM and DMT performance comparison in high capacity point-to-point fibre links for intra/inter-datacentre connections

NASA Astrophysics Data System (ADS)

Gatto, A.; Parolari, P.; Boffi, P.

2018-05-01

Frequency division multiplexing (FDM) is attractive to achieve high capacities in multiple access networks characterized by direct modulation and direct detection. In this paper we take into account point-to-point intra- and inter-datacenter connections to understand the performance of FDM operation compared with the ones achievable with standard multiple carrier modulation approach based on discrete multitone (DMT). DMT and FDM allow to match the non-uniform and bandwidth-limited response of the system under test, associated with the employment of low-cost directly-modulated sources, such as VCSELs with high-frequency chirp, and with fibre-propagation in presence of chromatic dispersion. While for very short distances typical of intra-datacentre communications, the huge number of DMT subcarriers permits to increase the transported capacity with respect to the FDM employment, in case of few tens-km reaches typical of inter-datacentre connections, the capabilities of FDM are more evident, providing system performance similar to the case of DMT application.

Effective Hydraulic Conductivity of Three-Dimensional Heterogeneous Formations of Lognormal Permeability Distribution: The Impact of Connectivity

NASA Astrophysics Data System (ADS)

Zarlenga, A.; Janković, I.; Fiori, A.; Dagan, G.

2018-03-01

Uniform mean flow takes place in a 3-D heterogeneous formation of normal hydraulic logconductivity Y=ln⁡K. The aim of the study is to derive the dependence of the horizontal Kefh and vertical Kefv effective conductivities on the structural parameters of hydraulic conductivity and investigate the impact of departure from multi-Gaussianity on Kef, by numerical simulations of flow in formations that share the same pdf and covariance of Y but differ in the connectivity of classes of Y. The main result is that for the extreme models of connected and disconnected high Y zones the ratio between the effective conductivities in isotropic media is much smaller than in 2-D. The dependence of Kefh and Kefv upon the logconductivity variance and the anisotropy ratio is compared with existing approximations (first-order, Landau-Matheron conjecture, self-consistent approximation). Besides the theoretical interest, the results offer a basis for empirical relationships to be used in applications.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eliazar, Iddo, E-mail: eliazar@post.tau.ac.il

The exponential, the normal, and the Poisson statistical laws are of major importance due to their universality. Harmonic statistics are as universal as the three aforementioned laws, but yet they fall short in their ‘public relations’ for the following reason: the full scope of harmonic statistics cannot be described in terms of a statistical law. In this paper we describe harmonic statistics, in their full scope, via an object termed harmonic Poisson process: a Poisson process, over the positive half-line, with a harmonic intensity. The paper reviews the harmonic Poisson process, investigates its properties, and presents the connections of thismore » object to an assortment of topics: uniform statistics, scale invariance, random multiplicative perturbations, Pareto and inverse-Pareto statistics, exponential growth and exponential decay, power-law renormalization, convergence and domains of attraction, the Langevin equation, diffusions, Benford’s law, and 1/f noise. - Highlights: • Harmonic statistics are described and reviewed in detail. • Connections to various statistical laws are established. • Connections to perturbation, renormalization and dynamics are established.« less

Asymmetric planar gradiometer for rejection of uniform ambient magnetic noise

DOEpatents

Dantsker, Eugene; Clarke, John

2000-01-01

An asymmetric planar gradiometer for use in making biomagnetic measurements. The gradiometer is formed from a magnetometer which is inductively-coupled to the smaller of two connected loops patterned in a superconducting film which form a flux transformer. The magnetometer is based on a SQUID formed from a high T.sub.c superconducting material. The flux transformer and magnetometer may be formed on separate substrates, allowing the baseline to be increased relative to presently available devices.

Crumb Rubber-Concrete Panels Under Blast Loads

DTIC Science & Technology

2010-05-01

and the samples were labeled. Samples were picked up with an overhead crane and a form spreader connected to two points on the sample, each outside...uniform loading. Shortly after test started 8 to 9 cracks developed within quarter points and 2 cracks developed through pick points where form spreader ...dynamic behaviour of recycled tyre rubber-filled concrete.” Cem. Concr. Res., 32, 1587–1596. Huang, B., Li, G., Pang, S. S., and Eggers, J. (2004

Decompositions of large-scale biological systems based on dynamical properties.

PubMed

Soranzo, Nicola; Ramezani, Fahimeh; Iacono, Giovanni; Altafini, Claudio

2012-01-01

Given a large-scale biological network represented as an influence graph, in this article we investigate possible decompositions of the network aimed at highlighting specific dynamical properties. The first decomposition we study consists in finding a maximal directed acyclic subgraph of the network, which dynamically corresponds to searching for a maximal open-loop subsystem of the given system. Another dynamical property investigated is strong monotonicity. We propose two methods to deal with this property, both aimed at decomposing the system into strongly monotone subsystems, but with different structural characteristics: one method tends to produce a single large strongly monotone component, while the other typically generates a set of smaller disjoint strongly monotone subsystems. Original heuristics for the methods investigated are described in the article. altafini@sissa.it

Centralities in simplicial complexes. Applications to protein interaction networks.

PubMed

Estrada, Ernesto; Ross, Grant J

2018-02-07

Complex networks can be used to represent complex systems which originate in the real world. Here we study a transformation of these complex networks into simplicial complexes, where cliques represent the simplices of the complex. We extend the concept of node centrality to that of simplicial centrality and study several mathematical properties of degree, closeness, betweenness, eigenvector, Katz, and subgraph centrality for simplicial complexes. We study the degree distributions of these centralities at the different levels. We also compare and describe the differences between the centralities at the different levels. Using these centralities we study a method for detecting essential proteins in PPI networks of cells and explain the varying abilities of the centrality measures at the different levels in identifying these essential proteins. Copyright © 2017 Elsevier Ltd. All rights reserved.

Accessible triple-phase boundary length: A performance metric to account for transport pathways in heterogeneous electrochemical materials

NASA Astrophysics Data System (ADS)

Nakajo, A.; Cocco, A. P.; DeGostin, M. B.; Peracchio, A. A.; Cassenti, B. N.; Cantoni, M.; Van herle, J.; Chiu, W. K. S.

2016-09-01

The performance of materials for electrochemical energy conversion and storage depends upon the number of electrocatalytic sites available for reaction and their accessibility by the transport of reactants and products. For solid oxide fuel/electrolysis cell materials, standard 3-D measurements such as connected triple-phase boundary (TPB) length and effective transport properties partially inform on how local geometry and network topology causes variability in TPB accessibility. A new measurement, the accessible TPB, is proposed to quantify these effects in detail and characterize material performance. The approach probes the reticulated pathways to each TPB using an analytical electrochemical fin model applied to a 3-D discrete representation of the heterogeneous structure provided by skeleton-based partitioning. The method is tested on artificial and real structures imaged by 3-D x-ray and electron microscopy. The accessible TPB is not uniform and the pattern varies depending upon the structure. Connected TPBs can be even passivated. The sensitivity to manipulations of the local 3-D geometry and topology that standard measurements cannot capture is demonstrated. The clear presence of preferential pathways showcases a non-uniform utilization of the 3-D structure that potentially affects the performance and the resilience to alterations due to degradation phenomena. The concepts presented also apply to electrochemical energy storage and conversion devices such as other types of fuel cells, electrolyzers, batteries and capacitors.

Measurement and simulation of millimeter wave scattering cross-sections from steel-reinforced concrete

NASA Astrophysics Data System (ADS)

Hassan, A. M.; Martys, N. S.; Garboczi, E. J.; McMichael, R. D.; Stiles, M. D.; Plusquellic, D. F.; Stutzman, P. E.; Wang, S.; Provenzano, V.; Surek, J. T.; Novotny, D. R.; Coder, J. B.; Janezic, M. D.; Kim, S.

2014-02-01

Some iron oxide corrosion products exhibit antiferromagnetic magnetic resonances (AFMR) at frequencies on the order of 100 GHz at ambient temperatures. AFMR can be detected in laboratory conditions, which serves as the basis for a new non-destructive spectroscopic method for detecting early corrosion. When attempting to measure the steel corrosion in reinforced concrete in the field, rebar geometry must be taken into account. Experiments and numerical simulations have been developed at frequencies near 100 GHz to sort out these effects. The experimental setup involves a vector network analyzer with converter heads to up-convert the output frequency, which is then connected to a horn antenna followed by a 7.5 cm diameter polymer lens to focus the waves on the sample. Two sets of samples were studied: uniform cylindrical rods and rebar corrosion samples broken out of concrete with different kinds of coatings. Electromagnetic scattering from uniform rods were calculated numerically using classical modal expansion. A finite-element electromagnetic solver was used to model more complex rebar geometry and non-uniform corrosion layers. Experimental and numerical data were compared to help quantify and understand the anticipated effect of local geometrical features on AFMR measurements.

Behavior of Industrial Steel Rack Connections

NASA Astrophysics Data System (ADS)

Shah, S. N. R.; Ramli Sulong, N. H.; Khan, R.; Jumaat, M. Z.; Shariati, M.

2016-03-01

Beam-to-column connections (BCCs) used in steel pallet racks (SPRs) play a significant role to maintain the stability of rack structures in the down-aisle direction. The variety in the geometry of commercially available beam end connectors hampers the development of a generalized analytic design approach for SPR BCCs. The experimental prediction of flexibility in SPR BCCs is prohibitively expensive and difficult for all types of commercially available beam end connectors. A suitable solution to derive a particular uniform M-θ relationship for each connection type in terms of geometric parameters may be achieved through finite element (FE) modeling. This study first presents a comprehensive description of the experimental investigations that were performed and used as the calibration bases for the numerical study that constituted its main contribution. A three dimensioned (3D) non-linear finite element (FE) model was developed and calibrated against the experimental results. The FE model took into account material nonlinearities, geometrical properties and large displacements. Comparisons between numerical and experimental data for observed failure modes and M-θ relationship showed close agreement. The validated FE model was further extended to perform parametric analysis to identify the effects of various parameters which may affect the overall performance of the connection.

Winners don't take all: Characterizing the competition for links on the web

NASA Astrophysics Data System (ADS)

Pennock, David M.; Flake, Gary W.; Lawrence, Steve; Glover, Eric J.; Giles, C. Lee

2002-04-01

As a whole, the World Wide Web displays a striking "rich get richer" behavior, with a relatively small number of sites receiving a disproportionately large share of hyperlink references and traffic. However, hidden in this skewed global distribution, we discover a qualitatively different and considerably less biased link distribution among subcategories of pagesfor example, among all university homepages or all newspaper homepages. Although the connectivity distribution over the entire web is close to a pure power law, we find that the distribution within specific categories is typically unimodal on a log scale, with the location of the mode, and thus the extent of the rich get richer phenomenon, varying across different categories. Similar distributions occur in many other naturally occurring networks, including research paper citations, movie actor collaborations, and United States power grid connections. A simple generative model, incorporating a mixture of preferential and uniform attachment, quantifies the degree to which the rich nodes grow richer, and how new (and poorly connected) nodes can compete. The model accurately accounts for the true connectivity distributions of category-specific web pages, the web as a whole, and other social networks.

Electron emitting filaments for electron discharge devices

DOEpatents

Leung, Ka-Ngo; Pincosy, Philip A.; Ehlers, Kenneth W.

1988-01-01

Electrons are copiously emitted by a device comprising a loop-shaped filament made of lanthanum hexaboride. The filament is directly heated by an electrical current produced along the filament by a power supply connected to the terminal legs of the filament. To produce a filament, a diamond saw or the like is used to cut a slice from a bar made of lanthanum hexaboride. The diamond saw is then used to cut the slice into the shape of a loop which may be generally rectangular, U-shaped, hairpin-shaped, zigzag-shaped, or generally circular. The filaments provide high electron emission at a relatively low operating temperature, such as 1600.degree. C. To achieve uniform heating, the filament is formed with a cross section which is tapered between the opposite ends of the filament to compensate for non-uniform current distribution along the filament due to the emission of electrons from the filament.

Intrinsic synchronization of an array of spin-torque oscillators driven by the spin-Hall effect

DOE Office of Scientific and Technical Information (OSTI.GOV)

Siracusano, G., E-mail: giuliosiracusano@gmail.com; Puliafito, V.; Giordano, A.

2015-05-07

This paper micromagnetically studies the magnetization dynamics driven by the spin-Hall effect in a Platinum/Permalloy bi-layer. For a certain field and current range, the excitation of a uniform mode, characterized by a power with a spatial distribution in the whole ferromagnetic cross section, is observed. We suggest to use the ferromagnet of the bi-layer as basis for the realization of an array of spin-torque oscillators (STOs): the Permalloy ferromagnet will act as shared free layer, whereas the spacers and the polarizers are built on top of it. Following this strategy, the frequency of the uniform mode will be the samemore » for the whole device, creating an intrinsic synchronization. The synchronization of an array of parallely connected STOs will allow to increase the output power, as necessary for technological applications.« less

Suppression of Space Charge Induced Beam Halo in Nonlinear Focusing Channel

DOE PAGES

Batygin, Yuri Konstantinovich; Scheinker, Alexander; Kurennoy, Sergey; ...

2016-01-29

An intense non-uniform particle beam exhibits strong emittance growth and halo formation in focusing channels due to nonlinear space charge forces of the beam. This phenomenon limits beam brightness and results in particle losses. The problem is connected with irreversible distortion of phase space volume of the beam in conventional focusing structures due to filamentation in phase space. Emittance growth is accompanied by halo formation in real space, which results in inevitable particle losses. We discuss a new approach for solving a self-consistent problem for a matched non-uniform beam in two-dimensional geometry. The resulting solution is applied to the problemmore » of beam transport, while avoiding emittance growth and halo formation by the use of nonlinear focusing field. Conservation of a beam distribution function is demonstrated analytically and by particle-in-cell simulation for a beam with a realistic beam distribution.« less

The effect of cell design and test criteria on the series/parallel performance of nickel cadmium cells and batteries

NASA Technical Reports Server (NTRS)

Halpert, G.; Webb, D. A.

1983-01-01

Three batteries were operated in parallel from a common bus during charge and discharge. SMM utilized NASA Standard 20AH cells and batteries, and LANDSAT-D NASA 50AH cells and batteries of a similar design. Each battery consisted of 22 series connected cells providing the nominal 28V bus. The three batteries were charged in parallel using the voltage limit/current taper mode wherein the voltage limit was temperature compensated. Discharge occurred on the demand of the spacecraft instruments and electronics. Both flights were planned for three to five year missions. The series/parallel configuration of cells and batteries for the 3-5 yr mission required a well controlled product with built-in reliability and uniformity. Examples of how component, cell and battery selection methods affect the uniformity of the series/parallel operation of the batteries both in testing and in flight are given.

Gliding Motility of Mycoplasma mobile on Uniform Oligosaccharides.

PubMed

Kasai, Taishi; Hamaguchi, Tasuku; Miyata, Makoto

2015-09-01

The binding and gliding of Mycoplasma mobile on a plastic plate covered by 53 uniform oligosaccharides were analyzed. Mycoplasmas bound to and glided on only 21 of the fixed sialylated oligosaccharides (SOs), showing that sialic acid is essential as the binding target. The affinities were mostly consistent with our previous results on the inhibitory effects of free SOs and suggested that M. mobile recognizes SOs from the nonreducing end with four continuous sites as follows. (i and ii) A sialic acid at the nonreducing end is tightly recognized by tandemly connected two sites. (iii) The third site is recognized by a loose groove that may be affected by branches. (iv) The fourth site is recognized by a large groove that may be enhanced by branches, especially those with a negative charge. The cells glided on uniform SOs in manners apparently similar to those of the gliding on mixed SOs. The gliding speed was related inversely to the mycoplasma's affinity for SO, suggesting that the detaching step may be one of the speed determinants. The cells glided faster and with smaller fluctuations on the uniform SOs than on the mixtures, suggesting that the drag caused by the variation in SOs influences gliding behaviors. Mycoplasma is a group of bacteria generally parasitic to animals and plants. Some Mycoplasma species form a protrusion at a pole, bind to solid surfaces, and glide in the direction of the protrusion. These procedures are essential for parasitism. Usually, mycoplasmas glide on mixed sialylated oligosaccharides (SOs) derived from glycoprotein and glycolipid. Since gliding motility on uniform oligosaccharides has never been observed, this study gives critical information about recognition and interaction between receptors and SOs. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Modeling and reconfiguration of solar photovoltaic arrays under non-uniform shadow conditions

NASA Astrophysics Data System (ADS)

Nguyen, Dung Duc

Mass production and use of electricity generated from solar energy has become very common recently because of the environmental threats arising from the production of electricity from fossil fuels and nuclear power. The obvious benefits of solar energy are clean energy production and infinite supply of daylight. The main disadvantage is the high cost. In these photovoltaic systems, semiconductor materials convert the solar light into electrical energy. Current versus voltage characteristics of the solar cells are nonlinear, thus leading to technical control challenges. In the first order approximation, output power of a solar array is proportional to the irradiance of sunlight. However, in many applications, such as solar power plants, building integrated photovoltaic or solar tents, the solar photovoltaic arrays might be illuminated non-uniformly. The cause of non-uniform illumination may be the shadow of clouds, the trees, booms, neighbor's houses, or the shadow of one solar array on the other, etc. This further leads to nonlinearities in characteristics. Because of the nature of the electrical characteristics of solar cells, the maximum power losses are not proportional to the shadow, but magnify nonlinearly [1]. Further, shadows of solar PV array can cause other undesired effects: (1) The power actually generated from the solar PV array is much less than designed. At some systems, the annual losses because of the shadow effects can be reached 10%. Thus, the probability for "loss of load" increases [2]. (2) The local hot spot in the shaded part of the solar PV array can damage the solar cells. The shaded solar cells may be work on the negative voltage region and become a resistive load and absorb power. Bypass diodes are sometimes connected parallel to solar cells to protect them from damage. However, in most cases, just one diode is connected in parallel to group of solar cells [3], and this hidden the potential power output of the array. This proposed research will focus on the development of an adaptable solar array that is able to optimize power output, reconfigure itself when solar cells are damaged and create controllable output voltages and currents. This study will be a technological advancement over the existing technology of solar PV. Presently solar arrays are fixed arrays that require external device to control their output. In this research, the solar array will be able to self-reconfigure, leading to the following advantages: (1) Higher efficiency because no external devices are used. (2) Can reach maximum possible output power that is much higher than the maximum power of fixed solar arrays by arranging the solar cells in optimized connections. (3) Elimination of the hot spot effects. The proposed research has the following goals: First, to create a modeling and computing algorithm, which is able to simulate and analyze the effects of non-uniform changing shadows on the output power of solar PV arrays. Our model will be able to determine the power losses in each solar cell and the collective hot spots of an array. Second, to propose new methods, which are able to predict the performance of solar PV arrays under shadow conditions for long term (days, months, years). Finally, to develop adaptive reconfiguration algorithms to reconfigure connections within solar PV arrays in real time, under shadow conditions, in order to optimize output power.

Steel Rack Connections: Identification of Most Influential Factors and a Comparison of Stiffness Design Methods.

PubMed

Shah, S N R; Sulong, N H Ramli; Shariati, Mahdi; Jumaat, M Z

2015-01-01

Steel pallet rack (SPR) beam-to-column connections (BCCs) are largely responsible to avoid the sway failure of frames in the down-aisle direction. The overall geometry of beam end connectors commercially used in SPR BCCs is different and does not allow a generalized analytic approach for all types of beam end connectors; however, identifying the effects of the configuration, profile and sizes of the connection components could be the suitable approach for the practical design engineers in order to predict the generalized behavior of any SPR BCC. This paper describes the experimental behavior of SPR BCCs tested using a double cantilever test set-up. Eight sets of specimens were identified based on the variation in column thickness, beam depth and number of tabs in the beam end connector in order to investigate the most influential factors affecting the connection performance. Four tests were repeatedly performed for each set to bring uniformity to the results taking the total number of tests to thirty-two. The moment-rotation (M-θ) behavior, load-strain relationship, major failure modes and the influence of selected parameters on connection performance were investigated. A comparative study to calculate the connection stiffness was carried out using the initial stiffness method, the slope to half-ultimate moment method and the equal area method. In order to find out the more appropriate method, the mean stiffness of all the tested connections and the variance in values of mean stiffness according to all three methods were calculated. The calculation of connection stiffness by means of the initial stiffness method is considered to overestimate the values when compared to the other two methods. The equal area method provided more consistent values of stiffness and lowest variance in the data set as compared to the other two methods.

Adaptive control of structural balance for complex dynamical networks based on dynamic coupling of nodes

NASA Astrophysics Data System (ADS)

Gao, Zilin; Wang, Yinhe; Zhang, Lili

2018-02-01

In the existing research results of the complex dynamical networks controlled, the controllers are mainly used to guarantee the synchronization or stabilization of the nodes’ state, and the terms coupled with connection relationships may affect the behaviors of nodes, this obviously ignores the dynamic common behavior of the connection relationships between the nodes. In fact, from the point of view of large-scale system, a complex dynamical network can be regarded to be composed of two time-varying dynamic subsystems, which can be called the nodes subsystem and the connection relationships subsystem, respectively. Similar to the synchronization or stabilization of the nodes subsystem, some characteristic phenomena can be also emerged in the connection relationships subsystem. For example, the structural balance in the social networks and the synaptic facilitation in the biological neural networks. This paper focuses on the structural balance in dynamic complex networks. Generally speaking, the state of the connection relationships subsystem is difficult to be measured accurately in practical applications, and thus it is not easy to implant the controller directly into the connection relationships subsystem. It is noted that the nodes subsystem and the relationships subsystem are mutually coupled, which implies that the state of the connection relationships subsystem can be affected by the controllable state of nodes subsystem. Inspired by this observation, by using the structural balance theory of triad, the controller with the parameter adaptive law is proposed for the nodes subsystem in this paper, which may ensure the connection relationship matrix to approximate a given structural balance matrix in the sense of the uniformly ultimately bounded (UUB). That is, the structural balance may be obtained by employing the controlling state of the nodes subsystem. Finally, the simulations are used to show the validity of the method in this paper.

Connections of the juxtaventromedial region of the lateral hypothalamic area in the male rat

PubMed Central

Hahn, Joel D.; Swanson, Larry W.

2015-01-01

Evolutionary conservation of the hypothalamus attests to its critical role in the control of fundamental behaviors. However, our knowledge of hypothalamic connections is incomplete, particularly for the lateral hypothalamic area (LHA). Here we present the results of neuronal pathway-tracing experiments to investigate connections of the LHA juxtaventromedial region, which is parceled into dorsal (LHAjvd) and ventral (LHAjvv) zones. Phaseolus vulgaris leucoagglutinin (PHAL, for outputs) and cholera toxin B subunit (CTB, for inputs) coinjections were targeted stereotaxically to the LHAjvd/v. Results: LHAjvd/v connections overlapped highly but not uniformly. Major joint outputs included: Bed nuc. stria terminalis (BST), interfascicular nuc. (BSTif) and BST anteromedial area, rostral lateral septal (LSr)- and ventromedial hypothalamic (VMH) nuc., and periaqueductal gray. Prominent joint LHAjvd/v input sources included: BSTif, BST principal nuc., LSr, VMH, anterior hypothalamic-, ventral premammillary-, and medial amygdalar nuc., and hippocampal formation (HPF) field CA1. However, LHAjvd HPF retrograde labeling was markedly more abundant than from the LHAjvv; in the LSr this was reversed. Furthermore, robust LHAjvv (but not LHAjvd) targets included posterior- and basomedial amygdalar nuc., whereas the midbrain reticular nuc. received a dense input from the LHAjvd alone. Our analyses indicate the existence of about 500 LHAjvd and LHAjvv connections with about 200 distinct regions of the cerebral cortex, cerebral nuclei, and cerebrospinal trunk. Several highly LHAjvd/v-connected regions have a prominent role in reproductive behavior. These findings contrast with those from our previous pathway-tracing studies of other LHA medial and perifornical tier regions, with different connectional behavioral relations. The emerging picture is of a highly differentiated LHA with extensive and far-reaching connections that point to a role as a central coordinator of behavioral control. PMID:26074786

Exploration of a possible cause of magnetic reconfiguration/reconnection due to generation, rather than annihilation, of magnetic field in a nun-uniform thin current sheet

NASA Astrophysics Data System (ADS)

Huang, Y. C.; Lyu, L. H.

2014-12-01

Magnetic reconfiguration/reconnection plays an important role on energy and plasma transport in the space plasma. It is known that magnetic field lines on two sides of a tangential discontinuity can connect to each other only at a neutral point, where the strength of the magnetic field is equal to zero. Thus, the standard reconnection picture with magnetic field lines intersecting at the neutral point is not applicable to the component reconnection events observed at the magnetopause and in the solar corona. In our early study (Yu, Lyu, & Wu, 2011), we have shown that annihilation of magnetic field near a thin current sheet can lead to the formation of normal magnetic field component (normal to the current sheet) to break the frozen-in condition and to accelerate the reconnected plasma flux, even without the presence of a neutral point. In this study, we examine whether or not a generation, rather than annihilation, of magnetic field in a nun-uniform thin current sheet can also lead to reconnection of plasma flux. Our results indicate that a non-uniform enhancement of electric current can yield formation of field-aligned currents. The normal-component magnetic field generated by the field-aligned currents can yield reconnection of plasma flux just outside the current-enhancement region. The particle motion that can lead to non-uniform enhancement of electric currents will be discussed.

Templated assembly of BiFeO3 nanocrystals into 3D mesoporous networks for catalytic applications

NASA Astrophysics Data System (ADS)

Papadas, I. T.; Subrahmanyam, K. S.; Kanatzidis, M. G.; Armatas, G. S.

2015-03-01

The self-assembly of uniform nanocrystals into large porous architectures is currently of immense interest for nanochemistry and nanotechnology. These materials combine the respective advantages of discrete nanoparticles and mesoporous structures. In this article, we demonstrate a facile nanoparticle templating process to synthesize a three-dimensional mesoporous BiFeO3 material. This approach involves the polymer-assisted aggregating assembly of 3-aminopropanoic acid-stabilized bismuth ferrite (BiFeO3) nanocrystals followed by thermal decomposition of the surfactant. The resulting material consists of a network of tightly connected BiFeO3 nanoparticles (~6-7 nm in diameter) and has a moderately high surface area (62 m2 g-1) and uniform pores (ca. 6.3 nm). As a result of the unique mesostructure, the porous assemblies of BiFeO3 nanoparticles show an excellent catalytic activity and chemical stability for the reduction of p-nitrophenol to p-aminophenol with NaBH4.The self-assembly of uniform nanocrystals into large porous architectures is currently of immense interest for nanochemistry and nanotechnology. These materials combine the respective advantages of discrete nanoparticles and mesoporous structures. In this article, we demonstrate a facile nanoparticle templating process to synthesize a three-dimensional mesoporous BiFeO3 material. This approach involves the polymer-assisted aggregating assembly of 3-aminopropanoic acid-stabilized bismuth ferrite (BiFeO3) nanocrystals followed by thermal decomposition of the surfactant. The resulting material consists of a network of tightly connected BiFeO3 nanoparticles (~6-7 nm in diameter) and has a moderately high surface area (62 m2 g-1) and uniform pores (ca. 6.3 nm). As a result of the unique mesostructure, the porous assemblies of BiFeO3 nanoparticles show an excellent catalytic activity and chemical stability for the reduction of p-nitrophenol to p-aminophenol with NaBH4. Electronic supplementary information (ESI) available: IR spectra and TG profiles of as-made BiFeO3 NPs and MBFA samples, TEM images of 3-APA-capped BiFeO3 NPs, EDS spectrum of MBFAs, N2 adsorption-desorption isotherms of randomly aggregated BiFeO3 NPs and catalytic data for 4-NP reduction by MBFAs and other nanostructured catalysts. See DOI: 10.1039/c5nr00185d

Superconducting magnet for a Ku-band maser.

NASA Technical Reports Server (NTRS)

Berwin, R.; Wiebe, E.; Dachel, P.

1972-01-01

A superconducting magnet to provide a uniform magnetic field of up to 8000 G in a 1.14-cm gap for the 15.3-GHz (Ku-band) traveling wave maser is described. The magnet operates in a persistent mode in the vacuum environment of a closed-cycle helium refrigerator (4.5 K). The features of a superconducting switch, which has both leads connected to 4.5 K heat stations and thereby does not receive heat generated by the magnet charging leads, are described.

Holding Fixture For Making Piezoelectric Acoustic Sensors

NASA Technical Reports Server (NTRS)

Hall, E. Thomas, Jr.

1993-01-01

Vacuum holding device provides quick and easy method of bonding together two strips of thin film with fast-setting epoxy adhesive. Fixture holds films in place by vacuum while adhesive applied, maintaining uniform bond line between films, providing internal connection port between nickel coats on films for center conductor of coaxial cable, and eliminating need to clean up excessive adhesive. Used to fabricate acoustic sensors for use in ambulatory fetal heart monitors. Potential for other heart-monitoring applications and other applications in which acoustic sensors used.

A Nonfullerene Small Molecule Acceptor with 3D Interlocking Geometry Enabling Efficient Organic Solar Cells.

PubMed

Lee, Jaewon; Singh, Ranbir; Sin, Dong Hun; Kim, Heung Gyu; Song, Kyu Chan; Cho, Kilwon

2016-01-06

A new 3D nonfullerene small-molecule acceptor is reported. The 3D interlocking geometry of the small-molecule acceptor enables uniform molecular conformation and strong intermolecular connectivity, facilitating favorable nanoscale phase separation and electron charge transfer. By employing both a novel polymer donor and a nonfullerene small-molecule acceptor in the solution-processed organic solar cells, a high-power conversion efficiency of close to 6% is demonstrated. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pribram-Jones, A.; Burke, K.

We show that the adiabatic connection formula of ground-state density functional theory relates the correlation energy to a coupling-constant integral over a purely potential contribution, and is widely used to understand and improve approximations. The corresponding formula for thermal density functional theory is cast as an integral over temperatures instead, ranging upward from the system's physical temperature. We also show how to relate different correlation components to each other, either in terms of temperature or coupling-constant integrations. Lastly, we illustrate our results on the uniform electron gas.

The Effects of Various Levels of Ascorbic Acid Intake Upon Oral Wound Healing in Guinea Pigs.

DTIC Science & Technology

1983-01-01

82174 7’ 4 8 Alfano observed increased permeability of oral tissue with decreased vitamin C supplementation. Periodontal tissues are susceptible to...make a uniform wound in the midline of the oral mucosa, anterior to the maxillary premolars. (Figure 2). The trephine bur penetrated the tissues until...grids across the wound site and dividing by two. This area encompassed the edges of the bone wound or residual mature soft connective tissue . The

Equilibrium and Non-Equilibrium Condensation Phenomena in Tuneable 3D and 2D Bose Gases

DTIC Science & Technology

2016-04-01

condensed gas " which remains condensed above the expected critical temperature, and performed one of the first studies of the strongly-interacting "unitary...34 Bose gas . With the 2d harmonic trap we showed how the interaction-driven BKT phase is connected with purely statistical theory, and with the 3d...box trap we created the world’s first atomic BEC in a quasi-uniform potential. 15. SUBJECT TERMS EOARD, Bose gas , ultracold, condensation, equilibrium

The effects of neuron morphology on graph theoretic measures of network connectivity: the analysis of a two-level statistical model.

PubMed

Aćimović, Jugoslava; Mäki-Marttunen, Tuomo; Linne, Marja-Leena

2015-01-01

We developed a two-level statistical model that addresses the question of how properties of neurite morphology shape the large-scale network connectivity. We adopted a low-dimensional statistical description of neurites. From the neurite model description we derived the expected number of synapses, node degree, and the effective radius, the maximal distance between two neurons expected to form at least one synapse. We related these quantities to the network connectivity described using standard measures from graph theory, such as motif counts, clustering coefficient, minimal path length, and small-world coefficient. These measures are used in a neuroscience context to study phenomena from synaptic connectivity in the small neuronal networks to large scale functional connectivity in the cortex. For these measures we provide analytical solutions that clearly relate different model properties. Neurites that sparsely cover space lead to a small effective radius. If the effective radius is small compared to the overall neuron size the obtained networks share similarities with the uniform random networks as each neuron connects to a small number of distant neurons. Large neurites with densely packed branches lead to a large effective radius. If this effective radius is large compared to the neuron size, the obtained networks have many local connections. In between these extremes, the networks maximize the variability of connection repertoires. The presented approach connects the properties of neuron morphology with large scale network properties without requiring heavy simulations with many model parameters. The two-steps procedure provides an easier interpretation of the role of each modeled parameter. The model is flexible and each of its components can be further expanded. We identified a range of model parameters that maximizes variability in network connectivity, the property that might affect network capacity to exhibit different dynamical regimes.

A Universal Portable Appliance for Stellarator W7-X Power Supply Controlling

NASA Astrophysics Data System (ADS)

Xu, Wei-hua; Wolfgang, Foerster; Guenter, Mueller

2001-06-01

In the project Wendelstein 7-X (W7-X), the popular fieldbus Profibus has been determined as a uniform connection between the central control system and all the subordinate systems. A universal embedded control system has been developed for W7-X power supply controlling. Siemens 80C167CR microcontroller is used as the central control unit of the system. With a user-defined printed circuit board (PCB) several control buses, i.e., Profibus, CAN, IEEE 488, RS485 and RS 232 have been connected to the microcontroller. The corresponding hardware interfaces for the control buses have been designed. A graphic liquid crystal display(LCD) and a user-defined keyboard are used as user interface. The control software will be developed with a C-like language, i.e., C166 for the controller.

Electric Current Flow Through Two-Dimensional Networks

NASA Astrophysics Data System (ADS)

Gaspard, Mallory

In modern nanotechnology, two-dimensional atomic network structures boast promising applications as nanoscale circuit boards to serve as the building blocks of more sustainable and efficient, electronic devices. However, properties associated with the network connectivity can be beneficial or deleterious to the current flow. Taking a computational approach, we will study large uniform networks, as well as large random networks using Kirchhoff's Equations in conjunction with graph theoretical measures of network connectedness and flows, to understand how network connectivity affects overall ability for successful current flow throughout a network. By understanding how connectedness affects flow, we may develop new ways to design more efficient two-dimensional materials for the next generation of nanoscale electronic devices, and we will gain a deeper insight into the intricate balance between order and chaos in the universe. Rensselaer Polytechnic Institute, SURP Institutional Grant.

Comparing Networks from a Data Analysis Perspective

NASA Astrophysics Data System (ADS)

Li, Wei; Yang, Jing-Yu

To probe network characteristics, two predominant ways of network comparison are global property statistics and subgraph enumeration. However, they suffer from limited information and exhaustible computing. Here, we present an approach to compare networks from the perspective of data analysis. Initially, the approach projects each node of original network as a high-dimensional data point, and the network is seen as clouds of data points. Then the dispersion information of the principal component analysis (PCA) projection of the generated data clouds can be used to distinguish networks. We applied this node projection method to the yeast protein-protein interaction networks and the Internet Autonomous System networks, two types of networks with several similar higher properties. The method can efficiently distinguish one from the other. The identical result of different datasets from independent sources also indicated that the method is a robust and universal framework.

Assembly planning based on subassembly extraction

NASA Technical Reports Server (NTRS)

Lee, Sukhan; Shin, Yeong Gil

1990-01-01

A method is presented for the automatic determination of assembly partial orders from a liaison graph representation of an assembly through the extraction of preferred subassemblies. In particular, the authors show how to select a set of tentative subassemblies by decomposing a liaison graph into a set of subgraphs based on feasibility and difficulty of disassembly, how to evaluate each of the tentative subassemblies in terms of assembly cost using the subassembly selection indices, and how to construct a hierarchical partial order graph (HPOG) as an assembly plan. The method provides an approach to assembly planning by identifying spatial parallelism in assembly as a means of constructing temporal relationships among assembly operations and solves the problem of finding a cost-effective assembly plan in a flexible environment. A case study of the assembly planning of a mechanical assembly is presented.

Quantum Clique Gossiping.

PubMed

Li, Bo; Li, Shuang; Wu, Junfeng; Qi, Hongsheng

2018-02-09

This paper establishes a framework of quantum clique gossiping by introducing local clique operations to networks of interconnected qubits. Cliques are local structures in complex networks being complete subgraphs, which can be used to accelerate classical gossip algorithms. Based on cyclic permutations, clique gossiping leads to collective multi-party qubit interactions. We show that at reduced states, these cliques have the same acceleration effects as their roles in accelerating classical gossip algorithms. For randomized selection of cliques, such improved rate of convergence is precisely characterized. On the other hand, the rate of convergence at the coherent states of the overall quantum network is proven to be decided by the spectrum of a mean-square error evolution matrix. Remarkably, the use of larger quantum cliques does not necessarily increase the speed of the network density aggregation, suggesting quantum network dynamics is not entirely decided by its classical topology.

Spectra of random networks in the weak clustering regime

NASA Astrophysics Data System (ADS)

Peron, Thomas K. DM.; Ji, Peng; Kurths, Jürgen; Rodrigues, Francisco A.

2018-03-01

The asymptotic behavior of dynamical processes in networks can be expressed as a function of spectral properties of the corresponding adjacency and Laplacian matrices. Although many theoretical results are known for the spectra of traditional configuration models, networks generated through these models fail to describe many topological features of real-world networks, in particular non-null values of the clustering coefficient. Here we study effects of cycles of order three (triangles) in network spectra. By using recent advances in random matrix theory, we determine the spectral distribution of the network adjacency matrix as a function of the average number of triangles attached to each node for networks without modular structure and degree-degree correlations. Implications to network dynamics are discussed. Our findings can shed light in the study of how particular kinds of subgraphs influence network dynamics.

New graph polynomials in parametric QED Feynman integrals

NASA Astrophysics Data System (ADS)

Golz, Marcel

2017-10-01

In recent years enormous progress has been made in perturbative quantum field theory by applying methods of algebraic geometry to parametric Feynman integrals for scalar theories. The transition to gauge theories is complicated not only by the fact that their parametric integrand is much larger and more involved. It is, moreover, only implicitly given as the result of certain differential operators applied to the scalar integrand exp(-ΦΓ /ΨΓ) , where ΨΓ and ΦΓ are the Kirchhoff and Symanzik polynomials of the Feynman graph Γ. In the case of quantum electrodynamics we find that the full parametric integrand inherits a rich combinatorial structure from ΨΓ and ΦΓ. In the end, it can be expressed explicitly as a sum over products of new types of graph polynomials which have a combinatoric interpretation via simple cycle subgraphs of Γ.

A spatially resolved network spike in model neuronal cultures reveals nucleation centers, circular traveling waves and drifting spiral waves.

PubMed

Paraskevov, A V; Zendrikov, D K

2017-03-23

We show that in model neuronal cultures, where the probability of interneuronal connection formation decreases exponentially with increasing distance between the neurons, there exists a small number of spatial nucleation centers of a network spike, from where the synchronous spiking activity starts propagating in the network typically in the form of circular traveling waves. The number of nucleation centers and their spatial locations are unique and unchanged for a given realization of neuronal network but are different for different networks. In contrast, if the probability of interneuronal connection formation is independent of the distance between neurons, then the nucleation centers do not arise and the synchronization of spiking activity during a network spike occurs spatially uniform throughout the network. Therefore one can conclude that spatial proximity of connections between neurons is important for the formation of nucleation centers. It is also shown that fluctuations of the spatial density of neurons at their random homogeneous distribution typical for the experiments in vitro do not determine the locations of the nucleation centers. The simulation results are qualitatively consistent with the experimental observations.

Two-port connecting-layer-based sandwiched grating by a polarization-independent design.

PubMed

Li, Hongtao; Wang, Bo

2017-05-02

In this paper, a two-port connecting-layer-based sandwiched beam splitter grating with polarization-independent property is reported and designed. Such the grating can separate the transmission polarized light into two diffraction orders with equal energies, which can realize the nearly 50/50 output with good uniformity. For the given wavelength of 800 nm and period of 780 nm, a simplified modal method can design a optimal duty cycle and the estimation value of the grating depth can be calculated based on it. In order to obtain the precise grating parameters, a rigorous coupled-wave analysis can be employed to optimize grating parameters by seeking for the precise grating depth and the thickness of connecting layer. Based on the optimized design, a high-efficiency two-port output grating with the wideband performances can be gained. Even more important, diffraction efficiencies are calculated by using two analytical methods, which are proved to be coincided well with each other. Therefore, the grating is significant for practical optical photonic element in engineering.

A spatially resolved network spike in model neuronal cultures reveals nucleation centers, circular traveling waves and drifting spiral waves

NASA Astrophysics Data System (ADS)

Paraskevov, A. V.; Zendrikov, D. K.

2017-04-01

We show that in model neuronal cultures, where the probability of interneuronal connection formation decreases exponentially with increasing distance between the neurons, there exists a small number of spatial nucleation centers of a network spike, from where the synchronous spiking activity starts propagating in the network typically in the form of circular traveling waves. The number of nucleation centers and their spatial locations are unique and unchanged for a given realization of neuronal network but are different for different networks. In contrast, if the probability of interneuronal connection formation is independent of the distance between neurons, then the nucleation centers do not arise and the synchronization of spiking activity during a network spike occurs spatially uniform throughout the network. Therefore one can conclude that spatial proximity of connections between neurons is important for the formation of nucleation centers. It is also shown that fluctuations of the spatial density of neurons at their random homogeneous distribution typical for the experiments in vitro do not determine the locations of the nucleation centers. The simulation results are qualitatively consistent with the experimental observations.

Markov Networks of Collateral Resistance: National Antimicrobial Resistance Monitoring System Surveillance Results from Escherichia coli Isolates, 2004-2012

PubMed Central

Love, William J.; Zawack, Kelson A.; Booth, James G.; Grӧhn, Yrjo T.

2016-01-01

Surveillance of antimicrobial resistance (AMR) is an important component of public health. Antimicrobial drug use generates selective pressure that may lead to resistance against to the administered drug, and may also select for collateral resistances to other drugs. Analysis of AMR surveillance data has focused on resistance to individual drugs but joint distributions of resistance in bacterial populations are infrequently analyzed and reported. New methods are needed to characterize and communicate joint resistance distributions. Markov networks are a class of graphical models that define connections, or edges, between pairs of variables with non-zero partial correlations and are used here to describe AMR resistance relationships. The graphical least absolute shrinkage and selection operator is used to estimate sparse Markov networks from AMR surveillance data. The method is demonstrated using a subset of Escherichia coli isolates collected by the National Antimicrobial Resistance Monitoring System between 2004 and 2012 which included AMR results for 16 drugs from 14418 isolates. Of the 119 possible unique edges, 33 unique edges were identified at least once during the study period and graphical density ranged from 16.2% to 24.8%. Two frequent dense subgraphs were noted, one containing the five β-lactam drugs and the other containing both sulfonamides, three aminoglycosides, and tetracycline. Density did not appear to change over time (p = 0.71). Unweighted modularity did not appear to change over time (p = 0.18), but a significant decreasing trend was noted in the modularity of the weighted networks (p < 0.005) indicating relationships between drugs of different classes tended to increase in strength and frequency over time compared to relationships between drugs of the same class. The current method provides a novel method to study the joint resistance distribution, but additional work is required to unite the underlying biological and genetic characteristics of the isolates with the current results derived from phenotypic data. PMID:27851767

Markov Networks of Collateral Resistance: National Antimicrobial Resistance Monitoring System Surveillance Results from Escherichia coli Isolates, 2004-2012.

PubMed

Love, William J; Zawack, Kelson A; Booth, James G; Grӧhn, Yrjo T; Lanzas, Cristina

2016-11-01

Surveillance of antimicrobial resistance (AMR) is an important component of public health. Antimicrobial drug use generates selective pressure that may lead to resistance against to the administered drug, and may also select for collateral resistances to other drugs. Analysis of AMR surveillance data has focused on resistance to individual drugs but joint distributions of resistance in bacterial populations are infrequently analyzed and reported. New methods are needed to characterize and communicate joint resistance distributions. Markov networks are a class of graphical models that define connections, or edges, between pairs of variables with non-zero partial correlations and are used here to describe AMR resistance relationships. The graphical least absolute shrinkage and selection operator is used to estimate sparse Markov networks from AMR surveillance data. The method is demonstrated using a subset of Escherichia coli isolates collected by the National Antimicrobial Resistance Monitoring System between 2004 and 2012 which included AMR results for 16 drugs from 14418 isolates. Of the 119 possible unique edges, 33 unique edges were identified at least once during the study period and graphical density ranged from 16.2% to 24.8%. Two frequent dense subgraphs were noted, one containing the five β-lactam drugs and the other containing both sulfonamides, three aminoglycosides, and tetracycline. Density did not appear to change over time (p = 0.71). Unweighted modularity did not appear to change over time (p = 0.18), but a significant decreasing trend was noted in the modularity of the weighted networks (p < 0.005) indicating relationships between drugs of different classes tended to increase in strength and frequency over time compared to relationships between drugs of the same class. The current method provides a novel method to study the joint resistance distribution, but additional work is required to unite the underlying biological and genetic characteristics of the isolates with the current results derived from phenotypic data.

Markov Dynamics as a Zooming Lens for Multiscale Community Detection: Non Clique-Like Communities and the Field-of-View Limit

PubMed Central

Schaub, Michael T.; Delvenne, Jean-Charles; Yaliraki, Sophia N.; Barahona, Mauricio

2012-01-01

In recent years, there has been a surge of interest in community detection algorithms for complex networks. A variety of computational heuristics, some with a long history, have been proposed for the identification of communities or, alternatively, of good graph partitions. In most cases, the algorithms maximize a particular objective function, thereby finding the ‘right’ split into communities. Although a thorough comparison of algorithms is still lacking, there has been an effort to design benchmarks, i.e., random graph models with known community structure against which algorithms can be evaluated. However, popular community detection methods and benchmarks normally assume an implicit notion of community based on clique-like subgraphs, a form of community structure that is not always characteristic of real networks. Specifically, networks that emerge from geometric constraints can have natural non clique-like substructures with large effective diameters, which can be interpreted as long-range communities. In this work, we show that long-range communities escape detection by popular methods, which are blinded by a restricted ‘field-of-view’ limit, an intrinsic upper scale on the communities they can detect. The field-of-view limit means that long-range communities tend to be overpartitioned. We show how by adopting a dynamical perspective towards community detection [1], [2], in which the evolution of a Markov process on the graph is used as a zooming lens over the structure of the network at all scales, one can detect both clique- or non clique-like communities without imposing an upper scale to the detection. Consequently, the performance of algorithms on inherently low-diameter, clique-like benchmarks may not always be indicative of equally good results in real networks with local, sparser connectivity. We illustrate our ideas with constructive examples and through the analysis of real-world networks from imaging, protein structures and the power grid, where a multiscale structure of non clique-like communities is revealed. PMID:22384178

Comparison of directed and weighted co-occurrence networks of six languages

NASA Astrophysics Data System (ADS)

Gao, Yuyang; Liang, Wei; Shi, Yuming; Huang, Qiuling

2014-01-01

To study commonalities and differences among different languages, we select 100 reports from the documents of the United Nations, each of which was written in Arabic, Chinese, English, French, Russian and Spanish languages, separately. Based on these corpora, we construct 6 weighted and directed word co-occurrence networks. Besides all the networks exhibit scale-free and small-world features, we find several new non-trivial results, including connections among English words are denser, and the expression of English language is more flexible and powerful; the connection way among Spanish words is more stringent and this indicates that the Spanish grammar is more rigorous; values of many statistical parameters of the French and Spanish networks are very approximate and this shows that these two languages share many commonalities; Arabic and Russian words have many varieties, which result in rich types of words and a sparse connection among words; connections among Chinese words obey a more uniform distribution, and one inclines to use the least number of Chinese words to express the same complex information as those in other five languages. This shows that the expression of Chinese language is quite concise. In addition, several topics worth further investigating by the complex network approach have been observed in this study.

Mathematical estimates of recovery after loss of activity: II. Long-range connectivity facilitates rapid functional recovery.

PubMed

Hübler, Merla J; Buchman, Timothy G

2008-02-01

To model the effects of system connectedness on recovery of dysfunctional tissues. One-dimensional elementary cellular automata models with small-world features, where the center-input for a few cells comes not from itself but, with a given probability, from another cell. This probability represents the connectivity of the network. The long-range connections are chosen randomly to survey the potential influences of distant information flowing into a local region. MATLAB and Mathematica computing environments. None. None. We determined the recovery rate of the entropy after perturbing a uniformly dormant system. We observed that the recovery of normal activity after perturbation of a dormant system had the characteristics of an epidemic. Moreover, we found that the rate of recovery to normal steady-state activity increased rapidly even for small amounts of long-range connectivity. Findings obtained through numerical simulation were verified through analytical solutions. This study links our hypothesis that multiple organ function syndromes represent recoupling failure with a mathematical model showing the contribution of such coupling to reactivation of dormant systems. The implication is that strategies aimed not at target tissues or target organs but rather at restoring the quality and quantity of interconnections across those tissues and organs may be a novel therapeutic strategy.

Implications of tristability in pattern-forming ecosystems

NASA Astrophysics Data System (ADS)

Zelnik, Yuval R.; Gandhi, Punit; Knobloch, Edgar; Meron, Ehud

2018-03-01

Many ecosystems show both self-organized spatial patterns and multistability of possible states. The combination of these two phenomena in different forms has a significant impact on the behavior of ecosystems in changing environments. One notable case is connected to tristability of two distinct uniform states together with patterned states, which has recently been found in model studies of dryland ecosystems. Using a simple model, we determine the extent of tristability in parameter space, explore its effects on the system dynamics, and consider its implications for state transitions or regime shifts. We analyze the bifurcation structure of model solutions that describe uniform states, periodic patterns, and hybrid states between the former two. We map out the parameter space where these states exist, and note how the different states interact with each other. We further focus on two special implications with ecological significance, breakdown of the snaking range and complex fronts. We find that the organization of the hybrid states within a homoclinic snaking structure breaks down as it meets a Maxwell point where simple fronts are stationary. We also discover a new series of complex fronts between the uniform states, each with its own velocity. We conclude with a brief discussion of the significance of these findings for the dynamics of regime shifts and their potential control.

Validation of color Doppler sonography for evaluating relative displacement between the flexor tendon and subsynovial connective tissue.

PubMed

Tat, Jimmy; Kociolek, Aaron M; Keir, Peter J

2015-04-01

A common pathologic finding in carpal tunnel syndrome is fibrosis and thickening of the subsynovial connective tissue. This finding suggests an etiology of excessive shear forces, with relative longitudinal displacement between the flexor tendon and adjacent subsynovial connective tissue. The purpose of this study was to validate color Doppler sonography for measurement of tendon displacement over time. Eight unmatched fresh frozen cadaver arms were used to evaluate color Doppler sonography for measurement of tendon displacement. The middle flexor digitorum superficialis tendon was moved through a physiologic excursion of 20 mm at 3 different tendon velocities (50, 100, and 150 mm/s). We found that color Doppler sonography provided accurate measurement of tendon displacement, with absolute errors of -0.05 mm (50 mm/s), -1.24 mm (100 mm/s), and -2.36 mm (150 mm/s) on average throughout the tendon excursion range. Evaluating relative displacement between the tendon and subsynovial connective tissue during finger flexion-extension movements also offered insight into the gliding mechanism of the subsynovial connective tissue. During flexion, we observed a curvilinear increase in relative displacement, with greater differential motion at the end range of displacement, likely due to the sequential stretch of the fibrils between successive layers of the subsynovial connective tissue. In extension, there was a linear return in relative displacement, suggesting a different unloading mechanism characterized by uniform relaxation of fibrils. We demonstrated the validity of color Doppler displacement for use in the evaluation of relative motion. Color Doppler sonography is useful in our understanding of the behavior of the subsynovial connective tissue during tendon excursion, which may elucidate the role of finger motion in the etiology of shear injury. © 2015 by the American Institute of Ultrasound in Medicine.

Ceria nanoparticles uniformly decorated on graphene nanosheets with coral-like morphology for high-performance supercapacitors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tao, Yan; Ruiyi, Li; Haiyan, Zhu

Graphical abstract: The study reported the synthesis of coral-like CeO{sub 2}/GNs for supercapacitors. The unique architecture with overall connected framework and good conducting network of the graphene greatly boosts the Faradaic redox reaction. Therefore, the CeO{sub 2}/GNs delivers an excellent electrochemical performance. - Highlights: • The study reported the synthesis of CeO{sub 2}/GNs. • The graphene was woven into CeO{sub 2}, acting as a good conducting network. • The CeO{sub 2}/GNs shows a coral-like structure. • The architecture creates an overall connected framework. • The CeO{sub 2}/GNs delivers good capacitive performances. - Abstract: CeO{sub 2}/graphene was synthesized by a simplemore » microwave method along with subsequent calcination. CeO{sub 2} nanoparticles with an average size of 68.8 nm are uniformly decorated on graphene nanosheets (CeO{sub 2}/GNs). The CeO{sub 2}/GNs displays a like-coral morphology. The architecture including overall connected framework, abundant intercrossed and interconnected nanochannels and perfect conducting network of the graphene, endows the CeO{sub 2}/GNs material with a superior electron and mass transport. As a result, the CeO{sub 2}/GNs gives a high specific capacitance of 503.4 F/g at 2 A/g and good cycle performance with 91.8% capacitance retention after 3000 cycles. Further, an asymmetric supercapacitors was assembled by using CeO{sub 2}/GNs as the positive electrode and activated carbon as the negative electrode, the asymmetric device demonstrate a favorable energy density of 30.2 Wh/kg at the power density of 750.0 W/kg and superior cycle life with 86.4% the capacitance retenion at 5 A/g after 3000 cycles.« less

Abnormal structural connectivity between the basal ganglia, thalamus, and frontal cortex in patients with disorders of consciousness.

PubMed

Weng, Ling; Xie, Qiuyou; Zhao, Ling; Zhang, Ruibin; Ma, Qing; Wang, Junjing; Jiang, Wenjie; He, Yanbin; Chen, Yan; Li, Changhong; Ni, Xiaoxiao; Xu, Qin; Yu, Ronghao; Huang, Ruiwang

2017-05-01

Consciousness loss in patients with severe brain injuries is associated with reduced functional connectivity of the default mode network (DMN), fronto-parietal network, and thalamo-cortical network. However, it is still unclear if the brain white matter connectivity between the above mentioned networks is changed in patients with disorders of consciousness (DOC). In this study, we collected diffusion tensor imaging (DTI) data from 13 patients and 17 healthy controls, constructed whole-brain white matter (WM) structural networks with probabilistic tractography. Afterward, we estimated and compared topological properties, and revealed an altered structural organization in the patients. We found a disturbance in the normal balance between segregation and integration in brain structural networks and detected significantly decreased nodal centralities primarily in the basal ganglia and thalamus in the patients. A network-based statistical analysis detected a subnetwork with uniformly significantly decreased structural connections between the basal ganglia, thalamus, and frontal cortex in the patients. Further analysis indicated that along the WM fiber tracts linking the basal ganglia, thalamus, and frontal cortex, the fractional anisotropy was decreased and the radial diffusivity was increased in the patients compared to the controls. Finally, using the receiver operating characteristic method, we found that the structural connections within the NBS-derived component that showed differences between the groups demonstrated high sensitivity and specificity (>90%). Our results suggested that major consciousness deficits in DOC patients may be related to the altered WM connections between the basal ganglia, thalamus, and frontal cortex. Copyright © 2017 Elsevier Ltd. All rights reserved.

Effects of nonuniform Mach-number entrance on scramjet nozzle flowfield and performance

NASA Astrophysics Data System (ADS)

Zhang, Pu; Xu, Jinglei; Quan, Zhibin; Mo, Jianwei

2016-12-01

Considering the non-uniformities of nozzle entrance influenced by the upstream, the effects of nonuniform Mach-number coupled with shock and expansion-wave on the flowfield and performances of single expansion ramp nozzle (SERN) are numerically studied using Reynolds-Averaged Navier-Stokes equations. The adopted Reynolds-averaged Navier-Stokes methodology is validated by comparing the numerical results with the cold experimental data, and the average method used in this paper is discussed. Uniform and nonuniform facility nozzles are designed to generate different Mach-number profile for the inlet of SERN, which is direct-connected with different facility nozzle, and the whole flowfield is simulated. Because of the coupling of shock and expansion-wave, flow direction of nonuniform SERN entrance is distorted. Compared with Mach contour of uniform case, the line is more curved for coupling shock-wave entrance (SWE) case, and flatter for the coupling expansion-wave entrance (EWE) case. Wall pressure distribution of SWE case appears rising region, whereas decreases like stairs of EWE case. The numerical results reveal that the coupled shock and expansion-wave play significant roles on nozzle performances. Compared with the SERN performances of uniform entrance case at the same work conditions, the thrust of nonuniform entrance cases reduces by 3-6%, pitch moment decreases by 2.5-7%. The negative lift presents an incremental trend with EWE while the situation is the opposite with SWE. These results confirm that considering the entrance flow parameter nonuniformities of a scramjet nozzle coupled with shock or expansion-wave from the upstream is necessary.

Topographic Constraints on the Evolution and Connectivity of Titan's Lacustrine Basins

NASA Astrophysics Data System (ADS)

Hayes, A. G.; Birch, S. P. D.; Dietrich, W. E.; Howard, A. D.; Kirk, R. L.; Poggiali, V.; Mastrogiuseppe, M.; Michaelides, R. J.; Corlies, P. M.; Moore, J. M.; Malaska, M. J.; Mitchell, K. L.; Lorenz, R. D.; Wood, C. A.

2017-12-01

The topography provided by altimetry, synthetic aperture radar-topography, and stereo radargrammetry has opened new doors for Titan research by allowing for quantitative analysis of morphologic form. Using altimetry measurements, we show that Titan's Maria are consistent with an equipotential surface but that several filled lakes are found to be hundreds of meters above this sea level, suggesting that they exist in isolated or perched basins. Within a given drainage basin, empty lake floors are typically higher than the liquid elevation of nearby lakes/seas, suggesting local subsurface connectivity. The majority of Titan's lakes reside in topographically closed, sharp-edged depressions whose planform curvature suggests lateral expansion through uniform scarp retreat. Many, but not all, empty lake basins exhibit flat floors and hectometer-scale raised rims that present a challenge to formation models. We conclude that dissolution erosion can best match the observed constraints but that challenges remain in the interpretation of formation processes and materials.

Spread of risk across financial markets: better to invest in the peripheries

NASA Astrophysics Data System (ADS)

Pozzi, F.; Di Matteo, T.; Aste, T.

2013-04-01

Risk is not uniformly spread across financial markets and this fact can be exploited to reduce investment risk contributing to improve global financial stability. We discuss how, by extracting the dependency structure of financial equities, a network approach can be used to build a well-diversified portfolio that effectively reduces investment risk. We find that investments in stocks that occupy peripheral, poorly connected regions in financial filtered networks, namely Minimum Spanning Trees and Planar Maximally Filtered Graphs, are most successful in diversifying, improving the ratio between returns' average and standard deviation, reducing the likelihood of negative returns, while keeping profits in line with the general market average even for small baskets of stocks. On the contrary, investments in subsets of central, highly connected stocks are characterized by greater risk and worse performance. This methodology has the added advantage of visualizing portfolio choices directly over the graphic layout of the network.

Spread of risk across financial markets: better to invest in the peripheries

PubMed Central

Pozzi, F.; Di Matteo, T.; Aste, T.

2013-01-01

Risk is not uniformly spread across financial markets and this fact can be exploited to reduce investment risk contributing to improve global financial stability. We discuss how, by extracting the dependency structure of financial equities, a network approach can be used to build a well-diversified portfolio that effectively reduces investment risk. We find that investments in stocks that occupy peripheral, poorly connected regions in financial filtered networks, namely Minimum Spanning Trees and Planar Maximally Filtered Graphs, are most successful in diversifying, improving the ratio between returns' average and standard deviation, reducing the likelihood of negative returns, while keeping profits in line with the general market average even for small baskets of stocks. On the contrary, investments in subsets of central, highly connected stocks are characterized by greater risk and worse performance. This methodology has the added advantage of visualizing portfolio choices directly over the graphic layout of the network. PMID:23588852

Optimal operation of turbo blowers serially connected using inlet vanes

NASA Astrophysics Data System (ADS)

Jang, Choon-Man

2011-03-01

Optimal operation of the turbo blowers having an inlet vane has been studied to understand the blowers' operating performance. To analyze three-dimensional flow field in the turbo blowers serially connected, general analysis code, CFX, is introduced in the present work. SST turbulence model is employed to estimate the eddy viscosity. Throughout the numerical analysis, it is found that the flow rates of the turbo blowers can be controlled at the vane angle between 90 (full open condition) degrees and 60 degrees effectively, because pressure loss rapidly increases below 60 degree of a vane angle. Efficiency also has almost the same values from 90 degrees to 60 degrees of a vane angle. It is noted that the distorted inlet velocity generated in the small vane angle makes performance deterioration of the turbo blowers due to the local leading edge separation and the following non-uniform blade loading.

A lake-centric geospatial database to guide research and inform management decisions in an Arctic watershed in northern Alaska experiencing climate and land-use changes

USGS Publications Warehouse

Jones, Benjamin M.; Arp, Christopher D.; Whitman, Matthew S.; Nigro, Debora A.; Nitze, Ingmar; Beaver, John; Gadeke, Anne; Zuck, Callie; Liljedahl, Anna K.; Daanen, Ronald; Torvinen, Eric; Fritz, Stacey; Grosse, Guido

2017-01-01

Lakes are dominant and diverse landscape features in the Arctic, but conventional land cover classification schemes typically map them as a single uniform class. Here, we present a detailed lake-centric geospatial database for an Arctic watershed in northern Alaska. We developed a GIS dataset consisting of 4362 lakes that provides information on lake morphometry, hydrologic connectivity, surface area dynamics, surrounding terrestrial ecotypes, and other important conditions describing Arctic lakes. Analyzing the geospatial database relative to fish and bird survey data shows relations to lake depth and hydrologic connectivity, which are being used to guide research and aid in the management of aquatic resources in the National Petroleum Reserve in Alaska. Further development of similar geospatial databases is needed to better understand and plan for the impacts of ongoing climate and land-use changes occurring across lake-rich landscapes in the Arctic.

LINEAR COUNT-RATE METER

DOEpatents

Henry, J.J.

1961-09-01

A linear count-rate meter is designed to provide a highly linear output while receiving counting rates from one cycle per second to 100,000 cycles per second. Input pulses enter a linear discriminator and then are fed to a trigger circuit which produces positive pulses of uniform width and amplitude. The trigger circuit is connected to a one-shot multivibrator. The multivibrator output pulses have a selected width. Feedback means are provided for preventing transistor saturation in the multivibrator which improves the rise and decay times of the output pulses. The multivibrator is connected to a diode-switched, constant current metering circuit. A selected constant current is switched to an averaging circuit for each pulse received, and for a time determined by the received pulse width. The average output meter current is proportional to the product of the counting rate, the constant current, and the multivibrator output pulse width.

A 1.8K refrigeration cryostat with 100 hours continuous cooling

NASA Astrophysics Data System (ADS)

Xu, Dong; Li, Jian; Huang, Rongjin; Li, Laifeng

2017-02-01

A refrigeration cryostat has been developed to produce continuous cooling to a sample below 1.8 K over 100 hours by using a cryocooler. A two-stage 4K G-M cryocooler is used to liquefy helium gas from evacuated vapor and cylinder helium bottle which can be replaced during the cooling process. The liquid helium transfer into superfluid helium in a Joule-Thomson valve in connection with a 1000 m3/h pumping unit. The pressure of evacuated helium vapor is controlled by air bag and valves. A copper decompression chamber, which is designed as a cooling station to control the superfluid helium, is used to cool the sample attached on it uniformly. The sample connects to the copper chamber in cryostat with screw thread. The cryostat can reach the temperature of 1.7 K without load and the continuous working time is more than 100 hours.

Use of laser drilling in the manufacture of organic inverter circuits.

PubMed

Iba, Shingo; Kato, Yusaku; Sekitani, Tsuyoshi; Kawaguchi, Hiroshi; Sakurai, Takayasu; Someya, Takao

2006-01-01

Inverter circuits have been made by connecting two high-quality pentacene field-effect transistors. A uniform and pinhole-free 900 nm thick polyimide gate-insulating layer was formed on a flexible polyimide film with gold gate electrodes and partially removed by using a CO2 laser drilling machine to make via holes and contact holes. Subsequent evaporation of the gold layer results in good electrical connection with a gold gate layer underneath the gate-insulating layer. By optimization of the settings of the CO2 laser drilling machine, contact resistance can be reduced to as low as 3 ohms for 180 microm square electrodes. No degradation of the transport properties of the organic transistors was observed after the laser-drilling process. This study demonstrates the feasibility of using the laser drilling process for implementation of organic transistors in integrated circuits on flexible polymer films.

NuSTAR Observations of Water Megamaser AGN

NASA Technical Reports Server (NTRS)

Masini, A.; Comastri, A.; Balokvic, M.; Zaw, I.; Puccetti, S.; Ballantyne, D. R.; Bauer, F. E.; Boggs, S. E.; Brandt, W. N.; Zhang, William W.

2016-01-01

Aims. We study the connection between the masing disk and obscuring torus in Seyfert 2 galaxies. Methods. We present a uniform X-ray spectral analysis of the high energy properties of 14 nearby megamaser active galactic nuclei observed by NuSTAR. We use a simple analytical model to localize the maser disk and understand its connection with the torus by combining NuSTAR spectral parameters with the available physical quantities from VLBI mapping.Results. Most of the sources that we analyzed are heavily obscured, showing a column density in excess of approx.10(exp 23) cm(exp -2); in particular, 79% are Compton-thick [NH is greater than 1.5 x 10(exp 24) cm(exp -2)]. When using column densities measured by NuSTAR with the assumption that the torus is the extension of the maser disk, and further assuming a reasonable density profile, we can predict the torus dimensions. They are found to be consistent with mid-IR interferometry parsec-scale observations of Circinus and NGC 1068. In this picture, the maser disk is intimately connected to the inner part of the torus. It is probably made of a large number of molecular clouds that connect the torus and the outer part of the accretion disk, giving rise to a thin disk rotating in most cases in Keplerian or sub-Keplerian motion. This toy model explains the established close connection between water megamaser emission and nuclear obscuration as a geometric effect.

Degree-of-Freedom Strengthened Cascade Array for DOD-DOA Estimation in MIMO Array Systems.

PubMed

Yao, Bobin; Dong, Zhi; Zhang, Weile; Wang, Wei; Wu, Qisheng

2018-05-14

In spatial spectrum estimation, difference co-array can provide extra degrees-of-freedom (DOFs) for promoting parameter identifiability and parameter estimation accuracy. For the sake of acquiring as more DOFs as possible with a given number of physical sensors, we herein design a novel sensor array geometry named cascade array. This structure is generated by systematically connecting a uniform linear array (ULA) and a non-uniform linear array, and can provide more DOFs than some exist array structures but less than the upper-bound indicated by minimum redundant array (MRA). We further apply this cascade array into multiple input multiple output (MIMO) array systems, and propose a novel joint direction of departure (DOD) and direction of arrival (DOA) estimation algorithm, which is based on a reduced-dimensional weighted subspace fitting technique. The algorithm is angle auto-paired and computationally efficient. Theoretical analysis and numerical simulations prove the advantages and effectiveness of the proposed array structure and the related algorithm.

Stationary states in quantum walk search

NASA Astrophysics Data System (ADS)

PrÅ«sis, Krišjānis; Vihrovs, Jevgěnijs; Wong, Thomas G.

2016-09-01

When classically searching a database, having additional correct answers makes the search easier. For a discrete-time quantum walk searching a graph for a marked vertex, however, additional marked vertices can make the search harder by causing the system to approximately begin in a stationary state, so the system fails to evolve. In this paper, we completely characterize the stationary states, or 1-eigenvectors, of the quantum walk search operator for general graphs and configurations of marked vertices by decomposing their amplitudes into uniform and flip states. This infinitely expands the number of known stationary states and gives an optimization procedure to find the stationary state closest to the initial uniform state of the walk. We further prove theorems on the existence of stationary states, with them conditionally existing if the marked vertices form a bipartite connected component and always existing if nonbipartite. These results utilize the standard oracle in Grover's algorithm, but we show that a different type of oracle prevents stationary states from interfering with the search algorithm.

System for concentrating and analyzing particles suspended in a fluid

DOEpatents

Fiechtner, Gregory J [Bethesda, MD; Cummings, Eric B [Livermore, CA; Singh, Anup K [Danville, CA

2011-04-26

Disclosed is a device for separating and concentrating particles suspended in a fluid stream by using dielectrophoresis (DEP) to trap and/or deflect those particles as they migrate through a fluid channel. The method uses fluid channels designed to constrain a liquid flowing through it to uniform electrokinetic flow velocities. This behavior is achieved by connecting deep and shallow sections of channels, with the channel depth varying abruptly along an interface. By careful design of abrupt changes in specific permeability at the interface, an abrupt and spatially uniform change in electrokinetic force can be selected. Because these abrupt interfaces also cause a sharp gradient in applied electric fields, a DEP force also can be established along the interface. Depending on the complex conductivity of the suspended particles and the immersion liquid, the DEP force can controllably complement or oppose the local electrokinetic force transporting the fluid through the channel allowing for manipulation of particles suspended in the transporting liquid.

Apparatus and method for concentrating and filtering particles suspended in a fluid

DOEpatents

Fiechtner, Gregory J [Bethesda, MD; Cummings, Eric B [Livermore, CA; Singh, Anup K [Danville, CA

2009-05-19

Disclosed is a device for separating and concentrating particles suspended in a fluid stream by using dielectrophoresis (DEP) to trap and/or deflect those particles as they migrate through a fluid channel. The method uses fluid channels designed to constrain a liquid flowing through it to uniform electrokinetic flow velocities. This behavior is achieved by connecting deep and shallow sections of channels, with the channel depth varying abruptly along an interface. By careful design of abrupt changes in specific permeability at the interface, an abrupt and spatially uniform change in electrokinetic force can be selected. Because these abrupt interfaces also cause a sharp gradient in applied electric fields, a DEP force also can be established along the interface. Depending on the complex conductivity of the suspended particles and the immersion liquid, the DEP force can controllably complement or oppose the local electrokinetic force transporting the fluid through the channel allowing for manipulation of particles suspended in the transporting liquid.

Method for uniformly distributing carbon flakes in a positive electrode, the electrode made thereby and compositions

DOEpatents

Mrazek, Franklin C.; Smaga, John A.; Battles, James E.

1983-01-01

A positive electrode for a secondary electrochemical cell wherein an electrically conductive current collector is in electrical contact with a particulate mixture of gray cast iron and an alkali metal sulfide and an electrolyte including alkali metal halides or alkaline earth metal halides. Also present may be a transition metal sulfide and graphite flakes from the conversion of gray cast iron to iron sulfide. Also disclosed is a method of distributing carbon flakes in a cell wherein there is formed an electrochemical cell of a positive electrode structure of the type described and a suitable electrolyte and a second electrode containing a material capable of alloying with alkali metal ions. The cell is connected to a source of electrical potential to electrochemically convert gray cast iron to an iron sulfide and uniformly to distribute carbon flakes formerly in the gray cast iron throughout the positive electrode while forming an alkali metal alloy in the negative electrode. Also disclosed are compositions useful in preparing positive electrodes.

Designing in vivo concentration gradients with discrete controlled release: a computational model

NASA Astrophysics Data System (ADS)

Walker, Edgar Y.; Barbour, Dennis L.

2010-08-01

One promising neurorehabilitation therapy involves presenting neurotrophins directly into the brain to induce growth of new neural connections. The precise control of neurotrophin concentration gradients deep within neural tissue that would be necessary for such a therapy is not currently possible, however. Here we evaluate the theoretical potential of a novel method of drug delivery, discrete controlled release (DCR), to control effective neurotrophin concentration gradients in an isotropic region of neocortex. We do so by constructing computational models of neurotrophin concentration profiles resulting from discrete release locations into the cortex and then optimizing their design for uniform concentration gradients. The resulting model indicates that by rationally selecting initial neurotrophin concentrations for drug-releasing electrode coatings in a square 16-electrode array, nearly uniform concentration gradients (i.e. planar concentration profiles) from one edge of the electrode array to the other should be obtainable. DCR therefore represents a promising new method of precisely directing neuronal growth in vivo over a wider spatial profile than would be possible with single release points.

Trapped one-dimensional ideal Fermi gas with a single impurity

NASA Astrophysics Data System (ADS)

Astrakharchik, G. E.; Brouzos, I.

2013-08-01

Ground-state properties of a single impurity in a one-dimensional Fermi gas are investigated in uniform and trapped geometries. The energy of a trapped system is obtained (i) by generalizing the McGuire expression from a uniform to trapped system (ii) within the local density approximation (iii) using the perturbative approach in the case of a weakly interacting impurity and (iv) diffusion Monte Carlo method. We demonstrate that there is a closed formula based on the exact solution of the homogeneous case which provides a precise estimation for the energy of a trapped system even for a small number of fermions and arbitrary coupling constant of the impurity. Using this expression, we analyze energy contributions from kinetic, interaction, and potential components, as well as spatial properties such as the system size and the pair-correlation function. Finally, we calculate the frequency of the breathing mode. Our analysis is directly connected and applicable to the recent experiments in microtraps.

Snake states and their symmetries in graphene

NASA Astrophysics Data System (ADS)

Liu, Yang; Tiwari, Rakesh P.; Brada, Matej; Bruder, C.; Kusmartsev, F. V.; Mele, E. J.

2015-12-01

Snake states are open trajectories for charged particles propagating in two dimensions under the influence of a spatially varying perpendicular magnetic field. In the quantum limit they are protected edge modes that separate topologically inequivalent ground states and can also occur when the particle density rather than the field is made nonuniform. We examine the correspondence of snake trajectories in single-layer graphene in the quantum limit for two families of domain walls: (a) a uniform doped carrier density in an antisymmetric field profile and (b) antisymmetric carrier distribution in a uniform field. These families support different internal symmetries but the same pattern of boundary and interface currents. We demonstrate that these physically different situations are gauge equivalent when rewritten in a Nambu doubled formulation of the two limiting problems. Using gauge transformations in particle-hole space to connect these problems, we map the protected interfacial modes to the Bogoliubov quasiparticles of an interfacial one-dimensional p -wave paired state. A variational model is introduced to interpret the interfacial solutions of both domain wall problems.

Snake states and their symmetries in graphene

NASA Astrophysics Data System (ADS)

Tiwari, Rakesh; Liu, Yang; Brada, Matej; Bruder, C.; Kusmartsev, F. V.; Mele, E. J.

Snake states are open trajectories for charged particles moving in two dimensions under the influence of a spatially varying perpendicular magnetic field. They can also occur in a constant perpendicular magnetic field when the particle density is made nonuniform as realized at a pn junction in a semiconductor, or in graphene. We examine the correspondence of such trajectories in monolayer graphene in the quantum limit for two families of domain walls: (a) a uniform doped carrier density in an antisymmetric perpendicular magnetic field and (b) antisymmetric carrier density distribution in a uniform perpendicular magnetic field. Although, these families support different internal symmetries, the pattern of the boundary and interface currents is the same in both cases. We demonstrate that these two physically different situations are gauge equivalent when rewritten in a Nambu doubled formulation of the two limiting problems. Using gauge transformations in particle-hole space to connect these two problems, we map the protected interfacial modes to the Bogoliubov quasiparticles of an interfacial one-dimensional p-wave paired state.

Price dynamics and market power in an agent-based power exchange

NASA Astrophysics Data System (ADS)

Cincotti, Silvano; Guerci, Eric; Raberto, Marco

2005-05-01

This paper presents an agent-based model of a power exchange. Supply of electric power is provided by competing generating companies, whereas demand is assumed to be inelastic with respect to price and is constant over time. The transmission network topology is assumed to be a fully connected graph and no transmission constraints are taken into account. The price formation process follows a common scheme for real power exchanges: a clearing house mechanism with uniform price, i.e., with price set equal across all matched buyer-seller pairs. A single class of generating companies is considered, characterized by linear cost function for each technology. Generating companies compete for the sale of electricity through repeated rounds of the uniform auction and determine their supply functions according to production costs. However, an individual reinforcement learning algorithm characterizes generating companies behaviors in order to attain the expected maximum possible profit in each auction round. The paper investigates how the market competitive equilibrium is affected by market microstructure and production costs.

Type Ia Supernova Cosmology

NASA Astrophysics Data System (ADS)

Leibundgut, B.; Sullivan, M.

2018-03-01

The primary agent for Type Ia supernova cosmology is the uniformity of their appearance. We present the current status, achievements and uncertainties. The Hubble constant and the expansion history of the universe are key measurements provided by Type Ia supernovae. They were also instrumental in showing time dilation, which is a direct observational signature of expansion. Connections to explosion physics are made in the context of potential improvements of the quality of Type Ia supernovae as distance indicators. The coming years will see large efforts to use Type Ia supernovae to characterise dark energy.

Little-Parks oscillations in superconducting ring with Josephson junctions

NASA Astrophysics Data System (ADS)

Sharon, Omri J.; Sharoni, Amos; Berger, Jorge; Shaulov, Avner; Yeshurun, Yosi

2018-03-01

Nb nano-rings connected serially by Nb wires exhibit, at low bias currents, the typical parabolic Little-Parks magnetoresistance oscillations. As the bias current increases, these oscillations become sinusoidal. This result is ascribed to the generation of Josephson junctions caused by the combined effect of current-induced phase slips and the non-uniformity of the order parameter along each ring due to the Nb wires attached to it. This interpretation is validated by further increasing the bias current, which results in magnetoresistance oscillations typical of a SQUID.

Atomic oxygen reactor having at least one sidearm conduit

NASA Technical Reports Server (NTRS)

Koontz, Steven L. (Inventor)

1994-01-01

An apparatus for treating a microporous structure with atomic oxygen is presented. The apparatus includes a main gas chamber for flowing gas in an axial direction and a source of gas, containing atomic oxygen, connected for introducing the gas into the main gas chamber. The apparatus employs at least one side arm extending from the main atomic oxygen-containing chamber. The side arm has characteristic relaxation times such that a uniform atomic oxygen dose rate is delivered to a specimen positioned transversely in the side arm spaced from the main gas chamber.

Predicting disease-related proteins based on clique backbone in protein-protein interaction network.

PubMed

Yang, Lei; Zhao, Xudong; Tang, Xianglong

2014-01-01

Network biology integrates different kinds of data, including physical or functional networks and disease gene sets, to interpret human disease. A clique (maximal complete subgraph) in a protein-protein interaction network is a topological module and possesses inherently biological significance. A disease-related clique possibly associates with complex diseases. Fully identifying disease components in a clique is conductive to uncovering disease mechanisms. This paper proposes an approach of predicting disease proteins based on cliques in a protein-protein interaction network. To tolerate false positive and negative interactions in protein networks, extending cliques and scoring predicted disease proteins with gene ontology terms are introduced to the clique-based method. Precisions of predicted disease proteins are verified by disease phenotypes and steadily keep to more than 95%. The predicted disease proteins associated with cliques can partly complement mapping between genotype and phenotype, and provide clues for understanding the pathogenesis of serious diseases.

From near to eternity: Spin-glass planting, tiling puzzles, and constraint-satisfaction problems

NASA Astrophysics Data System (ADS)

Hamze, Firas; Jacob, Darryl C.; Ochoa, Andrew J.; Perera, Dilina; Wang, Wenlong; Katzgraber, Helmut G.

2018-04-01

We present a methodology for generating Ising Hamiltonians of tunable complexity and with a priori known ground states based on a decomposition of the model graph into edge-disjoint subgraphs. The idea is illustrated with a spin-glass model defined on a cubic lattice, where subproblems, whose couplers are restricted to the two values {-1 ,+1 } , are specified on unit cubes and are parametrized by their local degeneracy. The construction is shown to be equivalent to a type of three-dimensional constraint-satisfaction problem known as the tiling puzzle. By varying the proportions of subproblem types, the Hamiltonian can span a dramatic range of typical computational complexity, from fairly easy to many orders of magnitude more difficult than prototypical bimodal and Gaussian spin glasses in three space dimensions. We corroborate this behavior via experiments with different algorithms and discuss generalizations and extensions to different types of graphs.

Topics on data transmission problem in software definition network

NASA Astrophysics Data System (ADS)

Gao, Wei; Liang, Li; Xu, Tianwei; Gan, Jianhou

2017-08-01

In normal computer networks, the data transmission between two sites go through the shortest path between two corresponding vertices. However, in the setting of software definition network (SDN), it should monitor the network traffic flow in each site and channel timely, and the data transmission path between two sites in SDN should consider the congestion in current networks. Hence, the difference of available data transmission theory between normal computer network and software definition network is that we should consider the prohibit graph structures in SDN, and these forbidden subgraphs represent the sites and channels in which data can't be passed by the serious congestion. Inspired by theoretical analysis of an available data transmission in SDN, we consider some computational problems from the perspective of the graph theory. Several results determined in the paper imply the sufficient conditions of data transmission in SDN in the various graph settings.

A general method for computing Tutte polynomials of self-similar graphs

NASA Astrophysics Data System (ADS)

Gong, Helin; Jin, Xian'an

2017-10-01

Self-similar graphs were widely studied in both combinatorics and statistical physics. Motivated by the construction of the well-known 3-dimensional Sierpiński gasket graphs, in this paper we introduce a family of recursively constructed self-similar graphs whose inner duals are of the self-similar property. By combining the dual property of the Tutte polynomial and the subgraph-decomposition trick, we show that the Tutte polynomial of this family of graphs can be computed in an iterative way and in particular the exact expression of the formula of the number of their spanning trees is derived. Furthermore, we show our method is a general one that is easily extended to compute Tutte polynomials for other families of self-similar graphs such as Farey graphs, 2-dimensional Sierpiński gasket graphs, Hanoi graphs, modified Koch graphs, Apollonian graphs, pseudofractal scale-free web, fractal scale-free network, etc.

Effect of tumor resection on the characteristics of functional brain networks.

PubMed

Wang, H; Douw, L; Hernández, J M; Reijneveld, J C; Stam, C J; Van Mieghem, P

2010-08-01

Brain functioning such as cognitive performance depends on the functional interactions between brain areas, namely, the functional brain networks. The functional brain networks of a group of patients with brain tumors are measured before and after tumor resection. In this work, we perform a weighted network analysis to understand the effect of neurosurgery on the characteristics of functional brain networks. Statistically significant changes in network features have been discovered in the beta (13-30 Hz) band after neurosurgery: the link weight correlation around nodes and within triangles increases which implies improvement in local efficiency of information transfer and robustness; the clustering of high link weights in a subgraph becomes stronger, which enhances the global transport capability; and the decrease in the synchronization or virus spreading threshold, revealed by the increase in the largest eigenvalue of the adjacency matrix, which suggests again the improvement of information dissemination.

A tool for filtering information in complex systems

NASA Astrophysics Data System (ADS)

Tumminello, M.; Aste, T.; Di Matteo, T.; Mantegna, R. N.

2005-07-01

We introduce a technique to filter out complex data sets by extracting a subgraph of representative links. Such a filtering can be tuned up to any desired level by controlling the genus of the resulting graph. We show that this technique is especially suitable for correlation-based graphs, giving filtered graphs that preserve the hierarchical organization of the minimum spanning tree but containing a larger amount of information in their internal structure. In particular in the case of planar filtered graphs (genus equal to 0), triangular loops and four-element cliques are formed. The application of this filtering procedure to 100 stocks in the U.S. equity markets shows that such loops and cliques have important and significant relationships with the market structure and properties. This paper was submitted directly (Track II) to the PNAS office.Abbreviations: MST, minimum spanning tree; PMFG, Planar Maximally Filtered Graph; r-clique, clique of r elements.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hamilton, Kathleen E.; Humble, Travis S.

Using quantum annealing to solve an optimization problem requires minor embedding a logic graph into a known hardware graph. We introduce the minor set cover (MSC) of a known graph GG : a subset of graph minors which contain any remaining minor of the graph as a subgraph, in an effort to reduce the complexity of the minor embedding problem. Any graph that can be embedded into GG will be embeddable into a member of the MSC. Focusing on embedding into the hardware graph of commercially available quantum annealers, we establish the MSC for a particular known virtual hardware, whichmore » is a complete bipartite graph. Furthermore, we show that the complete bipartite graph K N,N has a MSC of N minors, from which K N+1 is identified as the largest clique minor of K N,N. In the case of determining the largest clique minor of hardware with faults we briefly discussed this open question.« less

Ndarts

NASA Technical Reports Server (NTRS)

Jain, Abhinandan

2011-01-01

Ndarts software provides algorithms for computing quantities associated with the dynamics of articulated, rigid-link, multibody systems. It is designed as a general-purpose dynamics library that can be used for the modeling of robotic platforms, space vehicles, molecular dynamics, and other such applications. The architecture and algorithms in Ndarts are based on the Spatial Operator Algebra (SOA) theory for computational multibody and robot dynamics developed at JPL. It uses minimal, internal coordinate models. The algorithms are low-order, recursive scatter/ gather algorithms. In comparison with the earlier Darts++ software, this version has a more general and cleaner design needed to support a larger class of computational dynamics needs. It includes a frames infrastructure, allows algorithms to operate on subgraphs of the system, and implements lazy and deferred computation for better efficiency. Dynamics modeling modules such as Ndarts are core building blocks of control and simulation software for space, robotic, mechanism, bio-molecular, and material systems modeling.

Quantify spatial relations to discover handwritten graphical symbols

NASA Astrophysics Data System (ADS)

Li, Jinpeng; Mouchère, Harold; Viard-Gaudin, Christian

2012-01-01

To model a handwritten graphical language, spatial relations describe how the strokes are positioned in the 2-dimensional space. Most of existing handwriting recognition systems make use of some predefined spatial relations. However, considering a complex graphical language, it is hard to express manually all the spatial relations. Another possibility would be to use a clustering technique to discover the spatial relations. In this paper, we discuss how to create a relational graph between strokes (nodes) labeled with graphemes in a graphical language. Then we vectorize spatial relations (edges) for clustering and quantization. As the targeted application, we extract the repetitive sub-graphs (graphical symbols) composed of graphemes and learned spatial relations. On two handwriting databases, a simple mathematical expression database and a complex flowchart database, the unsupervised spatial relations outperform the predefined spatial relations. In addition, we visualize the frequent patterns on two text-lines containing Chinese characters.

Scalable Faceted Ranking in Tagging Systems

NASA Astrophysics Data System (ADS)

Orlicki, José I.; Alvarez-Hamelin, J. Ignacio; Fierens, Pablo I.

Nowadays, web collaborative tagging systems which allow users to upload, comment on and recommend contents, are growing. Such systems can be represented as graphs where nodes correspond to users and tagged-links to recommendations. In this paper we analyze the problem of computing a ranking of users with respect to a facet described as a set of tags. A straightforward solution is to compute a PageRank-like algorithm on a facet-related graph, but it is not feasible for online computation. We propose an alternative: (i) a ranking for each tag is computed offline on the basis of tag-related subgraphs; (ii) a faceted order is generated online by merging rankings corresponding to all the tags in the facet. Based on the graph analysis of YouTube and Flickr, we show that step (i) is scalable. We also present efficient algorithms for step (ii), which are evaluated by comparing their results with two gold standards.

A binary-decision-diagram-based two-bit arithmetic logic unit on a GaAs-based regular nanowire network with hexagonal topology.

PubMed

Zhao, Hong-Quan; Kasai, Seiya; Shiratori, Yuta; Hashizume, Tamotsu

2009-06-17

A two-bit arithmetic logic unit (ALU) was successfully fabricated on a GaAs-based regular nanowire network with hexagonal topology. This fundamental building block of central processing units can be implemented on a regular nanowire network structure with simple circuit architecture based on graphical representation of logic functions using a binary decision diagram and topology control of the graph. The four-instruction ALU was designed by integrating subgraphs representing each instruction, and the circuitry was implemented by transferring the logical graph structure to a GaAs-based nanowire network formed by electron beam lithography and wet chemical etching. A path switching function was implemented in nodes by Schottky wrap gate control of nanowires. The fabricated circuit integrating 32 node devices exhibits the correct output waveforms at room temperature allowing for threshold voltage variation.

The braingraph.org database of high resolution structural connectomes and the brain graph tools.

PubMed

Kerepesi, Csaba; Szalkai, Balázs; Varga, Bálint; Grolmusz, Vince

2017-10-01

Based on the data of the NIH-funded Human Connectome Project, we have computed structural connectomes of 426 human subjects in five different resolutions of 83, 129, 234, 463 and 1015 nodes and several edge weights. The graphs are given in anatomically annotated GraphML format that facilitates better further processing and visualization. For 96 subjects, the anatomically classified sub-graphs can also be accessed, formed from the vertices corresponding to distinct lobes or even smaller regions of interests of the brain. For example, one can easily download and study the connectomes, restricted to the frontal lobes or just to the left precuneus of 96 subjects using the data. Partially directed connectomes of 423 subjects are also available for download. We also present a GitHub-deposited set of tools, called the Brain Graph Tools, for several processing tasks of the connectomes on the site http://braingraph.org.

Computing the Edge-Neighbour-Scattering Number of Graphs

NASA Astrophysics Data System (ADS)

Wei, Zongtian; Qi, Nannan; Yue, Xiaokui

2013-11-01

A set of edges X is subverted from a graph G by removing the closed neighbourhood N[X] from G. We denote the survival subgraph by G=X. An edge-subversion strategy X is called an edge-cut strategy of G if G=X is disconnected, a single vertex, or empty. The edge-neighbour-scattering number of a graph G is defined as ENS(G) = max{ω(G/X)-|X| : X is an edge-cut strategy of G}, where w(G=X) is the number of components of G=X. This parameter can be used to measure the vulnerability of networks when some edges are failed, especially spy networks and virus-infected networks. In this paper, we prove that the problem of computing the edge-neighbour-scattering number of a graph is NP-complete and give some upper and lower bounds for this parameter.

Significant Scales in Community Structure

NASA Astrophysics Data System (ADS)

Traag, V. A.; Krings, G.; van Dooren, P.

2013-10-01

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

Steel Rack Connections: Identification of Most Influential Factors and a Comparison of Stiffness Design Methods

PubMed Central

Shah, S. N. R.; Sulong, N. H. Ramli; Shariati, Mahdi; Jumaat, M. Z.

2015-01-01

Steel pallet rack (SPR) beam-to-column connections (BCCs) are largely responsible to avoid the sway failure of frames in the down-aisle direction. The overall geometry of beam end connectors commercially used in SPR BCCs is different and does not allow a generalized analytic approach for all types of beam end connectors; however, identifying the effects of the configuration, profile and sizes of the connection components could be the suitable approach for the practical design engineers in order to predict the generalized behavior of any SPR BCC. This paper describes the experimental behavior of SPR BCCs tested using a double cantilever test set-up. Eight sets of specimens were identified based on the variation in column thickness, beam depth and number of tabs in the beam end connector in order to investigate the most influential factors affecting the connection performance. Four tests were repeatedly performed for each set to bring uniformity to the results taking the total number of tests to thirty-two. The moment-rotation (M-θ) behavior, load-strain relationship, major failure modes and the influence of selected parameters on connection performance were investigated. A comparative study to calculate the connection stiffness was carried out using the initial stiffness method, the slope to half-ultimate moment method and the equal area method. In order to find out the more appropriate method, the mean stiffness of all the tested connections and the variance in values of mean stiffness according to all three methods were calculated. The calculation of connection stiffness by means of the initial stiffness method is considered to overestimate the values when compared to the other two methods. The equal area method provided more consistent values of stiffness and lowest variance in the data set as compared to the other two methods. PMID:26452047

Cascaded Converters for Integration and Management of Grid Level Energy Storage Systems

NASA Astrophysics Data System (ADS)

Alaas, Zuhair

This research work proposes two cascaded multilevel inverter structures for BESS. The gating and switching control of switching devices in both inverter typologies are done by using a phase-shifted PWM scheme. The first proposed isolated multilevel inverter is made up of three-phase six-switch inverter blocks with a reduced number of power components compared with traditional isolated CHB. The suggested isolated converter has only one battery string for three-phase system that can be used for high voltage and high power applications such as grid connected BESS and alternative energy systems. The isolated inverter enables dq frame based simple control and eliminates the issues of single-phase pulsating power, which can cause detrimental impacts on certain dc sources. Simulation studies have been carried out to compare the proposed isolated multi-level inverter with an H-bridge cascaded transformer inverter. The simulation results verified the performance of the isolated inverter. The second proposed topology is a Hierarchal Cascaded Multilevel Converter (HCMC) with phase to phase SOC balancing capability which also for high voltage and high power battery energy storage systems. The HCMC has a hybrid structure of half-bridge converters and H-bridge inverters and the voltage can be hierarchically cascaded to reach the desired value at the half-bridge and the H-bridge levels. The uniform SOC battery management is achieved by controlling the half-bridge converters that are connected to individual battery modules/cells. Simulation studies and experimental results have been carried on a large scale battery system under different operating conditions to verify the effectiveness of the proposed inverters. Moreover, this dissertation presents a new three-phase SOC equalizing circuit, called six-switch energy-level balancing circuit (SSBC), which can be used to realize uniform SOC operation for full utilization of the battery capacity in proposed HCMC or any CMI inverter while keeping balanced three-phase operation. A sinusoidal PWM modulation technique is used to control power transferring between phases. Simulation results have been carried out to verify the performance of the proposed SSBC circuit of uniform three-phase SOC balancing.

Incongruent genetic connectivity patterns for VME indicator taxa: implications for the management of New Zealand's vulnerable marine ecosystems

NASA Astrophysics Data System (ADS)

Clark, M. R.; Gardner, J.; Holland, L.; Zeng, C.; Hamilton, J. S.; Rowden, A. A.

2016-02-01

In the New Zealand region vulnerable marine ecosystems (VMEs) are at risk from commercial fishing activity and future seabed mining. Understanding connectivity among VMEs is important for the design of effective spatial management strategies, i.e. a network of protected areas. To date however, genetic connectivity in the New Zealand region has rarely been documented. As part of a project developing habitat suitability models and spatial management options for VMEs we used DNA sequence data and microsatellite genotyping to assess genetic connectivity for a range of VME indicator taxa, including the coral Desmophyllum dianthus, and the sponges Poecilastra laminaris and Penares palmatoclada. Overall, patterns of connectivity were inconsistent amonst taxa. Nonetheless, genetic data from each taxon were relevant to inform management at a variety of spatial scales. D. dianthus populations in the Kermadec volcanic arc and the Louisville Seamount Chain were indistinguishable, highlighting the importance of considering source-sink dynamics between populations beyond the EEZ in conservation planning. Poecilastra laminaris populations showed significant divergence across the Chatham Rise, in contrast to P. palmatoclada, which had a uniform haplotypic distribution. However, both sponge species exhibited the highest genetic diversity on the Chatham Rise, suggesting that this area is a genetic hotspot. The spatial heterogeneity of genetic patterns of structure suggest that inclusion of several taxa is necessary to facilitate understanding of regional connectivity patterns, variation in which may be attributed to alternate life history strategies, local hydrodynamic regimes, or in some cases, suboptimal sample sizes. Our findings provide important information for use by environmental managers, including summary maps of genetic diversity and barriers to gene flow, which will be used in spatial management decision-support tools.

Semantic processing in connected speech at a uniformly early stage of autopsy-confirmed Alzheimer's disease.

PubMed

Ahmed, Samrah; de Jager, Celeste A; Haigh, Anne-Marie; Garrard, Peter

2013-01-01

The aim of the present study was to quantify the semantic content of connected speech produced by patients at a uniformly early stage of pathologically proven Alzheimer's disease (AD). A secondary aim was to establish whether semantic units were reduced globally, or whether there was a disproportionate reduction of specific classes of information. Discourse samples were obtained from 18 AD patients and 18 matched controls, all pathologically confirmed. Semantic unit identification was scored overall and for four subclasses: subjects, locations, objects, and actions. Idea density and efficiency were calculated. AD transcripts showed significantly reduced units overall, particularly actions and subjects, as well as reduced efficiency. Total semantic units and a combination of subject-, location-, and object-related units ("noun" units) correlated with the Expression subscore on the Cambridge Cognitive Examination (CAMCOG). Subject related units correlated with the CAMCOG Abstract Thinking scale. Logistic regression analyses confirmed that all measures that were lower in AD than controls were predictive of group membership. An exploratory comparison between units expressed mainly using nouns and those mainly using verbs showed that the latter was the stronger of these two predictors. The present study adds a lexico-semantic dimension to the linguistic profile based on discourse analysis in typical AD, recently described by the same authors. 2012, 83(11): 1056-1062). The suggestion of differential importance of verb and noun use in the present study may be related to the reduction in syntactic complexity that was reported, using the same set of discourse samples, in the earlier study.

Two-dimensional array of cold-electron bolometers for high-sensitivity polarization measurements

NASA Astrophysics Data System (ADS)

Kuzmin, L. S.

2012-01-01

A new concept of a two-dimensional array of cold-electron bolometers with distributed dipole antennas in the focal plane for high-sensitivity polarization measurements is proposed. The concept gives a unique combination of high polarization resolution due to a large uniforms array of cold-electron bolometers and optimal matching with junction field effect transistor (JFET) amplifiers because of flexibility in direct-current connections. The noise characteristics are improved due to arriving-signal power distribution among numerous cold-electron bolometers and an increase in their response. This should lead to a significant increase in the sensitivity and dynamic range compared with competing alternative bolometer technologies. The reliability of the twodimensional array significantly increases due to a series-parallel connection of a large number of cold-electron bolometers. High polarization resolution should be ensured due to uniform covering of a substrate by a two-dimensional array over a large area and the absence of the beam compression to small lumped elements. The fundamental sensitivity limit of the cold-electron bolometer array is smaller than photon noise which is considered to be the ultimate level restricted by the background radiation. Estimates of noise of bolometers with the JFET reading system show the possibility of realizing the ultimate sensitivity below the photon-noise level 5 ・10-17 W/Hz1/2 at a frequency of 350 GHz for an optical load with a power of 5 pW. These parameters correspond to the requirements to the receiving system of a BOOMERanG balloon telescope.

The value of residential photovoltaic systems: A comprehensive assessment

NASA Technical Reports Server (NTRS)

Borden, C. S.

1983-01-01

Utility-interactive photovoltaic (PV) arrays on residential rooftops appear to be a potentially attractive, large-scale application of PV technology. Results of a comprehensive assessment of the value (i.e., break-even cost) of utility-grid connected residential photovoltaic power systems under a variety of technological and economic assumptions are presented. A wide range of allowable PV system costs are calculated for small (4.34 kW (p) sub ac) residential PV systems in various locales across the United States. Primary factor in this variation are differences in local weather conditions, utility-specific electric generation capacity, fuel types, and customer-load profiles that effect purchase and sell-back rates, and non-uniform state tax considerations. Additional results from this analysis are: locations having the highest insolation values are not necessary the most economically attractive sites; residential PV systems connected in parallel to the utility demonstrate high percentages of energy sold back to the grid, and owner financial and tax assumptions cause large variations in break-even costs. Significant cost reduction and aggressive resolution of potential institutional impediments (e.g., liability, standards, metering, and technical integration) are required for a residential PV marker to become a major electric-grid-connected energy-generation source.

STEAM GENERATOR FOR GAS COOLED NUCLEAR REACTORS

DOE Office of Scientific and Technical Information (OSTI.GOV)

None

1960-03-14

A steam generator for a gas-cooled nuclear reactor is disposed inside the same pressure vessel as the reactor and has a tube system heated by the gas circulating through the reactor; the pressure vessel is double-walled, and the interspace between these two walls is filled with concrete serving as radiation shielding. The steam generator has a cylindricaIly shaped vertical casing, through which the heating gas circulates, while the tubes are arranged in a plurality of parallel horizontal planes and each of them have the shape of an involute of a circle. The tubes are uniformly distributed over the available surfacemore » in the plane, all the tubes of the same plane being connected in parallel. The exterior extremities of these involute-shaped tubes are each connected with similar tubes disposed in the adjacent lower situated plane, while the interior extremities are connected with tubes in the adjacent higher situated plane. The alimentation of the tubes is performed over annular headers. The tube system is self-supporting, the tubes being joined together by welded spacers. The fluid flow in the tubes is performed by forced circulation. (NPO)« less

Self-assembly of the yeast actomyosin contractile ring as an aggregation process: kinetics of formation and instability regimes

NASA Astrophysics Data System (ADS)

Ojkic, Nikola; Vavylonis, Dimitrios

2009-03-01

Fission yeast cells assemble an equatorial contractile ring for cytokinesis, the last step of mitosis. The ring assembles from ˜ 65 membrane-bound ``nodes''' containing myosin motors and other proteins. Actin filaments that grow out from the nodes establish transient connections among the nodes and aid in pulling them together in a process that appears as pair-wise attraction (Vavylonis et al. Science 97:319, 2008). We used scaling arguments, coarse grained stability analysis of homogeneous states, and Monte Carlo simulations of simple models, to explore the conditions that yield fast and efficient ring formation, as opposed to formation of isolated clumps. We described our results as a function of: number of nodes, rate of establishing connections, range of node interaction, distance traveled per node interaction and broad band width, w. Uniform cortical 2d distributions of nodes are stable over short times due to randomness of connections among nodes, but become unstable over long times due to fluctuations in the initial node distribution. Successful condensation of nodes into a ring requires sufficiently small w such that lateral contraction occurs faster then clump formation.

Apparatus and method for continuous electroplating. [Patent application

DOEpatents

Conlon, T.P. Jr.; Holmes, S.D.

1981-11-19

An apparatus and method are disclosed for performing a continuous electroplating process upon an elongate conductive stock article. A closed housing assembly retaining an electroplating solution and having a conductive housing body and flexible, nonconductive end walls is connected to the positive pole of a source of electromotive force. The end walls have an aperture for receiving the conducting stock article in sliding and sealing contact. The stock article is connected to the negative pole of the source of electromotive force. The conductive housing body and the section of the conductive stock article within the housing body are coextensive, coaxial and spaced a uniform distance apart. The housing body has an inlet at the bottom and an outlet at the top allowing the housing assembly to fill completely with plating solution. The inlet has a reduced nozzle to create turbulence and spiral circulating motion of the plating solution moved by a pump connected by nonconductive conduits. The solution is circulated through an open reservoir. A coolant may be conveyed through the interior in a hollow stock article to cool the surface being electroplated. Different sizes of coaxial metal insert sleeves may be telescopically received in the housing body.

Investigation of OSL signal of resistors from mobile phones for accidental dosimetry

NASA Astrophysics Data System (ADS)

Mrozik, A.; Marczewska, B.; Bilski, P.; Gieszczyk, W.

2014-12-01

Resistors from mobile phones, usually located near the human body, are considered as individual dosimeters of ionizing radiation in emergency situations. The resistors contain Al2O3, which is optically stimulated luminescence (OSL) material sensitive to ionizing radiation. This work is focused on determination of dose homogeneity within a mobile phones which was carried out by OSL measurements of resistors placed in different parts inside the mobile phone. Separate, commercially available resistors, similar in the shape and size to the resistors from circuit board of the studied mobile phone, were situated in different locations inside it. The irradiations were performed in uniform 60Co and 137Cs radiation fields, with the mobile phones connected and not connected to the cellular network. The dose decrease of 9% was measured for original resistors situated between layer of copper-clad laminate and battery, in comparison to the dose at the front of the phone. The resistors showed the lower signal when the mobile phone was connected to the cellular network, due to higher temperature inside the housing. The profile of fading was investigated within 3 month period for resistors irradiated with 1 Gy of gamma rays to estimate of the fading coefficient.

The value of residential photovoltaic systems: A comprehensive assessment

NASA Astrophysics Data System (ADS)

Borden, C. S.

1983-09-01

Utility-interactive photovoltaic (PV) arrays on residential rooftops appear to be a potentially attractive, large-scale application of PV technology. Results of a comprehensive assessment of the value (i.e., break-even cost) of utility-grid connected residential photovoltaic power systems under a variety of technological and economic assumptions are presented. A wide range of allowable PV system costs are calculated for small (4.34 kW (p) sub ac) residential PV systems in various locales across the United States. Primary factor in this variation are differences in local weather conditions, utility-specific electric generation capacity, fuel types, and customer-load profiles that effect purchase and sell-back rates, and non-uniform state tax considerations. Additional results from this analysis are: locations having the highest insolation values are not necessary the most economically attractive sites; residential PV systems connected in parallel to the utility demonstrate high percentages of energy sold back to the grid, and owner financial and tax assumptions cause large variations in break-even costs. Significant cost reduction and aggressive resolution of potential institutional impediments (e.g., liability, standards, metering, and technical integration) are required for a residential PV marker to become a major electric-grid-connected energy-generation source.

Method and device for microwave sintering large ceramic articles

DOEpatents

Kimrey, Jr., Harold D.

1990-01-01

A microwave sintering system and method are provided for extremely uniform sintering of large and/or irregular shaped ceramic articles at microwave frequencies of at least 28 GHz in the hundreds of kilowatts power range in an untuned cavity. A 28 GHz, 200 kw gyrotron with variable power output is used as the microwave source connected to an untuned microwave cavity formed of an electrically conductive housing through an overmoded waveguide arrangement which acts in conjunction with a mode promoter within the cavity to achieve unexpected field uniformity. The part to be sintered is placed in the cavity and supported on a removable high temperature table in a central location within the cavity. The part is surrounded by a microwave transparent bulk insulating material to reduce thermal heat loss at the part surfaces and maintain more uniform temperature. The cavity may be operated at a high vacuum to aid in preventing arcing. The system allows controlled increased heating rates of greater than 200.degree. C./min to provide rapid heating of a ceramic part to a selected sintering temperature where it is maintained by regulating the microwave power applied to the part. As a result of rapid heating, the extent of non-isothermal processes such as segregation of impurities to the grain boundaries are minimized and exaggerated grain growth is reduced, thereby strengthening the mechanical properties of the ceramic part being sintered.

Influence of the normal modes on the plasma uniformity in large scale CCP reactors

NASA Astrophysics Data System (ADS)

Eremin, Denis; Brinkmann, Ralf Peter; Mussenbrock, Thomas; Lane, Barton; Matsukuma, Masaaki; Ventzek, Peter

2016-09-01

Large scale capacitively coupled plasmas (CCP) driven by sources with high frequency components often exhibit phenomena which are absent in relatively well understood small scale CCPs driven at low frequencies. Of particular interest are such phenomena which affect discharge parameters of direct relevance to the plasma processing applications. One of such parameters is plasma uniformity. By using a self-consistent 2d3v Particle-in-cell/Monte-Carlo (PIC/MCC) code parallelized on GPU we have been able to show that uniformity of the plasma generated is influenced predominantly by two factors, the ionization pattern caused by high-energy electrons and the average temperature of low-energy plasma electrons. The heating mechanisms for these two groups of electrons appear to be different leading to different transversal (radial) profiles of the corresponding factors, which is well captured by the kinetic PIC/MCC code. We find that the heating mechanisms are intrinsically connected with excitation of normal modes inherent to a plasma-filled CCP reactor. In this work we study the wave nature of these phenomena, such as their excitation, propagation, and interaction with electrons. Supported by SFB-TR 87 project of the German Research Foundation and by the ``Experimental and numerical analysis of very high frequency capacitively coupled plasma discharges'' mutual research project between RUB and Tokyo Electron Ltd.

Anomalously Strong and Rapid Drying of the Tropical Lower Stratosphere in 2016: Connections to Both the QBO and ENSO

NASA Astrophysics Data System (ADS)

Hurst, D. F.; Davis, S. M.; Rosenlof, K. H.; Lambert, A.; Read, W. G.; Hall, E.; Jordan, A. F.

2017-12-01

Variations in tropical lower stratospheric water vapor are generally attributable to annual cycles in the Brewer-Dobson circulation and inter-annual phenomenon like the quasi-biennial oscillation (QBO) and the El Niño Southern Oscillation (ENSO). Extremes in tropical lower stratospheric water vapor (SWV) occur when these annual and inter-annual changes are constructively superimposed. The atypical progression of the 2015-16 QBO led to a strong and rapid cooling of the tropical lower stratosphere during 2016. From December 2015 to November 2016, monthly tropical mean (15°S-15°N) coldpoint temperature (CPT) anomalies decreased 3.2°C, from 1.1 to -2.1°C. Accordingly, monthly tropical mean SWV anomalies at 83 hPa dropped 1.9 ppm, from 0.85 to -1.05 ppm. This decline in SWV anomalies is equivalent to 40% of the long-term December average tropical abundance of SWV at 83 hPa. The 2016 decreases in tropical anomalies of both CPTs and SWV were not zonally uniform, with average Eastern Hemisphere reductions greater by 2°C and 0.9 ppm (50%), respectively. Since the QBO typically has a zonally uniform effect on tropical CPTs, this implies a zonally non-uniform mechanism like ENSO also influenced CPTs during 2016. The transition of ENSO from strong El Niño to weak La Niña conditions in 2016 would induce this zonal non-uniformity by shifting convective activity from the Eastern Pacific to the Western Pacific and Indian Ocean regions. Evidence indicates the simultaneous cooling of tropical CPTs by both the QBO and ENSO during 2016 rapidly dried the tropical lower stratosphere with anomalous strength, especially in the Eastern Hemisphere.

Flow Webs: Mechanism and Architecture for the Implementation of Sensor Webs

NASA Astrophysics Data System (ADS)

Gorlick, M. M.; Peng, G. S.; Gasster, S. D.; McAtee, M. D.

2006-12-01

The sensor web is a distributed, federated infrastructure much like its predecessors, the internet and the world wide web. It will be a federation of many sensor webs, large and small, under many distinct spans of control, that loosely cooperates and share information for many purposes. Realistically, it will grow piecemeal as distinct, individual systems are developed and deployed, some expressly built for a sensor web while many others were created for other purposes. Therefore, the architecture of the sensor web is of fundamental import and architectural strictures that inhibit innovation, experimentation, sharing or scaling may prove fatal. Drawing upon the architectural lessons of the world wide web, we offer a novel system architecture, the flow web, that elevates flows, sequences of messages over a domain of interest and constrained in both time and space, to a position of primacy as a dynamic, real-time, medium of information exchange for computational services. The flow web captures; in a single, uniform architectural style; the conflicting demands of the sensor web including dynamic adaptations to changing conditions, ease of experimentation, rapid recovery from the failures of sensors and models, automated command and control, incremental development and deployment, and integration at multiple levels—in many cases, at different times. Our conception of sensor webs—dynamic amalgamations of sensor webs each constructed within a flow web infrastructure—holds substantial promise for earth science missions in general, and of weather, air quality, and disaster management in particular. Flow webs, are by philosophy, design and implementation a dynamic infrastructure that permits massive adaptation in real-time. Flows may be attached to and detached from services at will, even while information is in transit through the flow. This concept, flow mobility, permits dynamic integration of earth science products and modeling resources in response to real-time demands. Flows are the connective tissue of flow webs—massive computational engines organized as directed graphs whose nodes are semi-autonomous components and whose edges are flows. The individual components of a flow web may themselves be encapsulated flow webs. In other words, a flow web subgraph may be presented to a yet larger flow web as a single, seamless component. Flow webs, at all levels, may be edited and modified while still executing. Within a flow web individual components may be added, removed, started, paused, halted, reparameterized, or inspected. The topology of a flow web may be changed at will. Thus, flow webs exhibit an extraordinary degree of adaptivity and robustness as they are explicitly designed to be modified on the fly, an attribute well suited for dynamic model interactions in sensor webs. We describe our concept for a sensor web, implemented as a flow web, in the context of a wildfire disaster management system for the southern California region. Comprehensive wildfire management requires cooperation among multiple agencies. Flow webs allow agencies to share resources in exactly the manner they choose. We will explain how to employ flow webs and agents to integrate satellite remote sensing data, models, in-situ sensors, UAVs and other resources into a sensor web that interconnects organizations and their disaster management tools in a manner that simultaneously preserves their independence and builds upon the individual strengths of agency-specific models and data sources.

Incorporating Sulfur Inside the Pores of Carbons for Advanced Lithium-Sulfur Batteries: An Electrolysis Approach.

PubMed

He, Bin; Li, Wen-Cui; Yang, Chao; Wang, Si-Qiong; Lu, An-Hui

2016-01-26

We have developed an electrolysis approach that allows effective and uniform incorporation of sulfur inside the micropores of carbon nanosheets for advanced lithium-sulfur batteries. The sulfur-carbon hybrid can be prepared with a 70 wt % sulfur loading, in which no nonconductive sulfur agglomerations are formed. Because the incorporated sulfur is electrically connected to the carbon matrix in nature, the hybrid cathode shows excellent electrochemical performance, including a high reversible capacity, good rate capability, and good cycling stability, as compared to one prepared using the popular melt-diffusion method.

Turbine component cooling channel mesh with intersection chambers

DOEpatents

Lee, Ching-Pang; Marra, John J

2014-05-06

A mesh (35) of cooling channels (35A, 35B) with an array of cooling channel intersections (42) in a wall (21, 22) of a turbine component. A mixing chamber (42A-C) at each intersection is wider (W1, W2)) than a width (W) of each of the cooling channels connected to the mixing chamber. The mixing chamber promotes swirl, and slows the coolant for more efficient and uniform cooling. A series of cooling meshes (M1, M2) may be separated by mixing manifolds (44), which may have film cooling holes (46) and/or coolant refresher holes (48).

Apparatus for electroplating particles of small dimension

DOEpatents

Yu, C.M.; Illige, J.D.

1980-09-19

The thickness, uniformity, and surface smoothness requirements for surface coatings of glass microspheres for use as targets for laser fusion research are critical. Because of thier minute size, the microspheres are difficult to manipulate and control in electroplating systems. The electroplating apparatus of the present invention addresses these problems by providing a cathode cell having a cell chamber, a cathode and an anode electrically isolated from each other and connected to an electrical power source. During the plating process, the cathode is controllably vibrated along with solution pulse to maintain the particles in random free motion so as to attain the desired properties.

Field alignment of bent-core smectic liquid crystals for analog optical phase modulation

NASA Astrophysics Data System (ADS)

Shen, Y.; Goodhew, L.; Shao, R.; Moran, M.; Korblova, E.; Walba, D. M.; Clark, N. A.; Maclennan, J. E.; Rudquist, P.

2015-05-01

A general method for aligning bent-core smectic liquid crystal materials is described. Alternating electric fields between interdigitated electrodes patterned on one cell surface create torques on the liquid crystal that result in uniform "bookshelf" orientation of the smectic layers. The aligned cell can then be driven in the conventional way by applying an electric field between all of the stripe electrodes connected together and a monolithic electrode on the other cell surface. Fast, analog, optical phase-only modulation is demonstrated in a device containing a polar, bent-core SmAPF material aligned using this technique.

Determination of vertical pressures on running wheels of freight trolleys of bridge type cranes

NASA Astrophysics Data System (ADS)

Goncharov, K. A.; Denisov, I. A.

2018-03-01

The problematic issues of the design of the bridge-type trolley crane, connected with ensuring uniform load distribution between the running wheels, are considered. The shortcomings of the existing methods of calculation of reference pressures are described. The results of the analytical calculation of the pressure of the support wheels are compared with the results of the numerical solution of this problem for various schemes of trolley supporting frames. Conclusions are given on the applicability of various methods for calculating vertical pressures, depending on the type of metal structures used in the trolley.