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1

Directed network modules  

NASA Astrophysics Data System (ADS)

A search technique locating network modules, i.e. internally densely connected groups of nodes in directed networks is introduced by extending the clique percolation method originally proposed for undirected networks. After giving a suitable definition for directed modules we investigate their percolation transition in the Erdos Rényi graph both analytically and numerically. We also analyse four real-world directed networks, including Google's own web-pages, an email network, a word association graph and the transcriptional regulatory network of the yeast Saccharomyces cerevisiae. The obtained directed modules are validated by additional information available for the nodes. We find that directed modules of real-world graphs inherently overlap and the investigated networks can be classified into two major groups in terms of the overlaps between the modules. Accordingly, in the word-association network and Google's web-pages, overlaps are likely to contain in-hubs, whereas the modules in the email and transcriptional regulatory network tend to overlap via out-hubs.

Palla, Gergely; Farkas, Illés J.; Pollner, Péter; Derényi, Imre; Vicsek, Tamás

2007-06-01

2

Tunable directly modulated fiber ring laser using a reflective semiconductor optical amplifier for WDM access networks.  

PubMed

We have proposed a stable, wideband, and tunable directly modulated fiber ring laser (TDMFRL) by using a reflective semiconductor optical amplifier (RSOA) and an optical tunable filter (OTF). For use in a bidirectional access network, the TDMFRL not only generates downstream data traffic but also serves as the wavelength-selecting injection light source for the Fabry-Pérot laser diode (FP-LD) located at the subscriber site. We experimentally demonstrated a bidirectional transmission at 1.25-Gb/s direct modulation over a 25-km single-mode fiber (SMF), thereby showing good performance in a wavelength division multiplexing (WDM) access network. PMID:20721147

Lin, Zih-Rong; Liu, Cheng-Kuang; Jhang, Yu-Jhu; Keiser, Gerd

2010-08-16

3

Extremely High Frequency Directly Modulated Lasers.  

National Technical Information Service (NTIS)

Several novel directly modulated semiconductor laser structures have been investigated to increase the bandwidth of direct modulation. Detailed theoretical models were developed and a high speed directly modulated laser was fabricated and tested. Corner r...

R. Spencer J. Greenberg L. Eastman

1997-01-01

4

MINE: Module Identification in Networks  

PubMed Central

Background Graphical models of network associations are useful for both visualizing and integrating multiple types of association data. Identifying modules, or groups of functionally related gene products, is an important challenge in analyzing biological networks. However, existing tools to identify modules are insufficient when applied to dense networks of experimentally derived interaction data. To address this problem, we have developed an agglomerative clustering method that is able to identify highly modular sets of gene products within highly interconnected molecular interaction networks. Results MINE outperforms MCODE, CFinder, NEMO, SPICi, and MCL in identifying non-exclusive, high modularity clusters when applied to the C. elegans protein-protein interaction network. The algorithm generally achieves superior geometric accuracy and modularity for annotated functional categories. In comparison with the most closely related algorithm, MCODE, the top clusters identified by MINE are consistently of higher density and MINE is less likely to designate overlapping modules as a single unit. MINE offers a high level of granularity with a small number of adjustable parameters, enabling users to fine-tune cluster results for input networks with differing topological properties. Conclusions MINE was created in response to the challenge of discovering high quality modules of gene products within highly interconnected biological networks. The algorithm allows a high degree of flexibility and user-customisation of results with few adjustable parameters. MINE outperforms several popular clustering algorithms in identifying modules with high modularity and obtains good overall recall and precision of functional annotations in protein-protein interaction networks from both S. cerevisiae and C. elegans.

2011-01-01

5

Single package directly modulated laser bidirectional optical subassembly using a modified mini-dual-in-line package for 10 Gbps passive optical networks  

NASA Astrophysics Data System (ADS)

A bidirectional optical subassembly comprised of a 2.5 Gbps distributed feedback (DFB) laser diode (LD) directly modulated laser transmitter and a 10 Gbps positive intrinsic negative photodiode receiver was developed for an optical network unit of a 10 Gbps passive optical network. Here, a low-cost mini-dual-in-line package was modified to contain whole components of a transmitter and receiver in a single space while satisfying the requirements of 10 Gbps micro-device package standards. The transmitter was fabricated to achieve high optical output power by placing a micro aspheric lens very close to the DFB LD and reducing the thermal resistance between an LD chip and heat sink to bring down the DFB LD chip temperature. As a result, the transmitter output power was 3.5 dB higher than a conventional transistor outline can BOSA due to a high optical coupling efficiency of more than 70% and a low thermal resistance for heat dissipation. The receiver sensitivity was -21 dBm at a bit error rate of 10-3 and the sensitivity penalty of the receiver due to signal crosstalk was less than 0.3 dB.

Lee, Jong Jin; Kim, Jongdeog; Lee, Seihyoung

2012-12-01

6

Potential theory for directed networks.  

PubMed

Uncovering factors underlying the network formation is a long-standing challenge for data mining and network analysis. In particular, the microscopic organizing principles of directed networks are less understood than those of undirected networks. This article proposes a hypothesis named potential theory, which assumes that every directed link corresponds to a decrease of a unit potential and subgraphs with definable potential values for all nodes are preferred. Combining the potential theory with the clustering and homophily mechanisms, it is deduced that the Bi-fan structure consisting of 4 nodes and 4 directed links is the most favored local structure in directed networks. Our hypothesis receives strongly positive supports from extensive experiments on 15 directed networks drawn from disparate fields, as indicated by the most accurate and robust performance of Bi-fan predictor within the link prediction framework. In summary, our main contribution is twofold: (i) We propose a new mechanism for the local organization of directed networks; (ii) We design the corresponding link prediction algorithm, which can not only testify our hypothesis, but also find out direct applications in missing link prediction and friendship recommendation. PMID:23408979

Zhang, Qian-Ming; Lü, Linyuan; Wang, Wen-Qiang; Zhou, Tao

2013-02-11

7

Sampling properties of directed networks  

NASA Astrophysics Data System (ADS)

For many real-world networks only a small “sampled” version of the original network may be investigated; those results are then used to draw conclusions about the actual system. Variants of breadth-first search (BFS) sampling, which are based on epidemic processes, are widely used. Although it is well established that BFS sampling fails, in most cases, to capture the IN component(s) of directed networks, a description of the effects of BFS sampling on other topological properties is all but absent from the literature. To systematically study the effects of sampling biases on directed networks, we compare BFS sampling to random sampling on complete large-scale directed networks. We present new results and a thorough analysis of the topological properties of seven complete directed networks (prior to sampling), including three versions of Wikipedia, three different sources of sampled World Wide Web data, and an Internet-based social network. We detail the differences that sampling method and coverage can make to the structural properties of sampled versions of these seven networks. Most notably, we find that sampling method and coverage affect both the bow-tie structure and the number and structure of strongly connected components in sampled networks. In addition, at a low sampling coverage (i.e., less than 40%), the values of average degree, variance of out-degree, degree autocorrelation, and link reciprocity are overestimated by 30% or more in BFS-sampled networks and only attain values within 10% of the corresponding values in the complete networks when sampling coverage is in excess of 65%. These results may cause us to rethink what we know about the structure, function, and evolution of real-world directed networks.

Son, S.-W.; Christensen, C.; Bizhani, G.; Foster, D. V.; Grassberger, P.; Paczuski, M.

2012-10-01

8

Is My Network Module Preserved and Reproducible?  

PubMed Central

In many applications, one is interested in determining which of the properties of a network module change across conditions. For example, to validate the existence of a module, it is desirable to show that it is reproducible (or preserved) in an independent test network. Here we study several types of network preservation statistics that do not require a module assignment in the test network. We distinguish network preservation statistics by the type of the underlying network. Some preservation statistics are defined for a general network (defined by an adjacency matrix) while others are only defined for a correlation network (constructed on the basis of pairwise correlations between numeric variables). Our applications show that the correlation structure facilitates the definition of particularly powerful module preservation statistics. We illustrate that evaluating module preservation is in general different from evaluating cluster preservation. We find that it is advantageous to aggregate multiple preservation statistics into summary preservation statistics. We illustrate the use of these methods in six gene co-expression network applications including 1) preservation of cholesterol biosynthesis pathway in mouse tissues, 2) comparison of human and chimpanzee brain networks, 3) preservation of selected KEGG pathways between human and chimpanzee brain networks, 4) sex differences in human cortical networks, 5) sex differences in mouse liver networks. While we find no evidence for sex specific modules in human cortical networks, we find that several human cortical modules are less preserved in chimpanzees. In particular, apoptosis genes are differentially co-expressed between humans and chimpanzees. Our simulation studies and applications show that module preservation statistics are useful for studying differences between the modular structure of networks. Data, R software and accompanying tutorials can be downloaded from the following webpage: http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/ModulePreservation.

Langfelder, Peter; Luo, Rui; Oldham, Michael C.; Horvath, Steve

2011-01-01

9

Distributed Pulse Forming Network for Magnetic Modulator.  

National Technical Information Service (NTIS)

A pulse forming network with distributed inductance and capacitance is disclosed for use in a magnetic modulator. The magnetic modulator has a magnetic core with a primary winding and a secondary winding around it. The pulse forming network includes an in...

M. Weiner J. L. Carter R. J. Youmans

1984-01-01

10

Dense module enumeration in biological networks  

NASA Astrophysics Data System (ADS)

Analysis of large networks is a central topic in various research fields including biology, sociology, and web mining. Detection of dense modules (a.k.a. clusters) is an important step to analyze the networks. Though numerous methods have been proposed to this aim, they often lack mathematical rigorousness. Namely, there is no guarantee that all dense modules are detected. Here, we present a novel reverse-search-based method for enumerating all dense modules. Furthermore, constraints from additional data sources such as gene expression profiles or customer profiles can be integrated, so that we can systematically detect dense modules with interesting profiles. We report successful applications in human protein interaction network analyses.

Tsuda, Koji; Georgii, Elisabeth

2009-12-01

11

Directed module detection in a large-scale expression compendium.  

PubMed

Public online microarray databases contain tremendous amounts of expression data. Mining these data sources can provide a wealth of information on the underlying transcriptional networks. In this chapter, we illustrate how the web services COLOMBOS and DISTILLER can be used to identify condition-dependent coexpression modules by exploring compendia of public expression data. COLOMBOS is designed for user-specified query-driven analysis, whereas DISTILLER generates a global regulatory network overview. The user is guided through both web services by means of a case study in which condition-dependent coexpression modules comprising a gene of interest (i.e., "directed") are identified. PMID:22144152

Fu, Qiang; Lemmens, Karen; Sanchez-Rodriguez, Aminael; Thijs, Inge M; Meysman, Pieter; Sun, Hong; Fierro, Ana Carolina; Engelen, Kristof; Marchal, Kathleen

2012-01-01

12

Optimal pinning synchronization on directed complex network  

NASA Astrophysics Data System (ADS)

In this paper, pinning synchronization on directed network was considered. By analyzing, some general synchronization criteria on directed network were established. And then, we verified it on directed globally coupled network, directed scale-free network, and directed small-world network, respectively. The pinning nodes were selected, respectively, according to order of in-degrees and out-degrees. Through comparing and analyzing simulations, the optimal pinning scheme was found, and a practical principle was induced finally.

Nian, Fuzhong; Wang, Xingyuan

2011-12-01

13

Modulation for emergent networks: serotonin and dopamine.  

PubMed

In autonomous learning, value-sensitive experiences can improve the efficiency of learning. A learning network needs be motivated so that the limited computational resources and the limited lifetime are devoted to events that are of high value for the agent to compete in its environment. The neuromodulatory system of the brain is mainly responsible for developing such a motivation system. Although reinforcement learning has been extensively studied, many existing models are symbolic whose internal nodes or modules have preset meanings. Neural networks have been used to automatically generate internal emergent representations. However, modeling an emergent motivational system for neural networks is still a great challenge. By emergent, we mean that the internal representations emerge autonomously through interactions with the external environments. This work proposes a generic emergent modulatory system for emergent networks, which includes two subsystems - the serotonin system and the dopamine system. The former signals a large class of stimuli that are intrinsically aversive (e.g., stress or pain). The latter signals a large class of stimuli that are intrinsically appetitive (e.g., pleasure or sweet). We experimented with this motivational system for two settings. The first is a visual recognition setting to investigate how such a system can learn through interactions with a teacher, who does not directly give answers, but only punishments and rewards. The second is a setting for wandering in the presence of a friend and a foe. PMID:23294763

Weng, Juyang; Paslaski, Stephen; Daly, James; VanDam, Courtland; Brown, Jacob

2012-12-08

14

DIRECT PERFORMANCE COMPARISON OF PV MODULES  

Microsoft Academic Search

The real electrical parameters rarely correspond to the nominal electrical parameters supplied by the manufacturers. Moreover initial degradation occurs in almost all types of modules during the first period of exposure. Project planners and installers are increasingly asked to provide production and behaviour estimates for the systems they install. Therefore a direct performance comparison of PV modules is needed. The

D. Chianese; G. Friesen; P. Pasinelli; I. Pola; A. Realini; N. Cereghetti; A. Bernasconi

15

Direct modulation of a tuneable slotted Fabry-Pérot laser with adaptive modulation OFDM.  

PubMed

Next generation optical access networks will require low cost lasers in conjunction with network flexibility and higher data rates. This work presents the direct modulation of a low cost tuneable slotted Fabry-Pérot laser (tuneable over 14 nm) with AM-OFDM. Characteristics of this dual section laser are presented and transmission of 10 Gb/s over 50 km is achieved with this device. PMID:23262880

Browning, C; Shi, K; Anandarajah, P M; Phelan, R; Barry, L P

2012-12-10

16

Coarse graining for synchronization in directed networks.  

PubMed

Coarse-graining model is a promising way to analyze and visualize large-scale networks. The coarse-grained networks are required to preserve statistical properties as well as the dynamic behaviors of the initial networks. Some methods have been proposed and found effective in undirected networks, while the study on coarse-graining directed networks lacks of consideration. In this paper we proposed a path-based coarse-graining (PCG) method to coarse grain the directed networks. Performing the linear stability analysis of synchronization and numerical simulation of the Kuramoto model on four kinds of directed networks, including tree networks and variants of Barabási-Albert networks, Watts-Strogatz networks, and Erdös-Rényi networks, we find our method can effectively preserve the network synchronizability. PMID:21728621

Zeng, An; Lü, Linyuan

2011-05-25

17

Coarse graining for synchronization in directed networks  

NASA Astrophysics Data System (ADS)

Coarse-graining model is a promising way to analyze and visualize large-scale networks. The coarse-grained networks are required to preserve statistical properties as well as the dynamic behaviors of the initial networks. Some methods have been proposed and found effective in undirected networks, while the study on coarse-graining directed networks lacks of consideration. In this paper we proposed a path-based coarse-graining (PCG) method to coarse grain the directed networks. Performing the linear stability analysis of synchronization and numerical simulation of the Kuramoto model on four kinds of directed networks, including tree networks and variants of Barabási-Albert networks, Watts-Strogatz networks, and Erdös-Rényi networks, we find our method can effectively preserve the network synchronizability.

Zeng, An; Lü, Linyuan

2011-05-01

18

Chirp-managed directly modulated laser (CML)  

Microsoft Academic Search

We demonstrate a new highly dispersion tolerant modulation format using a chirp-managed directly modulated laser (CML) for uncompensated 10-Gb\\/s transmission over >200 km at 1.55 ?m. The CML consists of a distributed feedback (DFB) laser followed by an optical filter. We show that the combination of adiabatic chirp from the DFB and filter edge response produces high extinction ratio pulses

Yasuhiro Matsui; Daniel Mahgerefteh; Xueyan Zheng; Charlie Liao; Zhencan Frank Fan; Kevin McCallion; Parviz Tayebati

2006-01-01

19

A direct density modulation cathode in magnetron  

NASA Astrophysics Data System (ADS)

A direct Density Modulation Cathode (DMC) in magnetron is proposed in this paper. By removing the velocity modulation process, electron spokes corresponding to the dominant operating mode can be quickly formed when the DMC is used. Based on theoretical analysis, particle-in-cell simulations and experimental investigations are carried out for demonstration. The final results show that compared with conventional solid cathode and transparent cathode, the DMC can increase 68% and even 146% of relative microwave widths, respectively.

Li, Wei; Zhang, Jun; Liu, Yong-gui; Yang, Han-wu; Shu, Ting

2013-09-01

20

Caffeine Modulates Attention Network Function.  

National Technical Information Service (NTIS)

The present work investigated the effects of caffeine (0 mg, 100 mg, 200 mg, 400 mg) on a flanker task designed to test Posner's three visual attention network functions: alerting, orienting, and executive control Posner, M. I. (2004). Cognitive Neuroscie...

C. R. Mahoney H. A. Tyalor H. R. Lieberman T. T. Brunye

2010-01-01

21

Optimal design of reverse osmosis module networks  

SciTech Connect

The structure of individual reverse osmosis modules, the configuration of the module network, and the operating conditions were optimized for seawater and brackish water desalination. The system model included simple mathematical equations to predict the performance of the reverse osmosis modules. The optimization problem was formulated as a constrained multivariable nonlinear optimization. The objective function was the annual profit for the system, consisting of the profit obtained from the permeate, capital cost for the process units, and operating costs associated with energy consumption and maintenance. Optimization of several dual-stage reverse osmosis systems were investigated and compared. It was found that optimal network designs are the ones that produce the most permeate. It may be possible to achieve economic improvements by refining current membrane module designs and their operating pressures.

Maskan, F.; Wiley, D.E.; Johnston, L.P.M.; Clements, D.J.

2000-05-01

22

Optimization of directional antenna network topology in Airborne Networks  

Microsoft Academic Search

Future IP-based Airborne Networks, important components in net-centric military communications, are envisioned to consist of a persistent backbone core network and dynamic tactical edge networks. The backbone would consist of quasi-stable platforms equipped with multiple high-capacity directional wireless links. The tactical edge networks would consist of highly dynamic platforms such as fighter jets equipped with omni-directional wireless links, and these

G. Hadynski; S. B. Lee; G. Rajappan; R. Sundaram; X. Wang; F. Zhou

2010-01-01

23

Caffeine Modulates Attention Network Function  

ERIC Educational Resources Information Center

|The present work investigated the effects of caffeine (0 mg, 100 mg, 200 mg, 400 mg) on a flanker task designed to test Posner's three visual attention network functions: alerting, orienting, and executive control [Posner, M. I. (2004). "Cognitive neuroscience of attention". New York, NY: Guilford Press]. In a placebo-controlled, double-blind…

Brunye, Tad T.; Mahoney, Caroline R.; Lieberman, Harris R.; Taylor, Holly A.

2010-01-01

24

Caffeine modulates attention network function.  

PubMed

The present work investigated the effects of caffeine (0mg, 100mg, 200mg, 400mg) on a flanker task designed to test Posner's three visual attention network functions: alerting, orienting, and executive control [Posner, M. I. (2004). Cognitive neuroscience of attention. New York, NY: Guilford Press]. In a placebo-controlled, double-blind study using a repeated-measures design, we found that the effects of caffeine on visual attention vary as a function of dose and the attention network under examination. Caffeine improved alerting and executive control function in a dose-response manner, asymptoting at 200mg; this effect is congruent with caffeine's adenosine-mediated effects on dopamine-rich areas of brain, and the involvement of these areas in alerting and the executive control of visual attention. Higher doses of caffeine also led to a marginally less efficient allocation of visual attention towards cued regions during task performance (i.e., orienting). Taken together, results of this study demonstrate that caffeine has differential effects on visual attention networks as a function of dose, and such effects have implications for hypothesized interactions of caffeine, adenosine and dopamine in brain areas mediating visual attention. PMID:19733954

Brunyé, Tad T; Mahoney, Caroline R; Lieberman, Harris R; Taylor, Holly A

2009-09-05

25

Network management, status and directions  

SciTech Connect

It has been said that the ``network is the system``. This implies providing levels of service, reliability, predictability and availability that are commensurate with or better than those that individual computers provide today. To provide this requires integrated network management for interconnected networks of heterogeneous devices covering both the local campus and across the world and spanning many administrative domains. This talk will review the status of existing tools to address management for networks. It draws on experience from both within and outside the HEP community.

Cottrell, R.L.A.; Streater, T.C.

1992-09-01

26

Network management, status and directions  

SciTech Connect

It has been said that the network is the system''. This implies providing levels of service, reliability, predictability and availability that are commensurate with or better than those that individual computers provide today. To provide this requires integrated network management for interconnected networks of heterogeneous devices covering both the local campus and across the world and spanning many administrative domains. This talk will review the status of existing tools to address management for networks. It draws on experience from both within and outside the HEP community.

Cottrell, R.L.A.; Streater, T.C.

1992-09-01

27

Traffic predictor for network-accessible information modules  

US Patent & Trademark Office Database

Methods, apparatuses and systems directed to predicting the performance of an information package or module presented on a network addressable resource, such as a web page. A particular implementation relies on regression models that utilize statistical measures of user interest in terms, concepts and other subject matter as revealed in on-line search activity of a pool of users. A model receives as inputs a plurality of attribute values corresponding to an information package or module (including one or more statistical measures of interest) and outputs an estimated click-thru rate.

Gamble; Nathan E. (Redwood Shores, CA)

2011-07-26

28

MoNetFamily: a web server to infer homologous modules and module-module interaction networks in vertebrates  

PubMed Central

A module is a fundamental unit forming with highly connected proteins and performs a certain kind of biological functions. Modules and module–module interaction (MMI) network are essential for understanding cellular processes and functions. The MoNetFamily web server can identify the modules, homologous modules (called module family) and MMI networks across multiple species for the query protein(s). This server first finds module candidates of the query by using BLASTP to search the module template database (1785 experimental and 1252 structural templates). MoNetFamily then infers the homologous modules of the selected module candidate using protein–protein interaction (PPI) families. According to homologous modules and PPIs, we statistically calculated MMIs and MMI networks across multiple species. For each module candidate, MoNetFamily identifies its neighboring modules and their MMIs in module networks of Homo sapiens, Mus musculus and Danio rerio. Finally, MoNetFamily shows the conserved proteins, PPI profiles and functional annotations of the module family. Our results indicate that the server can be useful for MMI network (e.g. 1818 modules and 9678 MMIs in H. sapiens) visualizations and query annotations using module families and neighboring modules. We believe that the server is able to provide valuable insights to determine homologous modules and MMI networks across multiple species for studying module evolution and cellular processes. The MoNetFamily sever is available at http://monetfamily.life.nctu.edu.tw.

Lin, Chun-Yu; Lin, Yi-Wei; Yu, Shang-Wen; Lo, Yu-Shu; Yang, Jinn-Moon

2012-01-01

29

Parsimonious Module Inference in Large Networks  

NASA Astrophysics Data System (ADS)

We investigate the detectability of modules in large networks when the number of modules is not known in advance. We employ the minimum description length principle which seeks to minimize the total amount of information required to describe the network, and avoid overfitting. According to this criterion, we obtain general bounds on the detectability of any prescribed block structure, given the number of nodes and edges in the sampled network. We also obtain that the maximum number of detectable blocks scales as N, where N is the number of nodes in the network, for a fixed average degree ?k?. We also show that the simplicity of the minimum description length approach yields an efficient multilevel Monte Carlo inference algorithm with a complexity of O(?Nlog?N), if the number of blocks is unknown, and O(?N) if it is known, where ? is the mixing time of the Markov chain. We illustrate the application of the method on a large network of actors and films with over 106 edges, and a dissortative, bipartite block structure.

Peixoto, Tiago P.

2013-04-01

30

Core organization of directed complex networks  

NASA Astrophysics Data System (ADS)

The recursive removal of leaves (dead end vertices) and their neighbors from an undirected network results, when this pruning algorithm stops, in a so-called core of the network. This specific subgraph should be distinguished from k-cores, which are principally different subgraphs in networks. If the vertex mean degree of a network is sufficiently large, the core is a giant cluster containing a finite fraction of vertices. We find that generalization of this pruning algorithm to directed networks provides a significantly more complex picture of cores. By implementing a rate equation approach to this pruning procedure for directed uncorrelated networks, we identify a set of cores progressively embedded into each other in a network and describe their birth points and structure.

Azimi-Tafreshi, N.; Dorogovtsev, S. N.; Mendes, J. F. F.

2013-03-01

31

Edge direction and the structure of networks  

PubMed Central

Directed networks are ubiquitous and are necessary to represent complex systems with asymmetric interactions—from food webs to the World Wide Web. Despite the importance of edge direction for detecting local and community structure, it has been disregarded in studying a basic type of global diversity in networks: the tendency of nodes with similar numbers of edges to connect. This tendency, called assortativity, affects crucial structural and dynamic properties of real-world networks, such as error tolerance or epidemic spreading. Here we demonstrate that edge direction has profound effects on assortativity. We define a set of four directed assortativity measures and assign statistical significance by comparison to randomized networks. We apply these measures to three network classes—online/social networks, food webs, and word-adjacency networks. Our measures (i) reveal patterns common to each class, (ii) separate networks that have been previously classified together, and (iii) expose limitations of several existing theoretical models. We reject the standard classification of directed networks as purely assortative or disassortative. Many display a class-specific mixture, likely reflecting functional or historical constraints, contingencies, and forces guiding the system’s evolution.

Foster, Jacob G.; Foster, David V.; Grassberger, Peter; Paczuski, Maya

2010-01-01

32

Edge direction and the structure of networks.  

PubMed

Directed networks are ubiquitous and are necessary to represent complex systems with asymmetric interactions--from food webs to the World Wide Web. Despite the importance of edge direction for detecting local and community structure, it has been disregarded in studying a basic type of global diversity in networks: the tendency of nodes with similar numbers of edges to connect. This tendency, called assortativity, affects crucial structural and dynamic properties of real-world networks, such as error tolerance or epidemic spreading. Here we demonstrate that edge direction has profound effects on assortativity. We define a set of four directed assortativity measures and assign statistical significance by comparison to randomized networks. We apply these measures to three network classes--online/social networks, food webs, and word-adjacency networks. Our measures (i) reveal patterns common to each class, (ii) separate networks that have been previously classified together, and (iii) expose limitations of several existing theoretical models. We reject the standard classification of directed networks as purely assortative or disassortative. Many display a class-specific mixture, likely reflecting functional or historical constraints, contingencies, and forces guiding the system's evolution. PMID:20505119

Foster, Jacob G; Foster, David V; Grassberger, Peter; Paczuski, Maya

2010-05-26

33

Complex propagation on directed small world networks  

NASA Astrophysics Data System (ADS)

The effect of directionality on the information propagation in a contagion model with complex propagation, i.e., that takes into account the need for simultaneous exposure to multiple activation sources, is studied. While it is known that complex propagation is blocked with increasing network randomness, here it is shown that network directionality affects such a result, leading to several different behaviors depending on the preservation of the in-degree or out-degree. The critical points for the occurrence of complex propagation in 1D directed small world networks are determined. It is shown that these points only depend on the number of outgoing links.

Gandica, Yérali; Bonalde, Ismardo; Cabrera, Juan Luis

2010-10-01

34

Organization of signal flow in directed networks  

NASA Astrophysics Data System (ADS)

Confining an answer to the question of whether and how the coherent operation of network elements is determined by the network structure is the topic of our work. We map the structure of signal flow in directed networks by analysing the degree of edge convergence and the overlap between the in- and output sets of an edge. Definitions of convergence degree and overlap are based on the shortest paths, thus they encapsulate global network properties. Using the defining notions of convergence degree and overlapping set we clarify the meaning of network causality and demonstrate the crucial role of chordless circles. In real-world networks the flow representation distinguishes nodes according to their signal transmitting, processing and control properties. The analysis of real-world networks in terms of flow representation was in accordance with the known functional properties of the network nodes. It is shown that nodes with different signal processing, transmitting and control properties are randomly connected at the global scale, while local connectivity patterns depart from randomness. The grouping of network nodes according to their signal flow properties was unrelated to the network's community structure. We present evidence that the signal flow properties of small-world-like, real-world networks cannot be reconstructed by algorithms used to generate small-world networks. Convergence degree values were calculated for regular oriented trees, and the probability density function for networks grown with the preferential attachment mechanism. For Erdos-Rényi graphs we calculated the probability density function of both convergence degrees and overlaps.

Bányai, M.; Négyessy, L.; Bazsó, F.

2011-06-01

35

Hierarchy in directed random networks  

NASA Astrophysics Data System (ADS)

In recent years, the theory and application of complex networks have been quickly developing in a markable way due to the increasing amount of data from real systems and the fruitful application of powerful methods used in statistical physics. Many important characteristics of social or biological systems can be described by the study of their underlying structure of interactions. Hierarchy is one of these features that can be formulated in the language of networks. In this paper we present some (qualitative) analytic results on the hierarchical properties of random network models with zero correlations and also investigate, mainly numerically, the effects of different types of correlations. The behavior of the hierarchy is different in the absence and the presence of giant components. We show that the hierarchical structure can be drastically different if there are one-point correlations in the network. We also show numerical results suggesting that the hierarchy does not change monotonically with the correlations and there is an optimal level of nonzero correlations maximizing the level of hierarchy.

Mones, Enys

2013-02-01

36

Weighted and Directed Network on Traveling Patterns  

Microsoft Academic Search

The importance of weighted and directed networks is brought into discussion. On this study we analyze the arrivals of international\\u000a tourism (edges) over 206 countries and territories (nodes) around the world, on the year 2004. Using tools from network theory\\u000a we characterize the topology and weighted properties of the resulting network. International tourist arrivals are analyzed\\u000a over in strength and

J. I. L. Miguens; J. F. F. Mendes

37

Impact of hierarchical modular structure on ranking of individual nodes in directed networks  

NASA Astrophysics Data System (ADS)

Many systems, ranging from biological and engineering systems to social systems, can be modeled as directed networks, with links representing directed interaction between two nodes. To assess the importance of a node in a directed network, various centrality measures based on different criteria have been proposed. However, calculating the centrality of a node is often difficult because of the overwhelming size of the network or because the information held about the network is incomplete. Thus, developing an approximation method for estimating centrality measures is needed. In this study, we focus on modular networks; many real-world networks are composed of modules, where connection is dense within a module and sparse across different modules. We show that ranking-type centrality measures, including the PageRank, can be efficiently estimated once the modular structure of a network is extracted. We develop an analytical method to evaluate the centrality of nodes by combining the local property (i.e. indegree and outdegree of nodes) and the global property (i.e. centrality of modules). The proposed method is corroborated by real data. Our results provide a linkage between the ranking-type centrality values of modules and those of individual nodes. They also reveal the hierarchical structure of networks in the sense of subordination (not nestedness) laid out by connectivity among modules of different relative importance. The present study raises a novel motive for identifying modules in networks.

Masuda, Naoki; Kawamura, Yoji; Kori, Hiroshi

2009-11-01

38

Mutual exclusivity analysis identifies oncogenic network modules  

PubMed Central

Although individual tumors of the same clinical type have surprisingly diverse genomic alterations, these events tend to occur in a limited number of pathways, and alterations that affect the same pathway tend to not co-occur in the same patient. While pathway analysis has been a powerful tool in cancer genomics, our knowledge of oncogenic pathway modules is incomplete. To systematically identify such modules, we have developed a novel method, Mutual Exclusivity Modules in cancer (MEMo). The method uses correlation analysis and statistical tests to identify network modules by three criteria: (1) Member genes are recurrently altered across a set of tumor samples; (2) member genes are known to or are likely to participate in the same biological process; and (3) alteration events within the modules are mutually exclusive. Applied to data from the Cancer Genome Atlas (TCGA), the method identifies the principal known altered modules in glioblastoma (GBM) and highlights the striking mutual exclusivity of genomic alterations in the PI(3)K, p53, and Rb pathways. In serous ovarian cancer, we make the novel observation that inactivation of BRCA1 and BRCA2 is mutually exclusive of amplification of CCNE1 and inactivation of RB1, suggesting distinct alternative causes of genomic instability in this cancer type; and, we identify RBBP8 as a candidate oncogene involved in Rb-mediated cell cycle control. When applied to any cancer genomics data set, the algorithm can nominate oncogenic alterations that have a particularly strong selective effect and may also be useful in the design of therapeutic combinations in cases where mutual exclusivity reflects synthetic lethality.

Ciriello, Giovanni; Cerami, Ethan; Sander, Chris; Schultz, Nikolaus

2012-01-01

39

Predicting network instabilities in mobile directional wireless networks  

NASA Astrophysics Data System (ADS)

We have been investigating the dynamics of molecular systems as analogies for directional wireless networks. This has provided significant insight into reconfigurations of mobile wireless networks using directional point-to-point links (e.g. free-space optics or radio frequency). In this effort, we conceptualize the network as a giant molecule comprised of atoms that exert forces (attraction and repulsion) that stretch and relax the corresponding links. We monitor second-order variations of a potential energy function to gain an improved understanding of the large dimensionality of the optimized reconfiguration for network topology management. Ultimately, we envision this approach will allow for the prediction of two distinct events: 1) localized link failures and 2) catastrophic network events such as a partition. Our results show the detection of localized link failures and the availability for resource allocation more than one minute ahead of the failure (due to known events such as range and antenna blockage) with <80% accuracy.

Coleman, David M.; Milner, Stuart D.; Davis, Christopher C.

2013-09-01

40

An effective method for network module extraction from microarray data  

PubMed Central

Background The development of high-throughput Microarray technologies has provided various opportunities to systematically characterize diverse types of computational biological networks. Co-expression network have become popular in the analysis of microarray data, such as for detecting functional gene modules. Results This paper presents a method to build a co-expression network (CEN) and to detect network modules from the built network. We use an effective gene expression similarity measure called NMRS (Normalized mean residue similarity) to construct the CEN. We have tested our method on five publicly available benchmark microarray datasets. The network modules extracted by our algorithm have been biologically validated in terms of Q value and p value. Conclusions Our results show that the technique is capable of detecting biologically significant network modules from the co-expression network. Biologist can use this technique to find groups of genes with similar functionality based on their expression information.

2012-01-01

41

Directed diffusion for wireless sensor networking  

Microsoft Academic Search

Advances in processor, memory, and radio technology will enable small and cheap nodes capable of sensing, communication, and computation. Networks of such nodes can coordinate to perform distributed sensing of environmental phenomena. In this paper, we explore the directed-diffusion paradigm for such coordination. Directed diffusion is data-centric in that all communication is for named data. All nodes in a directed-diffusion-based

Chalermek Intanagonwiwat; Ramesh Govindan; Deborah Estrin; John S. Heidemann; Fabio Silva

2003-01-01

42

An Instructional Module for Protecting Privacy on Social Networking Sites  

Microsoft Academic Search

Many college students are misled into making uninformed choices about what to disclose online and avoid taking the necessary precautions to protect their privacy on social networking sites. This study was aimed at developing and evaluating a multimedia, Web-based, instructional module to educate college students about protecting privacy on social networking sites. The module covered privacy, threats to one's privacy,

Rachael L. M. Inake

2009-01-01

43

A generalized maximum neural network for the module orientation problem  

Microsoft Academic Search

Several neuron models and artificial neural networks have been intensively studied since McCulloch and Pitts proposed the simplified neuron model in 1943. In this paper a generalized maximum neural network for parallel computing is introduced to solve the module orientation problem which belongs to the class of NP-complete problems. The goal of the module orientation problem in VLSI circuits or

KUO CHUN LEE; YOSHIYASU TAKEFUJI

1992-01-01

44

Gaussian Networks for Direct Adaptive Control  

Microsoft Academic Search

A direct adaptive tracking control architecture is proposed and evaluated for a class of continuous-time nonlinear dynamic systems for which an explicit linear parameterization of the uncertainty in the dynamics is either unknown or impossible. The architecture employs a network of gausian radial basis functions to adaptively compensate for the plant nonlinearities. Under mild assumptions about the degree of smoothness

Robert M. Sanner; Jean-Jacques E. Slotine

1991-01-01

45

Functional modules by relating protein interaction networks and gene expression  

Microsoft Academic Search

Genes and proteins are organized on the basis of their particular mutual relations or according to their interactions in cellular and genetic networks. These include metabolic or signaling pathways and protein interaction, regulatory or co-expression net- works. Integrating the information from the different types of networks may lead to the notion of a func- tional network and functional modules. To

Sabine Tornow; H. W. Mewes

2003-01-01

46

Identification of biochemical network modules based on shortest retroactive distances.  

PubMed

Modularity analysis offers a route to better understand the organization of cellular biochemical networks as well as to derive practically useful, simplified models of these complex systems. While there is general agreement regarding the qualitative properties of a biochemical module, there is no clear consensus on the quantitative criteria that may be used to systematically derive these modules. In this work, we investigate cyclical interactions as the defining characteristic of a biochemical module. We utilize a round trip distance metric, termed Shortest Retroactive Distance (ShReD), to characterize the retroactive connectivity between any two reactions in a biochemical network and to group together network components that mutually influence each other. We evaluate the metric on two types of networks that feature feedback interactions: (i) epidermal growth factor receptor (EGFR) signaling and (ii) liver metabolism supporting drug transformation. For both networks, the ShReD partitions found hierarchically arranged modules that confirm biological intuition. In addition, the partitions also revealed modules that are less intuitive. In particular, ShReD-based partition of the metabolic network identified a 'redox' module that couples reactions of glucose, pyruvate, lipid and drug metabolism through shared production and consumption of NADPH. Our results suggest that retroactive interactions arising from feedback loops and metabolic cycles significantly contribute to the modularity of biochemical networks. For metabolic networks, cofactors play an important role as allosteric effectors that mediate the retroactive interactions. PMID:22102800

Sridharan, Gautham Vivek; Hassoun, Soha; Lee, Kyongbum

2011-11-10

47

Identify Dynamic Network Modules with Temporal and Spatial Constraints  

SciTech Connect

Despite the rapid accumulation of systems-level biological data, understanding the dynamic nature of cellular activity remains a difficult task. The reason is that most biological data are static, or only correspond to snapshots of cellular activity. In this study, we explicitly attempt to detangle the temporal complexity of biological networks by using compilations of time-series gene expression profiling data.We define a dynamic network module to be a set of proteins satisfying two conditions: (1) they form a connected component in the protein-protein interaction (PPI) network; and (2) their expression profiles form certain structures in the temporal domain. We develop the first efficient mining algorithm to discover dynamic modules in a temporal network, as well as frequently occurring dynamic modules across many temporal networks. Using yeast as a model system, we demonstrate that the majority of the identified dynamic modules are functionally homogeneous. Additionally, many of them provide insight into the sequential ordering of molecular events in cellular systems. We further demonstrate that identifying frequent dynamic network modules can significantly increase the signal to noise separation, despite the fact that most dynamic network modules are highly condition-specific. Finally, we note that the applicability of our algorithm is not limited to the study of PPI systems, instead it is generally applicable to the combination of any type of network and time-series data.

Jin, R; McCallen, S; Liu, C; Almaas, E; Zhou, X J

2007-09-24

48

Exploring the randomness of directed acyclic networks  

NASA Astrophysics Data System (ADS)

The feed-forward relationship naturally observed in time-dependent processes and in a diverse number of real systems—such as some food webs and electronic and neural wiring—can be described in terms of the so-called directed acyclic graphs (DAGs). An important ingredient of the analysis of such networks is a proper comparison of their observed architecture against an ensemble of randomized graphs, thereby quantifying the randomness of the real systems with respect to suitable null models. This approximation is particularly relevant when the finite size and/or large connectivity of real systems make inadequate a comparison with the predictions obtained from the so-called configuration model. In this paper we analyze two methods of DAG randomization as defined by the desired combination of two topological invariants (directed degree sequence and component distributions) aimed to be preserved. A highly ordered DAG, called snake graph, and an Erdös-Rényi DAG were used to validate the performance of the algorithms. Finally, three real case studies, namely, the C. elegans cell lineage network, a Ph.D. student-supervisor network, and the Milgram’s citation network, were analyzed using each randomization method. Results show how the interpretation of degree-degree relations in DAGs with respect to their randomized ensembles depends on the topological invariants imposed.

Gońi, Joaquín; Corominas-Murtra, Bernat; Solé, Ricard V.; Rodríguez-Caso, Carlos

2010-12-01

49

Serotonin modulation of cortical neurons and networks  

PubMed Central

The serotonergic pathways originating in the dorsal and median raphe nuclei (DR and MnR, respectively) are critically involved in cortical function. Serotonin (5-HT), acting on postsynaptic and presynaptic receptors, is involved in cognition, mood, impulse control and motor functions by (1) modulating the activity of different neuronal types, and (2) varying the release of other neurotransmitters, such as glutamate, GABA, acetylcholine and dopamine. Also, 5-HT seems to play an important role in cortical development. Of all cortical regions, the frontal lobe is the area most enriched in serotonergic axons and 5-HT receptors. 5-HT and selective receptor agonists modulate the excitability of cortical neurons and their discharge rate through the activation of several receptor subtypes, of which the 5-HT1A, 5-HT1B, 5-HT2A, and 5-HT3 subtypes play a major role. Little is known, however, on the role of other excitatory receptors moderately expressed in cortical areas, such as 5-HT2C, 5-HT4, 5-HT6, and 5-HT7. In vitro and in vivo studies suggest that 5-HT1A and 5-HT2A receptors are key players and exert opposite effects on the activity of pyramidal neurons in the medial prefrontal cortex (mPFC). The activation of 5-HT1A receptors in mPFC hyperpolarizes pyramidal neurons whereas that of 5-HT2A receptors results in neuronal depolarization, reduction of the afterhyperpolarization and increase of excitatory postsynaptic currents (EPSCs) and of discharge rate. 5-HT can also stimulate excitatory (5-HT2A and 5-HT3) and inhibitory (5-HT1A) receptors in GABA interneurons to modulate synaptic GABA inputs onto pyramidal neurons. Likewise, the pharmacological manipulation of various 5-HT receptors alters oscillatory activity in PFC, suggesting that 5-HT is also involved in the control of cortical network activity. A better understanding of the actions of 5-HT in PFC may help to develop treatments for mood and cognitive disorders associated with an abnormal function of the frontal lobe.

Celada, Pau; Puig, M. Victoria; Artigas, Francesc

2013-01-01

50

Decreased Default Mode Neural Network Modulation with Age in Schizophrenia  

PubMed Central

Objective Previous studies have shown that patients with schizophrenia have less modulation of the task-positive and default mode networks of the brain during novelty detection. To date, the relationship between network modulation and age has not been assessed in patients with a long duration of illness. Method Seventeen patients with schizophrenia with a minimum disorder duration of 15 years and 28 age-matched healthy controls from the Mind Clinical Imaging Consortium database completed the auditory oddball discrimination task. Independent component analysis identified temporally cohesive but spatially distributed neural networks. This study examined whether age was associated with modulation of executive control and default mode networks during novelty detection in the patient and control groups. Analyses also tested whether duration of illness, chlorpromazine equivalents and symptoms were predictive of network modulation in the patient group. Results The modulation for the anterior default mode network had a main effect by group (F1, 41 = 7.17, p = 0.011) and an interaction of group and age (F1, 41 = 6.92, p = 0.012). Older patients with schizophrenia tended to have less negative modulation of the anterior default mode network with age. Exploratory analyses revealed patients with schizophrenia had less positive modulation of the task-positive network than healthy controls (F1, 43 = 4.01, p = 0.052). Conclusions Decreased negative modulation of the anterior default mode network occurs late in the disease course of schizophrenia. This may be related to inability of older patients to allocate attentional resources away from task-irrelevant stimuli in the environment.

Abbott, Christopher; Kim, Dae Il; Sponheim, Scott; Bustillo, Juan; Calhoun, Vince D.

2010-01-01

51

Modulation of function and gated learning in a network memory  

SciTech Connect

Memory and learning are studied in a model neural network made from component cells with a variety of realistic intrinsic dynamic behaviors. Modulation of intrinsic cellular characteristics causes a network to switch between two entirely different modes of operation. In one mode the network acts as a selective, long-term associative memory, whereas in the other it is a nonselective, short-term latching memory. Such functional modulation can be used as a mechanism for initiating and terminating learning in a network associative memory.

Abbott, L.F. (Brandeis Univ., Waltham, MA (United States))

1990-12-01

52

Modulation of function and gated learning in a network memory.  

PubMed Central

Memory and learning are studied in a model neural network made from component cells with a variety of realistic intrinsic dynamic behaviors. Modulation of intrinsic cellular characteristics causes a network to switch between two entirely different modes of operation. In one mode the network acts as a selective, long-term associative memory, whereas in the other it is a nonselective, short-term latching memory. Such functional modulation can be used as a mechanism for initiating and terminating learning in a network associative memory. Images

Abbott, L F

1990-01-01

53

Gaze direction modulates visual aftereffects in depth and color  

Microsoft Academic Search

Prior physiological studies indicate that gaze direction modulates the gain of neural responses to visual stimuli. Here, we test gaze modulation in the perceptual domain using color and depth aftereffects. After confirming retinotopy of the effects, we employed a balanced alternating adaptation paradigm (adaptation alternates between opponent stimuli) to demonstrate that opposite color and depth aftereffects can co-develop at the

Dylan R. Nieman; Ryusuke Hayashi; Richard A. Andersen; Shinsuke Shimojo

2005-01-01

54

Microwave phase stability of directly modulated semiconductor injection lasers  

SciTech Connect

The microwave phase stability of directly modulated high-speed semiconductor lasers was studied. It was shown that optical feedback had a serious effect on microwave phase stability of the modulated signal and must be reduced to below -40 dB for satisfactory phase performance.

Lau, K.Y.

1988-04-25

55

Community Landscapes: An Integrative Approach to Determine Overlapping Network Module Hierarchy, Identify Key Nodes and Predict Network Dynamics  

PubMed Central

Background Network communities help the functional organization and evolution of complex networks. However, the development of a method, which is both fast and accurate, provides modular overlaps and partitions of a heterogeneous network, has proven to be rather difficult. Methodology/Principal Findings Here we introduce the novel concept of ModuLand, an integrative method family determining overlapping network modules as hills of an influence function-based, centrality-type community landscape, and including several widely used modularization methods as special cases. As various adaptations of the method family, we developed several algorithms, which provide an efficient analysis of weighted and directed networks, and (1) determine pervasively overlapping modules with high resolution; (2) uncover a detailed hierarchical network structure allowing an efficient, zoom-in analysis of large networks; (3) allow the determination of key network nodes and (4) help to predict network dynamics. Conclusions/Significance The concept opens a wide range of possibilities to develop new approaches and applications including network routing, classification, comparison and prediction.

Kovacs, Istvan A.; Palotai, Robin; Szalay, Mate S.; Csermely, Peter

2010-01-01

56

Differential Frequency Hopping (DFH) Modulation For Mobile Underwater Sensor Networks.  

National Technical Information Service (NTIS)

The long-term goal of this research effort is to develop underwater acoustic communications algorithms based on differential frequency hopping (DFH) modulation that enable networked operations (i.e. multiple simultaneous users), as well as providing low p...

A. Das L. Cazzanti

2011-01-01

57

Analog spatial light modulator for learning in neural networks  

NASA Astrophysics Data System (ADS)

This paper presents a FELC/VLSI spatial light modulator which has been built as a component for optoelectronic neural networks. The device exhibits analogue optical modulation and is capable of optical memory. It is the first parallel optical device that implements a learning algorithm in its pixels.

Yu, T. C.; Mears, Robert J.; Davey, A. B.; Crossland, W. A.; Snook, M. W.; Collings, Neil; Birch, Martin J.

1996-05-01

58

Data-driven reconstruction of directed networks  

NASA Astrophysics Data System (ADS)

We investigate the properties of a recently introduced asymmetric association measure, called inner composition alignment (IOTA), aimed at inferring regulatory links (couplings). We show that the measure can be used to determine the direction of coupling, detect superfluous links, and to account for autoregulation. In addition, the measure can be extended to infer the type of regulation (positive or negative). The capabilities of IOTA to correctly infer couplings together with their directionality are compared against Kendall's rank correlation for time series of different lengths, particularly focussing on biological examples. We demonstrate that an extended version of the measure, bidirectional inner composition alignment (biIOTA), increases the accuracy of the network reconstruction for short time series. Finally, we discuss the applicability of the measure to infer couplings in chaotic systems.

Hempel, Sabrina; Koseska, Aneta; Nikoloski, Zoran

2013-06-01

59

Inspiring Climate Education Excellence (ICEE): Developing self-directed professional development modules for secondary science teachers  

NASA Astrophysics Data System (ADS)

Inspiring Climate Education Excellence (ICEE) is a NASA-funded project to develop online course modules and self-directed learning resources aligned with the Essential Principles of Climate Science. Following a national needs assessment survey and a face to face workshop to pilot test topics, a suite of online modules is being developed suitable for self-directed learning by secondary science teachers. Modules are designed around concepts and topics in which teachers express the most interest and need for instruction. Module design also includes attention to effective teaching strategies, such as awareness of student misconceptions, strategies for forestalling controversy and advice from master teachers on implementation and curriculum development. The resources are being developed in partnership with GLOBE, and the National Science Digital Library (NSDL) and is informed by the work of the Climate Literacy and Energy Awareness Network (CLEAN) project. ICEE will help to meet the professional development needs of teachers, including those participating in the GLOBE Student Climate Research Campaign. Modules and self-directed learning resources will be developed and disseminated in partnership with the National Science Digital Library (NSDL). This presentation introduces the needs assessment and pilot workshop data upon which the modules are based, and describes the modules that are available and in development.

Buhr, S. M.; Lynds, S. E.; McCaffrey, M. S.; Morton, E.

2010-12-01

60

Directed network topologies of smart grain sensors  

NASA Astrophysics Data System (ADS)

We employ a recent technique for building complex networks from time series data to construct a directed network embodying time structure to collate the predictive properties of individual granular sensors in a series of biaxial compression tests. For each grain, we reconstruct a static predictive model. This combines a subset selection algorithm and an information theory fitting criterion that selects which other grains in the assembly are best placed to predict a given grain's local stress throughout loading history. The local stress of a grain at each time step is summarized by the magnitude of its particle load vector. A directed network is constructed by representing each grain as a node, and assigning an in-link to a grain from another grain if the latter is selected within the best predictive model of the first grain. The grains with atypically large out-degree are thus the most responsible for predicting the stress history of the other grains: These turn out to be only a few grains which reside inside shear bands. Moreover, these “smart grains” prove to be strongly linked to the mechanism of force chain buckling and intermittent rattler events. That only a small number of grain sensors situated in the shear band are required to accurately capture the rheological response of all other grains in the assembly underlines the crucial importance of nonlocal interactions, espoused by extended continuum theories which posit nonlocal evolution laws. Findings here cast the spotlight on two specific mechanisms as being key to the formulation of robust evolution laws in deforming granular materials under compression and shear: the long held mechanism for energy dissipation of force chain buckling and the sudden switch in roles that a rattler plays as it enters in and out of force chains.

Walker, David M.; Tordesillas, Antoinette; Nakamura, Tomomichi; Tanizawa, Toshihiro

2013-03-01

61

Optical phase modulation based on directly modulated reflection-mode OIL-VCSEL.  

PubMed

Optical phase modulation based on directly modulated reflection-mode optically injection-locked VCSEL is investigated based on standard OIL rate equations and reflection-mode OIL model. The phase information of both static and dynamic state is simulated. The difference of static state phase information between transmission- and reflection-mode OIL is numerically analyzed. With specific OIL parameters, the output power of directly modulated OIL-VCSEL remains constant and phase deviation of 0.934? rad is obtained. Results show that a directly modulated OIL-VCSEL can function as a key component in QPSK or 8PSK transmitters. Preliminary 2.5 Gb/s PSK modulation characteristic is demonstrated experimentally. PMID:24104103

Guo, Peng; Sun, Tao; Yang, Weijian; Parekh, Devang; Zhang, Cheng; Xie, Xiaopeng; Chang-Hasnain, Connie J; Xu, Anshi; Chen, Zhangyuan

2013-09-23

62

Differential Network Analysis Reveals Genetic Effects on Catalepsy Modules  

PubMed Central

We performed short-term bi-directional selective breeding for haloperidol-induced catalepsy, starting from three mouse populations of increasingly complex genetic structure: an F2 intercross, a heterogeneous stock (HS) formed by crossing four inbred strains (HS4) and a heterogeneous stock (HS-CC) formed from the inbred strain founders of the Collaborative Cross (CC). All three selections were successful, with large differences in haloperidol response emerging within three generations. Using a custom differential network analysis procedure, we found that gene coexpression patterns changed significantly; importantly, a number of these changes were concordant across genetic backgrounds. In contrast, absolute gene-expression changes were modest and not concordant across genetic backgrounds, in spite of the large and similar phenotypic differences. By inferring strain contributions from the parental lines, we are able to identify significant differences in allelic content between the selected lines concurrent with large changes in transcript connectivity. Importantly, this observation implies that genetic polymorphisms can affect transcript and module connectivity without large changes in absolute expression levels. We conclude that, in this case, selective breeding acts at the subnetwork level, with the same modules but not the same transcripts affected across the three selections.

Iancu, Ovidiu D.; Oberbeck, Denesa; Darakjian, Priscila; Kawane, Sunita; Erk, Jason; McWeeney, Shannon; Hitzemann, Robert

2013-01-01

63

Transcranial alternating current stimulation modulates large-scale cortical network activity by network resonance.  

PubMed

Transcranial direct current stimulation (tDCS) has emerged as a potentially safe and effective brain stimulation modality that alters cortical excitability by passing a small, constant electric current through the scalp. tDCS creates an electric field that weakly modulates the membrane voltage of a large number of cortical neurons. Recent human studies have suggested that sine-wave stimulation waveforms [transcranial alternating current stimulation (tACS)] represent a more targeted stimulation paradigm for the enhancement of cortical oscillations. Yet, the underlying mechanisms of how periodic, weak global perturbations alter the spatiotemporal dynamics of large-scale cortical network dynamics remain a matter of debate. Here, we simulated large-scale networks of spiking neuron models to address this question in endogenously rhythmic networks. We identified distinct roles of the depolarizing and hyperpolarizing phases of tACS in entrainment, which entailed moving network activity toward and away from a strong nonlinearity provided by the local excitatory coupling of pyramidal cells. Together, these mechanisms gave rise to resonance dynamics characterized by an Arnold tongue centered on the resonance frequency of the network. We then performed multichannel extracellular recordings of multiunit firing activity during tACS in anesthetized ferrets (Mustela putoris furo), a model species with a gyrencephalic brain, to verify that weak global perturbations can selectively enhance oscillations at the applied stimulation frequency. Together, these results provide a detailed mechanistic understanding of tACS at the level of large-scale network dynamics and support the future design of activity-dependent feedback tACS paradigms that dynamically tailor stimulation frequency to the spectral peak of ongoing brain activity. PMID:23825429

Ali, Mohsin M; Sellers, Kristin K; Fröhlich, Flavio

2013-07-01

64

Low-cost adaptive directly modulated optical OFDM based on semiconductor optical amplifier  

NASA Astrophysics Data System (ADS)

Low cost optical OFDM has great potential for next generation optical access networks and PONs, due to its high flexibility in bandwidth manipulation, and high spectral efficiency. Here, a low cost optical OFDM is proposed, based on adaptive direct modulation semiconductor optical amplifier. Adaptive current loading techniques for PAPR (peak to average power ratio) reduction are proposed and analyzed. Simulations show that the proposed adaptive techniques enable significant BER improvement.

Kashany-Mizrahi, Inbal; Sadot, Dan

2013-10-01

65

Directly modulated cable television transport systems using negative dispersion fiber  

NASA Astrophysics Data System (ADS)

A directly modulated AM-VSB cable-television transport system using negative dispersion fiber (NDF) as the transmission medium is proposed and successfully demonstrated. Good performances of carrier-to-noise radio, composite second order, and composite triple beat were obtained over a 70-km NDF transport without optical amplification. The directly modulated laser has a positive chirp, while NDF has a negative dispersion property in the transmission fiber. This negative dispersion property compensates for the laser chirp and results in a system with better transmission performance.

Lu, Hai-Han; Liaw, Je-Wei; Lee, Yi-Shiuan; Tsai, Wan-Lin; Ji, Yu-Jie

2005-03-01

66

Interaction of Motility, Directional Sensing, and Polarity Modules Recreates the Behaviors of Chemotaxing Cells  

PubMed Central

Chemotaxis involves the coordinated action of separable but interrelated processes: motility, gradient sensing, and polarization. We have hypothesized that these are mediated by separate modules that account for these processes individually and that, when combined, recreate most of the behaviors of chemotactic cells. Here, we describe a mathematical model where the modules are implemented in terms of reaction-diffusion equations. Migration and the accompanying changes in cellular morphology are demonstrated in simulations using a mechanical model of the cell cortex implemented in the level set framework. The central module is an excitable network that accounts for random migration. The response to combinations of uniform stimuli and gradients is mediated by a local excitation, global inhibition module that biases the direction in which excitability is directed. A polarization module linked to the excitable network through the cytoskeleton allows unstimulated cells to move persistently and, for cells in gradients, to gradually acquire distinct sensitivity between front and back. Finally, by varying the strengths of various feedback loops in the model we obtain cellular behaviors that mirror those of genetically altered cell lines.

Shi, Changji; Huang, Chuan-Hsiang; Devreotes, Peter N.; Iglesias, Pablo A.

2013-01-01

67

Protein complexes and functional modules in molecular networks  

NASA Astrophysics Data System (ADS)

Proteins, nucleic acids, and small molecules form a dense network of molecular interactions in a cell. Molecules are nodes of this network, and the interactions between them are edges. The architecture of molecular networks can reveal important principles of cellular organization and function, similarly to the way that protein structure tells us about the function and organization of a protein. Computational analysis of molecular networks has been primarily concerned with node degree [Wagner, A. & Fell, D. A. (2001) Proc. R. Soc. London Ser. B 268, 1803-1810; Jeong, H., Tombor, B., Albert, R., Oltvai, Z. N. & Barabasi, A. L. (2000) Nature 407, 651-654] or degree correlation [Maslov, S. & Sneppen, K. (2002) Science 296, 910-913], and hence focused on single/two-body properties of these networks. Here, by analyzing the multibody structure of the network of protein-protein interactions, we discovered molecular modules that are densely connected within themselves but sparsely connected with the rest of the network. Comparison with experimental data and functional annotation of genes showed two types of modules: (i) protein complexes (splicing machinery, transcription factors, etc.) and (ii) dynamic functional units (signaling cascades, cell-cycle regulation, etc.). Discovered modules are highly statistically significant, as is evident from comparison with random graphs, and are robust to noise in the data. Our results provide strong support for the network modularity principle introduced by Hartwell et al. [Hartwell, L. H., Hopfield, J. J., Leibler, S. & Murray, A. W. (1999) Nature 402, C47-C52], suggesting that found modules constitute the "building blocks" of molecular networks.

Spirin, Victor; Mirny, Leonid A.

2003-10-01

68

Module detection in complex networks using integer optimisation  

PubMed Central

Background The detection of modules or community structure is widely used to reveal the underlying properties of complex networks in biology, as well as physical and social sciences. Since the adoption of modularity as a measure of network topological properties, several methodologies for the discovery of community structure based on modularity maximisation have been developed. However, satisfactory partitions of large graphs with modest computational resources are particularly challenging due to the NP-hard nature of the related optimisation problem. Furthermore, it has been suggested that optimising the modularity metric can reach a resolution limit whereby the algorithm fails to detect smaller communities than a specific size in large networks. Results We present a novel solution approach to identify community structure in large complex networks and address resolution limitations in module detection. The proposed algorithm employs modularity to express network community structure and it is based on mixed integer optimisation models. The solution procedure is extended through an iterative procedure to diminish effects that tend to agglomerate smaller modules (resolution limitations). Conclusions A comprehensive comparative analysis of methodologies for module detection based on modularity maximisation shows that our approach outperforms previously reported methods. Furthermore, in contrast to previous reports, we propose a strategy to handle resolution limitations in modularity maximisation. Overall, we illustrate ways to improve existing methodologies for community structure identification so as to increase its efficiency and applicability.

2010-01-01

69

Nicotinic modulation of intrinsic brain networks in schizophrenia.  

PubMed

The nicotinic receptor is a promising drug target currently being investigated for the treatment of cognitive symptoms in schizophrenia. A key step in this process is the development of noninvasive functional neuroimaging biomarkers that can be used to determine if nicotinic agents are eliciting their targeted biological effect, ideally through modulation of a fundamental aspect of neuronal function. To that end, neuroimaging researchers are beginning to understand how nicotinic modulation affects "intrinsic" brain networks to elicit potentially therapeutic effects. An intrinsic network is a functionally and (often) structurally connected network of brain areas whose activity reflects a fundamental neurobiological organizational principle of the brain. This review summarizes findings of the effects of nicotinic drugs on three topics related to intrinsic brain network activity: (1) the default mode network, a group of brain areas for which activity is maximal at rest and reduced during cognitive tasks, (2) the salience network, which integrates incoming sensory data with prior internal representations to guide future actions and change predictive values, and (3) multi-scale complex network dynamics, which describe these brain's ability to efficiency integrate information while preserving local functional specialization. These early findings can be used to inform future neuroimaging studies that examine the network effects of nicotinic agents. PMID:23796751

Smucny, Jason; Tregellas, Jason

2013-06-21

70

Control strategies for direct torque control using discrete pulse modulation  

Microsoft Academic Search

A scheme for direct torque control of AC machines using discrete pulse-modulated inverters such as the resonant DC link inverter is presented. A unique feature of the control method is that only one current sensor in the DC link is required. Excellent control of torque, stator flux, and motor current waveshapes is seen to be obtained without affecting the high

Thomas G. Habetler; Deepakraj M. Divan

1991-01-01

71

Control strategies for direct torque control using discrete pulse modulation  

Microsoft Academic Search

A scheme for direct torque control of AC machines using discrete pulse modulated inverters, such as the resonant DC link inverter, is presented. A unique feature of the control method presented is that only one current sensor in the DC link is required. Excellent control of torque, stator flux and motor current waveshapes is obtained without affecting the high dynamic

Thomas G. Habetler; Deepakraj M. Divan

1989-01-01

72

Federal Statutes & Directives Regarding National Origin Students. Technical Assistance Module.  

ERIC Educational Resources Information Center

|Federal statutes and directives regarding national origin students is the subject of this technical assistance module. It is a guide for trainers who seek to familiarize education personnel with the legal aspects of providing services to limited English proficient (LEP) students. Nine activities are described and materials, including 17…

Gonzales, Frank

73

NeMo: Network Module identification in Cytoscape  

PubMed Central

Background As the size of the known human interactome grows, biologists increasingly rely on computational tools to identify patterns that represent protein complexes and pathways. Previous studies have shown that densely connected network components frequently correspond to community structure and functionally related modules. In this work, we present a novel method to identify densely connected and bipartite network modules based on a log odds score for shared neighbours. Results To evaluate the performance of our method (NeMo), we compare it to other widely used tools for community detection including kMetis, MCODE, and spectral clustering. We test these methods on a collection of synthetically constructed networks and the set of MIPS human complexes. We apply our method to the CXC chemokine pathway and find a high scoring functional module of 12 disconnected phospholipase isoforms. Conclusion We present a novel method that combines a unique neighbour-sharing score with hierarchical agglomerative clustering to identify diverse network communities. The approach is unique in that we identify both dense network and dense bipartite network structures in a single approach. Our results suggest that the performance of NeMo is better than or competitive with leading approaches on both real and synthetic datasets. We minimize model complexity and generalization error in the Bayesian spirit by integrating out nuisance parameters. An implementation of our method is freely available for download as a plugin to Cytoscape through our website and through Cytoscape itself.

2010-01-01

74

Learning biological networks: from modules to dynamics  

Microsoft Academic Search

Learning regulatory networks from genomics data is an important problem with applications spanning all of biology and biomedicine. Functional genomics projects offer a cost-effective means of greatly expanding the completeness of our regulatory models, and for some prokaryotic organisms they offer a means of learning accurate models that incorporate the majority of the genome. There are, however, several reasons to

Richard Bonneau

2008-01-01

75

Analysis of reflex modulation with a biologically realistic neural network  

Microsoft Academic Search

In this study, a neuromusculoskeletal model was built to give insight into the mechanisms behind the modulation of reflexive feedback strength as exper- imentally identified in the human shoulder joint. The model is an integration of a biologically realistic neural network consisting of motoneurons and interneurons, modeling 12 populations of spinal neurons, and a one degree-of-freedom musculoskeletal model, including proprioceptors.

Arno H. A. Stienen; Alfred C. Schouten; Jasper Schuurmans; Frans C. T. Van Der Helm

2007-01-01

76

Functionally guided alignment of protein interaction networks for module detection  

PubMed Central

Motivation: Functional module detection within protein interaction networks is a challenging problem due to the sparsity of data and presence of errors. Computational techniques for this task range from purely graph theoretical approaches involving single networks to alignment of multiple networks from several species. Current network alignment methods all rely on protein sequence similarity to map proteins across species. Results: Here we carry out network alignment using a protein functional similarity measure. We show that using functional similarity to map proteins across species improves network alignment in terms of functional coherence and overlap with experimentally verified protein complexes. Moreover, the results from functional similarity-based network alignment display little overlap (<15%) with sequence similarity-based alignment. Our combined approach integrating sequence and function-based network alignment alongside graph clustering properties offers a 200% increase in coverage of experimental datasets and comparable accuracy to current network alignment methods. Availability: Program binaries and source code is freely available at http://www.stats.ox.ac.uk/research/bioinfo/resources Contact: ali@stats.ox.ac.uk Supplementary Information: Supplementary data are available at Bioinformatics online.

Ali, Waqar; Deane, Charlotte M.

2009-01-01

77

Directions in Packet Classification for Network Processors  

Microsoft Academic Search

To classify a packet as belonging to a flow often requires network systems—such as routers and firewalls—to maintain large data structures and perform several memory accesses. Network processors, on the other hand, are generally configured with only a small amount of memory with limited access bandwidth. Hence, a key challenge is to design packet classification algorithms that can be implemented

Michael E. Kounavis; Alok Kumar; Harrick Vin; Raj Yavatkar; Andrew T. Campbell

78

Direct self control of induction motor based on neural network  

Microsoft Academic Search

This paper presents an artificial-neural-network-based direct-self-control (ANN-DSC) scheme for an input inverter-fed three-phase induction motor. In order to cope with the complex calculations required in direct self control (DSC), the proposed artificial-neural-network (ANN) system employs the individual training strategy with fixed-weight and supervised models. A computer simulation program is developed using Matlab\\/Simulink together with the Neural Network Toolbox. The simulated

K. L. Shi; T. F. Chan; Y. K. Wong; S. L. Ho

2001-01-01

79

Dopamine differentially modulates the excitability of striatal neurons of the direct and indirect pathways in lamprey.  

PubMed

The functions of the basal ganglia are critically dependent on dopamine. In mammals, dopamine differentially modulates the excitability of the direct and indirect striatal projection neurons, and these populations selectively express dopamine D1 and D2 receptors, respectively. Although the detailed organization of the basal ganglia is conserved throughout the vertebrate phylum, it was unknown whether the differential dopamine modulation of the direct and indirect pathways is present in non-mammalian species. We aim here to determine whether the receptor expression and opposing dopaminergic modulation of the direct and indirect pathways is present in one of the phylogenetically oldest vertebrates, the river lamprey. Using in situ hybridization and patch-clamp recordings, we show that D1 receptors are almost exclusively expressed in the striatal neurons projecting directly to the homolog of the substantia nigra pars reticulata. In addition, the majority of striatal neurons projecting to the homolog of the globus pallidus interna/globus pallidus externa express D1 or D2 receptors. As in mammals, application of dopamine receptor agonists differentially modulates the excitability of these neurons, increasing the excitability of the D1-expressing neurons and decreasing the excitability of D2-expressing neurons. Our results suggest that the segregated expression of the D1 and D2 receptors in the direct and indirect striatal projection neurons has been conserved across the vertebrate phylum. Because dopamine receptor agonists differentially modulate these pathways, increasing the excitability of the direct pathway and decreasing the excitability of the indirect pathway, this organization may be conserved as a mechanism that biases the networks toward action selection. PMID:23637194

Ericsson, Jesper; Stephenson-Jones, Marcus; Pérez-Fernández, Juan; Robertson, Brita; Silberberg, Gilad; Grillner, Sten

2013-05-01

80

Direct modulation of stably injection-locked semiconductor lasers for photonic microwave transmission  

NASA Astrophysics Data System (ADS)

Photonic transmission of microwave signals from a central office to remote base stations is a key functionality in broadband radio-over-fiber access networks. Because of chromatic dispersion, a strong fluctuation of the microwave power along fiber transmission happens to microwave-modulated optical carriers with double-sideband features. Therefore, optical single-sideband modulation characteristics are preferred. Direct modulation of a semiconductor laser is the simplest scheme for photonic microwave generation and transmission. However, the symmetric property of the laser in the modulation sideband intensity makes the scheme unattractive for radio-over-fiber applications. In this study, we apply the injection locking technique to the laser for optical single-sideband generation. Proper optical injection can drive the laser to the stable-locking dynamical state before entering the Hopf bifurcation. The field-carrier coupling of the injected laser is radically modified due to the dynamical interaction between the injection-shifted cavity resonance and the injection-imposed oscillation. Therefore, the relaxation resonance sidebands of the injected laser are considerably shifted in frequency and asymmetrically modified in intensity, the extent of which depends strongly on the injection condition. Under the range of our study, direct modulation of the injected laser can thus generate microwave signals that are broadly tunable up to 4 times its free-funning relaxation resonance frequency and are highly asymmetric up to 20 dB in modulation sidebands. The microwave frequency can be tuned over a broad range while keeping a similar level of modulation sideband asymmetry, or different levels of modulation sideband asymmetry can be obtained while keeping a similar microwave frequency. This adds the flexibility and re-configurability to the proposed system. No optical phase-locking electronics, no high driving voltages, and no narrow-bandwidth optical filters are necessary as in many other systems.

Hwang, Sheng-Kwang; Chan, Sze-Chun; Hsieh, Shie-Chin; Li, Cheng-Yu

2010-04-01

81

Studies on controllability of directed networks with extremal optimization  

NASA Astrophysics Data System (ADS)

Almost all natural, social and man-made-engineered systems can be represented by a complex network to describe their dynamic behaviors. To make a real-world complex network controllable with its desired topology, the study on network controllability has been one of the most critical and attractive subjects for both network and control communities. In this paper, based on a given directed-weighted network with both state and control nodes, a novel optimization tool with extremal dynamics to generate an optimal network topology with minimum control nodes and complete controllability under Kalman's rank condition has been developed. The experimental results on a number of popular benchmark networks show the proposed tool is effective to identify the minimum control nodes which are sufficient to guide the whole network's dynamics and provide the evolution of network topology during the optimization process. We also find the conclusion: "the sparse networks need more control nodes than the dense, and the homogeneous networks need fewer control nodes compared to the heterogeneous" (Liu et al., 2011 [18]), is also applicable to network complete controllability. These findings help us to understand the network dynamics and make a real-world network under the desired control. Moreover, compared with the relevant research results on structural controllability with minimum driver nodes, the proposed solution methodology may also be applied to other constrained network optimization problems beyond complete controllability with minimum control nodes.

Ding, Jin; Lu, Yong-Zai; Chu, Jian

2013-12-01

82

Trajectory generation and modulation using dynamic neural networks.  

PubMed

Generation of desired trajectory behavior using neural networks involves a particularly challenging spatio-temporal learning problem. This paper introduces a novel solution, i.e., designing a dynamic system whose terminal behavior emulates a prespecified spatio-temporal pattern independently of its initial conditions. The proposed solution uses a dynamic neural network (DNN), a hybrid architecture that employs a recurrent neural network (RNN) in cascade with a nonrecurrent neural network (NRNN). The RNN generates a simple limit cycle, which the NRNN reshapes into the desired trajectory. This architecture is simple to train. A systematic synthesis procedure based on the design of relay control systems is developed for configuring an RNN that can produce a limit cycle of elementary complexity. It is further shown that a cascade arrangement of this RNN and an appropriately trained NRNN can emulate any desired trajectory behavior irrespective of its complexity. An interesting solution to the trajectory modulation problem, i.e., online modulation of the generated trajectories using external inputs, is also presented. Results of several experiments are included to demonstrate the capabilities and performance of the DNN in handling trajectory generation and modulation problems. PMID:18238036

Zegers, P; Sundareshan, M K

2003-01-01

83

Pseudophosphorylation of tau protein directly modulates its aggregation kinetics  

PubMed Central

Hyperphosphorylation of tau protein is associated with neurofibrillary lesion formation in Alzheimer’s disease and other tauopathic neurodegenerative diseases. It fosters lesion formation by increasing the concentration of free tau available for aggregation and by directly modulating the tau aggregation reaction. To clarify how negative charge incorporation into tau directly affects aggregation behavior, the fibrillization of pseudophosphorylation mutant T212E prepared in a full-length four-repeat tau background was examined in vitro as a function of time and submicromolar tau concentrations using electron microscopy assay methods. Kinetic constants for nucleation and extension phases of aggregation were then estimated by direct measurement and mathematical simulation. Kinetic analysis revealed that pseudophosphorylation increased tau aggregation rate by increasing the rate of filament nucleation. In addition, it increased aggregation propensity by stabilizing mature filaments against disaggregation. The data suggest that incorporation of negative charge into the T212 site can directly promote tau filament formation at multiple steps in the aggregation pathway.

Chang, Edward; Kim, Sohee; Schafer, Kelsey N.; Kuret, Jeff

2010-01-01

84

Performance of a cascadable neural network VME-module with Intel 80170NX chips  

Microsoft Academic Search

We describe an experimental research prototype VME-module with three commercially available Intel 80170NX analog neural network chips. Each chip can hold one layer with up to 64 neurons of a feedforward network and a single module can thus be configured for 1 to 3 layer networks. Multiple boards can be cascaded together to build broad structured networks. We discuss tests

C. S. Lindsey; Th. Lindblad; J. R. Vollaro; G. Szčkely; J. Molnar

1994-01-01

85

Network modules help the identification of key transport routes, signaling pathways in cellular and other networks  

NASA Astrophysics Data System (ADS)

Complex systems are successfully reduced to interacting elements via the network concept. Transport plays a key role in the survival of networks. For example the specialized signaling cascades of cellular networks filter noise and efficiently adapt the network structure to new stimuli. However, our general understanding of transport mechanisms and signaling pathways in complex systems is yet limited. Here we summarize the key network structures involved in transport, list the solutions available to overloaded systems for relaxing their load and outline a possible method for the computational determination of signaling pathways. We highlight that in addition to hubs, bridges and the network skeleton, the overlapping modular structure is also essential in network transport. Moreover, by locating network elements in the space of overlapping network modules and evaluating their distance in this "module space", it may be possible to approximate signaling pathways computationally, which, in turn could serve the identification of signaling pathways of complex systems. Our model may be applicable in a wide range of fields including traffic control or drug design.

Palotai, R.; Csermely, P.

2009-12-01

86

Modulation format identification in heterogeneous fiber-optic networks using artificial neural networks.  

PubMed

We propose a simple and cost-effective technique for modulation format identification (MFI) in next-generation heterogeneous fiber-optic networks using an artificial neural network (ANN) trained with the features extracted from the asynchronous amplitude histograms (AAHs). Results of numerical simulations conducted for six different widely-used modulation formats at various data rates demonstrate that the proposed technique can effectively classify all these modulation formats with an overall estimation accuracy of 99.6% and also in the presence of various link impairments. The proposed technique employs extremely simple hardware and digital signal processing (DSP) to enable MFI and can also be applied for the identification of other modulation formats at different data rates without necessitating hardware changes. PMID:22714229

Khan, Faisal Nadeem; Zhou, Yudi; Lau, Alan Pak Tao; Lu, Chao

2012-05-21

87

A neural network model of attention-modulated neurodynamics  

Microsoft Academic Search

Visual attention appears to modulate cortical neurodynamics and synchronization through various cholinergic mechanisms. In\\u000a order to study these mechanisms, we have developed a neural network model of visual cortex area V4, based on psychophysical,\\u000a anatomical and physiological data. With this model, we want to link selective visual information processing to neural circuits\\u000a within V4, bottom-up sensory input pathways, top-down attention

Yuqiao Gu; Hans Liljenström

2007-01-01

88

Compression of Flow Can Reveal Overlapping-Module Organization in Networks  

NASA Astrophysics Data System (ADS)

To better understand the organization of overlapping modules in large networks with respect to flow, we introduce the map equation for overlapping modules. In this information-theoretic framework, we use the correspondence between compression and regularity detection. The generalized map equation measures how well we can compress a description of flow in the network when we partition it into modules with possible overlaps. When we minimize the generalized map equation over overlapping network partitions, we detect modules that capture flow and determine which nodes at the boundaries between modules should be classified in multiple modules and to what degree. With a novel greedy-search algorithm, we find that some networks, for example, the neural network of the nematode Caenorhabditis elegans, are best described by modules dominated by hard boundaries, but that others, for example, the sparse European-roads network, have an organization of highly overlapping modules.

Viamontes Esquivel, Alcides; Rosvall, Martin

2011-10-01

89

Pro-cognitive drug effects modulate functional brain network organization  

PubMed Central

Previous studies document that cholinergic and noradrenergic drugs improve attention, memory and cognitive control in healthy subjects and patients with neuropsychiatric disorders. In humans neural mechanisms of cholinergic and noradrenergic modulation have mainly been analyzed by investigating drug-induced changes of task-related neural activity measured with functional magnetic resonance imaging (fMRI). Endogenous neural activity has often been neglected. Further, although drugs affect the coupling between neurons, only a few human studies have explicitly addressed how drugs modulate the functional connectome, i.e., the functional neural interactions within the brain. These studies have mainly focused on synchronization or correlation of brain activations. Recently, there are some drug studies using graph theory and other new mathematical approaches to model the brain as a complex network of interconnected processing nodes. Using such measures it is possible to detect not only focal, but also subtle, widely distributed drug effects on functional network topology. Most important, graph theoretical measures also quantify whether drug-induced changes in topology or network organization facilitate or hinder information processing. Several studies could show that functional brain integration is highly correlated with behavioral performance suggesting that cholinergic and noradrenergic drugs which improve measures of cognitive performance should increase functional network integration. The purpose of this paper is to show that graph theory provides a mathematical tool to develop theory-driven biomarkers of pro-cognitive drug effects, and also to discuss how these approaches can contribute to the understanding of the role of cholinergic and noradrenergic modulation in the human brain. Finally we discuss the “global workspace” theory as a theoretical framework of pro-cognitive drug effects and argue that pro-cognitive effects of cholinergic and noradrenergic drugs might be related to higher network integration.

Giessing, Carsten; Thiel, Christiane M.

2012-01-01

90

Pro-cognitive drug effects modulate functional brain network organization.  

PubMed

Previous studies document that cholinergic and noradrenergic drugs improve attention, memory and cognitive control in healthy subjects and patients with neuropsychiatric disorders. In humans neural mechanisms of cholinergic and noradrenergic modulation have mainly been analyzed by investigating drug-induced changes of task-related neural activity measured with functional magnetic resonance imaging (fMRI). Endogenous neural activity has often been neglected. Further, although drugs affect the coupling between neurons, only a few human studies have explicitly addressed how drugs modulate the functional connectome, i.e., the functional neural interactions within the brain. These studies have mainly focused on synchronization or correlation of brain activations. Recently, there are some drug studies using graph theory and other new mathematical approaches to model the brain as a complex network of interconnected processing nodes. Using such measures it is possible to detect not only focal, but also subtle, widely distributed drug effects on functional network topology. Most important, graph theoretical measures also quantify whether drug-induced changes in topology or network organization facilitate or hinder information processing. Several studies could show that functional brain integration is highly correlated with behavioral performance suggesting that cholinergic and noradrenergic drugs which improve measures of cognitive performance should increase functional network integration. The purpose of this paper is to show that graph theory provides a mathematical tool to develop theory-driven biomarkers of pro-cognitive drug effects, and also to discuss how these approaches can contribute to the understanding of the role of cholinergic and noradrenergic modulation in the human brain. Finally we discuss the "global workspace" theory as a theoretical framework of pro-cognitive drug effects and argue that pro-cognitive effects of cholinergic and noradrenergic drugs might be related to higher network integration. PMID:22973209

Giessing, Carsten; Thiel, Christiane M

2012-08-28

91

Optical modulation of astrocyte network using ultrashort pulsed laser  

NASA Astrophysics Data System (ADS)

Astrocyte, the most abundant cell type in the central nervous system, has been one of major topics in neuroscience. Even though many tools have been developed for the analysis of astrocyte function, there has been no adequate tool that can modulates astrocyte network without pharmaceutical or genetic interventions. Here we found that ultrashort pulsed laser stimulation can induce label-free activation of astrocytes as well as apoptotic-like cell death in a dose-dependent manner. Upon irradiation with high intensity pulsed lasers, the irradiated cells with short exposure time showed very rapid mitochondria fragmentation, membrane blebbing and cytoskeletal retraction. We applied this technique to investigate in vivo function of astrocyte network in the CNS: in the aspect of neurovascular coupling and blood-brain barrier. We propose that this noninvasive technique can be widely applied for in vivo study of complex cellular network.

Yoon, Jonghee; Ku, Taeyun; Chong, Kyuha; Ryu, Seung-Wook; Choi, Chulhee

2012-02-01

92

Topology formulation algorithms for wireless networks with reconfigurable directional links  

Microsoft Academic Search

In future airborne networks, high rate connectivity between platforms will be heterogeneous and provided over directional free space optical (FSO) or RF wireless links. It is essential for large scale high performance networks that the creation and maintenance of link adjacencies between airborne nodes proceed in an automated manner. Precisely which steerable transmit beams should form connections with available receivers

T. J. Vitolo; Jian-Qiang Hu; L. Servi; V. Mehta

2005-01-01

93

Local Search in Weighted and Directed Social Networks: The Case of Enron Email Networks  

Microsoft Academic Search

Although they have small-world and searchable characteristics, social networks always protect local structure which makes local search very hard. Social networks not only have power-law distribution, but also have higher connectivity or clustering characteristics. Meanwhile, several social networks are weighted and directed. Hence we should utilize these extra information. In this paper, we propose and theoretically analyze local search strategies

Ning Zhong; Rui Guo; Wenbin Li

2009-01-01

94

Errorless and errorful learning modulated by transcranial direct current stimulation  

PubMed Central

Background Errorless learning is advantageous over trial and error learning (errorful learning) as errors are avoided during learning resulting in increased memory performance. Errorful learning challenges the executive control system of memory processes as the erroneous items compete with the correct items during retrieval. The left dorsolateral prefrontal cortex (DLPFC) is a core region involved in this executive control system. Transcranial direct current stimulation (tDCS) can modify the excitability of underlying brain functioning. Results In a single blinded tDCS study one group of young healthy participants received anodal and another group cathodal tDCS of the left DLPFC each compared to sham stimulation. Participants had to learn words in an errorless and an errorful manner using a word stem completion paradigm. The results showed that errorless compared to errorful learning had a profound effect on the memory performance in terms of quality. Anodal stimulation of the left DLPFC did not modulate the memory performance following errorless or errorful learning. By contrast, cathodal stimulation hampered memory performance after errorful learning compared to sham, whereas there was no modulation after errorless learning. Conclusions Concluding, the study further supports the advantages of errorless learning over errorful learning. Moreover, cathodal stimulation of the left DLPFC hampered memory performance following the conflict-inducing errorful learning as compared to no modulation after errorless learning emphasizing the importance of the left DLPFC in executive control of memory.

2011-01-01

95

Limitations of Gene Duplication Models: Evolution of Modules in Protein Interaction Networks  

PubMed Central

It has been generally acknowledged that the module structure of protein interaction networks plays a crucial role with respect to the functional understanding of these networks. In this paper, we study evolutionary aspects of the module structure of protein interaction networks, which forms a mesoscopic level of description with respect to the architectural principles of networks. The purpose of this paper is to investigate limitations of well known gene duplication models by showing that these models are lacking crucial structural features present in protein interaction networks on a mesoscopic scale. This observation reveals our incomplete understanding of the structural evolution of protein networks on the module level.

Emmert-Streib, Frank

2012-01-01

96

Distributed Neighbor Discovery in Ad Hoc Networks Using Directional Antennas  

Microsoft Academic Search

In this paper, we propose a distributed neighbor discov- ery algorithm in ad hoc networks using directional anten- nas. A newly joining node obtains the information about its neighbors in both its omnidirectional and directional range by querying a subset of its omnidirectional neighbors. The main contribution of the proposed algorithm is that it does not require all neighbor nodes

Rully Adrian Santosa; Bu-sung Lee; Chai Kiat Yeo; Teck Meng Lim

2006-01-01

97

Directed Altruism and Enforced Reciprocity in Social Networks  

Microsoft Academic Search

We conduct online field experiments in large real-world social networks in order to decompose prosocial giving into three components: (1) baseline altruism toward randomly selected strangers, (2) directed altruism that favors friends over random strangers, and (3) giving motivated by the prospect of future interaction. Directed altruism increases giving to friends by 52 percent relative to random strangers, while future

Tanya Rosenblat; Markus M. Möbius

2009-01-01

98

Capacity achieving modulation format for high-speed optical networks  

NASA Astrophysics Data System (ADS)

In recent years, we have witnessed an increased demand on optical-networks transmission-capacities due to the growing popularity of the Internet and multimedia in everyday life. According to industry expert estimates, 1Tb/s-Ethernet should be standardized by the year 2012-2013. To this end, we propose a non-uniform modulation format that achieves the channel capacity for SNRs of up to 25dB. The proposed modulation format is optimized for ASE-noise-dominated channels and can achieve 400Gb/s data rate per polarization utilizing the currently-available components operating at 50-GSymbols/s. One major benefit of the current scheme is that it is an affordable upgrade to the current systems.

Batshon, Hussam G.; Djordjevic, Ivan B.; Xu, Lei; Wang, Ting

2010-01-01

99

Prefrontal transcranial direct current stimulation changes connectivity of resting-state networks during fMRI.  

PubMed

Transcranial direct current stimulation (tDCS) has been proposed for experimental and therapeutic modulation of regional brain function. Specifically, anodal tDCS of the dorsolateral prefrontal cortex (DLPFC) together with cathodal tDCS of the supraorbital region have been associated with improvement of cognition and mood, and have been suggested for the treatment of several neurological and psychiatric disorders. Although modeled mathematically, the distribution, direction, and extent of tDCS-mediated effects on brain physiology are not well understood. The current study investigates whether tDCS of the human prefrontal cortex modulates resting-state network (RSN) connectivity measured by functional magnetic resonance imaging (fMRI). Thirteen healthy subjects underwent real and sham tDCS in random order on separate days. tDCS was applied for 20 min at 2 mA with the anode positioned over the left DLPFC and the cathode over the right supraorbital region. Patterns of resting-state brain connectivity were assessed before and after tDCS with 3 T fMRI, and changes were analyzed for relevant networks related to the stimulation-electrode localizations. At baseline, four RSNs were detected, corresponding to the default mode network (DMN), the left and right frontal-parietal networks (FPNs) and the self-referential network. After real tDCS and compared with sham tDCS, significant changes of regional brain connectivity were found for the DMN and the FPNs both close to the primary stimulation site and in connected brain regions. These findings show that prefrontal tDCS modulates resting-state functional connectivity in distinct functional networks of the human brain. PMID:22031874

Keeser, Daniel; Meindl, Thomas; Bor, Julie; Palm, Ulrich; Pogarell, Oliver; Mulert, Christoph; Brunelin, Jerome; Möller, Hans-Jürgen; Reiser, Maximilian; Padberg, Frank

2011-10-26

100

MOfinder: A Novel Algorithm for Detecting Overlapping Modules from Protein-Protein Interaction Network  

PubMed Central

Since organism development and many critical cell biology processes are organized in modular patterns, many algorithms have been proposed to detect modules. In this study, a new method, MOfinder, was developed to detect overlapping modules in a protein-protein interaction (PPI) network. We demonstrate that our method is more accurate than other 5 methods. Then, we applied MOfinder to yeast and human PPI network and explored the overlapping information. Using the overlapping modules of human PPI network, we constructed the module-module communication network. Functional annotation showed that the immune-related and cancer-related proteins were always together and present in the same modules, which offer some clues for immune therapy for cancer. Our study around overlapping modules suggests a new perspective on the analysis of PPI network and improves our understanding of disease.

Yu, Qi; Li, Gong-Hua; Huang, Jing-Fei

2012-01-01

101

Optimal Opportunistic Scheduling and Adaptive Modulation Policies in Wireless Ad-Hoc Networks with Network Coding  

NASA Astrophysics Data System (ADS)

In this paper, we study an opportunistic scheduling and adaptive modulation scheme for a wireless network with an XOR network coding scheme, which results in a cross-layer problem for MAC and physical layers. A similar problem was studied in [2] which considered an idealized system with the Shannon capacity. They showed that it may not be optimal for a relay node to encode all possible native packets and there exists the optimal subset of native packets that depends on the channel condition at the receiver node of each native packet. In this paper, we consider a more realistic model than that of [2] with a practical modulation scheme such as M-PSK. We show that the optimal policy is to encode native as many native packets as possible in the network coding group into a coded packet regardless of the channel condition at the receiver node for each native packet, which is a different conclusion from that of [2]. However, we show that adaptive modulation, in which the constellation size of a coded packet is adjusted based on the channel condition of each receiver node, provides a higher throughput than fixed modulation, in which its constellation size is always fixed regardless of the channel condition at each receiver node.

Gong, Seong-Lyong; Kim, Byung-Gook; Lee, Jang-Won

102

IEEE1451-based smart module for in-vehicle networking systems of intelligent vehicles  

Microsoft Academic Search

As vehicles become intelligent for the convenience and safety of drivers, in-vehicle networking (IVN) systems and smart modules are essential components of intelligent vehicles. However, there are obstacles for the wide acceptance of smart modules. First, there exist numerous IVN protocols that a smart module should be able to support. Second, the whole smart module has to be replaced when

Kyung Chang Lee; Man Ho Kim; Suk Lee; Hong Hee Lee

2004-01-01

103

Directly driven Rayleigh—Taylor instability of modulated CH targets  

NASA Astrophysics Data System (ADS)

Directly driven ablative Rayleigh—Taylor (R—T) instability of modulated CH targets was studied using the face-on X-ray radiography on the Shen-Guang II device. We obtained temporal evolution images of the R—T instability perturbation. The R—T instability growth factor has been obtained by using the methods of fast Fourier transform and seeking the difference of light intensity between the peak and the valley of the targets. Through comparison with the the theoretical simulation, we found that the experimental data had a good agreement with the theoretical simulation results before 1.8 ns, and was lower than the theoretical simulation results after that.

Jia, Guo; Xiong, Jun; Dong, Jia-Qin; Xie, Zhi-Yong; Wu, Jiang

2012-09-01

104

Both hand position and movement direction modulate visual attention  

PubMed Central

The current study explored effects of continuous hand motion on the allocation of visual attention. A concurrent paradigm was used to combine visually concealed continuous hand movements with an attentionally demanding letter discrimination task. The letter probe appeared contingent upon the moving right hand passing through one of six positions. Discrimination responses were then collected via a keyboard press with the static left hand. Both the right hand's position and its movement direction systematically contributed to participants' visual sensitivity. Discrimination performance increased substantially when the right hand was distant from, but moving toward the visual probe location (replicating the far-hand effect, Festman et al., 2013). However, this effect disappeared when the probe appeared close to the static left hand, supporting the view that static and dynamic features of both hands combine in modulating pragmatic maps of attention.

Festman, Yariv; Adam, Jos J.; Pratt, Jay; Fischer, Martin H.

2013-01-01

105

Excitability modulation of the motor system induced by transcranial direct current stimulation: A multimodal approach.  

PubMed

Anodal and cathodal transcranial direct current stimulations (tDCS) are both established techniques to induce cortical excitability changes. Typically, in the human motor system, such cortical modulations are inferred through changes in the amplitude of the motor evoked potentials (MEPs). However, it is now possible to directly evaluate tDCS-induced changes at the cortical level by recording the transcranial magnetic stimulation evoked potentials (TEPs) using electroencephalography (EEG). The present study investigated the modulation induced by the tDCS on the motor system. The study evaluates changes in the MEPs, in the amplitude and distribution of the TEPs, in resting state oscillatory brain activity and in behavioral performance in a simple manual response task. Both the short- and long-term tDCS effects were investigated by evaluating their time course at ~0 and 30min after tDCS. Anodal tDCS over the left primary motor cortex (M1) induced an enhancement of corticospinal excitability, whereas cathodal stimulation produced a reduction. These changes in excitability were indexed by changes in MEP amplitude. More interestingly, tDCS modulated the cortical reactivity, which is the neuronal activity evoked by TMS, in a polarity-dependent and site-specific manner. Cortical reactivity increased after anodal stimulation over the left M1, whereas it decreased with cathodal stimulation. These effects were partially present also at long term evaluation. No polarity-specific effect was found either on behavioral measures or on oscillatory brain activity. The latter showed a general increase in the power density of low frequency oscillations (theta and alpha) at both stimulation polarities. Our results suggest that tDCS is able to modulate motor cortical reactivity in a polarity-specific manner, inducing a complex pattern of direct and indirect cortical activations or inhibitions of the motor system-related network, which might be related to changes in synaptic efficacy of the motor cortex. PMID:23845429

Pellicciari, Maria Concetta; Brignani, Debora; Miniussi, Carlo

2013-07-09

106

Interarrival times of message propagation on directed networks  

NASA Astrophysics Data System (ADS)

One of the challenges in fighting cybercrime is to understand the dynamics of message propagation on botnets, networks of infected computers used to send viruses, unsolicited commercial emails (SPAM) or denial of service attacks. We map this problem to the propagation of multiple random walkers on directed networks and we evaluate the interarrival time distribution between successive walkers arriving at a target. We show that the temporal organization of this process, which models information propagation on unstructured peer to peer networks, has the same features as SPAM reaching a single user. We study the behavior of the message interarrival time distribution on three different network topologies using two different rules for sending messages. In all networks the propagation is not a pure Poisson process. It shows universal features on Poissonian networks and a more complex behavior on scale free networks. Results open the possibility to indirectly learn about the process of sending messages on networks with unknown topologies, by studying interarrival times at any node of the network.

Mihaljev, Tamara; de Arcangelis, Lucilla; Herrmann, Hans J.

2011-08-01

107

Interarrival times of message propagation on directed networks.  

PubMed

One of the challenges in fighting cybercrime is to understand the dynamics of message propagation on botnets, networks of infected computers used to send viruses, unsolicited commercial emails (SPAM) or denial of service attacks. We map this problem to the propagation of multiple random walkers on directed networks and we evaluate the interarrival time distribution between successive walkers arriving at a target. We show that the temporal organization of this process, which models information propagation on unstructured peer to peer networks, has the same features as SPAM reaching a single user. We study the behavior of the message interarrival time distribution on three different network topologies using two different rules for sending messages. In all networks the propagation is not a pure Poisson process. It shows universal features on Poissonian networks and a more complex behavior on scale free networks. Results open the possibility to indirectly learn about the process of sending messages on networks with unknown topologies, by studying interarrival times at any node of the network. PMID:21929069

Mihaljev, Tamara; de Arcangelis, Lucilla; Herrmann, Hans J

2011-08-15

108

Multi-transceiver simulation modules for free-space optical mobile ad hoc networks  

NASA Astrophysics Data System (ADS)

This paper presents realistic simulation modules to assess characteristics of multi-transceiver free-space-optical (FSO) mobile ad-hoc networks. We start with a physical propagation model for FSO communications in the context of mobile ad-hoc networks (MANETs). We specifically focus on the drop in power of the light beam and probability of error in the decoded signal due to a number of parameters (such as separation between transmitter and receiver and visibility in the propagation medium), comparing our results with well-known theoretical models. Then, we provide details on simulating multi-transceiver mobile wireless nodes in Network Simulator 2 (NS-2), realistic obstacles in the medium and communication between directional optical transceivers. We introduce new structures in the networking protocol stack at lower layers to deliver such functionality. At the end, we provide our findings resulted from detailed modeling and simulation of FSO-MANETs regarding effects of such directionality on higher layers in the networking stack.

Bilgi, Mehmet; Yuksel, Murat

2010-04-01

109

Input-rate modulation of ? oscillations is sensitive to network topology, delays and short-term plasticity.  

PubMed

Simulated networks of excitatory and inhibitory neurons have previously been shown to reproduce critical features of experimental data regarding neural coding in V1, such as a positive relationship between thalamic input spike rate and the power of gamma frequency oscillations. This effect, referred to as modulated gamma power, could represent a neural code in V1 for stimulus characteristics that affect thalamic spike rate such as contrast or intensity. The simulated network's assumptions included homogeneous random connectivity, equal synaptic delays after spike arrival, and constant synaptic efficacies. Plausible alternative assumptions include small world connectivity, a wide distribution of axonal propagation delays, and short term synaptic plasticity, and here we assess the individual impact of each of these on the model's success in reproducing modulated gamma power. First, we developed several alternative algorithms for simulating directed networks with clustered connectivity and balanced excitation and inhibition. We found that modulated gamma power was absent in all small-world networks that had a relatively low abundance of reciprocal connectivity, which suggests that such motifs are present in V1 cortical networks at levels at least equal to those found in random networks. We also found in a different network type that the balance of excitation and inhibition could be destroyed when the network was in the small-world regime. Given all neurons had identical in-degrees, this result suggests that balance relies on motif distributions as well as mean connectivity. Second, altering the distribution of axonal delays had little effect, but increasing the mean delay led to a secondary gamma modulation at harmonics of the main peak, and since this is not observed experimentally, it suggests a mean delay in V1 networks less than 2 ms. Finally, we compared two types of excitatory synaptic plasticity, and found that modulated beta power emerged in addition to gamma power for one type, in the presence of short term depression in interneurons. This article is part of a Special Issue entitled "Neural Coding". PMID:22000590

McDonnell, Mark D; Mohan, Ashutosh; Stricker, Christian; Ward, Lawrence M

2011-09-08

110

Direct Marketing Modeling Using Evolutionary Bayesian Network Learning Algorithm  

Microsoft Academic Search

\\u000a Direct marketing modeling identifies effective models for improving managerial decision making in marketing. This paper proposes\\u000a a novel system for discovering models represented as Bayesian networks from incomplete databases in the presence of missing\\u000a values. It combines an evolutionary algorithm with the traditional Expectation-Maximization(EM) algorithm to find better network structures in each iteration round. A data completing method is also

Man Leung Wong

111

Reliable MAC broadcast protocol in directional and omni-directional transmissions for vehicular ad hoc networks  

Microsoft Academic Search

This paper presents the design, implementation and simulation results of a reliable Medium Access Control (MAC) broadcast protocol for Vehicular Ad hoc Networks for omni-directional and directional transmissions. The IEEE 802.11 MAC protocol uses control frames for handshaking to reliably communicate unicast data. In contrast, the broadcast data is transmitted without any control frames. This results in increased collisions due

Ravi M. Yadumurthy; Mohan Sadashivaiah; Ranga Makanaboyina

2005-01-01

112

DMesh: Incorporating Practical Directional Antennas in Multichannel Wireless Mesh Networks  

Microsoft Academic Search

Wireless mesh networks (WMNs) have been proposed as an effective solution for ubiquitous last-mile broadband access. Three key factors that affect the usability of WMNs are high throughput, cost-effectiveness, and ease of deployability. In this paper, we propose DMesh, a WMN architecture that combines spatial separation from directional antennas with frequency separation from orthogonal channels to improve the throughput of

Saumitra M. Das; Himabindu Pucha; Dimitrios Koutsonikolas; Y. Charlie Hu; Dimitrios Peroulis

2006-01-01

113

UDB: Using Directional Beacons for Localization in Underwater Sensor Networks  

Microsoft Academic Search

Underwater sensor networks (UWSN) are widely used in many applications, such as oceanic resource exploration, pollution monitoring, tsunami warnings and mine reconnaissance. In UWSNs, determining the location information of each sensor node is a critical issue, because many services are based on the localization results. In this paper, we introduce a novel underwater localization approach based on directional signals, which

Hanjiang Luo; Yiyang Zhao; Zhongwen Guo; Siyuan Liu; Pengpeng Chen; Lionel M. Ni

2008-01-01

114

Intelligent video content routing in a direct access network  

Microsoft Academic Search

The video content is growing rapidly in the Internet. This demand has raised a great deal of challenges. One of the crucial problems is to figure out an efficient content routing approach to quickly find and transport right titles to users. This paper presents a direct access network (DAN) which can automatically fetch interesting subject to the users' community in

Zhu Wang; Tiejian Luo

2011-01-01

115

Coverage directed test generation for functional verification using bayesian networks  

Microsoft Academic Search

Functional verification is widely acknowledged as the bottleneck in the hardware design cycle. This paper addresses one of the main challenges of simulation based verification (or dynamic verification), by providing a new approach for Coverage Directed Test Generation (CDG). This approach is based on Bayesian networks and computer learning techniques. It provides an efficient way for closing a feedback loop

Shai Fine; Avi Ziv

2003-01-01

116

Adaptive modulation in ad hoc DS\\/CDMA packet radio networks  

Microsoft Academic Search

This paper investigates the benefit of adaptive modulation based on channel state information (CSI) in DS\\/CDMA multihop packet radio networks. By exploiting varying channel conditions on different links, adaptive modulation can be used in ad hoc networks to provide upper layers with higher capacity links over which to route traffic. Performance is evaluated in terms of the information efficiency, a

Michael R. Souryal; Branimir R. Vojcic; Raymond L. Pickholtz

2003-01-01

117

High-frequency neuronal network modulations encoded in scalp EEG precede the onset of focal seizures  

PubMed Central

Modulations of neuronal network interactions by seizure precursors are only partially understood and difficult to measure, in part due to inherent intra- and inter-patient seizure heterogeneity and EEG variability. This study investigated preictal neuromodulations associated with seizures originating in the temporal and/or frontal lobes, using information theoretic parameters estimated from awake scalp EEGs in two frequency ranges, ?100 Hz and >100 Hz, respectively. Seizure-related activity at high frequencies has not been extensively estimated in awake scalp EEGs. Based on the statistical similarity of preictal and ictal information parameters, preictal network interactions appeared to be specifically modulated at frequencies >100 Hz, but not at lower frequencies. The dynamics of these parameters varied distinctly according to the origin of seizure onset (temporal versus frontal). Although preliminary, and based on a small patient sample for which the potential heterogeneity of multiple anticonvulsive medications was difficult to control, these results suggest that preictal modulations may be estimated from high-frequency scalp EEGs using directional information measures with high specificity to ictal events, and may thus be promising for improving seizure prediction.

Stamoulis, Catherine; Gruber, Lawrence J.; Schomer, Donald L.; Chang, Bernard S.

2012-01-01

118

Heterogeneous optical networking using orthogonal OAM multimode modulation  

NASA Astrophysics Data System (ADS)

In order to solve capacity and energy-efficiency problems of future Internet technologies simultaneously, in this paper, we propose the use of energy-efficient N-dimensional (ND) orbital angular momentum (OAM) coded-modulation. The energy-efficient signal constellation is obtained by employing the energy-efficient signal constellation design algorithm. This scheme can achieve beyond 100 Gb/s transmission while employing the state-of-the-art 10 Gb/s technology. The proposed scheme significantly outperforms conventional M-ary PAM. The proposed scheme represents a promising candidate for indoor optical wireless communication, terrestrial free-space optical (FSO) communication, data center applications and can be used as enabling technology for heterogeneous optical networking, thanks to its transparency to both free-space optical and few-mode/multimode fiber links.

Djordjevic, Ivan B.; Anguita, Jaime

2012-10-01

119

Modulation of glutamine metabolism by the PI(3)K-PKB-FOXO network regulates autophagy.  

PubMed

The PI(3)K-PKB-FOXO signalling network provides a major intracellular hub for the regulation of cell proliferation, survival and stress resistance. Here we report an unexpected role for FOXO transcription factors in regulating autophagy by modulating intracellular glutamine levels. To identify transcriptional targets of this network, we performed global transcriptional analyses after conditional activation of the key components PI(3)K, PKB/Akt, FOXO3 and FOXO4. Using this pathway approach, we identified glutamine synthetase as being transcriptionally regulated by PI(3)K-PKB-FOXO signalling. Conditional activation of FOXO also led to an increased level of glutamine production. FOXO activation resulted in mTOR inhibition by preventing the translocation of mTOR to lysosomal membranes in a glutamine-synthetase-dependent manner. This resulted in an increased level of autophagy as measured by LC3 lipidation, p62 degradation and fluorescent imaging of multiple autophagosomal markers. Inhibition of FOXO3-mediated autophagy increased the level of apoptosis, suggesting that the induction of autophagy by FOXO3-mediated glutamine synthetase expression is important for cellular survival. These findings reveal a growth-factor-responsive network that can directly modulate autophagy through the regulation of glutamine metabolism. PMID:22820375

van der Vos, Kristan E; Eliasson, Pernilla; Proikas-Cezanne, Tassula; Vervoort, Stephin J; van Boxtel, Ruben; Putker, Marrit; van Zutphen, Iris J; Mauthe, Mario; Zellmer, Sebastian; Pals, Cornelieke; Verhagen, Liesbeth P; Groot Koerkamp, Marian J A; Braat, A Koen; Dansen, Tobias B; Holstege, Frank C; Gebhardt, Rolf; Burgering, Boudewijn M; Coffer, Paul J

2012-07-22

120

Unbiased degree-preserving randomization of directed binary networks.  

PubMed

Randomizing networks using a naive "accept-all" edge-swap algorithm is generally biased. Building on recent results for nondirected graphs, we construct an ergodic detailed balance Markov chain with nontrivial acceptance probabilities for directed graphs, which converges to a strictly uniform measure and is based on edge swaps that conserve all in and out degrees. The acceptance probabilities can also be generalized to define Markov chains that target any alternative desired measure on the space of directed graphs in order to generate graphs with more sophisticated topological features. This is demonstrated by defining a process tailored to the production of directed graphs with specified degree-degree correlation functions. The theory is implemented numerically and tested on synthetic and biological network examples. PMID:22680534

Roberts, E S; Coolen, A C C

2012-04-05

121

Allosteric modulators for the treatment of schizophrenia: targeting glutamatergic networks.  

PubMed

Schizophrenia is a highly debilitating mental disorder which afflicts approximately 1% of the global population. Cognitive and negative deficits account for the lifelong disability associated with schizophrenia, whose symptoms are not effectively addressed by current treatments. New medicines are needed to treat these aspects of the disease. Neurodevelopmental, neuropathological, genetic, and behavioral pharmacological data indicate that schizophrenia stems from a dysfunction of glutamate synaptic transmission, particularly in frontal cortical networks. A number of novel pre- and postsynaptic mechanisms affecting glutamatergic synaptic transmission have emerged as viable targets for schizophrenia. While developing orthosteric glutamatergic agents for these targets has proven extremely difficult, targeting allosteric sites of these targets has emerged as a promising alternative. From a medicinal chemistry perspective, allosteric sites provide an opportunity of finding agents with better drug-like properties and greater target specificity. Furthermore, allosteric modulators are better suited to maintaining the highly precise temporal and spatial aspects of glutamatergic synaptic transmission. Herein, we review neuropathological and genomic/genetic evidence underscoring the importance of glutamate synaptic dysfunction in the etiology of schizophrenia and make a case for allosteric targets for therapeutic intervention. We review progress in identifying allosteric modulators of AMPA receptors, NMDA receptors, and metabotropic glutamate receptors, all with the aim of restoring physiological glutamatergic synaptic transmission. Challenges remain given the complexity of schizophrenia and the difficulty in studying cognition in animals and humans. Nonetheless, important compounds have emerged from these efforts and promising preclinical and variable clinical validation has been achieved. PMID:23409764

Menniti, Frank S; Lindsley, Craig W; Conn, P Jeffrey; Pandit, Jayvardhan; Zagouras, Panayiotis; Volkmann, Robert A

2013-01-01

122

Allosteric Modulators for the Treatment of Schizophrenia: Targeting Glutamatergic Networks  

PubMed Central

Schizophrenia is a highly debilitating mental disorder which afflicts approximately 1% of the global population. Cognitive and negative deficits account for the lifelong disability associated with schizophrenia, whose symptoms are not effectively addressed by current treatments. New medicines are needed to treat these aspects of the disease. Neurodevelopmental, neuropathological, genetic, and behavioral pharmacological data indicate that schizophrenia stems from a dysfunction of glutamate synaptic transmission, particularly in frontal cortical networks. A number of novel pre- and postsynaptic mechanisms affecting glutamatergic synaptic transmission have emerged as viable targets for schizophrenia. While developing orthosteric glutamatergic agents for these targets has proven extremely difficult, targeting allosteric sites of these targets has emerged as a promising alternative. From a medicinal chemistry perspective, allosteric sites provide an opportunity of finding agents with better drug-like properties and greater target specificity. Furthermore, allosteric modulators are better suited to maintaining the highly precise temporal and spatial aspects of glutamatergic synaptic transmission. Herein, we review neuropathological and genomic/genetic evidence underscoring the importance of glutamate synaptic dysfunction in the etiology of schizophrenia and make a case for allosteric targets for therapeutic intervention. We review progress in identifying allosteric modulators of AMPA receptors, NMDA receptors, and metabotropic glutamate receptors, all with the aim of restoring physiological glutamatergic synaptic transmission. Challenges remain given the complexity of schizophrenia and the difficulty in studying cognition in animals and humans. Nonetheless, important compounds have emerged from these efforts and promising preclinical and variable clinical validation has been achieved.

Menniti, Frank S.; Lindsley, Craig W.; Conn, P. Jeffrey; Pandit, Jayvardhan; Zagouras, Panayiotis; Volkmann, Robert A.

2013-01-01

123

Directed partial correlation: inferring large-scale gene regulatory network through induced topology disruptions.  

PubMed

Inferring regulatory relationships among many genes based on their temporal variation in transcript abundance has been a popular research topic. Due to the nature of microarray experiments, classical tools for time series analysis lose power since the number of variables far exceeds the number of the samples. In this paper, we describe some of the existing multivariate inference techniques that are applicable to hundreds of variables and show the potential challenges for small-sample, large-scale data. We propose a directed partial correlation (DPC) method as an efficient and effective solution to regulatory network inference using these data. Specifically for genomic data, the proposed method is designed to deal with large-scale datasets. It combines the efficiency of partial correlation for setting up network topology by testing conditional independence, and the concept of Granger causality to assess topology change with induced interruptions. The idea is that when a transcription factor is induced artificially within a gene network, the disruption of the network by the induction signifies a genes role in transcriptional regulation. The benchmarking results using GeneNetWeaver, the simulator for the DREAM challenges, provide strong evidence of the outstanding performance of the proposed DPC method. When applied to real biological data, the inferred starch metabolism network in Arabidopsis reveals many biologically meaningful network modules worthy of further investigation. These results collectively suggest DPC is a versatile tool for genomics research. The R package DPC is available for download (http://code.google.com/p/dpcnet/). PMID:21494330

Yuan, Yinyin; Li, Chang-Tsun; Windram, Oliver

2011-04-06

124

Directed Partial Correlation: Inferring Large-Scale Gene Regulatory Network through Induced Topology Disruptions  

PubMed Central

Inferring regulatory relationships among many genes based on their temporal variation in transcript abundance has been a popular research topic. Due to the nature of microarray experiments, classical tools for time series analysis lose power since the number of variables far exceeds the number of the samples. In this paper, we describe some of the existing multivariate inference techniques that are applicable to hundreds of variables and show the potential challenges for small-sample, large-scale data. We propose a directed partial correlation (DPC) method as an efficient and effective solution to regulatory network inference using these data. Specifically for genomic data, the proposed method is designed to deal with large-scale datasets. It combines the efficiency of partial correlation for setting up network topology by testing conditional independence, and the concept of Granger causality to assess topology change with induced interruptions. The idea is that when a transcription factor is induced artificially within a gene network, the disruption of the network by the induction signifies a genes role in transcriptional regulation. The benchmarking results using GeneNetWeaver, the simulator for the DREAM challenges, provide strong evidence of the outstanding performance of the proposed DPC method. When applied to real biological data, the inferred starch metabolism network in Arabidopsis reveals many biologically meaningful network modules worthy of further investigation. These results collectively suggest DPC is a versatile tool for genomics research. The R package DPC is available for download (http://code.google.com/p/dpcnet/).

Yuan, Yinyin; Li, Chang-Tsun; Windram, Oliver

2011-01-01

125

The Southern California Integrated GPS Network Education Module  

NSDL National Science Digital Library

This educational module was designed to allow students to interactively explore the use of SCIGN (Southern California Integrated GPS Network) and its data in earthquake studies. It is divided into four major sections: Plate Tectonics, Earthquakes, GPS (Global Positioning System), and Space Technology at Work. All of the sections include background material and activities; the first three sections focus primarily on introducing satellite technology and tectonic phenomena, and the final section serves to integrate knowledge learned in the first three by allowing students to use real SCIGN data in their investigations into plate tectonics, earthquakes, and GPS. Primary concepts include: Forces in the Earth cause its surface to change over time, earthquakes release stress causing permanent change in the Earth's crust, GPS is a satellite technology used as a tool to measure crustal change, and SCIGN is a network of GPS stations used to study tectonics and earthquakes in Southern California. The activities include: How many earthquakes does it take to build a mountain?, Are GPS measurements accurate or precise? What is a rate? How far away are satellites? How fast is the Jet Propulsion Laboratory's station moving? How long will it take for Los Angeles and San Francisco to meet?

Glasscoe, Maggi; Mikolajcik, Anne; Donnellan, Andrea; Watkins, Michael; Smith, Mark

126

The Southern California Integrated GPS Network Education Module  

NSDL National Science Digital Library

This educational module was designed to allow students to interactively explore the use of SCIGN (Southern California Integrated GPS Network) and its data in earthquake studies. It is divided into four major sections: Plate Tectonics, Earthquakes, GPS (Global Positioning System), and Space Technology at Work. All of the sections include background material and activities; the first three sections focus primarily on introducing satellite technology and tectonic phenomena, and the final section serves to integrate knowledge learned in the first three by allowing students to use real SCIGN data in their investigations into plate tectonics, earthquakes, and GPS. Primary concepts include: Forces in the Earth cause its surface to change over time, earthquakes release stress causing permanent change in the Earth\\'s crust, GPS is a satellite technology used as a tool to measure crustal change, and SCIGN is a network of GPS stations used to study tectonics and earthquakes in Southern California. The activities include: How many earthquakes does it take to build a mountain?, Are GPS measurements accurate or precise? What is a rate? How far away are satellites? How fast is the Jet Propulsion Laboratory\\'s station moving? How long will it take for Los Angeles and San Francisco to meet?

Glasscoe, Maggi; Watkins, Michael; Smith, Mark; Donnellan, Andrea; Mikolajcik, Anne

2006-12-21

127

Secure Upgrade of Hardware Security Modules in Bank Networks  

NASA Astrophysics Data System (ADS)

We study the secure upgrade of critical components in wide networked systems, focussing on the case study of PIN processing Hardware Security Modules (HSMs). These tamper-resistant devices, used by banks to securely transmit and verify the PIN typed at the ATMs, have been shown to suffer from API level attacks that allow an insider to recover user PINs and, consequently, clone cards. Proposed fixes require to reduce and modify the HSM functionality by, e.g., sticking on a single format of the transmitted PIN or adding MACs for the integrity of user data. Upgrading HSMs worldwide is, of course, unaffordable. We thus propose strategies to incrementally upgrade the network so to obtain upgraded, secure subnets, while preserving the compatibility towards the legacy system. Our strategies aim at finding tradeoffs between the cost for special "guardian" HSMs used on the borderline between secure and insecure nodes, and the size of the team working in the upgrade process, representing the maximum number of nodes that can be simultaneously upgraded.

Focardi, Riccardo; Luccio, Flaminia L.

128

Gene duplication models for directed networks with limits on growth  

NASA Astrophysics Data System (ADS)

Background: Duplication of genes is important for evolution of molecular networks. Many authors have therefore considered gene duplication as a driving force in shaping the topology of molecular networks. In particular it has been noted that growth via duplication would act as an implicit means of preferential attachment, and thereby provide the observed broad degree distributions of molecular networks. Results: We extend current models of gene duplication and rewiring by including directions and the fact that molecular networks are not a result of unidirectional growth. We introduce upstream sites and downstream shapes to quantify potential links during duplication and rewiring. We find that this in itself generates the observed scaling of transcription factors for genome sites in prokaryotes. The dynamical model can generate a scale-free degree distribution, p(k)\\propto 1/k^{\\gamma } , with exponent ? = 1 in the non-growing case, and with ?>1 when the network is growing. Conclusions: We find that duplication of genes followed by substantial recombination of upstream regions could generate features of genetic regulatory networks. Our steady state degree distribution is however too broad to be consistent with data, thereby suggesting that selective pruning acts as a main additional constraint on duplicated genes. Our analysis shows that gene duplication can only be a main cause for the observed broad degree distributions if there are also substantial recombinations between upstream regions of genes.

Enemark, Jakob; Sneppen, Kim

2007-11-01

129

Early fragmentation in the adaptive voter model on directed networks.  

PubMed

We consider voter dynamics on a directed adaptive network with fixed out-degree distribution. A transition between an active phase and a fragmented phase is observed. This transition is similar to the undirected case if the networks are sufficiently dense and have a narrow out-degree distribution. However, if a significant number of nodes with low out degree is present, then fragmentation can occur even far below the estimated critical point due to the formation of self-stabilizing structures that nucleate fragmentation. This process may be relevant for fragmentation in current political opinion formation processes. PMID:22680538

Zschaler, Gerd; Böhme, Gesa A; Seißinger, Michael; Huepe, Cristián; Gross, Thilo

2012-04-13

130

Dopaminergic modulation of local network activity in rat prefrontal cortex.  

PubMed

Dopamine modulates prefrontal cortex excitability in complex ways. Dopamine's net effect on local neuronal networks is therefore difficult to predict based on studies on pharmacologically isolated excitatory or inhibitory connections. In the present work, we have studied the effects of dopamine on evoked activity in acute rat brain slices when both excitation and inhibition are intact. Whole cell recordings from layer II/III pyramidal cells under conditions of normal synaptic transmission showed that bath-applied dopamine (30 microM) increased the outward inhibitory component of composite postsynaptic currents, whereas inward excitatory currents were not significantly affected. Optical imaging with the voltage-sensitive dye N-(3-(triethylammonium)propyl)-4-(4-(p-diethylaminophenyl)buta-dienyl)pyridinium dibromide revealed that bath application of dopamine significantly decreased the amplitude, duration, and lateral spread of activity in local cortical networks. This effect of dopamine was observed both with single and train (5 at 20 Hz) stimuli. The effect was mimicked by the D1-like receptor agonistR(+)-6-chloro-7,8-dihydroxy-1-methyl-1-phenyl-2,3,4,5-tetrahydro-1H-3-benzazepine hydrobromide (1 microM) and was blocked by R(+)-7-chloro-8-hydroxy-3-methyl-1-phenyl-2,3,4,5-tetrahydro-1H-3-benzazepine hydrochloride (10 microM), a selective antagonist for D1-like receptors. The D2-like receptor agonist quinpirole (10 microM) had no significant effect on evoked dye signals. Our results suggest that dopamine's effect on inhibition dominates over that on excitation under conditions of normal synaptic transmission. Such neuromodulation by dopamine may be important for maintenance of stability in local neuronal networks in the prefrontal cortex. PMID:17392423

Bandyopadhyay, Susanta; Hablitz, John J

2007-03-28

131

C-element: A New Clustering Algorithm to Find High Quality Functional Modules in PPI Networks  

PubMed Central

Graph clustering algorithms are widely used in the analysis of biological networks. Extracting functional modules in protein-protein interaction (PPI) networks is one such use. Most clustering algorithms whose focuses are on finding functional modules try either to find a clique like sub networks or to grow clusters starting from vertices with high degrees as seeds. These algorithms do not make any difference between a biological network and any other networks. In the current research, we present a new procedure to find functional modules in PPI networks. Our main idea is to model a biological concept and to use this concept for finding good functional modules in PPI networks. In order to evaluate the quality of the obtained clusters, we compared the results of our algorithm with those of some other widely used clustering algorithms on three high throughput PPI networks from Sacchromyces Cerevisiae, Homo sapiens and Caenorhabditis elegans as well as on some tissue specific networks. Gene Ontology (GO) analyses were used to compare the results of different algorithms. Each algorithm's result was then compared with GO-term derived functional modules. We also analyzed the effect of using tissue specific networks on the quality of the obtained clusters. The experimental results indicate that the new algorithm outperforms most of the others, and this improvement is more significant when tissue specific networks are used.

Ghasemi, Mahdieh; Rahgozar, Maseud; Bidkhori, Gholamreza; Masoudi-Nejad, Ali

2013-01-01

132

C-element: A New Clustering Algorithm to Find High Quality Functional Modules in PPI Networks.  

PubMed

Graph clustering algorithms are widely used in the analysis of biological networks. Extracting functional modules in protein-protein interaction (PPI) networks is one such use. Most clustering algorithms whose focuses are on finding functional modules try either to find a clique like sub networks or to grow clusters starting from vertices with high degrees as seeds. These algorithms do not make any difference between a biological network and any other networks. In the current research, we present a new procedure to find functional modules in PPI networks. Our main idea is to model a biological concept and to use this concept for finding good functional modules in PPI networks. In order to evaluate the quality of the obtained clusters, we compared the results of our algorithm with those of some other widely used clustering algorithms on three high throughput PPI networks from Sacchromyces Cerevisiae, Homo sapiens and Caenorhabditis elegans as well as on some tissue specific networks. Gene Ontology (GO) analyses were used to compare the results of different algorithms. Each algorithm's result was then compared with GO-term derived functional modules. We also analyzed the effect of using tissue specific networks on the quality of the obtained clusters. The experimental results indicate that the new algorithm outperforms most of the others, and this improvement is more significant when tissue specific networks are used. PMID:24039752

Ghasemi, Mahdieh; Rahgozar, Maseud; Bidkhori, Gholamreza; Masoudi-Nejad, Ali

2013-09-05

133

Bose-Einstein condensation in random directed networks.  

PubMed

We consider the phenomenon of Bose-Einstein condensation in a random growing directed network. The network grows by the addition of vertices and edges. At each time step the network gains a vertex with probability p and an edge with probability 1-p. The new vertex has a fitness (a,b) a,b>0, with probability f(a,b). A vertex with fitness (a,b), with in-degree i and out-degree j, gains a new incoming edge with rate a(i+1) and an outgoing edge with rate b(j+1). The Bose-Einstein condensation occurs as a function of fitness distribution f(a,b). PMID:14682857

Sotolongo-Costa, O; Rodgers, G J

2003-11-21

134

Temperature modulated differential scanning calorimetry during isothermal curing of phase separating polymer networks  

Microsoft Academic Search

Temperature modulated differential scanning calorimetry (TMDSC) and conventional differential scanning calorimetry (DSC) have been applied for investigation of isothermal curing of two component polymer networks separating into two phases during network formation. The network component consists of diglycidylether of bisphenol A (DGEBA) cross-linked with diaminodiphenyl methane (DDM) and the linear polymer component is polyethersulfone (PES). Isothermal curing experiments at 373

I. Alig; W. Jenninger; J. E. K. Schawe

1998-01-01

135

Direct and remote modulation of l -channels in chromaffin cells  

Microsoft Academic Search

Understanding precisely the functioning of voltage-gated Ca2+ channels and their modulation by signaling molecules will help clarifying the Ca2+-dependent mechanisms controlling exocytosis in chromaffin cells. In recent years, we have learned more about the various\\u000a pathways through which Ca2+ channels can be up- or down-modulated by hormones and neurotransmitters and how these changes may condition chromaffin cell\\u000a activity and catecolamine

Pietro Baldelli; Jesus Miguel Hernández-Guijo; Valentina Carabelli; Monica Novara; Tiziana Cesetti; Eva Andrés-Mateos; Carmen Montiel; Emilio Carbone

2004-01-01

136

Learning module networks from genome-wide location and expression data.  

PubMed

We develop a systematic algorithm for discovering network of regulatory modules, which identifies regulatory modules and their regulation program by integrating genome-wide location and expression data. Unlike previous approaches [Eisen, M.B., Spellman, P.T., Brown, P.O. and Botstein, D. (1998) Proc. Natl. Acad. Sci. USA 95, 14863-14868; Tavazoie, S., Hughes, J.D., Campbell, M.J., Cho, R.J. and Church, G.M. (1999) Nat. Genet. 22, 281-285; Ihmels, J., Friedlander, G., Bergmann, S., Sarig, O., Ziv, Y. and Barkai, N. (2002) Nat. Genet. 31, 370-377; Segal, E., Shapira, M., Regev, A., Pe'er, D., Botstein, D., Koller, D. and Friedman, N. (2003) Nat. Genet. 34, 166-176] that relied primarily on gene expression data, our algorithm regards the regulator binding data as prior knowledge that provide direct evidence of physical regulatory interactions. We applied the method to a Saccharomyces cerevisiae genome-wide location data [Lee, T.I., Rinaldi, N.J., Robert, F., Odom, D.T., Bar-Joseph, Z., Gerber, G.K., Hannett, N.M., Harbison, C.T., Thompson, C.M., Simon, I., Zeitlinger, J., Jennings, E.G., Murray, H.L. Gordon, D.B., Ren, B., Wyrick, J.J., Tagne, J.B., Volkert, T.L., Fraenkel, E., Gifford, D.K. and Young, R.A. (2002) Science 298, 799-804] for 106 DNA-binding transcription factors and 250 gene expression experiments under the conditions from the cell cycle to responses to various stress conditions. The results show that our method is able to identify functionally coherent modules and their proper regulators. Supplementary materials are available at http://compbio.sibnet.org/projects/module-network/. PMID:15589836

Xu, Xiaojiang; Wang, Lianshui; Ding, Dafu

2004-12-17

137

Modulating cortico-striatal and thalamo-cortical functional connectivity with transcranial direct current stimulation.  

PubMed

Transcranial direct current stimulation (tDCS) is a noninvasive brain stimulation technique that has been shown to alter cortical excitability and activity via application of weak direct currents. Beyond intracortical effects, functional imaging as well as behavioral studies are suggesting additional tDCS-driven alterations of subcortical areas, however, direct evidence for such effects is scarce. We aimed to investigate the impact of tDCS on cortico-subcortical functional networks by seed functional connectivity analysis of different striatal and thalamic regions to prove tDCS-induced alterations of the cortico-striato-thalamic circuit. fMRI resting state data sets were acquired immediately before and after 10 min of bipolar tDCS during rest, with the anode/cathode placed over the left primary motor cortex (M1) and the cathode/anode over the contralateral frontopolar cortex. To control for possible placebo effects, an additional sham stimulation session was carried out. Functional coupling between the left thalamus and the ipsilateral primary motor cortex (M1) significantly increased following anodal stimulation over M1. Additionally, functional connectivity between the left caudate nucleus and parietal association cortices was significantly strengthened. In contrast, cathodal tDCS over M1 decreased functional coupling between left M1 and contralateral putamen. In summary, in this study, we show for the first time that tDCS modulates functional connectivity of cortico-striatal and thalamo-cortical circuits. Here we highlight that anodal tDCS over M1 is capable of modulating elements of the cortico-striato-thalamo-cortical functional motor circuit. PMID:21922602

Polanía, Rafael; Paulus, Walter; Nitsche, Michael A

2011-09-16

138

Serotonergic modulation of spatial working memory: predictions from a computational network model  

PubMed Central

Serotonin (5-HT) receptors of types 1A and 2A are strongly expressed in prefrontal cortex (PFC) neurons, an area associated with cognitive function. Hence, 5-HT could be effective in modulating prefrontal-dependent cognitive functions, such as spatial working memory (SWM). However, a direct association between 5-HT and SWM has proved elusive in psycho-pharmacological studies. Recently, a computational network model of the PFC microcircuit was used to explore the relationship between 5-HT and SWM (Cano-Colino et al., 2013). This study found that both excessive and insufficient 5-HT levels lead to impaired SWM performance in the network, and it concluded that analyzing behavioral responses based on confidence reports could facilitate the experimental identification of SWM behavioral effects of 5-HT neuromodulation. Such analyses may have confounds based on our limited understanding of metacognitive processes. Here, we extend these results by deriving three additional predictions from the model that do not rely on confidence reports. Firstly, only excessive levels of 5-HT should result in SWM deficits that increase with delay duration. Secondly, excessive 5-HT baseline concentration makes the network vulnerable to distractors at distances that were robust to distraction in control conditions, while the network still ignores distractors efficiently for low 5-HT levels that impair SWM. Finally, 5-HT modulates neuronal memory fields in neurophysiological experiments: Neurons should be better tuned to the cued stimulus than to the behavioral report for excessive 5-HT levels, while the reverse should happen for low 5-HT concentrations. In all our simulations agonists of 5-HT1A receptors and antagonists of 5-HT2A receptors produced behavioral and physiological effects in line with global 5-HT level increases. Our model makes specific predictions to be tested experimentally and advance our understanding of the neural basis of SWM and its neuromodulation by 5-HT receptors.

Cano-Colino, Maria; Almeida, Rita; Compte, Albert

2013-01-01

139

Integrated Brain Circuits: Astrocytic Networks Modulate Neuronal Activity and Behavior  

PubMed Central

The past decade has seen an explosion of research on roles of neuron-astrocyte interactions in the control of brain function. We highlight recent studies performed on the tripartite synapse, the structure consisting of pre- and postsynaptic elements of the synapse and an associated astrocytic process. Astrocytes respond to neuronal activity and neuro-transmitters, through the activation of metabotropic receptors, and can release the gliotransmitters ATP, D-serine, and glutamate, which act on neurons. Astrocyte-derived ATP modulates synaptic transmission, either directly or through its metabolic product adenosine. D-serine modulates NMDA receptor function, whereas glia-derived glutamate can play important roles in relapse following withdrawal from drugs of abuse. Cell type–specific molecular genetics has allowed a new level of examination of the function of astrocytes in brain function and has revealed an important role of these glial cells that is mediated by adenosine accumulation in the control of sleep and in cognitive impairments that follow sleep deprivation.

Halassa, Michael M.; Haydon, Philip G.

2011-01-01

140

Performance of directly modulated OFDM data over multimode fiber link  

NASA Astrophysics Data System (ADS)

The performance of orthogonal-frequency-division-multiplexing (OFDM) technology in the multimode fiber (MMF) optical communication system is investigated numerically. The mode dispersion in MMF is analyzed by utilizing the optical angular spectrum analysis method. Simulation results in terms of bit-error-rate (BER) and signal-to-noise ratio (SNR) show that the transmission distance can reach up to 2.5-km at 10- 3 BER for 40-Gb/s data. Results of different modulation formats further indicate that better performance can be achieved by adopting multi-level modulation format.

Chen, Tianhua; Pan, Wei; Yan, Lianshan; Luo, Bin; Yi, Anlin; Ye, Jia

2010-11-01

141

Intermodulation distortion in a directly modulated semiconductor injection laser  

SciTech Connect

A most important quantity in high-frequency analog transmission is the intermodulation distortion product. Experimental studies of the third order intermodulation distortion products in the modulation response of high-speed semiconductor lasers give very low values (<-60 dB) at low frequencies, an increase at a rate of 40 dB/dec as the modulation frequency is increased, and a leveling off at one-half of the relaxation oscillation resonance frequency. These experimental results can be well explained by a theory based on a perturbative analysis of laser dynamics.

Lau, K.Y.; Yariv, A.

1984-11-15

142

Integrated Module and Gene-Specific Regulatory Inference Implicates Upstream Signaling Networks  

PubMed Central

Regulatory networks that control gene expression are important in diverse biological contexts including stress response and development. Each gene's regulatory program is determined by module-level regulation (e.g. co-regulation via the same signaling system), as well as gene-specific determinants that can fine-tune expression. We present a novel approach, Modular regulatory network learning with per gene information (MERLIN), that infers regulatory programs for individual genes while probabilistically constraining these programs to reveal module-level organization of regulatory networks. Using edge-, regulator- and module-based comparisons of simulated networks of known ground truth, we find MERLIN reconstructs regulatory programs of individual genes as well or better than existing approaches of network reconstruction, while additionally identifying modular organization of the regulatory networks. We use MERLIN to dissect global transcriptional behavior in two biological contexts: yeast stress response and human embryonic stem cell differentiation. Regulatory modules inferred by MERLIN capture co-regulatory relationships between signaling proteins and downstream transcription factors thereby revealing the upstream signaling systems controlling transcriptional responses. The inferred networks are enriched for regulators with genetic or physical interactions, supporting the inference, and identify modules of functionally related genes bound by the same transcriptional regulators. Our method combines the strengths of per-gene and per-module methods to reveal new insights into transcriptional regulation in stress and development.

Roy, Sushmita; Lagree, Stephen; Hou, Zhonggang; Thomson, James A.; Stewart, Ron; Gasch, Audrey P.

2013-01-01

143

An AWG-based 10 Gbit/s colorless WDM-PON system using a chirp-managed directly modulated laser  

NASA Astrophysics Data System (ADS)

We propose an arrayed waveguide grating (AWG)-based 10 Gbit/s per channel full duplex wavelength division multiplexing passive optical network (WDM-PON). A chirp managed directly modulated laser with return-to-zero (RZ) differential phase shift keying (DPSK) modulation technique is utilized for downlink (DL) direction, and then the downlink signal is re-modulated for the uplink (UL) direction using intensity modulation technique with the data rate of 10 Gbit/s per channel. A successful WDM-PON transmission operation with the data rate of 10 Gbit/s per channel over a distance of 25 km without any optical amplification or dispersion compensation is demonstrated with low power penalty.

Latif, Abdul; Yu, Chong-xiu; Xin, Xiang-jun; Husain, Aftab; Hussain, Ashiq; Munir, Abid; Khan, Yousaf

2012-09-01

144

Emulation of modulated data channels in optical networks using a programmable optical processor  

Microsoft Academic Search

We demonstrate a method of filtering broadband ASE to emulate high bit rate optically modulated signals, allowing accurately shaped artificial channels to be loaded into a channel plan for optical networks.

Cibby Pulikkaseril; Jochen Schroder; Michael A. F. Roelens

2011-01-01

145

Predicting Fault Prone Modules by the Dempster-Shafer Belief Networks  

Microsoft Academic Search

This paper describes a novel methodology for predicting fault prone modules. The methodology is based on Dempster-Shafer (D-S) belief networks. Our approach consists of three steps: First, building the Dempster- Shafer network by the induction algorithm; Second, selecting the predictors (attributes) by the logistic procedure; Third, feeding the predictors describing the modules of the current project into the inducted Dempster-Shafer

Lan Guo; Bojan Cukic; Harshinder Singh

2003-01-01

146

Assessing the functional coherence of modules found in multiple-evidence networks from Arabidopsis  

Microsoft Academic Search

Background  Combining multiple evidence-types from different information sources has the potential to reveal new relationships in biological\\u000a systems. The integrated information can be represented as a relationship network, and clustering the network can suggest possible\\u000a functional modules. The value of such modules for gaining insight into the underlying biological processes depends on their\\u000a functional coherence. The challenges that we wish to

Artem Lysenko; Michael Defoin-Platel; Keywan Hassani-Pak; Jan Taubert; Charlie Hodgman; Christopher J. Rawlings; Mansoor Saqi

2011-01-01

147

Identification of susceptibility modules for coronary artery disease using a genome wide integrated network analysis.  

PubMed

Although recent genome-wide association studies (GWAS) have identified a handful of variants with best significance for coronary artery disease (CAD), it remains a challenge to summarize the underlying biological information from the abundant genotyping data. Here, we propose an integrated network analysis that effectively combines GWAS genotyping dataset, protein-protein interaction (PPI) database, literature and pathway annotation information. This three-step approach was illustrated for a comprehensive network analysis of CAD as the following. First, a network was constructed from PPI database and CAD seed genes mined from the available literatures. Then, susceptibility network modules were captured from the results of gene-based association tests. Finally, susceptibility modules were annotated with potential mechanisms for CAD via the KEGG pathway database. Our network analysis identified four susceptibility modules for CAD including a complex module that consisted of 15 functional inter-connected sub-modules, AGPAT3-AGPAT4-PPAP2B module, ITGA11-ITGB1 module and EMCN-SELL module. MAPK10 and COL4A2 among the top-scored focal adhesion pathway related module were the most significant genes (MAPK10: OR=32.5, P=3.5×10(-11); COL4A2: OR=2.7, P=2.8×10(-10)). The significance of the two genes were further validated by other two gene-based association tests (MAPK10: P=0.009 and 0.007; COL4A2: P=0.001 and 0.023) and another independent GWAS dataset (MAPK10: P=0.001; COL4A2: P=0.0004). Furthermore, 34 out of 44 previously reported CAD susceptibility genes were captured by our CAD PPI network and 17 of them were also significant genes. The susceptibility modules identified in our study might provide novel clues for the clarification of CAD pathogenesis in the future. PMID:23994195

Duan, Shiwei; Luo, Xuhong; Dong, Changzheng

2013-08-29

148

Modulation of cortical-subcortical networks in Parkinson's disease by applied field effects  

PubMed Central

Studies suggest that endogenous field effects may play a role in neuronal oscillations and communication. Non-invasive transcranial electrical stimulation with low-intensity currents can also have direct effects on the underlying cortex as well as distant network effects. While Parkinson’s disease (PD) is amenable to invasive neuromodulation in the basal ganglia by deep brain stimulation (DBS), techniques of non-invasive neuromodulation like transcranial direct current stimulation (tDCS) and transcranial alternating current stimulation (tACS) are being investigated as possible therapies. tDCS and tACS have the potential to influence the abnormal cortical-subcortical network activity that occurs in PD through sub-threshold changes in cortical excitability or through entrainment or disruption of ongoing rhythmic cortical activity. This may allow for the targeting of specific features of the disease involving abnormal oscillatory activity, as well as the enhancement of potential cortical compensation for basal ganglia dysfunction and modulation of cortical plasticity in neurorehabilitation. However, little is currently known about how cortical stimulation will affect subcortical structures, the size of any effect, and the factors of stimulation that will influence these effects.

Hess, Christopher W.

2013-01-01

149

Wavelength channel data rewrite using saturated SOA modulator for WDM networks with centralized light sources  

Microsoft Academic Search

This paper describes a method for realizing the efficient utilization of wavelength resources in wavelength-division multiplexing networks with centralized light sources. Using a deeply saturated semiconductor optical amplifier (SOA) modulator located in a remote node (RN), we erase the data on a downstream signal with a low extinction ratio and modulate it with new data to generate an upstream signal.

Hiroki Takesue; Toshihiko Sugie

2003-01-01

150

Implementation and design analysis of a network messaging module using virtual interface architecture  

Microsoft Academic Search

The buffered message interface (BMI) of PVFSv2 is a low level network abstraction that allows PVFSv2 to operate on any protocol that has BMI support. This work presents a BMI module that supports the VIA over an early release version of InfiniBand and also over Myrinet. The baseline bandwidth and latency of the implementation were compared to the BMI modules

Gregory Amerson; Amy W. Apon

2004-01-01

151

Branched networks by directed assembly of shape anisotropic magnetic particles.  

PubMed

The directed assembly of shape anisotropic magnetic particles into targeted macrostructures requires judicious particle design. We present a framework to understand the self-assembly of magnetic non-Brownian H-shaped particles and the formation of branched networks under an applied magnetic field. A finite element integration (FEI) method is developed to identify the preferred particle orientation (relative to the applied field) at different values of the geometric parameters defining H shapes, and used to construct a phase diagram to generalize the results. Theoretical predictions are validated by comparing with experiments performed using magnetic hydrogels synthesized using stop-flow lithography (SFL). We demonstrate the ability of H-shaped particles to form chains parallel to the field that can thicken in a direction orthogonal to the field, and in some cases with branching. The assembly of a suspension containing H-shaped particles, or rods, or a combination of both, is reported. PMID:21932770

Panda, Priyadarshi; Bong, Ki Wan; Hatton, T Alan; Doyle, Patrick S

2011-10-21

152

Electromagnetic Modeling and Simulation of a Directly-Modulated L-band Microstrip Patch Antenna.  

National Technical Information Service (NTIS)

The direct pulse modulation of a carrier wave by incorporating fast- switching semiconductor devices into an antenna structure and biasing them with a baseband information signal has recently emerged as a promising technique for improving communication sy...

S. D. Keller W. D. Palmer W. T. Joines

2007-01-01

153

Direct modulation of semiconductor lasers at f>10 GHz by low-temperature operation  

SciTech Connect

Using a 175-..mu..m-long buried-heterostructure laser fabricated on a semi-insulating substrate operating at -50 /sup 0/C, a direct amplitude modulation bandwidth in excess of 10 GHz has been achieved.

Lau, K.Y.; Harder, C.; Yariv, A.

1984-02-01

154

Illumimote: A High Performance Light Sensor Module for Wireless Sensor Networks  

Microsoft Academic Search

We describe application requirements, design, integration and performance evaluation of the Illumimote, a light sens- ing module for wireless sensor networks. Achieving perfor- mance comparable to commercial light meters while con- forming to the beneficial size and energy constraints of sen- sor networks, the Illumimote includes light intensity, RGB color, incident light angle, attitude and temperature sensors. Its maximum power

Jonathan Friedman; Mani B. Srivastava; Pablo Gutierrez; Vids Samanta; Jeff Burke

155

Cellular and Synaptic Modulation Underlying Substance P-Mediated Plasticity of the Lamprey Locomotor Network  

Microsoft Academic Search

The tachykinin substance P modulates the lamprey locomotor network by increasing the frequency of NMDA-evoked ventral root bursts and by making the burst activity more regular. These effects can last in excess of 24 hr. In this paper, the effects of substance P on the synaptic and cellular properties of motor neurons and identified network interneurons have been examined. Substance

David Parker; Sten Grillner

1998-01-01

156

Directly modulated transmission systems using half-split-band and wavelength division multiplexing techniques  

NASA Astrophysics Data System (ADS)

We present a directly modulated NTSC AM-VSB 80 channels fiber optical CATV long-distance transmission systems by using 1550nm digital DFB laser diodes, half-split-band, wavelength division multiplexing and EDGA-repeated techniques. Good performances of CNR, CSO and CTB are obtained after 80 km standard single mode fiber transmission. The direct transmission systems are simpler and cost lower than externally modulated transmission systems. 8

Lu, Hai-Han; Lee, Ching-Ting

1998-07-01

157

Employing split-band technique and Fabry Perot etalon filter to improve directly modulated fiber optical CATV system performances  

NASA Astrophysics Data System (ADS)

We proposed and demonstrated a directly modulated NTSC 77-channel fiber optical CATV transport system using split-band technique at the transmitting site and Fabry Perot (FP) etalon filter at the receiving site to improve system performance. Good performance of carrier-to-noise ratio (CNR), composite second-order (CSO), and composite triple beat (CTB) were obtained in our proposed systems over a 100-km standard single-mode fiber (SMF) transmission. Employing a FP etalon filter in fiber optical CATV transport systems is useful in real network, as it is simple, passive, and potentially low cost. This proposed system reveals an outstanding one with simpler and more economic advantages than that of externally modulated transport system.

Lu, Hai-Han; Patra, Ardhendu Sekhar; Wu, Hsiao-Wen; Tzeng, Shah-Jye; Ho, Wen-Jeng; Yee, Hoshin

2008-07-01

158

Functional Influence-Based Approach to Identify Overlapping Modules in Biological Networks  

Microsoft Academic Search

\\u000a The inherent, dynamic, and structural behaviors of complex biological networks in a topological perspective have been widely\\u000a studied recently. These studies have attempted to discover hidden functional knowledge on a system level since biological\\u000a networks provide insights into the underlying mechanisms of biological processes and molecular functions within a cell. Functional\\u000a modules can be identified from biological networks as a

Young-Rae Cho; Aidong Zhang

159

How biologically relevant are interaction-based modules in protein networks?  

PubMed Central

By applying a graph-based algorithm to yeast protein-interaction networks we have extracted modular structures and show that they can be validated using information from the phylogenetic conservation of the network components. We show that the module cores, the parts with the highest intramodular connectivity, are biologically relevant components of the networks. These constituents correlate only weakly with other levels of organization. We also discuss how such structures could be used for finding targets for antimicrobial drugs.

Poyatos, Juan F; Hurst, Laurence D

2004-01-01

160

Directional blood flow imaging in volumetric optical microangiography achieved by digital frequency modulation  

PubMed Central

An effective digital frequency modulation approach to achieve directional blood flow imaging within microcirculations in tissue beds in vivo for optical microangiography is presented. The method only requires the system to capture one three-dimensional data set within which the interferograms are modulated by a constant frequency modulation that gives one directional flow information. The result is that the imaging speed is doubled and the computational load is halved. The method is experimentally validated by a flow phantom and is tested for imaging of cerebral vascular blood perfusion in a live mouse with the cranium left intact.

Wang, Ruikang K.

2009-01-01

161

The Her7 node modulates the network topology of the zebrafish segmentation clock via sequestration of the Hes6 hub  

PubMed Central

Using in vitro and in vivo assays, we define a network of Her/Hes dimers underlying transcriptional negative feedback within the zebrafish segmentation clock. Some of the dimers do not appear to be DNA-binding, whereas those dimers that do interact with DNA have distinct preferences for cis regulatory sequences. Dimerization is specific, with Hes6 serving as the hub of the network. Her1 binds DNA only as a homodimer but will also dimerize with Hes6. Her12 and Her15 bind DNA both as homodimers and as heterodimers with Hes6. Her7 dimerizes strongly with Hes6 and weakly with Her15. This network structure engenders specific network dynamics and imparts greater influence to the Her7 node. Computational analysis supports the hypothesis that Her7 disproportionately influences the availability of Hes6 to heterodimerize with other Her proteins. Genetic experiments suggest that this regulation is important for operation of the network. Her7 therefore has two functions within the zebrafish segmentation clock. Her7 acts directly within the delayed negative feedback as a DNA-binding heterodimer with Hes6. Her7 also has an emergent function, independent of DNA binding, in which it modulates network topology via sequestration of the network hub.

Trofka, Anna; Schwendinger-Schreck, Jamie; Brend, Tim; Pontius, William; Emonet, Thierry; Holley, Scott A.

2012-01-01

162

Identification of functional modules using network topology and high-throughput data  

PubMed Central

Background With the advent of systems biology, biological knowledge is often represented today by networks. These include regulatory and metabolic networks, protein-protein interaction networks, and many others. At the same time, high-throughput genomics and proteomics techniques generate very large data sets, which require sophisticated computational analysis. Usually, separate and different analysis methodologies are applied to each of the two data types. An integrated investigation of network and high-throughput information together can improve the quality of the analysis by accounting simultaneously for topological network properties alongside intrinsic features of the high-throughput data. Results We describe a novel algorithmic framework for this challenge. We first transform the high-throughput data into similarity values, (e.g., by computing pairwise similarity of gene expression patterns from microarray data). Then, given a network of genes or proteins and similarity values between some of them, we seek connected sub-networks (or modules) that manifest high similarity. We develop algorithms for this problem and evaluate their performance on the osmotic shock response network in S. cerevisiae and on the human cell cycle network. We demonstrate that focused, biologically meaningful and relevant functional modules are obtained. In comparison with extant algorithms, our approach has higher sensitivity and higher specificity. Conclusion We have demonstrated that our method can accurately identify functional modules. Hence, it carries the promise to be highly useful in analysis of high throughput data.

Ulitsky, Igor; Shamir, Ron

2007-01-01

163

An in silico method for detecting overlapping functional modules from composite biological networks  

PubMed Central

Background The ever-increasing flow of gene expression and protein-protein interaction (PPI) data has assisted in understanding the dynamics of the cell. The detection of functional modules is the first step in deciphering the apparent modularity of biological networks. However, most network-partitioning algorithms consider only the topological aspects and ignore the underlying functional relationships. Results In the current study we integrate proteomics and microarray data of yeast, in the form of a weighted PPI graph. We partition the enriched PPI network with the novel DetMod algorithm and we identify 335 modules. One of the main advantages of DetMod is that it manages to capture the inter-module cross-talk by allowing a controlled degree of overlap among the detected modules. The obtained modules are densely connected in terms of protein interactions, while their members share up to a high degree similar biological process GO terms. Moreover, known protein complexes are largely incorporated in the assessed modules. Finally, we display the prevalence of our method against modules resulting from other computational approaches. Conclusion The successful integration of heterogeneous data and the concept of the proposed algorithm provide confident functional modules. We also proved that our approach is superior to methods restricted to PPI data only.

Maraziotis, Ioannis A; Dimitrakopoulou, Konstantina; Bezerianos, Anastasios

2008-01-01

164

Stealth constrained routing optimization using directional antennas in mobile ad-hoc networks  

Microsoft Academic Search

Low probability of detection (LPD) is an important requirement of mobile ad-hoc networks in battlefield applications. Although directional antennas are a suitable means to achieve LPD, related work on the use of directional antennas at the MAC and network layer has been mostly centered on improving network utilization and QoS, while LPD has been mostly addressed at the physical layer.

Antonio Grilo; Mario Macedo; Pedro Sebastiao; Mario Nunes

2004-01-01

165

Application of directed transfer function and network formalism for the assessment of functional connectivity in working memory task.  

PubMed

The dynamic pattern of functional connectivity during a working memory task was investigated by means of the short-time directed transfer function. A clear-cut picture of transmissions was observed with the main centres of propagation located in the frontal and parietal regions, in agreement with imaging studies and neurophysiological hypotheses concerning the mechanisms of working memory. The study of the time evolution revealed that most of the time short-range interactions prevailed, whereas the communication between the main centres of activity occurred more sparsely and changed dynamically in time. The patterns of connectivity were quantified by means of a network formalism based on assortative mixing--an approach novel in the field of brain networks study. By means of application of the above method, we have demonstrated the existence of a modular structure of brain networks. The strength of interaction inside the modules was higher than between modules. The obtained results are compatible with theories concerning metabolic energy saving and efficient wiring in the brain, which showed that preferred organization includes modular structure with dense connectivity inside the modules and more sparse connections between the modules. The presented detailed temporal and spatial patterns of propagation are in line with the neurophysiological hypotheses concerning the role of gamma and theta activity in information processing during a working memory task. PMID:23858482

Blinowska, Katarzyna J; Kami?ski, Maciej; Brzezicka, Aneta; Kami?ski, Jan

2013-07-15

166

Selective Attention to Semantic and Syntactic Features Modulates Sentence Processing Networks in Anterior Temporal Cortex  

PubMed Central

Numerous studies have identified an anterior temporal lobe (ATL) region that responds preferentially to sentence-level stimuli. It is unclear, however, whether this activity reflects a response to syntactic computations or some form of semantic integration. This distinction is difficult to investigate with the stimulus manipulations and anomaly detection paradigms traditionally implemented. The present functional magnetic resonance imaging study addresses this question via a selective attention paradigm. Subjects monitored for occasional semantic anomalies or occasional syntactic errors, thus directing their attention to semantic integration, or syntactic properties of the sentences. The hemodynamic response in the sentence-selective ATL region (defined with a localizer scan) was examined during anomaly/error-free sentences only, to avoid confounds due to error detection. The majority of the sentence-specific region of interest was equally modulated by attention to syntactic or compositional semantic features, whereas a smaller subregion was only modulated by the semantic task. We suggest that the sentence-specific ATL region is sensitive to both syntactic and integrative semantic functions during sentence processing, with a smaller portion of this area preferentially involved in the later. This study also suggests that selective attention paradigms may be effective tools to investigate the functional diversity of networks involved in sentence processing.

Rogalsky, Corianne

2009-01-01

167

A network-aware MAC and routing protocol for effective load balancing in ad hoc wireless networks with directional antenna  

Microsoft Academic Search

Use of directional antenna in the context of ad hoc wireless networks can largely reduce radio interference, thereby improving the utilization of wireless medium. Our major contribution in this paper is to devise a routing strategy, along with a MAC protocol, that exploits the advantages of directional antenna in ad hoc networks for improved system performance. In this paper, we

Siuli Roy; Dola Saha; Somprakash Bandyopadhyay; Tetsuro Ueda; Shinsuke Tanaka

2003-01-01

168

Spatially resolved non-invasive chemical stimulation for modulation of signalling in reconstructed neuronal networks  

PubMed Central

Functional coupling of reconstructed neuronal networks with microelectronic circuits has potential for the development of bioelectronic devices, pharmacological assays and medical engineering. Modulation of the signal processing properties of on-chip reconstructed neuronal networks is an important aspect in such applications. It may be achieved by controlling the biochemical environment, preferably with cellular resolution. In this work, we attempt to design cell–cell and cell–medium interactions in confined geometries with the aim to manipulate non-invasively the activity pattern of an individual neuron in neuronal networks for long-term modulation. Therefore, we have developed a biohybrid system in which neuronal networks are reconstructed on microstructured silicon chips and interfaced to a microfluidic system. A high degree of geometrical control over the network architecture and alignment of the network with the substrate features has been achieved by means of aligned microcontact printing. Localized non-invasive on-chip chemical stimulation of micropatterned rat cortical neurons within a network has been demonstrated with an excitatory neurotransmitter glutamate. Our system will be useful for the investigation of the influence of localized chemical gradients on network formation and long-term modulation.

Mourzina, Yulia; Steffen, Alfred; Kaliaguine, Dmitri; Wolfrum, Bernhard; Schulte, Petra; Bocker-Meffert, Simone; Offenhausser, Andreas

2005-01-01

169

State-dependent, bidirectional modulation of neural network activity by endocannabinoids.  

PubMed

The endocannabinoid (eCB) system and the cannabinoid CB1 receptor (CB1R) play key roles in the modulation of brain functions. Although actions of eCBs and CB1Rs are well described at the synaptic level, little is known of their modulation of neural activity at the network level. Using microelectrode arrays, we have examined the role of CB1R activation in the modulation of the electrical activity of rat and mice cortical neural networks in vitro. We find that exogenous activation of CB1Rs expressed on glutamatergic neurons decreases the spontaneous activity of cortical neural networks. Moreover, we observe that the net effect of the CB1R antagonist AM251 inversely correlates with the initial level of activity in the network: blocking CB1Rs increases network activity when basal network activity is low, whereas it depresses spontaneous activity when its initial level is high. Our results reveal a complex role of CB1Rs in shaping spontaneous network activity, and suggest that the outcome of endogenous neuromodulation on network function might be state dependent. PMID:22090486

Piet, Richard; Garenne, André; Farrugia, Fanny; Le Masson, Gwendal; Marsicano, Giovanni; Chavis, Pascale; Manzoni, Olivier J

2011-11-16

170

Directional Gossip: Gossip in a Wide Area Network  

Microsoft Academic Search

this paper is the wide area network gossip protocol# wedonotaddress local area network issues further. In Section 1 we argued that to have a high reliabilityofmessage delivery, a wide area network gossip protocol needs to have some information about thenetwork topology. Wide area networks can be large and their topology maychange frequently,andso we decided not to require each gossip server

Meng-jang Lin; Keith Marzullo

1999-01-01

171

Nswap: A Network Swapping Module for Linux Clusters  

Microsoft Academic Search

Cluster applications that process large amounts of data, such as parallel scientic or multimedia applications, are likely to cause swap- ping on individual cluster nodes. These applications will perform better on clusters with network swapping support. Network swapping allows any cluster node with over-committed memory to use idle memory of a re- mote node as its backing store and to

Tia Newhall; Sean Finney; Kuzman Ganchev; Michael Spiegel

2003-01-01

172

Molecular transport modulates the adaptive response of branched actin networks to an external force.  

PubMed

Actin networks are an integral part of the cytoskeleton of eukaryotic cells and play an essential role in determining cellular shape and movement. Understanding the underlying mechanism of actin network assembly is of fundamental importance. We developed in this work a minimal motility model and performed stochastic simulations to study mechanical regulation of the growth dynamics of lamellipodia-like branched actin networks, characterized by various force-velocity relations. In such networks, the treadmilling process leads to a concentration gradient of G-actin, and thus G-actin transport is essential to effective actin network assembly. We first explore how capping protein modulates force-velocity relations and then discuss how actin transport due to diffusion and facilitated transport such as advective flow tunes the growth dynamics of the branched actin network. Our work demonstrates the important role of molecular transport in determining the adaptive response of the actin network to an external force. PMID:23962335

Hu, Longhua; Papoian, Garegin A

2013-09-05

173

Modulating lexical and semantic processing by transcranial direct current stimulation.  

PubMed

Here we aim to evaluate the ability of transcranial direct current stimulation (tDCS), which is applied over Wernicke's area and its right homologue, to influence lexical decisions and semantic priming and establish an involvement for temporo-parietal areas in lexical and semantic processing. Thirty-two subjects (17 women) completed a lexical decision task and a semantic priming task while receiving 20 min of bilateral tDCS stimulation (right anodal/left cathodal or left anodal/right cathodal stimulation) or sham stimulation. We hypothesized that right anodal/left cathodal stimulation over temporo-parietal areas would selectively interrupt the typical lexical processing dominance of the left hemisphere and facilitate mediated priming, while left anodal/right cathodal stimulation would selectively facilitate lexical processing and direct priming. Results showed impaired lexical processing under right anodal/left cathodal stimulation in comparison with sham and left anodal/right cathodal stimulation. Results are discussed in light of previous findings and hemispheric lateralization models. PMID:23371750

Weltman, Keren; Lavidor, Michal

2013-02-01

174

An overlapping module identification method in protein-protein interaction networks  

PubMed Central

Background Previous studies have shown modular structures in PPI (protein-protein interaction) networks. More recently, many genome and metagenome investigations have focused on identifying modules in PPI networks. However, most of the existing methods are insufficient when applied to networks with overlapping modular structures. In our study, we describe a novel overlapping module identification method (OMIM) to address this problem. Results Our method is an agglomerative clustering method merging modules according to their contributions to modularity. Nodes that have positive effects on more than two modules are defined as overlapping parts. As well, we designed de-noising steps based on a clustering coefficient and hub finding steps based on nodal weight. Conclusions The low computational complexity and few control parameters prove that our method is suitable for large scale PPI network analysis. First, we verified OMIM on a small artificial word association network which was able to provide us with a comprehensive evaluation. Then experiments on real PPI networks from the MIPS Saccharomyces Cerevisiae dataset were carried out. The results show that OMIM outperforms several other popular methods in identifying high quality modular structures.

2012-01-01

175

A 45nm low-power SAW-less WCDMA transmit modulator using direct quadrature voltage modulation  

Microsoft Academic Search

To address the low-noise low-power requirement of the WCDMA transmitter this paper describes an innovative approach using direct quadrature voltage modulation via a passive voltage mixer driven by a 25%-duty-cycle LO. As shown in Fig. 6.5.2, first the IF l\\/Q voltage inputs are filtered by the passive LPF to lower the far-out noise. By switching on\\/off the transistors M1 to

Xin He; Jan van Sinderen

2009-01-01

176

On Reducing Broadcast Transmission Cost and Redundancy in Ad Hoc Wireless Networks Using Directional Antennas  

Microsoft Academic Search

Using directional antennas to conserve bandwidth and energy consumption in ad hoc wireless networks has at- tracted much attention of the research community in recent years. However, very few research has focused on applying directional antennas to broadcasting. In this paper, we propose a virtual link reduction (VLR) based broadcasting protocol for ad hoc wireless networks using directional antennas. Based

Ling Ding; Yifeng Shao; Minglu Li

2008-01-01

177

Electroptic Polymer Linear Modulators Based on Multiple-Domain Y-Fed Directional Coupler  

Microsoft Academic Search

We developed an analytical method to optimize the design of Y-fed direction couplers at large modulation depth from 10% to 50%. Simulation results indicate that three and four-domain devices can obtain 45 dB higher distortion suppression than two-domain devices, which can potentially achieve 120 dB spurious free dynamic range. We also experimentally demonstrated that the two-domain electrooptic modulator obtained 94

Xiaolong Wang; Boem-Suk Lee; Che-Yun Lin; Dechang An; Ray T. Chen

2010-01-01

178

6GHz Radio-Over-Fiber Upstream Transmission Using a Directly Modulated RSOA  

Microsoft Academic Search

We propose and demonstrate 40-km upstream trans- mission of a 2-Gb\\/s 6-GHz binary phase-shift keyed radio signal using a directly modulated reflective semiconductor optical ampli- fier (RSOA). A delay interferometer, acting as an optical equal- izer, compensates for limited RSOA modulation bandwidth and si- multaneously performs single sideband filtering to relieve disper- sion-induced radio-frequency (RF) fading effect. Furthermore, ex- tended

Adaickalavan Meiyappan; Pooi Yuen Kam; Hoon Kim

2011-01-01

179

Multi-equilibrium property of metabolic networks: SSI module  

Microsoft Academic Search

Background  Revealing the multi-equilibrium property of a metabolic network is a fundamental and important topic in systems biology. Due\\u000a to the complexity of the metabolic network, it is generally a difficult task to study the problem as a whole from both analytical\\u000a and numerical viewpoint. On the other hand, the structure-oriented modularization idea is a good choice to overcome such a

Hong-Bo Lei; Ji-Feng Zhang; Luonan Chen

2011-01-01

180

Advanced Glycation End Products Are Direct Modulators of ?-Cell Function  

PubMed Central

OBJECTIVE Excess accumulation of advanced glycation end products (AGEs) contributes to aging and chronic diseases. We aimed to obtain evidence that exposure to AGEs plays a role in the development of type 1 diabetes (T1D). RESEARCH DESIGN AND METHODS The effect of AGEs was examined on insulin secretion by MIN6N8 cells and mouse islets and in vivo in three separate rodent models: AGE-injected or high AGE–fed Sprague-Dawley rats and nonobese diabetic (NODLt) mice. Rodents were also treated with the AGE-lowering agent alagebrium. RESULTS ?-Cells exposed to AGEs displayed acute glucose-stimulated insulin secretory defects, mitochondrial abnormalities including excess superoxide generation, a decline in ATP content, loss of MnSOD activity, reduced calcium flux, and increased glucose uptake, all of which were improved with alagebrium treatment or with MnSOD adenoviral overexpression. Isolated mouse islets exposed to AGEs had decreased glucose-stimulated insulin secretion, increased mitochondrial superoxide production, and depletion of ATP content, which were improved with alagebrium or with MnTBAP, an SOD mimetic. In rats, transient or chronic exposure to AGEs caused progressive insulin secretory defects, superoxide generation, and ?-cell death, ameliorated with alagebrium. NODLt mice had increased circulating AGEs in association with an increase in islet mitochondrial superoxide generation, which was prevented by alagebrium, which also reduced the incidence of autoimmune diabetes. Finally, at-risk children who progressed to T1D had higher AGE concentrations than matched nonprogressors. CONCLUSIONS These findings demonstrate that AGEs directly cause insulin secretory defects, most likely by impairing mitochondrial function, which may contribute to the development of T1D.

Coughlan, Melinda T.; Yap, Felicia Y.T.; Tong, David C.K.; Andrikopoulos, Sofianos; Gasser, Anna; Thallas-Bonke, Vicki; Webster, Diane E.; Miyazaki, Jun-ichi; Kay, Thomas W.; Slattery, Robyn M.; Kaye, David M.; Drew, Brian G.; Kingwell, Bronwyn A.; Fourlanos, Spiros; Groop, Per-Henrik; Harrison, Leonard C.; Knip, Mikael; Forbes, Josephine M.

2011-01-01

181

Modulating human procedural learning by cerebellar transcranial direct current stimulation.  

PubMed

Neuroimaging studies suggest that the cerebellum contributes to human cognitive processing, particularly procedural learning. This type of learning is often described as implicit learning and involves automatic, associative, and unintentional learning processes. Our aim was to investigate whether cerebellar transcranial direct current stimulation (tDCS) influences procedural learning as measured by the serial reaction time task (SRTT), in which subjects make speeded key press responses to visual cues. A preliminary modeling study demonstrated that our electrode montage (active electrode over the cerebellum with an extra-cephalic reference) generated the maximum electric field amplitude in the cerebellum. We enrolled 21 healthy subjects (aged 20-49 years). Participants did the SRTT, a visual analogue scale and a visual attention task, before and 35 min after receiving 20-min anodal and sham cerebellar tDCS in a randomized order. To avoid carry-over effects, experimental sessions were held at least 1 week apart. For our primary outcome measure (difference in RTs for random and repeated blocks) anodal versus sham tDCS, RTs were significantly slower for sham tDCS than for anodal cerebellar tDCS (p = 0.04), demonstrating that anodal tDCS influenced implicit learning processes. When we assessed RTs for procedural learning across the one to eight blocks, we found that RTs changed significantly after anodal stimulation (interaction "time" × "blocks 1/8": anodal, p = 0.006), but after sham tDCS, they remained unchanged (p = 0.094). No significant changes were found in the other variables assessed. Our finding that anodal cerebellar tDCS improves an implicit learning type essential to the development of several motor skills or cognitive activity suggests that the cerebellum has a critical role in procedural learning. tDCS could be a new tool for improving procedural learning in daily life in healthy subjects and for correcting abnormal learning in neuropsychiatric disorders. PMID:23328908

Ferrucci, Roberta; Brunoni, Andre R; Parazzini, Marta; Vergari, Maurizio; Rossi, Elena; Fumagalli, Manuela; Mameli, Francesca; Rosa, Manuela; Giannicola, Gaia; Zago, Stefano; Priori, Alberto

2013-08-01

182

A Multilevel Approach to Identify Functional Modules in a Yeast Protein-Protein Interaction Network  

Microsoft Academic Search

\\u000a Identifying functional modules is believed to reveal most cellular processes. There have been many computational approaches\\u000a to investigate the underlying biological structures [9, 4, 10, 6]. A spectral clustering method plays a critical role identifying\\u000a functional modules in a yeast protein-protein network in [6, 4]. We present an unweighted-graph version of a multilevel spectral\\u000a algorithm which more accurately identifies protein

Suely Oliveira; Sang-cheol Seok

2006-01-01

183

CATV/radio-on-fiber transport system based on direct modulation  

NASA Astrophysics Data System (ADS)

A directly modulated CATV/radio-on-fiber (ROF) transport system based on external light injection technique, optical single sideband (SSB) filter, and RF amplifier predistorter is proposed and demonstrated. To the best of my knowledge, it is the first time to transmit CATV and ROF signals simultaneously in a directly modulated form. Good performances of carrier-to-noise ratio (CNR), composite second order (CSO) and composite triple beat (CTB) were obtained for CATV band; and low third order intermodulation distortion to carrier ratio (IMD3/C), and bit error rate (BER) values were achieved for ROF application.

Tzeng, Shah-Jye

2006-03-01

184

Highly spectrum efficient OFDM\\/PDM wireless networks by using optical SSB modulation  

Microsoft Academic Search

Optical frequency division multiplexing (OFDM) wireless access network using optical single-sideband modulation is proposed, which allows to deliver different wireless signals from a central station to each base station over an optical fiber network. The optical single-sideband (SSB) OFDM can achieve the highest spectrum efficiency of 0.25 b\\/s\\/Hz. A 0.25 b\\/s\\/Hz has been experimentally verified by the error-free transport of

Ken-Ichi Kitayama

1998-01-01

185

VisANT: data-integrating visual framework for biological networks and modules  

Microsoft Academic Search

VisANT is a web-based software framework for visu- alizing and analyzing many types of networks of bio- logical interactions and associations. Networks are a useful computational tool for representing many types of biological data, such as biomolecular inter- actions, cellular pathways and functional modules. Given user-defined sets of interactions or groupings between genes or proteins, VisANT provides: (i) a visual

Zhenjun Hu; Joe Mellor; Jie Wu; Takuji Yamada; Dustin T. Holloway; Charles Delisi

2005-01-01

186

Multicarrier modulation and cooperative communication in multihop cognitive radio networks  

Microsoft Academic Search

For high-data-rate wireless communication systems, two major issues are the underutilization of limited available radio spectrum and the effect of channel fading. Using dynamic spectrum access, cognitive radio can improve spectrum utilization. Almost all proposed CR systems are based on multicarrier modulation since multiple users can access the MCM systems by allocating subcarriers. Generally, MCM mainly includes two different schemes,

Tao Luo; Fei Lin; Tao Jiang; Mohsen Guizani; Wen Chen

2011-01-01

187

Modulating the Precision of Recurrent Bursts in Cultured Neural Networks  

NASA Astrophysics Data System (ADS)

Synchronized bursts are a very common feature in biological neural networks, and they play an important role in various brain functions and neurological diseases. This Letter investigates “recurrent synchronized bursts” induced by a single pulse stimulation in cultured networks of rat cortical neurons. We look at how the precision in their arrival times can be modified by a noble time-delayed stimulation protocol, which we term as “?t training.” The emergence of recurrent bursts and the change of the precision in their arrival times can be explained by the stochastic resonance of a damped, subthreshold, neural oscillation.

Choi, Joon Ho; Kim, June Hoan; Heo, Ryoun; Lee, Kyoung J.

2012-03-01

188

A testbed to emulate next-generation directional RF and free-space optical tactical networks  

Microsoft Academic Search

The tactical edge network emulation tool (TENET) hardware integration system (THIS) is designed to characterize higher layer responses to the dynamic physical layer topology of a tactical network utilizing directional communication links. THIS emulates the mobile, tactical, network environment using the hardware in a static infrastructure. MATLAB-based tools implement the TENET emulation to simulate mobility induced link fragility, and the

William M. Turner; Daniel J. Tebben; Jason R. Madsen; Anurag Dwivedi

2009-01-01

189

Secure network coding for wireless mesh networks: Threats, challenges, and directions  

Microsoft Academic Search

In recent years, network coding has emerged as a new communication paradigm that can significantly improve the efficiency of network protocols by requiring intermediate nodes to mix packets before forwarding them. Recently, several real-world systems have been proposed to leverage network coding in wireless networks. Although the theoretical foundations of network coding are well understood, a real-world system needs to

Jing Dong; Reza Curtmola; Cristina Nita-Rotaru

2009-01-01

190

A networked viewpoint controller based on a spatiotemporal attention module for the future 3D TV  

Microsoft Academic Search

A networked viewpoint controller exploits a spatiotemporal attention module for the smart user interaction of the future 3D TV. In this paper, a new approach to locate a focus of attention for the generation of candidate viewpoints is suggested. The suggested method combines spatial and temporal features given from a series of images to provide viewers with several viewpoints.

Min-Chul Park; Wonhyuk Choi; Sung Kyu Kim; Jung-Young Son

2007-01-01

191

Direct gain modulation of a semiconductor laser by a GaAs picosecond optoelectronic switch  

SciTech Connect

We report a novel application of high-speed optoelectronic switches for direct gain modulation of semiconductor lasers. A GaAs/GaAlAs buried heterostructure laser is driven by a Cr-doped GaAs photoconducting switch activated by a synchronously mode-locked cw dye laser. Infrared light pulses of 55-ps width are emitted from the semiconductor laser.

Goebel, E.O.; Veith, G.; Kuhl, J.; Habermeier, H.; Luebke, K.; Perger, A.

1983-01-01

192

Effect of modulation format and jamming spectrum on performance of direct sequence spread spectrum systems  

Microsoft Academic Search

The processing gain of a direct sequence spread spectrum system is approximately the ratio of the spreading code chip rate to the data rate. This paper provides a more accurate understanding of the performance of such systems as a function of the modulation scheme and jammer characteristics. Bibtex entry for this abstract Preferred format for this abstract (see Preferences) Find

B. K. Levitt

1980-01-01

193

Urban road network evolution mechanism based on the 'direction preferred connection' and 'degree constraint'  

NASA Astrophysics Data System (ADS)

The urban road network is a complex system that exhibits the properties of self-organization and emergence. Recent theoretical and empirical studies have mainly focused on the structural properties of the urban road networks. This research concentrates on some important parameters such as degree, average degree, meshedness coefficient, betweeness, etc. These parameters of the real road network exhibit specific statistical properties. Some studies show that perhaps these specific statistical properties are caused by a compromise mechanism of the formation of a minimum spanning tree and the greedy triangulation. Inspired by these results, we propose a principle to construct the network (we call it a MG network in this paper) whose structure is located between the minimum spanning tree and the greedy triangulation at first. The structural properties of the MG network are analyzed. We find the formation mechanism of the MG network cannot explain the urban road network evolution well. Then, based on the formation mechanism of the MG network, we add the 'direction preferred connection' and 'degree constraint' principles to the urban road network evolution simulation process. The result of the simulation network turns out to be a planar network that is in accordance with reality. Compared with the real road network's structural properties, we find the simulation results are so consistent with it. It indicates the validation of the model and also demonstrates perhaps the 'direction preferred connection' and 'degree constraint' principle can explain the urban road network evolution better.

Yuan, PengCheng; Juan, ZhiCai

2013-10-01

194

Channel estimation for OFDM modulated two-way relay networks  

Microsoft Academic Search

In this work, we introduce the model of employing orthogonal-frequency-division multiplexing (OFDM) for transmission over time-dispersive channels in the two-way relay network (TWRN), where two source terminals exchange their information through a relay terminal using the amplify-and-forward (AF) relaying scheme. We propose a two-phase training protocol for the channel estimation, which is compatible with the two-phase data transmission scheme. In

Feifei Gao; Rui Zhang; Ying-Chang Liang

2009-01-01

195

Spectral properties of the Google matrix of the World Wide Web and other directed networks  

NASA Astrophysics Data System (ADS)

We study numerically the spectrum and eigenstate properties of the Google matrix of various examples of directed networks such as vocabulary networks of dictionaries and university World Wide Web networks. The spectra have gapless structure in the vicinity of the maximal eigenvalue for Google damping parameter ? equal to unity. The vocabulary networks have relatively homogeneous spectral density, while university networks have pronounced spectral structures which change from one university to another, reflecting specific properties of the networks. We also determine specific properties of eigenstates of the Google matrix, including the PageRank. The fidelity of the PageRank is proposed as a characterization of its stability.

Georgeot, Bertrand; Giraud, Olivier; Shepelyansky, Dima L.

2010-05-01

196

Upstream multi-wavelength shared TDM-PON using RSOA based directly modulated tunable fiber ring laser  

NASA Astrophysics Data System (ADS)

We have proposed to use a directly modulated tunable fiber ring laser based on reflective semiconductor optical amplifiers(RSOA) and tunable optical filter (TOF) as an upstream source in multi-wavelength shared(UMWS) time division multiplexing-passive optical network (TDM-PON) configuration. Downstream signal is broadcasted in TDM way while upstream signals are multiplexed in hybrid time/wavelength division multiplexed way, which upgrades the upstream capacity greatly. Bidirectional transmission of downstream data at 10-Gb/s and upstream data at 1.25-Gb/s per wavelength over 25-km single mode fiber (SMF) is demonstrated with a power penalty of ~0.5 dB at both ends. A stable performance is observed for the upstream wavelength tuned from 1530 nm to 1595 nm.

Li, Zhengxuan; Yi, Lilin; Zhang, Yan; Xiao, Shilin; Hu, Weisheng

2011-11-01

197

Integration of turbo-generator modules in digital transient network analyzer  

SciTech Connect

The behavior of a small power system consisting of two interconnected generators is simulated in real-time by a prototype Digital Transient Network Analyzer (TNA). The prototype Digital TNA consists of two Computational Modules and one I/O Module. The Modules communicate with each other through ribbon cables. Each Computational Module simulates one Turbo-Generator, its Transformer, its Governor, Exciter, and Power System Stabilizer Systems. The numerical integration is shared by two TMS320C30 DSPs at a step-size of 100 microseconds in real-time. The I/O module post-processes the state variables and presents selected information for analog display. The paper presents oscillograms from a test program which includes symmetry checks and behavioral checks against well known waveforms of hunting oscillations, synchronization out-of-phase torques, and subsynchronous resonance phenomena. The success of the Digital TNA depends on: (a) the theoretical method of Decoupled Partitioning so that different portions of the power system can be allocated to different DSP-modules, (b) the architecture of the DSP-modules which can communicate the numerical integration results of one module to its contiguous neighbors with minimum delay.

Guo, Y.; Ooi, B.T.; Lee, H.C. (McGill Univ., Montreal, Quebec (Canada). Dept. of Electrical Engineering)

1994-05-01

198

Influences of impedance matching network on pulse-modulated radio frequency atmospheric pressure glow discharges  

SciTech Connect

Pulse-modulated RF atmospheric pressure glow discharges (APDGs) were investigated in recent years to reduce the thermal accumulation and extend the operation region of the stable alpha glow mode. Different pulse-modulated voltage and current waveforms were acquired in previous experiments, but no attention was paid to the interpretation. We investigated this issue and associated phenomenon via positive and negative feedback effects derived from varying the series capacitor in the inversely L-shaped matching network used in our pulse-modulated RF APGD source. The evolutions of pulse-modulated RF waveforms were found to be associated with the feedback region and the pulsed plasma absorbed RF power. In the positive feedback region, pulse-modulated RF APGDs are relatively stable. In the negative feedback region, wide spikes as well as undershoots occur in RF voltage and current waveforms and the plasma absorbed RF power. In case of a high RF power discharge with a low modulation frequency, the pulse-modulated RF APGD is extinguished and re-ignited due to the enhanced undershoot during the initial pulse phase. The pulse-modulated RF APGD can transit from positive to negative feedback region in a range of series capacitance. Experimental results are discussed by the aid of equivalent circuit, negative and positive feedback effects.

Huo, W. G. [School of Physics and Optoelectronic Technology, Dalian University of Technology, Dalian 116023 (China); School of Physics and Electronic Technology, Liaoning Normal University, Dalian 116029 (China); Xu, K.; Sun, B.; Ding, Z. F. [School of Physics and Optoelectronic Technology, Dalian University of Technology, Dalian 116023 (China)

2012-08-15

199

Influences of impedance matching network on pulse-modulated radio frequency atmospheric pressure glow discharges  

NASA Astrophysics Data System (ADS)

Pulse-modulated RF atmospheric pressure glow discharges (APDGs) were investigated in recent years to reduce the thermal accumulation and extend the operation region of the stable alpha glow mode. Different pulse-modulated voltage and current waveforms were acquired in previous experiments, but no attention was paid to the interpretation. We investigated this issue and associated phenomenon via positive and negative feedback effects derived from varying the series capacitor in the inversely L-shaped matching network used in our pulse-modulated RF APGD source. The evolutions of pulse-modulated RF waveforms were found to be associated with the feedback region and the pulsed plasma absorbed RF power. In the positive feedback region, pulse-modulated RF APGDs are relatively stable. In the negative feedback region, wide spikes as well as undershoots occur in RF voltage and current waveforms and the plasma absorbed RF power. In case of a high RF power discharge with a low modulation frequency, the pulse-modulated RF APGD is extinguished and re-ignited due to the enhanced undershoot during the initial pulse phase. The pulse-modulated RF APGD can transit from positive to negative feedback region in a range of series capacitance. Experimental results are discussed by the aid of equivalent circuit, negative and positive feedback effects.

Huo, W. G.; Xu, K.; Sun, B.; Ding, Z. F.

2012-08-01

200

A Scheduling Algorithm for Connected Target Coverage in Rotatable Directional Sensor Networks  

NASA Astrophysics Data System (ADS)

A key challenge in developing energy-efficient sensor networks is to extend network lifetime in resource-limited environments. As sensors are often densely distributed, they can be scheduled on alternative duty cycles to conserve energy while satisfying the system requirements. Directional sensor networks composed of a large number of directional sensors equipped with a limited battery and with a limited angle of sensing have recently attracted attention. Many types of directional sensors can rotate to face a given direction. Maximizing network lifetime while covering all of the targets in a given area and forwarding sensor data to the sink is a challenge in developing such rotatable directional sensor networks. In this paper, we address the maximum directional cover tree (MDCT) problem of organizing directional sensors into a group of non-disjoint subsets to extend network lifetime. One subset, in which the directional sensors cover all of the targets and forward the data to the sink, is activated at a time, while the others sleep to conserve energy. For the MDCT problem, we first present an energy-consumption model that mainly takes into account the energy expenditure for sensor rotation as well as for the sensing and relaying of data. We also develop a heuristic scheduling algorithm called directional coverage and connectivity (DCC)-greedy to solve the MDCT problem. To verify and evaluate the algorithm, we conduct extensive simulations and show that it extends network lifetime to a reasonable degree.

Han, Youn-Hee; Kim, Chan-Myung; Gil, Joon-Min

201

Nonuniversality in Semi-Directed BARABÁSI-ALBERT Networks  

NASA Astrophysics Data System (ADS)

In usual scale-free networks of Barabási-Albert type, a newly added node selects randomly m neighbors from the already existing network nodes, proportionally to the number of links these had before. Then the number n(k) of nodes with k links each decays as 1/k? where ? = 3 is universal, i.e. independent of m. Now we use a limited directedness in building the network, as a result of which the exponent ? decreases from 3 to 2 for increasing m.

Sumour, M. A.; Radwan, M. A.

2012-09-01

202

Moral enhancement via direct emotion modulation: a reply to John Harris.  

PubMed

Some argue that humans should enhance their moral capacities by adopting institutions that facilitate morally good motives and behaviour. I have defended a parallel claim: that we could permissibly use biomedical technologies to enhance our moral capacities, for example by attenuating certain counter-moral emotions. John Harris has recently responded to my argument by raising three concerns about the direct modulation of emotions as a means to moral enhancement. He argues (1) that such means will be relatively ineffective in bringing about moral improvements, (2) that direct modulation of emotions would invariably come at an unacceptable cost to our freedom, and (3) that we might end up modulating emotions in ways that actually lead to moral decline. In this article I outline some counter-intuitive potential implications of Harris' claims. I then respond individually to his three concerns, arguing that they license only the very weak conclusion that moral enhancement via direct emotion modulation is sometimes impermissible. However I acknowledge that his third concern might, with further argument, be developed into a more troubling objection to such enhancements. PMID:22092503

Douglas, Thomas

2011-11-17

203

Horizontally slotted photonic crystal nanobeam cavity with embedded active nanopillars for ultrafast direct modulation  

NASA Astrophysics Data System (ADS)

A horizontally slotted photonic crystal nanobeam cavity with an embedded active nanopillar structure is proposed for ultrafast direct modulation. By designing the thicknesses of both the nanobeam and the horizontal slot layer, the quality factor (Q factor) and the mode volume (Vn) of the proposed cavity can be engineered independently. As a result, the spontaneous emission (SpE) rate is enhanced with a small Vn of 2.4 while the SpE rate and the cavity photon lifetime have an optimal Q factor of ~ 1000. In our simulation, the modulation bandwidth could be enhanced up to 170 GHz with different emission linewidths of the active nanopillar.

Wang, Da; Cui, Kai-Yu; Feng, Xue; Huang, Yi-Dong; Li, Yong-Zhuo; Liu, Fang; Zhang, Wei

2013-09-01

204

Social status modulates neural activity in the mentalizing network.  

PubMed

The current research explored the neural mechanisms linking social status to perceptions of the social world. Two fMRI studies provide converging evidence that individuals lower in social status are more likely to engage neural circuitry often involved in 'mentalizing' or thinking about others' thoughts and feelings. Study 1 found that college students' perception of their social status in the university community was related to neural activity in the mentalizing network (e.g., DMPFC, MPFC, precuneus/PCC) while encoding social information, with lower social status predicting greater neural activity in this network. Study 2 demonstrated that socioeconomic status, an objective indicator of global standing, predicted adolescents' neural activity during the processing of threatening faces, with individuals lower in social status displaying greater activity in the DMPFC, previously associated with mentalizing, and the amygdala, previously associated with emotion/salience processing. These studies demonstrate that social status is fundamentally and neurocognitively linked to how people process and navigate their social worlds. PMID:22289808

Muscatell, Keely A; Morelli, Sylvia A; Falk, Emily B; Way, Baldwin M; Pfeifer, Jennifer H; Galinsky, Adam D; Lieberman, Matthew D; Dapretto, Mirella; Eisenberger, Naomi I

2012-01-25

205

Ethanol Modulation of Gene Networks: Implications for Alcoholism  

PubMed Central

Alcoholism is a complex disease caused by a confluence of environmental and genetic factors influencing multiple brain pathways to produce a variety of behavioral sequelae, including addiction. Genetic factors contribute to over 50% of the risk for alcoholism and recent evidence points to a large number of genes with small effect sizes as the likely molecular basis for this disease. Recent progress in genomics (microarrays or RNA-Seq) and genetics has led to the identification of a large number of potential candidate genes influencing ethanol behaviors or alcoholism itself. To organize this complex information, investigators have begun to focus on the contribution of gene networks, rather than individual genes, for various ethanol-induced behaviors in animal models or behavioral endophenotypes comprising alcoholism. This chapter reviews some of the methods used for constructing gene networks from genomic data and some of the recent progress made in applying such approaches to the study of the neurobiology of ethanol. We show that rapid technology development in gathering genomic data, together with sophisticated experimental design and a growing collection of sophisticated tools are producing novel insights for understanding the molecular basis of alcoholism and that such approaches promise new opportunities for therapeutic development.

Farris, Sean P.; Miles, Michael F.

2011-01-01

206

Global Analysis of the Human Pathophenotypic Similarity Gene Network Merges Disease Module Components  

PubMed Central

The molecular complexity of genetic diseases requires novel approaches to break it down into coherent biological modules. For this purpose, many disease network models have been created and analyzed. We highlight two of them, “the human diseases networks” (HDN) and “the orphan disease networks” (ODN). However, in these models, each single node represents one disease or an ambiguous group of diseases. In these cases, the notion of diseases as unique entities reduces the usefulness of network-based methods. We hypothesize that using the clinical features (pathophenotypes) to define pathophenotypic connections between disease-causing genes improve our understanding of the molecular events originated by genetic disturbances. For this, we have built a pathophenotypic similarity gene network (PSGN) and compared it with the unipartite projections (based on gene-to-gene edges) similar to those used in previous network models (HDN and ODN). Unlike these disease network models, the PSGN uses semantic similarities. This pathophenotypic similarity has been calculated by comparing pathophenotypic annotations of genes (human abnormalities of HPO terms) in the “Human Phenotype Ontology”. The resulting network contains 1075 genes (nodes) and 26197 significant pathophenotypic similarities (edges). A global analysis of this network reveals: unnoticed pairs of genes showing significant pathophenotypic similarity, a biological meaningful re-arrangement of the pathological relationships between genes, correlations of biochemical interactions with higher similarity scores and functional biases in metabolic and essential genes toward the pathophenotypic specificity and the pleiotropy, respectively. Additionally, pathophenotypic similarities and metabolic interactions of genes associated with maple syrup urine disease (MSUD) have been used to merge into a coherent pathological module. Our results indicate that pathophenotypes contribute to identify underlying co-dependencies among disease-causing genes that are useful to describe disease modularity.

Reyes-Palomares, Armando; Rodriguez-Lopez, Rocio; Ranea, Juan A. G.; Jimenez, Francisca Sanchez; Medina, Miguel Angel

2013-01-01

207

Feature-based attention modulates direction-selective hemodynamic activity within human MT.  

PubMed

Attending to the spatial location or to nonspatial features of a stimulus modulates neural activity in cortical areas that process its perceptual attributes. The feature-based attentional selection of the direction of a moving stimulus is associated with increased firing of individual neurons tuned to the direction of the movement in area V5/MT, while responses of neurons tuned to opposite directions are suppressed. However, it is not known how these multiplicatively scaled responses of individual neurons tuned to different motion-directions are integrated at the population level, in order to facilitate the processing of stimuli that match the perceptual goals. Using functional magnetic resonance imaging (fMRI) the present study revealed that attending to the movement direction of a dot field enhances the response in a number of areas including the human MT region (hMT) as a function of the coherence of the stimulus. Attending the opposite direction, however, lead to a suppressed response in hMT that was inversely correlated with stimulus-coherence. These findings demonstrate that the multiplicative scaling of single-neuron responses by feature-based attention results in an enhanced direction-selective population response within those cortical modules that processes the physical attributes of the attended stimuli. Our results provide strong support for the validity of the "feature similarity gain model" on the integrated population response as quantified by parametric fMRI in humans. PMID:21305663

Stoppel, Christian Michael; Boehler, Carsten Nicolas; Strumpf, Hendrik; Heinze, Hans-Jochen; Noesselt, Toemme; Hopf, Jens-Max; Schoenfeld, Mircea Ariel

2011-02-08

208

Directional MAC Approach for Wireless Body Area Networks  

PubMed Central

Wireless Body Area Networks (WBANs) designed for medical, sports, and entertainment applications, have drawn the attention of academia and industry alike. A WBAN is a special purpose network, designed to operate autonomously to connect various medical sensors and appliances, located inside and/or outside of a human body. This network enables physicians to remotely monitor vital signs of patients and provide real time feedback for medical diagnosis and consultations. The WBAN system can offer two significant advantages: patient mobility due to their use of portable monitoring devices and a location independent monitoring facility. With its appealing dimensions, it brings about a new set of challenges, which we do not normally consider in such small sensor networks. It requires a scalable network in terms of heterogeneous data traffic, low power consumption of sensor nodes, integration in and around the body networking and coexistence. This work presents a medium access control protocol for WBAN which tries to overcome the aforementioned challenges. We consider the use of multiple beam adaptive arrays (MBAA) at BAN Coordinator (BAN_C) node. When used as a BAN_C, an MBAA can successfully receive two or more overlapping packets at the same time. Each beam captures a different packet by automatically pointing its pattern toward one packet while annulling other contending packets. This paper describes how an MBAA can be integrated into a single hope star topology as a BAN_C. Simulation results show the performance of our proposed protocol.

Hussain, Md. Asdaque; Alam, Md. Nasre; Kwak, Kyung Sup

2011-01-01

209

Frequency locking of self-modulated oscillations and hysteresis of a nonautonomous two-directional ring solid-state laser  

SciTech Connect

The effect of the pump modulation on the lasing dynamics of a two-directional ring solid-state laser operating in the self-modulated regime is studied experimentally. The frequency locking was observed when the pump modulation frequency approached the self-modulation frequency. The dependence of the locking band on the laser characteristics and parameters of an external signal is studied. The frequency locking exhibits hysteresis. (control of laser radiation parameters)

Kravtsov, Nikolai V; Firsov, V V [D.V. Skobel'tsyn Institute of Nuclear Physics, M.V. Lomonosov Moscow State University, Moscow (Russian Federation); Pashinin, Pavel P; Sidorov, S S [A.M. Prokhorov General Physics Institute, Russian Academy of Sciences, Moscow (Russian Federation)

2002-06-30

210

Differential modulation of the default mode network via serotonin-1A receptors.  

PubMed

Reflecting one's mental self is a fundamental process for evaluating the personal relevance of life events and for moral decision making and future envisioning. Although the corresponding network has been receiving growing attention, the driving neurochemical mechanisms of the default mode network (DMN) remain unknown. Here we combined positron emission tomography and functional magnetic resonance imaging to investigate modulations of the DMN via serotonin-1A receptors (5-HT(1A)), separated for 5-HT autoinhibition (dorsal raphe nucleus) and local inhibition (heteroreceptors in projection areas). Using two independent approaches, regional 5-HT(1A) binding consistently predicted DMN activity in the retrosplenial cortex for resting-state functional magnetic resonance imaging and the Tower of London task. On the other hand, both local and autoinhibitory 5-HT(1A) binding inversely modulated the posterior cingulate cortex, the strongest hub in the resting human brain. In the frontal part of the DMN, a negative association was found between the dorsal medial prefrontal cortex and local 5-HT(1A) inhibition. Our results indicate a modulation of key areas involved in self-referential processing by serotonergic neurotransmission, whereas variations in 5-HT(1A) binding explained a considerable amount of the individual variability in the DMN. Moreover, the brain regions associated with distinct introspective functions seem to be specifically regulated by the different 5-HT(1A) binding sites. Together with previously reported modulations of dopamine and GABA, this regional specialization suggests complex interactions of several neurotransmitters driving the default mode network. PMID:22308408

Hahn, Andreas; Wadsak, Wolfgang; Windischberger, Christian; Baldinger, Pia; Höflich, Anna S; Losak, Jan; Nics, Lukas; Philippe, Cécile; Kranz, Georg S; Kraus, Christoph; Mitterhauser, Markus; Karanikas, Georgios; Kasper, Siegfried; Lanzenberger, Rupert

2012-01-30

211

Neuronal Network Pharmacodynamics of GABAergic Modulation in the Human Cortex Determined Using Pharmaco-Magnetoencephalography  

PubMed Central

Neuronal network oscillations are a unifying phenomenon in neuroscience research, with comparable measurements across scales and species. Cortical oscillations are of central importance in the characterization of neuronal network function in health and disease and are influential in effective drug development. Whilst animal in vitro and in vivo electrophysiology is able to characterize pharmacologically induced modulations in neuronal activity, present human counterparts have spatial and temporal limitations. Consequently, the potential applications for a human equivalent are extensive. Here, we demonstrate a novel implementation of contemporary neuroimaging methods called pharmaco-magnetoencephalography. This approach determines the spatial profile of neuronal network oscillatory power change across the cortex following drug administration and reconstructs the time course of these modulations at focal regions of interest. As a proof of concept, we characterize the nonspecific GABAergic modulator diazepam, which has a broad range of therapeutic applications. We demonstrate that diazepam variously modulates ? (4–7 Hz), ? (7–14 Hz), ? (15–25 Hz), and ? (30–80 Hz) frequency oscillations in specific regions of the cortex, with a pharmacodynamic profile consistent with that of drug uptake. We examine the relevance of these results with regard to the spatial and temporal observations from other modalities and the various therapeutic consequences of diazepam and discuss the potential applications of such an approach in terms of drug development and translational neuroscience. Hum Brain Mapp, 2010. © 2009 Wiley-Liss, Inc.

Hall, Stephen D; Barnes, Gareth R; Furlong, Paul L; Seri, Stefano; Hillebrand, Arjan

2010-01-01

212

Driving and Driven Architectures of Directed Small-World Human Brain Functional Networks  

PubMed Central

Recently, increasing attention has been focused on the investigation of the human brain connectome that describes the patterns of structural and functional connectivity networks of the human brain. Many studies of the human connectome have demonstrated that the brain network follows a small-world topology with an intrinsically cohesive modular structure and includes several network hubs in the medial parietal regions. However, most of these studies have only focused on undirected connections between regions in which the directions of information flow are not taken into account. How the brain regions causally influence each other and how the directed network of human brain is topologically organized remain largely unknown. Here, we applied linear multivariate Granger causality analysis (GCA) and graph theoretical approaches to a resting-state functional MRI dataset with a large cohort of young healthy participants (n?=?86) to explore connectivity patterns of the population-based whole-brain functional directed network. This directed brain network exhibited prominent small-world properties, which obviously improved previous results of functional MRI studies showing weak small-world properties in the directed brain networks in terms of a kernel-based GCA and individual analysis. This brain network also showed significant modular structures associated with 5 well known subsystems: fronto-parietal, visual, paralimbic/limbic, subcortical and primary systems. Importantly, we identified several driving hubs predominantly located in the components of the attentional network (e.g., the inferior frontal gyrus, supplementary motor area, insula and fusiform gyrus) and several driven hubs predominantly located in the components of the default mode network (e.g., the precuneus, posterior cingulate gyrus, medial prefrontal cortex and inferior parietal lobule). Further split-half analyses indicated that our results were highly reproducible between two independent subgroups. The current study demonstrated the directions of spontaneous information flow and causal influences in the directed brain networks, thus providing new insights into our understanding of human brain functional connectome.

Yan, Chaogan; He, Yong

2011-01-01

213

Driving and driven architectures of directed small-world human brain functional networks.  

PubMed

Recently, increasing attention has been focused on the investigation of the human brain connectome that describes the patterns of structural and functional connectivity networks of the human brain. Many studies of the human connectome have demonstrated that the brain network follows a small-world topology with an intrinsically cohesive modular structure and includes several network hubs in the medial parietal regions. However, most of these studies have only focused on undirected connections between regions in which the directions of information flow are not taken into account. How the brain regions causally influence each other and how the directed network of human brain is topologically organized remain largely unknown. Here, we applied linear multivariate Granger causality analysis (GCA) and graph theoretical approaches to a resting-state functional MRI dataset with a large cohort of young healthy participants (n?=?86) to explore connectivity patterns of the population-based whole-brain functional directed network. This directed brain network exhibited prominent small-world properties, which obviously improved previous results of functional MRI studies showing weak small-world properties in the directed brain networks in terms of a kernel-based GCA and individual analysis. This brain network also showed significant modular structures associated with 5 well known subsystems: fronto-parietal, visual, paralimbic/limbic, subcortical and primary systems. Importantly, we identified several driving hubs predominantly located in the components of the attentional network (e.g., the inferior frontal gyrus, supplementary motor area, insula and fusiform gyrus) and several driven hubs predominantly located in the components of the default mode network (e.g., the precuneus, posterior cingulate gyrus, medial prefrontal cortex and inferior parietal lobule). Further split-half analyses indicated that our results were highly reproducible between two independent subgroups. The current study demonstrated the directions of spontaneous information flow and causal influences in the directed brain networks, thus providing new insights into our understanding of human brain functional connectome. PMID:21858129

Yan, Chaogan; He, Yong

2011-08-12

214

Predicted Modulated Differential Rates for Direct WIMP Searches at Low Energy Transfers  

NASA Astrophysics Data System (ADS)

The differential event rate for direct detection of dark matter, both the time averaged and the modulated one due to the motion of the Earth, are discussed. The calculations focus on relatively light cold dark matter candidates (WIMP) and low energy transfers. It is shown that for sufficiently light WIMPs the extraction of relatively large nucleon cross sections is possible. Furthermore for some WIMP masses the modulation amplitude may change sign, meaning that, in such a case, the maximum rate may occur six months later than naively expected. This effect can be exploited to yield information about the mass of the dark matter candidate, if and when the observation of the modulation of the event rate is established.

J. D., Vergados

2012-03-01

215

Sex-Specific Modulation of Gene Expression Networks in Murine Hypothalamus  

PubMed Central

The hypothalamus contains nuclei and cell populations that are critical in reproduction and that differ significantly between the sexes in structure and function. To examine the molecular and genetic basis for these differences, we quantified gene expression in the hypothalamus of 39 pairs of adult male and female mice belonging to the BXD strains. This experimental design enabled us to define hypothalamic gene coexpression networks and provided robust estimates of absolute expression differences. As expected, sex has the strongest effect on the expression of genes on the X and Y chromosomes (e.g., Uty, Xist, Kdm6a). Transcripts associated with the endocrine system and neuropeptide signaling also differ significantly. Sex-differentiated transcripts often have well delimited expression within specific hypothalamic nuclei that have roles in reproduction. For instance, the estrogen receptor (Esr1) and neurokinin B (Tac2) genes have intense expression in the medial preoptic and arcuate nuclei and comparatively high expression in females. Despite the strong effect of sex on single transcripts, the global pattern of covariance among transcripts is well preserved, and consequently, males and females have well matched coexpression modules. However, there are sex-specific hub genes in functionally equivalent modules. For example, only in males is the Y-linked gene, Uty, a highly connected transcript in a network that regulates chromatin modification and gene transcription. In females, the X chromosome paralog, Kdm6a, takes the place of Uty in the same network. We also find significant effect of sex on genetic regulation and the same network in males and females can be associated with markedly different regulatory loci. With the exception of a few sex-specific modules, our analysis reveals a system in which sets of functionally related transcripts are organized into stable sex-independent networks that are controlled at a higher level by sex-specific modulators.

Mozhui, Khyobeni; Lu, Lu; Armstrong, William E.; Williams, Robert W.

2012-01-01

216

Advanced modulation formats for delivery of heterogeneous wired and wireless access networks  

NASA Astrophysics Data System (ADS)

It is believed that the integration of wired and wireless access networks (or heterogeneous network) will provide high bandwidth and flexibility for both fixed and mobile users in a single and cost-effective platform. Here, we propose and demonstrate a signal remodulated wired and wireless network with wireless signal broadcast. Dark-return-to-zero (DRZ) and polarization-shift-keying (PolSK) signals are used for the downstream wired and wireless applications respectively. At the remote antenna unit (RAU), the PolSK signal is demodulated to produce the binary-phase-shift-keying (BPSK) signal, which will be used for the wireless broadcast application. Signal remodulation is demonstrated using reflective semiconductor optical amplifier (RSOA) as a colorless reflective modulator in the optical networking unit (ONU)/RAU. The downstream signal is remodulated at the ONU/RAU to produce the non-return-to-zero (NRZ) upstream signal.

Chow, C. W.; Yeh, C. H.

2009-12-01

217

Social Working Memory: Neurocognitive Networks and Directions for Future Research  

PubMed Central

Navigating the social world requires the ability to maintain and manipulate information about people’s beliefs, traits, and mental states. We characterize this capacity as social working memory (SWM). To date, very little research has explored this phenomenon, in part because of the assumption that general working memory systems would support working memory for social information. Various lines of research, however, suggest that social cognitive processing relies on a neurocognitive network (i.e., the “mentalizing network”) that is functionally distinct from, and considered antagonistic with, the canonical working memory network. Here, we review evidence suggesting that demanding social cognition requires SWM and that both the mentalizing and canonical working memory neurocognitive networks support SWM. The neural data run counter to the common finding of parametric decreases in mentalizing regions as a function of working memory demand and suggest that the mentalizing network can support demanding cognition, when it is demanding social cognition. Implications for individual differences in social cognition and pathologies of social cognition are discussed.

Meyer, Meghan L.; Lieberman, Matthew D.

2012-01-01

218

Directly phase-modulation-mode-locked doubly-resonant optical parametric oscillator.  

PubMed

We present results on direct mode-locking of a doubly-resonant optical parametric oscillator (DRO) using an electro-optic phase modulator with low resonant frequency of 80 MHz as the single mode-locking element. Pumped by a cw laser at 532 nm and based on MgO:sPPLT as the nonlinear material, the DRO generates 533 ps pulses at 80 MHz and 471 ps pulses at 160 MHz. Stable train of mode-locked pulses is obtained at a modulation depth of 1.83 radians when the modulation frequency is precisely tuned and the cavity length is carefully adjusted. The effects of frequency detuning, modulation depth, input laser pump power, crystal temperature and position of modulator inside the cavity, on pulse duration and repetition rate have been studied. Operating at degeneracy, under mode-locked condition, the signal-idler spectrum exhibits a bandwidth of ~31 nm, and the spectrum has been investigated for different phase-matching temperatures. Mode-locked operation has been confirmed by second-harmonic-generation of the DRO output in a ?-BaB2O4 crystal, where a 4 times enhancement in green power is observed compared to cw operation. PMID:24104250

Devi, Kavita; Kumar, S Chaitanya; Ebrahim-Zadeh, M

2013-10-01

219

Wireless Multimedia Sensor Networks: current trends and future directions.  

PubMed

Wireless Multimedia Sensor Networks (WMSNs) have emerged and shifted the focus from the typical scalar wireless sensor networks to networks with multimedia devices that are capable to retrieve video, audio, images, as well as scalar sensor data. WMSNs are able to deliver multimedia content due to the availability of inexpensive CMOS cameras and microphones coupled with the significant progress in distributed signal processing and multimedia source coding techniques. In this paper, we outline the design challenges of WMSNs, give a comprehensive discussion of the proposed architectures, algorithms and protocols for the different layers of the communication protocol stack for WMSNs, and evaluate the existing WMSN hardware and testbeds. The paper will give the reader a clear view of the state of the art at all aspects of this research area, and shed the light on its main current challenges and future trends. We also hope it will foster discussions and new research ideas among its researchers. PMID:22163571

Almalkawi, Islam T; Zapata, Manel Guerrero; Al-Karaki, Jamal N; Morillo-Pozo, Julian

2010-07-09

220

A direct torque control scheme for permanent magnet synchronous motors based on space vector modulation  

NASA Astrophysics Data System (ADS)

In order to solve the problem of direct torque control (DTC) for permanent magnet synchronous motor (PMSM) related to the flux and the torque ripple and the uncertainty of switching frequency, A novel direct torque control system based on space vector modulation(SVM-DTC) for permanent magnet synchronous motor was proposed. In this method flux and torque are controlled through stator voltage components in stator flux linkage coordinate axes and space vector modulation is used to control inverters. Therefore, the errors of torque and flux linkage could be compensated accurately. The whole system has only one easily adjustable PI adjuster and needs no high for hardware and easy for realize. The simulation results verify the feasibility of this method, reduction of the flux and the torque ripple, and the good performance of DTC.

Su, Xiao-hui; Xu, Shu-Ping

2013-03-01

221

Acupuncture Modulates Resting State Connectivity in Default and Sensorimotor Brain Networks  

PubMed Central

Previous studies have defined low-frequency, spatially consistent networks in resting fMRI data which may reflect functional connectivity. We sought to explore how a complex somatosensory stimulation, acupuncture, influences intrinsic connectivity in two of these networks: the default mode network (DMN) and sensorimotor network (SMN). We analyzed resting fMRI data taken before and after verum and sham acupuncture. Electrocardiography data was used to infer autonomic modulation through measures of heart rate variability (HRV). Probabilistic independent component analysis was used to separate resting fMRI data into DMN and SMN components. Following verum, but not sham, acupuncture there was increased DMN connectivity with pain (anterior cingulate cortex (ACC), periaqueductal gray), affective (amygdala, ACC), and memory (hippocampal formation, middle temporal gyrus) related brain regions. Furthermore, increased DMN connectivity with the hippocampal formation, a region known to support memory and interconnected with autonomic brain regions, was negatively correlated with acupuncture-induced increase in a sympathetic related HRV metric (LFu), and positively correlated with a parasympathetic related metric (HFu). Following verum, but not sham, acupuncture there was also increased SMN connectivity with pain related brain regions (ACC, cerebellum). We attribute differences between verum and sham acupuncture to more varied and stronger sensations evoked by verum acupuncture. Our results demonstrate for the first time that acupuncture can enhance the post-stimulation spatial extent of resting brain networks to include anti-nociceptive, memory, and affective brain regions. This modulation and sympathovagal response may relate to acupuncture analgesia and other potential therapeutic effects.

Dhond, Rupali P.; Yeh, Calvin; Park, Kyungmo; Kettner, Norman; Napadow, Vitaly

2008-01-01

222

Regulatory Snapshots: Integrative Mining of Regulatory Modules from Expression Time Series and Regulatory Networks  

PubMed Central

Explaining regulatory mechanisms is crucial to understand complex cellular responses leading to system perturbations. Some strategies reverse engineer regulatory interactions from experimental data, while others identify functional regulatory units (modules) under the assumption that biological systems yield a modular organization. Most modular studies focus on network structure and static properties, ignoring that gene regulation is largely driven by stimulus-response behavior. Expression time series are key to gain insight into dynamics, but have been insufficiently explored by current methods, which often (1) apply generic algorithms unsuited for expression analysis over time, due to inability to maintain the chronology of events or incorporate time dependency; (2) ignore local patterns, abundant in most interesting cases of transcriptional activity; (3) neglect physical binding or lack automatic association of regulators, focusing mainly on expression patterns; or (4) limit the discovery to a predefined number of modules. We propose Regulatory Snapshots, an integrative mining approach to identify regulatory modules over time by combining transcriptional control with response, while overcoming the above challenges. Temporal biclustering is first used to reveal transcriptional modules composed of genes showing coherent expression profiles over time. Personalized ranking is then applied to prioritize prominent regulators targeting the modules at each time point using a network of documented regulatory associations and the expression data. Custom graphics are finally depicted to expose the regulatory activity in a module at consecutive time points (snapshots). Regulatory Snapshots successfully unraveled modules underlying yeast response to heat shock and human epithelial-to-mesenchymal transition, based on regulations documented in the YEASTRACT and JASPAR databases, respectively, and available expression data. Regulatory players involved in functionally enriched processes related to these biological events were identified. Ranking scores further suggested ability to discern the primary role of a gene (target or regulator). Prototype is available at: http://kdbio.inesc-id.pt/software/regulatorysnapshots.

Goncalves, Joana P.; Aires, Ricardo S.; Francisco, Alexandre P.; Madeira, Sara C.

2012-01-01

223

Lightweight PV Inverters: Dual Bi-Directional IGBTs Modules Enables Breakthrough PV Inverter Using Current Modulation Topology  

SciTech Connect

Solar ADEPT Project: PV inverters convert DC power generated by modules into usable AC power. IPC’s initial 30kW 94lb. PV inverter reduces the weight of comparable 30kW PV inverters by 90%—reducing the cost of materials, manufacturing, shipping, and installation. With ARPA-E support, new bi-directional silicon power switches will be developed, commercialized, and utilized in IPC’s next-generation PV inverter. With these components, IPC will produce 100kW inverters that weight less than 100lb., reducing the weight of conventional 3,000lb. 100kW inverters by more than 95%. The new power switches will cut IPC’s $/W manufacturing cost in half, as well as further reduce indirect shipping and installation costs.

None

2012-01-30

224

Modularized bi-directional grid-tied inverter with asynchronous sigma-delta modulation  

Microsoft Academic Search

The objective of this paper is to propose a modularized bi-directional grid-tied inverter (BGI) with asynchronous sigma-delta modulation (ASDM) control for the renewable energy (RE)-supplied DC power system. The proposed BGI can be operated either in the grid-tied mode (GTM) or the power factor correction mode (PFCM) which is necessary features for the RE-supplied DC power system. The proposed BGI

Yaow-Ming Chen; Chia-Hsi Chang

2010-01-01

225

Directly modulated sampled grating DBR lasers for long-haul WDM communication systems  

Microsoft Academic Search

The limitations on high-speed data transmission, using widely tunable sampled-grating distributed Bragg reflector (SGDBR) lasers, are investigated. We demonstrate 1.244-Gb\\/s data transmission over a wavelength range of 45 nm using a single directly modulated tunable SGDBR laser diode. Data transmission was evaluated on four separate wavelength channels each spaced 15 nm apart. Less than 0.6 dB of dispersion penalty was

Beck Mason; San-Liang Lee; Mark E. Heimbuch; Larry A. Coldren

1997-01-01

226

Direct aperture optimization–based intensity-modulated radiotherapy for whole breast irradiation  

Microsoft Academic Search

Purpose: To investigate the technical and dosimetric advantages and the efficacy of direct aperture optimized intensity-modulated radiation therapy (DAO-IMRT) over standard (e.g., beamlet optimized) IMRT and conventional three-dimensional conformal radiotherapy (3D-CRT) for whole breast irradiation in supine and prone positions. Methods and Materials: We retrospectively designed DAO-IMRT plans for 15 breast cancer patients in supine (10 patients) and prone (5

Ergun E.. Ahunbay; Guang-Pei Chen; Steven Thatcher; Paul A. Jursinic; Julia White; Katherine Albano; X. Allen Li

2007-01-01

227

A 1 GHz CMOS current-folded direct digital RF quadrature modulator  

Microsoft Academic Search

This paper describes a CMOS current-folded direct digital RF quadrature modulator, which uses two 10-bit linear interpolation current steering digital-to-analog converters (DACs) and two current-folded double-balanced mixers. The attenuation of the DAC image components is significantly increased with linear interpolation, and the reconstruction filter is therefore eliminated. The DAC baseband differential current signals are fed to the mixer by current-folded

Yijun Zhou; Jiren Yuan

2005-01-01

228

Transcranial direct current stimulation of the prefrontal cortex modulates the desire for specific foods  

Microsoft Academic Search

We aimed to assess whether modulation of the dorsolateral prefrontal cortex (DLFPC) with noninvasive brain stimulation, namely transcranial direct current stimulation (tDCS), modifies food craving in healthy subjects. We performed a randomized sham-controlled cross-over study in which 23 subjects received sham and active tDCS (anode left\\/cathode right and anode right\\/cathode left) of the DLPFC. Subjects were exposed to food and

Felipe Fregni; Fernanda Orsati; Waldelle Pedrosa; Shirley Fecteau; Fatima A. M. Tome; Michael A. Nitsche; Tatiana Mecca; Elizeu C. Macedo; Alvaro Pascual-Leone; Paulo S. Boggio

2008-01-01

229

V-band single chip, direct carrier BPSK modulation transmitter with integrated patch antenna  

Microsoft Academic Search

A single chip V-Band pHEMT technology transmitter with wideband direct BPSK modulation and on-chip dual band patch antenna is reported. The transmitter features, 10% bandwidth electronic tuning range, substantial power output, injection locking capability, low power consumption and good patch antenna radiation characteristics. As such it is well suited to wireless digital communications systems as well in radar and phased

G. Passiopoulos; S. Nam; A. Georgiou; A. E. Ashtiani; I. D. Robertson; E. A. Grindrod

1998-01-01

230

V-band single chip, direct carrier BPSK modulation transmitter with integrated patch antenna  

Microsoft Academic Search

A single chip V-band pHEMT technology transmitter with wideband direct BPSK modulation and on-chip dual band patch antenna is reported. The transmitter features, 10% bandwidth electronic tuning range, substantial power output, injection locking capability, low power consumption and good patch antenna radiation characteristics. As such it is well suited to wireless digital communications systems as well in radar and phased

G. Passiopoulos; S. Nam; A. Georgiou; A. E. Ashtiani; I. D. Robertson; E. A. Grindrod

1998-01-01

231

Analyzing Data from Multivariate Directed Graphs: An Application to Social Networks.  

National Technical Information Service (NTIS)

A multivariate directed graph consists of a set of g nodes, and a family of directed arcs (one for each relation) connecting pairs of nodes. Such multivariate directed graphs provide natural representations for social networks. In this paper, methods to a...

S. E. Fienberg M. M. Meyer S. S. Wasserman

1980-01-01

232

CDR-MAC: A Protocol for Full Exploitation of Directional Antennas in Ad Hoc Wireless Networks  

Microsoft Academic Search

In this paper, we propose a new Medium Access Control (MAC) protocol for full exploitation of directional antennas in wireless networks. The protocol introduces a circular directional transmission of the Request To Send (RTS) control packet, spreading around a station information about the intended communication. The stations that receive the directional RTS, using a simple scheme of tracking the neighbors'

Thanasis Korakis; Gentian Jakllari; Leandros Tassiulas

2008-01-01

233

Shaping Embodied Neural Networks for Adaptive Goal-directed Behavior  

Microsoft Academic Search

The acts of learning and memory are thought to emerge from the modifications of synaptic connections between neurons, as guided by sensory feedback during behavior. However, much is unknown about how such synaptic processes can sculpt and are sculpted by neuronal population dynamics and an interaction with the environment. Here, we embodied a simulated network, inspired by dissociated cortical neuronal

Zenas C. Chao; Douglas J. Bakkum; Steve M. Potter

2008-01-01

234

Direct retrieval of Kerr and plasma effects from alignment-induced spatiotemporal modulation.  

PubMed

We developed a direct measurement method for comprehensive analyses of Kerr and plasma effects that cooperated or competed with molecular alignment-induced spatiotemporal modulation for intense aligning and weak probing pulses around zero time delay. The mixed influences were revealed by time-resolving the combined spatial focusing or defocusing dynamics under different molecular alignment directions and degrees. The nonlinear refractive index and plasma density were extracted straightforwardly, facilitating accurate explorations on multiphoton ionization and nonlinear optical Kerr effects of aligned molecular gases. PMID:23041879

Feng, Yahui; Li, Wenxue; Liu, Jia; Pan, Haifeng; Wu, Jian; Zeng, Heping

2012-09-15

235

A novel prediction methodology for detecting failures and instabilities in directional wireless networks  

NASA Astrophysics Data System (ADS)

Even though advances in wireless technology have yielded lower power consumption, higher data rates, and numerous other improvements, the ability to develop a proactive strategy towards handling degradations and failures in directional wireless networks has evaded the research community. In this paper, we introduce a methodology using an analogy to molecular systems in which a directional wireless network utilizing free space optical (FSO) or RF links is modeled as a molecule whose links can grow/retract similarly to bonds. A normal mode analysis (NMA) is performed to identify link instabilities (degradations and failures) and an N-dimensional potential energy surface (PES) is derived with respect to network and environmental parameters to aide in the detection of when a new topology is available ahead of the topology computation stage. Together, the NMA and PES form a basis for a proactive network methodology aimed at improving performance in directional wireless networks.

Coleman, David M.; Milner, Stuart D.; Davis, Christopher C.

2012-10-01

236

Early appraisal of the fixation probability in directed networks  

NASA Astrophysics Data System (ADS)

In evolutionary dynamics, the probability that a mutation spreads through the whole population, having arisen from a single individual, is known as the fixation probability. In general, it is not possible to find the fixation probability analytically given the mutant’s fitness and the topological constraints that govern the spread of the mutation, so one resorts to simulations instead. Depending on the topology in use, a great number of evolutionary steps may be needed in each of the simulation events, particularly in those that end with the population containing mutants only. We introduce two techniques to accelerate the determination of the fixation probability. The first one skips all evolutionary steps in which the number of mutants does not change and thereby reduces the number of steps per simulation event considerably. This technique is computationally advantageous for some of the so-called layered networks. The second technique, which is not restricted to layered networks, consists of aborting any simulation event in which the number of mutants has grown beyond a certain threshold value and counting that event as having led to a total spread of the mutation. For advantageous mutations in large populations and regardless of the network’s topology, we demonstrate, both analytically and by means of simulations, that using a threshold of about [N/(r-1)]1/4 mutants, where N is the number of simulation events and r is the ratio of the mutants’ fitness to that of the remainder of the population, leads to an estimate of the fixation probability that deviates in no significant way from that obtained from the full-fledged simulations. We have observed speedups of two orders of magnitude for layered networks with 10000 nodes.

Barbosa, Valmir C.; Donangelo, Raul; Souza, Sergio R.

2010-10-01

237

Hierarchical structure and modules in the Escherichia coli transcriptional regulatory network revealed by a new top-down approach  

PubMed Central

Background Cellular functions are coordinately carried out by groups of genes forming functional modules. Identifying such modules in the transcriptional regulatory network (TRN) of organisms is important for understanding the structure and function of these fundamental cellular networks and essential for the emerging modular biology. So far, the global connectivity structure of TRN has not been well studied and consequently not applied for the identification of functional modules. Moreover, network motifs such as feed forward loop are recently proposed to be basic building blocks of TRN. However, their relationship to functional modules is not clear. Results In this work we proposed a top-down approach to identify modules in the TRN of E. coli. By studying the global connectivity structure of the regulatory network, we first revealed a five-layer hierarchical structure in which all the regulatory relationships are downward. Based on this regulatory hierarchy, we developed a new method to decompose the regulatory network into functional modules and to identify global regulators governing multiple modules. As a result, 10 global regulators and 39 modules were identified and shown to have well defined functions. We then investigated the distribution and composition of the two basic network motifs (feed forward loop and bi-fan motif) in the hierarchical structure of TRN. We found that most of these network motifs include global regulators, indicating that these motifs are not basic building blocks of modules since modules should not contain global regulators. Conclusion The transcriptional regulatory network of E. coli possesses a multi-layer hierarchical modular structure without feedback regulation at transcription level. This hierarchical structure builds the basis for a new and simple decomposition method which is suitable for the identification of functional modules and global regulators in the transcriptional regulatory network of E. coli. Analysis of the distribution of feed forward loops and bi-fan motifs in the hierarchical structure suggests that these network motifs are not elementary building blocks of functional modules in the transcriptional regulatory network of E. coli.

Ma, Hong-Wu; Buer, Jan; Zeng, An-Ping

2004-01-01

238

Comparison of Modules of Wild Type and Mutant Huntingtin and TP53 Protein Interaction Networks: Implications in Biological Processes and Functions  

PubMed Central

Disease-causing mutations usually change the interacting partners of mutant proteins. In this article, we propose that the biological consequences of mutation are directly related to the alteration of corresponding protein protein interaction networks (PPIN). Mutation of Huntingtin (HTT) which causes Huntington's disease (HD) and mutations to TP53 which is associated with different cancers are studied as two example cases. We construct the PPIN of wild type and mutant proteins separately and identify the structural modules of each of the networks. The functional role of these modules are then assessed by Gene Ontology (GO) enrichment analysis for biological processes (BPs). We find that a large number of significantly enriched () GO terms in mutant PPIN were absent in the wild type PPIN indicating the gain of BPs due to mutation. Similarly some of the GO terms enriched in wild type PPIN cease to exist in the modules of mutant PPIN, representing the loss. GO terms common in modules of mutant and wild type networks indicate both loss and gain of BPs. We further assign relevant biological function(s) to each module by classifying the enriched GO terms associated with it. It turns out that most of these biological functions in HTT networks are already known to be altered in HD and those of TP53 networks are altered in cancers. We argue that gain of BPs, and the corresponding biological functions, are due to new interacting partners acquired by mutant proteins. The methodology we adopt here could be applied to genetic diseases where mutations alter the ability of the protein to interact with other proteins.

Basu, Mahashweta; Bhattacharyya, Nitai P.; Mohanty, Pradeep K.

2013-01-01

239

Identification of Gene Modules Associated with Drought Response in Rice by Network-Based Analysis  

PubMed Central

Understanding the molecular mechanisms that underlie plant responses to drought stress is challenging due to the complex interplay of numerous different genes. Here, we used network-based gene clustering to uncover the relationships between drought-responsive genes from large microarray datasets. We identified 2,607 rice genes that showed significant changes in gene expression under drought stress; 1,392 genes were highly intercorrelated to form 15 gene modules. These drought-responsive gene modules are biologically plausible, with enrichments for genes in common functional categories, stress response changes, tissue-specific expression and transcription factor binding sites. We observed that a gene module (referred to as module 4) consisting of 134 genes was significantly associated with drought response in both drought-tolerant and drought-sensitive rice varieties. This module is enriched for genes involved in controlling the response of the plant to water and embryonic development, including a heat shock transcription factor as the key regulator in the expression of ABRE-containing genes. These results suggest that module 4 is highly conserved in the ABA-mediated drought response pathway in different rice varieties. Moreover, our study showed that many hub genes clustered in rice chromosomes had significant associations with QTLs for drought stress tolerance. The relationship between hub gene clusters and drought tolerance QTLs may provide a key to understand the genetic basis of drought tolerance in rice.

Zuo, Kaijing; Luo, Lijun; Tang, Kexuan

2012-01-01

240

Directed Diffusion Based on Link-Stabilizing Clustering for Wireless Sensor Networks  

Microsoft Academic Search

Reducing power consumption to extend network lifetime with limited energy resource is one of the most important challenges\\u000a in wireless sensor networks. In addition, the issue of real-time communication is also very important in some practical applications.\\u000a A directed diffusion algorithm based on link-stabilizing clustering (DDLSC), which is a delay-energy aware routing protocol\\u000a for wireless sensor networks is proposed in

Zude Zhou; Wenjun Xu; Fangmin Li; Xuehong Wu

2007-01-01

241

Expression changes in mouse brains following nicotine-induced seizures: the modulation of transcription factor networks  

Microsoft Academic Search

Kedmi M, Orr-Urtreger A. Expression changes in mouse brains following nicotine-induced seizures: the modulation of transcription factor networks. Physiol Genomics 30: 242-252, 2007. First published April 24, 2007; doi:10.1152\\/physiolgenomics.00288.2006.—Nico- tine, acting through the neuronal nicotinic acetylcholine receptors (nAChRs), can induce seizures in mice. We aimed to study brain transcriptional response to seizure and to identify genes whose ex- pression is

Merav Kedmi; Avi Orr-Urtreger

2007-01-01

242

From complete to modulated synchrony in networks of identical Hindmarsh-Rose neurons  

NASA Astrophysics Data System (ADS)

In most cases tendency to synchrony in networks of oscillatory units increases with the coupling strength. Using the popular Hindmarsh-Rose neuronal model, we demonstrate that even for identical neurons and simple coupling the dynamics can be more complicated. Our numerical analysis for globally coupled systems and oscillator lattices reveals a new scenario of synchrony breaking with the increase of coupling, resulting in a quasiperiodic, modulated synchronous state.

Ehrich, Sebastian; Pikovsky, Arkady; Rosenblum, Michael

2013-10-01

243

Temperature modulated DSC study of the kinetics of free radical isothermal network polymerization  

Microsoft Academic Search

Temperature modulated differential scanning calorimetry (TMDSC) is used to study the kinetics of the free radical isothermal\\u000a polymerization of triethyleneglycol dimethacrylate (TEGDMA). Azo-bis-isobutironitrile was used as initiator. The polymerization’s temperature is lower than the final glass transition temperature\\u000a of the polymer network. The measurement of the average heat flow released and the heat capacity during the reaction allows\\u000a identifying the

M. T. Viciosa; J. Quiles Hoyo; M. Dionísio; J. L. Gómez Ribelles

2007-01-01

244

Estradiol interacts with an opioidergic network to achieve rapid modulation of a vocal pattern generator  

Microsoft Academic Search

Estrogens rapidly regulate neuronal activity within seconds-to-minutes, yet it is unclear how estrogens interact with neural\\u000a circuits to rapidly coordinate behavior. This study examines whether 17-beta-estradiol interacts with an opioidergic network\\u000a to achieve rapid modulation of a vocal control circuit. Adult plainfin midshipman fish emit vocalizations that mainly differ\\u000a in duration, and rhythmic activity of a hindbrain–spinal vocal pattern generator

Luke Remage-Healey; Andrew H. Bass

2010-01-01

245

Extending the direct laser modulation bandwidth by exploiting the photon-photon resonance: modeling, simulations and experiments  

NASA Astrophysics Data System (ADS)

The direct laser modulation bandwidth can be extended substantially by introducing a supplementary photon-photon resonance (PPR) at a higher frequency than the carrier-photon resonance (CPR). The paper presents a modified rate equation model that takes into account the PPR by treating the longitudinal confinement factor as a dynamic variable. The conditions required for obtaining a strong PPR and an enhancement of the small-signal modulation bandwidth are analyzed and experimental results confirming the model are presented. Since the small-signal modulation bandwidth may not be indicative of the large-signal modulation capability, particularly in case of a small-signal modulation response with substantial variations across the bandwidth, we have also analyzed the influence of the PPR-enhanced small-signal modulation response shape on the large-signal modulation capability as well as the methods that can be employed to flatten the small-signal modulation transfer function between the CPR and PPR.

Dumitrescu, M.; Laakso, A.; Viheriala, J.; Kamp, M.; Bardella, P.; Eisenstein, G.

2013-03-01

246

A neural network approach to off-line signature verification using directional PDF  

Microsoft Academic Search

A neural network approach is proposed to build the first stage of an Automatic Handwritten Signature Verification System. The directional Probability Density Function was used as a global shape factor and its discriminating power was enhanced by reducing its cardinality via filtering. Various experimental protocols were used to implement the backpropagation network (BPN) classifier. A comparison, on the same database

Jean-pierre Drouhard; Robert Sabourin; Mario Godbout

1996-01-01

247

NRC TLD direct radiation monitoring network: Progress report, January--March 1996, Volume 16, No. 1  

SciTech Connect

This report provides the status and results of the NRC Thermoluminescent Dosimeter (TLD) Direct Radiation Monitoring Network. It presents the radiation levels measured in the vicinity of NRC licensed facilities throughout the country for the first quarter of 1996.

Struckmeyer, R.

1996-05-01

248

NRC TLD direct radiation monitoring network: Progress report, April--June 1997. Volume 17, Number 2  

SciTech Connect

This report provides the status and results of the NRC Thermoluminescent Dosimeter (TLD) Direct Radiation Monitoring Network. It presents the radiation levels measured in the vicinity of NRC licensed facilities throughout the country for the second quarter of 1997.

Struckmeyer, R.

1997-09-01

249

Optimizing Environmental Monitoring Networks with Direction-Dependent Distance Thresholds.  

ERIC Educational Resources Information Center

In the direction-dependent approach to location modeling developed herein, the distance within which a point of demand can find service from a facility depends on direction of measurement. The utility of the approach is illustrated through an application to groundwater remediation. (Author/MDH)

Hudak, Paul F.

1993-01-01

250

Localized energy efficient broadcast for wireless networks with directional antennas  

Microsoft Academic Search

Directional antennas reduce the beamwidth angle to diffuse the radio transmission to one direction and thus use less energy than omnidirectional antennas. Combined with the idea of reducing the transmission power, these devices can be used for the minimal energy broadcasting problem. The problem is to mini- mize the total energy consumption but still enable a message orig- inated from

Julien Cartigny; David Simplot; Ivan Stojmenovi

2002-01-01

251

A ?-amyloid oligomer directly modulates P/Q-type calcium currents in Xenopus oocytes  

PubMed Central

BACKGROUND AND PURPOSE ?-amyloid (A?) oligomers have been implicated in the early pathophysiology of Alzheimer's disease (AD). While the precise nature of the molecular target has not been fully revealed, a number of studies have indicated that A? oligomers modulate neuron-specific ion channels. We recently provided evidence that A? oligomers suppress isolated P/Q-type calcium currents in cultured nerve cells. Using a heterologous expression system, we aimed to prove a direct effect on the membrane channel mediating such current. EXPERIMENTAL APPROACH The effects of a synthetically generated A? oligomer, A? globulomer, were investigated on P/Q-type currents recorded from Xenopus laevis oocytes expressing the full P/Q-type calcium channel or the pore-forming subunit only. We also examined the effects of A? globulomer on recombinant NMDA receptor currents. Finally, we compared the modulation by A? globulomer with that induced by a synthetic monomeric A?. KEY RESULTS A? globulomer directly and dose-dependently modulated P/Q-type calcium channels. A leftward shift of the current-voltage curve indicated that the threshold for channel opening was reduced. The effect of A? globulomer was also present when only the ?1A subunit of the normally tripartite channel was expressed. In contrast, the monomeric A? had no effect on P/Q current. Also globulomer A? had no effect on glutamate-induced NMDA currents. CONCLUSIONS AND IMPLICATIONS The ?1A subunit of the P/Q-type calcium channel is directly modulated by oligomeric A?. Threshold reduction as well as an increase in current at synaptic terminals may facilitate vesicle release and could trigger excitotoxic events in the brains of patients with AD.

Mezler, M; Barghorn, S; Schoemaker, H; Gross, G; Nimmrich, V

2012-01-01

252

Mining Bayesian Networks from Direct Marketing Databases with Missing Values  

Microsoft Academic Search

Discovering knowledge from huge databases with missing values is a challenging problem in Data Mining. In this paper, a novel\\u000a hybrid algorithm for learning knowledge represented in Bayesian Networks is discussed. The new algorithm combines an evolutionary\\u000a algorithm with the Expectation-Maximization (EM) algorithm to overcome the problem of getting stuck in sub-optimal solutions\\u000a which occurs in most existing learning algorithms.

Yuan Yuan Guo; Man Leung Wong

253

Directed Assembly of One-Dimensional Nanostructures into Functional Networks  

Microsoft Academic Search

One-dimensional nanostructures, such as nanowires and nanotubes, represent the smallest dimension for efficient transport of electrons and excitons and thus are ideal building blocks for hierarchical assembly of functional nanoscale electronic and photonic structures. We report an approach for the hierarchical assembly of one-dimensional nanostructures into well-defined functional networks. We show that nanowires can be assembled into parallel arrays with

Yu Huang; Xiangfeng Duan; Qingqiao Wei; Charles M. Lieber

2001-01-01

254

Wireless ATM networks: technology status and future directions  

Microsoft Academic Search

The concept of “wireless ATM” (WATM), first proposed in 1992, is now being actively considered as a potential framework for new-generation wireless communication networks capable of supporting integrated, quality-of service (QoS) based multimedia services. In this review paper, we outline the technological rationale for wireless ATM, present a system-level architecture, and discuss key design issues for both mobile ATM switching

DIPANKAR RAYCHAUDHURI

1999-01-01

255

Adaptive modulation in ad hoc DS\\/CDMA packet radio networks  

Microsoft Academic Search

This paper investigates the benefit of adaptive modu- lation based on channel state information (CSI) in direct-sequence\\/ code-division multiple-access (DS\\/CDMA) multihop packet radio networks. By exploiting varying channel conditions, adaptive mod- ulation can be used in ad hoc networks to provide upper layers with higher capacity links over which to relay traffic. Using the -stable interference model, the distribution of

Michael R. Souryal; Branimir R. Vojcic; Raymond L. Pickholtz

2006-01-01

256

Circuit level Alternating-Direction-Implicit approach to transient analysis of power distribution networks  

Microsoft Academic Search

This paper presents an efficient method for transient analysis of power distribution networks. We employ an iterative approach-Alternating-Direction-Implicit (ADI) method-to solving the circuit matrices of power distribution networks. In contrast to the existing finite-difference based ADI approach to power\\/ground grid analysis, where transmission-line was used to model the mesh-structured P\\/G grids (TLM-ADI), we apply ADI scheme to directly solve P\\/G

Weikun Guo; S. X.-D. Tan

2003-01-01

257

Automatic modulation recognition based on spatial pattern classification using artificial neural networks  

NASA Astrophysics Data System (ADS)

In an electronic countermeasures project, an automatic modulation recognition system has been designed and tested based on backpropagation neural networks. The system successfully distinguishes between the specified 10 signal classes to a very high degree and uses a Welch periodogram processor. Experimental results show that the neural networks match and even outdo the performance of the conventional K-nearest neighbor classifier for the same preprocessor, upper 90's percentages. Significant optimization of the neural networks is also shown using the optimal brain damage pruning algorithm. The design issues, preprocessing techniques, backpropagation algorithms, implementation details, and results of the project are fully discussed. A user manual of the software developed during the project, complete with program listings in the C language, is included.

Ghani, Nasir

1992-07-01

258

Towards a direction-sensitive optical module for neutrino telescopes based on a hybrid photon detector  

NASA Astrophysics Data System (ADS)

The optical modules of all currently operating neutrino telescopes contain one standard PMT with a large hemispherical photo-cathode. The maximum spatial resolution of this detection principle is thus limited to the photo-cathode area and no information is obtained on the direction of the incoming photons. We propose a new direction-sensitive design featuring a fisheye lens and a hybrid photon detector. The lens system maps incoming photons from one direction on a well-defined point on the photo-cathode of the hybrid photon detector. The photo-electrons are accelerated in a cross-focussed optics and detected using a pixelated anode, which allows for very high spatial resolution. As a candidate chip for the photo-electron detection we propose the Timepix detector of the Medipix family. We have successfully shown its capability to detect photo-electrons in the experiment and evaluated the time resolution by simulation and measurement.

Rügheimer, Tilman K.; Gebert, Ulrike; Michel, Thilo; Anton, Gisela; Séguinot, Jacques; Joram, Christian

2009-12-01

259

Performance evaluation of ePTFE and PVDF flat-sheet module direct contact membrane distillation.  

PubMed

This paper reports experiments using a flat-sheet module with 0.18 approximately 0.45 microm ePTFE (expanded polytetrafluoroethylene) and PVDF (polyvinylidene fluoride) membranes to show the effects of membrane properties, salt concentration and fluid hydrodynamics on the permeate flux and salt rejection of DCMD (direct contact membrane distillation). A theoretical prediction of the permeate flux was carried out, and was in close agreement with the experimental results. In addition, the energy integration of the process was also analyzed in order to evaluate module design to increase energy efficiency. According to the simulated results of the energy integration design, a combination of simultaneous cooling of the permeate stream and an additional heat exchanger to lower the temperature of the permeate stream not only enhances the MD flux, but also reduces energy consumption. PMID:20651439

Chuang, Ching-Jung; Tung, Kuo-Lun; Fan, Yang-Hsiang; Ho, Chii-Dong; Huang, James

2010-01-01

260

Data Rewrite of Wavelength Channel Using Saturated SOA Modulator for WDM Metro\\/Access Networks with Centralized Light Sources  

Microsoft Academic Search

We propose a simple wavelength reuse technique for WDM metro\\/access networks with centralized light sources. Using a deeply saturated SOA modulator located in a remote node, we erase the data on a low-extinction-ratio downstream signal and modulate it with new data to generate an upstream signal.

H. Takesue; T. Sugie

2002-01-01

261

Direct Detection of RDX Vapor Using a Conjugated Polymer Network.  

PubMed

1,3,5-Trinitroperhydro-1,3,5-triazine (RDX) is a principal component of plastic explosives used in acts of terrorism and within improvised explosive devices, among others. Approaches to detect RDX compatible with remote, "stand-off" sampling that do not require preconcentration strategies, such as the swabs commonly employed in airports, will benefit military and civilian security. Such detection remains a significant challenge because RDX is 10(3) less volatile than 1,3,5-trinitrotoluene (TNT), corresponding to a parts-per-trillion vapor pressure under ambient conditions. Therefore, while fluorescence quenching of conjugated polymers is sufficiently sensitive to detect TNT vapors, RDX vapor detection is undemonstrated. Here we report a cross-linked phenylene vinylene polymer network whose fluorescence is quenched by trace amounts of RDX introduced from solution or the vapor phase. Fluorescence quenching is reduced, but remains significant, when partially degraded RDX is employed, suggesting that the polymer responds to RDX itself. The polymer network also responds to TNT and PETN similarly introduced from solution or the vapor phase. Pure solvents, volatile amines, and the outgassed vapors from lipstick or sunscreen do not quench polymer fluorescence. The established success of TNT sensors based on fluorescence quenching makes this a material of interest for real-world explosive sensors and will motivate further interest in cross-linked polymers and framework materials for sensing applications. PMID:23641956

Gopalakrishnan, Deepti; Dichtel, William R

2013-05-23

262

Direct2Experts: a pilot national network to demonstrate interoperability among research-networking platforms.  

PubMed

Research-networking tools use data-mining and social networking to enable expertise discovery, matchmaking and collaboration, which are important facets of team science and translational research. Several commercial and academic platforms have been built, and many institutions have deployed these products to help their investigators find local collaborators. Recent studies, though, have shown the growing importance of multiuniversity teams in science. Unfortunately, the lack of a standard data-exchange model and resistance of universities to share information about their faculty have presented barriers to forming an institutionally supported national network. This case report describes an initiative, which, in only 6 months, achieved interoperability among seven major research-networking products at 28 universities by taking an approach that focused on addressing institutional concerns and encouraging their participation. With this necessary groundwork in place, the second phase of this effort can begin, which will expand the network's functionality and focus on the end users. PMID:22037890

Weber, Griffin M; Barnett, William; Conlon, Mike; Eichmann, David; Kibbe, Warren; Falk-Krzesinski, Holly; Halaas, Michael; Johnson, Layne; Meeks, Eric; Mitchell, Donald; Schleyer, Titus; Stallings, Sarah; Warden, Michael; Kahlon, Maninder

2011-10-28

263

A 45nm WCDMA transmitter using direct quadrature voltage modulator with high oversampling digital front-end  

Microsoft Academic Search

A 45 nm WCDMA transmitter using a direct quadrature voltage modulator with high oversampling digital front-end is described. The highly digitized transmitter realizes modulation in the voltage domain. Delivering 1 dBm WCDMA output power, the transmitter achieves -158 dBc\\/Hz noise and 2% EVM, while consuming 30 mW including the digital front-end.

Xin He; Jan van Sinderen; Robert Rutten

2010-01-01

264

Directed Altruism and Granting Favors in Social Networks  

Microsoft Academic Search

We study why socially close neighbors make better agents than strangers. Using a series of modified dictator games and a new helping game we find that agents pass about 50 percent more surplus to friends compared to strangers when decision making is anonymous. This directed altruism ef- fect is complemented by an enforcement effect which increases giving by an additional

Stephen Leider; Markus M. Mobius; Tanya Rosenblat; Quoc-Anh Do

2006-01-01

265

AN IMPROVED METHOD FOR RADIO FREQUENCY DIRECTION FINDING USING WIRELESS SENSOR NETWORKS  

Microsoft Academic Search

We present the design of a remotely deployable distributed wireless antenna system formed from wireless sensor network nodes. Specifically, the focus is on enhancing the detection range of a distributed wireless antenna system. The primary objective is to create a methodology to steer the beam in the desired direction to enhance radio frequency (RF) direction finding and follow-on signal reception.

Mickey S. Batson; John C. McEachen; Murali Tummala

266

Capacity improvement of high density wireless LAN networks using adaptive directional antenna  

Microsoft Academic Search

This paper evaluates capacity improvement of high density wireless LAN networks using adaptive directional antenna, in terms of channel capacity and system capacity based on IEE802.11a OFDM PHY with CSMA based MAC protocol. Simulation results show that the utilization of adaptive directional antenna increases channel and system capacity and the improvement becomes large as the AP deployment density becomes scarcer.

Masahiro UMEHIRA; Rihito MATSUOKA

2009-01-01

267

A Method for Fast Radio Frequency Direction Finding Using Wireless Sensor Networks  

Microsoft Academic Search

We present the design of a remotely deployable distributed wireless antenna system formed from wireless sensor network nodes. Specifically, the focus is on enhancing the detection range of a distributed wireless antenna system. The primary objective is to create a methodology to steer the beam in the desired direction to enhance radio frequency (RF) direction finding and follow-on signal reception.

Mickey S. Batson; John C. Mceachen; Murali Tummala

2008-01-01

268

Study on application of the asynchronous motor direct torque control based on neural network  

Microsoft Academic Search

A new improved direct torque control (DTC) method is proposed for an asynchronous motor direct torque control system, in this paper, after studying and analyzing model reference adaptive control (MRAC) and adaptive linear neural network motor speed identification. This method adopts an MRAC identification model with high-pass filter part and low-pass filter part. Based on this condition, we design a

Xiucheng Dong; Guijuan Wang; Jun Wang; Xiaoxiao Zhao

2005-01-01

269

Direct solutions of sparse network equations by optimally ordered triangular factorization  

Microsoft Academic Search

Matrix inversion is very inefficient for computing direct solutions of the large sparse systems of linear equations that arise in many network problems. Optimally ordered triangular factorization of sparse matrices is more efficient and offers other important computational advantages in some applications. With this method, direct solutions are computed from sparse matrix factors instead of from a full inverse matrix,

W. F. Tinney; J. W. Walker

1967-01-01

270

An Integrated Neighbor Discovery and MAC Protocol for Ad Hoc Networks Using Directional Antennas  

Microsoft Academic Search

Many MAC sub-layer protocols for supporting the usage of directional antennas in ad hoc networks have been proposed in literature. However, there remain two open issues that are yet to be resolved completely. First, in order to fully exploit the spatial diversity gains possible due to the use of directional antennas, it is essential to shift to the exclusive usage

Gentian Jakllari; Wenjie Luo; Srikanth V. Krishnamurthy

2005-01-01

271

An Integrated Neighbor Discovery and MAC Protocol for Ad Hoc Networks Using Directional Antennas  

Microsoft Academic Search

Many MAC sub-layer protocols for supporting the usage of directional antennas in ad hoc networks have been proposed in literature. However, there remain two open issues that are yet to be resolved completely. First, in order to fully exploit the spatial diversity gains possible due to the use of directional antennas, it is essential to shift to the exclusive usage

Gentian Jakllari; Wenjie Luo; Srikanth V. Krishnamurthy

2007-01-01

272

BinTree Seeking: A Novel Approach to Mine Both Bi-Sparse and Cohesive Modules in Protein Interaction Networks  

PubMed Central

Modern science of networks has brought significant advances to our understanding of complex systems biology. As a representative model of systems biology, Protein Interaction Networks (PINs) are characterized by a remarkable modular structures, reflecting functional associations between their components. Many methods were proposed to capture cohesive modules so that there is a higher density of edges within modules than those across them. Recent studies reveal that cohesively interacting modules of proteins is not a universal organizing principle in PINs, which has opened up new avenues for revisiting functional modules in PINs. In this paper, functional clusters in PINs are found to be able to form unorthodox structures defined as bi-sparse module. In contrast to the traditional cohesive module, the nodes in the bi-sparse module are sparsely connected internally and densely connected with other bi-sparse or cohesive modules. We present a novel protocol called the BinTree Seeking (BTS) for mining both bi-sparse and cohesive modules in PINs based on Edge Density of Module (EDM) and matrix theory. BTS detects modules by depicting links and nodes rather than nodes alone and its derivation procedure is totally performed on adjacency matrix of networks. The number of modules in a PIN can be automatically determined in the proposed BTS approach. BTS is tested on three real PINs and the results demonstrate that functional modules in PINs are not dominantly cohesive but can be sparse. BTS software and the supporting information are available at: www.csbio.sjtu.edu.cn/bioinf/BTS/.

Shen, Hong-Bin

2011-01-01

273

Viral immune modulators perturb the human molecular network by common and unique strategies.  

PubMed

Viruses must enter host cells to replicate, assemble and propagate. Because of the restricted size of their genomes, viruses have had to evolve efficient ways of exploiting host cell processes to promote their own life cycles and also to escape host immune defence mechanisms. Many viral open reading frames (viORFs) with immune-modulating functions essential for productive viral growth have been identified across a range of viral classes. However, there has been no comprehensive study to identify the host factors with which these viORFs interact for a global perspective of viral perturbation strategies. Here we show that different viral perturbation patterns of the host molecular defence network can be deduced from a mass-spectrometry-based host-factor survey in a defined human cellular system by using 70 innate immune-modulating viORFs from 30 viral species. The 579 host proteins targeted by the viORFs mapped to an unexpectedly large number of signalling pathways and cellular processes, suggesting yet unknown mechanisms of antiviral immunity. We further experimentally verified the targets heterogeneous nuclear ribonucleoprotein?U, phosphatidylinositol-3-OH kinase, the WNK (with-no-lysine) kinase family and USP19 (ubiquitin-specific peptidase 19) as vulnerable nodes in the host cellular defence system. Evaluation of the impact of viral immune modulators on the host molecular network revealed perturbation strategies used by individual viruses and by viral classes. Our data are also valuable for the design of broad and specific antiviral therapies. PMID:22810585

Pichlmair, Andreas; Kandasamy, Kumaran; Alvisi, Gualtiero; Mulhern, Orla; Sacco, Roberto; Habjan, Matthias; Binder, Marco; Stefanovic, Adrijana; Eberle, Carol-Ann; Goncalves, Adriana; Bürckstümmer, Tilmann; Müller, André C; Fauster, Astrid; Holze, Cathleen; Lindsten, Kristina; Goodbourn, Stephen; Kochs, Georg; Weber, Friedemann; Bartenschlager, Ralf; Bowie, Andrew G; Bennett, Keiryn L; Colinge, Jacques; Superti-Furga, Giulio

2012-07-26

274

AMBIENT: Active Modules for Bipartite Networks - using high-throughput transcriptomic data to dissect metabolic response  

PubMed Central

Background With the continued proliferation of high-throughput biological experiments, there is a pressing need for tools to integrate the data produced in ways that produce biologically meaningful conclusions. Many microarray studies have analysed transcriptomic data from a pathway perspective, for instance by testing for KEGG pathway enrichment in sets of upregulated genes. However, the increasing availability of species-specific metabolic models provides the opportunity to analyse these data in a more objective, system-wide manner. Results Here we introduce ambient (Active Modules for Bipartite Networks), a simulated annealing approach to the discovery of metabolic subnetworks (modules) that are significantly affected by a given genetic or environmental change. The metabolic modules returned by ambient are connected parts of the bipartite network that change coherently between conditions, providing a more detailed view of metabolic changes than standard approaches based on pathway enrichment. Conclusions ambient is an effective and flexible tool for the analysis of high-throughput data in a metabolic context. The same approach can be applied to any system in which reactions (or metabolites) can be assigned a score based on some biological observation, without the limitation of predefined pathways. A Python implementation of ambient is available at http://www.theosysbio.bio.ic.ac.uk/ambient.

2013-01-01

275

Dopaminergic modulation of tracer coupling in a ganglion-amacrine cell network.  

PubMed

Many retinal ganglion cells are coupled via gap junctions with neighboring amacrine cells and ganglion cells. We investigated the extent and dynamics of coupling in one such network, the OFF alpha ganglion cell of rabbit retina and its associated amacrine cells. We also observed the relative spread of Neurobiotin injected into a ganglion cell in the presence of modulators of gap junctional permeability. We found that gap junctions between amacrine cells were closed via stimulation of a D(1) dopamine receptor, while the gap junctions between ganglion cells were closed via stimulation of a D(2) dopamine receptor. The pairs of hemichannels making up the heterologous gap junctions between the ganglion and amacrine cells were modulated independently, so that elevations of cAMP in the ganglion cell open the ganglion cell hemichannels, while elevations of cAMP in the amacrine cell close its hemichannels. We also measured endogenous dopamine release from an eyecup preparation and found a basal release from the dark-adapted retina of approximately 2 pmol/min during the day. Maximal stimulation with light increased the rate of dopamine release from rabbit retina by 66%. The results suggest that coupling between members of the OFF alpha ganglion cell/amacrine cell network is differentially modulated with changing levels of dopamine. PMID:17711603

Mills, Stephen L; Xia, Xiao-Bo; Hoshi, Hideo; Firth, Sally I; Rice, Margaret E; Frishman, Laura J; Marshak, David W

2007-08-22

276

Directionality in hyperbrain networks discriminates between leaders and followers in guitar duets.  

PubMed

To investigate whether directionality in hyperbrain networks reflects different roles during interpersonal action coordination (IAC), we recorded EEG data from pairs of guitarists playing together as musical leaders versus followers. We used an asymmetric index of in-phase synchronization to analyze hyperbrain networks of directed functional connectivity in the alpha and beta frequency ranges for time segments around coordinated play onsets. After exploring the small-world characteristics of the networks at different thresholds, we examined the directed connection strengths within and between brains. As predicted, we found evidence suggesting that the musical roles of leader and follower are associated with different patterns of directed between-brain couplings. The functional significance of these differences for IAC requires further study. PMID:23761745

Sänger, Johanna; Müller, Viktor; Lindenberger, Ulman

2013-06-04

277

Fiber-Optic Transceiver Module for High-Speed Intrasatellite Networks  

NASA Astrophysics Data System (ADS)

High-speed intrasatellite networks are needed to interconnect units such as synthetic aperture radars, high-resolution cameras, and fast image-compression processors that produce data beyond gigabits per second. We have developed a fiber-optic link, named SpaceFibre, which operates up to 3.125 Gb/s and is compatible with the existing SpaceWire network. The link provides symmetrical, bidirectional, full-duplex, and point-to-point communication. It employs 850-nm vertical-cavity surface emitting lasers, radiation-hardened laser-optimized 50/125 µm graded-index fibers, and GaAs p-i-n photo diodes. The transceiver electronics is realized using a multilayer-ceramic-substrate technology that enables the passive alignment of optical fibers to active devices. The SpaceFibre link demonstrator was tested to transfer data at 2.5 Gb/s over 100 m with a bit error rate of less than 1.3 · 10-14. Fiber-pigtailed modules were stressed with temperature variations from -40 °C to +85 °C, vibrations up to 30 g, and mechanical shocks up to 3900 g. The test results of 20 modules show that the SpaceFibre link is a promising candidate for the upcoming high-speed intrasatellite networks.

Heikkinen, Veli; Alajoki, Teemu; Juntunen, Eveliina; Karppinen, Mikko; Kautio, Kari; Mäkinen, Jukka-Tapani; Ollila, Jyrki; Tanskanen, Antti; Toivonen, Jaakko; Casey, Rory; Scott, Shane; Pintzka, Wilhelm; Thériault, Sylvain; McKenzie, Iain

2007-05-01

278

Multi-Dimensional Prioritization of Dental Caries Candidate Genes and Its Enriched Dense Network Modules  

PubMed Central

A number of genetic studies have suggested numerous susceptibility genes for dental caries over the past decade with few definite conclusions. The rapid accumulation of relevant information, along with the complex architecture of the disease, provides a challenging but also unique opportunity to review and integrate the heterogeneous data for follow-up validation and exploration. In this study, we collected and curated candidate genes from four major categories: association studies, linkage scans, gene expression analyses, and literature mining. Candidate genes were prioritized according to the magnitude of evidence related to dental caries. We then searched for dense modules enriched with the prioritized candidate genes through their protein-protein interactions (PPIs). We identified 23 modules comprising of 53 genes. Functional analyses of these 53 genes revealed three major clusters: cytokine network relevant genes, matrix metalloproteinases (MMPs) family, and transforming growth factor-beta (TGF-?) family, all of which have been previously implicated to play important roles in tooth development and carious lesions. Through our extensive data collection and an integrative application of gene prioritization and PPI network analyses, we built a dental caries-specific sub-network for the first time. Our study provided insights into the molecular mechanisms underlying dental caries. The framework we proposed in this work can be applied to other complex diseases.

Wang, Quan; Jia, Peilin; Cuenco, Karen T.; Feingold, Eleanor; Marazita, Mary L.; Wang, Lily; Zhao, Zhongming

2013-01-01

279

Multi-dimensional prioritization of dental caries candidate genes and its enriched dense network modules.  

PubMed

A number of genetic studies have suggested numerous susceptibility genes for dental caries over the past decade with few definite conclusions. The rapid accumulation of relevant information, along with the complex architecture of the disease, provides a challenging but also unique opportunity to review and integrate the heterogeneous data for follow-up validation and exploration. In this study, we collected and curated candidate genes from four major categories: association studies, linkage scans, gene expression analyses, and literature mining. Candidate genes were prioritized according to the magnitude of evidence related to dental caries. We then searched for dense modules enriched with the prioritized candidate genes through their protein-protein interactions (PPIs). We identified 23 modules comprising of 53 genes. Functional analyses of these 53 genes revealed three major clusters: cytokine network relevant genes, matrix metalloproteinases (MMPs) family, and transforming growth factor-beta (TGF-?) family, all of which have been previously implicated to play important roles in tooth development and carious lesions. Through our extensive data collection and an integrative application of gene prioritization and PPI network analyses, we built a dental caries-specific sub-network for the first time. Our study provided insights into the molecular mechanisms underlying dental caries. The framework we proposed in this work can be applied to other complex diseases. PMID:24146904

Wang, Quan; Jia, Peilin; Cuenco, Karen T; Feingold, Eleanor; Marazita, Mary L; Wang, Lily; Zhao, Zhongming

2013-10-11

280

Bimodal Modulation and Continuous Stimulation in Optical Imaging to Map Direction Selectivity  

PubMed Central

In the visual system, neurons with similar functional properties such as orientation and direction selectivity are clustered together to form modules. Optical imaging recordings in combination with episodic paradigms have been previously used to estimate direction selectivity, a fundamental property of visual neurons. The major drawback of the episodic approach is that the extraction of the signal from various forms of physiological noise is difficult, leading to a poor estimation of direction. Recent work, based on periodic stimulation and Fourier decomposition improved the extraction of periodic stimulus responses from noise and thus, reduced the recording time considerably. Given the success of this new paradigm in mapping orientation, the present study evaluated its reliability to measure direction selectivity in the visual cortex of anesthetised cats. Here, a model that exploits the harmonics of the Fourier decomposition is proposed where the first harmonic is related to direction responses, and the second to orientation. As expected, the first harmonic was absent when a static stimulus was presented. Contrarily, the first harmonic was present when moving stimuli were presented and the amplitude was greater with random dots kinematograms than with drifting gratings. The phase of the first harmonic showed a good agreement with direction preference measured by episodic paradigm. The ratio of the first/the second harmonic amplitude, related to a direction index, was weaker in fracture. It was also weaker in areas of the ventral pathway (areas 17 and 21a) where direction selectivity is known to be reduced. These results indicate that a periodic paradigm can be easily used to measure specific parameters in optical signals, particularly in situations when short acquisition periods are needed.

Vanni, M. P.; Provost, J.; Casanova, C.; Lesage, F.

2009-01-01

281

Calaxin drives sperm chemotaxis by Ca2+-mediated direct modulation of a dynein motor  

PubMed Central

Sperm chemotaxis occurs widely in animals and plants and plays an important role in the success of fertilization. Several studies have recently demonstrated that Ca2+ influx through specific Ca2+ channels is a prerequisite for sperm chemotactic movement. However, the regulator that modulates flagellar movement in response to Ca2+ is unknown. Here we show that a neuronal calcium sensor, calaxin, directly acts on outer-arm dynein and regulates specific flagellar movement during sperm chemotaxis. Calaxin inhibition resulted in significant loss of sperm chemotactic movement, despite normal increases in intracellular calcium concentration. Using a demembranated sperm model, we demonstrate that calaxin is essential for generation and propagation of Ca2+-induced asymmetric flagellar bending. An in vitro motility assay revealed that calaxin directly suppressed the velocity of microtubule sliding by outer-arm dynein at high Ca2+ concentrations. This study describes the missing link between chemoattractant-mediated Ca2+ signaling and motor-driven microtubule sliding during sperm chemotaxis.

Mizuno, Katsutoshi; Shiba, Kogiku; Okai, Masahiko; Takahashi, Yusuke; Shitaka, Yuji; Oiwa, Kazuhiro; Tanokura, Masaru; Inaba, Kazuo

2012-01-01

282

Directional spike propagation in a recurrent network: dynamical firewall as anisotropic recurrent inhibition.  

PubMed

It has been demonstrated that theta rhythm propagates along the septotemporal axis of the hippocampal CA1 of the rat running on a track, and it has been suggested that directional spike propagation in the hippocampal CA3 is reflected in CA1. In this paper, we show that directional spike propagation occurs in a recurrent network model in which neurons are connected locally and connection weights are modified through STDP. The recurrent network model consists of excitatory and inhibitory neurons, which are intrinsic bursting and fast spiking neurons developed by Izhikevich, respectively. The maximum length of connections from excitatory neurons is shorter in the horizontal direction than the vertical direction. Connections from inhibitory neurons have the same maximum length in both directions, and the maximum length of inhibitory connections is the same as that of excitatory connections in the vertical direction. When connection weights between excitatory neurons (E?E) were modified through STDP and those from excitatory neurons to inhibitory neurons (E?I) were constant, spikes propagated in the vertical direction as expected from the network structure. However, when E?I connection weights were modified through STDP, as well as E?E connection weights, spikes propagated in the horizontal direction against the above expectation. This paradoxical propagation was produced by strengthened E?I connections which shifted the timing of inhibition forward. When E?I connections are enhanced, the direction of effective inhibition changes from horizontal to vertical, as if a gate for spike propagation is opened in the horizontal direction and firewalls come out in the vertical direction. These results suggest that the advance of timing of inhibition caused by potentiation of E?I connections is influential in network activity and is an important element in determining the direction of spike propagation. PMID:22717450

Samura, Toshikazu; Hayashi, Hatsuo

2012-06-05

283

Identification of dysfunctional modules and disease genes in congenital heart disease by a network-based approach  

PubMed Central

Background The incidence of congenital heart disease (CHD) is continuously increasing among infants born alive nowadays, making it one of the leading causes of infant morbidity worldwide. Various studies suggest that both genetic and environmental factors lead to CHD, and therefore identifying its candidate genes and disease-markers has been one of the central topics in CHD research. By using the high-throughput genomic data of CHD which are available recently, network-based methods provide powerful alternatives of systematic analysis of complex diseases and identification of dysfunctional modules and candidate disease genes. Results In this paper, by modeling the information flow from source disease genes to targets of differentially expressed genes via a context-specific protein-protein interaction network, we extracted dysfunctional modules which were then validated by various types of measurements and independent datasets. Network topology analysis of these modules revealed major and auxiliary pathways and cellular processes in CHD, demonstrating the biological usefulness of the identified modules. We also prioritized a list of candidate CHD genes from these modules using a guilt-by-association approach, which are well supported by various kinds of literature and experimental evidence. Conclusions We provided a network-based analysis to detect dysfunctional modules and disease genes of CHD by modeling the information transmission from source disease genes to targets of differentially expressed genes. Our method resulted in 12 modules from the constructed CHD subnetwork. We further identified and prioritized candidate disease genes of CHD from these dysfunctional modules. In conclusion, module analysis not only revealed several important findings with regard to the underlying molecular mechanisms of CHD, but also suggested the distinct network properties of causal disease genes which lead to identification of candidate CHD genes.

2011-01-01

284

RV filling modulates LV function by direct ventricular interaction during mechanical ventilation.  

PubMed

During mechanical ventilation, phasic changes in systemic venous return modulate right ventricular output but may also affect left ventricular function by direct ventricular interaction. In 13 anesthetized, closed-chest, normal dogs, we measured inferior vena cava flow and left and right ventricular dimensions and output during mechanical ventilation, during an inspiratory hold, and (during apnea) vena caval constriction and abdominal compression. During a single ventilation cycle preceded by apnea, positive pressure inspiration decreased caval flow and right ventricular dimension; the transseptal pressure gradient increased, the septum shifted rightward, reflecting an increased left ventricular volume (the anteroposterior diameter did not change); and stroke volume increased. The opposite occurred during expiration. Similarly, the maneuvers that decreased venous return shifted the septum rightward, and left ventricular volume and stroke volume increased. Increased venous return had opposite effects. Changes in left ventricular function caused by changes in venous return alone were similar to those during mechanical ventilation except for minor quantitative differences. We conclude that phasic changes in systemic venous return during mechanical ventilation modulate left ventricular function by direct ventricular interaction. PMID:15792988

Mitchell, Jamie R; Whitelaw, William A; Sas, Rozsa; Smith, Eldon R; Tyberg, John V; Belenkie, Israel

2005-03-25

285

Impedance is modulated to meet accuracy demands during goal-directed arm movements.  

PubMed

The neuromuscular system is inherently noisy and joint impedance may serve to filter this noise. In the present experiment, we investigated whether individuals modulate joint impedance to meet spatial accuracy demands. Twelve subjects were instructed to make rapid, time constrained, elbow extensions to three differently sized targets. Some trials (20 out of 140 for each target, randomly assigned) were perturbed mechanically at 75% of movement amplitude. Inertia, damping and stiffness were estimated from the torque and angle deviation signal using a forward simulation and optimization routine. Increases in endpoint accuracy were not always reflected in a decrease in trajectory variability. Only in the final quarter of the trajectory the variability decreased as target width decreased. Stiffness estimates increased significantly with accuracy constraints. Damping estimates only increased for perturbations that were initially directed against the movement direction. We concluded that joint impedance modulation is one of the strategies used by the neuromuscular system to generate accurate movements, at least during the final part of the movement. PMID:16372169

Selen, Luc P J; Beek, Peter J; van Dieën, Jaap H

2005-12-22

286

RadSensor: Xray Detection by Direct Modulation of an Optical Probe Beam  

SciTech Connect

We present a new x-ray detection technique based on optical measurement of the effects of x-ray absorption and electron hole pair creation in a direct band-gap semiconductor. The electron-hole pairs create a frequency dependent shift in optical refractive index and absorption. This is sensed by simultaneously directing an optical carrier beam through the same volume of semiconducting medium that has experienced an xray induced modulation in the electron-hole population. If the operating wavelength of the optical carrier beam is chosen to be close to the semiconductor band-edge, the optical carrier will be modulated significantly in phase and amplitude. This approach should be simultaneously capable of very high sensitivity and excellent temporal response, even in the difficult high-energy xray regime. At xray photon energies near 10 keV and higher, we believe that sub-picosecond temporal responses are possible with near single xray photon sensitivity. The approach also allows for the convenient and EMI robust transport of high-bandwidth information via fiber optics. Furthermore, the technology can be scaled to imaging applications. The basic physics of the detector, implementation considerations, and preliminary experimental data are presented and discussed.

Lowry, M E; Bennett, C V; Vernon, S P; Bond, T; Welty, R; Behymer, E; Petersen, H; Krey, A; Stewart, R; Kobayashi, N P; Sperry, V; Stephan, P; Reinhardt, C; Simpson, S; Stratton, P; Bionta, R; McKernan, M; Ables, E; Ott, L; Bond, S; Ayers, J.; Landen, O L; Bell, P M

2003-08-01

287

Direction-Aware Time Slot Assignment for Largest Bandwidth in Slotted Wireless Ad Hoc Networks  

NASA Astrophysics Data System (ADS)

Slotted wireless ad hoc networks are drawing more and more attention because of their advantage of QoS (Quality of Service) support for multimedia applications owing to their collision-free packet transmission. Time slot assignment is an unavoidable and important problem in such networks. The existing time slot assignment methods have in general a drawback of limited available bandwidth due to their local assignment optimization without the consideration of directions of the radio wave transmission of wireless links along the routes in such networks. A new time slot assignment is proposed in this paper in order to overcome this drawback. The proposed assignment is different from the existing methods in the following aspects: a) consideration of link directions during time slot assignment; b) largest bandwidth to be achieved; c) feasibility in resource limited ad hoc networks because of its fast assignment. Moreover, the effectiveness of the proposal is confirmed by some simulation results.

Li, Jianping; Wakahara, Yasushi

288

Posterior Association Networks and Functional Modules Inferred from Rich Phenotypes of Gene Perturbations  

PubMed Central

Combinatorial gene perturbations provide rich information for a systematic exploration of genetic interactions. Despite successful applications to bacteria and yeast, the scalability of this approach remains a major challenge for higher organisms such as humans. Here, we report a novel experimental and computational framework to efficiently address this challenge by limiting the ‘search space’ for important genetic interactions. We propose to integrate rich phenotypes of multiple single gene perturbations to robustly predict functional modules, which can subsequently be subjected to further experimental investigations such as combinatorial gene silencing. We present posterior association networks (PANs) to predict functional interactions between genes estimated using a Bayesian mixture modelling approach. The major advantage of this approach over conventional hypothesis tests is that prior knowledge can be incorporated to enhance predictive power. We demonstrate in a simulation study and on biological data, that integrating complementary information greatly improves prediction accuracy. To search for significant modules, we perform hierarchical clustering with multiscale bootstrap resampling. We demonstrate the power of the proposed methodologies in applications to Ewing's sarcoma and human adult stem cells using publicly available and custom generated data, respectively. In the former application, we identify a gene module including many confirmed and highly promising therapeutic targets. Genes in the module are also significantly overrepresented in signalling pathways that are known to be critical for proliferation of Ewing's sarcoma cells. In the latter application, we predict a functional network of chromatin factors controlling epidermal stem cell fate. Further examinations using ChIP-seq, ChIP-qPCR and RT-qPCR reveal that the basis of their genetic interactions may arise from transcriptional cross regulation. A Bioconductor package implementing PAN is freely available online at http://bioconductor.org/packages/release/bioc/html/PANR.html.

Wang, Xin; Castro, Mauro A.

2012-01-01

289

A network module-based method for identifying cancer prognostic signatures  

PubMed Central

Discovering robust prognostic gene signatures as biomarkers using genomics data can be challenging. We have developed a simple but efficient method for discovering prognostic biomarkers in cancer gene expression data sets using modules derived from a highly reliable gene functional interaction network. When applied to breast cancer, we discover a novel 31-gene signature associated with patient survival. The signature replicates across 5 independent gene expression studies, and outperforms 48 published gene signatures. When applied to ovarian cancer, the algorithm identifies a 75-gene signature associated with patient survival. A Cytoscape plugin implementation of the signature discovery method is available at http://wiki.reactome.org/index.php/Reactome_FI_Cytoscape_Plugin

2012-01-01

290

Impulsive consensus in directed networks of identical nonlinear oscillators with switching topologies  

NASA Astrophysics Data System (ADS)

In this paper, we investigate the problem of impulsive consensus of multi-agent systems, where each agent can be modeled as an identical nonlinear oscillator. Firstly, an impulsive control protocol is designed for directed networks with switching topologies based on the local information of agents. Then sufficient conditions are given to guarantee the consensus of the networked nonlinear oscillators. How to select the discrete instants and impulsive constants is also discussed. Numerical simulations show the effectiveness of our theoretical results.

Jiang, Haibo; Bi, Qinsheng; Zheng, Song

2012-01-01

291

Reconfigurable Radio-Over-Fiber Networks: Multiple-Access Functionality Directly Over the Optical Layer  

Microsoft Academic Search

This paper explores different functionalities that can be implemented directly over the optical layer, paving the way for the future for converged wireless and wired services optical networks. Wireless technologies operating over optical networks mainly employ radio-over-fiber (RoF) technologies, which effectively help to manipulate microwave and millimeter-wave band signals. We have experimented with different generation technologies in order to achieve

J. J. Vegas Olmos; Toshiaki Kuri; Ken-ichi Kitayama

2010-01-01

292

Reconstructing Cortical Networks: Case of Directed Graphs with High Level of Reciprocity  

Microsoft Academic Search

\\u000a The problem of prediction of yet uncharted connections in the large scale network of the cerebral cortex is addressed. Our\\u000a approach was determined by the fact that the cortical network is highly reciprocal although directed, i.e. the input and output\\u000a connection patterns of vertices are slightly different. In order to solve the problem of predicting missing connections in\\u000a the cerebral

Tamás Nepusz; László Négyessy; Gábor Tusnády; Fülöp Bazsó

293

Gene-Disease Network Analysis Reveals Functional Modules in Mendelian, Complex and Environmental Diseases  

PubMed Central

Background Scientists have been trying to understand the molecular mechanisms of diseases to design preventive and therapeutic strategies for a long time. For some diseases, it has become evident that it is not enough to obtain a catalogue of the disease-related genes but to uncover how disruptions of molecular networks in the cell give rise to disease phenotypes. Moreover, with the unprecedented wealth of information available, even obtaining such catalogue is extremely difficult. Principal Findings We developed a comprehensive gene-disease association database by integrating associations from several sources that cover different biomedical aspects of diseases. In particular, we focus on the current knowledge of human genetic diseases including mendelian, complex and environmental diseases. To assess the concept of modularity of human diseases, we performed a systematic study of the emergent properties of human gene-disease networks by means of network topology and functional annotation analysis. The results indicate a highly shared genetic origin of human diseases and show that for most diseases, including mendelian, complex and environmental diseases, functional modules exist. Moreover, a core set of biological pathways is found to be associated with most human diseases. We obtained similar results when studying clusters of diseases, suggesting that related diseases might arise due to dysfunction of common biological processes in the cell. Conclusions For the first time, we include mendelian, complex and environmental diseases in an integrated gene-disease association database and show that the concept of modularity applies for all of them. We furthermore provide a functional analysis of disease-related modules providing important new biological insights, which might not be discovered when considering each of the gene-disease association repositories independently. Hence, we present a suitable framework for the study of how genetic and environmental factors, such as drugs, contribute to diseases. Availability The gene-disease networks used in this study and part of the analysis are available at http://ibi.imim.es/DisGeNET/DisGeNETweb.html#Download.

Bauer-Mehren, Anna; Bundschus, Markus; Rautschka, Michael; Mayer, Miguel A.; Sanz, Ferran; Furlong, Laura I.

2011-01-01

294

Single-chip fully integrated direct-modulation CMOS RF transmitters for short-range wireless applications.  

PubMed

Ultra-low power radio frequency (RF) transceivers used in short-range application such as wireless sensor networks (WSNs) require efficient, reliable and fully integrated transmitter architectures with minimal building blocks. This paper presents the design, implementation and performance evaluation of single-chip, fully integrated 2.4 GHz and 433 MHz RF transmitters using direct-modulation power voltage-controlled oscillators (PVCOs) in addition to a 2.0 GHz phase-locked loop (PLL) based transmitter. All three RF transmitters have been fabricated in a standard mixed-signal CMOS 0.18 µm technology. Measurement results of the 2.4 GHz transmitter show an improvement in drain efficiency from 27% to 36%. The 2.4 GHz and 433 MHz transmitters deliver an output power of 8 dBm with a phase noise of -122 dBc/Hz at 1 MHz offset, while drawing 15.4 mA of current and an output power of 6.5 dBm with a phase noise of -120 dBc/Hz at 1 MHz offset, while drawing 20.8 mA of current from 1.5 V power supplies, respectively. The PLL transmitter delivers an output power of 9 mW with a locking range of 128 MHz and consumes 26 mA from 1.8 V power supply. The experimental results demonstrate that the RF transmitters can be efficiently used in low power WSN applications. PMID:23917260

El-Desouki, Munir M; Qasim, Syed Manzoor; BenSaleh, Mohammed; Deen, M Jamal

2013-08-02

295

Neural feedback for instantaneous spatiotemporal modulation of afferent pathways in bi-directional brain-machine interfaces.  

PubMed

In bi-directional brain-machine interfaces (BMIs), precisely controlling the delivery of microstimulation, both in space and in time, is critical to continuously modulate the neural activity patterns that carry information about the state of the brain-actuated device to sensory areas in the brain. In this paper, we investigate the use of neural feedback to control the spatiotemporal firing patterns of neural ensembles in a model of the thalamocortical pathway. Control of pyramidal (PY) cells in the primary somatosensory cortex (S1) is achieved based on microstimulation of thalamic relay cells through multiple-input multiple-output (MIMO) feedback controllers. This closed loop feedback control mechanism is achieved by simultaneously varying the stimulation parameters across multiple stimulation electrodes in the thalamic circuit based on continuous monitoring of the difference between reference patterns and the evoked responses of the cortical PY cells. We demonstrate that it is feasible to achieve a desired level of performance by controlling the firing activity pattern of a few "key" neural elements in the network. Our results suggest that neural feedback could be an effective method to facilitate the delivery of information to the cortex to substitute lost sensory inputs in cortically controlled BMIs. PMID:21859634

Liu, Jianbo; Khalil, Hassan K; Oweiss, Karim G

2011-08-18

296

Single-Chip Fully Integrated Direct-Modulation CMOS RF Transmitters for Short-Range Wireless Applications  

PubMed Central

Ultra-low power radio frequency (RF) transceivers used in short-range application such as wireless sensor networks (WSNs) require efficient, reliable and fully integrated transmitter architectures with minimal building blocks. This paper presents the design, implementation and performance evaluation of single-chip, fully integrated 2.4 GHz and 433 MHz RF transmitters using direct-modulation power voltage-controlled oscillators (PVCOs) in addition to a 2.0 GHz phase-locked loop (PLL) based transmitter. All three RF transmitters have been fabricated in a standard mixed-signal CMOS 0.18 ?m technology. Measurement results of the 2.4 GHz transmitter show an improvement in drain efficiency from 27% to 36%. The 2.4 GHz and 433 MHz transmitters deliver an output power of 8 dBm with a phase noise of ?122 dBc/Hz at 1 MHz offset, while drawing 15.4 mA of current and an output power of 6.5 dBm with a phase noise of ?120 dBc/Hz at 1 MHz offset, while drawing 20.8 mA of current from 1.5 V power supplies, respectively. The PLL transmitter delivers an output power of 9 mW with a locking range of 128 MHz and consumes 26 mA from 1.8 V power supply. The experimental results demonstrate that the RF transmitters can be efficiently used in low power WSN applications.

El-Desouki, Munir M.; Qasim, Syed Manzoor; BenSaleh, Mohammed; Deen, M. Jamal

2013-01-01

297

Bi-directional astrocytic regulation of neuronal activity within a network  

PubMed Central

The concept of a tripartite synapse holds that astrocytes can affect both the pre- and post-synaptic compartments through the Ca2+-dependent release of gliotransmitters. Because astrocytic Ca2+ transients usually last for a few seconds, we assumed that astrocytic regulation of synaptic transmission may also occur on the scale of seconds. Here, we considered the basic physiological functions of tripartite synapses and investigated astrocytic regulation at the level of neural network activity. The firing dynamics of individual neurons in a spontaneous firing network was described by the Hodgkin–Huxley model. The neurons received excitatory synaptic input driven by the Poisson spike train with variable frequency. The mean field concentration of the released neurotransmitter was used to describe the presynaptic dynamics. The amplitudes of the excitatory postsynaptic currents (PSCs) obeyed the gamma distribution law. In our model, astrocytes depressed the presynaptic release and enhanced the PSCs. As a result, low frequency synaptic input was suppressed while high frequency input was amplified. The analysis of the neuron spiking frequency as an indicator of network activity revealed that tripartite synaptic transmission dramatically changed the local network operation compared to bipartite synapses. Specifically, the astrocytes supported homeostatic regulation of the network activity by increasing or decreasing firing of the neurons. Thus, the astrocyte activation may modulate a transition of neural network into bistable regime of activity with two stable firing levels and spontaneous transitions between them.

Gordleeva, S. Yu; Stasenko, S. V.; Semyanov, A. V.; Dityatev, A. E.; Kazantsev, V. B.

2012-01-01

298

Bi-directional astrocytic regulation of neuronal activity within a network.  

PubMed

The concept of a tripartite synapse holds that astrocytes can affect both the pre- and post-synaptic compartments through the Ca(2+)-dependent release of gliotransmitters. Because astrocytic Ca(2+) transients usually last for a few seconds, we assumed that astrocytic regulation of synaptic transmission may also occur on the scale of seconds. Here, we considered the basic physiological functions of tripartite synapses and investigated astrocytic regulation at the level of neural network activity. The firing dynamics of individual neurons in a spontaneous firing network was described by the Hodgkin-Huxley model. The neurons received excitatory synaptic input driven by the Poisson spike train with variable frequency. The mean field concentration of the released neurotransmitter was used to describe the presynaptic dynamics. The amplitudes of the excitatory postsynaptic currents (PSCs) obeyed the gamma distribution law. In our model, astrocytes depressed the presynaptic release and enhanced the PSCs. As a result, low frequency synaptic input was suppressed while high frequency input was amplified. The analysis of the neuron spiking frequency as an indicator of network activity revealed that tripartite synaptic transmission dramatically changed the local network operation compared to bipartite synapses. Specifically, the astrocytes supported homeostatic regulation of the network activity by increasing or decreasing firing of the neurons. Thus, the astrocyte activation may modulate a transition of neural network into bistable regime of activity with two stable firing levels and spontaneous transitions between them. PMID:23129997

Gordleeva, S Yu; Stasenko, S V; Semyanov, A V; Dityatev, A E; Kazantsev, V B

2012-11-02

299

Modification of a neuronal network direction using stepwise photo-thermal etching of an agarose architecture.  

PubMed

Control over spatial distribution of individual neurons and the pattern of neural network provides an important tool for studying information processing pathways during neural network formation. Moreover, the knowledge of the direction of synaptic connections between cells in each neural network can provide detailed information on the relationship between the forward and feedback signaling. We have developed a method for topographical control of the direction of synaptic connections within a living neuronal network using a new type of individual-cell-based on-chip cell-cultivation system with an agarose microchamber array (AMCA). The advantages of this system include the possibility to control positions and number of cultured cells as well as flexible control of the direction of elongation of axons through stepwise melting of narrow grooves. Such micrometer-order microchannels are obtained by photo-thermal etching of agarose where a portion of the gel is melted with a 1064-nm infrared laser beam. Using this system, we created neural network from individual Rat hippocampal cells. We were able to control elongation of individual axons during cultivation (from cells contained within the AMCA) by non-destructive stepwise photo-thermal etching. We have demonstrated the potential of our on-chip AMCA cell cultivation system for the controlled development of individual cell-based neural networks. PMID:15230976

Suzuki, Ikurou; Sugio, Yoshihiro; Moriguchi, Hiroyuki; Jimbo, Yasuhiko; Yasuda, Kenji

2004-07-01

300

Exploration and Modulation of Brain Network Interactions with Noninvasive Brain Stimulation in Combination with Neuroimaging  

PubMed Central

Much recent work in systems neuroscience has focused on how dynamic interactions between different cortical regions underlie complex brain functions such as motor coordination, language, and emotional regulation. Various studies using neuroimaging and neurophysiologic techniques have suggested that in many neuropsychiatric disorders, these dynamic brain networks are dysregulated. Here we review the utility of combined noninvasive brain stimulation and neuroimaging approaches towards greater understanding of dynamic brain networks in health and disease. Brain stimulation techniques, such as transcranial magnetic stimulation and transcranial direct current stimulation, use electromagnetic principles to noninvasively alter brain activity, and induce focal but also network effects beyond the stimulation site. When combined with brain imaging techniques such as functional MRI, PET and EEG, these brain stimulation techniques enable a causal assessment of the interaction between different network components, and their respective functional roles. The same techniques can also be applied to explore hypotheses regarding the changes in functional connectivity that occur during task performance and in various disease states such as stroke, depression and schizophrenia. Finally, in diseases characterized by pathologic alterations in either the excitability within a single region or in the activity of distributed networks, such techniques provide a potential mechanism to alter cortical network function and architectures in a beneficial manner.

Shafi, Mouhsin M.; Westover, M. Brandon; Fox, Michael D.; Pascual-Leone, Alvaro

2012-01-01

301

Geometric detection of coupling directions by means of inter-system recurrence networks  

NASA Astrophysics Data System (ADS)

We introduce a geometric method for identifying the coupling direction between two dynamical systems based on a bivariate extension of recurrence network analysis. Global characteristics of the resulting inter-system recurrence networks provide a correct discrimination for weakly coupled Rössler oscillators not yet displaying generalised synchronisation. Investigating two real-world palaeoclimate time series representing the variability of the Asian monsoon over the last 10,000 years, we observe indications for a considerable influence of the Indian summer monsoon on climate in Eastern China rather than vice versa. The proposed approach can be directly extended to studying K>2 coupled subsystems.

Feldhoff, Jan H.; Donner, Reik V.; Donges, Jonathan F.; Marwan, Norbert; Kurths, Jürgen

2012-10-01

302

Fast changes in direction during human locomotion are executed by impulsive activation of motor modules.  

PubMed

This study investigated the modular control of complex locomotor tasks that require fast changes in direction, i.e., cutting manoeuvres. It was hypothesized that such tasks are accomplished by an impulsive (burst-like) activation of a few motor modules, as observed during walking and running. It was further hypothesized that the performance in cutting manoeuvres would be associated to the relative timing of the activation impulses. Twenty-two healthy men performed 90° side-step cutting manoeuvres while electromyography (EMG) activity from 16 muscles of the supporting limb and trunk, kinematics, and ground reaction forces were recorded. Motor modules and their respective temporal activations were extracted from the EMG signals by non-negative matrix factorization. The kinematic analysis provided the velocity of the centre of mass and the external work absorbed during the load acceptance (negative work, external work during absorption (W-Abs)) and propulsion phases (positive work, external work during propulsion (W-Prp)) of the cutting manoeuvres. Five motor modules explained the EMG activity of all muscles and were driven in an impulsive way, with timing related to the initial contact (M2), load acceptance (M3), and propulsion (M4). The variability in timing between impulses across subjects was greater for cutting manoeuvres than for running. The timing difference between M2 and M3 in the cutting manoeuvres was significantly associated to W-Abs (r(2)=0.45) whereas the timing between M3 and M4 was associated to W-Prp (r(2)=0.43). These results suggest that complex locomotor tasks can be achieved by impulsive activation of muscle groups, and that performance is associated to the specific timing of the activation impulses. PMID:23085217

Oliveira, A S; Silva, P B; Lund, M E; Kersting, U G; Farina, D

2012-10-22

303

Modulation of LTP at rat hippocampal CA3-CA1 synapses by direct current stimulation.  

PubMed

Transcranial direct current stimulation (tDCS) can produce a lasting polarity-specific modulation of cortical excitability in the brain, and it is increasingly used in experimental and clinical settings. Recent studies suggest that the after-effects of tDCS are related to molecular mechanisms of activity-dependent synaptic plasticity. Here we investigated the effect of DCS on the induction of one of the most studied N-methyl-d-aspartate receptor-dependent forms of long-term potentiation (LTP) of synaptic activity at CA3-CA1 synapses in the hippocampus. We show that DCS applied to rat brain slices determines a modulation of LTP that is increased by anodal and reduced by cathodal DCS. Immediate early genes, such as c-fos and zif268 (egr1/NGFI-A/krox24), are rapidly induced following neuronal activation, and a specific role of zif268 in the induction and maintenance of LTP has been demonstrated. We found that both anodal and cathodal DCS produce a marked subregion-specific increase in the expression of zif268 protein in the cornus ammonis (CA) region, whereas the same protocols of stimulation produce a less pronounced increase in c-fos protein expression in the CA and in dentate gyrus regions of the hippocampus. Brain-derived neurotrophic factor expression was also investigated, and it was found to be reduced in cathodal-stimulated slices. The present data demonstrate that it is possible to modulate LTP by using DCS and provide the rationale for the use of DCS in neurological diseases to promote the adaptive and suppress the maladaptive forms of brain plasticity. PMID:22236710

Ranieri, F; Podda, M V; Riccardi, E; Frisullo, G; Dileone, M; Profice, P; Pilato, F; Di Lazzaro, V; Grassi, C

2012-01-11

304

Short duration transcranial direct current stimulation (tDCS) modulates verbal memory.  

PubMed

Transcranial direct current stimulation (tDCS) is a noninvasive method of modulating cortical excitability. The aim of this study was to investigate the effects of short-duration tDCS (1.6 seconds per trial) on memory performance, and whether the effects were affected by stimulation administered early or late in a trial. Participants memorize words under anodal and cathodal tDCS to the left dorsolateral prefrontal cortex (DLPFC) in two separate sessions in no-stimulation, early stimulation, and late stimulation trials. Early stimulation occurred during word presentation, whereas late stimulation occurred after word presentation. Early anodal tDCS led to significantly better accuracy and speed in a subsequent recognition test compared to anodal late or no-stimulation conditions. Early cathodal tDCS, on the other hand, led to significantly worse accuracy and speed in a subsequent recognition test compared with cathodal late or no-stimulation conditions. The results of this study suggest that short-duration tDCS can modulate memory performance and highlight the importance of period of stimulation. PMID:21962975

Javadi, Amir Homayoun; Cheng, Paul; Walsh, Vincent

2011-08-25

305

Bi-directional modulation of fast inhibitory synaptic transmission by leptin  

PubMed Central

The hormone leptin has widespread actions in the CNS. Indeed, leptin markedly influences hippocampal excitatory synaptic transmission and synaptic plasticity. However, the effects of leptin on fast inhibitory synaptic transmission in the hippocampus have not been evaluated. Here we show that leptin modulates GABAA receptor-mediated synaptic transmission onto hippocampal CA1 pyramidal cells. Leptin promotes a rapid and reversible increase in the amplitude of evoked GABAA receptor-mediated IPSCs; an effect that was paralleled by increases in the frequency and amplitude of miniature IPSCs, but with no change in paired pulse ratio or CV, suggesting a postsynaptic expression mechanism. Following washout of leptin, a persistent depression (I-LTD) of evoked IPSCs was observed. Whole cell dialysis or bath application of inhibitors of PI 3-kinase or Akt prevented leptin-induced enhancement of IPSCs indicating involvement of a postsynaptic PI 3-kinase/Akt-dependent pathway. In contrast, blockade of PI 3-kinase or Akt activity failed to alter the ability of leptin to induce I-LTD, suggesting that this process is independent of PI 3-kinase/Akt. In conclusion these data indicate that the hormone leptin bi-directionally modulates GABAA receptor-mediated synaptic transmission in the hippocampus. These findings have important implications for the role of this hormone in regulating hippocampal pyramidal neuron excitability.

Solovyova, N.; Moult, P.R.; Milojkovic, B.; Lambert, J.J.; Harvey, J.

2008-01-01

306

Transcranial direct current stimulation of the prefrontal cortex modulates the desire for specific foods.  

PubMed

We aimed to assess whether modulation of the dorsolateral prefrontal cortex (DLFPC) with noninvasive brain stimulation, namely transcranial direct current stimulation (tDCS), modifies food craving in healthy subjects. We performed a randomized sham-controlled cross-over study in which 23 subjects received sham and active tDCS (anode left/cathode right and anode right/cathode left) of the DLPFC. Subjects were exposed to food and also watched a movie of food associated with strong craving. Desire for food consumption was evaluated by visual analogue scales (VAS) and food consumption before and after treatment. In addition we measured visual attention to food using an eye tracking system. Craving for viewed foods as indexed by VAS was reduced by anode right/cathode left tDCS. After sham stimulation, exposure to real food or food-related movie increased craving; whereas after anode left/cathode right tDCS, the food-related stimuli did not increase craving levels, as revealed by the VAS scale. Moreover, compared with sham stimulation, subjects fixated food-related pictures less frequently after anode right/cathode left tDCS and consumed less food after both active stimulation conditions. These changes were not related to mood changes after any type of tDCS treatment. The effects of tDCS on food craving might be related to a modulation of neural circuits associated with reward and decision-making. PMID:18243412

Fregni, Felipe; Orsati, Fernanda; Pedrosa, Waldelle; Fecteau, Shirley; Tome, Fatima A M; Nitsche, Michael A; Mecca, Tatiana; Macedo, Elizeu C; Pascual-Leone, Alvaro; Boggio, Paulo S

2007-12-23

307

A novel functional module detection algorithm for protein-protein interaction networks  

PubMed Central

Background The sparse connectivity of protein-protein interaction data sets makes identification of functional modules challenging. The purpose of this study is to critically evaluate a novel clustering technique for clustering and detecting functional modules in protein-protein interaction networks, termed STM. Results STM selects representative proteins for each cluster and iteratively refines clusters based on a combination of the signal transduced and graph topology. STM is found to be effective at detecting clusters with a diverse range of interaction structures that are significant on measures of biological relevance. The STM approach is compared to six competing approaches including the maximum clique, quasi-clique, minimum cut, betweeness cut and Markov Clustering (MCL) algorithms. The clusters obtained by each technique are compared for enrichment of biological function. STM generates larger clusters and the clusters identified have p-values that are approximately 125-fold better than the other methods on biological function. An important strength of STM is that the percentage of proteins that are discarded to create clusters is much lower than the other approaches. Conclusion STM outperforms competing approaches and is capable of effectively detecting both densely and sparsely connected, biologically relevant functional modules with fewer discards.

Hwang, Woochang; Cho, Young-Rae; Zhang, Aidong; Ramanathan, Murali

2006-01-01

308

Aldolase directly interacts with ARNO and modulates cell morphology and acidic vesicle distribution  

PubMed Central

Previously, we demonstrated that the vacuolar-type H+-ATPase (V-ATPase) a2-subunit functions as an endosomal pH sensor that interacts with the ADP-ribosylation factor (Arf) guanine nucleotide exchange factor, ARNO. In the present study, we showed that ARNO directly interacts not only with the a2-subunit but with all a-isoforms (a1–a4) of the V-ATPase, indicating a widespread regulatory interaction between V-ATPase and Arf GTPases. We then extended our search for other ARNO effectors that may modulate V-ATPase-dependent vesicular trafficking events and actin cytoskeleton remodeling. Pull-down experiments using cytosol of mouse proximal tubule cells (MTCs) showed that ARNO interacts with aldolase, but not with other enzymes of the glycolytic pathway. Direct interaction of aldolase with the pleckstrin homology domain of ARNO was revealed by pull-down assays using recombinant proteins, and surface plasmon resonance revealed their high avidity interaction with a dissociation constant: KD = 2.84 × 10?10 M. MTC cell fractionation revealed that aldolase is also associated with membranes of early endosomes. Functionally, aldolase knockdown in HeLa cells produced striking morphological changes accompanied by long filamentous cell protrusions and acidic vesicle redistribution. However, the 50% knockdown we achieved did not modulate the acidification capacity of endosomal/lysosomal compartments. Finally, a combination of small interfering RNA knockdown and overexpression revealed that the expression of aldolase is inversely correlated with gelsolin levels in HeLa cells. In summary, we have shown that aldolase forms a complex with ARNO/Arf6 and the V-ATPase and that it may contribute to remodeling of the actin cytoskeleton and/or the trafficking and redistribution of V-ATPase-dependent acidic compartments via a combination of protein-protein interaction and gene expression mechanisms.

Merkulova, Maria; Hurtado-Lorenzo, Andres; Hosokawa, Hiroyuki; Zhuang, Zhenjie; Brown, Dennis; Ausiello, Dennis A.

2011-01-01

309

Stealth optimized fisheye state routing in mobile ad-hoc networks using directional antennas  

Microsoft Academic Search

Research on the use of directional antennas in mobile ad-hoc networks has been mostly centered on improving spatial reuse, extending the transmission range and minimizing flooding overhead. However, directional antennas are also a suitable means to achieve low probability of detection in battlefield applications. This paper proposes mechanisms to minimize the number of hops and end-to-end delay when routing packets

António Grilo; Mário Macedo; Pedro Sebastiăo; Mário Nunes

2005-01-01

310

Clustering and overlapping modules detection in PPI network based on IBFO.  

PubMed

As is known to all, traditional clustering algorithms do not work well due to the topological features of protein-protein interaction networks. An improved clustering method based on bacteria foraging optimization (BFO) mechanism and intuitionistic fuzzy set, short for improved BFO, is proposed in this paper, in which the trigonometric function is used to define the membership degrees and the indeterminacy degree is introduced to detect the overlapping modules. In chemotactic operation of BFO, the algorithm initializes a cluster center according to comprehensive network feature value of node and eliminates the isolated point in accordance with edge-clustering coefficient. In the reproduction operation of BFO, the nodes possessing high membership degrees are merged into the cluster that the cluster center belongs to and labeled as visited nodes. Meanwhile, the nodes that also have high indeterminacy degrees are visited again when generating another cluster. The procedure of elimination-dispersal operation is equivalent to the selection of the next cluster center. Finally, the algorithm merges the clusters having high similarity. The results show that the algorithm not only determines the cluster number automatically, improves the f-measure value of cluster results, but also identify the overlaps in protein-protein interaction network successfully. PMID:23229795

Lei, Xiujuan; Wu, Shuang; Ge, Liang; Zhang, Aidong

2013-01-01

311

Metabolomic correlation-network modules in Arabidopsis based on a graph-clustering approach  

PubMed Central

Background Deciphering the metabolome is essential for a better understanding of the cellular metabolism as a system. Typical metabolomics data show a few but significant correlations among metabolite levels when data sampling is repeated across individuals grown under strictly controlled conditions. Although several studies have assessed topologies in metabolomic correlation networks, it remains unclear whether highly connected metabolites in these networks have specific functions in known tissue- and/or genotype-dependent biochemical pathways. Results In our study of metabolite profiles we subjected root tissues to gas chromatography-time-of-flight/mass spectrometry (GC-TOF/MS) and used published information on the aerial parts of 3 Arabidopsis genotypes, Col-0 wild-type, methionine over-accumulation 1 (mto1), and transparent testa4 (tt4) to compare systematically the metabolomic correlations in samples of roots and aerial parts. We then applied graph clustering to the constructed correlation networks to extract densely connected metabolites and evaluated the clusters by biochemical-pathway enrichment analysis. We found that the number of significant correlations varied by tissue and genotype and that the obtained clusters were significantly enriched for metabolites included in biochemical pathways. Conclusions We demonstrate that the graph-clustering approach identifies tissue- and/or genotype-dependent metabolomic clusters related to the biochemical pathway. Metabolomic correlations complement information about changes in mean metabolite levels and may help to elucidate the organization of metabolically functional modules.

2011-01-01

312

Evolution of ethnocentrism on undirected and directed Barabási-Albert networks  

NASA Astrophysics Data System (ADS)

Using Monte Carlo simulations, we study the evolution of contingent cooperation and ethnocentrism in the one-shot game. Interactions and reproduction among computational agents are simulated on undirected and directed Barabási-Albert (BA) networks. We first replicate the Hammond-Axelrod model of in-group favoritism on a square lattice and then generalize this model on undirected and directed BA networks for both asexual and sexual reproduction cases. Our simulations demonstrate that irrespective of the mode of reproduction, the ethnocentric strategy becomes common even though cooperation is individually costly and mechanisms such as reciprocity or conformity are absent. Moreover, our results indicate that the spread of favoritism towards similar others highly depends on the network topology and the associated heterogeneity of the studied population.

Lima, F. W. S.; Hadzibeganovic, Tarik; Stauffer, Dietrich

2009-12-01

313

TCP fiber: direct measurement optical transport congestion control for beyond 10 gigabit networks  

NASA Astrophysics Data System (ADS)

Optical or gigabit communication links could currently allow petabytes of data to be transferred to geographically distributed tera-scale computing facilities at beyond 10Gbps rates. While the bandwidth is available in network link technology, transport protocols like TCP/IP and common network host architectures severely limit the attainable throughput over such links. Traditional layering -that is implemented through excessive per-byte (word) memory bandwidth constrained buffer copying- transport processing complexity, combined error and congestion control and trial and error timeout-based approaches result in prohibitively increasing performance degradation as network speeds increase. In this paper we present TCP-Fiber, a TCP version that is based on direct measurements of available and bottleneck link bandwidth and is able to perform decoupled error and congestion control while supporting zero-copy from application to network interface. A key innovation in TCP-Fiber is a variable length "packet train" based method that allows sensing ultra high bandwidth related quantities in a network independent fashion with relaxed requirements to timers and system resources (as related to interrupts, system calls etc). A TCP-Fiber connection is able to fairly send at the full network rate without extensive trial-and-error convergence procedures or waiting on time-out for unacknowledged packets, while maintaining network stability.

Kazantzidis, Matheos

2006-06-01

314

Direct torque controlled space vector modulated induction motor fed by a Z-source inverter for electric vehicles  

Microsoft Academic Search

This paper proposes a new closed loop speed control of an induction motor fed by a high performance Z-source inverter (ZSI), the speed control is based on direct torque control space vector modulation (DTC-SVM) control strategy. The modified space vector modulation (MSVM) is used to insert the shoot-through state within the switching signals for the ZSI. A dual loop controller

Omar Ellabban; Joeri Van Mierlo; Philippe Lataire

2011-01-01

315

Magnetoencephalographic evidence for the modulation of cortical swallowing processing by transcranial direct current stimulation.  

PubMed

Swallowing is a complex neuromuscular task that is processed within multiple regions of the human brain. Rehabilitative treatment options for dysphagia due to neurological diseases are limited. Because the potential for adaptive cortical changes in compensation of disturbed swallowing is recognized, neuromodulation techniques like transcranial direct current stimulation (tDCS) are currently considered as a treatment option. Here we evaluate the effect of tDCS on cortical swallowing network activity and behavior. In a double-blind crossover study, anodal tDCS (20min, 1mA) or sham stimulation was administered over the left or right swallowing motor cortex in 21 healthy subjects in separate sessions. Cortical activation was measured using magnetoencephalography (MEG) before and after tDCS during cued "simple", "fast" and "challenged" swallow tasks with increasing levels of difficulty. Swallowing response times and accuracy were measured. Significant bilateral enhancement of cortical swallowing network activation was found in the theta frequency range after left tDCS in the fast swallow task (p=0.006) and following right tDCS in the challenged swallow task (p=0.007), but not after sham stimulation. No relevant behavioral effects were observed on swallow response time, but swallow precision improved after left tDCS (p<0.05). Anodal tDCS applied over the swallowing motor cortex of either hemisphere was able to increase bilateral swallow-related cortical network activation in a frequency specific manner. These neuroplastic effects were associated with subtle behavioral gains during complex swallow tasks in healthy individuals suggesting that tDCS deserves further evaluation as a treatment tool for dysphagia. PMID:23800793

Suntrup, Sonja; Teismann, Inga; Wollbrink, Andreas; Winkels, Martin; Warnecke, Tobias; Flöel, Agnes; Pantev, Christo; Dziewas, Rainer

2013-06-23

316

NRC TLD Direct Radiation Monitoring Network. Progress report, October--December 1996  

SciTech Connect

This report presents the results of the NRC Direct Radiation Monitoring Network for the fourth quarter of 1996. It provides the ambient radiation levels measured in the vicinity of 74 sites throughout the United States. In addition, it describes the equipment used, monitoring station selection criteria, characterization of the dosimeter response, calibration procedures, statistical methods, intercomparison, and quality assurance program. 3 figs., 4 tabs.

Struckmeyer, R.

1997-03-01

317

Conservation laws for voter-like models on random directed networks  

Microsoft Academic Search

We study the voter model, under node and link update, and the related invasion process on a single strongly connected component of a directed network. We implement an analytical treatment in the thermodynamic limit using the heterogeneous mean field assumption. From the dynamical rules at the microscopic level, we find the equations for the evolution of the relative densities of

Angeles Serrano; Konstantin Klemm; Federico Vazquez; V ´ őctor; M. Egu ´ őluz; Maxi San Miguel

318

Modeling of a Direct Expansion Solar Assisted Heat Pump Using Artificial Neural Networks  

Microsoft Academic Search

This study presents the applicability of artificial neural networks (ANNs) to model a direct expansion solar assisted heat pump (DXSAHP). The experiments were conducted to determine the effects of solar intensity under the meteorological conditions of Calicut, India. The parameters such as coefficient of performance, compressor pressure ratio, air temperature at condenser outlet, and solar energy input ratio predicted from

M. Mohanraj; S. Jayaraj; C. Muraleedharan

2008-01-01

319

Direct-detection WiMax orthogonal frequency division multiplexing over fiber access networks  

NASA Astrophysics Data System (ADS)

We have investigated novel optical-wireless architecture to provide WiMax orthogonal frequency division multiplexing (OFDM) signals over fiber access network by simulation. The proposed architecture utilizes direct detection for WiMax OFDM. The simulation results show that it can transmit a high capacity WiMax OFDM signal over 250km SMF successfully.

He, Jing; Su, Jinshu; Huang, Yuan; Liu, Hao

2012-11-01

320

Direct adaptive regulation of unknown nonlinear dynamical systems via dynamic neural networks  

Microsoft Academic Search

A direct nonlinear adaptive state regulator, for unknown dynamical systems that are modeled by dynamic neural networks is discussed. In the ideal case of complete model matching, convergence of the state to zero plus boundedness of all signals in the closed loop is ensured. Moreover, the behavior of the closed loop system is analyzed for cases in which the true

George A. Rovithakis; Manolis A. Christodoulou

1995-01-01

321

O(/E/) Time Algorithm for Computing the Reliability of a Class of Directed Networks.  

National Technical Information Service (NTIS)

This paper is concerned with the problem of computing the source-to-terminal reliability, the probability that a source s can send communication to a terminal t, in a probabilistic directed network. A set of reliability-preserving reductions, called 2-nei...

A. Agrawal A. Satyanarayana

1982-01-01

322

Transient simulation of multilayered power distribution network based on block-type alternating direction implicit scheme  

Microsoft Academic Search

This paper describes an alternating direction implicit (ADI) formulation of a block-type scheme to circumvent the time step size limitation of an existing block-type leapfrog scheme. Numerical results show that the proposed block-type ADI scheme can use a larger time step size and perform faster simulations of power distribution networks than the existing method.

Tadatoshi Sekine; Tomoki Ishimaru; Hideki Asai

2012-01-01

323

Spreading codes for direct sequence CDMA and wideband CDMA cellular networks  

Microsoft Academic Search

This article presents an overview of the spreading techniques for use in direct sequence CDMA cellular networks. We review the theoretical background for sequences used in CDMA and wideband CDMA, and discuss the main characteristics of the maximal length, Gold (1967, 1968), and Kasami sequences, as well as variable- and fixed-length orthogonal codes. We also describe different methods of multiple

Esmael H. Dinan; Bijan Jabbari

1998-01-01

324

A new artificial neural network controller for direct control method for matrix converters  

Microsoft Academic Search

This work presents a new artificial neural network (ANN) Controller for implementing the Direct control method (DCM) for Matrix converters (MC) to decrease the time of calculation of the conventional DSP control system. To avoid the difficult calculation of ANN-DCM, the design uses the individual training strategy with the fixed weight and the supervised models. A computer simulation program is

Hong Hee Lee; Phan Quoc Dzung; Le Minh Phuong; Le Dinh Khoa

2009-01-01

325

Selection of input parameters to model direct solar irradiance by using artificial neural networks  

Microsoft Academic Search

A very important factor in the assessment of solar energy resources is the availability of direct irradiance data of high quality. However, this component of solar radiation is seldom measured and thus must be estimated from data of global solar irradiance, which is registered in most radiometric stations. In recent years, artificial neural networks (ANN) have shown to be a

G. López; F. J. Batlles; J. Tovar-Pescador

2005-01-01

326

Direct, physically motivated derivation of the contagion condition for spreading processes on generalized random networks.  

PubMed

For a broad range of single-seed contagion processes acting on generalized random networks, we derive a unifying analytic expression for the possibility of global spreading events in a straightforward, physically intuitive fashion. Our reasoning lays bare a direct mechanical understanding of an archetypal spreading phenomena that is not evident in circuitous extant mathematical approaches. PMID:21728620

Dodds, Peter Sheridan; Harris, Kameron Decker; Payne, Joshua L

2011-05-25

327

Direct, physically motivated derivation of the contagion condition for spreading processes on generalized random networks  

NASA Astrophysics Data System (ADS)

For a broad range of single-seed contagion processes acting on generalized random networks, we derive a unifying analytic expression for the possibility of global spreading events in a straightforward, physically intuitive fashion. Our reasoning lays bare a direct mechanical understanding of an archetypal spreading phenomena that is not evident in circuitous extant mathematical approaches.

Dodds, Peter Sheridan; Harris, Kameron Decker; Payne, Joshua L.

2011-05-01

328

Gene Coexpression Network Alignment and Conservation of Gene Modules between Two Grass Species: Maize and Rice[C][W][OA  

PubMed Central

One major objective for plant biology is the discovery of molecular subsystems underlying complex traits. The use of genetic and genomic resources combined in a systems genetics approach offers a means for approaching this goal. This study describes a maize (Zea mays) gene coexpression network built from publicly available expression arrays. The maize network consisted of 2,071 loci that were divided into 34 distinct modules that contained 1,928 enriched functional annotation terms and 35 cofunctional gene clusters. Of note, 391 maize genes of unknown function were found to be coexpressed within modules along with genes of known function. A global network alignment was made between this maize network and a previously described rice (Oryza sativa) coexpression network. The IsoRankN tool was used, which incorporates both gene homology and network topology for the alignment. A total of 1,173 aligned loci were detected between the two grass networks, which condensed into 154 conserved subgraphs that preserved 4,758 coexpression edges in rice and 6,105 coexpression edges in maize. This study provides an early view into maize coexpression space and provides an initial network-based framework for the translation of functional genomic and genetic information between these two vital agricultural species.

Ficklin, Stephen P.; Feltus, F. Alex

2011-01-01

329

Efavirenz directly modulates estrogen receptor and induces breast cancer cell growth  

PubMed Central

Objectives Efavirenz-based HIV therapy is associated with breast hypertrophy and gynecomastia. Here, we tested the hypothesis that efavirenz induces gynecomastia through direct binding and modulation of estrogen receptor (ER). Methods To determine the effect of efavirenz on growth, the estrogen-dependent, ER-positive breast cancer cell lines MCF-7, T47D and ZR-75-1 were treated with efavirenz under estrogen-free conditions in the presence or absence of the anti-estrogen ICI 182,780. Cells treated with 17?-estradiol in the absence or presence of ICI 182,780 served as positive and negative controls, respectively. Cellular growth was assayed using the crystal violet staining method and an in vitro receptor binding assay was used to measure efavirenz’s ER binding affinity. Results Efavirenz induced growth in MCF-7 cells with an estimated EC50 of 15.7µM. This growth was reversed by ICI 182,780. Further, efavirenz binds directly to ER (IC50 of ~52µM) at roughly 1000-fold higher concentration than observed with E2. Conclusions Our data suggest that efavirenz-induced gynecomastia may be due, at least in part, to drug-induced ER activation in breast tissues.

Sikora, Matthew J.; Rae, James M.; Johnson, Michael D.; Desta, Zeruesenay

2010-01-01

330

Calaxin drives sperm chemotaxis by Ca˛?-mediated direct modulation of a dynein motor.  

PubMed

Sperm chemotaxis occurs widely in animals and plants and plays an important role in the success of fertilization. Several studies have recently demonstrated that Ca(2+) influx through specific Ca(2+) channels is a prerequisite for sperm chemotactic movement. However, the regulator that modulates flagellar movement in response to Ca(2+) is unknown. Here we show that a neuronal calcium sensor, calaxin, directly acts on outer-arm dynein and regulates specific flagellar movement during sperm chemotaxis. Calaxin inhibition resulted in significant loss of sperm chemotactic movement, despite normal increases in intracellular calcium concentration. Using a demembranated sperm model, we demonstrate that calaxin is essential for generation and propagation of Ca(2+)-induced asymmetric flagellar bending. An in vitro motility assay revealed that calaxin directly suppressed the velocity of microtubule sliding by outer-arm dynein at high Ca(2+) concentrations. This study describes the missing link between chemoattractant-mediated Ca(2+) signaling and motor-driven microtubule sliding during sperm chemotaxis. PMID:23169663

Mizuno, Katsutoshi; Shiba, Kogiku; Okai, Masahiko; Takahashi, Yusuke; Shitaka, Yuji; Oiwa, Kazuhiro; Tanokura, Masaru; Inaba, Kazuo

2012-11-20

331

INFORMAS (International Network for Food and Obesity/non-communicable diseases Research, Monitoring and Action Support): summary and future directions.  

PubMed

This supplement presents the foundational elements for INFORMAS (International Network for Food and Obesity/non-communicable diseases Research, Monitoring and Action Support). As explained in the overview article by Swinburn and colleagues, INFORMAS has a compelling rationale and has set forth clear objectives, outcomes, principles and frameworks for monitoring and benchmarking key aspects of food environments and the policies and actions that influence the healthiness of food environments. This summary highlights the proposed monitoring approaches for the 10 interrelated INFORMAS modules: public and private sector policies and actions; key aspects of food environments (food composition, labelling, promotion, provision, retail, prices, and trade and investment) and population outcomes (diet quality). This ambitious effort should be feasible when approached in a step-wise manner, taking into account existing monitoring efforts, data sources, country contexts and capacity, and when adequately resourced. After protocol development and pilot testing of the modules, INFORMAS aims to be a sustainable, low-cost monitoring framework. Future directions relate to institutionalization, implementation and, ultimately, to leveraging INFORMAS data in ways that will bring key drivers of food environments into alignment with public health goals. PMID:24074219

Kumanyika, S

2013-10-01

332

Network-state modulation of power-law frequency-scaling in visual cortical neurons.  

PubMed

Various types of neural-based signals, such as EEG, local field potentials and intracellular synaptic potentials, integrate multiple sources of activity distributed across large assemblies. They have in common a power-law frequency-scaling structure at high frequencies, but it is still unclear whether this scaling property is dominated by intrinsic neuronal properties or by network activity. The latter case is particularly interesting because if frequency-scaling reflects the network state it could be used to characterize the functional impact of the connectivity. In intracellularly recorded neurons of cat primary visual cortex in vivo, the power spectral density of V(m) activity displays a power-law structure at high frequencies with a fractional scaling exponent. We show that this exponent is not constant, but depends on the visual statistics used to drive the network. To investigate the determinants of this frequency-scaling, we considered a generic recurrent model of cortex receiving a retinotopically organized external input. Similarly to the in vivo case, our in computo simulations show that the scaling exponent reflects the correlation level imposed in the input. This systematic dependence was also replicated at the single cell level, by controlling independently, in a parametric way, the strength and the temporal decay of the pairwise correlation between presynaptic inputs. This last model was implemented in vitro by imposing the correlation control in artificial presynaptic spike trains through dynamic-clamp techniques. These in vitro manipulations induced a modulation of the scaling exponent, similar to that observed in vivo and predicted in computo. We conclude that the frequency-scaling exponent of the V(m) reflects stimulus-driven correlations in the cortical network activity. Therefore, we propose that the scaling exponent could be used to read-out the "effective" connectivity responsible for the dynamical signature of the population signals measured at different integration levels, from Vm to LFP, EEG and fMRI. PMID:19779556

El Boustani, Sami; Marre, Olivier; Béhuret, Sébastien; Baudot, Pierre; Yger, Pierre; Bal, Thierry; Destexhe, Alain; Frégnac, Yves

2009-09-25

333

A radio-aware routing algorithm for reliable directed diffusion in lossy wireless sensor networks.  

PubMed

In Wireless Sensor Networks (WSNs), transmission errors occur frequently due to node failure, battery discharge, contention or interference by objects. Although Directed Diffusion has been considered as a prominent data-centric routing algorithm, it has some weaknesses due to unexpected network errors. In order to address these problems, we proposed a radio-aware routing algorithm to improve the reliability of Directed Diffusion in lossy WSNs. The proposed algorithm is aware of the network status based on the radio information from MAC and PHY layers using a cross-layer design. The cross-layer design can be used to get detailed information about current status of wireless network such as a link quality or transmission errors of communication links. The radio information indicating variant network conditions and link quality was used to determine an alternative route that provides reliable data transmission under lossy WSNs. According to the simulation result, the radio-aware reliable routing algorithm showed better performance in both grid and random topologies with various error rates. The proposed solution suggested the possibility of providing a reliable transmission method for QoS requests in lossy WSNs based on the radio-awareness. The energy and mobility issues will be addressed in the future work. PMID:22408493

Kim, Yong-Pyo; Jung, Euihyun; Park, Yong-Jin

2009-10-13

334

A Radio-Aware Routing Algorithm for Reliable Directed Diffusion in Lossy Wireless Sensor Networks  

PubMed Central

In Wireless Sensor Networks (WSNs), transmission errors occur frequently due to node failure, battery discharge, contention or interference by objects. Although Directed Diffusion has been considered as a prominent data-centric routing algorithm, it has some weaknesses due to unexpected network errors. In order to address these problems, we proposed a radio-aware routing algorithm to improve the reliability of Directed Diffusion in lossy WSNs. The proposed algorithm is aware of the network status based on the radio information from MAC and PHY layers using a cross-layer design. The cross-layer design can be used to get detailed information about current status of wireless network such as a link quality or transmission errors of communication links. The radio information indicating variant network conditions and link quality was used to determine an alternative route that provides reliable data transmission under lossy WSNs. According to the simulation result, the radio-aware reliable routing algorithm showed better performance in both grid and random topologies with various error rates. The proposed solution suggested the possibility of providing a reliable transmission method for QoS requests in lossy WSNs based on the radio-awareness. The energy and mobility issues will be addressed in the future work.

Kim, Yong-Pyo; Jung, Euihyun; Park, Yong-Jin

2009-01-01

335

Modulating parameters of excitability during and after transcranial direct current stimulation of the human motor cortex  

PubMed Central

Weak transcranial direct current stimulation (tDCS) of the human motor cortex results in excitability shifts which occur during and after stimulation. These excitability shifts are polarity-specific with anodal tDCS enhancing excitability, and cathodal reducing it. To explore the origin of this excitability modulation in more detail, we measured the input–output curve and motor thresholds as global parameters of cortico-spinal excitability, and determined intracortical inhibition and facilitation, as well as facilitatory indirect wave (I-wave) interactions. Measurements were performed during short-term tDCS, which elicits no after-effects, and during other tDCS protocols which do elicit short- and long-lasting after-effects. Resting and active motor thresholds remained stable during and after tDCS. The slope of the input–output curve was increased by anodal tDCS and decreased by cathodal tDCS. Anodal tDCS of the primary motor cortex reduced intracortical inhibition and enhanced facilitation after tDCS but not during tDCS. Cathodal tDCS reduced facilitation during, and additionally increased inhibition after its administration. During tDCS, I-wave facilitation was not influenced but, for the after-effects, anodal tDCS increased I-wave facilitation, while cathodal tDCS had only minor effects. These results suggest that the effect of tDCS on cortico-spinal excitability during a short period of stimulation (which does not induce after-effects) primarily depends on subthreshold resting membrane potential changes, which are able to modulate the input-output curve, but not motor thresholds. In contrast, the after-effects of tDCS are due to shifts in intracortical inhibition and facilitation, and at least partly also to facilitatory I-wave interaction, which is controlled by synaptic activity.

Nitsche, Michael A; Seeber, Antje; Frommann, Kai; Klein, Cornelia Carmen; Rochford, Christian; Nitsche, Maren S; Fricke, Kristina; Liebetanz, David; Lang, Nicolas; Antal, Andrea; Paulus, Walter; Tergau, Frithjof

2005-01-01

336

Single Stage Inverter for a Direct AC Connection of a Photovoltaic Cell Module  

Microsoft Academic Search

There are several possibilities to transfer the energy taken from a photovoltaic cell to the grid. In the past, several cell modules used the same centralized inverter to transfer the energy to the grid. Nowadays, decentralized modules are preferred because of their versatility to harvest a larger amount of power, even when some of the modules of the total surface

A. Fernandez; J. Sebastian; M. M. Hernando; M. Arias; G. Perez

2006-01-01

337

Cortical Hubs Form a Module for Multisensory Integration on Top of the Hierarchy of Cortical Networks  

PubMed Central

Sensory stimuli entering the nervous system follow particular paths of processing, typically separated (segregated) from the paths of other modal information. However, sensory perception, awareness and cognition emerge from the combination of information (integration). The corticocortical networks of cats and macaque monkeys display three prominent characteristics: (i) modular organisation (facilitating the segregation), (ii) abundant alternative processing paths and (iii) the presence of highly connected hubs. Here, we study in detail the organisation and potential function of the cortical hubs by graph analysis and information theoretical methods. We find that the cortical hubs form a spatially delocalised, but topologically central module with the capacity to integrate multisensory information in a collaborative manner. With this, we resolve the underlying anatomical substrate that supports the simultaneous capacity of the cortex to segregate and to integrate multisensory information.

Zamora-Lopez, Gorka; Zhou, Changsong; Kurths, Jurgen

2009-01-01

338

Astrocytes Modulate Neural Network Activity by Ca2+-Dependent Uptake of Extracellular K+  

PubMed Central

Astrocytes are electrically nonexcitable cells that display increases in cytosolic calcium ion (Ca2+) in response to various neurotransmitters and neuromodulators. However, the physiological role of astrocytic Ca2+ signaling remains controversial. We show here that astrocytic Ca2+ signaling ex vivo and in vivo stimulated the Na+,K+-ATPase (Na+- and K+-dependent adenosine triphosphatase), leading to a transient decrease in the extracellular potassium ion (K+) concentration. This in turn led to neuronal hyperpolarization and suppressed baseline excitatory synaptic activity, detected as a reduced frequency of excitatory postsynaptic currents. Synaptic failures decreased in parallel, leading to an increase in synaptic fidelity. The net result was that astrocytes, through active uptake of K+, improved the signal-to-noise ratio of synaptic transmission. Active control of the extracellular K+ concentration thus provides astrocytes with a simple yet powerful mechanism to rapidly modulate network activity.

Wang, Fushun; Smith, Nathan A.; Xu, Qiwu; Fujita, Takumi; Baba, Akemichi; Matsuda, Toshio; Takano, Takahiro; Bekar, Lane; Nedergaard, Maiken

2012-01-01

339

A Polygon Model for Wireless Sensor Network Deployment with Directional Sensing Areas  

PubMed Central

The modeling of the sensing area of a sensor node is essential for the deployment algorithm of wireless sensor networks (WSNs). In this paper, a polygon model is proposed for the sensor node with directional sensing area. In addition, a WSN deployment algorithm is presented with topology control and scoring mechanisms to maintain network connectivity and improve sensing coverage rate. To evaluate the proposed polygon model and WSN deployment algorithm, a simulation is conducted. The simulation results show that the proposed polygon model outperforms the existed disk model and circular sector model in terms of the maximum sensing coverage rate.

Wu, Chun-Hsien; Chung, Yeh-Ching

2009-01-01

340

Synthetic nanomotors in microchannel networks: directional microchip motion and controlled manipulation of cargo.  

PubMed

We illustrate the use of catalytic nanowire motors for directional motion and microscale transport of cargo within microfluidic channel networks. The CNT-based synthetic nanomotor can propel a large cargo load at high speeds through predetermined paths and junctions of the microchannel network. The magnetic properties of the nickel-containing nanomotors offer controlled cargo manipulations, including en-route load, drag, and release. Such use of synthetic nanomachines can lead to chemically powered versatile laboratory-on-a-chip devices performing a series of tasks simultaneously or sequentially. PMID:18533716

Burdick, Jared; Laocharoensuk, Rawiwan; Wheat, Philip M; Posner, Jonathan D; Wang, Joseph

2008-06-06

341

Algorithm to Identify Frequent Coupled Modules from Two-Layered Network Series: Application to Study Transcription and Splicing Coupling  

PubMed Central

Abstract Current network analysis methods all focus on one or multiple networks of the same type. However, cells are organized by multi-layer networks (e.g., transcriptional regulatory networks, splicing regulatory networks, protein-protein interaction networks), which interact and influence each other. Elucidating the coupling mechanisms among those different types of networks is essential in understanding the functions and mechanisms of cellular activities. In this article, we developed the first computational method for pattern mining across many two-layered graphs, with the two layers representing different types yet coupled biological networks. We formulated the problem of identifying frequent coupled clusters between the two layers of networks into a tensor-based computation problem, and proposed an efficient solution to solve the problem. We applied the method to 38 two-layered co-transcription and co-splicing networks, derived from 38 RNA-seq datasets. With the identified atlas of coupled transcription-splicing modules, we explored to what extent, for which cellular functions, and by what mechanisms transcription-splicing coupling takes place.

Li, Wenyuan; Dai, Chao; Liu, Chun-Chi

2012-01-01

342

Algorithm to identify frequent coupled modules from two-layered network series: application to study transcription and splicing coupling.  

PubMed

Current network analysis methods all focus on one or multiple networks of the same type. However, cells are organized by multi-layer networks (e.g., transcriptional regulatory networks, splicing regulatory networks, protein-protein interaction networks), which interact and influence each other. Elucidating the coupling mechanisms among those different types of networks is essential in understanding the functions and mechanisms of cellular activities. In this article, we developed the first computational method for pattern mining across many two-layered graphs, with the two layers representing different types yet coupled biological networks. We formulated the problem of identifying frequent coupled clusters between the two layers of networks into a tensor-based computation problem, and proposed an efficient solution to solve the problem. We applied the method to 38 two-layered co-transcription and co-splicing networks, derived from 38 RNA-seq datasets. With the identified atlas of coupled transcription-splicing modules, we explored to what extent, for which cellular functions, and by what mechanisms transcription-splicing coupling takes place. PMID:22697243

Li, Wenyuan; Dai, Chao; Liu, Chun-Chi; Zhou, Xianghong Jasmine

2012-06-01

343

Je pense donc je fais: transcranial direct current stimulation modulates brain oscillations associated with motor imagery and movement observation  

PubMed Central

Motor system neural networks are activated during movement imagery, observation and execution, with a neural signature characterized by suppression of the Mu rhythm. In order to investigate the origin of this neurophysiological marker, we tested whether transcranial direct current stimulation (tDCS) modifies Mu rhythm oscillations during tasks involving observation and imagery of biological and non-biological movements. We applied tDCS (anodal, cathodal, and sham) in 21 male participants (mean age 23.8 ± 3.06), over the left M1 with a current of 2 mA for 20 min. Following this, we recorded the EEG at C3, C4, and Cz and surrounding C3 and C4 electrodes. Analyses of C3 and C4 showed significant effects for biological vs. non-biological movement (p = 0.005), and differential hemisphere effects according to the type of stimulation (p = 0.04) and type of movement (p = 0.02). Analyses of surrounding electrodes revealed significant interaction effects considering type of stimulation and imagery or observation of biological or non-biological movement (p = 0.03). The main findings of this study were (1) Mu desynchronization during biological movement of the hand region in the contralateral hemisphere after sham tDCS; (2) polarity-dependent modulation effects of tDCS on the Mu rhythm, i.e., anodal tDCS led to Mu synchronization while cathodal tDCS led to Mu desynchronization during movement observation and imagery (3) specific focal and opposite inter-hemispheric effects, i.e., contrary effects for the surrounding electrodes during imagery condition and also for inter-hemispheric electrodes (C3 vs. C4). These findings provide insights into the cortical oscillations during movement observation and imagery. Furthermore, it shows that tDCS can be highly focal when guided by a behavioral task.

Lapenta, Olivia M.; Minati, Ludovico; Fregni, Felipe; Boggio, Paulo S.

2013-01-01

344

Cholinergic control of cortical network interactions enables feedback-mediated attentional modulation.  

PubMed

Attention increases our ability to detect behaviorally relevant stimuli. At the neuronal level this is supported by increased firing rates of neurons representing the attended object. In primary visual cortex an attention-mediated activity increase depends on the presence of the neuromodulator acetylcholine. Using a spiking network model of visual cortex we have investigated how acetylcholine interacts with biased feedback to enable attentional processing. Although acetylcholine affects cortical processing in a multitude of manners, we restricted our analysis to four of its main established actions. These were (i) a reduction in firing rate adaptation by reduction in M-currents (muscarinic), (ii) an increase in thalamocortical synaptic efficacy by nicotinic presynaptic receptors, (iii) a reduction in lateral interactions by muscarinic presynaptic receptors, and (iv) an increase in inhibitory drive by muscarinic receptors located on inhibitory interneurons. We found that acetylcholine contributes to feedback-mediated attentional modulation, mostly by reducing intracortical interactions and also to some extent by increasing the inhibitory drive. These findings help explain why acetylcholine is necessary for top-down-driven attentional modulation, and suggest a close interdependence of cholinergic and feedback drive in mediating cognitive function. PMID:21692884

Deco, Gustavo; Thiele, Alexander

2011-06-21

345

Efficient direct magneto-optical phase modulation of light waves in spun microstructured fibres  

SciTech Connect

We have proposed a phase modulator of optical radiation for an interferometric electric-current sensor. The modulator takes advantage of the Faraday effect in spun microstructured optical fibres. Such fibres enable small-diameter multiturn fibre coils to be produced, which is necessary for achieving a preset phase modulation amplitude at a moderate drive current. The principal characteristics of the modulator have been studied experimentally: frequency response, magneto-optical sensitivity and output signal contrast. The results demonstrate that the modulator ensures high efficiency, approaching the theoretical one, provided the modulation period exceeds the time it takes light to pass through the fibre. We have examined the influence of spun fibre parameters on the performance of the modulator.

Gubin, Vladimir P; Morshnev, Sergey K; Starostin, Nikolay I; Chamorovsky, Yury K; Sazonov, Aleksandr I; Przhiyalkovskii, Ya V; Boev, A I [V.A.Kotel'nikov Institute of Radio Engineering and Electronics, Fryazino Branch, Russian Academy of Sciences, Fryazino, Moscow Region (Russian Federation)

2011-09-30

346

The Proximal Hydrogen Bond Network Modulates Bacillus subtilis Nitric-oxide Synthase Electronic and Structural Properties  

PubMed Central

Bacterial nitric-oxide synthase (NOS)-like proteins are believed to be genuine NOSs. As for cytochromes P450 (CYPs), NOS-proximal ligand is a thiolate that exerts a push effect crucial for the process of dioxygen activation. Unlike CYPs, this catalytic electron donation seems controlled by a hydrogen bond (H-bond) interaction between the thiolate ligand and a vicinal tryptophan. Variations of the strength of this H-bond could provide a direct way to tune the stability along with the electronic and structural properties of NOS. We generated five different mutations of bsNOS Trp66, which can modulate this proximal H-bond. We investigated the effects of these mutations on different NOS complexes (FeIII, FeIICO, and FeIINO), using a combination of UV-visible absorption, EPR, FTIR, and resonance Raman spectroscopies. Our results indicate that (i) the proximal H-bond modulation can selectively decrease or increase the electron donating properties of the proximal thiolate, (ii) this modulation controls the ?-competition between distal and proximal ligands, (iii) this H-bond controls the stability of various NOS intermediates, and (iv) a fine tuning of the electron donation by the proximal ligand is required to allow at the same time oxygen activation and to prevent uncoupling reactions.

Brunel, Albane; Wilson, Adjele; Henry, Laura; Dorlet, Pierre; Santolini, Jerome

2011-01-01

347

Arachidonic Acid: An Evolutionarily Conserved Signaling Molecule Modulates Plant Stress Signaling Networks[C][W  

PubMed Central

Fatty acid structure affects cellular activities through changes in membrane lipid composition and the generation of a diversity of bioactive derivatives. Eicosapolyenoic acids are released into plants upon infection by oomycete pathogens, suggesting they may elicit plant defenses. We exploited transgenic Arabidopsis thaliana plants (designated EP) producing eicosadienoic, eicosatrienoic, and arachidonic acid (AA), aimed at mimicking pathogen release of these compounds. We also examined their effect on biotic stress resistance by challenging EP plants with fungal, oomycete, and bacterial pathogens and an insect pest. EP plants exhibited enhanced resistance to all biotic challenges, except they were more susceptible to bacteria than the wild type. Levels of jasmonic acid (JA) were elevated and levels of salicylic acid (SA) were reduced in EP plants. Altered expression of JA and SA pathway genes in EP plants shows that eicosapolyenoic acids effectively modulate stress-responsive transcriptional networks. Exogenous application of various fatty acids to wild-type and JA-deficient mutants confirmed AA as the signaling molecule. Moreover, AA treatment elicited heightened expression of general stress-responsive genes. Importantly, tomato (Solanum lycopersicum) leaves treated with AA exhibited reduced susceptibility to Botrytis cinerea infection, confirming AA signaling in other plants. These studies support the role of AA, an ancient metazoan signaling molecule, in eliciting plant stress and defense signaling networks.

Savchenko, Tatyana; Walley, Justin W.; Chehab, E. Wassim; Xiao, Yanmei; Kaspi, Roy; Pye, Matthew F.; Mohamed, Maged E.; Lazarus, Colin M.; Bostock, Richard M.; Dehesh, Katayoon

2010-01-01

348

The core regulation module of stress-responsive regulatory networks in yeast  

PubMed Central

How does a cell respond to numerous external stresses with a limited number of internal molecular components? It has been observed that there are some common responses of yeast to various stresses, but most observations were based on gene-expression profiles and only some part of the common responses were intensively investigated. So far there has been no system-level analysis to identify commonly responsive or regulated genes against various stresses. In this study, we identified a core regulation module (CRM), a commonly involved regulation structure in the regulatory networks of yeast, which cells reuse in response to an array of environmental stresses. We found that regulators in the CRM constitute a hierarchical backbone of the yeast regulatory network and that the CRM is evolutionarily well conserved, stable against genetic variations and crucial for cell growth. All these findings were consistently held up to considerable noise levels that we introduced to address experimental noise and the resulting false positives of regulatory interactions. We conclude that the CRM of yeast might be an evolutionarily conserved information processing unit that endows a cell with enhanced robustness and efficiency in dealing with numerous environmental stresses with a limited number of internal elements.

Kim, Dongsan; Kim, Man-Sun; Cho, Kwang-Hyun

2012-01-01

349

Network Offoaded Hierarchical Collectives Using ConnectX-2's CORE-Direct Capabilities  

SciTech Connect

As the scale of High Performance Computing (HPC) systems continues to increase, demanding that we extract even more parallelism from applications, the need to move communication management away from the Central Processing Unit (CPU) becomes even greater. Moving this management to the network, frees up CPU cycles for computation, making it possible to overlap computation and communication. In this paper we continue to investigate how to best use the new CORE-Direct support added in the ConnectX-2 Host Channel Adapter (HCA) for creating high performance, asynchronous collective operations that are managed by the HCA. Specifically we consider the network topology, creating a two-level communication hierarchy, reducing the MPI Barrier completion time by 45%, from 26.59 microseconds, when not considering network topology, to 14.72 microseconds, with the CPU based collective barrier operation completing in 19.04 microseconds. The nonblocking barrier algorithm has similar performance, with about 50% of that time available for computation.

Rabinovitz, Ishai [Mellanox Technologies, Inc.; Shamis, Pavel [ORNL; Graham, Richard L [ORNL; Bloch, Noam [Mellanox Technologies, Inc.; Shainer, Gilad [Mellanox Technologies, Inc.

2010-01-01

350

Labeling the planar face of crystalline cellulose using quantum dots directed by type-I carbohydrate-binding modules  

Microsoft Academic Search

We report a new method for the direct labeling and visualization of crystalline cellulose using quantum dots (QDs) directed\\u000a by carbohydrate-binding modules (CBMs). Two type-I (surface binding) CBMs belonging to families 2 and 3a were cloned and expressed\\u000a with dual histidine tags at the N- and C-termini. Semiconductor (CdSe)ZnS QDs were used to label these CBMs following their binding to

Qi Xu; Melvin P. Tucker; Phil Arenkiel; Xin Ai; Garry Rumbles; Junji Sugiyama; Michael E. Himmel; Shi-You Ding

2009-01-01

351

Intricate environment-modulated genetic networks control isoflavone accumulation in soybean seeds  

PubMed Central

Background Soybean (Glycine max [L] Merr.) seed isoflavones have long been considered a desirable trait to target in selection programs for their contribution to human health and plant defense systems. However, attempts to modify seed isoflavone contents have not always produced the expected results because their genetic basis is polygenic and complex. Undoubtedly, the extreme variability that seed isoflavones display over environments has obscured our understanding of the genetics involved. Results In this study, a mapping population of RILs with three replicates was analyzed in four different environments (two locations over two years). We found a total of thirty-five main-effect genomic regions and many epistatic interactions controlling genistein, daidzein, glycitein and total isoflavone accumulation in seeds. The use of distinct environments permitted detection of a great number of environment-modulated and minor-effect QTL. Our findings suggest that isoflavone seed concentration is controlled by a complex network of multiple minor-effect loci interconnected by a dense epistatic map of interactions. The magnitude and significance of the effects of many of the nodes and connections in the network varied depending on the environmental conditions. In an attempt to unravel the genetic architecture underlying the traits studied, we searched on a genome-wide scale for genomic regions homologous to the most important identified isoflavone biosynthetic genes. We identified putative candidate genes for several of the main-effect and epistatic QTL and for QTL reported by other groups. Conclusions To better understand the underlying genetics of isoflavone accumulation, we performed a large scale analysis to identify genomic regions associated with isoflavone concentrations. We not only identified a number of such regions, but also found that they can interact with one another and with the environment to form a complex adaptable network controlling seed isoflavone levels. We also found putative candidate genes in several regions and overall we advanced the knowledge of the genetics underlying isoflavone synthesis.

2010-01-01

352

A role for direct interactions in the modulation of rhodopsin by -3 polyunsaturated lipids  

NASA Astrophysics Data System (ADS)

Rhodopsin, the G protein-coupled receptor primarily responsible for sensing light, is found in an environment rich in polyunsaturated lipid chains and cholesterol. Biophysical experiments have shown that lipid unsaturation and cholesterol both have significant effects on rhodopsin's stability and function; -3 polyunsaturated chains, such as docosahexaenoic acid (DHA), destabilize rhodopsin and enhance the kinetics of the photocycle, whereas cholesterol has the opposite effect. Here, we use molecular dynamics simulations to investigate the possibility that polyunsaturated chains modulate rhodopsin stability and kinetics via specific direct interactions. By analyzing the results of 26 independent 100-ns simulations of dark-adapted rhodopsin, we found that DHA routinely forms tight associations with the protein in a small number of specific locations qualitatively different from the nonspecific interactions made by saturated chains and cholesterol. Furthermore, the presence of tightly packed DHA molecules tends to weaken the interhelical packing. These results are consistent with recent NMR work, which proposes that rhodopsin binds DHA, and they suggest a molecular rationale for DHA's effects on rhodopsin stability and kinetics. cholesterol | molecular dynamics | fatty acid | protein-lipid interactions

Grossfield, Alan; Feller, Scott E.; Pitman, Michael C.

2006-03-01

353

Structures of ? repressors bound to direct and inverted DNA repeats explain modulation of transcription  

PubMed Central

Repressor ? regulates transcription of genes required for copy number control, accurate segregation and stable maintenance of inc18 plasmids hosted by Gram-positive bacteria. ? belongs to homodimeric ribbon-helix-helix (RHH2) repressors typified by a central, antiparallel ?-sheet for DNA major groove binding. Homodimeric ?2 binds cooperatively to promotors with 7 to 10 consecutive non-palindromic DNA heptad repeats (5?-A/TATCACA/T-3?, symbolized by ?) in palindromic inverted, converging (??) or diverging (??) orientation and also, unique to ?2 and contrasting other RHH2 repressors, to non-palindromic direct (??) repeats. Here we investigate with crystal structures how ?2 binds specifically to heptads in minimal operators with (??) and (??) repeats. Since the pseudo-2-fold axis relating the monomers in ?2 passes the central C–G base pair of each heptad with ?0.3 ? downstream offset, the separation between the pseudo-2-fold axes is exactly 7 bp in (??), ?0.6 ? shorter in (??) but would be ?0.6 ? longer in (??). These variations grade interactions between adjacent ?2 and explain modulations in cooperative binding affinity of ?2 to operators with different heptad orientations.

Weihofen, Wilhelm Andreas; Cicek, Aslan; Pratto, Florencia; Alonso, Juan Carlos; Saenger, Wolfram

2006-01-01

354

A new device concept for directly modulating spinal cord pathways: initial in vivo experimental results.  

PubMed

We describe a novel spinal cord (SC) stimulator that is designed to overcome a major shortcoming of existing stimulator devices: their restricted capacity to selectively activate targeted axons within the dorsal columns. This device overcomes that limitation by delivering electrical stimuli directly to the pial surface of the SC. Our goal in testing this device was to measure its ability to physiologically activate the SC and examine its capacity to modulate somatosensory evoked potentials (SSEPs) triggered by peripheral stimulation. In this acute study on adult sheep (n = 7), local field potentials were recorded from a grid placed in the subdural space of the right hemisphere during electrical stimulation of the left tibial nerve and the spinal cord. Large amplitude SSEPs (>200 µV) in response to SC stimulation were consistently obtained at stimulation strengths well below the thresholds inducing neural injury. Moreover, stimulation of the dorsal columns with signals employed routinely by devices in standard clinical use, e.g., 50 Hz, 0.2 ms pulse width, produced long-lasting changes (>4.5 h) in the SSEP patterns produced by subsequent tibial nerve stimulation. The results of these acute experiments demonstrate that this device can be safely secured to the SC surface and effectively activate somatosensory pathways. PMID:23151433

Flouty, Oliver; Oya, Hiroyuki; Kawasaki, Hiroto; Wilson, Saul; Reddy, Chandan G; Jeffery, Nicholas D; Brennan, Timothy J; Gibson-Corley, Katherine N; Utz, Marcel; Gillies, George T; Howard, Matthew A

2012-11-15

355

Direct modulation of calmodulin targets by the neuronal calcium sensor NCS-1.  

PubMed Central

Ca2+ and its ubiquitous intracellular receptor calmodulin (CaM) are required in the nervous system, among a host of cellular responses, for the modulation of several important enzymes and ion channels involved in synaptic efficacy and neuronal plasticity. Here, we report that CaM can be replaced by the neuronal calcium sensor NCS-1 both in vitro and in vivo. NCS-1 is a calcium binding protein with two Ca(2+)-binding domains that shares only 21% of homology with CaM. We observe that NCS-1 directly activates two Ca2+/CaM-dependent enzymes (3':5'-cyclic nucleotide phosphodiesterase and protein phosphatase calcineurin). Co-activation of nitric oxide synthase by NCS-1 and CaM results in a higher activity than with CaM alone. Moreover, NCS-1 is coexpressed with calcineurin and nitric oxide synthase in several neuron populations. Finally, injections of NCS-1 into calmodulin-defective cam1 Paramecium partially restore wildtype behavioral responses. With this highly purified preparation of NCS-1, we have obtained crystals suitable for crystallographic structure studies. NCS-1, despite its very different structure, distribution, and Ca(2+)-binding affinity as compared with CaM, can substitute for or potentiate CaM functions. Therefore, NCS-1 represents a novel protein capable of mediating multiple Ca(2+)-signaling pathways in the nervous system. Images Fig. 3 Fig. 4 Fig. 5

Schaad, N C; De Castro, E; Nef, S; Hegi, S; Hinrichsen, R; Martone, M E; Ellisman, M H; Sikkink, R; Rusnak, F; Sygush, J; Nef, P

1996-01-01

356

Study of capillary network directionality and irrigation of hypoxic tissue in an angiogenesis lattice model  

NASA Astrophysics Data System (ADS)

To shed light on the understanding of the angiogenesis process, we study a simplified lattice model for the capillary network formation between an existing blood vessel and an initially hypoxic tissue. We consider that the cells of the tissue surface can release growth factors that will diffuse, leading to the formation of new capillaries that ultimately arrive at the tissue. Additionally, we consider the local production of growth factors by the growing capillary network. We also propose the existence of an inhibition mechanism at the hypoxic surface, i.e., a fixed number of neighboring sites of an already irrigated site of the hypoxic tissue stop releasing growth factors due to the arrival of nutrients. Particularly, the goal of this work is to study the effect of the release of local growth factors and the inhibition mechanism on properties such as the directionality of the growing network and the irrigation of the hypoxic tissue. Therefore we propose the quantification of these two relevant features for angiogenesis modeling. We establish a relationship between the model behavior without the release of local growth factors in the presence of the inhibition mechanism and a normal angiogenesis process. In this situation, the model gives a directional capillary network and a good irrigation of the hypoxic tissue. On the other hand, for a large number of released local growth factors in the absence of the inhibition mechanism, the model could be appropriate for the description of tumor angiogenesis. In this case, the model provides a rather small directionality for the growing structure, with a worse degree of irrigation of the hypoxic tissue, as well as a more tortuous capillary network with many closed branches and loops.

Moglia, Belén; Guisoni, Nara; Albano, Ezequiel V.

2013-12-01

357

Neuro-fuzzy speed tracking control of traveling-wave ultrasonic motor drives using direct pulsewidth modulation  

Microsoft Academic Search

The traveling-wave ultrasonic motor (TWUM) drive offers many distinct advantages but suffers from severe system nonlinearities and parameter variations, especially during speed control. This paper presents a new speed tracking control system for the TWUM drive, which newly incorporates neuro-fuzzy control and direct pulsewidth modulation to solve the problem of nonlinearities and variations. The proposed control system is digitally implemented

K. T. Chau; S. W. Chung; C. C. Chan

2003-01-01

358

Neuro-fuzzy speed tracking control of traveling-wave ultrasonic motor drives using direct pulse width modulation  

Microsoft Academic Search

The traveling-wave ultrasonic motor (TUSM) drive offers many distinct advantages but suffers from severe system nonlinearities and parameter variations especially during speed control. This paper presents a new speed tracking control system for the TUSM drive, which newly incorporates neuro-fuzzy control and direct pulse width modulation to solve the problem of nonlinearities and variations. Increasingly, the proposed control system is

K. T. Chau; S. W. Chung

2002-01-01

359

Detection, direction discrimination, and off-frequency interference of center-frequency modulations and glides for vowel formants  

NASA Astrophysics Data System (ADS)

Vowels are mainly classified by the positions of peaks in their frequency spectra, the formants. For normal-hearing subjects, change detection and direction discrimination were measured for linear glides in the center frequency (CF) of formantlike sounds. A CF rove was used to prevent subjects from using either the start or end points of the glides as cues. In addition, change detection and starting-phase (start-direction) discrimination were measured for similar stimuli with a sinusoidal 5-Hz formant-frequency modulation. The stimuli consisted of single formants generated using a number of different stimulus parameters including fundamental frequency, spectral slope, frequency region, and position of the formant relative to the harmonic spectrum. The change detection thresholds were in good agreement with the predictions of a model which analyzed and combined the effects of place-of-excitation and temporal cues. For most stimuli, thresholds were approximately equal for change detection and start-direction discrimination. Exceptions were found for stimuli that consisted of only one or two harmonics. In a separate experiment, it was shown that change detection and start-direction discrimination of linear and sinusoidal formant-frequency modulations were impaired by off-frequency frequency-modulated interferers. This frequency modulation detection interference was larger for formants with shallow than for those with steep spectral slopes. .

Lyzenga, J.; Carlyon, R. P.

2005-05-01

360

Octave-spanning spectra directly from a two-foci Ti:sapphire laser with enhanced self-phase modulation  

Microsoft Academic Search

Summary form only given. The generation of spectra extending over one octave directly from a laser oscillator is challenging in many aspects. First of all, the limited gain bandwidth of the laser material, about 200 nm in the case of Ti:sapphire, has to be overcome by nonlinear spectral broadening (SB) via self phase modulation (SPM). The amount of SPM and

R. Ell; U. Morgner; F. X. Kartner; J. G. Fujimoto; E. P. Ippen; V. Scheuer; G. Angelow; T. Tschudi; M. J. Lederer; A. Boiko; B. Luther-Davies

2001-01-01

361

Evaluation of four-dimensional nonbinary LDPC-coded modulation for next-generation long-haul optical transport networks.  

PubMed

Leveraging the advanced coherent optical communication technologies, this paper explores the feasibility of using four-dimensional (4D) nonbinary LDPC-coded modulation (4D-NB-LDPC-CM) schemes for long-haul transmission in future optical transport networks. In contrast to our previous works on 4D-NB-LDPC-CM which considered amplified spontaneous emission (ASE) noise as the dominant impairment, this paper undertakes transmission in a more realistic optical fiber transmission environment, taking into account impairments due to dispersion effects, nonlinear phase noise, Kerr nonlinearities, and stimulated Raman scattering in addition to ASE noise. We first reveal the advantages of using 4D modulation formats in LDPC-coded modulation instead of conventional two-dimensional (2D) modulation formats used with polarization-division multiplexing (PDM). Then we demonstrate that 4D LDPC-coded modulation schemes with nonbinary LDPC component codes significantly outperform not only their conventional PDM-2D counterparts but also the corresponding 4D bit-interleaved LDPC-coded modulation (4D-BI-LDPC-CM) schemes, which employ binary LDPC codes as component codes. We also show that the transmission reach improvement offered by the 4D-NB-LDPC-CM over 4D-BI-LDPC-CM increases as the underlying constellation size and hence the spectral efficiency of transmission increases. Our results suggest that 4D-NB-LDPC-CM can be an excellent candidate for long-haul transmission in next-generation optical networks. PMID:22513641

Zhang, Yequn; Arabaci, Murat; Djordjevic, Ivan B

2012-04-01

362

Computational Intelligence in Multimedia Networking and Communications: Trends and Future Directions  

Microsoft Academic Search

This paper presents a review of the current literature on computational intelligence based approaches to various problems\\u000a in multimedia networking and communications such as call admission control, management of resources and traffic, routing,\\u000a multicasting, media composition, encoding, media streaming and synchronization, and on-demand servers and services. Challenges\\u000a to be addressed and future directions of research are also presented.

Parthasarathy Guturu

363

Template-directed carbon nanotube network using self-organized Si nanocrystals  

Microsoft Academic Search

We demonstrate a way to direct carbon nanotube growth using Si nanocrystals that are self-ordered via the thermal decomposition of thin silicon-on-insulator substrates. The Si nanocrystals are about 90 nm wide and 100–150 nm tall, with 200 nm spacing. Nanotubes connect the silicon nanocrystals to form a network. Nanotubes selectively appear between tops of the Si nanocrystals. We show that

B. Yang; M. S. Marcus; D. G. Keppel; P. P. Zhang; Z. W. Li; B. J. Larson; D. E. Savage; J. M. Simmons; O. M. Castellini; M. A. Eriksson; M. G. Lagally

2005-01-01

364

Template-directed carbon nanotube network using self-organized Si nanocrystals  

Microsoft Academic Search

We demonstrate a way to direct carbon nanotube growth using Si nanocrystals that are self-ordered via the thermal decomposition of thin silicon-on-insulator substrates. The Si nanocrystals are about 90 nm wide and 100-150 nm tall, with 200 nm spacing. Nanotubes connect the silicon nanocrystals to form a network. Nanotubes selectively appear between tops of the Si nanocrystals. We show that

B. Yang; M. S. Marcus; D. G. Keppel; P. P. Zhang; Z. W. Li; B. J. Larson; D. E. Savage; J. M. Simmons; O. M. Castellini; M. A. Eriksson; M. G. Lagally

2005-01-01

365

Calibration of a magnetic direction finding network using measured triggered lightning return stroke peak currents  

Microsoft Academic Search

Triggered lightning return stroke peak currents were measured in 1985-1988 at the NASA Kennedy Space Center, an area covered by six wideband magnetic direction finders (DFs) in the SUNYA lightning detection network. Analysis of the data reveals that the high-gain-normalized signal strength amplitudes can be used to estimate the peak current in lightning return strokes. Range-normalized signal strength amplitudes for

Richard E. Orville

1991-01-01

366

Modulation of gravity waves by planetary waves (2 and 16 d): observations with the North American-Pacific MLT-MFR radar network  

NASA Astrophysics Data System (ADS)

In an earlier study based upon medium frequency radar (MFR) data from Saskatoon /(52°N) the variability of time-sequences of gravity wave (GW) variances was linked to tidal (12,24h) and planetary wave (2d) oscillations of the wind. Fifty days of data were chosen from each of winter, spring and autumn seasons for this most comprehensive assessment of wave interactions. While modulations of the GW variances were observed, the results indicated considerable intermittency in the strength and direction of waves from the GW sources. Here we extend the study to other sites in the MLT-MFR (mesosphere, lower-thermosphere) network, and focus upon the planetary waves (PWs) and their modulating influences upon the GW variances. The PW events include the 2d waves as seen at Saskatoon, London, Hawaii and Christmas Island during the summer of 1994; and 16d wave activity evidenced at Saskatoon and London throughout 1994, and also during 12 and 7 years of observations, respectively. The modulations of the sequences of GW variances (10-100/150min, 2-6h periods) are significant, and the phase-differences between the PW (2d,16d) oscillations in the time-sequences of the winds and of the GW variances allow the propagation directions for the GW fluxes to be inferred. These are eastward in summer months and westward in winter at MLT (60-90km) altitudes.

Manson, A. H.; Meek, C. E.; Luo, Y.; Hocking, W. K.; MacDougall, J.; Riggin, D.; Fritts, D. C.; Vincent, R. A.

2003-01-01

367

Direct aperture optimization-based intensity-modulated radiotherapy for whole breast irradiation  

SciTech Connect

Purpose: To investigate the technical and dosimetric advantages and the efficacy of direct aperture optimized intensity-modulated radiation therapy (DAO-IMRT) over standard (e.g., beamlet optimized) IMRT and conventional three-dimensional conformal radiotherapy (3D-CRT) for whole breast irradiation in supine and prone positions. Methods and Materials: We retrospectively designed DAO-IMRT plans for 15 breast cancer patients in supine (10 patients) and prone (5 patients) positions with a goal of uniform dose coverage of the whole breast. These DAO-IMRT plans were compared with standard IMRT using beamlet optimization and conventional 3D-CRT plans using wedges. All plans used opposed tangential beam arrangements. Results: In all cases, the DAO-IMRT plans were equal to or better than those generated with 3D-CRT and standard beamlet-IMRT. For supine cases, DAO-IMRT provided higher uniformity index (UI, defined as the ratio of the dose to 95% of breast volume to the maximum dose) than either 3D-CRT (0.88 vs. 0.82; p = 0.026) or beamlet-IMRT (0.89 vs. 0.85; p = 0.003). Direct aperture optimized IMRT also gave lower lung doses than either 3D-CRT (V20 = 7.9% vs. 8.6%; p = 0.024) or beamlet-IMRT (V20 = 8.4% vs. 9.7%; p = 0.0008) for supine patients. For prone patients, DAO-IMRT provided higher UI than either 3D-CRT (0.89 vs. 0.83; p = 0.027) or beamlet-IMRT (0.89 vs. 0.85; p = 0.003). The planning time for DAO-IMRT was approximately 75% less than that of 3D-CRT. The monitor units for DAO-IMRT were approximately 60% less than those of beamlet-IMRT. Conclusion: Direct aperture optimized IMRT improved the overall quality of dose distributions as well as the planning and delivery efficiency for treating whole breast in both supine and prone positions.

Ahunbay, Ergun E. [Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, WI (United States)]. E-mail: eahunbay@radonc.mcw.edu; Chen, G.-P. [Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, WI (United States); Thatcher, Steven [Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, WI (United States); Jursinic, Paul A. [Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, WI (United States); White, Julia [Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, WI (United States); Albano, Katherine [Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, WI (United States); Li, X. Allen [Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, WI (United States)

2007-03-15

368

Cost-effective 33-Gbps intensity modulation direct detection multi-band OFDM LR-PON system employing a 10-GHz-based transceiver.  

PubMed

We develop a dynamic multi-band OFDM subcarrier allocation scheme to fully utilize the available bandwidth under the restriction of dispersion- and chirp-related power fading. The experimental results successfully demonstrate an intensity-modulation-direct-detection 34.78-Gbps OFDM signal transmissions over 100-km long-reach (LR) passive-optical networks (PONs) based on a cost-effective 10-GHz EAM and a 10-GHz PIN. Considering 0-100-km transmission bandwidth of a 10-GHz EAM, the narrowest bandwidth is theoretically evaluated to occur at ~40 km, instead of 100 km. Consequently, the performances of 20-100-km PONs are experimentally investigated, and at least 33-Gbps capacity is achieved to support LR-PONs of all possible 20-100-km radii. PMID:21935121

Hsu, Dar-Zu; Wei, Chia-Chien; Chen, Hsing-Yu; Li, Wei-Yuan; Chen, Jyehong

2011-08-29

369

Allosteric modulation of Ras positions Q61 for a direct role in catalysis  

PubMed Central

Ras and its effector Raf are key mediators of the Ras/Raf/MEK/ERK signal transduction pathway. Mutants of residue Q61 impair the GTPase activity of Ras and are found prominently in human cancers. Yet the mechanism through which Q61 contributes to catalysis has been elusive. It is thought to position the catalytic water molecule for nucleophilic attack on the ?-phosphate of GTP. However, we previously solved the structure of Ras from crystals with symmetry of the space group R32 in which switch II is disordered and found that the catalytic water molecule is present. Here we present a structure of wild-type Ras with calcium acetate from the crystallization mother liquor bound at a site remote from the active site and likely near the membrane. This results in a shift in helix 3/loop 7 and a network of H-bonding interactions that propagates across the molecule, culminating in the ordering of switch II and placement of Q61 in the active site in a previously unobserved conformation. This structure suggests a direct catalytic role for Q61 where it interacts with a water molecule that bridges one of the ?-phosphate oxygen atoms to the hydroxyl group of Y32 to stabilize the transition state of the hydrolysis reaction. We propose that Raf together with the binding of Ca2+ and a negatively charged group mimicked in our structure by the acetate molecule induces the ordering of switch I and switch II to complete the active site of Ras.

Buhrman, Greg; Holzapfel, Genevieve; Fetics, Susan; Mattos, Carla

2010-01-01

370

Stitching together Multiple Data Dimensions Reveals Interacting Metabolomic and Transcriptomic Networks That Modulate Cell Regulation  

PubMed Central

Cells employ multiple levels of regulation, including transcriptional and translational regulation, that drive core biological processes and enable cells to respond to genetic and environmental changes. Small-molecule metabolites are one category of critical cellular intermediates that can influence as well as be a target of cellular regulations. Because metabolites represent the direct output of protein-mediated cellular processes, endogenous metabolite concentrations can closely reflect cellular physiological states, especially when integrated with other molecular-profiling data. Here we develop and apply a network reconstruction approach that simultaneously integrates six different types of data: endogenous metabolite concentration, RNA expression, DNA variation, DNA–protein binding, protein–metabolite interaction, and protein–protein interaction data, to construct probabilistic causal networks that elucidate the complexity of cell regulation in a segregating yeast population. Because many of the metabolites are found to be under strong genetic control, we were able to employ a causal regulator detection algorithm to identify causal regulators of the resulting network that elucidated the mechanisms by which variations in their sequence affect gene expression and metabolite concentrations. We examined all four expression quantitative trait loci (eQTL) hot spots with colocalized metabolite QTLs, two of which recapitulated known biological processes, while the other two elucidated novel putative biological mechanisms for the eQTL hot spots.

Dombek, Kenneth M.; Xu, Ethan Y.; Vu, Heather; Tu, Zhidong; Brem, Rachel B.; Bumgarner, Roger E.; Schadt, Eric E.

2012-01-01

371

Temporal dynamics of direct reciprocal and indirect effects in a host-parasite network.  

PubMed

Temporal variation in the direct and indirect influence that hosts and parasites exert on each other is still poorly understood. However, variation in species' influence due to species and interactions turnover can have important consequences for host community dynamics and/or for parasite transmission dynamics, and eventually for the risk of zoonotic diseases. We used data on a network of small mammals and their ectoparasites surveyed over 6 years to test hypotheses exploring (i) the temporal variability in direct and indirect influences species exert on each other in a community, and (ii) the differences in temporal variability of direct/indirect influences between temporally persistent (TP) and temporally intermittent species. We modelled the temporal variation in (i) direct reciprocal influence between hosts and parasites (hosts providing resources to parasites and parasites exploiting the resources of hosts), using an asymmetry index, and (ii) indirect influence among species within a community (e.g. facilitation of parasite infestation by other parasites), using betweenness centrality. We also correlated asymmetry and centrality to examine the relationship between them. Network dynamics was determined by TP species but even those species had strong among-species heterogeneity in the temporal variation of the direct/indirect effects they exerted. In addition, there was a significant positive linear correlation between asymmetry and centrality. We conclude that the temporal dynamics of host-parasite interactions is driven by TP hosts. However, even within this group of persistent species, some exhibit large temporal variation, such that the functional roles they play (e.g. in promoting parasite transmission) change over time. In addition, parasites having a large negative impact on hosts are also those facilitating the spread of other parasites through the entire host community. Our results provide new insights into community dynamics and can be applied in the management of antagonistic networks aimed at preventing disease outbreaks. PMID:23672501

Pilosof, Shai; Fortuna, Miguel A; Vinarski, Maxim V; Korallo-Vinarskaya, Natalia P; Krasnov, Boris R

2013-05-14

372

Transcranial Direct Current Stimulation Modulates Human Color Discrimination in a Pathway-Specific Manner  

PubMed Central

Previous research showed that transcranial direct current stimulation (tDCS) can modulate visual cortex excitability. However, there is no experiment on the effects of tDCS on color perception to date. The present study aimed to investigate the effects of tDCS on color discrimination tasks. Fifteen healthy subjects (mean age of 25.6?±?4.4?years) were tested with Cambridge Color Test 2.0 (Trivector and ellipses protocols) and a Forced-choice Spatial Color Contrast Sensitivity task (vertical red-green sinusoidal grating) while receiving tDCS. Anodal, cathodal, and sham tDCS were delivered at Oz for 22?min using two square electrodes (25?cm2 with a current of 1.5?mA) in sessions separated by 7?days. Anodal tDCS significantly increased tritan sensitivity (p?

Costa, Thiago L.; Nagy, Balazs V.; Barboni, Mirella T. S.; Boggio, Paulo S.; Ventura, Dora F.

2012-01-01

373

The 22-Year Hale Cycle in Cosmic Ray Flux - Evidence for Direct Heliospheric Modulation  

NASA Astrophysics Data System (ADS)

The ability to predict times of greater galactic cosmic ray (GCR) fluxes is important for reducing the hazards caused by these particles to satellite communications, aviation, or astronauts. The 11-year solar-cycle variation in cosmic rays is highly correlated with the strength of the heliospheric magnetic field. Differences in GCR flux during alternate solar cycles yield a 22-year cycle, known as the Hale Cycle, which is thought to be due to different particle drift patterns when the northern solar pole has predominantly positive (denoted as qA>0 cycle) or negative (qA<0) polarities. This results in the onset of the peak cosmic-ray flux at Earth occurring earlier during qA>0 cycles than for qA<0 cycles, which in turn causes the peak to be more dome-shaped for qA>0 and more sharply peaked for qA<0. In this study, we demonstrate that properties of the large-scale heliospheric magnetic field are different during the declining phase of the qA<0 and qA>0 solar cycles, when the difference in GCR flux is most apparent. This suggests that particle drifts may not be the sole mechanism responsible for the Hale Cycle in GCR flux at Earth. However, we also demonstrate that these polarity-dependent heliospheric differences are evident during the space-age but are much less clear in earlier data: using geomagnetic reconstructions, we show that for the period of 1905 - 1965, alternate polarities do not give as significant a difference during the declining phase of the solar cycle. Thus we suggest that the 22-year cycle in cosmic-ray flux is at least partly the result of direct modulation by the heliospheric magnetic field and that this effect may be primarily limited to the grand solar maximum of the space-age.

Thomas, S. R.; Owens, M. J.; Lockwood, M.

2013-07-01

374

Modulation of adult hippocampal neurogenesis during myelin-directed autoimmune neuroinflammation.  

PubMed

In chronic autoimmune diseases of the central nervous system (CNS) such as multiple sclerosis (MS) clinical signs of cognitive dysfunction have been associated with structural changes in the hippocampus. Moreover, experimental studies indicate that inflammatory responses within the CNS modulate the homeostasis of newborn cells in the adult dentate gyrus (DG). However, it remained open whether such changes happen regardless of the primary immunological target or whether a CNS antigen-directed T lymphocyte-mediated autoimmune response may exert a specific impact. We therefore induced experimental autoimmune encephalomyelitis (EAE), a common model of MS serving as a paradigm for a CNS-specific immune response, by immunizing C57BL/6 mice with encephalitogenic myelin oligodendrocyte glycoprotein (MOG) p35-55. In EAE animals, we found enhanced de novo generation and survival of doublecortin (DCX)-positive immature neurons when compared with controls immunized with CNS-irrelevant antigen (ovalbumine). However, despite activation of neurogenesis, we observed a reduced capacity of these cells to generate mature neurons. Moreover, the high number of newly born cells retained the expression of the glial marker GFAP. These effects were associated with downregulation of pro-neurogenic factors Neurogenin1 and Neurogenin2 and dysregulation of Notch, ?-catenin, Sonic Hedgehog (Shh) signaling as suggested by altered gene expression of effector molecules. Thus, a CNS antigen-specific immune response leads to an aberrant differentiation of neural precursors associated with dysbalance of signaling pathways relevant for adult hippocampal neurogenesis. These results may further extend our understanding of disturbed regeneration in the course of chronic inflammatory CNS diseases such as MS. PMID:20967885

Huehnchen, Petra; Prozorovski, Timour; Klaissle, Philipp; Lesemann, Anne; Ingwersen, Jens; Wolf, Susanne A; Kupsch, Andreas; Aktas, Orhan; Steiner, Barbara

2010-10-21

375

Trans-spinal direct current stimulation modulates motor cortex-induced muscle contraction in mice.  

PubMed

The present study investigated the effect of trans-spinal direct current (tsDC) on the firing rate, pattern, and amplitude of spontaneous activity of the tibial nerve and on the magnitude of cortically elicited triceps surae (TS) muscle contractions. The effect of combined tsDC and repetitive cortical electrical stimulation (rCES) on the amplitude of cortically elicited TS twitches was also investigated. Stimulation was applied by two disk electrodes (0.79 cm(2)): one was located subcutaneously over the vertebral column (T(10)-L(1)) and was used to deliver anodal DC (a-tsDC) or cathodal DC (c-tsDC) (density range: ± 0.64 to ± 38.2 A/m(2)), whereas the other was located subcutaneously on the lateral aspect of the abdomen and served as a reference. While the application of a-tsDC significantly increased the spike frequency and amplitude of spontaneous discharges compared with c-tsDC, c-tsDC made the spontaneous discharges more rhythmic. Cortically elicited TS twitches were depressed during a-tsDC and potentiated after termination. Conversely, cortically elicited TS twitches were enhanced during c-tsDC and depressed after termination. While combined a-tsDC and rCES produced similar effects as a-tsDC alone, combined c-tsDC and rCES showed the greatest increase in cortically elicited TS twitches. tsDC appears to be a powerful neurostimulation tool that can differentially modulate spinal cord excitability and corticospinal transmission. PMID:21350028

Ahmed, Zaghloul

2011-02-24

376

CONTROL OF LASER RADIATION PARAMETERS: Frequency locking of self-modulated oscillations and hysteresis of a nonautonomous two-directional ring solid-state laser  

Microsoft Academic Search

The effect of the pump modulation on the lasing dynamics of a two-directional ring solid-state laser operating in the self-modulated regime is studied experimentally. The frequency locking was observed when the pump modulation frequency approached the self-modulation frequency. The dependence of the locking band on the laser characteristics and parameters of an external signal is studied. The frequency locking exhibits

Nikolai V. Kravtsov; Pavel P. Pashinin; S. S. Sidorov; V. V. Firsov

2002-01-01

377

A directed network analysis of heterospecific pollen transfer in a biodiverse community.  

PubMed

Community studies have shown that plant species are often pollinated by multiple pollinators; however, networks of heterospecific pollen transfer (HPT) in natural communities remain largely unexplored. We analyzed pollen deposition on stigmas of 57 flowering species to build a picture of plant-plant interactions via HPT in a biodiverse alpine meadow in southwest China. Plant species were categorized as pollen donors or recipients by their link numbers and link qualities. We identified 3609 heterospecific pollen grains, representing 410 links among 69 pollen species. Each plant species received on average 7.2 pollen species and donated its pollen to 5.5 species; only a few species donated or received large amounts of pollen or pollen from a large number of species. Compared to specialized plants, generalized plants tended to receive more heterospecific pollen but exported no more pollen to other species. Plant position in the network was related to both floral traits (stigma position) and pollinator generalization level. When different species share the same pollinator, bidirectional HPT may occur, but this was rarely observed in the species-rich community, indicating that interspecific pollen interference was largely unidirectional. Our study highlights the importance of understanding how sympatric flowering plants reduce deleterious effects of HPT, for example via stigma position. This study is the first to present a pollen transfer network for an entire community and to unravel its properties using directed network analysis. PMID:23858657

Fang, Qiang; Huang, Shuang-Quan

2013-05-01

378

Large-scale directional connections among multi resting-state neural networks in human brain: a functional MRI and Bayesian network modeling study.  

PubMed

This study examined the large-scale connectivity among multiple resting-state networks (RSNs) in the human brain. Independent component analysis was first applied to the resting-state functional MRI (fMRI) data acquired from 12 healthy young subjects for the separation of RSNs. Four sensory (lateral and medial visual, auditory, and sensory-motor) RSNs and four cognitive (default-mode, self-referential, dorsal and ventral attention) RSNs were identified. Gaussian Bayesian network (BN) learning approach was then used for the examination of the conditional dependencies among these RSNs and the construction of the network-to-network directional connectivity patterns. The BN based results demonstrated that sensory networks and cognitive networks were hierarchically organized. Specially, we found the sensory networks were highly intra-dependent and the cognitive networks were strongly intra-influenced. In addition, the results depicted dominant bottom-up connectivity from sensory networks to cognitive networks in which the self-referential and the default-mode networks might play respectively important roles in the process of resting-state information transfer and integration. The present study characterized the global connectivity relations among RSNs and delineated more characteristics of spontaneous activity dynamics. PMID:21396456

Li, Rui; Chen, Kewei; Fleisher, Adam S; Reiman, Eric M; Yao, Li; Wu, Xia

2011-03-17

379

29 GHz directly modulated 980 nm vertical-cavity surface emitting lasers with bow-tie shape transverse coupled cavity  

NASA Astrophysics Data System (ADS)

A concept for the bandwidth enhancement of directly modulated vertical-cavity surface emitting lasers (VCSELs) using a transverse-coupled-cavity (TCC) scheme is proposed, which enables us to tailor the modulation-transfer function. A bow-tie shaped oxide aperture forms the transverse-coupled cavity resulting in optical feedback to boost the modulation speed. While the bandwidth of conventional VCSELs is 9-10 GHz, the 3 dB-bandwidth of the TCC VCSEL is increased by a factor of 3 far beyond the relaxation-oscillation frequency. The maximum bandwidth is currently limited by the photo-detector used in the experiment. Clear 36 Gbps eye opening was attained with an extinction ratio of 4 dB.

Dalir, Hamed; Koyama, Fumio

2013-08-01

380

Efficient narrow-band direct modulation of semiconductor injection lasers at millimeter wave frequencies of 100 GHz and beyond  

SciTech Connect

It has been demonstrated both theoretically and experimentally that it is possible to mode lock semiconductor lasers at millimeter wave frequencies approaching and beyond 100 GHz. The mode-locked output usually takes the form of sinusoidal modulation, and can be regarded for practical purposes as a highly efficient means of directly modulating an optical carrier in a narrow band at millimeter wave frequencies. In active mode locking, the external signal efficiently creates the optical modulation, while in passive mode locking a small external signal imposes its information on the optical carrier by injection locking the passive mode-locked output. Experimentally, we have demonstrated passive mode locking at 70 GHz using a tandem contact GaAs laser.

Lau, K.Y.

1988-06-27

381

HSP27 modulates survival signaling networks in cells treated with curcumin and TRAIL.  

PubMed

The combination of curcumin and TRAIL and their role in enhancing apoptotic cell death has been reported by many studies. However, the exact molecular mechanism of apoptosis mediated by curcumin and tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) is not yet completely understood. In this study, we observed a close connection between dephosphorylated Akt and an increase in phosphorylated heat shock protein 27 (HSP27) during combined treatment with curcumin and TRAIL. Akt dephosphorylation was cumulatively regulated by protein phosphatase 1 (PP1), phosphoinositide-dependent kinase-1 (PDK1), and src. PP1 and PDK1 directly interacted with HSP27, whereas src indirectly interacted with HSP27 via the tumor necrosis factor receptor-associated factor 6 complex. In conclusion, HSP27 modulated cell survival by its interactions with various binding partners, depending on the level of phosphorylated HSP27. PMID:22449710

Kim, Jina; Kim, So Y; Kang, Sujin; Yoon, Hyo R; Sun, Bo K; Kang, Dongxu; Kim, Joo-Hang; Song, Jae J

2012-03-15

382

10 Gb/s bidirectional optical subassembly module for the application of FTTH network  

NASA Astrophysics Data System (ADS)

A 10 Gb/s bi-directional optical subassembly (BOSA) with an uncooled 1300nm DFB laser and a receiving PIN-TIA had been assembled and characterized. This 10 Gb/s BOSA integrated a 45o-tilted thin film WDM filter which can transmit the 1300nm light into the fiber and reflect the 1550nm light into the PIN-TIA. At the transmitter side, the -3dB modulation bandwidth was measured to be 11.86GHz and an OC-192 eye diagram with 19% mask margin was obtained. At the receiver side, the sensitivity was -13.1dBm at the bit error rate of 10-9 and the eye mask margin of OC-192 was more than 30%.

Shih, Tien-Tsorng; Lin, Min-Ching; Tseng, Pei-Hau; Chiu, Yi-Jen; Li, Chang-You; Hung, Tuan-Yu; Cheng, Wood-Hi

2007-03-01

383

Oppositional transcranial direct current stimulation (tDCS) of parietal substrates of attention during encoding modulates episodic memory.  

PubMed

Effective learning requires that attentional resources be focused on target information and withheld from irrelevant events in the learner's surroundings. This requires engagement of the brain substrates of selective attention and the concurrent disengagement of brain substrates of orienting toward changes in the environment. In the present study, we attempted to modulate activation of cortical substrates of attention during learning by physiological intervention, using transcranial direct current stimulation (tDCS). To effect adversarial modulation, we applied anodal stimulation directed toward left intraparietal sulcus/superior parietal cortex (IPS/SPL; a substrate of selective attention) and cathodal stimulation directed toward right inferior parietal cortex (IPL; a substrate of orienting). Such stimulation during study of verbal materials led to superior subsequent recognition memory relative to the opposite polarity of stimulation. To our knowledge, this is the first application of direct current stimulation to parietal regions implicated in different forms of attention in an oppositional manner in order to modulate learning in a verbal recognition memory task. Additionally, these results may have practical implications for the development of interventions to benefit persons with various types of attentional deficits. PMID:22265704

Jacobson, Liron; Goren, Nir; Lavidor, Michal; Levy, Daniel A

2011-12-29

384

Modeling Reveals Bistability and Low-Pass Filtering in the Network Module Determining Blood Stem Cell Fate  

PubMed Central

Combinatorial regulation of gene expression is ubiquitous in eukaryotes with multiple inputs converging on regulatory control elements. The dynamic properties of these elements determine the functionality of genetic networks regulating differentiation and development. Here we propose a method to quantitatively characterize the regulatory output of distant enhancers with a biophysical approach that recursively determines free energies of protein-protein and protein-DNA interactions from experimental analysis of transcriptional reporter libraries. We apply this method to model the Scl-Gata2-Fli1 triad—a network module important for cell fate specification of hematopoietic stem cells. We show that this triad module is inherently bistable with irreversible transitions in response to physiologically relevant signals such as Notch, Bmp4 and Gata1 and we use the model to predict the sensitivity of the network to mutations. We also show that the triad acts as a low-pass filter by switching between steady states only in response to signals that persist for longer than a minimum duration threshold. We have found that the auto-regulation loops connecting the slow-degrading Scl to Gata2 and Fli1 are crucial for this low-pass filtering property. Taken together our analysis not only reveals new insights into hematopoietic stem cell regulatory network functionality but also provides a novel and widely applicable strategy to incorporate experimental measurements into dynamical network models.

Narula, Jatin; Smith, Aileen M.; Gottgens, Berthold; Igoshin, Oleg A.

2010-01-01

385

Low-Power Direct-Sequence Spread-Spectrum Modem Architecture for Distributed Wireless Sensor Networks  

SciTech Connect

Emerging CMOS and MEMS technologies enable the implementation of a large number of wireless distributed microsensors that can be easily and rapidly deployed to form highly redundant, self-configuring, and ad hoc sensor networks. To facilitate ease of deployment, these sensors should operate on battery for extended periods of time. A particular challenge in maintaining extended battery lifetime lies in achieving communications with low power. This paper presents a direct-sequence spread-spectrum modem architecture that provides robust communications for wireless sensor networks while dissipating very low power. The modem architecture has been verified in an FPGA implementation that dissipates only 33 mW for both transmission and reception. The implementation can be easily mapped to an ASIC technology, with an estimated power performance of less than 1 mW.

Chien, C; Elgorriaga, I; McConaghy, C

2001-07-03

386

Direct adaptive control of wind energy conversion systems using Gaussian networks.  

PubMed

Grid connected wind energy conversion systems (WECS) present interesting control demands, due to the intrinsic nonlinear characteristics of windmills and electric generators. In this paper a direct adaptive control strategy for WECS control is proposed. It is based on the combination of two control actions: a radial basis zfunction network-based adaptive controller, which drives the tracking error to zero with user specified dynamics, and a supervisory controller, based on crude bounds of the system's nonlinearities. The supervisory controller fires when the finite neural-network approximation properties cannot be guaranteed. The form of the supervisor control and the adaptation law for the neural controller are derived from a Lyapunov analysis of stability. The results are applied to a typical turbine/generator pair, showing the feasibility of the proposed solution. PMID:18252585

Mayosky, M A; Cancelo, I E

1999-01-01

387

Design, implementation and testing of an artificial neural network based fault direction discriminator for protecting transmission lines  

Microsoft Academic Search

This paper describes a fault direction discriminator that uses an Artificial Neural Network (ANN) for protecting transmission lines. The discriminator uses various attributes to reach a decision and tends to emulate the conventional pattern classification problem. An equation of the boundary describing the classification is embedded in the Multilayer Feedforward Neural Network (MFNN) by training through the use of an

T. S. Sidhu; H. Singh; M. S. Sachdev

1995-01-01

388

Direct incorporation of fault level constraints in optimal power flow as a tool for network capacity analysis  

Microsoft Academic Search

The aim of this paper is to present a method for the direct incorporation of fault level constraints (FLCs) in the optimal power flow (OPF) as a tool for network capacity analysis, i.e., optimal generation expansion planning within an existing network. A mathematical methodology to convert constraints imposed by fault levels to simple nonlinear inequality constraints is developed. No new

Panagis N. Vovos; Janusz W. Bialek

2005-01-01

389

Direct aperture optimization as a means of reducing the complexity of Intensity Modulated Radiation Therapy plans.  

PubMed

Intensity Modulated Radiation Therapy (IMRT) is a means of delivering radiation therapy where the intensity of the beam is varied within the treatment field. This is done by dividing a large beam into many small beamlets. Dose constraints are assigned to both the target and sensitive structures and computerised inverse optimization is performed to find the individual weights of this large number of beamlets. The computer adjusts the intensities of these beamlets according to the required planning dose objectives. The optimized intensity patterns are then decomposed into a series of deliverable multi leaf collimator (MLC) shapes in the sequencing step. One of the main problems of IMRT, which becomes even more apparent as the complexity of the IMRT plan increases, is the dramatic increase in the number of Monitor Units (MU) required to deliver a fractionated treatment. The difficulty with this increase in MU is its association with increased treatment times and a greater leakage of radiation from the MLCs increasing the total body dose and the risk of secondary cancers in patients. Therefore one attempts to find ways of reducing these MU without compromising plan quality. The design of inverse planning systems where the beam is divided into small beamlets to produce the required intensity map automatically introduces complexity into IMRT treatment planning. Plan complexity is associated with many negative factors such as dosimetric uncertainty and delivery issues A large search space is required necessitating much computing power. However, the limitations of the delivery technology are not taken into consideration when designing the ideal intensity map therefore a further step termed the sequencing step is required to convert the ideal intensity map into a deliverable one. Many approaches have been taken to reduce the complexity. These include setting intensity limits, putting penalties on the cost function and using smoothing filters Direct Aperture optimization (DAO) incorporates the limitations of the delivery technology at the initial design of the intensity map thereby eliminating the sequencing step. It also gives control over the number of segments and hence control over the complexity of the plan although the design of the segments is independent of the person preparing the plan. PMID:19220906

Broderick, Maria; Leech, Michelle; Coffey, Mary

2009-02-16

390

High-Power, Low RIN 1.55-$\\\\mu{\\\\rm m}$ Directly Modulated DFB Lasers for Analog Signal Transmission  

Microsoft Academic Search

We report the demonstration of high-power and low relative intensity noise (RIN) directly modulated distributed feedback lasers at 1.55 $\\\\mu{\\\\rm m}$. We have developed a structure with asymmetrical cladding to reduce internal losses due to the p-doped upper cladding. We obtain an output power of 140 mW at 550 mA and an RIN below ${-}{\\\\rm 157}~{\\\\rm dB}\\/{\\\\rm Hz}$ in the

Mickaël Faugeron; Michaël Tran; François Lelarge; Mourad Chtioui; Yannick Robert; Eric Vinet; Alain Enard; Joël Jacquet; Frederic Van Dijk

2012-01-01

391

Band structure of Si\\/Ge core-shell nanowires along the [110] direction modulated by external uniaxial strain  

Microsoft Academic Search

Strain modulated electronic properties of Si\\/Ge core-shell nanowires along the [110] direction were reported, on the basis of first principles density-functional theory calculations. In particular, the energy dispersion relationship of the conduction\\/valence band was explored in detail. At the Gamma point, the energy levels of both bands are significantly altered by applied uniaxial strain, which results in an evident change

Xihong Peng; Fu Tang; Paul Logan

2011-01-01

392

Band structure of Si\\/Ge core-shell nanowires along [110] direction modulated by external uniaxial strain  

Microsoft Academic Search

Strain modulated electronic properties of Si\\/Ge core-shell nanowires along\\u000a[110] direction were reported based on first principles density-functional\\u000atheory calculations. Particularly, the energy dispersion relationship of the\\u000aconduction\\/valence band was explored in detail. At the {\\\\Gamma} point, the\\u000aenergy levels of both bands are significantly altered by applied uniaxial\\u000astrain, which results in an evident change of band gap. In

Xihong Peng; Fu Tang; Paul Logan

2010-01-01

393

Direct Modulation of Activity and Body Temperature of Owl Monkeys (Aotus lemurinus griseimembra) by Low Light Intensities  

Microsoft Academic Search

The activity pattern of Aotus lemurinus griseimembra can be predictably altered by varying the illuminance during the dark phase of a 12:12-hour light:dark rhythm. Intensities well below full-moon brightness (0.1–0.5 1x) severely inhibit activity. This modulation is not the result of a light-induced phase shift of the circadian rhythm, but it is primarily caused by masking due to direct effects

H. G. Erkert; J. Gröber

1986-01-01

394

Neural Feedback for Instantaneous Spatiotemporal Modulation of Afferent Pathways in BiDirectional Brain–Machine Interfaces  

Microsoft Academic Search

In bi-directional brain-machine interfaces (BMIs), precisely controlling the delivery of microstimulation, both in space and in time, is critical to continuously modulate the neural activity patterns that carry information about the state of the brain-actuated device to sensory areas in the brain. In this paper, we investigate the use of neural feedback to control the spatiotemporal firing patterns of neural

Jianbo Liu; Hassan K. Khalil; Karim G. Oweiss

2011-01-01

395

Fault Diagnosis of Steam Generator Using Signed Directed Graph and Artificial Neural Networks  

SciTech Connect

Diagnosis is a very complex and important task for finding the root cause of faults in nuclear power plants. The objective of this paper is to investigate the feasibility of using the combination of signed directed graph (SDG) and artificial neural networks for fault diagnosis in nuclear power plants especially in U-Tube steam generator. Signed directed graph has been the most widely used form of qualitative based model methods for process fault diagnosis. It is constructed to represent the cause-effect relations among the dynamic process variables. Signed directed graph consists of nodes represent the process variables and branches. The branch represents the qualitative influence of a process variable on the related variable. The main problem in fault diagnosis using the signed directed graph is the unmeasured variables. Therefore, neural networks are used to estimate the values of unmeasured nodes. In this work, different four cases of faults in the steam generator ( SG) have been diagnosed, three of them are single fault and the fourth is multiple fault. The first three faults are by pass valve leakage (Vbp(+)), main feed water valve opening increase (Vfw(+)), main feed water valve opening decrease (Vfw (-)). The fourth fault is a multiple fault where by-pass valve leakage and main feed water valve opening decrease (Vbp(+) and Vfw (-)) in the same time. The used data are collected from a basic principle simulator of pressurized water reactor 925 Mwe. The signed directed graph of the steam generator is constructed to represent the cause-effect relations among SG variables. It consists of 26 nodes represent the SG variables, and 48 branches represent the cause effect relations among this variables. For each fault the values of measured nodes are coming from sensors and the values of unmeasured nodes are coming from the trained neural networks. These values of the nodes are compared by normal values to get the sign of the nodes. The cause-effect graph for each fault is constructed from the steam generator signed directed graph by removing the invalid (normal) nodes and inconsistent branches. Then in the cause-effect graph we search about the node which does not have an input branch. This node is the fault origin node. The result of this work demonstrated that this method can be used in nuclear power plant fault diagnosis. The advantages of this method are, it enables us to diagnose a multi fault, it is not restricted by pre-defined faults, and it is fast method. (authors)

Aly, Mohamed N. [Nuclear Eng. Department, Fac. of Eng., Alex. Univ., Alex. (Egypt); Hegazy, Hesham N. [Nuclear Power Plants Authority, Cairo (Egypt)

2006-07-01

396

Decomposition of metabolic network into functional modules based on the global connectivity structure of reaction graph  

Microsoft Academic Search

Motivation: Metabolic networks are organized in a modular, hierarchical manner. Methods for a rational decomposition of the metabolic network into relatively independent functional subsets are essential to better understand the modularity and organization principle of a large-scale, genome-wide network. Network decomposition is also necessary for functional ana- lysis of metabolism by pathway analysis methods that are often hampered by the

Hongwu Ma; Xue-ming Zhao; Ying-jin Yuan; An-ping Zeng

2004-01-01

397

Direct imaging of the percolation network in a three-dimensional disordered conductor-insulator composite  

NASA Astrophysics Data System (ADS)

We have directly imaged the percolation network at the surface of a three-dimensional carbon-black-polymer composite using an electric force microscope. At intermediate length scales the conductive area exposed at the surface increases with surface area according to a power law corresponding to a three-dimensional infinite cluster of fractal dimension D=2.6+/-0.1. This value is in good agreement with the scaling theory prediction, D=2.53. At large length scales the behavior is homogenous with the classical exponent D=3.

Viswanathan, Ravi; Heaney, Michael B.

1995-12-01

398

Polymer-networked liquid crystal cell for omni-directional viewing-angle switching  

NASA Astrophysics Data System (ADS)

A novel method for switching the viewing-angle of a liquid crystal display is proposed by using a polymernetworked liquid crystal cell in combination with a collimated backlight system. The bright state for a wide viewing-angle is obtained aligning liquid crystals randomly in polymer-networked structure, which diffuses a collimated backlight. The liquid crystals homogeneous-aligned by in-plane switching are operated as the bright state for a narrow viewing-angle since a collimated backlight passes through the liquid crystal layer intactly. It is demonstrated experimentally that the viewing-angle can be controlled omni-directionally without an additional panel or an additional backlight system.

Yoon, Tae-Hoon; Baek, Jong-In; Kim, Ki-Han; Kim, Jae-Chang

2010-02-01

399

Metaplastic facilitation and ultrastructural changes in synaptic properties are associated with long-term modulation of the lamprey locomotor network.  

PubMed

The neuropeptide substance P evokes a long-term protein synthesis-dependent increase in the cycle frequency of locomotor network activity in the lamprey. Although cellular and synaptic mechanisms that could induce this effect have been identified, nothing is known of the underlying maintenance mechanisms. These mechanisms have been examined here. Substance P potentiates low-frequency-evoked EPSPs from excitatory network interneurons. It also converts the depression of the EPSP during spike trains into facilitation, an example of metaplasticity. The metaplasticity was associated with a reduction of the transmitter release probability but an increase in the number of release sites. Although the potentiation of low-frequency-evoked EPSPs recovered within 1 hr, the metaplastic facilitation had not recovered 3-4 hr after substance P application. The metaplasticity thus extended into the protein synthesis-dependent maintenance phase of the network modulation, making it the only identified cellular or synaptic effect of substance P to last this long. It also had the same induction and maintenance features as the network burst frequency modulation, further suggesting that the two effects were related. Long-term changes in synaptic properties are often associated with changes in synaptic organization. We have thus also examined the effects of substance P on synaptic ultrastructure up to 5 hr after substance P application. Substance P had several significant effects. These included an increase in the number of docked vesicles and a reduction of the synaptic gap. Substance P thus has long-term effects on synaptic organization and function. The relevance of these effects to the long-term locomotor network modulation is discussed. PMID:15496682

Bevan, Sarah; Parker, David

2004-10-20

400

Network analysis of genomic alteration profiles reveals co-altered functional modules and driver genes for glioblastoma.  

PubMed

The heterogeneity of genetic alterations in human cancer genomes presents a major challenge to advancing our understanding of cancer mechanisms and identifying cancer driver genes. To tackle this heterogeneity problem, many approaches have been proposed to investigate genetic alterations and predict driver genes at the individual pathway level. However, most of these approaches ignore the correlation of alteration events between pathways and miss many genes with rare alterations collectively contributing to carcinogenesis. Here, we devise a network-based approach to capture the cooperative functional modules hidden in genome-wide somatic mutation and copy number alteration profiles of glioblastoma (GBM) from The Cancer Genome Atlas (TCGA), where a module is a set of altered genes with dense interactions in the protein interaction network. We identify 7 pairs of significantly co-altered modules that involve the main pathways known to be altered in GBM (TP53, RB and RTK signaling pathways) and highlight the striking co-occurring alterations among these GBM pathways. By taking into account the non-random correlation of gene alterations, the property of co-alteration could distinguish oncogenic modules that contain driver genes involved in the progression of GBM. The collaboration among cancer pathways suggests that the redundant models and aggravating models could shed new light on the potential mechanisms during carcinogenesis and provide new indications for the design of cancer therapeutic strategies. PMID:23344900

Gu, Yunyan; Wang, Hongwei; Qin, Yao; Zhang, Yujing; Zhao, Wenyuan; Qi, Lishuang; Zhang, Yuannv; Wang, Chenguang; Guo, Zheng

2013-01-23

401

Dynamical Systems for Discovering Protein Complexes and Functional Modules from Biological Networks  

Microsoft Academic Search

Recent advances in high throughput experiments and annotations via published literature have provided a wealth of interaction maps of several biomolecular networks, including metabolic, protein-protein, and protein-DNA interaction networks. The architecture of these molecular networks reveals important principles of cellular organization and molecular functions. Analyzing such networks, i.e., discovering dense regions in the network, is an important way to identify

Wenyuan Li; Ying Liu; Hung-Chung Huang; Yanxiong Peng; Yongjing Lin; Wee-Keong Ng; Kok-Leong Ong

2007-01-01

402

Advanced ATM-layer function MCM-D module for ATM wide-area network  

Microsoft Academic Search

This paper describes a high-performance and cost-effective MCM-D module for an ATM-layer function device. The MCM-D module is fabricated on a Si-substrate using the stacking RAM technique to reduce module size. The MCM has a 4-layer Si substrate, a high-performance ASIC, 8 high-speed SRAMs, and an FPGA. By using the stacking RAM technique, MCM-D module size was reduced to 50.8

Tomoaki Kawamura; Naoaki Yamanaka; Katsumi Kaizu

1997-01-01

403

NRC TLD direct radiation monitoring network: Progress report, April--June 1996. Volume 16, Number 2  

SciTech Connect

The US Nuclear Regulatory Commission (NRC) Direct Radiation Monitoring network is operated by the NRC in cooperation with participating states to provide continuous measurement of the ambient radiation levels around licensed NRC facilities, primarily power reactors. Ambient radiation levels result from naturally occurring radionuclides present in the soil, cosmic radiation constantly bombarding the earth from outer space, and the contribution, if any, from the monitored facilities and other man-made sources. The Network is intended to measure radiation levels during routine facility operations and to establish background radiation levels used to assess the radiological impact of an unusual condition, such as an accident. This report presents the radiation levels measured around all facilities in the Network for the second quarter of 1996. A complete listing of the site facilities monitored is included. In some instances, two power reactor facilities are monitored by the same set of dosimeters. All radiation measurements are made using small, passive detectors called thermoluminescent dosimeters (TLDs), which provide a quantitative measurement of the radiation levels in the area in which they are placed. Each site is monitored by arranging approximately 40 to 50 TLD stations in two concentric rings extending to about five miles from the facility. All TLD stations are outside the site boundary of the facility.

Struckmeyer, R.

1996-08-01

404

Gel-expanded to gel-condensed transition in neurofilament networks revealed by direct force measurements  

NASA Astrophysics Data System (ADS)

Neurofilaments (NF)-the principal cytoskeletal constituent of myelinated axons in vertebrates-consist of three molecular-weight subunit proteins NF-L (low), NF-M (medium) and NF-H (high), assembled to form mature filaments with protruding unstructured C-terminus side arms. Liquid-crystal gel networks of side-arm-mediated neurofilament assemblies have a key role in the mechanical stability of neuronal processes. Disruptions of the neurofilament network, owing to neurofilament over-accumulation or incorrect side-arm interactions, are a hallmark of motor-neuron diseases including amyotrophic lateral sclerosis. Using synchrotron X-ray scattering, we report on a direct measurement of forces in reconstituted neurofilament gels under osmotic pressure (P). With increasing pressure near physiological salt and average phosphorylation conditions, NF-LMH, comprising the three subunits near in vivo composition, or NF-LH gels, undergo for P>Pc~10kPa, an abrupt non-reversible gel-expanded to gel-condensed transition. The transition indicates side-arm-mediated attractions between neurofilaments consistent with an electrostatic model of interpenetrating chains. In contrast, NF-LM gels remain in a collapsed state for PPc. These findings, which delineate the distinct roles of NF-M and NF-H in regulating neurofilament interactions, shed light on possible mechanisms for disruptions of optimal mechanical network properties.

Beck, Roy; Deek, Joanna; Jones, Jayna B.; Safinya, Cyrus R.

2010-01-01

405

Neural network approach to continuous-time direct adaptive optimal control for partially unknown nonlinear systems.  

PubMed

In this paper we present in a continuous-time framework an online approach to direct adaptive optimal control with infinite horizon cost for nonlinear systems. The algorithm converges online to the optimal control solution without knowledge of the internal system dynamics. Closed-loop dynamic stability is guaranteed throughout. The algorithm is based on a reinforcement learning scheme, namely Policy Iterations, and makes use of neural networks, in an Actor/Critic structure, to parametrically represent the control policy and the performance of the control system. The two neural networks are trained to express the optimal controller and optimal cost function which describes the infinite horizon control performance. Convergence of the algorithm is proven under the realistic assumption that the two neural networks do not provide perfect representations for the nonlinear control and cost functions. The result is a hybrid control structure which involves a continuous-time controller and a supervisory adaptation structure which operates based on data sampled from the plant and from the continuous-time performance dynamics. Such control structure is unlike any standard form of controllers previously seen in the literature. Simulation results, obtained considering two second-order nonlinear systems, are provided. PMID:19362449

Vrabie, Draguna; Lewis, Frank

2009-03-26

406

Herb network construction and co-module analysis for uncovering the combination rule of traditional Chinese herbal formulae  

PubMed Central

Background Traditional Chinese Medicine (TCM) is characterized by the wide use of herbal formulae, which are capable of systematically treating diseases determined by interactions among various herbs. However, the combination rule of TCM herbal formulae remains a mystery due to the lack of appropriate methods. Methods From a network perspective, we established a method called Distance-based Mutual Information Model (DMIM) to identify useful relationships among herbs in numerous herbal formulae. DMIM combines mutual information entropy and “between-herb-distance” to score herb interactions and construct herb network. To evaluate the efficacy of the DMIM-extracted herb network, we conducted in vitro assays to measure the activities of strongly connected herbs and herb pairs. Moreover, using the networked Liu-wei-di-huang (LWDH) formula as an example, we proposed a novel concept of “co-module” across herb-biomolecule-disease multilayer networks to explore the potential combination mechanism of herbal formulae. Results DMIM, when used for retrieving herb pairs, achieves a good balance among the herb’s frequency, independence, and distance in herbal formulae. A herb network constructed by DMIM from 3865 Collaterals-related herbal formulae can not only nicely recover traditionally-defined herb pairs and formulae, but also generate novel anti-angiogenic herb ingredients (e.g. Vitexicarpin with IC50=3.2 ?M, and Timosaponin A-III with IC50=3.4 ?M) as well as herb pairs with synergistic or antagonistic effects. Based on gene and phenotype information associated with both LWDH herbs and LWDH-treated diseases, we found that LWDH-treated diseases show high phenotype similarity and identified certain “co-modules” enriched in cancer pathways and neuro-endocrine-immune pathways, which may be responsible for the action of treating different diseases by the same LWDH formula. Conclusions DMIM is a powerful method to identify the combination rule of herbal formulae and lead to new discoveries. We also provide the first evidence that the co-module across multilayer networks may underlie the combination mechanism of herbal formulae and demonstrate the potential of network biology approaches in the studies of TCM.

2010-01-01

407

ADHERENS JUNCTIONS AND THE ACTOMYOSIN NETWORK REGULATE ORGAN GROWTH BY MODULATING HIPPO PATHWAY ACTIVITY IN DROSOPHILA  

Microsoft Academic Search

Adherens junctions (AJs) and basolateral modules are important for the establishment and maintenance of apico-basal polarity. Loss of AJs and basolateral module members lead to tumor formation, as well as poor prognosis for metastasis. Recently, in mammalian studies it has been shown that loss of either AJ or basolateral module members deregulate Yorkie activity, the downstream transcriptional effector of the

Chih-Chao Yang

2012-01-01

408

Reconstruction of an integrated genome-scale co-expression network reveals key modules involved in lung adenocarcinoma.  

PubMed

Our goal of this study was to reconstruct a "genome-scale co-expression network" and find important modules in lung adenocarcinoma so that we could identify the genes involved in lung adenocarcinoma. We integrated gene mutation, GWAS, CGH, array-CGH and SNP array data in order to identify important genes and loci in genome-scale. Afterwards, on the basis of the identified genes a co-expression network was reconstructed from the co-expression data. The reconstructed network was named "genome-scale co-expression network". As the next step, 23 key modules were disclosed through clustering. In this study a number of genes have been identified for the first time to be implicated in lung adenocarcinoma by analyzing the modules. The genes EGFR, PIK3CA, TAF15, XIAP, VAPB, Appl1, Rab5a, ARF4, CLPTM1L, SP4, ZNF124, LPP, FOXP1, SOX18, MSX2, NFE2L2, SMARCC1, TRA2B, CBX3, PRPF6, ATP6V1C1, MYBBP1A, MACF1, GRM2, TBXA2R, PRKAR2A, PTK2, PGF and MYO10 are among the genes that belong to modules 1 and 22. All these genes, being implicated in at least one of the phenomena, namely cell survival, proliferation and metastasis, have an over-expression pattern similar to that of EGFR. In few modules, the genes such as CCNA2 (Cyclin A2), CCNB2 (Cyclin B2), CDK1, CDK5, CDC27, CDCA5, CDCA8, ASPM, BUB1, KIF15, KIF2C, NEK2, NUSAP1, PRC1, SMC4, SYCE2, TFDP1, CDC42 and ARHGEF9 are present that play a crucial role in cell cycle progression. In addition to the mentioned genes, there are some other genes (i.e. DLGAP5, BIRC5, PSMD2, Src, TTK, SENP2, PSMD2, DOK2, FUS and etc.) in the modules. PMID:23874428

Bidkhori, Gholamreza; Narimani, Zahra; Hosseini Ashtiani, Saman; Moeini, Ali; Nowzari-Dalini, Abbas; Masoudi-Nejad, Ali

2013-07-11

409

Performance comparison between conventional direction-of-arrival algorithm and stereausis network based on cochlea model  

NASA Astrophysics Data System (ADS)

In this paper, we present experimental results comparing the conventional direction-of-arrival (DOA) algorithm and the stereausis network algorithm for the purpose of performing acoustic DOA estimation. The comparison would be focused on robustness, complexity and aperture size. Robustness is important because the acoustic signatures can vary significantly under different environmental conditions. Low complexity is also important because the DOA algorithm will be used in real time and systems need to identify a target instantly. Aperture size is another important issue in target positioning because fewer sensors could lead to small size and be located more freely. We show the DOA results of different algorithms on a simulated signal with given SNRs (Signal to Noise Ratio) and discuss issues such as robustness with respect to noise, computational complexity, and aperture sizes. The stereausis network algorithm could perform well under low SNR environment. When the SNR is above -5db, the accuracy is almost not affected. The complexity of computation of stereausis algorithm is much smaller than temporal delay algorithm because of the absence of neural delays, which means it has no time delay units. Therefore, stereausis algorithm could resolve the direction with less time cost compared to conventional time-delay methods so that it exhibits high real time feature. In addition, conventional algorithms usually require complex sensors array, which means the aperture size can't be small, while the stereausis algorithm could be implemented through only two sensors, which means a smaller aperture size.

Zhang, Yaoliang; Yin, Li; Liu, Wei

2009-10-01

410

The Local Structure of Globalization. The Network Dynamics of Foreign Direct Investments in the International Electricity Industry  

NASA Astrophysics Data System (ADS)

We study the evolution of the network of foreign direct investment (FDI) in the international electricity industry during the period 1994-2003. We assume that the ties in the network of investment relations between countries are created and deleted in continuous time, according to a conditional Gibbs distribution. This assumption allows us to take simultaneously into account the aggregate predictions of the well-established gravity model of international trade as well as local dependencies between network ties connecting the countries in our sample. According to the modified version of the gravity model that we specify, the probability of observing an investment tie between two countries depends on the mass of the economies involved, their physical distance, and the tendency of the network to self-organize into local configurations of network ties. While the limiting distribution of the data generating process is an exponential random graph model, we do not assume the system to be in equilibrium. We find evidence of the effects of the standard gravity model of international trade on evolution of the global FDI network. However, we also provide evidence of significant dyadic and extra-dyadic dependencies between investment ties that are typically ignored in available research. We show that local dependencies between national electricity industries are sufficient for explaining global properties of the network of foreign direct investments. We also show, however, that network dependencies vary significantly over time giving rise to a time-heterogeneous localized process of network evolution.

Koskinen, Johan; Lomi, Alessandro

2013-05-01

411