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Sample records for directed network modules

  1. Directed network modules

    NASA Astrophysics Data System (ADS)

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

    2007-06-01

    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.

  2. Centrality properties of directed module members in social networks

    NASA Astrophysics Data System (ADS)

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

    2008-08-01

    Several recent studies of complex networks have suggested algorithms for locating network communities, also called modules or clusters, which are mostly defined as groups of nodes with dense internal connections. Along with the rapid development of these clustering techniques, the ability of revealing overlaps between communities has become very important as well. An efficient search technique for locating overlapping modules is provided by the Clique Percolation Method (CPM) and its extension to directed graphs, the CPMd algorithm. Here we investigate the centrality properties of directed module members in social networks obtained from e-mail exchanges and from sociometric questionnaires. Our results indicate that nodes in the overlaps between modules play a central role in the studied systems. Furthermore, the two different types of networks show interesting differences in the relation between the centrality measures and the role of the nodes in the directed modules.

  3. Cycle-flow-based module detection in directed recurrence networks

    NASA Astrophysics Data System (ADS)

    Banisch, Ralf; Djurdjevac Conrad, Nataša

    2014-12-01

    We present a new cycle-flow-based method for finding fuzzy partitions of weighted directed networks coming from time series data. We show that this method overcomes essential problems of most existing clustering approaches, which tend to ignore important directional information by considering only one-step, one-directional node connections. Our method introduces a novel measure of communication between nodes using multi-step, bidirectional transitions encoded by a cycle decomposition of the probability flow. Symmetric properties of this measure enable us to construct an undirected graph that captures the information flow of the original graph seen by the data and apply clustering methods designed for undirected graphs. Finally, we demonstrate our algorithm by analyzing earthquake time series data, which naturally induce (time-)directed networks.

  4. System performance analysis of time-division-multiplexing passive optical network using directly modulated lasers or colorless optical network units

    NASA Astrophysics Data System (ADS)

    Gong, Xiaoxue; Guo, Lei; Liu, Yejun; Zhou, Yufang

    2015-05-01

    As a promising technology for broadband communication, passive optical network (PON) has been deployed to support the last-mile broadband access network. In particular, time-division-multiplexing PON (TDM-PON) has been widely used owing to its mature technology and low cost. To practically implement TDM-PONs, the combination of intensity modulation and direct detection is a very promising technique because it achieves cost reduction in system installation and maintenance. However, the current intensity-modulation and direct-detection TDM-PON still suffers from some problems, which mainly include a high-power penalty, detrimental Brillouin backscattering (BB), and so on. Thus, using directly modulated lasers (DMLs) and colorless optical network units (ONUs), respectively, two intensity-modulation and direct-detection TDM-PON architectures are proposed. Using VPI (an optical simulation software developed by VPIphotonics company) simulators, we first analyze the influences on DML-based intensity-modulation and direct-detection TDM-PON (system 1) performances, which mainly include bit error rate (BER) and power penalty. Next, the BB effect on the BER of the intensity-modulation and direct-detection TDM-PON that uses colorless ONUs (system 2) is also investigated. The simulation results show that: (1) a low-power penalty is achieved without degrading the BER of system 1, and (2) the BB can be effectively reduced using phase modulation of the optical carrier in system 2.

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

    PubMed

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

    2010-08-16

    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

  6. Sequence dependence of phase-induced intensity noise in optical networks that employ direct modulation

    NASA Astrophysics Data System (ADS)

    Tur, M.; Legg, P. J.; Shabeer, M.; Andonovic, I.

    1995-02-01

    Phase-induced intensity noise in optical networks that employ directly modulated laser sources is observed to be bit-sequence dependent. This dependence is explained by optical frequency variations that are due to the heating history of the laser chip and is accurately modeled. This effect may permit suppression of phase-induced intensity noise in many types of fiber system with multipaths.

  7. Dynamic Network-Based Relevance Score Reveals Essential Proteins and Functional Modules in Directed Differentiation

    PubMed Central

    Wu, Chia-Chou; Lin, Che

    2015-01-01

    The induction of stem cells toward a desired differentiation direction is required for the advancement of stem cell-based therapies. Despite successful demonstrations of the control of differentiation direction, the effective use of stem cell-based therapies suffers from a lack of systematic knowledge regarding the mechanisms underlying directed differentiation. Using dynamic modeling and the temporal microarray data of three differentiation stages, three dynamic protein-protein interaction networks were constructed. The interaction difference networks derived from the constructed networks systematically delineated the evolution of interaction variations and the underlying mechanisms. A proposed relevance score identified the essential components in the directed differentiation. Inspection of well-known proteins and functional modules in the directed differentiation showed the plausibility of the proposed relevance score, with the higher scores of several proteins and function modules indicating their essential roles in the directed differentiation. During the differentiation process, the proteins and functional modules with higher relevance scores also became more specific to the neuronal identity. Ultimately, the essential components revealed by the relevance scores may play a role in controlling the direction of differentiation. In addition, these components may serve as a starting point for understanding the systematic mechanisms of directed differentiation and for increasing the efficiency of stem cell-based therapies. PMID:25977693

  8. Direct-Sequence Spread-Spectrum Modulation for Utility Packet Transmission in Underwater Acoustic Communication Networks

    NASA Astrophysics Data System (ADS)

    Duke, Peter S.

    2002-09-01

    This thesis investigates the feasibility and performance of using Direct-Sequence Spread-Spectrum (DSSS) modulation for utility-packet transmission in Seaweb underwater wireless acoustic communications networks, Seaweb networks require robust channel-tolerant utility packets having a low probability of detection (LPD) and allowing for multi-user access, MATLAB code simulated the DSSS transmitter and receiver structures and a modeled channel impulse response represented the underwater environment, The specific modulation scheme implemented is direct-sequence, differentially encoded binary phase-shift keying (DS-DBPSK) with quadrature spreading, Performance is examined using Monte Carlo simulation Bit error rates and packet error rates for various signal-to-noise ratios and channel conditions are presented and the use of a RAKE receiver, forward error-correction coding and symbol interleaving are examined for improving system performance.

  9. Effects of aging on value-directed modulation of semantic network activity during verbal learning.

    PubMed

    Cohen, Michael S; Rissman, Jesse; Suthana, Nanthia A; Castel, Alan D; Knowlton, Barbara J

    2016-01-15

    While impairments in memory recall are apparent in aging, older adults show a remarkably preserved ability to selectively remember information deemed valuable. Here, we use fMRI to compare brain activation in healthy older and younger adults during encoding of high and low value words to determine whether there are differences in how older adults achieve value-directed memory selectivity. We find that memory selectivity in older adults is associated with value-related changes in activation during word presentation in left hemisphere regions that are involved in semantic processing, similar to young adults. However, highly selective young adults show a relatively greater increase in semantic network activity during encoding of high-value items, whereas highly selective older adults show relatively diminished activity during encoding of low-value items. Additionally, only younger adults showed value-related increases in activity in semantic and reward processing regions during presentation of the value cue preceding each to-be-remembered word. Young adults therefore respond to cue value more proactively than do older adults, yet the magnitude of value-related differences in cue period brain activity did not predict individual differences in memory selectivity. Thus, our data also show that age-related reductions in prestimulus activity do not always lead to inefficient performance. PMID:26244278

  10. Module bay with directed flow

    DOEpatents

    Torczynski, John R.

    2001-02-27

    A module bay requires less cleanroom airflow. A shaped gas inlet passage can allow cleanroom air into the module bay with flow velocity preferentially directed toward contaminant rich portions of a processing module in the module bay. Preferential gas flow direction can more efficiently purge contaminants from appropriate portions of the module bay, allowing a reduced cleanroom air flow rate for contaminant removal. A shelf extending from an air inlet slit in one wall of a module bay can direct air flowing therethrough toward contaminant-rich portions of the module bay, such as a junction between a lid and base of a processing module.

  11. Weighted network modules

    NASA Astrophysics Data System (ADS)

    Farkas, Illés; Ábel, Dániel; Palla, Gergely; Vicsek, Tamás

    2007-06-01

    The inclusion of link weights into the analysis of network properties allows a deeper insight into the (often overlapping) modular structure of real-world webs. We introduce a clustering algorithm clique percolation method with weights (CPMw) for weighted networks based on the concept of percolating k-cliques with high enough intensity. The algorithm allows overlaps between the modules. First, we give detailed analytical and numerical results about the critical point of weighted k-clique percolation on (weighted) Erdos Rényi graphs. Then, for a scientist collaboration web and a stock correlation graph we compute three-link weight correlations and with the CPMw the weighted modules. After reshuffling link weights in both networks and computing the same quantities for the randomized control graphs as well, we show that groups of three or more strong links prefer to cluster together in both original graphs.

  12. Modulation of large-scale brain networks by transcranial direct current stimulation evidenced by resting-state functional MRI

    PubMed Central

    Peña-Gómez, Cleofé; Sala-Lonch, Roser; Junqué, Carme; Clemente, Immaculada C.; Vidal, Dídac; Bargalló, Núria; Falcón, Carles; Valls-Solé, Josep; Pascual-Leone, Álvaro; Bartrés-Faz, David

    2013-01-01

    Background Brain areas interact mutually to perform particular complex brain functions such as memory or language. Furthermore, under resting-state conditions several spatial patterns have been identified that resemble functional systems involved in cognitive functions. Among these, the default-mode network (DMN), which is consistently deactivated during task periods and is related to a variety of cognitive functions, has attracted most attention. In addition, in resting-state conditions some brain areas engaged in focused attention (such as the anticorrelated network, AN) show a strong negative correlation with DMN; as task demand increases, AN activity rises, and DMN activity falls. Objective We combined transcranial direct current stimulation (tDCS) with functional magnetic resonance imaging (fMRI) to investigate these brain network dynamics. Methods Ten healthy young volunteers underwent four blocks of resting-state fMRI (10-minutes), each of them immediately after 20 minutes of sham or active tDCS (2 mA), on two different days. On the first day the anodal electrode was placed over the left dorsolateral prefrontal cortex (DLPFC) (part of the AN) with the cathode over the contralateral supraorbital area, and on the second day, the electrode arrangement was reversed (anode right-DLPFC, cathode left-supraorbital). Results After active stimulation, functional network connectivity revealed increased synchrony within the AN components and reduced synchrony in the DMN components. Conclusions Our study reveals a reconfiguration of intrinsic brain activity networks after active tDCS. These effects may help to explain earlier reports of improvements in cognitive functions after anodal-tDCS, where increasing cortical excitability may have facilitated reconfiguration of functional brain networks to address upcoming cognitive demands. PMID:21962981

  13. Reciprocity in directed networks

    NASA Astrophysics Data System (ADS)

    Yin, Mei; Zhu, Lingjiong

    2016-04-01

    Reciprocity is an important characteristic of directed networks and has been widely used in the modeling of World Wide Web, email, social, and other complex networks. In this paper, we take a statistical physics point of view and study the limiting entropy and free energy densities from the microcanonical ensemble, the canonical ensemble, and the grand canonical ensemble whose sufficient statistics are given by edge and reciprocal densities. The sparse case is also studied for the grand canonical ensemble. Extensions to more general reciprocal models including reciprocal triangle and star densities will likewise be discussed.

  14. Finding communities in directed networks

    NASA Astrophysics Data System (ADS)

    Kim, Youngdo; Son, Seung-Woo; Jeong, Hawoong

    2010-01-01

    To identify communities in directed networks, we propose a generalized form of modularity in directed networks by presenting the quantity LinkRank, which can be considered as the PageRank of links. This generalization is consistent with the original modularity in undirected networks and the modularity optimization methods developed for undirected networks can be directly applied to directed networks by optimizing our modified modularity. Also, a model network, which can be used as a benchmark network in further community studies, is proposed to verify our method. Our method is supposed to find communities effectively in citation- or reference-based directed networks.

  15. Modulated convection in directional solidification

    SciTech Connect

    Murray, B.T.

    1993-04-01

    It is well known that time-dependent modulation can significantly impact the stability behavior in fundamental fluid problems such as Rayleigh-Benard convection and Taylor-Couette flow. There are relevant applications in materials processing that require understanding of the effects of time-periodic forcing on hydrodynamic and interfacial instabilities in solidification from the melt. Studying temporal modulation is relevant as either a means of controlling the convective flows that can occur in the solidification of alloys under terrestrial conditions or to determine whether time-dependent accelerations can cause instabilities in low gravity conditions. One problem of particular interest is the effect of sinusoidal gravitational modulation on solutal or thermosolutal convection in directional solidification of a binary alloy. For solidification in a direction aligned with the gravitational acceleration vector a stability problem has been formulated based on Floquet theory; morphological stability can also be treated, and the influence of the solid-liquid interface on the convection instabilities in the presence of time-periodic modulation is considered. For high-frequency modulation, the method of averaging is employed which considerably simplifies the analysis. The stability behavior is highly dependent on how the temperature and solute fields contribute to the stratification of the melt density. Both semiconductor and metallic alloy systems are investigated.

  16. Dynamic behaviors in directed networks

    SciTech Connect

    Park, Sung Min; Kim, Beom Jun

    2006-08-15

    Motivated by the abundance of directed synaptic couplings in a real biological neuronal network, we investigate the synchronization behavior of the Hodgkin-Huxley model in a directed network. We start from the standard model of the Watts-Strogatz undirected network and then change undirected edges to directed arcs with a given probability, still preserving the connectivity of the network. A generalized clustering coefficient for directed networks is defined and used to investigate the interplay between the synchronization behavior and underlying structural properties of directed networks. We observe that the directedness of complex networks plays an important role in emerging dynamical behaviors, which is also confirmed by a numerical study of the sociological game theoretic voter model on directed networks.

  17. 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)

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

    2012-12-01

    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.

  18. Epidemic threshold in directed networks.

    PubMed

    Li, Cong; Wang, Huijuan; Van Mieghem, Piet

    2013-12-01

    Epidemics have so far been mostly studied in undirected networks. However, many real-world networks, such as the online social network Twitter and the world wide web, on which information, emotion, or malware spreads, are directed networks, composed of both unidirectional links and bidirectional links. We define the directionality ξ as the percentage of unidirectional links. The epidemic threshold τ(c) for the susceptible-infected-susceptible (SIS) epidemic is lower bounded by 1/λ(1) in directed networks, where λ(1), also called the spectral radius, is the largest eigenvalue of the adjacency matrix. In this work, we propose two algorithms to generate directed networks with a given directionality ξ. The effect of ξ on the spectral radius λ(1), principal eigenvector x(1), spectral gap (λ(1)-|λ(2)|), and algebraic connectivity μ(N-1) is studied. Important findings are that the spectral radius λ(1) decreases with the directionality ξ, whereas the spectral gap and the algebraic connectivity increase with the directionality ξ. The extent of the decrease of the spectral radius depends on both the degree distribution and the degree-degree correlation ρ(D). Hence, in directed networks, the epidemic threshold is larger and a random walk converges to its steady state faster than that in undirected networks with the same degree distribution. PMID:24483506

  19. Epidemic threshold in directed networks

    NASA Astrophysics Data System (ADS)

    Li, Cong; Wang, Huijuan; Van Mieghem, Piet

    2013-12-01

    Epidemics have so far been mostly studied in undirected networks. However, many real-world networks, such as the online social network Twitter and the world wide web, on which information, emotion, or malware spreads, are directed networks, composed of both unidirectional links and bidirectional links. We define the directionality ξ as the percentage of unidirectional links. The epidemic threshold τc for the susceptible-infected-susceptible (SIS) epidemic is lower bounded by 1/λ1 in directed networks, where λ1, also called the spectral radius, is the largest eigenvalue of the adjacency matrix. In this work, we propose two algorithms to generate directed networks with a given directionality ξ. The effect of ξ on the spectral radius λ1, principal eigenvector x1, spectral gap (λ1-λ2), and algebraic connectivity μN-1 is studied. Important findings are that the spectral radius λ1 decreases with the directionality ξ, whereas the spectral gap and the algebraic connectivity increase with the directionality ξ. The extent of the decrease of the spectral radius depends on both the degree distribution and the degree-degree correlation ρD. Hence, in directed networks, the epidemic threshold is larger and a random walk converges to its steady state faster than that in undirected networks with the same degree distribution.

  20. Direct modulation lowers VSAT equipment costs

    NASA Astrophysics Data System (ADS)

    Cannistraro, Vincent; Liou, Jenn-Chorng; McCarter, Steven

    1990-08-01

    The use of baseband digital waveform to modulate directly a very-small-aperture terminal (VSAT) as an alternative to frequency conversion in single-channel data communication systems is discussed. This method, known as direct microwave modulation (DMM), results in substantially lower manufacturing costs. The way that a DMM module works in this application is explained, and the use of such a module as a transmitter building block in a simulated VSAT earth station is described. Module performance specifications are given.

  1. Breakdown of interdependent directed networks.

    PubMed

    Liu, Xueming; Stanley, H Eugene; Gao, Jianxi

    2016-02-01

    Increasing evidence shows that real-world systems interact with one another via dependency connectivities. Failing connectivities are the mechanism behind the breakdown of interacting complex systems, e.g., blackouts caused by the interdependence of power grids and communication networks. Previous research analyzing the robustness of interdependent networks has been limited to undirected networks. However, most real-world networks are directed, their in-degrees and out-degrees may be correlated, and they are often coupled to one another as interdependent directed networks. To understand the breakdown and robustness of interdependent directed networks, we develop a theoretical framework based on generating functions and percolation theory. We find that for interdependent Erdős-Rényi networks the directionality within each network increases their vulnerability and exhibits hybrid phase transitions. We also find that the percolation behavior of interdependent directed scale-free networks with and without degree correlations is so complex that two criteria are needed to quantify and compare their robustness: the percolation threshold and the integrated size of the giant component during an entire attack process. Interestingly, we find that the in-degree and out-degree correlations in each network layer increase the robustness of interdependent degree heterogeneous networks that most real networks are, but decrease the robustness of interdependent networks with homogeneous degree distribution and with strong coupling strengths. Moreover, by applying our theoretical analysis to real interdependent international trade networks, we find that the robustness of these real-world systems increases with the in-degree and out-degree correlations, confirming our theoretical analysis. PMID:26787907

  2. Sampling properties of directed networks

    NASA Astrophysics Data System (ADS)

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

    2012-10-01

    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.

  3. Notational usage modulates attention networks in binumerates

    PubMed Central

    Koul, Atesh; Tyagi, Vaibhav; Singh, Nandini C.

    2014-01-01

    Multicultural environments require learning multiple number notations wherein some are encountered more frequently than others. This leads to differences in exposure and consequently differences in usage between notations. We find that differential notational usage imposes a significant neurocognitive load on number processing. Despite simultaneous acquisition, twenty four adult binumerates, familiar with two positional writing systems namely Hindu Nagari digits and Hindu Arabic digits, reported significantly lower preference and usage for Nagari as compared to Arabic. Twenty-four participants showed significantly increased reaction times and reduced accuracy while performing magnitude comparison tasks in Nagari with respect to Arabic. Functional magnetic resonance imaging revealed that processing Nagari elicited significantly greater activity in number processing and attention networks. A direct subtraction of networks for Nagari and Arabic notations revealed a neural circuit comprising of bilateral Intra-parietal Sulcus (IPS), Inferior and Mid Frontal Gyri, Fusiform Gyrus and the Anterior Cingulate Cortex (FDR p < 0.005). Additionally, whole brain correlation analysis showed that activity in the left inferior parietal region was modulated by task performance in Nagari. We attribute the increased activation in Nagari to increased task difficulty due to infrequent exposure and usage. Our results reiterate the role of left IPS in modulating performance in numeric tasks and highlight the role of the attention network for monitoring symbolic notation mode in binumerates. PMID:24904366

  4. Complex modulation and detection with directly modulated lasers.

    PubMed

    Hu, Qian; Che, Di; Wang, Yifei; Yuan, Feng; Yang, Qi; Shieh, William

    2015-12-14

    Due to the chirp effect, the modulation information is carried by both intensity and phase of the optical signal generated by a directly modulated laser (DML). Compared to the signal recovery based on intensity alone, the receiver sensitivity is significantly improved when phase is also involved for signal recovery. In this paper, we provide thorough analysis of two schemes to recover the directed modulated signal based on the combined information of intensity and phase. The intensity and phase combined recovery for polarization-division-multiplexed (PDM) directly modulated signal is demonstrated for the first time, achieving a data rate of 40 Gb/s over a transmission distance of 160 km. Compared with the conventional intensity-only recovery, the receiver sensitivity is improved by 5.5 dB and 10 dB respectively by using two intensity and phase combined recovery schemes. PMID:26699070

  5. Network Models of Frequency Modulated Sweep Detection

    PubMed Central

    Skorheim, Steven; Razak, Khaleel; Bazhenov, Maxim

    2014-01-01

    Frequency modulated (FM) sweeps are common in species-specific vocalizations, including human speech. Auditory neurons selective for the direction and rate of frequency change in FM sweeps are present across species, but the synaptic mechanisms underlying such selectivity are only beginning to be understood. Even less is known about mechanisms of experience-dependent changes in FM sweep selectivity. We present three network models of synaptic mechanisms of FM sweep direction and rate selectivity that explains experimental data: (1) The ‘facilitation’ model contains frequency selective cells operating as coincidence detectors, summing up multiple excitatory inputs with different time delays. (2) The ‘duration tuned’ model depends on interactions between delayed excitation and early inhibition. The strength of delayed excitation determines the preferred duration. Inhibitory rebound can reinforce the delayed excitation. (3) The ‘inhibitory sideband’ model uses frequency selective inputs to a network of excitatory and inhibitory cells. The strength and asymmetry of these connections results in neurons responsive to sweeps in a single direction of sufficient sweep rate. Variations of these properties, can explain the diversity of rate-dependent direction selectivity seen across species. We show that the inhibitory sideband model can be trained using spike timing dependent plasticity (STDP) to develop direction selectivity from a non-selective network. These models provide a means to compare the proposed synaptic and spectrotemporal mechanisms of FM sweep processing and can be utilized to explore cellular mechanisms underlying experience- or training-dependent changes in spectrotemporal processing across animal models. Given the analogy between FM sweeps and visual motion, these models can serve a broader function in studying stimulus movement across sensory epithelia. PMID:25514021

  6. Cross-Species Network Analysis Uncovers Conserved Nitrogen-Regulated Network Modules in Rice1[OPEN

    PubMed Central

    Obertello, Mariana; Shrivastava, Stuti; Katari, Manpreet S.; Coruzzi, Gloria M.

    2015-01-01

    In this study, we used a cross-species network approach to uncover nitrogen (N)-regulated network modules conserved across a model and a crop species. By translating gene network knowledge from the data-rich model Arabidopsis (Arabidopsis thaliana) to a crop, rice (Oryza sativa), we identified evolutionarily conserved N-regulatory modules as targets for translational studies to improve N use efficiency in transgenic plants. To uncover such conserved N-regulatory network modules, we first generated an N-regulatory network based solely on rice transcriptome and gene interaction data. Next, we enhanced the network knowledge in the rice N-regulatory network using transcriptome and gene interaction data from Arabidopsis and new data from Arabidopsis and rice plants exposed to the same N treatment conditions. This cross-species network analysis uncovered a set of N-regulated transcription factors (TFs) predicted to target the same genes and network modules in both species. Supernode analysis of the TFs and their targets in these conserved network modules uncovered genes directly related to N use (e.g. N assimilation) and to other shared biological processes indirectly related to N. This cross-species network approach was validated with members of two TF families in the supernode network, BASIC-LEUCINE ZIPPER TRANSCRIPTION FACTOR1-TGA and HYPERSENSITIVITY TO LOW PI-ELICITED PRIMARY ROOT SHORTENING1 (HRS1)/HRS1 Homolog family, which have recently been experimentally validated to mediate the N response in Arabidopsis. PMID:26045464

  7. Cross-Species Network Analysis Uncovers Conserved Nitrogen-Regulated Network Modules in Rice.

    PubMed

    Obertello, Mariana; Shrivastava, Stuti; Katari, Manpreet S; Coruzzi, Gloria M

    2015-08-01

    In this study, we used a cross-species network approach to uncover nitrogen (N)-regulated network modules conserved across a model and a crop species. By translating gene network knowledge from the data-rich model Arabidopsis (Arabidopsis thaliana) to a crop, rice (Oryza sativa), we identified evolutionarily conserved N-regulatory modules as targets for translational studies to improve N use efficiency in transgenic plants. To uncover such conserved N-regulatory network modules, we first generated an N-regulatory network based solely on rice transcriptome and gene interaction data. Next, we enhanced the network knowledge in the rice N-regulatory network using transcriptome and gene interaction data from Arabidopsis and new data from Arabidopsis and rice plants exposed to the same N treatment conditions. This cross-species network analysis uncovered a set of N-regulated transcription factors (TFs) predicted to target the same genes and network modules in both species. Supernode analysis of the TFs and their targets in these conserved network modules uncovered genes directly related to N use (e.g. N assimilation) and to other shared biological processes indirectly related to N. This cross-species network approach was validated with members of two TF families in the supernode network, BASIC-LEUCINE ZIPPER TRANSCRIPTION FACTOR1-TGA and HYPERSENSITIVITY TO LOW PI-ELICITED PRIMARY ROOT SHORTENING1 (HRS1)/HRS1 Homolog family, which have recently been experimentally validated to mediate the N response in Arabidopsis. PMID:26045464

  8. OM300 Direction Drilling Module

    SciTech Connect

    MacGugan, Doug

    2013-08-22

    OM300 – Geothermal Direction Drilling Navigation Tool: Design and produce a prototype directional drilling navigation tool capable of high temperature operation in geothermal drilling Accuracies of 0.1° Inclination and Tool Face, 0.5° Azimuth Environmental Ruggedness typical of existing oil/gas drilling Multiple Selectable Sensor Ranges High accuracy for navigation, low bandwidth High G-range & bandwidth for Stick-Slip and Chirp detection Selectable serial data communications Reduce cost of drilling in high temperature Geothermal reservoirs Innovative aspects of project Honeywell MEMS* Vibrating Beam Accelerometers (VBA) APS Flux-gate Magnetometers Honeywell Silicon-On-Insulator (SOI) High-temperature electronics Rugged High-temperature capable package and assembly process

  9. A direct density modulation cathode in magnetron

    SciTech Connect

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

    2013-09-15

    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.

  10. Investigation of direct integrated optics modulators

    NASA Technical Reports Server (NTRS)

    Batchman, T. E.; Mcwright, G. M.

    1981-01-01

    Direct optical modulation techniques applicable to integrated optical data preprocessors were studied. Emphasis was placed on the analysis and fabrication of a field effect type modulator. A series of computer modeling studies were performed to determine the effects of semiconductor cladding on the fields of propagating waves in planar dielectric waveguides. These studies predicted that changes in the propagation characteristics of waveguides clad with silicon and gallium arsenide could be made large enough to be useful in modulators. These effects are dependent on the complex permittivity and thickness of the cladding. Since the conductivity of the cladding can be changed by the photon generation of hole-electron pairs, incoherent light may be used as the input to modulate a coherent light beam. Waveguides were fabricated and silicon claddings were applied to verify the theoretical predictions.

  11. Optimal design of reverse osmosis module networks

    SciTech Connect

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

    2000-05-01

    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.

  12. Caffeine Modulates Attention Network Function

    ERIC Educational Resources Information Center

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

    2010-01-01

    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…

  13. Caffeine Modulates Attention Network Function

    ERIC Educational Resources Information Center

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

    2010-01-01

    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

  14. Local community extraction in directed networks

    NASA Astrophysics Data System (ADS)

    Ning, Xuemei; Liu, Zhaoqi; Zhang, Shihua

    2016-06-01

    Network is a simple but powerful representation of real-world complex systems. Network community analysis has become an invaluable tool to explore and reveal the internal organization of nodes. However, only a few methods were directly designed for community-detection in directed networks. In this article, we introduce the concept of local community structure in directed networks and provide a generic criterion to describe a local community with two properties. We further propose a stochastic optimization algorithm to rapidly detect a local community, which allows for uncovering the directional modular characteristics in directed networks. Numerical results show that the proposed method can resolve detailed local communities with directional information and provide more structural characteristics of directed networks than previous methods.

  15. Downhole drilling network using burst modulation techniques

    DOEpatents

    Hall; David R. , Fox; Joe

    2007-04-03

    A downhole drilling system is disclosed in one aspect of the present invention as including a drill string and a transmission line integrated into the drill string. Multiple network nodes are installed at selected intervals along the drill string and are adapted to communicate with one another through the transmission line. In order to efficiently allocate the available bandwidth, the network nodes are configured to use any of numerous burst modulation techniques to transmit data.

  16. Interconnection scheme for networks of online modules

    NASA Astrophysics Data System (ADS)

    Dormiani, Pouya; Ercegovac, Miloš D.

    2006-08-01

    In this paper we propose an interconnection scheme to compute any unfactored arithmetic expression as a network of online modules. This is accomplished through mapping the expression to a doubly-linked hypercube network of online units. The mapping algorithm guarantees a maximum dilation of 2, with unit load, and conjectures that any arbitrary unfactored expression can be mapped to the proposed architecture with a small delay overhead. The proposed architecture requires no form of reconfiguration to accomplish the mapping, providing us with an efficient way to compute any network of online operations.

  17. Adaptation to direction statistics modulates perceptual discrimination.

    PubMed

    Price, Nicholas S C; Prescott, Danielle L

    2012-01-01

    Perception depends on the relative activity of populations of sensory neurons with a range of tunings and response gains. Each neuron's tuning and gain are malleable and can be modified by sustained exposure to an adapting stimulus. Here, we used a combination of human psychophysical testing and models of neuronal population decoding to assess how rapid adaptation to moving stimuli might change neuronal tuning and thereby modulate direction perception. Using a novel motion stimulus in which the direction changed every 10 ms, we demonstrated that 1,500 ms of adaptation to a distribution of directions was capable of modifying human psychophysical direction discrimination performance. Consistent with previous reports, we found perceptual repulsion following adaptation to a single direction. Notably, compared with a uniform adaptation condition in which all motion directions were equiprobable, discrimination was impaired after adaptation to a stimulus comprising only directions ± 30-60° from the discrimination boundary and enhanced after adaptation to the complementary range of directions. Thus, stimulus distributions can be selectively chosen to either impair or improve discrimination performance through adaptation. A neuronal population decoding model incorporating adaptation-induced repulsive shifts in direction tuning curves can account for most aspects of our psychophysical data; however, changes in neuronal gain are sufficient to account for all aspects of our psychophysical data. PMID:22728681

  18. Pulse position modulation for local area networks

    NASA Astrophysics Data System (ADS)

    Martin, John D.

    1989-10-01

    The technique of Pulse-Position-Modulation offers greater receiver sensitivity than PCM, and is ideally suited to optical sources. A broad analysis shows that more taps could be made available on an existing multi-point fibre Local-Area-Network at a data rate of 10 Mb/s, by using PPM instead of PCM as a method of signalling.

  19. Google matrix analysis of directed networks

    NASA Astrophysics Data System (ADS)

    Ermann, Leonardo; Frahm, Klaus M.; Shepelyansky, Dima L.

    2015-10-01

    In the past decade modern societies have developed enormous communication and social networks. Their classification and information retrieval processing has become a formidable task for the society. Because of the rapid growth of the World Wide Web, and social and communication networks, new mathematical methods have been invented to characterize the properties of these networks in a more detailed and precise way. Various search engines extensively use such methods. It is highly important to develop new tools to classify and rank a massive amount of network information in a way that is adapted to internal network structures and characteristics. This review describes the Google matrix analysis of directed complex networks demonstrating its efficiency using various examples including the World Wide Web, Wikipedia, software architectures, world trade, social and citation networks, brain neural networks, DNA sequences, and Ulam networks. The analytical and numerical matrix methods used in this analysis originate from the fields of Markov chains, quantum chaos, and random matrix theory.

  20. The behaviour of basic autocatalytic signalling modules in isolation and embedded in networks

    SciTech Connect

    Krishnan, J.; Mois, Kristina; Suwanmajo, Thapanar

    2014-11-07

    In this paper, we examine the behaviour of basic autocatalytic feedback modules involving a species catalyzing its own production, either directly or indirectly. We first perform a systematic study of the autocatalytic feedback module in isolation, examining the effect of different factors, showing how this module is capable of exhibiting monostable threshold and bistable switch-like behaviour. We then study the behaviour of this module embedded in different kinds of basic networks including (essentially) irreversible cycles, open and closed reversible chains, and networks with additional feedback. We study the behaviour of the networks deterministically and also stochastically, using simulations, analytical work, and bifurcation analysis. We find that (i) there are significant differences between the behaviour of this module in isolation and in a network: thresholds may be altered or destroyed and bistability may be destroyed or even induced, even when the ambient network is simple. The global characteristics and topology of this network and the position of the module in the ambient network can play important and unexpected roles. (ii) There can be important differences between the deterministic and stochastic dynamics of the module embedded in networks, which may be accentuated by the ambient network. This provides new insights into the functioning of such enzymatic modules individually and as part of networks, with relevance to other enzymatic signalling modules as well.

  1. Giant components in directed multiplex networks

    NASA Astrophysics Data System (ADS)

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

    2014-11-01

    We describe the complex global structure of giant components in directed multiplex networks that generalizes the well-known bow-tie structure, generic for ordinary directed networks. By definition, a directed multiplex network contains vertices of one type and directed edges of m different types. In directed multiplex networks, we distinguish a set of different giant components based on the existence of directed paths of different types between their vertices such that for each type of edges, the paths run entirely through only edges of that type. If, in particular, m =2 , we define a strongly viable component as a set of vertices in which for each type of edges each two vertices are interconnected by at least two directed paths in both directions, running through the edges of only this type. We show that in this case, a directed multiplex network contains in total nine different giant components including the strongly viable component. In general, the total number of giant components is 3m. For uncorrelated directed multiplex networks, we obtain exactly the size and the emergence point of the strongly viable component and estimate the sizes of other giant components.

  2. On Functional Module Detection in Metabolic Networks

    PubMed Central

    Koch, Ina; Ackermann, Jörg

    2013-01-01

    Functional modules of metabolic networks are essential for understanding the metabolism of an organism as a whole. With the vast amount of experimental data and the construction of complex and large-scale, often genome-wide, models, the computer-aided identification of functional modules becomes more and more important. Since steady states play a key role in biology, many methods have been developed in that context, for example, elementary flux modes, extreme pathways, transition invariants and place invariants. Metabolic networks can be studied also from the point of view of graph theory, and algorithms for graph decomposition have been applied for the identification of functional modules. A prominent and currently intensively discussed field of methods in graph theory addresses the Q-modularity. In this paper, we recall known concepts of module detection based on the steady-state assumption, focusing on transition-invariants (elementary modes) and their computation as minimal solutions of systems of Diophantine equations. We present the Fourier-Motzkin algorithm in detail. Afterwards, we introduce the Q-modularity as an example for a useful non-steady-state method and its application to metabolic networks. To illustrate and discuss the concepts of invariants and Q-modularity, we apply a part of the central carbon metabolism in potato tubers (Solanum tuberosum) as running example. The intention of the paper is to give a compact presentation of known steady-state concepts from a graph-theoretical viewpoint in the context of network decomposition and reduction and to introduce the application of Q-modularity to metabolic Petri net models. PMID:24958145

  3. On functional module detection in metabolic networks.

    PubMed

    Koch, Ina; Ackermann, Jörg

    2013-01-01

    Functional modules of metabolic networks are essential for understanding the metabolism of an organism as a whole. With the vast amount of experimental data and the construction of complex and large-scale, often genome-wide, models, the computer-aided identification of functional modules becomes more and more important. Since steady states play a key role in biology, many methods have been developed in that context, for example, elementary flux modes, extreme pathways, transition invariants and place invariants. Metabolic networks can be studied also from the point of view of graph theory, and algorithms for graph decomposition have been applied for the identification of functional modules. A prominent and currently intensively discussed field of methods in graph theory addresses the Q-modularity. In this paper, we recall known concepts of module detection based on the steady-state assumption, focusing on transition-invariants (elementary modes) and their computation as minimal solutions of systems of Diophantine equations. We present the Fourier-Motzkin algorithm in detail. Afterwards, we introduce the Q-modularity as an example for a useful non-steady-state method and its application to metabolic networks. To illustrate and discuss the concepts of invariants and Q-modularity, we apply a part of the central carbon metabolism in potato tubers (Solanum tuberosum) as running example. The intention of the paper is to give a compact presentation of known steady-state concepts from a graph-theoretical viewpoint in the context of network decomposition and reduction and to introduce the application of Q-modularity to metabolic Petri net models. PMID:24958145

  4. Core organization of directed complex networks

    NASA Astrophysics Data System (ADS)

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

    2013-03-01

    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.

  5. Nonconsensus opinion model on directed networks.

    PubMed

    Qu, Bo; Li, Qian; Havlin, Shlomo; Stanley, H Eugene; Wang, Huijuan

    2014-11-01

    Dynamic social opinion models have been widely studied on undirected networks, and most of them are based on spin interaction models that produce a consensus. In reality, however, many networks such as Twitter and the World Wide Web are directed and are composed of both unidirectional and bidirectional links. Moreover, from choosing a coffee brand to deciding who to vote for in an election, two or more competing opinions often coexist. In response to this ubiquity of directed networks and the coexistence of two or more opinions in decision-making situations, we study a nonconsensus opinion model introduced by Shao et al. [Phys. Rev. Lett. 103, 018701 (2009)PRLTAO0031-900710.1103/PhysRevLett.103.018701] on directed networks. We define directionality ξ as the percentage of unidirectional links in a network, and we use the linear correlation coefficient ρ between the in-degree and out-degree of a node to quantify the relation between the in-degree and out-degree. We introduce two degree-preserving rewiring approaches which allow us to construct directed networks that can have a broad range of possible combinations of directionality ξ and linear correlation coefficient ρ and to study how ξ and ρ impact opinion competitions. We find that, as the directionality ξ or the in-degree and out-degree correlation ρ increases, the majority opinion becomes more dominant and the minority opinion's ability to survive is lowered. PMID:25493838

  6. Nonconsensus opinion model on directed networks

    NASA Astrophysics Data System (ADS)

    Qu, Bo; Li, Qian; Havlin, Shlomo; Stanley, H. Eugene; Wang, Huijuan

    2014-11-01

    Dynamic social opinion models have been widely studied on undirected networks, and most of them are based on spin interaction models that produce a consensus. In reality, however, many networks such as Twitter and the World Wide Web are directed and are composed of both unidirectional and bidirectional links. Moreover, from choosing a coffee brand to deciding who to vote for in an election, two or more competing opinions often coexist. In response to this ubiquity of directed networks and the coexistence of two or more opinions in decision-making situations, we study a nonconsensus opinion model introduced by Shao et al. [Phys. Rev. Lett. 103, 018701 (2009), 10.1103/PhysRevLett.103.018701] on directed networks. We define directionality ξ as the percentage of unidirectional links in a network, and we use the linear correlation coefficient ρ between the in-degree and out-degree of a node to quantify the relation between the in-degree and out-degree. We introduce two degree-preserving rewiring approaches which allow us to construct directed networks that can have a broad range of possible combinations of directionality ξ and linear correlation coefficient ρ and to study how ξ and ρ impact opinion competitions. We find that, as the directionality ξ or the in-degree and out-degree correlation ρ increases, the majority opinion becomes more dominant and the minority opinion's ability to survive is lowered.

  7. RNA Directed Modulation of Phenotypic Plasticity in Human Cells

    PubMed Central

    Burdach, Jon; Morris, Kevin V.

    2016-01-01

    Natural selective processes have been known to drive phenotypic plasticity, which is the emergence of different phenotypes from one genome following environmental stimulation. Long non-coding RNAs (lncRNAs) have been observed to modulate transcriptional and epigenetic states of genes in human cells. We surmised that lncRNAs are governors of phenotypic plasticity and drive natural selective processes through epigenetic modulation of gene expression. Using heat shocked human cells as a model we find several differentially expressed transcripts with the top candidates being lncRNAs derived from retro-elements. One particular retro-element derived transcripts, Retro-EIF2S2, was found to be abundantly over-expressed in heat shocked cells. Over-expression of Retro-EIF2S2 significantly enhanced cell viability and modulated a predisposition for an adherent cellular phenotype upon heat shock. Mechanistically, we find that this retro-element derived transcript interacts directly with a network of proteins including 40S ribosomal protein S30 (FAU), Eukaryotic translation initiation factor 5A (EIF5A), and Ubiquitin-60S ribosomal protein L40 (UBA52) to affect protein modulated cell adhesion pathways. We find one motif in Retro-EIF2S2 that exhibits binding to FAU and modulates phenotypic cell transitions from adherent to suspension states. The observations presented here suggest that retroviral derived transcripts actively modulate phenotypic plasticity in human cells in response to environmental selective pressures and suggest that natural selection may play out through the action of retro-elements in human cells. PMID:27082860

  8. Reconstructing Directed Networks From Noisy Dynamics

    NASA Astrophysics Data System (ADS)

    Tam, Hiu Ching; Ching, Emily Sc

    Complex systems can be fruitfully studied as networks of many elementary units, known as nodes, interacting with one another with the interactions being the links between the nodes. The overall behavior of the systems depends crucially on the network structure depicting how the nodes are linked with each other. It is usually possible to measure the dynamics of the individual nodes but difficult, if not impossible, to directly measure the interactions or links between the nodes. For most systems of interest, the links are directional in that one node affects the dynamics of the other but not vice versa. Moreover, the strength of interaction can vary for different links. Reconstructing directed and weighted networks from dynamics is one of the biggest challenges in network research. We have studied directed and weighted networks modelled by noisy dynamical systems with nonlinear dynamics and developed a method that reconstructs the links and their directions using only the dynamics of the nodes as input. Our method is motivated by a mathematical result derived for dynamical systems that approach a fixed point in the noise-free limit. We show that our method gives good reconstruction results for several directed and weighted networks with different nonlinear dynamics. Supported by Hong Kong Research Grants Council under Grant No. CUHK 14300914.

  9. Dynamics-based centrality for directed networks.

    PubMed

    Masuda, Naoki; Kori, Hiroshi

    2010-11-01

    Determining the relative importance of nodes in directed networks is important in, for example, ranking websites, publications, and sports teams, and for understanding signal flows in systems biology. A prevailing centrality measure in this respect is the PageRank. In this work, we focus on another class of centrality derived from the Laplacian of the network. We extend the Laplacian-based centrality, which has mainly been applied to strongly connected networks, to the case of general directed networks such that we can quantitatively compare arbitrary nodes. Toward this end, we adopt the idea used in the PageRank to introduce global connectivity between all the pairs of nodes with a certain strength. Numerical simulations are carried out on some networks. We also offer interpretations of the Laplacian-based centrality for general directed networks in terms of various dynamical and structural properties of networks. Importantly, the Laplacian-based centrality defined as the stationary density of the continuous-time random walk with random jumps is shown to be equivalent to the absorption probability of the random walk with sinks at each node but without random jumps. Similarly, the proposed centrality represents the importance of nodes in dynamics on the original network supplied with sinks but not with random jumps. PMID:21230545

  10. Dynamics-based centrality for directed networks

    NASA Astrophysics Data System (ADS)

    Masuda, Naoki; Kori, Hiroshi

    2010-11-01

    Determining the relative importance of nodes in directed networks is important in, for example, ranking websites, publications, and sports teams, and for understanding signal flows in systems biology. A prevailing centrality measure in this respect is the PageRank. In this work, we focus on another class of centrality derived from the Laplacian of the network. We extend the Laplacian-based centrality, which has mainly been applied to strongly connected networks, to the case of general directed networks such that we can quantitatively compare arbitrary nodes. Toward this end, we adopt the idea used in the PageRank to introduce global connectivity between all the pairs of nodes with a certain strength. Numerical simulations are carried out on some networks. We also offer interpretations of the Laplacian-based centrality for general directed networks in terms of various dynamical and structural properties of networks. Importantly, the Laplacian-based centrality defined as the stationary density of the continuous-time random walk with random jumps is shown to be equivalent to the absorption probability of the random walk with sinks at each node but without random jumps. Similarly, the proposed centrality represents the importance of nodes in dynamics on the original network supplied with sinks but not with random jumps.

  11. Predicting network instabilities in mobile directional wireless networks

    NASA Astrophysics Data System (ADS)

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

    2013-09-01

    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.

  12. Multifunction audio digitizer. [producing direct delta and pulse code modulation

    NASA Technical Reports Server (NTRS)

    Monford, L. G., Jr. (Inventor)

    1974-01-01

    An illustrative embodiment of the invention includes apparatus which simultaneously produces both direct delta modulation and pulse code modulation. An input signal, after amplification, is supplied to a window comparator which supplies a polarity control signal to gate the output of a clock to the appropriate input of a binary up-down counter. The control signals provide direct delta modulation while the up-down counter output provides pulse code modulation.

  13. Direct modulation at L-band using a quadrature modulator with feedback

    NASA Technical Reports Server (NTRS)

    Datta, Ravi; Crozier, Stewart N.

    1995-01-01

    This paper describes how a high quality modulated signal can be generated directly at the frequency of transmission, using a standard quadrature modulator and other commercially-available, low-cost building blocks. The method uses a feedback technique for automatic correction of carrier leakage, differential gain and phase mismatch errors in the quadrature modulator, and other building blocks, by providing guidance to the digital baseband portion of the modulator. Experimental results are presented for direct modulation at 1.65 GHz.

  14. Data reliability in complex directed networks

    NASA Astrophysics Data System (ADS)

    Sanz, Joaquín; Cozzo, Emanuele; Moreno, Yamir

    2013-12-01

    The availability of data from many different sources and fields of science has made it possible to map out an increasing number of networks of contacts and interactions. However, quantifying how reliable these data are remains an open problem. From Biology to Sociology and Economics, the identification of false and missing positives has become a problem that calls for a solution. In this work we extend one of the newest, best performing models—due to Guimerá and Sales-Pardo in 2009—to directed networks. The new methodology is able to identify missing and spurious directed interactions with more precision than previous approaches, which renders it particularly useful for analyzing data reliability in systems like trophic webs, gene regulatory networks, communication patterns and several social systems. We also show, using real-world networks, how the method can be employed to help search for new interactions in an efficient way.

  15. Advanced modulation format generation using high-speed directly modulated lasers for optical metro/access systems

    NASA Astrophysics Data System (ADS)

    Chan, Chun-Kit; Jia, Wei; Liu, Zhixin

    2011-12-01

    We propose and experimentally demonstrate the generation of various modulation formats using a directly modulated chirp-managed laser (CML), including phase-shaped binary transmission (PSBT), inverse-return-to-zero duobinary (IRZ-duobinary), Manchester-duobinary, return-to-zero differential phase shift keying (RZ-DPSK) and return-to-zero differential quadrature phase-shift-keying (RZ-DQPSK). The CML-based modulation formats improved dispersion tolerance and their corresponding transmitters have the features of compactness, low power consumption and costeffectiveness, which are desired in metro/access networks. System applications of such formats are also studied.

  16. Multiscale ensemble clustering for finding modules in complex networks

    NASA Astrophysics Data System (ADS)

    Kim, Eun-Youn; Hwang, Dong-Uk; Ko, Tae-Wook

    2012-02-01

    The identification of modules in complex networks is important for the understanding of systems. Here, we propose an ensemble clustering method incorporating node groupings in various sizes and the sequential removal of weak ties between nodes which are rarely grouped together. This method successfully detects modules in various networks, such as hierarchical random networks and the American college football network, with known modular structures. Some of the results are compared with those obtained by modularity optimization and K-means clustering.

  17. Optical waveform generation using a directly modulated laser

    NASA Astrophysics Data System (ADS)

    Cartledge, John C.; Karar, Abdullah S.; Roberts, Kim

    2013-10-01

    The capability of a directly modulated laser (DML) can be dramatically enhanced through precise control of the drive current waveform based on digital signal processing (DSP) and a digital-to-analog convertor (DAC). In this paper, a novel method to pre-compensate fiber dispersion for metro and regional networks is described for a bit rate of 10.709 Gb/s using a DML. A look-up table (LUT) for the drive current is optimized for dispersion mitigation. The entries of the LUT are determined based on the effects of the DML adiabatic and transient chirp on pulse propagation, the nonlinear mapping between the input current and the output optical power, and the bandwidth of the DML package. A DAC operating at 2 samples per bit (21.418 GSa/s with 6 bit resolution) converts the digital samples at the output of the LUT to an analog current waveform driving the DML. Experimental results for a bit rate of 10.709 Gb/s and on-off keying demonstrate a transmission reach of 252 km using a DML intended for 2.5 Gb/s operation and 608 km using a chirp managed laser intended for 10 Gb/s operation. Using this approach (DSP + DAC), the generation of 10.709 Gb/s differential phase shift keying (DPSK) and 56 Gb/s 16-ary quadrature amplitude modulation, sub-carrier multiplexed (QAM SCM) optical signals using the direct modulation of a passive feedback laser is also presented. 6-bit DACs operating at sampling rates of 21.418 GSa/s and 28 GSa/s, respectively, was used to generate the requisite analog current waveform.

  18. Modulating the default mode network using hypnosis.

    PubMed

    Deeley, Quinton; Oakley, David A; Toone, Brian; Giampietro, Vincent; Brammer, Michael J; Williams, Steven C R; Halligan, Peter W

    2012-01-01

    Debate regarding the neural basis of the hypnotic state continues, but a recent hypothesis suggests that it may produce alterations in the default mode network (DMN). DMN describes a network of brain regions more active during low-demand compared to high-demand task conditions and has been linked to processes such as task-independent thinking, episodic memory, semantic processing, and self-awareness. However, the experiential and cognitive correlates of DMN remain difficult to investigate directly. Using hypnosis as a means of altering the resting ("default") state in conjunction with subjective measures and brain imaging, the authors found that the state of attentional absorption following a hypnotic induction was associated with reduced activity in DMN and increased activity in prefrontal attentional systems, under invariant conditions of passive visual stimulation. The findings that hypnosis and spontaneous conceptual thought at rest were subjectively and neurally distinctive are also relevant to understanding hypnosis itself. PMID:22443526

  19. Robustness and dynamics of networks of coupled modules

    NASA Astrophysics Data System (ADS)

    Bagrow, James; Ahn, Yong-Yeol; Lehmann, Sune

    2011-03-01

    Many systems, from power grids and the internet, to the brain and society, can be modeled using networks of coupled overlapping modules. The elements of these networks perform individual and collective tasks such as generating and consuming electrical load or transmitting data. We study the robustness of these systems using percolation theory: a random fraction of the elements fail which may cause the network to lose global connectivity. We show that the modules themselves can become isolated or uncoupled (non-overlapping) well before the network falls apart. This has important structural and dynamical consequences for these networks and may explain how missing information hides pervasive overlap between communities in real networks.

  20. Clustering and community detection in directed networks: A survey

    NASA Astrophysics Data System (ADS)

    Malliaros, Fragkiskos D.; Vazirgiannis, Michalis

    2013-12-01

    Networks (or graphs) appear as dominant structures in diverse domains, including sociology, biology, neuroscience and computer science. In most of the aforementioned cases graphs are directed - in the sense that there is directionality on the edges, making the semantics of the edges nonsymmetric as the source node transmits some property to the target one but not vice versa. An interesting feature that real networks present is the clustering or community structure property, under which the graph topology is organized into modules commonly called communities or clusters. The essence here is that nodes of the same community are highly similar while on the contrary, nodes across communities present low similarity. Revealing the underlying community structure of directed complex networks has become a crucial and interdisciplinary topic with a plethora of relevant application domains. Therefore, naturally there is a recent wealth of research production in the area of mining directed graphs - with clustering being the primary method sought and the primary tool for community detection and evaluation. The goal of this paper is to offer an in-depth comparative review of the methods presented so far for clustering directed networks along with the relevant necessary methodological background and also related applications. The survey commences by offering a concise review of the fundamental concepts and methodological base on which graph clustering algorithms capitalize on. Then we present the relevant work along two orthogonal classifications. The first one is mostly concerned with the methodological principles of the clustering algorithms, while the second one approaches the methods from the viewpoint regarding the properties of a good cluster in a directed network. Further, we present methods and metrics for evaluating graph clustering results, demonstrate interesting application domains and provide promising future research directions.

  1. Automatic modulation format recognition for the next generation optical communication networks using artificial neural networks

    NASA Astrophysics Data System (ADS)

    Guesmi, Latifa; Hraghi, Abir; Menif, Mourad

    2015-03-01

    A new technique for Automatic Modulation Format Recognition (AMFR) in next generation optical communication networks is presented. This technique uses the Artificial Neural Network (ANN) in conjunction with the features of Linear Optical Sampling (LOS) of the detected signal at high bit rates using direct detection or coherent detection. The use of LOS method for this purpose mainly driven by the increase of bit rates which enables the measurement of eye diagrams. The efficiency of this technique is demonstrated under different transmission impairments such as chromatic dispersion (CD) in the range of -500 to 500 ps/nm, differential group delay (DGD) in the range of 0-15 ps and the optical signal tonoise ratio (OSNR) in the range of 10-30 dB. The results of numerical simulation for various modulation formats demonstrate successful recognition from a known bit rates with a higher estimation accuracy, which exceeds 99.8%.

  2. Random walks in directed modular networks

    NASA Astrophysics Data System (ADS)

    Comin, Cesar H.; Viana, Mateus P.; Antiqueira, Lucas; Costa, Luciano da F.

    2014-12-01

    Because diffusion typically involves symmetric interactions, scant attention has been focused on studying asymmetric cases. However, important networked systems underlain by diffusion (e.g. cortical networks and WWW) are inherently directed. In the case of undirected diffusion, it can be shown that the steady-state probability of the random walk dynamics is fully correlated with the degree, which no longer holds for directed networks. We investigate the relationship between such probability and the inward node degree, which we call efficiency, in modular networks. Our findings show that the efficiency of a given community depends mostly on the balance between its ingoing and outgoing connections. In addition, we derive analytical expressions to show that the internal degree of the nodes does not play a crucial role in their efficiency, when considering the Erdős-Rényi and Barabási-Albert models. The results are illustrated with respect to the macaque cortical network, providing subsidies for improving transportation and communication systems.

  3. Manipulating directed networks for better synchronization

    NASA Astrophysics Data System (ADS)

    Zeng, An; Lü, Linyuan; Zhou, Tao

    2012-08-01

    In this paper, we studied the strategies to enhance synchronization on directed networks by manipulating a fixed number of links. We proposed a centrality-based manipulating (CBM) method, where the node centrality is measured by the well-known PageRank algorithm. Extensive numerical simulation on many modeled networks demonstrated that the CBM method is more effective in facilitating synchronization than the degree-based manipulating method and the random manipulating method for adding or removing links. The reason is that the CBM method can effectively narrow the incoming degree distribution and reinforce the hierarchical structure of the network. Furthermore, we apply the CBM method to the links rewiring procedure where at each step one link is removed and one new link is added. The CBM method helps to decide which links should be removed or added. After several steps, the resulting networks are very close to the optimal structure from the theoretical analysis and the evolutionary optimization algorithm. The numerical simulations on the Kuramoto model further demonstrate that our method has an advantage in shortening the convergence time to synchronization on directed networks.

  4. Percolation of networks with directed dependency links

    NASA Astrophysics Data System (ADS)

    Niu, Dunbiao; Yuan, Xin; Du, Minhui; Stanley, H. Eugene; Hu, Yanqing

    2016-04-01

    The self-consistent probabilistic approach has proven itself powerful in studying the percolation behavior of interdependent or multiplex networks without tracking the percolation process through each cascading step. In order to understand how directed dependency links impact criticality, we employ this approach to study the percolation properties of networks with both undirected connectivity links and directed dependency links. We find that when a random network with a given degree distribution undergoes a second-order phase transition, the critical point and the unstable regime surrounding the second-order phase transition regime are determined by the proportion of nodes that do not depend on any other nodes. Moreover, we also find that the triple point and the boundary between first- and second-order transitions are determined by the proportion of nodes that depend on no more than one node. This implies that it is maybe general for multiplex network systems, some important properties of phase transitions can be determined only by a few parameters. We illustrate our findings using Erdős-Rényi networks.

  5. Essential Communication and Documentation Skills. Module: Giving Directions to Residents.

    ERIC Educational Resources Information Center

    Medina, Muriel; And Others

    This module is the fifth of 10 in the Essential Communication and Documentation Skills curriculum. It develops the ability to give directions, a workplace literacy skill identified as being directly related to the job of the direct care worker. The curriculum is designed to improve the competence of New York State Division for Youth direct care…

  6. Serotonin modulation of cortical neurons and networks

    PubMed Central

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

    2013-01-01

    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. PMID:23626526

  7. Dismissing Attachment Characteristics Dynamically Modulate Brain Networks Subserving Social Aversion.

    PubMed

    Krause, Anna Linda; Borchardt, Viola; Li, Meng; van Tol, Marie-José; Demenescu, Liliana Ramona; Strauss, Bernhard; Kirchmann, Helmut; Buchheim, Anna; Metzger, Coraline D; Nolte, Tobias; Walter, Martin

    2016-01-01

    Attachment patterns influence actions, thoughts and feeling through a person's "inner working model". Speech charged with attachment-dependent content was proposed to modulate the activation of cognitive-emotional schemata in listeners. We performed a 7 Tesla rest-task-rest functional magnetic resonance imaging (fMRI)-experiment, presenting auditory narratives prototypical of dismissing attachment representations to investigate their effect on 23 healthy males. We then examined effects of participants' attachment style and childhood trauma on brain state changes using seed-based functional connectivity (FC) analyses, and finally tested whether subjective differences in responsivity to narratives could be predicted by baseline network states. In comparison to a baseline state, we observed increased FC in a previously described "social aversion network" including dorsal anterior cingulated cortex (dACC) and left anterior middle temporal gyrus (aMTG) specifically after exposure to insecure-dismissing attachment narratives. Increased dACC-seeded FC within the social aversion network was positively related to the participants' avoidant attachment style and presence of a history of childhood trauma. Anxious attachment style on the other hand was positively correlated with FC between the dACC and a region outside of the "social aversion network", namely the dorsolateral prefrontal cortex, which suggests decreased network segregation as a function of anxious attachment. Finally, the extent of subjective experience of friendliness towards the dismissing narrative was predicted by low baseline FC-values between hippocampus and inferior parietal lobule (IPL). Taken together, our study demonstrates an activation of networks related to social aversion in terms of increased connectivity after listening to insecure-dismissing attachment narratives. A causal interrelation of brain state changes and subsequent changes in social reactivity was further supported by our observation of direct prediction of neuronal responses by individual attachment and trauma characteristics and reversely prediction of subjective experience by intrinsic functional connections. We consider these findings of activation of within-network and between-network connectivity modulated by inter-individual differences as substantial for the understanding of interpersonal processes, particularly in clinical settings. PMID:27014016

  8. Exploring the randomness of directed acyclic networks

    NASA Astrophysics Data System (ADS)

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

    2010-12-01

    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.

  9. A Novel Modulation Classification Approach Using Gabor Filter Network

    PubMed Central

    Ghauri, Sajjad Ahmed; Qureshi, Ijaz Mansoor; Cheema, Tanveer Ahmed; Malik, Aqdas Naveed

    2014-01-01

    A Gabor filter network based approach is used for feature extraction and classification of digital modulated signals by adaptively tuning the parameters of Gabor filter network. Modulation classification of digitally modulated signals is done under the influence of additive white Gaussian noise (AWGN). The modulations considered for the classification purpose are PSK 2 to 64, FSK 2 to 64, and QAM 4 to 64. The Gabor filter network uses the network structure of two layers; the first layer which is input layer constitutes the adaptive feature extraction part and the second layer constitutes the signal classification part. The Gabor atom parameters are tuned using Delta rule and updating of weights of Gabor filter using least mean square (LMS) algorithm. The simulation results show that proposed novel modulation classification algorithm has high classification accuracy at low signal to noise ratio (SNR) on AWGN channel. PMID:25126603

  10. A novel modulation classification approach using Gabor filter network.

    PubMed

    Ghauri, Sajjad Ahmed; Qureshi, Ijaz Mansoor; Cheema, Tanveer Ahmed; Malik, Aqdas Naveed

    2014-01-01

    A Gabor filter network based approach is used for feature extraction and classification of digital modulated signals by adaptively tuning the parameters of Gabor filter network. Modulation classification of digitally modulated signals is done under the influence of additive white Gaussian noise (AWGN). The modulations considered for the classification purpose are PSK 2 to 64, FSK 2 to 64, and QAM 4 to 64. The Gabor filter network uses the network structure of two layers; the first layer which is input layer constitutes the adaptive feature extraction part and the second layer constitutes the signal classification part. The Gabor atom parameters are tuned using Delta rule and updating of weights of Gabor filter using least mean square (LMS) algorithm. The simulation results show that proposed novel modulation classification algorithm has high classification accuracy at low signal to noise ratio (SNR) on AWGN channel. PMID:25126603

  11. Control range: a controllability-based index for node significance in directed networks

    NASA Astrophysics Data System (ADS)

    Wang, Bingbo; Gao, Lin; Gao, Yong

    2012-04-01

    While a large number of methods for module detection have been developed for undirected networks, it is difficult to adapt them to handle directed networks due to the lack of consensus criteria for measuring the node significance in a directed network. In this paper, we propose a novel structural index, the control range, motivated by recent studies on the structural controllability of large-scale directed networks. The control range of a node quantifies the size of the subnetwork that the node can effectively control. A related index, called the control range similarity, is also introduced to measure the structural similarity between two nodes. When applying the index of control range to several real-world and synthetic directed networks, it is observed that the control range of the nodes is mainly influenced by the network's degree distribution and that nodes with a low degree may have a high control range. We use the index of control range similarity to detect and analyze functional modules in glossary networks and the enzyme-centric network of homo sapiens. Our results, as compared with other approaches to module detection such as modularity optimization algorithm, dynamic algorithm and clique percolation method, indicate that the proposed indices are effective and practical in depicting structural and modular characteristics of sparse directed networks.

  12. Identify Dynamic Network Modules with Temporal and Spatial Constraints

    SciTech Connect

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

    2007-09-24

    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.

  13. Direct Gaze Modulates Face Recognition in Young Infants

    ERIC Educational Resources Information Center

    Farroni, Teresa; Massaccesi, Stefano; Menon, Enrica; Johnson, Mark H.

    2007-01-01

    From birth, infants prefer to look at faces that engage them in direct eye contact. In adults, direct gaze is known to modulate the processing of faces, including the recognition of individuals. In the present study, we investigate whether direction of gaze has any effect on face recognition in four-month-old infants. Four-month infants were shown…

  14. Network connectivity during mergers and growth: Optimizing the addition of a module

    NASA Astrophysics Data System (ADS)

    Taylor, Dane; Restrepo, Juan G.

    2011-06-01

    The principal eigenvalue ? of a networks adjacency matrix often determines dynamics on the network (e.g., in synchronization and spreading processes) and some of its structural properties (e.g., robustness against failure or attack) and is therefore a good indicator for how strongly a network is connected. We study how ? is modified by the addition of a module, or community, which has broad applications, ranging from those involving a single modification (e.g., introduction of a drug into a biological process) to those involving repeated additions (e.g., power-grid and transit development). We describe how to optimally connect the module to the network to either maximize or minimize the shift in ?, noting several applications of directing dynamics on networks.

  15. Dismissing Attachment Characteristics Dynamically Modulate Brain Networks Subserving Social Aversion

    PubMed Central

    Krause, Anna Linda; Borchardt, Viola; Li, Meng; van Tol, Marie-José; Demenescu, Liliana Ramona; Strauss, Bernhard; Kirchmann, Helmut; Buchheim, Anna; Metzger, Coraline D.; Nolte, Tobias; Walter, Martin

    2016-01-01

    Attachment patterns influence actions, thoughts and feeling through a person’s “inner working model”. Speech charged with attachment-dependent content was proposed to modulate the activation of cognitive-emotional schemata in listeners. We performed a 7 Tesla rest-task-rest functional magnetic resonance imaging (fMRI)-experiment, presenting auditory narratives prototypical of dismissing attachment representations to investigate their effect on 23 healthy males. We then examined effects of participants’ attachment style and childhood trauma on brain state changes using seed-based functional connectivity (FC) analyses, and finally tested whether subjective differences in responsivity to narratives could be predicted by baseline network states. In comparison to a baseline state, we observed increased FC in a previously described “social aversion network” including dorsal anterior cingulated cortex (dACC) and left anterior middle temporal gyrus (aMTG) specifically after exposure to insecure-dismissing attachment narratives. Increased dACC-seeded FC within the social aversion network was positively related to the participants’ avoidant attachment style and presence of a history of childhood trauma. Anxious attachment style on the other hand was positively correlated with FC between the dACC and a region outside of the “social aversion network”, namely the dorsolateral prefrontal cortex, which suggests decreased network segregation as a function of anxious attachment. Finally, the extent of subjective experience of friendliness towards the dismissing narrative was predicted by low baseline FC-values between hippocampus and inferior parietal lobule (IPL). Taken together, our study demonstrates an activation of networks related to social aversion in terms of increased connectivity after listening to insecure-dismissing attachment narratives. A causal interrelation of brain state changes and subsequent changes in social reactivity was further supported by our observation of direct prediction of neuronal responses by individual attachment and trauma characteristics and reversely prediction of subjective experience by intrinsic functional connections. We consider these findings of activation of within-network and between-network connectivity modulated by inter-individual differences as substantial for the understanding of interpersonal processes, particularly in clinical settings. PMID:27014016

  16. HyperModules: identifying clinically and phenotypically significant network modules with disease mutations for biomarker discovery

    PubMed Central

    Leung, Alvin; Bader, Gary D.; Reimand, Jüri

    2014-01-01

    Summary: Correlating disease mutations with clinical and phenotypic information such as drug response or patient survival is an important goal of personalized cancer genomics and a first step in biomarker discovery. HyperModules is a network search algorithm that finds frequently mutated gene modules with significant clinical or phenotypic signatures from biomolecular interaction networks. Availability and implementation: HyperModules is available in Cytoscape App Store and as a command line tool at www.baderlab.org/Sofware/HyperModules. Contact: Juri.Reimand@utoronto.ca or Gary.Bader@utoronto.ca Supplementary information: Supplementary data are available at Bioinformatics online PMID:24713437

  17. Functional module identification in protein interaction networks by interaction patterns

    PubMed Central

    Wang, Yijie; Qian, Xiaoning

    2014-01-01

    Motivation: Identifying functional modules in protein–protein interaction (PPI) networks may shed light on cellular functional organization and thereafter underlying cellular mechanisms. Many existing module identification algorithms aim to detect densely connected groups of proteins as potential modules. However, based on this simple topological criterion of ‘higher than expected connectivity’, those algorithms may miss biologically meaningful modules of functional significance, in which proteins have similar interaction patterns to other proteins in networks but may not be densely connected to each other. A few blockmodel module identification algorithms have been proposed to address the problem but the lack of global optimum guarantee and the prohibitive computational complexity have been the bottleneck of their applications in real-world large-scale PPI networks. Results: In this article, we propose a novel optimization formulation LCP2 (low two-hop conductance sets) using the concept of Markov random walk on graphs, which enables simultaneous identification of both dense and sparse modules based on protein interaction patterns in given networks through searching for LCP2 by random walk. A spectral approximate algorithm SLCP2 is derived to identify non-overlapping functional modules. Based on a bottom-up greedy strategy, we further extend LCP2 to a new algorithm (greedy algorithm for LCP2) GLCP2 to identify overlapping functional modules. We compare SLCP2 and GLCP2 with a range of state-of-the-art algorithms on synthetic networks and real-world PPI networks. The performance evaluation based on several criteria with respect to protein complex prediction, high level Gene Ontology term prediction and especially sparse module detection, has demonstrated that our algorithms based on searching for LCP2 outperform all other compared algorithms. Availability and implementation: All data and code are available at http://www.cse.usf.edu/∼xqian/fmi/slcp2hop/. Contact: yijie@mail.usf.edu or xqian@ece.tamu.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24085567

  18. Direct ink writing of microvascular networks

    NASA Astrophysics Data System (ADS)

    Wu, Willie

    Nature is replete with examples of embedded microvascular systems that enable efficient fluid flow and distribution for autonomic healing, cooling, and energy harvesting. The ability to incorporate microvascular networks in functional materials systems is therefore both scientifically and technologically important. In this PhD thesis, the direct-write assembly of planar and 3D biomimetic microvascular networks within polymer and hydrogel matrices is demonstrated. In addition, the influence of network design of fluid transport efficiency is characterized. Planar microvascular networks composed of periodic lattices of uniformal microchannels and hierarchical, branching architectures are constructed by direct-write assembly of a fugitive organic ink. Several advancements are required to facilitate their patterning, including pressure valving, dual ink printing, and dynamic pressure variation to allow tunable control of ink deposition. The hydraulic conductance is measured using a high pressure flow meter as a function of network design. For a constant vascular volume and areal coverage, 2- and 4-generation branched architectures that obey Murray's Law exhibited the highest hydraulic conductivity. These experimental observations are in good agreement with predictions made by analytic models. 3D microvascular networks are fabricated by omnidirectional printing a fugitive organic ink into a photopolymerizable hydrogel matrix that is capped with fluid filler of nearly identical composition. Using this approach, 3D networks of arbitrary design can be patterned. After ink deposition is complete, the matrix and fluid filler are chemically cross-linked via UV irradiation, and the ink is removed by liquefication. Aqueous solutions composed of a triblock copolymer of polyethylene oxide (PEO)-polypropylene oxide (PPO)-PEO constitute the materials system of choice due to their thermal- and concentration-dependent phase behavior. Specifically, the fugitive ink consists of a 23 w/w% PEO-PPO-PEO (Pluronic F127) solution, while matrix (25 w/w%) and fluid filler (20 w/w%) are composed of an acrylate-modified form of the Pluronic F127 that can be subsequently photopolymerized. The ink and matrix concentrations exceed the critical micelle concentration (CMC) of 22 w/w% and thus reside in a physical gel state. At their respective concentrations, they possess an elastic plateau modulus G' > 104 Pa needed for ink filament formation, shape retention, and support during the printing process. By contrast, the fluid filler is formulated below the CMC to facilitate its flow into void spaces created as the nozzle translates through the matrix during printing. After printing is completed, photopolymerization is carried out to yield a chemically cross-linked matrix from which the fugitive ink is removed leaving behind the desired 3D microvascular network. Due to the potential application of 3D microvasularized hydrogels in tissue engineering, dye diffusion through the cured Pluronic F127-diacrylate matrix is investigated via fluorescent microscopy. Image analysis is used to extract diffusion profiles of the dye as a function of time. Extraction of the 1-D Gaussian fitting parameters is used to determine the spatial peak variance sigma2 and plotted as a function of time to determine the dye diffusivity.

  19. Direct digital RF synthesis and modulation for MSAT mobile applications

    NASA Technical Reports Server (NTRS)

    Crozier, Stewart; Datta, Ravi; Sydor, John

    1993-01-01

    A practical method of performing direct digital RF synthesis using the Hilbert transform single sideband (SSB) technique is described. It is also shown that amplitude and phase modulation can be achieved directly at L-band with frequency stability and spurii performance exceeding stringent MSAT system requirements.

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

    PubMed

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

    2013-09-23

    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 0.934π 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

  1. eXamine: Exploring annotated modules in networks

    PubMed Central

    2014-01-01

    Background Biological networks have a growing importance for the interpretation of high-throughput “omics” data. Integrative network analysis makes use of statistical and combinatorial methods to extract smaller subnetwork modules, and performs enrichment analysis to annotate the modules with ontology terms or other available knowledge. This process results in an annotated module, which retains the original network structure and includes enrichment information as a set system. A major bottleneck is a lack of tools that allow exploring both network structure of extracted modules and its annotations. Results This paper presents a visual analysis approach that targets small modules with many set-based annotations, and which displays the annotations as contours on top of a node-link diagram. We introduce an extension of self-organizing maps to lay out nodes, links, and contours in a unified way. An implementation of this approach is freely available as the Cytoscape app eXamine Conclusions eXamine accurately conveys small and annotated modules consisting of several dozens of proteins and annotations. We demonstrate that eXamine facilitates the interpretation of integrative network analysis results in a guided case study. This study has resulted in a novel biological insight regarding the virally-encoded G-protein coupled receptor US28. PMID:25002203

  2. Hierarchical decomposition of metabolic networks using k-modules.

    PubMed

    Reimers, Arne C

    2015-12-01

    The optimal solutions obtained by flux balance analysis (FBA) are typically not unique. Flux modules have recently been shown to be a very useful tool to simplify and decompose the space of FBA-optimal solutions. Since yield-maximization is sometimes not the primary objective encountered in vivo, we are also interested in understanding the space of sub-optimal solutions. Unfortunately, the flux modules are too restrictive and not suited for this task. We present a generalization, called k-module, which compensates the limited applicability of flux modules to the space of sub-optimal solutions. Intuitively, a k-module is a sub-network with low connectivity to the rest of the network. Recursive application of k-modules yields a hierarchical decomposition of the metabolic network, which is also known as branch decomposition in matroid theory. In particular, decompositions computed by existing methods, like the null-space-based approach, introduced by Poolman et al. [(2007) J. Theor. Biol. 249: , 691-705] can be interpreted as branch decompositions. With k-modules we can now compare alternative decompositions of metabolic networks to the classical sub-systems of glycolysis, tricarboxylic acid (TCA) cycle, etc. They can be used to speed up algorithmic problems [theoretically shown for elementary flux modes (EFM) enumeration] and have the potential to present computational solutions in a more intuitive way independently from the classical sub-systems. PMID:26614652

  3. Module organization and variance in protein-protein interaction networks

    PubMed Central

    Lin, Chun-Yu; Lee, Tsai-Ling; Chiu, Yi-Yuan; Lin, Yi-Wei; Lo, Yu-Shu; Lin, Chih-Ta; Yang, Jinn-Moon

    2015-01-01

    A module is a group of closely related proteins that act in concert to perform specific biological functions through protein–protein interactions (PPIs) that occur in time and space. However, the underlying module organization and variance remain unclear. In this study, we collected module templates to infer respective module families, including 58,041 homologous modules in 1,678 species, and PPI families using searches of complete genomic database. We then derived PPI evolution scores and interface evolution scores to describe the module elements, including core and ring components. Functions of core components were highly correlated with those of essential genes. In comparison with ring components, core proteins/PPIs were conserved across multiple species. Subsequently, protein/module variance of PPI networks confirmed that core components form dynamic network hubs and play key roles in various biological functions. Based on the analyses of gene essentiality, module variance, and gene co-expression, we summarize the observations of module organization and variance as follows: 1) a module consists of core and ring components; 2) core components perform major biological functions and collaborate with ring components to execute certain functions in some cases; 3) core components are more conserved and essential during organizational changes in different biological states or conditions. PMID:25797237

  4. Module organization and variance in protein-protein interaction networks

    NASA Astrophysics Data System (ADS)

    Lin, Chun-Yu; Lee, Tsai-Ling; Chiu, Yi-Yuan; Lin, Yi-Wei; Lo, Yu-Shu; Lin, Chih-Ta; Yang, Jinn-Moon

    2015-03-01

    A module is a group of closely related proteins that act in concert to perform specific biological functions through protein-protein interactions (PPIs) that occur in time and space. However, the underlying module organization and variance remain unclear. In this study, we collected module templates to infer respective module families, including 58,041 homologous modules in 1,678 species, and PPI families using searches of complete genomic database. We then derived PPI evolution scores and interface evolution scores to describe the module elements, including core and ring components. Functions of core components were highly correlated with those of essential genes. In comparison with ring components, core proteins/PPIs were conserved across multiple species. Subsequently, protein/module variance of PPI networks confirmed that core components form dynamic network hubs and play key roles in various biological functions. Based on the analyses of gene essentiality, module variance, and gene co-expression, we summarize the observations of module organization and variance as follows: 1) a module consists of core and ring components; 2) core components perform major biological functions and collaborate with ring components to execute certain functions in some cases; 3) core components are more conserved and essential during organizational changes in different biological states or conditions.

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

    NASA Astrophysics Data System (ADS)

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

    2010-12-01

    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.

  6. Satellite-borne QPSK Direct Modulator for Ka Band

    NASA Astrophysics Data System (ADS)

    Zhang, Min; Li, Changsheng

    2016-02-01

    Ka band is referred to a microwave band whose frequency range is from 24.6 GHz to 40 GHz, it shares a wide available bandwidth, high frequency reuse rate and strong ability of anti-jamming. This paper presents a novel method to design a modulator for Ka-band satellite communication. Using QPSK to improve the ability of anti-jamming, using direct modulation to reduce the weight, volume and cost of electronic equipment, using sub-harmonic mixer to cut the LO power leakage, excellent modulation results are obtained.

  7. Identifying protein complexes and functional modules--from static PPI networks to dynamic PPI networks.

    PubMed

    Chen, Bolin; Fan, Weiwei; Liu, Juan; Wu, Fang-Xiang

    2014-03-01

    Cellular processes are typically carried out by protein complexes and functional modules. Identifying them plays an important role for our attempt to reveal principles of cellular organizations and functions. In this article, we review computational algorithms for identifying protein complexes and/or functional modules from protein-protein interaction (PPI) networks. We first describe issues and pitfalls when interpreting PPI networks. Then based on types of data used and main ideas involved, we briefly describe protein complex and/or functional module identification algorithms in four categories: (i) those based on topological structures of unweighted PPI networks; (ii) those based on characters of weighted PPI networks; (iii) those based on multiple data integrations; and (iv) those based on dynamic PPI networks. The PPI networks are modelled increasingly precise when integrating more types of data, and the study of protein complexes would benefit by shifting from static to dynamic PPI networks. PMID:23780996

  8. Differential Network Analysis Reveals Genetic Effects on Catalepsy Modules

    PubMed Central

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

    2013-01-01

    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. PMID:23555609

  9. New simple feed network for an array module of four microstrip elements

    NASA Technical Reports Server (NTRS)

    Oberhart, M. L.; Lo, Y. T.; Lee, R. Q. H.

    1987-01-01

    A simple microstripline feed network for an array module comprising four microstrip elements is described. The advantages and disadvantages of the network are discussed as well as a theoretical explanation for the radiation characteristics of array modules using the network.

  10. Inverter power module with distributed support for direct substrate cooling

    SciTech Connect

    Miller, David Harold; Korich, Mark D.; Ward, Terence G.; Mann, Brooks S.

    2012-08-21

    Systems and/or methods are provided for an inverter power module with distributed support for direct substrate cooling. An inverter module comprises a power electronic substrate. A first support frame is adapted to house the power electronic substrate and has a first region adapted to allow direct cooling of the power electronic substrate. A gasket is interposed between the power electronic substrate and the first support frame. The gasket is configured to provide a seal between the first region and the power electronic substrate. A second support frame is adapted to house the power electronic substrate and joined to the first support frame to form the seal.

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

    PubMed

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

    2013-07-01

    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

  12. An Integrative Approach to Inferring Gene Regulatory Module Networks

    PubMed Central

    Baitaluk, Michael; Kozhenkov, Sergey; Ponomarenko, Julia

    2012-01-01

    Background Gene regulatory networks (GRNs) provide insight into the mechanisms of differential gene expression at a system level. However, the methods for inference, functional analysis and visualization of gene regulatory modules and GRNs require the user to collect heterogeneous data from many sources using numerous bioinformatics tools. This makes the analysis expensive and time-consuming. Results In this work, the BiologicalNetworks application–the data integration and network based research environment–was extended with tools for inference and analysis of gene regulatory modules and networks. The backend database of the application integrates public data on gene expression, pathways, transcription factor binding sites, gene and protein sequences, and functional annotations. Thus, all data essential for the gene regulation analysis can be mined publicly. In addition, the user’s data can either be integrated in the database and become public, or kept private within the application. The capabilities to analyze multiple gene expression experiments are also provided. Conclusion The generated modular networks, regulatory modules and binding sites can be visualized and further analyzed within this same application. The developed tools were applied to the mouse model of asthma and the OCT4 regulatory network in embryonic stem cells. Developed methods and data are available through the Java application from BiologicalNetworks program at http://www.biologicalnetworks.org. PMID:23285197

  13. Protein complexes and functional modules in molecular networks

    NASA Astrophysics Data System (ADS)

    Spirin, Victor; Mirny, Leonid A.

    2003-10-01

    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.

  14. Reverse engineering module networks by PSO-RNN hybrid modeling

    PubMed Central

    Zhang, Yuji; Xuan, Jianhua; de los Reyes, Benildo G; Clarke, Robert; Ressom, Habtom W

    2009-01-01

    Background Inferring a gene regulatory network (GRN) from high throughput biological data is often an under-determined problem and is a challenging task due to the following reasons: (1) thousands of genes are involved in one living cell; (2) complex dynamic and nonlinear relationships exist among genes; (3) a substantial amount of noise is involved in the data, and (4) the typical small sample size is very small compared to the number of genes. We hypothesize we can enhance our understanding of gene interactions in important biological processes (differentiation, cell cycle, and development, etc) and improve the inference accuracy of a GRN by (1) incorporating prior biological knowledge into the inference scheme, (2) integrating multiple biological data sources, and (3) decomposing the inference problem into smaller network modules. Results This study presents a novel GRN inference method by integrating gene expression data and gene functional category information. The inference is based on module network model that consists of two parts: the module selection part and the network inference part. The former determines the optimal modules through fuzzy c-mean (FCM) clustering and by incorporating gene functional category information, while the latter uses a hybrid of particle swarm optimization and recurrent neural network (PSO-RNN) methods to infer the underlying network between modules. Our method is tested on real data from two studies: the development of rat central nervous system (CNS) and the yeast cell cycle process. The results are evaluated by comparing them to previously published results and gene ontology annotation information. Conclusion The reverse engineering of GRNs in time course gene expression data is a major obstacle in system biology due to the limited number of time points. Our experiments demonstrate that the proposed method can address this challenge by: (1) preprocessing gene expression data (e.g. normalization and missing value imputation) to reduce the data noise; (2) clustering genes based on gene expression data and gene functional category information to identify biologically meaningful modules, thereby reducing the dimensionality of the data; (3) modeling GRNs with the PSO-RNN method between the modules to capture their nonlinear and dynamic relationships. The method is shown to lead to biologically meaningful modules and networks among the modules. PMID:19594874

  15. Nicotinic modulation of intrinsic brain networks in schizophrenia

    PubMed Central

    Smucny, Jason; Tregellas, Jason

    2014-01-01

    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

  16. Identifying dynamic network modules with temporal and spatial constraints.

    PubMed

    Jin, Ruoming; McCallen, Scott; Liu, Chun-Chi; Xiang, Yang; Almaas, Eivind; Zhou, Xianghong Jasmine

    2009-01-01

    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 an efficient mining algorithm to discover dynamic modules in a temporal network. 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. Finally, we note that the applicability of our algorithm is not limited to the study of PPI networks, instead it is generally applicable to the combination of any type of network and time-series data. PMID:19209702

  17. Finding communities in directed networks by PageRank random walk induced network embedding

    NASA Astrophysics Data System (ADS)

    Lai, Darong; Lu, Hongtao; Nardini, Christine

    2010-06-01

    Community structure has been found to exist ubiquitously in many different kinds of real world complex networks. Most of the previous literature ignores edge directions and applies methods designed for community finding in undirected networks to find communities. Here, we address the problem of finding communities in directed networks. Our proposed method uses PageRank random walk induced network embedding to transform a directed network into an undirected one, where the information on edge directions is effectively incorporated into the edge weights. Starting from this new undirected weighted network, previously developed methods for undirected network community finding can be used without any modification. Moreover, our method improves on recent work in terms of community definition and meaning. We provide two simulated examples, a real social network and different sets of power law benchmark networks, to illustrate how our method can correctly detect communities in directed networks.

  18. Modulation of neuronal network activity using magnetic nanoparticle-based astrocytic network integration.

    PubMed

    Saito, Atsushi; Nakashima, Yutaro; Shimba, Kenta; Takayama, Yuzo; Kotani, Kiyoshi; Jimbo, Yasuhiko

    2015-08-01

    Investigating the mechanisms of the neuron-glia interaction is important in the basic research of neuroscience and neural transplantation. Synaptic transmission is modulated by astrocyte activation in the pre- and post-synaptic terminals, and this phenomenon is spread to the surrounding astrocytes through gap junctions. However, the modulation of network-wide neuronal activity dependent on extensive astrocyte activation is not well understood. In this study, we show network-wide neuronal modulation associated with a newly developed three-dimensional neuronal and astrocytic network co-culture method. To establish widespread neuronal and astrocytic network interactions in vitro, we performed integration of magnetic nanoparticle-injected astrocytes (Mag-AS) onto the matured monolayer of neuronal networks using an external magnetic force. The neuronal electrical activity was dynamically synchronized at 24 h after integration of the Mag-AS network. In addition, Mag-AS network activation using a caged calcium compound rapidly induced suppression and subsequent synchronization of neuronal electrical activity. These results indicate that the high-density astrocytic network integration onto the neuronal network can induce widespread neuronal modulation, and our in vitro co-culture method contributes to the advancement of neuronal and astrocytic transplantation research. PMID:26222038

  19. Investigation of direct integrated optics modulators. [applicable to data preprocessors

    NASA Technical Reports Server (NTRS)

    Batchman, T. E.

    1980-01-01

    Direct modulation techniques applicable to integrated optics data preprocessors were investigated. Several methods of modulating a coherent optical beam by interaction with an incoherent beam were studied. It was decided to investigate photon induced conductivity changes in thin semiconductor cladding layers on optical waveguides. Preliminary calculations indicate significant changes can be produced in the phase shift in a propagating wave when the conductivity is changed by ten percent or more. Experimental devices to verify these predicted phase changes and experiments designed to prove the concept are described.

  20. Modulation of behavioral networks by selective interneuronal inactivation

    PubMed Central

    Schmidt, MJ; Horvath, S; Ebert, P; Norris, JL; Seeley, EH; Brown, J; Gellert, L; Everheart, M; Garbett, KA; Grice, TW; Caprioli, RM; Mirnics, K

    2014-01-01

    Gamma-aminobutyric acid (GABA)-ergic disturbances are hallmark features of schizophrenia and other neuropsychiatric disorders and encompass multiple interneuronal cell types. Using bacterial artificial chromosome-driven, miRNA silencing technology we generated transgenic mouse lines that suppress glutamic acid decarboxylase 1 (GAD1) in either cholecystokinin (CCK)- or neuropeptide Y (NPY)-expressing interneurons. In situ lipidomic and proteomic analyses on brain tissue sections revealed distinct, brain region-specific profiles in each transgenic line. Behavioral analyses revealed that suppression of GAD1 in CCK+ interneurons resulted in locomotor and olfactory sensory changes, whereas suppression in NPY+ interneurons affected anxiety-related behaviors and social interaction. Both transgenic mouse lines had altered sensitivity to amphetamine albeit in opposite directions. Together, these data argue that reduced GAD1 expression leads to altered molecular and behavioral profiles in a cell type-dependent manner, and that these subpopulations of interneurons are strong and opposing modulators of dopamine system function. Furthermore, our findings also support the hypothesis that neuronal networks are differentially controlled by diverse inhibitory subnetworks. PMID:24322205

  1. Controllability and observability analysis for vertex domination centrality in directed networks

    NASA Astrophysics Data System (ADS)

    Wang, Bingbo; Gao, Lin; Gao, Yong; Deng, Yue; Wang, Yu

    2014-06-01

    Topological centrality is a significant measure for characterising the relative importance of a node in a complex network. For directed networks that model dynamic processes, however, it is of more practical importance to quantify a vertex's ability to dominate (control or observe) the state of other vertices. In this paper, based on the determination of controllable and observable subspaces under the global minimum-cost condition, we introduce a novel direction-specific index, domination centrality, to assess the intervention capabilities of vertices in a directed network. Statistical studies demonstrate that the domination centrality is, to a great extent, encoded by the underlying network's degree distribution and that most network positions through which one can intervene in a system are vertices with high domination centrality rather than network hubs. To analyse the interaction and functional dependence between vertices when they are used to dominate a network, we define the domination similarity and detect significant functional modules in glossary and metabolic networks through clustering analysis. The experimental results provide strong evidence that our indices are effective and practical in accurately depicting the structure of directed networks.

  2. Controllability and observability analysis for vertex domination centrality in directed networks.

    PubMed

    Wang, Bingbo; Gao, Lin; Gao, Yong; Deng, Yue; Wang, Yu

    2014-01-01

    Topological centrality is a significant measure for characterising the relative importance of a node in a complex network. For directed networks that model dynamic processes, however, it is of more practical importance to quantify a vertex's ability to dominate (control or observe) the state of other vertices. In this paper, based on the determination of controllable and observable subspaces under the global minimum-cost condition, we introduce a novel direction-specific index, domination centrality, to assess the intervention capabilities of vertices in a directed network. Statistical studies demonstrate that the domination centrality is, to a great extent, encoded by the underlying network's degree distribution and that most network positions through which one can intervene in a system are vertices with high domination centrality rather than network hubs. To analyse the interaction and functional dependence between vertices when they are used to dominate a network, we define the domination similarity and detect significant functional modules in glossary and metabolic networks through clustering analysis. The experimental results provide strong evidence that our indices are effective and practical in accurately depicting the structure of directed networks. PMID:24954137

  3. Direct Modulation of Small GTPase Activity and Function.

    PubMed

    Cromm, Philipp M; Spiegel, Jochen; Grossmann, Tom N; Waldmann, Herbert

    2015-11-01

    Small GTPases are a family of GDP-/GTP-binding proteins that serve as biomolecular switches inside cells to control a variety of essential cellular processes. Aberrant function and regulation of small GTPases is associated with a variety of human diseases, thus rendering these proteins highly interesting targets in drug discovery. However, this class of proteins has been considered "undruggable", as intensive decade-long efforts did not yield clinically relevant direct modulators of small GTPases. Recently, the targeting of small GTPases has gained fresh impetus through the discovery of novel transient cavities on the protein surfaces and the application of new targeting strategies. Besides Ras proteins, other small GTPases have attracted increased attention since improved biological insight in combination with novel targeting strategies identified them as promising targets in drug discovery. This Review gives an overview of relevant aspects of the superfamily of small GTPases and summarizes recent progress and perspectives for the direct modulation of these challenging targets. PMID:26470842

  4. Directed network motifs in Alzheimer's disease and mild cognitive impairment.

    PubMed

    Friedman, Eric J; Young, Karl; Tremper, Graham; Liang, Jason; Landsberg, Adam S; Schuff, Norbert

    2015-01-01

    Directed network motifs are the building blocks of complex networks, such as human brain networks, and capture deep connectivity information that is not contained in standard network measures. In this paper we present the first application of directed network motifs in vivo to human brain networks, utilizing recently developed directed progression networks which are built upon rates of cortical thickness changes between brain regions. This is in contrast to previous studies which have relied on simulations and in vitro analysis of non-human brains. We show that frequencies of specific directed network motifs can be used to distinguish between patients with Alzheimer's disease (AD) and normal control (NC) subjects. Especially interesting from a clinical standpoint, these motif frequencies can also distinguish between subjects with mild cognitive impairment who remained stable over three years (MCI) and those who converted to AD (CONV). Furthermore, we find that the entropy of the distribution of directed network motifs increased from MCI to CONV to AD, implying that the distribution of pathology is more structured in MCI but becomes less so as it progresses to CONV and further to AD. Thus, directed network motifs frequencies and distributional properties provide new insights into the progression of Alzheimer's disease as well as new imaging markers for distinguishing between normal controls, stable mild cognitive impairment, MCI converters and Alzheimer's disease. PMID:25879535

  5. Receiver bandwidth effects on complex modulation and detection using directly modulated lasers.

    PubMed

    Yuan, Feng; Che, Di; Shieh, William

    2016-05-01

    Directly modulated lasers (DMLs) have long been employed for short- and medium-reach optical communications due to their low cost. Recently, a new modulation scheme called complex modulated DMLs has been demonstrated showing a significant optical signal to noise ratio sensitivity enhancement compared with the traditional intensity-only detection scheme. However, chirp-induced optical spectrum broadening is inevitable in complex modulated systems, which may imply a need for high-bandwidth receivers. In this Letter, we study the impact of receiver bandwidth effects on the performance of complex modulation and coherent detection systems based on DMLs. We experimentally demonstrate that such systems exhibit a reasonable tolerance for the reduced receiver bandwidth. For 10 Gbaud 4-level pulse amplitude modulation signals, the required electrical bandwidth is as low as 8.5 and 7.5 GHz for 7% and 20% forward error correction, respectively. Therefore, it is feasible to realize DML-based complex modulated systems using cost-effective receivers with narrow bandwidth. PMID:27128069

  6. Module-Based Association Analysis for Omics Data with Network Structure

    PubMed Central

    Wang, Zhi; Maity, Arnab; Hsiao, Chuhsing Kate; Voora, Deepak; Kaddurah-Daouk, Rima; Tzeng, Jung-Ying

    2015-01-01

    Module-based analysis (MBA) aims to evaluate the effect of a group of biological elements sharing common features, such as SNPs in the same gene or metabolites in the same pathways, and has become an attractive alternative to traditional single bio-element approaches. Because bio-elements regulate and interact with each other as part of network, incorporating network structure information can more precisely model the biological effects, enhance the ability to detect true associations, and facilitate our understanding of the underlying biological mechanisms. How-ever, most MBA methods ignore the network structure information, which depicts the interaction and regulation relationship among basic functional units in biology system. We construct the con-nectivity kernel and the topology kernel to capture the relationship among bio-elements in a mod-ule, and use a kernel machine framework to evaluate the joint effect of bio-elements. Our proposed kernel machine approach directly incorporates network structure so to enhance the study effi-ciency; it can assess interactions among modules, account covariates, and is computational effi-cient. Through simulation studies and real data application, we demonstrate that the proposed network-based methods can have markedly better power than the approaches ignoring network information under a range of scenarios. PMID:25822417

  7. Extracting weights from edge directions to find communities in directed networks

    NASA Astrophysics Data System (ADS)

    Lai, Darong; Lu, Hongtao; Nardini, Christine

    2010-06-01

    Community structures are found to exist ubiquitously in real-world complex networks. We address here the problem of community detection in directed networks. Most of the previous literature ignores edge directions and applies methods designed for community detection in undirected networks, which discards valuable information and often fails when different communities are defined on the basis of incoming and outgoing edges. We suggest extracting information about edge directions using a PageRank random walk and translating such information into edge weights. After extraction we obtain a new weighted directed network in which edge directions can then be safely ignored. We thus transform community detection in directed networks into community detection in reweighted undirected networks. Such an approach can benefit directly from the large volume of algorithms for the detection of communities in undirected networks already developed, since it is not obvious how to extend these algorithms to account for directed networks and the procedure is often difficult. Validations on synthetic and real-world networks demonstrate that the proposed framework can effectively detect communities in directed networks.

  8. Fast Fragmentation of Networks Using Module-Based Attacks

    PubMed Central

    Requião da Cunha, Bruno; González-Avella, Juan Carlos; Gonçalves, Sebastián

    2015-01-01

    In the multidisciplinary field of Network Science, optimization of procedures for efficiently breaking complex networks is attracting much attention from a practical point of view. In this contribution, we present a module-based method to efficiently fragment complex networks. The procedure firstly identifies topological communities through which the network can be represented using a well established heuristic algorithm of community finding. Then only the nodes that participate of inter-community links are removed in descending order of their betweenness centrality. We illustrate the method by applying it to a variety of examples in the social, infrastructure, and biological fields. It is shown that the module-based approach always outperforms targeted attacks to vertices based on node degree or betweenness centrality rankings, with gains in efficiency strongly related to the modularity of the network. Remarkably, in the US power grid case, by deleting 3% of the nodes, the proposed method breaks the original network in fragments which are twenty times smaller in size than the fragments left by betweenness-based attack. PMID:26569610

  9. Fast Fragmentation of Networks Using Module-Based Attacks.

    PubMed

    Requio da Cunha, Bruno; Gonzlez-Avella, Juan Carlos; Gonalves, Sebastin

    2015-01-01

    In the multidisciplinary field of Network Science, optimization of procedures for efficiently breaking complex networks is attracting much attention from a practical point of view. In this contribution, we present a module-based method to efficiently fragment complex networks. The procedure firstly identifies topological communities through which the network can be represented using a well established heuristic algorithm of community finding. Then only the nodes that participate of inter-community links are removed in descending order of their betweenness centrality. We illustrate the method by applying it to a variety of examples in the social, infrastructure, and biological fields. It is shown that the module-based approach always outperforms targeted attacks to vertices based on node degree or betweenness centrality rankings, with gains in efficiency strongly related to the modularity of the network. Remarkably, in the US power grid case, by deleting 3% of the nodes, the proposed method breaks the original network in fragments which are twenty times smaller in size than the fragments left by betweenness-based attack. PMID:26569610

  10. Quantitative assessment of gene expression network module-validation methods

    PubMed Central

    Li, Bing; Zhang, Yingying; Yu, Yanan; Wang, Pengqian; Wang, Yongcheng; Wang, Zhong; Wang, Yongyan

    2015-01-01

    Validation of pluripotent modules in diverse networks holds enormous potential for systems biology and network pharmacology. An arising challenge is how to assess the accuracy of discovering all potential modules from multi-omic networks and validating their architectural characteristics based on innovative computational methods beyond function enrichment and biological validation. To display the framework progress in this domain, we systematically divided the existing Computational Validation Approaches based on Modular Architecture (CVAMA) into topology-based approaches (TBA) and statistics-based approaches (SBA). We compared the available module validation methods based on 11 gene expression datasets, and partially consistent results in the form of homogeneous models were obtained with each individual approach, whereas discrepant contradictory results were found between TBA and SBA. The TBA of the Zsummary value had a higher Validation Success Ratio (VSR) (51%) and a higher Fluctuation Ratio (FR) (80.92%), whereas the SBA of the approximately unbiased (AU) p-value had a lower VSR (12.3%) and a lower FR (45.84%). The Gray area simulated study revealed a consistent result for these two models and indicated a lower Variation Ratio (VR) (8.10%) of TBA at 6 simulated levels. Despite facing many novel challenges and evidence limitations, CVAMA may offer novel insights into modular networks. PMID:26470848

  11. Modules of human micro-RNA co-target network

    NASA Astrophysics Data System (ADS)

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

    2011-05-01

    Human micro RNAs (miRNAs) target about 90% of the coding genes and form a complex regulatory network. We study the community structure of the miRNA co-target network considering miRNAs as the nodes which are connected by weighted links. The weight of link that connects a pair of miRNAs denote the total number of common transcripts targeted by that pair. We argue that the network consists of about 74 modules, quite similar to the components (or clusters) obtained earlier [Online J Bioinformatics, 10,280], indicating that the components of the miRNA co-target network are self organized in a way to maximize the modularity.

  12. Link module for a downhole drilling network

    DOEpatents

    Hall, David R.; Fox, Joe

    2007-05-29

    A repeater is disclosed in one embodiment of the present invention as including a cylindrical housing, characterized by a proximal end and a distal end, and having a substantially cylindrical wall, the cylindrical wall defining a central bore passing therethrough. The cylindrical housing is formed to define at least one recess in the cylindrical wall, into which a repeater is inserted. The cylindrical housing also includes an annular recess formed into at least one of the proximal end and the distal end. An annular transmission element, operably connected to the repeater, is located in the annular recess. In selected embodiments, the annular transmission element inductively converts electrical energy to magnetic energy. In other embodiments, the annular transmission element includes an electrical contact to transmit electrical energy directly to another contact.

  13. Transient mode competition in directly modulated DFB semiconductor laser

    NASA Astrophysics Data System (ADS)

    Xiao, RuLei; Shi, YueChun; Zheng, JiLin; Zhang, YunShan; Zheng, JunShou; Chen, XiangFei

    2015-12-01

    A new effect of transient mode competition in directly modulated DFB laser based on equivalent phase-shift (EPS) technique is presented and studied. Since there are multi-order reflections in EPS structure and if the 0th order subgrating is properly designed, the transient lasing of 0th order will occur during the rising time of the injection current. As a result, transient mode competition between -1st order (main mode) and 0th order will occur accordingly. This can consume redundant carrier and suppress the transient relaxation oscillation, which may be applied in some areas like on-off switching modulation of DFB semiconductor lasers. As an example, an equivalent π phase shift (π-EPS) is carefully designed to realize the effect. In such a laser the 0th order wavelength is in the margin of the material gain region and the -1st order wavelength is around the gain peak, while the stable single longitudinal mode (SLM) operation of the -1st order is guaranteed. The simulation investigation is performed. Good results with suppressed relaxation oscillation and 1.25 Gb/s directly on-off modulation (32 dB extinction ratio) are demonstrated. We believe it provides a new kind of method for on-off switching with high extinction ratio and weak relaxation oscillation.

  14. A directed network of Greek and Roman mythology

    NASA Astrophysics Data System (ADS)

    Choi, Yeon-Mu; Kim, Hyun-Joo

    2007-08-01

    We construct a directed network using a dictionary of Greek and Roman mythology in which the nodes represent the entries listed in the dictionary and we make directional links from an entry to other entries that appear in its explanatory part. We find that this network is clearly not a random network but a directed scale-free network in which the distributions of out-degree and in-degree follow a power-law with exponents γout≈3.0 and γin≈2.5, respectively. Also we measure several quantities which describe the topological properties of the network and compare it to that of other real networks.

  15. Smelling directions: olfaction modulates ambiguous visual motion perception.

    PubMed

    Kuang, Shenbing; Zhang, Tao

    2014-01-01

    Senses of smells are often accompanied by simultaneous visual sensations. Previous studies have documented enhanced olfactory performance with concurrent presence of congruent color- or shape- related visual cues, and facilitated visual object perception when congruent smells are simultaneously present. These visual object-olfaction interactions suggest the existences of couplings between the olfactory pathway and the visual ventral processing stream. However, it is not known if olfaction can modulate visual motion perception, a function that is related to the visual dorsal stream. We tested this possibility by examining the influence of olfactory cues on the perceptions of ambiguous visual motion signals. We showed that, after introducing an association between motion directions and olfactory cues, olfaction could indeed bias ambiguous visual motion perceptions. Our result that olfaction modulates visual motion processing adds to the current knowledge of cross-modal interactions and implies a possible functional linkage between the olfactory system and the visual dorsal pathway. PMID:25052162

  16. Task induced modulation of neural oscillations in electrophysiological brain networks.

    PubMed

    Brookes, M J; Liddle, E B; Hale, J R; Woolrich, M W; Luckhoo, H; Liddle, P F; Morris, P G

    2012-12-01

    In recent years, one of the most important findings in systems neuroscience has been the identification of large scale distributed brain networks. These networks support healthy brain function and are perturbed in a number of neurological disorders (e.g. schizophrenia). Their study is therefore an important and evolving focus for neuroscience research. The majority of network studies are conducted using functional magnetic resonance imaging (fMRI) which relies on changes in blood oxygenation induced by neural activity. However recently, a small number of studies have begun to elucidate the electrical origin of fMRI networks by searching for correlations between neural oscillatory signals from spatially separate brain areas in magnetoencephalography (MEG) data. Here we advance this research area. We introduce two methodological extensions to previous independent component analysis (ICA) approaches to MEG network characterisation: 1) we show how to derive pan-spectral networks that combine independent components computed within individual frequency bands. 2) We show how to measure the temporal evolution of each network with millisecond temporal resolution. We apply our approach to ~10h of MEG data recorded in 28 experimental sessions during 3 separate cognitive tasks showing that a number of networks could be identified and were robust across time, task, subject and recording session. Further, we show that neural oscillations in those networks are modulated by memory load, and task relevance. This study furthers recent findings on electrodynamic brain networks and paves the way for future clinical studies in patients in which abnormal connectivity is thought to underlie core symptoms. PMID:22906787

  17. The Direct Digital Modulation of Traveling Wave Tubes

    NASA Technical Reports Server (NTRS)

    Radhamohan, Ranjan S.

    2004-01-01

    Traveling wave tube (TWT) technology, first described by Rudolf Kompfner in the early 1940s, has been a key component of space missions from the earliest communication satellites in the 1960s to the Cassini probe today. TWTs are essentially signal amplifiers that have the special capability of operating at microwave frequencies. The microwave frequency range, which spans from approximately 500 MHz to 300 GHz, is shared by many technologies including cellular phones, satellite television, space communication, and radar. TWT devices are superior in reliability, weight, and efficiency to solid-state amplifiers at the high power and frequency levels required for most space missions. TWTs have three main components -an electron gun, slow wave structure, and collector. The electron gun generates an electron beam that moves along the length of the tube axis, inside of the slow wave circuit. At the same time, the inputted signal is slowed by its travel through the coils of the helical slow wave circuit. The interaction of the electron beam and this slowed signal produces a transfer of kinetic energy to the signal, and in turn, amplification. At the end of its travel, the spent electron beam moves into the collector where its remaining energy is dissipated as heat or harnessed for reuse. TWTs can easily produce gains in the tens of decibels, numbers that are suitable for space missions. To date, however, TWTs have typically operated at fixed levels of gain. This gain is determined by various, unchanging, physical factors of the tube. Traditionally, to achieve varying gain, an input signal s amplitude has had to first be modulated by a separate device before being fed into the TWT. This is not always desirable, as significant distortion can occur in certain situations. My mentor, Mr. Dale Force, has proposed an innovative solution to this problem called direct digital modulation . The testing and implementation of this solution is the focus of my summer internship. The direct digital modulation of a TWT removes the need for a separate amplitude modulation device. Instead, different levels of gain are achieved by varying the electron beam current. The lower the current, the less kinetic energy is available to be transferred to the signal. To vary the current, a grid is placed in-between the electron gun and the slow wave circuit. By changing the voltage across the grid, the electron beam current can be controlled. Grid technology has mostly been used in pulse applications such as radar, where only two voltage states are necessary. For direct digital modulation, however, a continuous range of voltages is required.

  18. Nitric oxide-mediated modulation of the murine locomotor network

    PubMed Central

    Foster, Joshua D.; Dunford, Catherine; Sillar, Keith T.

    2013-01-01

    Spinal motor control networks are regulated by neuromodulatory systems to allow adaptability of movements. The present study aimed to elucidate the role of nitric oxide (NO) in the modulation of mammalian spinal locomotor networks. This was investigated with isolated spinal cord preparations from neonatal mice in which rhythmic locomotor-related activity was induced pharmacologically. Bath application of the NO donor diethylamine NONOate (DEA/NO) decreased the frequency and modulated the amplitude of locomotor-related activity recorded from ventral roots. Removal of endogenous NO with coapplication of a NO scavenger (PTIO) and a nitric oxide synthase (NOS) blocker [nitro-l-arginine methyl ester (l-NAME)] increased the frequency and decreased the amplitude of locomotor-related activity. This demonstrates that endogenously derived NO can modulate both the timing and intensity of locomotor-related activity. The effects of DEA/NO were mimicked by the cGMP analog 8-bromo-cGMP. In addition, the soluble guanylyl cyclase (sGC) inhibitor ODQ blocked the effects of DEA/NO on burst amplitude and frequency, although the frequency effect was only blocked at low concentrations of DEA/NO. This suggests that NO-mediated modulation involves cGMP-dependent pathways. Sources of NO were studied within the lumbar spinal cord during postnatal development (postnatal days 1–12) with NADPH-diaphorase staining. NOS-positive cells in the ventral horn exhibited a rostrocaudal gradient, with more cells in rostral segments. The number of NOS-positive cells was also found to increase during postnatal development. In summary, we have shown that NO, derived from sources within the mammalian spinal cord, modulates the output of spinal motor networks and is therefore likely to contribute to the fine-tuning of locomotor behavior. PMID:24259545

  19. Pro-cognitive drug effects modulate functional brain network organization

    PubMed Central

    Giessing, Carsten; Thiel, Christiane M.

    2012-01-01

    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

  20. Stimulation of Glia Reveals Modulation of Mammalian Spinal Motor Networks by Adenosine.

    PubMed

    Acton, David; Miles, Gareth B

    2015-01-01

    Despite considerable evidence that glia can release modulators to influence the excitability of neighbouring neurons, the importance of gliotransmission for the operation of neural networks and in shaping behaviour remains controversial. Here we characterise the contribution of glia to the modulation of the mammalian spinal central pattern generator for locomotion, the output of which is directly relatable to a defined behaviour. Glia were stimulated by specific activation of protease-activated receptor-1 (PAR1), an endogenous G-protein coupled receptor preferentially expressed by spinal glia during ongoing activity of the spinal central pattern generator for locomotion. Selective activation of PAR1 by the agonist TFLLR resulted in a reversible reduction in the frequency of locomotor-related bursting recorded from ventral roots of spinal cord preparations isolated from neonatal mice. In the presence of the gliotoxins methionine sulfoximine or fluoroacetate, TFLLR had no effect, confirming the specificity of PAR1 activation to glia. The modulation of burst frequency upon PAR1 activation was blocked by the non-selective adenosine-receptor antagonist theophylline and by the A1-receptor antagonist 8-cyclopentyl-1,3-dipropylxanthine, but not by the A2A-receptor antagonist SCH5826, indicating production of extracellular adenosine upon glial stimulation, followed by A1-receptor mediated inhibition of neuronal activity. Modulation of network output following glial stimulation was also blocked by the ectonucleotidase inhibitor ARL67156, indicating glial release of ATP and its subsequent degradation to adenosine rather than direct release of adenosine. Glial stimulation had no effect on rhythmic activity recorded following blockade of inhibitory transmission, suggesting that glial cell-derived adenosine acts via inhibitory circuit components to modulate locomotor-related output. Finally, the modulation of network output by endogenous adenosine was found to scale with the frequency of network activity, implying activity-dependent release of adenosine. Together, these data indicate that glia play an active role in the modulation of mammalian locomotor networks, providing negative feedback control that may stabilise network activity. PMID:26252389

  1. Stimulation of Glia Reveals Modulation of Mammalian Spinal Motor Networks by Adenosine

    PubMed Central

    Acton, David; Miles, Gareth B.

    2015-01-01

    Despite considerable evidence that glia can release modulators to influence the excitability of neighbouring neurons, the importance of gliotransmission for the operation of neural networks and in shaping behaviour remains controversial. Here we characterise the contribution of glia to the modulation of the mammalian spinal central pattern generator for locomotion, the output of which is directly relatable to a defined behaviour. Glia were stimulated by specific activation of protease-activated receptor-1 (PAR1), an endogenous G-protein coupled receptor preferentially expressed by spinal glia during ongoing activity of the spinal central pattern generator for locomotion. Selective activation of PAR1 by the agonist TFLLR resulted in a reversible reduction in the frequency of locomotor-related bursting recorded from ventral roots of spinal cord preparations isolated from neonatal mice. In the presence of the gliotoxins methionine sulfoximine or fluoroacetate, TFLLR had no effect, confirming the specificity of PAR1 activation to glia. The modulation of burst frequency upon PAR1 activation was blocked by the non-selective adenosine-receptor antagonist theophylline and by the A1-receptor antagonist 8-cyclopentyl-1,3-dipropylxanthine, but not by the A2A-receptor antagonist SCH5826, indicating production of extracellular adenosine upon glial stimulation, followed by A1-receptor mediated inhibition of neuronal activity. Modulation of network output following glial stimulation was also blocked by the ectonucleotidase inhibitor ARL67156, indicating glial release of ATP and its subsequent degradation to adenosine rather than direct release of adenosine. Glial stimulation had no effect on rhythmic activity recorded following blockade of inhibitory transmission, suggesting that glial cell-derived adenosine acts via inhibitory circuit components to modulate locomotor-related output. Finally, the modulation of network output by endogenous adenosine was found to scale with the frequency of network activity, implying activity-dependent release of adenosine. Together, these data indicate that glia play an active role in the modulation of mammalian locomotor networks, providing negative feedback control that may stabilise network activity. PMID:26252389

  2. Experimental demonstration of large capacity WSDM optical access network with multicore fibers and advanced modulation formats.

    PubMed

    Li, Borui; Feng, Zhenhua; Tang, Ming; Xu, Zhilin; Fu, Songnian; Wu, Qiong; Deng, Lei; Tong, Weijun; Liu, Shuang; Shum, Perry Ping

    2015-05-01

    Towards the next generation optical access network supporting large capacity data transmission to enormous number of users covering a wider area, we proposed a hybrid wavelength-space division multiplexing (WSDM) optical access network architecture utilizing multicore fibers with advanced modulation formats. As a proof of concept, we experimentally demonstrated a WSDM optical access network with duplex transmission using our developed and fabricated multicore (7-core) fibers with 58.7km distance. As a cost-effective modulation scheme for access network, the optical OFDM-QPSK signal has been intensity modulated on the downstream transmission in the optical line terminal (OLT) and it was directly detected in the optical network unit (ONU) after MCF transmission. 10 wavelengths with 25GHz channel spacing from an optical comb generator are employed and each wavelength is loaded with 5Gb/s OFDM-QPSK signal. After amplification, power splitting, and fan-in multiplexer, 10-wavelength downstream signal was injected into six outer layer cores simultaneously and the aggregation downstream capacity reaches 300 Gb/s. -16 dBm sensitivity has been achieved for 3.8 × 10-3 bit error ratio (BER) with 7% Forward Error Correction (FEC) limit for all wavelengths in every core. Upstream signal from ONU side has also been generated and the bidirectional transmission in the same core causes negligible performance degradation to the downstream signal. As a universal platform for wired/wireless data access, our proposed architecture provides additional dimension for high speed mobile signal transmission and we hence demonstrated an upstream delivery of 20Gb/s per wavelength with QPSK modulation formats using the inner core of MCF emulating a mobile backhaul service. The IQ modulated data was coherently detected in the OLT side. -19 dBm sensitivity has been achieved under the FEC limit and more than 18 dB power budget is guaranteed. PMID:25969194

  3. Optical modulation of astrocyte network using ultrashort pulsed laser

    NASA Astrophysics Data System (ADS)

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

    2012-03-01

    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.

  4. RMaNI: Regulatory Module Network Inference framework

    PubMed Central

    2013-01-01

    Background Cell survival and development are orchestrated by complex interlocking programs of gene activation and repression. Understanding how this gene regulatory network (GRN) functions in normal states, and is altered in cancers subtypes, offers fundamental insight into oncogenesis and disease progression, and holds great promise for guiding clinical decisions. Inferring a GRN from empirical microarray gene expression data is a challenging task in cancer systems biology. In recent years, module-based approaches for GRN inference have been proposed to address this challenge. Despite the demonstrated success of module-based approaches in uncovering biologically meaningful regulatory interactions, their application remains limited a single condition, without supporting the comparison of multiple disease subtypes/conditions. Also, their use remains unnecessarily restricted to computational biologists, as accurate inference of modules and their regulators requires integration of diverse tools and heterogeneous data sources, which in turn requires scripting skills, data infrastructure and powerful computational facilities. New analytical frameworks are required to make module-based GRN inference approach more generally useful to the research community. Results We present the RMaNI (Regulatory Module Network Inference) framework, which supports cancer subtype-specific or condition specific GRN inference and differential network analysis. It combines both transcriptomic as well as genomic data sources, and integrates heterogeneous knowledge resources and a set of complementary bioinformatic methods for automated inference of modules, their condition specific regulators and facilitates downstream network analyses and data visualization. To demonstrate its utility, we applied RMaNI to a hepatocellular microarray data containing normal and three disease conditions. We demonstrate that how RMaNI can be employed to understand the genetic architecture underlying three disease conditions. RMaNI is freely available at http://inspect.braembl.org.au/bi/inspect/rmani Conclusion RMaNI makes available a workflow with comprehensive set of tools that would otherwise be challenging for non-expert users to install and apply. The framework presented in this paper is flexible and can be easily extended to analyse any dataset with multiple disease conditions. PMID:24564496

  5. Almost decouplability of any directed weighted network topology

    NASA Astrophysics Data System (ADS)

    Cai, Ning; Cao, Jun-Wei; Khan, M. Junaid

    2015-10-01

    This paper introduces a conception that any weighted directed network topology is almost decouplable, which can help to transform the topology into a similar form composed of uncoupled vertices, and thus reduce the complexity of analysis for networked dynamical systems. As an example of its application, the consensus problem of linear multi-agent systems with time-varying network topologies is addressed. As a result, a necessary and sufficient condition for uniform consensus is proposed.

  6. Contextual Modulation is Related to Efficiency in a Spiking Network Model of Visual Cortex

    PubMed Central

    Sharifian, Fariba; Heikkinen, Hanna; Vigário, Ricardo; Vanni, Simo

    2016-01-01

    In the visual cortex, stimuli outside the classical receptive field (CRF) modulate the neural firing rate, without driving the neuron by themselves. In the primary visual cortex (V1), such contextual modulation can be parametrized with an area summation function (ASF): increasing stimulus size causes first an increase and then a decrease of firing rate before reaching an asymptote. Earlier work has reported increase of sparseness when CRF stimulation is extended to its surroundings. However, there has been no clear connection between the ASF and network efficiency. Here we aimed to investigate possible link between ASF and network efficiency. In this study, we simulated the responses of a biomimetic spiking neural network model of the visual cortex to a set of natural images. We varied the network parameters, and compared the V1 excitatory neuron spike responses to the corresponding responses predicted from earlier single neuron data from primate visual cortex. The network efficiency was quantified with firing rate (which has direct association to neural energy consumption), entropy per spike and population sparseness. All three measures together provided a clear association between the network efficiency and the ASF. The association was clear when varying the horizontal connectivity within V1, which influenced both the efficiency and the distance to ASF, DAS. Given the limitations of our biophysical model, this association is qualitative, but nevertheless suggests that an ASF-like receptive field structure can cause efficient population response. PMID:26834619

  7. Smart Capture Modules for Direct Sensor-to-FPGA Interfaces.

    PubMed

    Oballe-Peinado, Óscar; Vidal-Verdú, Fernando; Sánchez-Durán, José A; Castellanos-Ramos, Julián; Hidalgo-López, José A

    2015-01-01

    Direct sensor-digital device interfaces measure time dependent variables of simple circuits to implement analog-to-digital conversion. Field Programmable Gate Arrays (FPGAs) are devices whose hardware can be reconfigured to work in parallel. They usually do not have analog-to-digital converters, but have many general purpose I/O pins. Therefore, direct sensor-FPGA connection is a good choice in complex systems with many sensors because several capture modules can be implemented to perform parallel analog data acquisition. The possibility to work in parallel and with high frequency clock signals improves the bandwidth compared to sequential devices such as conventional microcontrollers. The price to pay is usually the resolution of measurements. This paper proposes capture modules implemented in an FPGA which are able to perform smart acquisition that filter noise and achieve high precision. A calibration technique is also proposed to improve accuracy. Resolutions of 12 effective number of bits are obtained for the reading of resistors in the range of an example piezoresistive tactile sensor. PMID:26694403

  8. Smart Capture Modules for Direct Sensor-to-FPGA Interfaces

    PubMed Central

    Oballe-Peinado, Óscar; Vidal-Verdú, Fernando; Sánchez-Durán, José A.; Castellanos-Ramos, Julián; Hidalgo-López, José A.

    2015-01-01

    Direct sensor–digital device interfaces measure time dependent variables of simple circuits to implement analog-to-digital conversion. Field Programmable Gate Arrays (FPGAs) are devices whose hardware can be reconfigured to work in parallel. They usually do not have analog-to-digital converters, but have many general purpose I/O pins. Therefore, direct sensor-FPGA connection is a good choice in complex systems with many sensors because several capture modules can be implemented to perform parallel analog data acquisition. The possibility to work in parallel and with high frequency clock signals improves the bandwidth compared to sequential devices such as conventional microcontrollers. The price to pay is usually the resolution of measurements. This paper proposes capture modules implemented in an FPGA which are able to perform smart acquisition that filter noise and achieve high precision. A calibration technique is also proposed to improve accuracy. Resolutions of 12 effective number of bits are obtained for the reading of resistors in the range of an example piezoresistive tactile sensor. PMID:26694403

  9. The theory of pattern formation on directed networks.

    PubMed

    Asllani, Malbor; Challenger, Joseph D; Pavone, Francesco Saverio; Sacconi, Leonardo; Fanelli, Duccio

    2014-01-01

    Dynamical processes on networks have generated widespread interest in recent years. The theory of pattern formation in reaction-diffusion systems defined on symmetric networks has often been investigated, due to its applications in a wide range of disciplines. Here we extend the theory to the case of directed networks, which are found in a number of different fields, such as neuroscience, computer networks and traffic systems. Owing to the structure of the network Laplacian, the dispersion relation has both real and imaginary parts, at variance with the case for a symmetric, undirected network. The homogeneous fixed point can become unstable due to the topology of the network, resulting in a new class of instabilities, which cannot be induced on undirected graphs. Results from a linear stability analysis allow the instability region to be analytically traced. Numerical simulations show travelling waves, or quasi-stationary patterns, depending on the characteristics of the underlying graph. PMID:25077521

  10. Identification of Important Nodes in Directed Biological Networks: A Network Motif Approach

    PubMed Central

    Wang, Pei; Lü, Jinhu; Yu, Xinghuo

    2014-01-01

    Identification of important nodes in complex networks has attracted an increasing attention over the last decade. Various measures have been proposed to characterize the importance of nodes in complex networks, such as the degree, betweenness and PageRank. Different measures consider different aspects of complex networks. Although there are numerous results reported on undirected complex networks, few results have been reported on directed biological networks. Based on network motifs and principal component analysis (PCA), this paper aims at introducing a new measure to characterize node importance in directed biological networks. Investigations on five real-world biological networks indicate that the proposed method can robustly identify actually important nodes in different networks, such as finding command interneurons, global regulators and non-hub but evolutionary conserved actually important nodes in biological networks. Receiver Operating Characteristic (ROC) curves for the five networks indicate remarkable prediction accuracy of the proposed measure. The proposed index provides an alternative complex network metric. Potential implications of the related investigations include identifying network control and regulation targets, biological networks modeling and analysis, as well as networked medicine. PMID:25170616

  11. Identification of important nodes in directed biological networks: a network motif approach.

    PubMed

    Wang, Pei; Lü, Jinhu; Yu, Xinghuo

    2014-01-01

    Identification of important nodes in complex networks has attracted an increasing attention over the last decade. Various measures have been proposed to characterize the importance of nodes in complex networks, such as the degree, betweenness and PageRank. Different measures consider different aspects of complex networks. Although there are numerous results reported on undirected complex networks, few results have been reported on directed biological networks. Based on network motifs and principal component analysis (PCA), this paper aims at introducing a new measure to characterize node importance in directed biological networks. Investigations on five real-world biological networks indicate that the proposed method can robustly identify actually important nodes in different networks, such as finding command interneurons, global regulators and non-hub but evolutionary conserved actually important nodes in biological networks. Receiver Operating Characteristic (ROC) curves for the five networks indicate remarkable prediction accuracy of the proposed measure. The proposed index provides an alternative complex network metric. Potential implications of the related investigations include identifying network control and regulation targets, biological networks modeling and analysis, as well as networked medicine. PMID:25170616

  12. Pseudophosphorylation of tau protein directly modulates its aggregation kinetics

    PubMed Central

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

    2010-01-01

    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. PMID:20974297

  13. Space station common module network topology and hardware development

    NASA Technical Reports Server (NTRS)

    Anderson, P.; Braunagel, L.; Chwirka, S.; Fishman, M.; Freeman, K.; Eason, D.; Landis, D.; Lech, L.; Martin, J.; Mccorkle, J.

    1990-01-01

    Conceptual space station common module power management and distribution (SSM/PMAD) network layouts and detailed network evaluations were developed. Individual pieces of hardware to be developed for the SSM/PMAD test bed were identified. A technology assessment was developed to identify pieces of equipment requiring development effort. Equipment lists were developed from the previously selected network schematics. Additionally, functional requirements for the network equipment as well as other requirements which affected the suitability of specific items for use on the Space Station Program were identified. Assembly requirements were derived based on the SSM/PMAD developed requirements and on the selected SSM/PMAD network concepts. Basic requirements and simplified design block diagrams are included. DC remote power controllers were successfully integrated into the DC Marshall Space Flight Center breadboard. Two DC remote power controller (RPC) boards experienced mechanical failure of UES 706 stud-mounted diodes during mechanical installation of the boards into the system. These broken diodes caused input to output shorting of the RPC's. The UES 706 diodes were replaced on these RPC's which eliminated the problem. The DC RPC's as existing in the present breadboard configuration do not provide ground fault protection because the RPC was designed to only switch the hot side current. If ground fault protection were to be implemented, it would be necessary to design the system so the RPC switched both the hot and the return sides of power.

  14. Serotonin targets inhibitory synapses to induce modulation of network functions

    PubMed Central

    Manzke, Till; Dutschmann, Mathias; Schlaf, Gerald; Mörschel, Michael; Koch, Uwe R.; Ponimaskin, Evgeni; Bidon, Olivier; Lalley, Peter M.; Richter, Diethelm W.

    2009-01-01

    The cellular effects of serotonin (5-HT), a neuromodulator with widespread influences in the central nervous system, have been investigated. Despite detailed knowledge about the molecular biology of cellular signalling, it is not possible to anticipate the responses of neuronal networks to a global action of 5-HT. Heterogeneous expression of various subtypes of serotonin receptors (5-HTR) in a variety of neurons differently equipped with cell-specific transmitter receptors and ion channel assemblies can provoke diverse cellular reactions resulting in various forms of network adjustment and, hence, motor behaviour. Using the respiratory network as a model for reciprocal synaptic inhibition, we demonstrate that 5-HT1AR modulation primarily affects inhibition through glycinergic synapses. Potentiation of glycinergic inhibition of both excitatory and inhibitory neurons induces a functional reorganization of the network leading to a characteristic change of motor output. The changes in network operation are robust and help to overcome opiate-induced respiratory depression. Hence, 5-HT1AR activation stabilizes the rhythmicity of breathing during opiate medication of pain. PMID:19651659

  15. Directed progression brain networks in Alzheimer's disease: properties and classification.

    PubMed

    Friedman, Eric J; Young, Karl; Asif, Danial; Jutla, Inderjit; Liang, Michael; Wilson, Scott; Landsberg, Adam S; Schuff, Norbert

    2014-06-01

    This article introduces a new approach in brain connectomics aimed at characterizing the temporal spread in the brain of pathologies like Alzheimer's disease (AD). The main instrument is the development of "directed progression networks" (DPNets), wherein one constructs directed edges between nodes based on (weakly) inferred directions of the temporal spreading of the pathology. This stands in contrast to many previously studied brain networks where edges represent correlations, physical connections, or functional progressions. In addition, this is one of a few studies showing the value of using directed networks in the study of AD. This article focuses on the construction of DPNets for AD using longitudinal cortical thickness measurements from magnetic resonance imaging data. The network properties are then characterized, providing new insights into AD progression, as well as novel markers for differentiating normal cognition (NC) and AD at the group level. It also demonstrates the important role of nodal variations for network classification (i.e., the significance of standard deviations, not just mean values of nodal properties). Finally, the DPNets are utilized to classify subjects based on their global network measures using a variety of data-mining methodologies. In contrast to most brain networks, these DPNets do not show high clustering and small-world properties. PMID:24901258

  16. Gaze Direction Modulates the Relation between Neural Responses to Faces and Visual Awareness.

    PubMed

    Madipakkam, Apoorva Rajiv; Rothkirch, Marcus; Guggenmos, Matthias; Heinz, Andreas; Sterzer, Philipp

    2015-09-30

    Gaze direction and especially direct gaze is a powerful nonverbal cue that plays an important role in social interactions. Here we studied the neural mechanisms underlying the privileged access of direct gaze to visual awareness. We performed functional magnetic resonance imaging in healthy human volunteers who were exposed to faces with direct or averted gaze under continuous flash suppression, thereby manipulating their awareness of the faces. A gaze processing network comprising fusiform face area (FFA), superior temporal sulcus, amygdala, and intraparietal sulcus showed overall reduced neural responses when participants reported to be unaware of the faces. Interestingly, direct gaze elicited greater responses than averted gaze when participants were aware of the faces, but smaller responses when they were unaware. Additional between-subject correlation and single-trial analyses indicated that this pattern of results was due to a modulation of the relationship between neural responses and awareness by gaze direction: with increasing neural activation in the FFA, direct-gaze faces entered awareness more readily than averted-gaze faces. These findings suggest that for direct gaze, lower levels of neural activity are sufficient to give rise to awareness than for averted gaze, thus providing a neural basis for privileged access of direct gaze to awareness. Significance statement: Another person's eye gaze directed at oneself is a powerful social signal acting as a catalyst for further communication. Here, we studied the neural mechanisms underlying the prioritized access of direct gaze to visual awareness in healthy human volunteers and show that with increasing neural activation, direct-gaze faces enter awareness more readily than averted-gaze faces. This suggests that for a socially highly relevant cue like direct gaze, lower levels of neural activity are sufficient to give rise to awareness compared with averted gaze, possibly because the human brain is attuned to the efficient neural processing of direct gaze due to the biological importance of eye contact for social interactions. PMID:26424878

  17. The cascading vulnerability of the directed and weighted network

    NASA Astrophysics Data System (ADS)

    Jin, Wei-Xin; Song, Ping; Liu, Guo-Zhu; Stanley, H. Eugene

    2015-06-01

    The cascading failure can bring a huge loss for most real-world networks; but, we cannot uncover fully the mechanism and law of the cascading events occurrence. Most networks in which the cascading failure occurred are based on the various 'flows', such as power, oils, and information; moreover, the same link degree of the different nodes likely contain the different meanings, where some are large pivotal nodes and some are mini switching centers. Thus, these networks must be described by the directed and weighted network model. Besides, the 'over-loading' cascading failures were more analyzed and studied; but the cascading failures caused by 'short-loading' were less studied relatively. However, for some directed networks, such as power grids, oil pipe nets, gas pipe nets and information networks, the large-scale failures of network nodes substantially could be induced by 'short-loading' in a such similar way as 'over-loading'. Based on the above reasons, in this paper, we first built the 'load-capacity' model of the directed and weighted network. Afterwards the 'over-loading' cascading failure model and the 'short-loading' cascading failure model based on the directed and weighted network were built. Meanwhile, applying the models to two typical real networks-Poisson distribution network and power law distribution network-intensive study and numerical analysis were carried out. Lastly, two classical networks simulation experiment results are provided. After the numerical and simulation analyses, we gained the following conclusions. For the power law network, the power exponent β of 'load-capacity' function should be taken value (0, 1) for a good robustness, and the minimum in-degree and out-degree should be increased respectively, meanwhile, the weight and the scaling exponents of the in-degree and the out-degree distributions should be increased synchronously in the interval (2, 3) for enhancing the resistibility of 'over-loading' and 'short-loading' failures. For the Poisson network, the power exponent β of loading function should be taken value (0, 3) for a good robustness, and the average weight and the average in-degree should be increased respectively restricting 2 < β < 3 for enhancing the resistibility of 'over-loading' and 'short-loading' failures.

  18. How familiarization and repetition modulate the picture naming network.

    PubMed

    Llorens, Anaïs; Trébuchon, Agnès; Riès, Stéphanie; Liégeois-Chauvel, Catherine; Alario, F-Xavier

    2014-06-01

    A common strategy to reveal the components of the speech production network is to use psycholinguistic manipulations previously tested in behavioral protocols. This often disregards how implementation aspects that are nonessential for interpreting behavior may affect the neural response. We compared the electrophysiological (EEG) signature of two popular picture naming protocols involving either unfamiliar pictures without repetitions or repeated familiar pictures. We observed significant semantic interference effects in behavior but not in the EEG, contrary to some previous findings. Remarkably, the two protocols elicited clearly distinct EEG responses. These were not due to naming latency differences nor did they reflect a homogeneous modulation of amplitude over the trial time-window. The effect of protocol is attributed to the familiarization induced by the first encounter with the materials. Picture naming processes can be substantially modulated by specific protocol requirements controlled by familiarity and, to a much lesser degree, the repetition of materials. PMID:24785306

  19. Sinusoidal modulation control method in a chaotic neural network

    NASA Astrophysics Data System (ADS)

    Zhang, Qihanyue; Xie, Xiaoping; Zhu, Ping; Chen, Hongping; He, Guoguang

    2014-08-01

    Chaotic neural networks (CNNs) have chaotic dynamic associative memory properties: The memory states appear non-periodically, and cannot be converged to a stored pattern. Thus, it is necessary to control chaos in a CNN in order to recognize associative memory. In this paper, a novel control method, the sinusoidal modulation control method, has been proposed to control chaos in a CNN. In this method, a sinusoidal wave simplified from brain waves is used as a control signal to modulate a parameter of the CNN. The simulation results demonstrate the effectiveness of this control method. The controlled CNN can be applied to information processing. Moreover, the method provides a way to associate brain waves by controlling CNNs.

  20. How familiarization and repetition modulate the picture naming network

    PubMed Central

    Llorens, Anaïs; Trébuchon, Agnès; Riès, Stéphanie; Liégeois-Chauvel, Catherine; Alario, F.-Xavier

    2014-01-01

    A common strategy to reveal the components of the speech production network is to use psycholinguistic manipulations previously tested in behavioral protocols. This often disregards how implementation aspects that are nonessential for interpreting behavior may affect the neural response. We compared the electrophysiological (EEG) signature of two popular picture naming protocols involving either unfamiliar pictures without repetitions or repeated familiar pictures. We observed significant semantic interference effects in behavior but not in the EEG, contrary to some previous findings. Remarkably, the two protocols elicited clearly distinct EEG responses. These were not due to naming latency differences nor did they reflect a homogeneous modulation of amplitude over the trial time-window. The effect of protocol is attributed to the familiarization induced by the first encounter with the materials. Picture naming processes can be substantially modulated by specific protocol requirements controlled by familiarity and, to a much lesser degree, the repetition of materials. PMID:24785306

  1. Magnetic vestibular stimulation modulates default mode network fluctuations.

    PubMed

    Boegle, Rainer; Stephan, Thomas; Ertl, Matthias; Glasauer, Stefan; Dieterich, Marianne

    2016-02-15

    Strong magnetic fields (>1Tesla) can cause dizziness and it was recently shown that healthy subjects (resting in total darkness) developed a persistent nystagmus even when remaining completely motionless within a MR tomograph. Consequently, it was speculated that this magnetic vestibular stimulation (MVS) might influence fMRI results, as nystagmus is indicative of an imbalance in the vestibular system, potentially influencing other systems via multisensory vestibular interactions. The objective of our study was to investigate whether MVS does indeed modulate BOLD signal fluctuations. We recorded eye movements, as well as, resting-state fMRI of 30 volunteers in darkness at 1.5T and 3.0T to answer the question whether MVS modulated parts of the default mode resting-state network (DMN) in accordance with the Lorentz-force model for MVS, while distinguishing this from the known signal increase due to field strength related imaging effects. Our results showed that modulation of the default mode network occurred mainly in areas associated with vestibular and ocular motor function, and was in accordance with the Lorentz-force model, i.e., double than the expected signal scaling due to field strength alone. We discuss the implications of our findings for the interpretation of studies using resting-state fMRI, especially those concerning vestibular research. We conclude that MVS needs to be considered in vestibular research to avoid biased results, but it might also offer the possibility of manipulating network dynamics and may thus help in studying the brain as a dynamical system. PMID:26666898

  2. Transcranial direct current stimulation modulates efficiency of reading processes

    PubMed Central

    Thomson, Jennifer M.; Doruk, Deniz; Mascio, Bryan; Fregni, Felipe; Cerruti, Carlo

    2015-01-01

    Transcranial direct current stimulation (tDCS) is a neuromodulatory technique that offers promise as an investigative method for understanding complex cognitive operations such as reading. This study explores the ability of a single session of tDCS to modulate reading efficiency and phonological processing performance within a group of healthy adults. Half the group received anodal or cathodal stimulation, on two separate days, of the left temporo-parietal junction while the other half received anodal or cathodal stimulation of the right homologue area. Pre- and post-stimulation assessment of reading efficiency and phonological processing was carried out. A larger pre-post difference in reading efficiency was found for participants who received right anodal stimulation compared to participants who received left anodal stimulation. Further, there was a significant post-stimulation increase in phonological processing speed following right hemisphere anodal stimulation. Implications for models of reading and reading impairment are discussed. PMID:25852513

  3. Network modules and hubs in plant-root fungal biomes.

    PubMed

    Toju, Hirokazu; Yamamoto, Satoshi; Tanabe, Akifumi S; Hayakawa, Takashi; Ishii, Hiroshi S

    2016-03-01

    Terrestrial plants host phylogenetically and functionally diverse groups of below-ground microbes, whose community structure controls plant growth/survival in both natural and agricultural ecosystems. Therefore, understanding the processes by which whole root-associated microbiomes are organized is one of the major challenges in ecology and plant science. We here report that diverse root-associated fungi can form highly compartmentalized networks of coexistence within host roots and that the structure of the fungal symbiont communities can be partitioned into semi-discrete types even within a single host plant population. Illumina sequencing of root-associated fungi in a monodominant south beech forest revealed that the network representing symbiont-symbiont co-occurrence patterns was compartmentalized into clear modules, which consisted of diverse functional groups of mycorrhizal and endophytic fungi. Consequently, terminal roots of the plant were colonized by either of the two largest fungal species sets (represented by Oidiodendron or Cenococcum). Thus, species-rich root microbiomes can have alternative community structures, as recently shown in the relationships between human gut microbiome type (i.e. 'enterotype') and host individual health. This study also shows an analytical framework for pinpointing network hubs in symbiont-symbiont networks, leading to the working hypothesis that a small number of microbial species organize the overall root-microbiome dynamics. PMID:26962029

  4. Directed Progression Brain Networks in Alzheimer's Disease: Properties and Classification

    PubMed Central

    Young, Karl; Asif, Danial; Jutla, Inderjit; Liang, Michael; Wilson, Scott; Landsberg, Adam S.; Schuff, Norbert

    2014-01-01

    Abstract This article introduces a new approach in brain connectomics aimed at characterizing the temporal spread in the brain of pathologies like Alzheimer's disease (AD). The main instrument is the development of “directed progression networks” (DPNets), wherein one constructs directed edges between nodes based on (weakly) inferred directions of the temporal spreading of the pathology. This stands in contrast to many previously studied brain networks where edges represent correlations, physical connections, or functional progressions. In addition, this is one of a few studies showing the value of using directed networks in the study of AD. This article focuses on the construction of DPNets for AD using longitudinal cortical thickness measurements from magnetic resonance imaging data. The network properties are then characterized, providing new insights into AD progression, as well as novel markers for differentiating normal cognition (NC) and AD at the group level. It also demonstrates the important role of nodal variations for network classification (i.e., the significance of standard deviations, not just mean values of nodal properties). Finally, the DPNets are utilized to classify subjects based on their global network measures using a variety of data-mining methodologies. In contrast to most brain networks, these DPNets do not show high clustering and small-world properties. PMID:24901258

  5. Chirped laser dispersion spectroscopy using a directly modulated quantum cascade laser

    SciTech Connect

    Hangauer, Andreas Nikodem, Michal; Wysocki, Gerard; Spinner, Georg; Institute for Quantum Electronics, ETH Zurich, 8093 Zurich

    2013-11-04

    Chirped laser dispersion spectroscopy (CLaDS) utilizing direct modulation of a quantum cascade laser (QCL) is presented. By controlling the laser bias nearly single- and dual-sideband CLaDS operation can be realized in an extremely simplified optical setup with no external optical modulators. Capability of direct single-sideband modulation is a unique feature of QCLs that exhibit a low linewidth enhancement factor. The developed analytical model shows excellent agreement with the experimental, directly modulated CLaDS spectra. This method overcomes major technical limitations of mid-infrared CLaDS systems by allowing significantly higher modulation frequencies and eliminating optical fringes introduced by external modulators.

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

    PubMed Central

    Emmert-Streib, Frank

    2012-01-01

    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. PMID:22530042

  7. Interarrival times of message propagation on directed networks

    NASA Astrophysics Data System (ADS)

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

    2011-08-01

    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.

  8. Interarrival times of message propagation on directed networks.

    PubMed

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

    2011-08-01

    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

  9. Discriminating direct and indirect connectivities in biological networks

    PubMed Central

    Kang, Taek; Moore, Richard; Li, Yi; Sontag, Eduardo; Bleris, Leonidas

    2015-01-01

    Reverse engineering of biological pathways involves an iterative process between experiments, data processing, and theoretical analysis. Despite concurrent advances in quality and quantity of data as well as computing resources and algorithms, difficulties in deciphering direct and indirect network connections are prevalent. Here, we adopt the notions of abstraction, emulation, benchmarking, and validation in the context of discovering features specific to this family of connectivities. After subjecting benchmark synthetic circuits to perturbations, we inferred the network connections using a combination of nonparametric single-cell data resampling and modular response analysis. Intriguingly, we discovered that recovered weights of specific network edges undergo divergent shifts under differential perturbations, and that the particular behavior is markedly different between topologies. Our results point to a conceptual advance for reverse engineering beyond weight inference. Investigating topological changes under differential perturbations may address the longstanding problem of discriminating direct and indirect connectivities in biological networks. PMID:26420864

  10. Modulation of GABA and resting state functional connectivity by transcranial direct current stimulation.

    PubMed

    Bachtiar, Velicia; Near, Jamie; Johansen-Berg, Heidi; Stagg, Charlotte J

    2015-01-01

    We previously demonstrated that network level functional connectivity in the human brain could be related to levels of inhibition in a major network node at baseline (Stagg et al., 2014). In this study, we build upon this finding to directly investigate the effects of perturbing M1 GABA and resting state functional connectivity using transcranial direct current stimulation (tDCS), a neuromodulatory approach that has previously been demonstrated to modulate both metrics. FMRI data and GABA levels, as assessed by Magnetic Resonance Spectroscopy, were measured before and after 20 min of 1 mA anodal or sham tDCS. In line with previous studies, baseline GABA levels were negatively correlated with the strength of functional connectivity within the resting motor network. However, although we confirm the previously reported findings that anodal tDCS reduces GABA concentration and increases functional connectivity in the stimulated motor cortex; these changes are not correlated, suggesting they may be driven by distinct underlying mechanisms. PMID:26381352

  11. Flux modulation scheme for direct current SQUID readout revisited

    NASA Astrophysics Data System (ADS)

    Hong, Tao; Wang, Hai; Zhang, Yi; Krause, Hans-Joachim; Braginski, Alex I.; Xie, Xiaoming; Offenhäusser, Andreas; Jiang, Mianheng

    2016-02-01

    The flux modulation scheme (FMS) is the standard readout technique of dc SQUIDs, where a step-up transformer links the SQUID to the preamplifier. The transformer's primary winding shunts the SQUID via a large capacitor while the secondary winding connects it to the preamplifier. A modulation flux having a frequency of typically 100 kHz generates an ac voltage across the SQUID, stepped up by the transformer. The SQUID with FMS is customarily operated in the current bias mode, because a constant dc bias current flows only through the SQUID due to the capacitor isolation. With FMS, however, the transformer ac shunts the SQUID so that in reality the operating mode is neither purely current-biased nor voltage-biased but rather nominal current-biased or "mixed biased." Our objective is to experimentally investigate the consequences of ac shunting of the dc SQUID in FMS and the transformer's transfer characteristics. For different shunt values we measure the change in the SQUID bias current due to the ac shunt using another SQUID in the two-stage readout scheme, and simultaneously monitor the SQUID output voltage signal. We then explain our measurements by a simplified graphic analysis of SQUID intrinsic current-voltage (I-V) characteristics. Since the total current flowing through the SQUID is not constant due to the shunting effect of the transformer, the amplitude of SQUID flux-to-voltage characteristics V(Φ) is less as compared to the direct readout scheme (DRS). Furthermore, we analyze and compare V(Φ) obtained by DRS and FMS. We show that in FMS, the transfer characteristics of the SQUID circuit also depend on the isolation capacitance and the dynamic resistance of the SQUID.

  12. Modulating Cognition Using Transcranial Direct Current Stimulation of the Cerebellum

    PubMed Central

    Pope, Paul A.

    2015-01-01

    Numerous studies have emerged recently that demonstrate the possibility of modulating, and in some cases enhancing, cognitive processes by exciting brain regions involved in working memory and attention using transcranial electrical brain stimulation. Some researchers now believe the cerebellum supports cognition, possibly via a remote neuromodulatory effect on the prefrontal cortex. This paper describes a procedure for investigating a role for the cerebellum in cognition using transcranial direct current stimulation (tDCS), and a selection of information-processing tasks of varying task difficulty, which have previously been shown to involve working memory, attention and cerebellar functioning. One task is called the Paced Auditory Serial Addition Task (PASAT) and the other a novel variant of this task called the Paced Auditory Serial Subtraction Task (PASST). A verb generation task and its two controls (noun and verb reading) were also investigated. All five tasks were performed by three separate groups of participants, before and after the modulation of cortico-cerebellar connectivity using anodal, cathodal or sham tDCS over the right cerebellar cortex. The procedure demonstrates how performance (accuracy, verbal response latency and variability) could be selectively improved after cathodal stimulation, but only during tasks that the participants rated as difficult, and not easy. Performance was unchanged by anodal or sham stimulation. These findings demonstrate a role for the cerebellum in cognition, whereby activity in the left prefrontal cortex is likely dis-inhibited by cathodal tDCS over the right cerebellar cortex. Transcranial brain stimulation is growing in popularity in various labs and clinics. However, the after-effects of tDCS are inconsistent between individuals and not always polarity-specific, and may even be task- or load-specific, all of which requires further study. Future efforts might also be guided towards neuro-enhancement in cerebellar patients presenting with cognitive impairment once a better understanding of brain stimulation mechanisms has emerged. PMID:25741744

  13. Flexible multi-dimensional modulation method for elastic optical networks

    NASA Astrophysics Data System (ADS)

    He, Zilong; Liu, Wentao; Shi, Sheping; Shen, Bailin; Chen, Xue; Gao, Xiqing; Zhang, Qi; Shang, Dongdong; Ji, Yongning; Liu, Yingfeng

    2016-01-01

    We demonstrate a flexible multi-dimensional modulation method for elastic optical networks. We compare the flexible multi-dimensional modulation formats PM-kSC-mQAM with traditional modulation formats PM-mQAM using numerical simulations in back-to-back and wavelength division multiplexed (WDM) transmission (50 GHz-spaced) scenarios at the same symbol rate of 32 Gbaud. The simulation results show that PM-kSC-QPSK and PM-kSC-16QAM can achieve obvious back-to-back sensitivity gain with respect to PM-QPSK and PM-16QAM at the expense of spectral efficiency reduction. And the WDM transmission simulation results show that PM-2SC-QPSK can achieve 57.5% increase in transmission reach compared to PM-QPSK, and 48.5% increase for PM-2SC-16QAM over PM-16QAM. Furthermore, we also experimentally investigate the back to back performance of PM-2SC-QPSK, PM-4SC-QPSK, PM-2SC-16QAM and PM-3SC-16QAM, and the experimental results agree well with the numerical simulations.

  14. IIIDB: a database for isoform-isoform interactions and isoform network modules

    PubMed Central

    2015-01-01

    Background Protein-protein interactions (PPIs) are key to understanding diverse cellular processes and disease mechanisms. However, current PPI databases only provide low-resolution knowledge of PPIs, in the sense that "proteins" of currently known PPIs generally refer to "genes." It is known that alternative splicing often impacts PPI by either directly affecting protein interacting domains, or by indirectly impacting other domains, which, in turn, impacts the PPI binding. Thus, proteins translated from different isoforms of the same gene can have different interaction partners. Results Due to the limitations of current experimental capacities, little data is available for PPIs at the resolution of isoforms, although such high-resolution data is crucial to map pathways and to understand protein functions. In fact, alternative splicing can often change the internal structure of a pathway by rearranging specific PPIs. To fill the gap, we systematically predicted genome-wide isoform-isoform interactions (IIIs) using RNA-seq datasets, domain-domain interaction and PPIs. Furthermore, we constructed an III database (IIIDB) that is a resource for studying PPIs at isoform resolution. To discover functional modules in the III network, we performed III network clustering, and then obtained 1025 isoform modules. To evaluate the module functionality, we performed the GO/pathway enrichment analysis for each isoform module. Conclusions The IIIDB provides predictions of human protein-protein interactions at the high resolution of transcript isoforms that can facilitate detailed understanding of protein functions and biological pathways. The web interface allows users to search for IIIs or III network modules. The IIIDB is freely available at http://syslab.nchu.edu.tw/IIIDB. PMID:25707505

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

    NASA Astrophysics Data System (ADS)

    Bilgi, Mehmet; Yuksel, Murat

    2010-04-01

    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.

  16. Gate modulation of anodically etched gallium arsenide nanowire random network

    NASA Astrophysics Data System (ADS)

    Aikawa, Shinya; Yamada, Kohei; Asoh, Hidetaka; Ono, Sachiko

    2016-06-01

    Gallium arsenide nanowires (GaAs NWs) formed by anodic etching show an electrically semi-insulating behavior because of charge carrier depletion caused by high interface state density. Here, we demonstrate the gate modulation of an anodically etched GaAs NW random network. By applying a reverse bias voltage after anodic etching of bulk GaAs, hydrogen ion exposure of the depleted NW region occurs, and then the interface state density is possibly decreased owing to the reduction in the amount of excess As generated at the interface between the amorphous Ga2O3 and GaAs layers. Consequently, the drain current of the thin-film transistor (TFT) with the GaAs NW random network was increased and was changed by the gate voltage. In contrast, the random network film remained in the insulator in the absence of reverse electrolysis treatment. The TFT performance is still insufficient but may be improved by optimizing the hydrogen ion exposure conditions.

  17. Part mutual information for quantifying direct associations in networks.

    PubMed

    Zhao, Juan; Zhou, Yiwei; Zhang, Xiujun; Chen, Luonan

    2016-05-01

    Quantitatively identifying direct dependencies between variables is an important task in data analysis, in particular for reconstructing various types of networks and causal relations in science and engineering. One of the most widely used criteria is partial correlation, but it can only measure linearly direct association and miss nonlinear associations. However, based on conditional independence, conditional mutual information (CMI) is able to quantify nonlinearly direct relationships among variables from the observed data, superior to linear measures, but suffers from a serious problem of underestimation, in particular for those variables with tight associations in a network, which severely limits its applications. In this work, we propose a new concept, "partial independence," with a new measure, "part mutual information" (PMI), which not only can overcome the problem of CMI but also retains the quantification properties of both mutual information (MI) and CMI. Specifically, we first defined PMI to measure nonlinearly direct dependencies between variables and then derived its relations with MI and CMI. Finally, we used a number of simulated data as benchmark examples to numerically demonstrate PMI features and further real gene expression data from Escherichia coli and yeast to reconstruct gene regulatory networks, which all validated the advantages of PMI for accurately quantifying nonlinearly direct associations in networks. PMID:27092000

  18. Eigengene networks for studying the relationships between co-expression modules

    PubMed Central

    Langfelder, Peter; Horvath, Steve

    2007-01-01

    Background There is evidence that genes and their protein products are organized into functional modules according to cellular processes and pathways. Gene co-expression networks have been used to describe the relationships between gene transcripts. Ample literature exists on how to detect biologically meaningful modules in networks but there is a need for methods that allow one to study the relationships between modules. Results We show that network methods can also be used to describe the relationships between co-expression modules and present the following methodology. First, we describe several methods for detecting modules that are shared by two or more networks (referred to as consensus modules). We represent the gene expression profiles of each module by an eigengene. Second, we propose a method for constructing an eigengene network, where the edges are undirected but maintain information on the sign of the co-expression information. Third, we propose methods for differential eigengene network analysis that allow one to assess the preservation of network properties across different data sets. We illustrate the value of eigengene networks in studying the relationships between consensus modules in human and chimpanzee brains; the relationships between consensus modules in brain, muscle, liver, and adipose mouse tissues; and the relationships between male-female mouse consensus modules and clinical traits. In some applications, we find that module eigengenes can be organized into higher level clusters which we refer to as meta-modules. Conclusion Eigengene networks can be effective and biologically meaningful tools for studying the relationships between modules of a gene co-expression network. The proposed methods may reveal a higher order organization of the transcriptome. R software tutorials, the data, and supplementary material can be found at the following webpage: . PMID:18031580

  19. Global network analysis of phenotypic effects: Protein networks and toxicity modulation in Saccharomyces cerevisiae

    PubMed Central

    Said, Maya R.; Begley, Thomas J.; Oppenheim, Alan V.; Lauffenburger, Douglas A.; Samson, Leona D.

    2004-01-01

    Using genome-wide information to understand holistically how cells function is a major challenge of the postgenomic era. Recent efforts to understand molecular pathway operation from a global perspective have lacked experimental data on phenotypic context, so insights concerning biologically relevant network characteristics of key genes or proteins have remained largely speculative. Here, we present a global network investigation of the genotype/phenotype data set we developed for the recovery of the yeast Saccharomyces cerevisiae from exposure to DNA-damaging agents, enabling explicit study of how proteinprotein interaction network characteristics may be associated with phenotypic functional effects. We show that toxicity-modulating proteins have similar topological properties as essential proteins, suggesting that cells initiate highly coordinated responses to damage similar to those needed for vital cellular functions. We also identify toxicologically important protein complexes, pathways, and modules. These results have potential implications for understanding toxicity-modulating processes relevant to a number of human diseases, including cancer and aging. PMID:15608068

  20. TRIM32 modulates pluripotency entry and exit by directly regulating Oct4 stability

    PubMed Central

    Bahnassawy, Lamia’a; Perumal, Thanneer M.; Gonzalez-Cano, Laura; Hillje, Anna-Lena; Taher, Leila; Makalowski, Wojciech; Suzuki, Yutaka; Fuellen, Georg; Sol, Antonio del; Schwamborn, Jens Christian

    2015-01-01

    Induced pluripotent stem cells (iPSCs) have revolutionized the world of regenerative medicine; nevertheless, the exact molecular mechanisms underlying their generation and differentiation remain elusive. Here, we investigated the role of the cell fate determinant TRIM32 in modulating such processes. TRIM32 is essential for the induction of neuronal differentiation of neural stem cells by poly-ubiquitinating cMyc to target it for degradation resulting in inhibition of cell proliferation. To elucidate the role of TRIM32 in regulating somatic cell reprogramming we analysed the capacity of TRIM32-knock-out mouse embryonic fibroblasts (MEFs) in generating iPSC colonies. TRIM32 knock-out MEFs produced a higher number of iPSC colonies indicating a role for TRIM32 in inhibiting this cellular transition. Further characterization of the generated iPSCs indicated that the TRIM32 knock-out iPSCs show perturbed differentiation kinetics. Additionally, mathematical modelling of global gene expression data revealed that during differentiation an Oct4 centred network in the wild-type cells is replaced by an E2F1 centred network in the TRIM32 deficient cells. We show here that this might be caused by a TRIM32-dependent downregulation of Oct4. In summary, the data presented here reveal that TRIM32 directly regulates at least two of the four Yamanaka Factors (cMyc and Oct4), to modulate cell fate transitions. PMID:26307407

  1. Quetiapine modulates functional connectivity in brain aggression networks.

    PubMed

    Klasen, Martin; Zvyagintsev, Mikhail; Schwenzer, Michael; Mathiak, Krystyna A; Sarkheil, Pegah; Weber, René; Mathiak, Klaus

    2013-07-15

    Aggressive behavior is associated with dysfunctions in an affective regulation network encompassing amygdala and prefrontal areas such as orbitofrontal (OFC), anterior cingulate (ACC), and dorsolateral prefrontal cortex (DLPFC). In particular, prefrontal regions have been postulated to control amygdala activity by inhibitory projections, and this process may be disrupted in aggressive individuals. The atypical antipsychotic quetiapine successfully attenuates aggressive behavior in various disorders; the underlying neural processes, however, are unknown. A strengthened functional coupling in the prefrontal-amygdala system may account for these anti-aggressive effects. An inhibition of this network has been reported for virtual aggression in violent video games as well. However, there have been so far no in-vivo observations of pharmacological influences on corticolimbic projections during human aggressive behavior. In a double-blind, placebo-controlled study, quetiapine and placebo were administered for three successive days prior to an fMRI experiment. In this experiment, functional brain connectivity was assessed during virtual aggressive behavior in a violent video game and an aggression-free control task in a non-violent modification. Quetiapine increased the functional connectivity of ACC and DLPFC with the amygdala during virtual aggression, whereas OFC-amygdala coupling was attenuated. These effects were observed neither for placebo nor for the non-violent control. These results demonstrate for the first time a pharmacological modification of aggression-related human brain networks in a naturalistic setting. The violence-specific modulation of prefrontal-amygdala networks appears to control aggressive behavior and provides a neurobiological model for the anti-aggressive effects of quetiapine. PMID:23501053

  2. Theory of interface: category theory, directed networks and evolution of biological networks.

    PubMed

    Haruna, Taichi

    2013-11-01

    Biological networks have two modes. The first mode is static: a network is a passage on which something flows. The second mode is dynamic: a network is a pattern constructed by gluing functions of entities constituting the network. In this paper, first we discuss that these two modes can be associated with the category theoretic duality (adjunction) and derive a natural network structure (a path notion) for each mode by appealing to the category theoretic universality. The path notion corresponding to the static mode is just the usual directed path. The path notion for the dynamic mode is called lateral path which is the alternating path considered on the set of arcs. Their general functionalities in a network are transport and coherence, respectively. Second, we introduce a betweenness centrality of arcs for each mode and see how the two modes are embedded in various real biological network data. We find that there is a trade-off relationship between the two centralities: if the value of one is large then the value of the other is small. This can be seen as a kind of division of labor in a network into transport on the network and coherence of the network. Finally, we propose an optimization model of networks based on a quality function involving intensities of the two modes in order to see how networks with the above trade-off relationship can emerge through evolution. We show that the trade-off relationship can be observed in the evolved networks only when the dynamic mode is dominant in the quality function by numerical simulations. We also show that the evolved networks have features qualitatively similar to real biological networks by standard complex network analysis. PMID:24012823

  3. Physiological modules for generating discrete and rhythmic movements: action identification by a dynamic recurrent neural network

    PubMed Central

    Bengoetxea, Ana; Leurs, Françoise; Hoellinger, Thomas; Cebolla, Ana M.; Dan, Bernard; McIntyre, Joseph; Cheron, Guy

    2014-01-01

    In this study we employed a dynamic recurrent neural network (DRNN) in a novel fashion to reveal characteristics of control modules underlying the generation of muscle activations when drawing figures with the outstretched arm. We asked healthy human subjects to perform four different figure-eight movements in each of two workspaces (frontal plane and sagittal plane). We then trained a DRNN to predict the movement of the wrist from information in the EMG signals from seven different muscles. We trained different instances of the same network on a single movement direction, on all four movement directions in a single movement plane, or on all eight possible movement patterns and looked at the ability of the DRNN to generalize and predict movements for trials that were not included in the training set. Within a single movement plane, a DRNN trained on one movement direction was not able to predict movements of the hand for trials in the other three directions, but a DRNN trained simultaneously on all four movement directions could generalize across movement directions within the same plane. Similarly, the DRNN was able to reproduce the kinematics of the hand for both movement planes, but only if it was trained on examples performed in each one. As we will discuss, these results indicate that there are important dynamical constraints on the mapping of EMG to hand movement that depend on both the time sequence of the movement and on the anatomical constraints of the musculoskeletal system. In a second step, we injected EMG signals constructed from different synergies derived by the PCA in order to identify the mechanical significance of each of these components. From these results, one can surmise that discrete-rhythmic movements may be constructed from three different fundamental modules, one regulating the co-activation of all muscles over the time span of the movement and two others elliciting patterns of reciprocal activation operating in orthogonal directions. PMID:25278868

  4. Maintain the structural controllability under malicious attacks on directed networks

    NASA Astrophysics Data System (ADS)

    Wang, Bingbo; Gao, Lin; Gao, Yong; Deng, Yue

    2013-03-01

    The directedness of the links in a network plays a critical role in determining many dynamical processes among which the controllability has received much recent attention. The control robustness of a network against malicious attack and random failure also becomes a significant issue. In this paper, we propose a novel control robustness index motivated by recent studies on the global connectivity and controllability. In its general form, the problem of optimizing the control robustness index is computationally infeasible for large-scale networks. By analysing the influences of several directed topological factors on the dynamical control process, we transform the control robustness problem into the problem of transitivity maximization for control routes, and propose an efficient greedy algorithm to make control routes transitive. A series of experiments on real-world and synthetic networks show that the global connectivity and controllability can be improved simultaneously and we can mitigate the destruction of malicious attack through backing up the control routes.

  5. Site-directed electronic tunneling through a vibrating molecular network

    NASA Astrophysics Data System (ADS)

    Caspary, Maytal; Peskin, Uri

    2006-11-01

    The effect of electronic-nuclear coupling on electronic transport through a complex molecular network is studied. Electronic tunneling dynamics in a network of N donor/acceptor sites, connected by molecular bridges, is shown to be controlled by electronic-nuclear coupling at the bridges. Particularly, electronic coupling to an accepting nuclear mode at the contact site between the donor and the rest of the network is shown to affect the tunneling path selection to specific acceptors. In the "deep" tunneling regime, the network is mapped onto an N-level system using a recursive perturbation expansion, enabling analytical treatment of the electronic dynamics. The analytic formulation is applied for two model systems, demonstrating site-directed tunneling by electronic-nuclear coupling. Numerical simulations suggest that this phenomenon is not limited to the deep tunneling regime.

  6. Direct Adaptive Aircraft Control Using Dynamic Cell Structure Neural Networks

    NASA Technical Reports Server (NTRS)

    Jorgensen, Charles C.

    1997-01-01

    A Dynamic Cell Structure (DCS) Neural Network was developed which learns topology representing networks (TRNS) of F-15 aircraft aerodynamic stability and control derivatives. The network is integrated into a direct adaptive tracking controller. The combination produces a robust adaptive architecture capable of handling multiple accident and off- nominal flight scenarios. This paper describes the DCS network and modifications to the parameter estimation procedure. The work represents one step towards an integrated real-time reconfiguration control architecture for rapid prototyping of new aircraft designs. Performance was evaluated using three off-line benchmarks and on-line nonlinear Virtual Reality simulation. Flight control was evaluated under scenarios including differential stabilator lock, soft sensor failure, control and stability derivative variations, and air turbulence.

  7. Transcriptional Analysis of the MrpJ Network: Modulation of Diverse Virulence-Associated Genes and Direct Regulation of mrp Fimbrial and flhDC Flagellar Operons in Proteus mirabilis

    PubMed Central

    Bode, Nadine J.; Debnath, Irina; Kuan, Lisa; Schulfer, Anjelique; Ty, Maureen

    2015-01-01

    The enteric bacterium Proteus mirabilis is associated with a significant number of catheter-associated urinary tract infections (UTIs). Strict regulation of the antagonistic processes of adhesion and motility, mediated by fimbriae and flagella, respectively, is essential for disease progression. Previously, the transcriptional regulator MrpJ, which is encoded by the mrp fimbrial operon, has been shown to repress both swimming and swarming motility. Here we show that MrpJ affects an array of cellular processes beyond adherence and motility. Microarray analysis found that expression of mrpJ mimicking levels observed during UTIs leads to differential expression of 217 genes related to, among other functions, bacterial virulence, type VI secretion, and metabolism. We probed the molecular mechanism of transcriptional regulation by MrpJ using transcriptional reporters and chromatin immunoprecipitation (ChIP). Binding of MrpJ to two virulence-associated target gene promoters, the promoters of the flagellar master regulator flhDC and mrp itself, appears to be affected by the condensation state of the native chromosome, although both targets share a direct MrpJ binding site proximal to the transcriptional start. Furthermore, an mrpJ deletion mutant colonized the bladders of mice at significantly lower levels in a transurethral model of infection. Additionally, we observed that mrpJ is widely conserved in a collection of recent clinical isolates. Altogether, these findings support a role of MrpJ as a global regulator of P. mirabilis virulence. PMID:25847961

  8. Allosteric Modulators for the Treatment of Schizophrenia: Targeting Glutamatergic Networks

    PubMed Central

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

    2013-01-01

    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

  9. Network burst dynamics under heterogeneous cholinergic modulation of neural firing properties and heterogeneous synaptic connectivity.

    PubMed

    Knudstrup, Scott; Zochowski, Michal; Booth, Victoria

    2016-05-01

    The characteristics of neural network activity depend on intrinsic neural properties and synaptic connectivity in the network. In brain networks, both of these properties are critically affected by the type and levels of neuromodulators present. The expression of many of the most powerful neuromodulators, including acetylcholine (ACh), varies tonically and phasically with behavioural state, leading to dynamic, heterogeneous changes in intrinsic neural properties and synaptic connectivity properties. Namely, ACh significantly alters neural firing properties as measured by the phase response curve in a manner that has been shown to alter the propensity for network synchronization. The aim of this simulation study was to build an understanding of how heterogeneity in cholinergic modulation of neural firing properties and heterogeneity in synaptic connectivity affect the initiation and maintenance of synchronous network bursting in excitatory networks. We show that cells that display different levels of ACh modulation have differential roles in generating network activity: weakly modulated cells are necessary for burst initiation and provide synchronizing drive to the rest of the network, whereas strongly modulated cells provide the overall activity level necessary to sustain burst firing. By applying several quantitative measures of network activity, we further show that the existence of network bursting and its characteristics, such as burst duration and intraburst synchrony, are dependent on the fraction of cell types providing the synaptic connections in the network. These results suggest mechanisms underlying ACh modulation of brain oscillations and the modulation of seizure activity during sleep states. PMID:26869313

  10. Detecting modules in biological networks by edge weight clustering and entropy significance

    PubMed Central

    Lecca, Paola; Re, Angela

    2015-01-01

    Detection of the modular structure of biological networks is of interest to researchers adopting a systems perspective for the analysis of omics data. Computational systems biology has provided a rich array of methods for network clustering. To date, the majority of approaches address this task through a network node classification based on topological or external quantifiable properties of network nodes. Conversely, numerical properties of network edges are underused, even though the information content which can be associated with network edges has augmented due to steady advances in molecular biology technology over the last decade. Properly accounting for network edges in the development of clustering approaches can become crucial to improve quantitative interpretation of omics data, finally resulting in more biologically plausible models. In this study, we present a novel technique for network module detection, named WG-Cluster (Weighted Graph CLUSTERing). WG-Cluster's notable features, compared to current approaches, lie in: (1) the simultaneous exploitation of network node and edge weights to improve the biological interpretability of the connected components detected, (2) the assessment of their statistical significance, and (3) the identification of emerging topological properties in the detected connected components. WG-Cluster utilizes three major steps: (i) an unsupervised version of k-means edge-based algorithm detects sub-graphs with similar edge weights, (ii) a fast-greedy algorithm detects connected components which are then scored and selected according to the statistical significance of their scores, and (iii) an analysis of the convolution between sub-graph mean edge weight and connected component score provides a summarizing view of the connected components. WG-Cluster can be applied to directed and undirected networks of different types of interacting entities and scales up to large omics data sets. Here, we show that WG-Cluster can be successfully used in the differential analysis of physical protein–protein interaction (PPI) networks. Specifically, applying WG-Cluster to a PPI network weighted by measurements of differential gene expression permits to explore the changes in network topology under two distinct (normal vs. tumor) conditions. WG-Cluster code is available at https://sites.google.com/site/paolaleccapersonalpage/. PMID:26379697

  11. Unbiased degree-preserving randomization of directed binary networks

    NASA Astrophysics Data System (ADS)

    Roberts, E. S.; Coolen, A. C. C.

    2012-04-01

    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.

  12. Secure Upgrade of Hardware Security Modules in Bank Networks

    NASA Astrophysics Data System (ADS)

    Focardi, Riccardo; Luccio, Flaminia L.

    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.

  13. Metastability and inter-band frequency modulation in networks of oscillating spiking neuron populations.

    PubMed

    Bhowmik, David; Shanahan, Murray

    2013-01-01

    Groups of neurons firing synchronously are hypothesized to underlie many cognitive functions such as attention, associative learning, memory, and sensory selection. Recent theories suggest that transient periods of synchronization and desynchronization provide a mechanism for dynamically integrating and forming coalitions of functionally related neural areas, and that at these times conditions are optimal for information transfer. Oscillating neural populations display a great amount of spectral complexity, with several rhythms temporally coexisting in different structures and interacting with each other. This paper explores inter-band frequency modulation between neural oscillators using models of quadratic integrate-and-fire neurons and Hodgkin-Huxley neurons. We vary the structural connectivity in a network of neural oscillators, assess the spectral complexity, and correlate the inter-band frequency modulation. We contrast this correlation against measures of metastable coalition entropy and synchrony. Our results show that oscillations in different neural populations modulate each other so as to change frequency, and that the interaction of these fluctuating frequencies in the network as a whole is able to drive different neural populations towards episodes of synchrony. Further to this, we locate an area in the connectivity space in which the system directs itself in this way so as to explore a large repertoire of synchronous coalitions. We suggest that such dynamics facilitate versatile exploration, integration, and communication between functionally related neural areas, and thereby supports sophisticated cognitive processing in the brain. PMID:23614040

  14. Intra-cavity loss modulation for ultrahigh-speed direct modulation lasers based on photon-photon resonance

    NASA Astrophysics Data System (ADS)

    Mieda, Shigeru; Shiratori, Satoshi; Yokota, Nobuhide; Kobayashi, Wataru; Yasaka, Hiroshi

    2015-08-01

    The characteristics of the intra-cavity loss modulation laser diode (ICLM-LD) proposed in this paper were numerically and experimentally evaluated. A lower modulation sensitivity degradation rate (MSDR) of -0.30 dB/GHz and a wider 3 dB bandwidth of 49 GHz compared to those of direct modulation lasers (-0.49 dB/Hz, 16 GHz) were numerically confirmed. In addition, an MSDR of -0.29 dB/GHz and a 3 dB bandwidth wider than 30 GHz were experimentally confirmed using the fabricated ICLM-LD. The ICLM-LD will thus become a key part of ultrahigh-speed direct modulation lasers with external cavities whose modulation sensitivity is enhanced by the photon-photon resonance effect.

  15. Network-based survival-associated module biomarker and its crosstalk with cell death genes in ovarian cancer

    PubMed Central

    Jin, Nana; Wu, Hao; Miao, Zhengqiang; Huang, Yan; Hu, Yongfei; Bi, Xiaoman; Wu, Deng; Qian, Kun; Wang, Liqiang; Wang, Changliang; Wang, Hongwei; Li, Kongning; Li, Xia; Wang, Dong

    2015-01-01

    Ovarian cancer remains a dismal disease with diagnosing in the late, metastatic stages, therefore, there is a growing realization of the critical need to develop effective biomarkers for understanding underlying mechanisms. Although existing evidences demonstrate the important role of the single genetic abnormality in pathogenesis, the perturbations of interactors in the complex network are often ignored. Moreover, ovarian cancer diagnosis and treatment still exist a large gap that need to be bridged. In this work, we adopted a network-based survival-associated approach to capture a 12-gene network module based on differential co-expression PPI network in the advanced-stage, high-grade ovarian serous cystadenocarcinoma. Then, regulatory genes (protein-coding genes and non-coding genes) direct interacting with the module were found to be significantly overlapped with cell death genes. More importantly, these overlapping genes tightly clustered together pointing to the module, deciphering the crosstalk between network-based survival-associated module and cell death in ovarian cancer. PMID:26099452

  16. Baseline effects of transcranial direct current stimulation on glutamatergic neurotransmission and large-scale network connectivity

    PubMed Central

    Hunter, Michael A.; Coffman, Brian A.; Gasparovic, Charles; Calhoun, Vince D.; Trumbo, Michael C.; Clark, Vincent P.

    2015-01-01

    Transcranial direct current stimulation (tDCS) modulates glutamatergic neurotransmission and can be utilized as a novel treatment intervention for a multitude of populations. However, the exact mechanism by which tDCS modulates the brain’s neural architecture, from the micro to macro scales, have yet to be illuminated. Using a within-subjects design, resting-state functional magnetic resonance imaging (rs-fMRI) and proton magnetic resonance spectroscopy (1H-MRS) were performed immediately before and after the administration of anodal tDCS over right parietal cortex. Group independent component analysis (ICA) was used to decompose fMRI scans into 75 brain networks, from which 12 resting-state networks were identified that had significant voxel-wise functional connectivity to anatomical regions of interest. 1H-MRS was used to obtain estimates of combined glutamate and glutamine (Glx) concentrations from bilateral intraparietal sulcus. Paired sample t-tests showed significantly increased Glx under the anodal electrode, but not in homologous regions of the contralateral hemisphere. Increases of within-network connectivity were observed within the superior parietal, inferior parietal, left frontal-parietal, salience and cerebellar intrinsic networks, and decreases in connectivity were observed in the anterior cingulate and the basal ganglia (p < 0.05, FDR-corrected). Individual differences in Glx concentrations predicted network connectivity in most of these networks. The observed relationships between glutamatergic neurotransmission and network connectivity may be used to guide future tDCS protocols that aim to target and alter neuroplastic mechanisms in healthy individuals as well as those with psychiatric and neurologic disorders. PMID:25312829

  17. Baseline effects of transcranial direct current stimulation on glutamatergic neurotransmission and large-scale network connectivity.

    PubMed

    Hunter, Michael A; Coffman, Brian A; Gasparovic, Charles; Calhoun, Vince D; Trumbo, Michael C; Clark, Vincent P

    2015-01-12

    Transcranial direct current stimulation (tDCS) modulates glutamatergic neurotransmission and can be utilized as a novel treatment intervention for a multitude of populations. However, the exact mechanism by which tDCS modulates the brain׳s neural architecture, from the micro to macro scales, have yet to be investigated. Using a within-subjects design, resting-state functional magnetic resonance imaging (rs-fMRI) and proton magnetic resonance spectroscopy ((1)H MRS) were performed immediately before and after the administration of anodal tDCS over right parietal cortex. Group independent component analysis (ICA) was used to decompose fMRI scans into 75 brain networks, from which 12 resting-state networks were identified that had significant voxel-wise functional connectivity to anatomical regions of interest. (1)H MRS was used to obtain estimates of combined glutamate and glutamine (Glx) concentrations from bilateral intraparietal sulcus. Paired sample t-tests showed significantly increased Glx under the anodal electrode, but not in homologous regions of the contralateral hemisphere. Increases of within-network connectivity were observed within the superior parietal, inferior parietal, left frontal-parietal, salience and cerebellar intrinsic networks, and decreases in connectivity were observed in the anterior cingulate and the basal ganglia (p<0.05, FDR-corrected). Individual differences in Glx concentrations predicted network connectivity in most of these networks. The observed relationships between glutamatergic neurotransmission and network connectivity may be used to guide future tDCS protocols that aim to target and alter neuroplastic mechanisms in healthy individuals as well as those with psychiatric and neurologic disorders. PMID:25312829

  18. Direct electrical-to-optical conversion and light modulation in micro whispering-gallery-mode resonators

    NASA Technical Reports Server (NTRS)

    Maleki, Lute (Inventor); Levi, Anthony F. J. (Inventor)

    2005-01-01

    Techniques for directly converting an electrical signal into an optical signal by using a whispering gallery mode optical resonator formed of a dielectric material that allows for direct modulation of optical absorption by the electrical signal.

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

    PubMed

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

    2011-01-01

    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

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

    PubMed Central

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

    2013-01-01

    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

  1. C-element: a new clustering algorithm to find high quality functional modules in PPI networks.

    PubMed

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

    2013-01-01

    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

  2. Discovering Distinct Functional Modules of Specific Cancer Types Using Protein-Protein Interaction Networks

    PubMed Central

    Shen, Ru; Wang, Xiaosheng; Guda, Chittibabu

    2015-01-01

    Background. The molecular profiles exhibited in different cancer types are very different; hence, discovering distinct functional modules associated with specific cancer types is very important to understand the distinct functions associated with them. Protein-protein interaction networks carry vital information about molecular interactions in cellular systems, and identification of functional modules (subgraphs) in these networks is one of the most important applications of biological network analysis. Results. In this study, we developed a new graph theory based method to identify distinct functional modules from nine different cancer protein-protein interaction networks. The method is composed of three major steps: (i) extracting modules from protein-protein interaction networks using network clustering algorithms; (ii) identifying distinct subgraphs from the derived modules; and (iii) identifying distinct subgraph patterns from distinct subgraphs. The subgraph patterns were evaluated using experimentally determined cancer-specific protein-protein interaction data from the Ingenuity knowledgebase, to identify distinct functional modules that are specific to each cancer type. Conclusion. We identified cancer-type specific subgraph patterns that may represent the functional modules involved in the molecular pathogenesis of different cancer types. Our method can serve as an effective tool to discover cancer-type specific functional modules from large protein-protein interaction networks. PMID:26495282

  3. Provider-sponsored networks. Physicians organize for direct contracting.

    PubMed

    Coile, R C

    1996-08-01

    The Provider Service Network (PSN) concept is part of a wider movement by physicians to restructure for managed care to improve bargaining leverage for America's more than 600,000 active medical practitioners. Direct contracting has a simple appeal--no intermediaries. Imagine managed care contracts without the costs or hassles of an HMO or third-party intermediary. The PSN is a new form of managed care organization, but without the middleman. Savvy, self-insured employers, business coalitions, and government health programs are the potential "buyers." Doctors and hospitals are the "sellers," organizing provider networks on a regional and statewide basis. Up for grabs are over 225 million consumers whose health benefits are currently managed by insurance plans, HMOs, and third parties. This new marketplace of direct contracting may sound to doctors like the Garden of Eden, but there is plenty of opposition. PSNs will not become a national trend without a fight. PMID:10160042

  4. Site-directed deep electronic tunneling through a molecular network

    NASA Astrophysics Data System (ADS)

    Caspary, Maytal; Peskin, Uri

    2005-10-01

    Electronic tunneling in a complex molecular network of N(>2) donor/acceptor sites, connected by molecular bridges, is analyzed. The "deep" tunneling dynamics is formulated using a recursive perturbation expansion, yielding a McConnell-type reduced N-level model Hamiltonian. Applications to models of molecular junctions demonstrate that the donor-bridge contact parameters can be tuned in order to control the tunneling dynamics and particularly to direct the tunneling pathway to either one of the various acceptors.

  5. Site-directed deep electronic tunneling through a molecular network

    SciTech Connect

    Caspary, Maytal; Peskin, Uri

    2005-10-15

    Electronic tunneling in a complex molecular network of N(>2) donor/acceptor sites, connected by molecular bridges, is analyzed. The 'deep' tunneling dynamics is formulated using a recursive perturbation expansion, yielding a McConnell-type reduced N-level model Hamiltonian. Applications to models of molecular junctions demonstrate that the donor-bridge contact parameters can be tuned in order to control the tunneling dynamics and particularly to direct the tunneling pathway to either one of the various acceptors.

  6. Interest communities and flow roles in directed networks: the Twitter network of the UK riots.

    PubMed

    Beguerisse-Díaz, Mariano; Garduño-Hernández, Guillermo; Vangelov, Borislav; Yaliraki, Sophia N; Barahona, Mauricio

    2014-12-01

    Directionality is a crucial ingredient in many complex networks in which information, energy or influence are transmitted. In such directed networks, analysing flows (and not only the strength of connections) is crucial to reveal important features of the network that might go undetected if the orientation of connections is ignored. We showcase here a flow-based approach for community detection through the study of the network of the most influential Twitter users during the 2011 riots in England. Firstly, we use directed Markov Stability to extract descriptions of the network at different levels of coarseness in terms of interest communities, i.e. groups of nodes within which flows of information are contained and reinforced. Such interest communities reveal user groupings according to location, profession, employer and topic. The study of flows also allows us to generate an interest distance, which affords a personalized view of the attention in the network as viewed from the vantage point of any given user. Secondly, we analyse the profiles of incoming and outgoing long-range flows with a combined approach of role-based similarity and the novel relaxed minimum spanning tree algorithm to reveal that the users in the network can be classified into five roles. These flow roles go beyond the standard leader/follower dichotomy and differ from classifications based on regular/structural equivalence. We then show that the interest communities fall into distinct informational organigrams characterized by a different mix of user roles reflecting the quality of dialogue within them. Our generic framework can be used to provide insight into how flows are generated, distributed, preserved and consumed in directed networks. PMID:25297320

  7. Interest communities and flow roles in directed networks: the Twitter network of the UK riots

    PubMed Central

    Beguerisse-Díaz, Mariano; Garduño-Hernández, Guillermo; Vangelov, Borislav; Yaliraki, Sophia N.; Barahona, Mauricio

    2014-01-01

    Directionality is a crucial ingredient in many complex networks in which information, energy or influence are transmitted. In such directed networks, analysing flows (and not only the strength of connections) is crucial to reveal important features of the network that might go undetected if the orientation of connections is ignored. We showcase here a flow-based approach for community detection through the study of the network of the most influential Twitter users during the 2011 riots in England. Firstly, we use directed Markov Stability to extract descriptions of the network at different levels of coarseness in terms of interest communities, i.e. groups of nodes within which flows of information are contained and reinforced. Such interest communities reveal user groupings according to location, profession, employer and topic. The study of flows also allows us to generate an interest distance, which affords a personalized view of the attention in the network as viewed from the vantage point of any given user. Secondly, we analyse the profiles of incoming and outgoing long-range flows with a combined approach of role-based similarity and the novel relaxed minimum spanning tree algorithm to reveal that the users in the network can be classified into five roles. These flow roles go beyond the standard leader/follower dichotomy and differ from classifications based on regular/structural equivalence. We then show that the interest communities fall into distinct informational organigrams characterized by a different mix of user roles reflecting the quality of dialogue within them. Our generic framework can be used to provide insight into how flows are generated, distributed, preserved and consumed in directed networks. PMID:25297320

  8. Moving target tracking through distributed clustering in directional sensor networks.

    PubMed

    Enayet, Asma; Razzaque, Md Abdur; Hassan, Mohammad Mehedi; Almogren, Ahmad; Alamri, Atif

    2014-01-01

    The problem of moving target tracking in directional sensor networks (DSNs) introduces new research challenges, including optimal selection of sensing and communication sectors of the directional sensor nodes, determination of the precise location of the target and an energy-efficient data collection mechanism. Existing solutions allow individual sensor nodes to detect the target's location through collaboration among neighboring nodes, where most of the sensors are activated and communicate with the sink. Therefore, they incur much overhead, loss of energy and reduced target tracking accuracy. In this paper, we have proposed a clustering algorithm, where distributed cluster heads coordinate their member nodes in optimizing the active sensing and communication directions of the nodes, precisely determining the target location by aggregating reported sensing data from multiple nodes and transferring the resultant location information to the sink. Thus, the proposed target tracking mechanism minimizes the sensing redundancy and maximizes the number of sleeping nodes in the network. We have also investigated the dynamic approach of activating sleeping nodes on-demand so that the moving target tracking accuracy can be enhanced while maximizing the network lifetime. We have carried out our extensive simulations in ns-3, and the results show that the proposed mechanism achieves higher performance compared to the state-of-the-art works. PMID:25529205

  9. Dynamic Modulation of the Action Observation Network by Movement Familiarity

    PubMed Central

    Gardner, Tom; Goulden, Nia

    2015-01-01

    When watching another person's actions, a network of sensorimotor brain regions, collectively termed the action observation network (AON), is engaged. Previous research suggests that the AON is more responsive when watching familiar compared with unfamiliar actions. However, most research into AON function is premised on comparisons of AON engagement during different types of task using univariate, magnitude-based approaches. To better understand the relationship between action familiarity and AON engagement, here we examine how observed movement familiarity modulates AON activity in humans using dynamic causal modeling, a type of effective connectivity analysis. Twenty-one subjects underwent fMRI scanning while viewing whole-body dance movements that varied in terms of their familiarity. Participants' task was to either predict the next posture the dancer's body would assume or to respond to a non–action-related attentional control question. To assess individuals' familiarity with each movement, participants rated each video on a measure of visual familiarity after being scanned. Parametric analyses showed more activity in left middle temporal gyrus, inferior parietal lobule, and inferior frontal gyrus as videos were rated as increasingly familiar. These clusters of activity formed the regions of interest for dynamic causal modeling analyses, which revealed attenuation of effective connectivity bidirectionally between parietal and temporal AON nodes when participants observed videos they rated as increasingly familiar. As such, the findings provide partial support for a predictive coding model of the AON, as well as illuminate how action familiarity manipulations can be used to explore simulation-based accounts of action understanding. PMID:25632133

  10. Dynamic modulation of the action observation network by movement familiarity.

    PubMed

    Gardner, Tom; Goulden, Nia; Cross, Emily S

    2015-01-28

    When watching another person's actions, a network of sensorimotor brain regions, collectively termed the action observation network (AON), is engaged. Previous research suggests that the AON is more responsive when watching familiar compared with unfamiliar actions. However, most research into AON function is premised on comparisons of AON engagement during different types of task using univariate, magnitude-based approaches. To better understand the relationship between action familiarity and AON engagement, here we examine how observed movement familiarity modulates AON activity in humans using dynamic causal modeling, a type of effective connectivity analysis. Twenty-one subjects underwent fMRI scanning while viewing whole-body dance movements that varied in terms of their familiarity. Participants' task was to either predict the next posture the dancer's body would assume or to respond to a non-action-related attentional control question. To assess individuals' familiarity with each movement, participants rated each video on a measure of visual familiarity after being scanned. Parametric analyses showed more activity in left middle temporal gyrus, inferior parietal lobule, and inferior frontal gyrus as videos were rated as increasingly familiar. These clusters of activity formed the regions of interest for dynamic causal modeling analyses, which revealed attenuation of effective connectivity bidirectionally between parietal and temporal AON nodes when participants observed videos they rated as increasingly familiar. As such, the findings provide partial support for a predictive coding model of the AON, as well as illuminate how action familiarity manipulations can be used to explore simulation-based accounts of action understanding. PMID:25632133

  11. Phase transitions in Ising models on directed networks

    NASA Astrophysics Data System (ADS)

    Lipowski, Adam; Ferreira, António Luis; Lipowska, Dorota; Gontarek, Krzysztof

    2015-11-01

    We examine Ising models with heat-bath dynamics on directed networks. Our simulations show that Ising models on directed triangular and simple cubic lattices undergo a phase transition that most likely belongs to the Ising universality class. On the directed square lattice the model remains paramagnetic at any positive temperature as already reported in some previous studies. We also examine random directed graphs and show that contrary to undirected ones, percolation of directed bonds does not guarantee ferromagnetic ordering. Only above a certain threshold can a random directed graph support finite-temperature ferromagnetic ordering. Such behavior is found also for out-homogeneous random graphs, but in this case the analysis of magnetic and percolative properties can be done exactly. Directed random graphs also differ from undirected ones with respect to zero-temperature freezing. Only at low connectivity do they remain trapped in a disordered configuration. Above a certain threshold, however, the zero-temperature dynamics quickly drives the model toward a broken symmetry (magnetized) state. Only above this threshold, which is almost twice as large as the percolation threshold, do we expect the Ising model to have a positive critical temperature. With a very good accuracy, the behavior on directed random graphs is reproduced within a certain approximate scheme.

  12. Oscillatory entrainment of the motor cortical network during motor imagery is modulated by the feedback modality.

    PubMed

    Vukelić, Mathias; Gharabaghi, Alireza

    2015-05-01

    Neurofeedback of self-regulated brain activity in circumscribed cortical regions is used as a novel strategy to facilitate functional restoration following stroke. Basic knowledge about its impact on motor system oscillations and functional connectivity is however scarce. Specifically, a direct comparison between different feedback modalities and their neural signatures is missing. We assessed a neurofeedback training intervention of modulating β-activity in circumscribed sensorimotor regions by kinesthetic motor imagery (MI). Right-handed healthy participants received two different feedback modalities contingent to their MI-associated brain activity in a cross-over design: (I) visual feedback with a brain-computer interface (BCI) and (II) proprioceptive feedback with a brain-robot interface (BRI) orthosis attached to the right hand. High-density electroencephalography was used to examine the reactivity of the cortical motor system during the training session of each task by studying both local oscillatory power entrainment and distributed functional connectivity. Both feedback modalities activated a distributed functional connectivity network of coherent oscillations. A significantly higher skill and lower variability of self-controlled sensorimotor β-band modulation could, however, be achieved in the BRI condition. This gain in controlling regional motor oscillations was accompanied by functional coupling of remote β-band and θ-band activity in bilateral fronto-central regions and left parieto-occipital regions, respectively. The functional coupling of coherent θ-band oscillations correlated moreover with the skill of regional β-modulation thus revealing a motor learning related network. Our findings indicate that proprioceptive feedback is more suitable than visual feedback to entrain the motor network architecture during the interplay between motor imagery and feedback processing thus resulting in better volitional control of regional brain activity. PMID:25665968

  13. Interaction of multiple networks modulated by the working memory training based on real-time fMRI

    NASA Astrophysics Data System (ADS)

    Shen, Jiahui; Zhang, Gaoyan; Zhu, Chaozhe; Yao, Li; Zhao, Xiaojie

    2015-03-01

    Neuroimaging studies of working memory training have identified the alteration of brain activity as well as the regional interactions within the functional networks such as central executive network (CEN) and default mode network (DMN). However, how the interaction within and between these multiple networks is modulated by the training remains unclear. In this paper, we examined the interaction of three training-induced brain networks during working memory training based on real-time functional magnetic resonance imaging (rtfMRI). Thirty subjects assigned to the experimental and control group respectively participated in two times training separated by seven days. Three networks including silence network (SN), CEN and DMN were identified by the training data with the calculated function connections within each network. Structural equation modeling (SEM) approach was used to construct the directional connectivity patterns. The results showed that the causal influences from the percent signal changes of target ROI to the SN were positively changed in both two groups, as well as the causal influence from the SN to CEN was positively changed in experimental group but negatively changed in control group from the SN to DMN. Further correlation analysis of the changes in each network with the behavioral improvements showed that the changes in SN were stronger positively correlated with the behavioral improvement of letter memory task. These findings indicated that the SN was not only a switch between the target ROI and the other networks in the feedback training but also an essential factor to the behavioral improvement.

  14. Dopaminergic modulation of motor network dynamics in Parkinson's disease.

    PubMed

    Michely, Jochen; Volz, Lukas J; Barbe, Michael T; Hoffstaedter, Felix; Viswanathan, Shivakumar; Timmermann, Lars; Eickhoff, Simon B; Fink, Gereon R; Grefkes, Christian

    2015-03-01

    Although characteristic motor symptoms of Parkinson's disease such as bradykinesia typically improve under dopaminergic medication, deficits in higher motor control are less responsive. We here investigated the dopaminergic modulation of network dynamics underlying basic motor performance, i.e. finger tapping, and higher motor control, i.e. internally and externally cued movement preparation and selection. Twelve patients, assessed ON and OFF medication, and 12 age-matched healthy subjects underwent functional magnetic resonance imaging. Dynamic causal modelling was used to assess effective connectivity in a motor network comprising cortical and subcortical regions. In particular, we investigated whether impairments in basic and higher motor control, and the effects induced by dopaminergic treatment are due to connectivity changes in (i) the mesial premotor loop comprising the supplementary motor area; (ii) the lateral premotor loop comprising lateral premotor cortex; and (iii) cortico-subcortical interactions. At the behavioural level, we observed a marked slowing of movement preparation and selection when patients were internally as opposed to externally cued. Preserved performance during external cueing was associated with enhanced connectivity between prefrontal cortex and lateral premotor cortex OFF medication, compatible with a context-dependent compensatory role of the lateral premotor loop in the hypodopaminergic state. Dopaminergic medication significantly improved finger tapping speed in patients, which correlated with a drug-induced coupling increase of prefrontal cortex with the supplementary motor area, i.e. the mesial premotor loop. In addition, only in the finger tapping condition, patients ON medication showed enhanced excitatory influences exerted by cortical premotor regions and the thalamus upon the putamen. In conclusion, the amelioration of bradykinesia by dopaminergic medication seems to be driven by enhanced connectivity within the mesial premotor loop and cortico-striatal interactions. In contrast, medication did not improve internal motor control deficits concurrent to missing effects at the connectivity level. This differential effect of dopaminergic medication on the network dynamics underlying motor control provides new insights into the clinical finding that in Parkinson's disease dopaminergic drugs especially impact on bradykinesia but less on executive functions. PMID:25567321

  15. Intrinsic functional network architecture of human semantic processing: Modules and hubs.

    PubMed

    Xu, Yangwen; Lin, Qixiang; Han, Zaizhu; He, Yong; Bi, Yanchao

    2016-05-15

    Semantic processing entails the activation of widely distributed brain areas across the temporal, parietal, and frontal lobes. To understand the functional structure of this semantic system, we examined its intrinsic functional connectivity pattern using a database of 146 participants. Focusing on areas consistently activated during semantic processing generated from a meta-analysis of 120 neuroimaging studies (Binder et al., 2009), we found that these regions were organized into three stable modules corresponding to the default mode network (Module DMN), the left perisylvian network (Module PSN), and the left frontoparietal network (Module FPN). These three dissociable modules were integrated by multiple connector hubs-the left angular gyrus (AG) and the left superior/middle frontal gyrus linking all three modules, the left anterior temporal lobe linking Modules DMN and PSN, the left posterior portion of dorsal intraparietal sulcus (IPS) linking Modules DMN and FPN, and the left posterior middle temporal gyrus (MTG) linking Modules PSN and FPN. Provincial hubs, which converge local information within each system, were also identified: the bilateral posterior cingulate cortices/precuneus, the bilateral border area of the posterior AG and the superior lateral occipital gyrus for Module DMN; the left supramarginal gyrus, the middle part of the left MTG and the left orbital inferior frontal gyrus (IFG) for Module FPN; and the left triangular IFG and the left IPS for Module FPN. A neuro-functional model for semantic processing was derived based on these findings, incorporating the interactions of memory, language, and control. PMID:26973170

  16. Study of Transcriptional Regulatory Network Based on CIS Module Database

    NASA Astrophysics Data System (ADS)

    Akasaka, Shizu; Urushibara, Tomoko; Suzuki, Tomonori; Miyazaki, Satoru

    2011-01-01

    Microarray analysis is a high-throughput method for analyzing expression levels of multiple genes, therefore the microarray have been regarded by many investigators as a powerful method. Treating a huge amount of data and judgment of differentially expressed genes require appropriate statistical analysis. When the microarray analysis suggests there are co-expressed genes under a specific condition, there is high possibility that the common transcriptional factors (TFs) control them. It is also difficult to identify the TFs involved in co-expression through only biochemical experiments. In view of cis-element pattern related to co expressed genes might be one of the solutions to infer the gene expression mechanism clearly. So far, we have constructed Cis-Module database in order to specify cis-element location and distribution on genome. Using this database and rat microarray data, we have investigated the TFs network related to co-expression of genes. If we could also extract the human genes that are orthologous to co-expressed gene in rat, it will allow us to compare their cis-elements and TFs and to consider difference of gene expression profiles between rat and human. It will be very useful to find out attention to drug discovery targeting gene expression mechanism.

  17. Network-Dependent Modulation of COMT and DRD2 Polymorphisms in Healthy Young Adults

    PubMed Central

    Zhao, Fangshi; Zhang, Xuejun; Qin, Wen; Liu, Feng; Wang, Qiuhui; Xu, Qiang; Wang, Junping; Yu, Chunshui

    2015-01-01

    Nonlinear modulation of the dopamine signaling on brain functions can be estimated by the interaction effects of dopamine-related genetic variations. We aimed to explore the interaction effects of COMT rs4680 and DRD2 rs1076560 on intra-network connectivity using independent component analysis. In 250 young healthy adults, we identified 11 meaningful resting-state networks (RSNs), including the salience, visual, auditory, default-mode, sensorimotor, attention and frontoparietal networks. A two-way analysis of covariance was used to investigate COMT×DRD2 interactions on intra-network connectivity in each network, controlling for age, gender and education. Significant COMT×DRD2 interaction was found in intra-network connectivity in the left medial prefrontal cortex of the anterior default-mode network, in the right dorsolateral frontal cortex of the right dorsal attention network, and in the left dorsal anterior cingulate cortex of the salience network. Post hoc tests revealed that these interactions were driven by the differential effects of DRD2 genotypes on intra-network connectivity in different COMT genotypic subgroups. Moreover, even in the same COMT subgroup, the modulation effects of DRD2 on intra-network connectivity were different across RSNs. These findings suggest a network-dependent modulation of the DA-related genetic variations on intra-network connectivity. PMID:26642826

  18. Opinion formation of free speech on the directed social network

    NASA Astrophysics Data System (ADS)

    Su, Jiongming; Ma, Hongxu; Liu, Baohong; Li, Qi

    2014-12-01

    A dynamical model with continuous opinion is proposed to study how the speech order and the topology of directed social network affect the opinion formation of free speech. In the model, agents express their opinions one by one with random order (RO) or probability order (PO), other agents paying attentions to the speaking agent, receive provider's opinion, update their opinions and then express their new opinions in their turns. It is proved that with the same agent j repeats its opinion more, other agents who pay their attentions to j and include j's opinion in their confidence level at initial time, will continue approaching j's opinion. Simulation results reveal that on directed scale-free network: (1) the model for PO forms fewer opinion clusters, larger maximum cluster (MC), smaller standard deviation (SD), and needs less waiting time to reach a middle level of consensus than RO; (2) as the parameter of scale-free degree distribution decreases or the confidence level increases, the results often get better for both speech orders; (3) the differences between PO and RO get smaller as the size of network decreases.

  19. A new kind of node centrality in directed weighted networks based on the demands of network clients

    NASA Astrophysics Data System (ADS)

    Ma, Lili; Jiang, Xin; Zhang, Zhanli; Tang, Shaoting; Zheng, Zhiming

    2011-08-01

    To reveal the correlation between the demands of network clients and the safety and robustness of real-world networks, we propose client demand centrality (CDC) in order to quantify the contributions of nodes in the transportation processes in directed weighted networks. CDC is defined by incorporating not only the topology and dynamics of the network but also the demands of network clients. The centrality measures node potential to ensure acceptable and successful transportation for clients and does quite well in distinguishing the roles of different nodes in the network. Simulation results show that node CDC has Gaussian distributions in directed networks with different link weight distributions, and the expected value of the Gaussian distribution increases from negative to positive with a decrease of the client demand. In particular, for directed scale-free networks with the scale-free link weight distribution, the network CDC is only correlated with the degree structure of the network when the client demand is large.

  20. Direct DPSK modulation of chirp-managed laser as cost-effective downstream transmitter for symmetrical 10-Gbit/s WDM PONs.

    PubMed

    Le, Quang Trung; Emsia, Ali; Briggmann, Dieter; Küppers, Franko

    2012-12-10

    This paper proposes the use of chirp-managed lasers (CML) as cost-effective downstream (DS) transmitters for next generation access networks. As the laser bandwidth is as high as 10 GHz, the CML could be directly modulated at 10 Gbit/s for downstream transmission in future wavelength division multiplexing passive optical networks (WDM PON). The laser adiabatic chirp, which is the main drawback limiting the transmission performance of directly modulated lasers, is now utilized to generate phase-shift keying (PSK) modulation format by direct modulation. At the user premise, the wavelength reuse technique based on reflective colorless upstream transmitter is applied. The optical network unit (ONU) reflects and orthogonally remodulates the received light with upstream data. A full-duplex transmission with symmetrical 10-Gbit/s bandwidth is demonstrated. Bit-error-rate measurement showed that optical power budgets of 29 dB at BER of 10(-9) or of 36 dB at BER of 10(-3) could be obtained with direct phase-shift-keying modulation of CML which proves that the proposed solution is a viable candidate for future WDM-PONs. PMID:23262890

  1. Nitrogen modulation on plant direct and indirect defenses

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Instead of being passively attacked by insect pests, plants possess a myriad of defense mechanisms to protect themselves. These mechanisms function broadly either by directly reducing herbivore fitness (direct plant defense), or by indirectly attracting natural enemies of the herbivores (indirect p...

  2. Polarization-interleave-multiplexed discrete multi-tone modulation with direct detection utilizing MIMO equalization.

    PubMed

    Zhou, Xian; Zhong, Kangping; Gao, Yuliang; Sui, Qi; Dong, Zhenghua; Yuan, Jinhui; Wang, Liang; Long, Keping; Lau, Alan Pak Tao; Lu, Chao

    2015-04-01

    Discrete multi-tone (DMT) modulation is an attractive modulation format for short-reach applications to achieve the best use of available channel bandwidth and signal noise ratio (SNR). In order to realize polarization-multiplexed DMT modulation with direct detection, we derive an analytical transmission model for dual polarizations with intensity modulation and direct diction (IM-DD) in this paper. Based on the model, we propose a novel polarization-interleave-multiplexed DMT modulation with direct diction (PIM-DMT-DD) transmission system, where the polarization de-multiplexing can be achieved by using a simple multiple-input-multiple-output (MIMO) equalizer and the transmission performance is optimized over two distinct received polarization states to eliminate the singularity issue of MIMO demultiplexing algorithms. The feasibility and effectiveness of the proposed PIM-DMT-DD system are investigated via theoretical analyses and simulation studies. PMID:25968680

  3. Identification of functional modules in a PPI network by clique percolation clustering.

    PubMed

    Zhang, Shihua; Ning, Xuemei; Zhang, Xiang-Sun

    2006-12-01

    Large-scale experiments and data integration have provided the opportunity to systematically analyze and comprehensively understand the topology of biological networks and biochemical processes in cells. Modular architecture which encompasses groups of genes/proteins involved in elementary biological functional units is a basic form of the organization of interacting proteins. Here we apply a graph clustering algorithm based on clique percolation clustering to detect overlapping network modules of a protein-protein interaction (PPI) network. Our analysis of the yeast Sacchromyces cerevisiae suggests that most of the detected modules correspond to one or more experimentally functional modules and half of these annotated modules match well with experimentally determined protein complexes. Our method of analysis can of course be applied to protein-protein interaction data for any species and even other biological networks. PMID:17098476

  4. RM-SORN: a reward-modulated self-organizing recurrent neural network.

    PubMed

    Aswolinskiy, Witali; Pipa, Gordon

    2015-01-01

    Neural plasticity plays an important role in learning and memory. Reward-modulation of plasticity offers an explanation for the ability of the brain to adapt its neural activity to achieve a rewarded goal. Here, we define a neural network model that learns through the interaction of Intrinsic Plasticity (IP) and reward-modulated Spike-Timing-Dependent Plasticity (STDP). IP enables the network to explore possible output sequences and STDP, modulated by reward, reinforces the creation of the rewarded output sequences. The model is tested on tasks for prediction, recall, non-linear computation, pattern recognition, and sequence generation. It achieves performance comparable to networks trained with supervised learning, while using simple, biologically motivated plasticity rules, and rewarding strategies. The results confirm the importance of investigating the interaction of several plasticity rules in the context of reward-modulated learning and whether reward-modulated self-organization can explain the amazing capabilities of the brain. PMID:25852533

  5. RM-SORN: a reward-modulated self-organizing recurrent neural network

    PubMed Central

    Aswolinskiy, Witali; Pipa, Gordon

    2015-01-01

    Neural plasticity plays an important role in learning and memory. Reward-modulation of plasticity offers an explanation for the ability of the brain to adapt its neural activity to achieve a rewarded goal. Here, we define a neural network model that learns through the interaction of Intrinsic Plasticity (IP) and reward-modulated Spike-Timing-Dependent Plasticity (STDP). IP enables the network to explore possible output sequences and STDP, modulated by reward, reinforces the creation of the rewarded output sequences. The model is tested on tasks for prediction, recall, non-linear computation, pattern recognition, and sequence generation. It achieves performance comparable to networks trained with supervised learning, while using simple, biologically motivated plasticity rules, and rewarding strategies. The results confirm the importance of investigating the interaction of several plasticity rules in the context of reward-modulated learning and whether reward-modulated self-organization can explain the amazing capabilities of the brain. PMID:25852533

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

    NASA Astrophysics Data System (ADS)

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

    2012-09-01

    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.

  7. Wideband phase modulator works directly on carrier. [application of varactor compensated microwave circuit

    NASA Technical Reports Server (NTRS)

    Rippy, R. R.

    1975-01-01

    Multiplier-induced problems related to undesirable effects of the varactor multiplier on the modulation spectrum are eliminated in a modulator circuit which operates directly at the desired output frequency. The principles of operation of the new circuit are discussed and attention is given to requirements for high-Q components and the possibility of linear frequency deviation.

  8. Teleconnection Paths via Climate Network Direct Link Detection

    NASA Astrophysics Data System (ADS)

    Zhou, Dong; Gozolchiani, Avi; Ashkenazy, Yosef; Havlin, Shlomo

    2015-12-01

    Teleconnections describe remote connections (typically thousands of kilometers) of the climate system. These are of great importance in climate dynamics as they reflect the transportation of energy and climate change on global scales (like the El Niño phenomenon). Yet, the path of influence propagation between such remote regions, and weighting associated with different paths, are only partially known. Here we propose a systematic climate network approach to find and quantify the optimal paths between remotely distant interacting locations. Specifically, we separate the correlations between two grid points into direct and indirect components, where the optimal path is found based on a minimal total cost function of the direct links. We demonstrate our method using near surface air temperature reanalysis data, on identifying cross-latitude teleconnections and their corresponding optimal paths. The proposed method may be used to quantify and improve our understanding regarding the emergence of climate patterns on global scales.

  9. Teleconnection Paths via Climate Network Direct Link Detection.

    PubMed

    Zhou, Dong; Gozolchiani, Avi; Ashkenazy, Yosef; Havlin, Shlomo

    2015-12-31

    Teleconnections describe remote connections (typically thousands of kilometers) of the climate system. These are of great importance in climate dynamics as they reflect the transportation of energy and climate change on global scales (like the El Niño phenomenon). Yet, the path of influence propagation between such remote regions, and weighting associated with different paths, are only partially known. Here we propose a systematic climate network approach to find and quantify the optimal paths between remotely distant interacting locations. Specifically, we separate the correlations between two grid points into direct and indirect components, where the optimal path is found based on a minimal total cost function of the direct links. We demonstrate our method using near surface air temperature reanalysis data, on identifying cross-latitude teleconnections and their corresponding optimal paths. The proposed method may be used to quantify and improve our understanding regarding the emergence of climate patterns on global scales. PMID:26765033

  10. Different types of laughter modulate connectivity within distinct parts of the laughter perception network.

    PubMed

    Wildgruber, Dirk; Szameitat, Diana P; Ethofer, Thomas; Brück, Carolin; Alter, Kai; Grodd, Wolfgang; Kreifelts, Benjamin

    2013-01-01

    Laughter is an ancient signal of social communication among humans and non-human primates. Laughter types with complex social functions (e.g., taunt and joy) presumably evolved from the unequivocal and reflex-like social bonding signal of tickling laughter already present in non-human primates. Here, we investigated the modulations of cerebral connectivity associated with different laughter types as well as the effects of attention shifts between implicit and explicit processing of social information conveyed by laughter using functional magnetic resonance imaging (fMRI). Complex social laughter types and tickling laughter were found to modulate connectivity in two distinguishable but partially overlapping parts of the laughter perception network irrespective of task instructions. Connectivity changes, presumably related to the higher acoustic complexity of tickling laughter, occurred between areas in the prefrontal cortex and the auditory association cortex, potentially reflecting higher demands on acoustic analysis associated with increased information load on auditory attention, working memory, evaluation and response selection processes. In contrast, the higher degree of socio-relational information in complex social laughter types was linked to increases of connectivity between auditory association cortices, the right dorsolateral prefrontal cortex and brain areas associated with mentalizing as well as areas in the visual associative cortex. These modulations might reflect automatic analysis of acoustic features, attention direction to informative aspects of the laughter signal and the retention of those in working memory during evaluation processes. These processes may be associated with visual imagery supporting the formation of inferences on the intentions of our social counterparts. Here, the right dorsolateral precentral cortex appears as a network node potentially linking the functions of auditory and visual associative sensory cortices with those of the mentalizing-associated anterior mediofrontal cortex during the decoding of social information in laughter. PMID:23667619

  11. Myosin lever arm directs collective motion on cellular actin network

    PubMed Central

    Hariadi, Rizal F.; Cale, Mario; Sivaramakrishnan, Sivaraj

    2014-01-01

    The molecular motor myosin teams up to drive muscle contraction, membrane traffic, and cell division in biological cells. Myosin function in cells emerges from the interaction of multiple motors tethered to a scaffold, with surrounding actin filaments organized into 3D networks. Despite the importance of myosin function, the influence of intermotor interactions on collective motion remains poorly understood. In this study, we used precisely engineered myosin assemblies to examine emergence in collective myosin movement. We report that tethering multiple myosin VI motors, but not myosin V motors, modifies their movement trajectories on keratocyte actin networks. Single myosin V and VI dimers display similar skewed trajectories, albeit in opposite directions, when traversing the keratocyte actin network. In contrast, tethering myosin VI motors, but not myosin V motors, progressively straightens the trajectories with increasing myosin number. Trajectory shape of multimotor scaffolds positively correlates with the stiffness of the myosin lever arm. Swapping the flexible myosin VI lever arm for the relatively rigid myosin V lever increases trajectory skewness, and vice versa. A simplified model of coupled motor movement demonstrates that the differences in flexural rigidity of the two myosin lever arms is sufficient to account for the differences in observed behavior of groups of myosin V and VI motors. In accordance with this model trajectory, shapes for scaffolds containing both myosin V and VI are dominated by the myosin with a stiffer lever arm. Our findings suggest that structural features unique to each myosin type may confer selective advantages in cellular functions. PMID:24591646

  12. Directed assembly of three-dimensional microvascular networks

    NASA Astrophysics Data System (ADS)

    Therriault, Daniel

    Three-dimensional (3-D) microvascular networks with pervasive, interconnected channels less than 300 mum in diameter may find widespread application in microfluidic devices, biotechnology, sensors, and autonomic healing materials. Although microchannel arrays are readily constructed in two-dimensions by photolithographic or soft lithographic techniques, their construction in three-dimensions remains a challenging problem. The development of a microfabrication method to build 3-D microvascular networks based on direct-write assembly is described is this thesis. The method is based on the robotic deposition of a fugitive organic ink to form a free-standing scaffold structure. Secondary infiltration of a structural resin followed by setting of the matrix and removal of the scaffold yields an embedded pervasive network of smooth cylindrical channels (˜10--500 mum) with defined connectivity. Rheological and other material properties studies of fugitive organic ink were performed in order to identify the critical characteristics required for successful deposition of 3-D scaffolds by direct-write assembly. Guided by the results of these studies, several new ink formulations were screened for improved deposition performance. The most successful of these inks (40wt% microcrystalline wax, 60wt% petroleum jelly) showed excellent deposition and had an equilibrium modulus at room temperature (G 'eq ˜ 7.70 kPa 1 Hz) nearly two orders of magnitude higher than the original ink. The optimized ink was used to successfully build thick (i.e., ˜100 layers) scaffold structures at room temperature with negligible time-dependent deformation post-deposition. Secondary infiltration of the resin was accomplished at room temperature while maintaining the scaffold architecture. The optimized ink was also successfully extruded through small micronozzles (1 mum). The construction of 3-D microvascular networks enables microfluidic devices with unparallel geometric complexity. In one example, a 3-D microfluidic mixing device was demonstrated with square-spiral mixing towers isolated within the vascular network by a secondary photopatterning process. These vertical towers give rise to chaotic advection of the fluid streams and dramatic improvements in mixing relative to simple straight (1-D) and square-wave (2-D) channels while significantly reducing the device planar footprint.

  13. Directed Dynamic Small-World Network Model for Worm Epidemics in Mobile ad hoc Networks

    NASA Astrophysics Data System (ADS)

    Zhu, Chen-Ping; Wang, Li; Liu, Xiao-Ting; Yan, Zhi-Jun

    2012-01-01

    We investigate the worm spreading process in mobile ad hoc networks with a susceptible-infected-recovered model on a two-dimensional plane. A medium access control mechanism operates within it, inhibiting transmission and relaying a message by using other nodes inside the node's transmitting circle during speaking. We measure the rewiring probability p with the transmitting range r and the average relative velocity v¯ of the moving nodes, and map the problem into a directed dynamic small-world network. A new scaling relation for the recovered portion of the nodes reveals the effect caused by geometric distance, which has been ignored by previous models.

  14. Integrin-Directed Modulation of Macrophage Responses to Biomaterials

    PubMed Central

    Zaveri, Toral D.; Lewis, Jamal S.; Dolgova, Natalia V.; Clare-Salzler, Michael J.; Keselowsky, Benjamin G.

    2014-01-01

    Macrophages are the primary mediator of chronic inflammatory responses to implanted biomaterials, in cases when the material is either in particulate or bulk form. Chronic inflammation limits the performance and functional life of numerous implanted medical devices, and modulating macrophage interactions with biomaterials to mitigate this response would be beneficial. The integrin family of cell surface receptors mediates cell adhesion through binding to adhesive proteins nonspecifically adsorbed onto biomaterial surfaces. In this work, the roles of integrin Mac-1 (αMβ2) and RGD-binding integrins were investigated using model systems for both particulate and bulk biomaterials. Specifically, the macrophage functions of phagocytosis and inflammatory cytokine secretion in response to a model particulate material, polystyrene microparticles were investigated. Opsonizing proteins modulated microparticle uptake, and integrin Mac-1 and RGD-binding integrins were found to control microparticle uptake in an opsonin-dependent manner. The presence of adsorbed endotoxin did not affect microparticle uptake levels, but was required for the production of inflammatory cytokines in response to microparticles. Furthermore, it was demonstrated that integrin Mac-1 and RGD-binding integrins influence the in vivo foreign body response to a bulk biomaterial, subcutaneously implanted polyethylene terephthalate. A thinner foreign body capsule was formed when integrin Mac-1 was absent (~30% thinner) or when RGD-binding integrins were blocked by controlled release of a blocking peptide (~45% thinner). These findings indicate integrin Mac-1 and RGD-binding integrins are involved and may serve as therapeutic targets to mitigate macrophage inflammatory responses to both particulate and bulk biomaterials. PMID:24462356

  15. Directed deposition of inorganic oxide networks on patterned polymer templates

    NASA Astrophysics Data System (ADS)

    Ford, Thomas James Robert

    Inspired by nature, we have successfully directed the deposition of inorganic oxide materials on polymer templates via a combination of top-down and bottom-up fabrication methods. We have functionally mimicked the hierarchical silica exoskeletons of diatoms, where specialized proteins chaperone the condensation of silicic acid into nanoscale silica networks confined by microscopic vesicle walls. We replaced the proteins with functionally analogous polyamines and vesicles with lithographically defined polymer templates. We grafted the polyamines either to the surface or throughout the template by changing the template chemistry and altering our grafting strategy. Exposure to an inorganic oxide precursor solution led to electrostatic aggregation at the polyamine chains, catalyzing hydrolysis and condensation to form long-range inorganic oxide nanoparticle networks. Grafted to epoxy surfaces, swelling effects and the hyperbranched brush morphology lead to the formation of nanofruit features that generated thin, conformal inorganic coatings. When the polyamines were grafted throughout hydrogel templates, we obtained composite networks that yielded faithful inorganic replicas of the original patterns. By varying the polyamine chain length and combustion parameters, we controlled the nanoparticle size, morphology, and crystalline phase. The polyamine morphology affected the resulting inorganic network in both fabrication schemes and we could control the depostion over multiple length scales. Because our methods were compatible with a variety of lithographic methods, we were able to generate inorganic replicas of 1D, 2D, and 3D polymer structures. These may be used for a wide range of applications, including sensing, catalysis, photonic, phononic, photovoltaic, and others that require well-defined inorganic structures.

  16. Traveling-wave electrode design for a directional-coupler-based polymeric electro-optical modulator

    NASA Astrophysics Data System (ADS)

    Zhou, Qingjun; Chen, Ray T.

    2003-12-01

    In order to find the optimal traveling-wave electrode formation for directional-coupler-based polymeric modulators, four electrode structures are evaluated by simulating the modulator's driving voltages and bandwidths, and by experimentally measuring their driving voltages. First, the characteristic parameters of these four structures are analyzed. Then, the driving votlages for modulators using these four structures are computed using beam propagation method, and their bandwidths are obtained using small-signal analysis. Finally modulators are fabricated using DR1/PMMA and CLD1/APC respectively, and their driving voltages for different electode structures are measured.

  17. ModuleRole: A Tool for Modulization, Role Determination and Visualization in Protein-Protein Interaction Networks

    PubMed Central

    Li, GuiPeng; Li, Ming; Zhang, YiWei; Wang, Dong; Li, Rong; Guimerà, Roger; Gao, Juntao Tony; Zhang, Michael Q.

    2014-01-01

    Rapidly increasing amounts of (physical and genetic) protein-protein interaction (PPI) data are produced by various high-throughput techniques, and interpretation of these data remains a major challenge. In order to gain insight into the organization and structure of the resultant large complex networks formed by interacting molecules, using simulated annealing, a method based on the node connectivity, we developed ModuleRole, a user-friendly web server tool which finds modules in PPI network and defines the roles for every node, and produces files for visualization in Cytoscape and Pajek. For given proteins, it analyzes the PPI network from BioGRID database, finds and visualizes the modules these proteins form, and then defines the role every node plays in this network, based on two topological parameters Participation Coefficient and Z-score. This is the first program which provides interactive and very friendly interface for biologists to find and visualize modules and roles of proteins in PPI network. It can be tested online at the website http://www.bioinfo.org/modulerole/index.php, which is free and open to all users and there is no login requirement, with demo data provided by “User Guide” in the menu Help. Non-server application of this program is considered for high-throughput data with more than 200 nodes or user’s own interaction datasets. Users are able to bookmark the web link to the result page and access at a later time. As an interactive and highly customizable application, ModuleRole requires no expert knowledge in graph theory on the user side and can be used in both Linux and Windows system, thus a very useful tool for biologist to analyze and visualize PPI networks from databases such as BioGRID. Availability ModuleRole is implemented in Java and C, and is freely available at http://www.bioinfo.org/modulerole/index.php. Supplementary information (user guide, demo data) is also available at this website. API for ModuleRole used for this program can be obtained upon request. PMID:24788790

  18. Effect of Modulated Alternating and Direct Current Iontophoresis on Transdermal Delivery of Lidocaine Hydrochloride

    PubMed Central

    Banga, Ajay K.

    2014-01-01

    The objective of this study was to investigate the iontophoretic delivery of lidocaine hydrochloride through porcine skin and to compare the effects of modulated alternating and direct current iontophoresis. Continuous and modulated iontophoresis was applied for one hour and two hours (0-1 h and 4-5th h) using a 1% w/v solution of lidocaine hydrochloride. Tape stripping was done to quantify the amount of drug permeated into stratum corneum and skin extraction studies were performed to determine the amount of drug in stripped skin. Receptor was sampled and analyzed over predefined time periods. The amount of lidocaine delivered across porcine skin after modulated direct current iontophoresis for 2 h was 1069.87 ± 120.03 μg/sq·cm compared to 744.81 ± 125.41 μg/sq·cm after modulated alternating current iontophoresis for 2 h. Modulated direct current iontophoresis also enhanced lidocaine delivery by twelvefold compared to passive delivery as 91.27 ± 18.71 μg/sq·cm of lidocaine was delivered after passive delivery. Modulated iontophoresis enhanced the delivery of lidocaine hydrochloride across porcine skin compared to the passive delivery. Modulated alternating current iontophoresis for duration of 2 h at frequency of 1 kHz was found to be comparable to the continuous direct current iontophoresis for 1 h. PMID:24959580

  19. Surface-directed modulation of supramolecular gel properties.

    PubMed

    Angelerou, Maria Galini Faidra; Sabri, Akmal; Creasey, Rhiannon; Angelerou, Polyxeni; Marlow, Maria; Zelzer, Mischa

    2016-03-10

    Supramolecular materials are widely studied and used for a variety of applications; in most applications, these materials are in contact with surfaces of other materials. Whilst much focus has been placed on elucidating factors that affect supramolecular material properties, the influence of the material surface on gel formation is poorly characterised. Here, we demonstrate that surface properties directly affect the fibre architecture and mechanical properties of self-assembled cytidine based gel films. PMID:26960905

  20. Index modulation Bragg gratings directly imprinted on sol gel layers

    NASA Astrophysics Data System (ADS)

    Moreau, Yves; Arguel, Philippe; Coudray, Paul; Porque, Jerome; Etienne, Pascal

    1998-01-01

    Among the fabrication techniques of integrated optical devices, the sol-gel chemistry is now performant enough to make thin films of transparent materials with controlled purity and composition, at low temperature. Semi-mineral semi-organic solutions allow dip coating followed by low temperature baking to deposit vitreous films up to eight micrometers thick which are free from cracks. A local polymerization process through UV exposure enables hybrid components compatible with electronic planar silicon or III- V components. This UV imprinting method is used here to make index modulation gratings with use of a holographic equipment as an alternative to the use of a costly phase mask. Gratings have been imprinted on various sol-gel films; single layer, with a protective coating, and/or with an isolating buffer layer from the substrate, which is silicon and glass. Diffraction magnitude is measured in the various cases, as well as analysis and computer simulations are performed. Wavelength filters are experimented and studied. This shows the potential of this low cost technology in integrated optics, for application in telecommunications.

  1. Multiple Differential Networks Strategy Reveals Carboplatin and Melphalan-Induced Dynamic Module Changes in Retinoblastoma.

    PubMed

    Chen, Cui; Ma, Feng-Wei; Du, Cui-Yun; Wang, Ping

    2016-01-01

    BACKGROUND Retinoblastoma (RB) is the most common malignant tumor of the eye in childhood. The objective of this paper was to investigate carboplatin (CAR)- and melphalan (MEL)-induced dynamic module changes in RB based on multiple (M) differential networks, and to generate systems-level insights into RB progression. MATERIAL AND METHODS To achieve this goal, we constructed M-differential co-expression networks (DCNs), assigned a weight to each edge, and identified seed genes in M DCNs by ranking genes based on their topological features. Starting with seed genes, a module search was performed to explore candidate modules in CAR and MEL condition. M-DMs were detected according to significance evaluations of M-modules, which originated from refinement of candidate modules. Further, we revealed dynamic changes in M-DM activity and connectivity on the basis of significance of Module Connectivity Dynamic Score (MCDS). RESULTS In the present study, M=2, a total of 21 seed genes were obtained. By assessing module search, refinement, and evaluation, we gained 18 2-DMs. Moreover, 3 significant 2-DMs (Module 1, Module 2, and Module 3) with dynamic changes across CAR and MEL condition were determined, and we denoted them as dynamic modules. Module 1 had 27 nodes of which 6 were seed genes and 56 edges. Module 2 was composed of 28 nodes and 54 edges. A total of 28 nodes interacted with 45 edges presented in Module 3. CONCLUSIONS We have identified 3 dynamic modules with changes induced by CAR and MEL in RB, which might give insights in revealing molecular mechanism for RB therapy. PMID:27144687

  2. FPGA-based artificial neural network using CORDIC modules

    NASA Astrophysics Data System (ADS)

    Liddicoat, Albert A.; Slivovsky, Lynne A.; McLenegan, Tim; Heyer, Don

    2006-08-01

    Artificial neural networks have been used in applications that require complex procedural algorithms and in systems which lack an analytical mathematic model. By designing a large network of computing nodes based on the artificial neuron model, new solutions can be developed for computational problems in fields such as image processing and speech recognition. Neural networks are inherently parallel since each neuron, or node, acts as an autonomous computational element. Artificial neural networks use a mathematical model for each node that processes information from other nodes in the same region. The information processing entails computing a weighted average computation followed by a nonlinear mathematical transformation. Some typical artificial neural network applications use the exponential function or trigonometric functions for the nonlinear transformation. Various simple artificial neural networks have been implemented using a processor to compute the output for each node sequentially. This approach uses sequential processing and does not take advantage of the parallelism of a complex artificial neural network. In this work a hardware-based approach is investigated for artificial neural network applications. A Field Programmable Gate Arrays (FPGAs) is used to implement an artificial neuron using hardware multipliers, adders and CORDIC functional units. In order to create a large scale artificial neural network, area efficient hardware units such as CORDIC units are needed. High performance and low cost bit serial CORDIC implementations are presented. Finally, the FPGA resources and the performance of a hardware-based artificial neuron are presented.

  3. A Genomic Strategy to Elucidate Modules of Oncogenic Pathway Signaling Networks

    PubMed Central

    Chang, Jeffrey T.; Carvalho, Carlos; Mori, Seiichi; Bild, Andrea H.; Gatza, Michael; Wang, Quanli; Lucas, Joseph; Potti, Anil; Febbo, Phillip; West, Mike; Nevins, Joseph R.

    2009-01-01

    Summary Recent studies have emphasized the importance of pathway-specific interpretations for understanding the functional relevance of gene alterations in human cancers. Although signaling activities are often conceptualized as linear events, in reality they reflect the activity of complex functional networks assembled from modules that each respond to input signals. To acquire a deeper understand of this network structure, we developed an approach to deconstruct pathways into modules represented by gene expression signatures. Our studies confirm that they represent units of underlying biological activity linked to known biochemical pathway structures. Importantly, we show that these signaling modules provide tools to dissect the complexity of oncogenic states that define disease outcomes as well as response to pathway-specific therapeutics. We propose that this model of pathway structure constitutes a framework to study the processes by which information propogates through cellular networks, and to elucidate the relationships of fundamental modules to cellular and clinical phenotypes. PMID:19362539

  4. A genomic strategy to elucidate modules of oncogenic pathway signaling networks.

    PubMed

    Chang, Jeffrey T; Carvalho, Carlos; Mori, Seiichi; Bild, Andrea H; Gatza, Michael L; Wang, Quanli; Lucas, Joseph E; Potti, Anil; Febbo, Phillip G; West, Mike; Nevins, Joseph R

    2009-04-10

    Recent studies have emphasized the importance of pathway-specific interpretations for understanding the functional relevance of gene alterations in human cancers. Although signaling activities are often conceptualized as linear events, in reality, they reflect the activity of complex functional networks assembled from modules that each respond to input signals. To acquire a deeper understanding of this network structure, we developed an approach to deconstruct pathways into modules represented by gene expression signatures. Our studies confirm that they represent units of underlying biological activity linked to known biochemical pathway structures. Importantly, we show that these signaling modules provide tools to dissect the complexity of oncogenic states that define disease outcomes as well as response to pathway-specific therapeutics. We propose that this model of pathway structure constitutes a framework to study the processes by which information propogates through cellular networks and to elucidate the relationships of fundamental modules to cellular and clinical phenotypes. PMID:19362539

  5. ModuleBlast: identifying activated sub-networks within and across species

    PubMed Central

    Zinman, Guy E.; Naiman, Shoshana; O'Dee, Dawn M.; Kumar, Nishant; Nau, Gerard J.; Cohen, Haim Y.; Bar-Joseph, Ziv

    2015-01-01

    Identifying conserved and divergent response patterns in gene networks is becoming increasingly important. A common approach is integrating expression information with gene association networks in order to find groups of connected genes that are activated or repressed. In many cases, researchers are also interested in comparisons across species (or conditions). Finding an active sub-network is a hard problem and applying it across species requires further considerations (e.g. orthology information, expression data and networks from different sources). To address these challenges we devised ModuleBlast, which uses both expression and network topology to search for highly relevant sub-networks. We have applied ModuleBlast to expression and interaction data from mouse, macaque and human to study immune response and aging. The immune response analysis identified several relevant modules, consistent with recent findings on apoptosis and NFκB activation following infection. Temporal analysis of these data revealed cascades of modules that are dynamically activated within and across species. We have experimentally validated some of the novel hypotheses resulting from the analysis of the ModuleBlast results leading to new insights into the mechanisms used by a key mammalian aging protein. PMID:25428368

  6. Wavelength tunable receiver for FSK modulated optical signals based on standard direct-detection circuitry

    NASA Astrophysics Data System (ADS)

    van Eijk, P.; Jennen, J. G.; Koonen, Antonius A.

    1995-02-01

    A WDM system has been realized, intended for digital broadband (e.g. video) distribution in an optically splitted subscriber access network. Four standard 565 Mbit/s optical transmitter units have been equipped with wavelength-matched 1557 nm DFB laser diodes. The four transmitters are wavelength-locked to a temperature-stabilized fiber Fabry-Perot (FFP). The lasers are FSK modulated with a tone spacing of 6.7 GHz; the 565 Mbit/s input signals are 7B8B coded to avoid problems with the laser's non-linear FM response. Another tunable FFP precedes a standard direct-detection receiver for both wavelength channel selection and FSK demodulation. A wavelength control circuit (WCC) ensures locking of the FFP to the correct tone of the selected channel. The WCC continuously maximizes the average FFP output power, by determining the time-derivative of the mean photodiode current. The main advantage of this approach is the absence of a dithering signal, which interferes with the data signal. BER curves have been measured for each of the four channels and compared with theory, discrepancies are < 0.75 dB. A net system power budget of > 28 dB for each channel has been achieved, and no evidence for BER floors has been found down to a BER of 10-11.

  7. Robust criticality of an Ising model on rewired directed networks

    NASA Astrophysics Data System (ADS)

    Lipowski, Adam; Gontarek, Krzysztof; Lipowska, Dorota

    2015-06-01

    We show that preferential rewiring, which is supposed to mimic the behavior of financial agents, changes a directed-network Ising ferromagnet with a single critical point into a model with robust critical behavior. For the nonrewired random graph version, due to a constant number of out-links for each site, we write a simple mean-field-like equation describing the behavior of magnetization; we argue that it is exact and support the claim with extensive Monte Carlo simulations. For the rewired version, this equation is obeyed only at low temperatures. At higher temperatures, rewiring leads to strong heterogeneities, which apparently invalidates mean-field arguments and induces large fluctuations and divergent susceptibility. Such behavior is traced back to the formation of a relatively small core of agents that influence the entire system.

  8. Lighting direction and visual field modulate perceived intensity of illumination

    PubMed Central

    McCourt, Mark E.; Blakeslee, Barbara; Padmanabhan, Ganesh

    2013-01-01

    When interpreting object shape from shading the visual system exhibits a strong bias that illumination comes from above and slightly from the left. We asked whether such biases in the perceived direction of illumination might also influence its perceived intensity. Arrays of nine cubes were stereoscopically rendered where individual cubes varied in their 3D pose, but possessed identical triplets of visible faces. Arrays were virtually illuminated from one of four directions: Above-Left, Above-Right, Below-Left, and Below-Right (±24.4° azimuth; ±90° elevation). Illumination intensity possessed 15 levels, resulting in mean cube array luminances ranging from 1.31–3.45 cd/m2. A “reference” array was consistently illuminated from Above-Left at mid-intensity (mean array luminance = 2.38 cd/m2). The reference array's illumination was compared to that of matching arrays which were illuminated from all four directions at all intensities. Reference and matching arrays appeared in the left and right visual field, respectively, or vice versa. Subjects judged which cube array appeared to be under more intense illumination. Using the method of constant stimuli we determined the illumination level of matching arrays required to establish subjective equality with the reference array as a function of matching cube visual field, illumination elevation, and illumination azimuth. Cube arrays appeared significantly more intensely illuminated when they were situated in the left visual field (p = 0.017), and when they were illuminated from below (p = 0.001), and from the left (p = 0.001). An interaction of modest strength was that the effect of illumination azimuth was greater for matching arrays situated in the left visual field (p = 0.042). We propose that objects lit from below appear more intensely illuminated than identical objects lit from above due to long-term adaptation to downward lighting. The amplification of perceived intensity of illumination for stimuli situated in the left visual field and lit from the left is best explained by tonic egocentric and allocentric leftward attentional biases, respectively. PMID:24399990

  9. A Modularity-Based Method Reveals Mixed Modules from Chemical-Gene Heterogeneous Network

    PubMed Central

    Song, Jianglong; Tang, Shihuan; Liu, Xi; Gao, Yibo; Yang, Hongjun; Lu, Peng

    2015-01-01

    For a multicomponent therapy, molecular network is essential to uncover its specific mode of action from a holistic perspective. The molecular system of a Traditional Chinese Medicine (TCM) formula can be represented by a 2-class heterogeneous network (2-HN), which typically includes chemical similarities, chemical-target interactions and gene interactions. An important premise of uncovering the molecular mechanism is to identify mixed modules from complex chemical-gene heterogeneous network of a TCM formula. We thus proposed a novel method (MixMod) based on mixed modularity to detect accurate mixed modules from 2-HNs. At first, we compared MixMod with Clauset-Newman-Moore algorithm (CNM), Markov Cluster algorithm (MCL), Infomap and Louvain on benchmark 2-HNs with known module structure. Results showed that MixMod was superior to other methods when 2-HNs had promiscuous module structure. Then these methods were tested on a real drug-target network, in which 88 disease clusters were regarded as real modules. MixMod could identify the most accurate mixed modules from the drug-target 2-HN (normalized mutual information 0.62 and classification accuracy 0.4524). In the end, MixMod was applied to the 2-HN of Buchang naoxintong capsule (BNC) and detected 49 mixed modules. By using enrichment analysis, we investigated five mixed modules that contained primary constituents of BNC intestinal absorption liquid. As a matter of fact, the findings of in vitro experiments using BNC intestinal absorption liquid were found to highly accord with previous analysis. Therefore, MixMod is an effective method to detect accurate mixed modules from chemical-gene heterogeneous networks and further uncover the molecular mechanism of multicomponent therapies, especially TCM formulae. PMID:25927435

  10. Experimental demonstration of a flat optical frequency comb generation based on cascaded directly modulated distributed feedback laser and polarization modulator

    NASA Astrophysics Data System (ADS)

    Chen, Dalei; Wang, Rong; Pu, Tao; Xiang, Peng; Fang, Tao; Zheng, Jiling; Huang, Long; Wang, Peng

    2016-03-01

    A scheme to generate a flat optical frequency comb (OFC) is proposed and experimentally demonstrated based on a directly modulated distributed feedback (DFB) laser cascaded with a polarization modulator (PolM). In the proposed scheme, the DFB laser is optically injection-locked by a tunable laser source and directly modulated by a radio frequency (RF) signal, which is amplified by a microwave power amplifier. The optical signal is then sent to PolM via a polarization controller (PC) and modulated by the amplified and phase-shifted RF signal from the same source. The optical signal is finally received and measured by an optical spectrum analyzer (OSA) after transmitting through another PC and a polarizer. Here, the OFC with their power variation within 3 dB is desired, and four OFCs with 6, 6, 5, and 4 comb lines are generated using the RF signals with different frequencies, which have a flatness of, respectively, 2.4, 2.5, 0.7, and 0.6 dB. Here, the number of comb lines is decreased, which is due to the RF signal power decrease while its frequency is raised.

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

    PubMed Central

    Rogalsky, Corianne

    2009-01-01

    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. PMID:18669589

  12. Social network modulation of reward-related signals

    PubMed Central

    Fareri, Dominic S.; Niznikiewicz, Michael A.; Lee, Victoria K.; Delgado, Mauricio R.

    2012-01-01

    Everyday goals and experiences are often shared with others who may hold different places within our social networks. We investigated whether the experience of sharing a reward differs with respect to social network. Twenty human participants played a card guessing game for shared monetary outcomes with three partners: a computer, a confederate (out-of-network), and a friend (in-network). Participants subjectively rated the experience of sharing a reward more positively with their friend than the other partners. Neuroimaging results support participants’ subjective reports, as ventral striatal BOLD responses were more robust when sharing monetary gains with a friend, as compared to with the confederate or computer, suggesting a higher value for sharing with an in-network partner. Interestingly, ratings of social closeness co-varied with this activity, resulting in a significant partner × closeness interaction: exploratory analysis showed that only participants reporting higher levels of closeness demonstrated partner-related differences in striatal BOLD response. These results suggest that reward valuation in social contexts is sensitive to distinctions of social network, such that sharing positive experiences with in-network others may carry higher value. PMID:22745503

  13. Dynamic identifying protein functional modules based on adaptive density modularity in protein-protein interaction networks

    PubMed Central

    2015-01-01

    Background The identification of protein functional modules would be a great aid in furthering our knowledge of the principles of cellular organization. Most existing algorithms for identifying protein functional modules have a common defect -- once a protein node is assigned to a functional module, there is no chance to move the protein to the other functional modules during the follow-up processes, which lead the erroneous partitioning occurred at previous step to accumulate till to the end. Results In this paper, we design a new algorithm ADM (Adaptive Density Modularity) to detect protein functional modules based on adaptive density modularity. In ADM algorithm, according to the comparison between external closely associated degree and internal closely associated degree, the partitioning of a protein-protein interaction network into functional modules always evolves quickly to increase the density modularity of the network. The integration of density modularity into the new algorithm not only overcomes the drawback mentioned above, but also contributes to identifying protein functional modules more effectively. Conclusions The experimental result reveals that the performance of ADM algorithm is superior to many state-of-the-art protein functional modules detection techniques in aspect of the accuracy of prediction. Moreover, the identified protein functional modules are statistically significant in terms of "Biological Process" annotated in Gene Ontology, which provides substantial support for revealing the principles of cellular organization. PMID:26330105

  14. The psychedelic state induced by ayahuasca modulates the activity and connectivity of the default mode network.

    PubMed

    Palhano-Fontes, Fernanda; Andrade, Katia C; Tofoli, Luis F; Santos, Antonio C; Crippa, Jose Alexandre S; Hallak, Jaime E C; Ribeiro, Sidarta; de Araujo, Draulio B

    2015-01-01

    The experiences induced by psychedelics share a wide variety of subjective features, related to the complex changes in perception and cognition induced by this class of drugs. A remarkable increase in introspection is at the core of these altered states of consciousness. Self-oriented mental activity has been consistently linked to the Default Mode Network (DMN), a set of brain regions more active during rest than during the execution of a goal-directed task. Here we used fMRI technique to inspect the DMN during the psychedelic state induced by Ayahuasca in ten experienced subjects. Ayahuasca is a potion traditionally used by Amazonian Amerindians composed by a mixture of compounds that increase monoaminergic transmission. In particular, we examined whether Ayahuasca changes the activity and connectivity of the DMN and the connection between the DMN and the task-positive network (TPN). Ayahuasca caused a significant decrease in activity through most parts of the DMN, including its most consistent hubs: the Posterior Cingulate Cortex (PCC)/Precuneus and the medial Prefrontal Cortex (mPFC). Functional connectivity within the PCC/Precuneus decreased after Ayahuasca intake. No significant change was observed in the DMN-TPN orthogonality. Altogether, our results support the notion that the altered state of consciousness induced by Ayahuasca, like those induced by psilocybin (another serotonergic psychedelic), meditation and sleep, is linked to the modulation of the activity and the connectivity of the DMN. PMID:25693169

  15. The Psychedelic State Induced by Ayahuasca Modulates the Activity and Connectivity of the Default Mode Network

    PubMed Central

    Palhano-Fontes, Fernanda; Andrade, Katia C.; Tofoli, Luis F.; Santos, Antonio C.; Crippa, Jose Alexandre S.; Hallak, Jaime E. C.; Ribeiro, Sidarta; de Araujo, Draulio B.

    2015-01-01

    The experiences induced by psychedelics share a wide variety of subjective features, related to the complex changes in perception and cognition induced by this class of drugs. A remarkable increase in introspection is at the core of these altered states of consciousness. Self-oriented mental activity has been consistently linked to the Default Mode Network (DMN), a set of brain regions more active during rest than during the execution of a goal-directed task. Here we used fMRI technique to inspect the DMN during the psychedelic state induced by Ayahuasca in ten experienced subjects. Ayahuasca is a potion traditionally used by Amazonian Amerindians composed by a mixture of compounds that increase monoaminergic transmission. In particular, we examined whether Ayahuasca changes the activity and connectivity of the DMN and the connection between the DMN and the task-positive network (TPN). Ayahuasca caused a significant decrease in activity through most parts of the DMN, including its most consistent hubs: the Posterior Cingulate Cortex (PCC)/Precuneus and the medial Prefrontal Cortex (mPFC). Functional connectivity within the PCC/Precuneus decreased after Ayahuasca intake. No significant change was observed in the DMN-TPN orthogonality. Altogether, our results support the notion that the altered state of consciousness induced by Ayahuasca, like those induced by psilocybin (another serotonergic psychedelic), meditation and sleep, is linked to the modulation of the activity and the connectivity of the DMN. PMID:25693169

  16. Direct and Propagated Effects of Small Molecules on Protein–Protein Interaction Networks

    PubMed Central

    Cesa, Laura C.; Mapp, Anna K.; Gestwicki, Jason E.

    2015-01-01

    Networks of protein–protein interactions (PPIs) link all aspects of cellular biology. Dysfunction in the assembly or dynamics of PPI networks is a hallmark of human disease, and as such, there is growing interest in the discovery of small molecules that either promote or inhibit PPIs. PPIs were once considered undruggable because of their relatively large buried surface areas and difficult topologies. Despite these challenges, recent advances in chemical screening methodologies, combined with improvements in structural and computational biology have made some of these targets more tractable. In this review, we highlight developments that have opened the door to potent chemical modulators. We focus on how allostery is being used to produce surprisingly robust changes in PPIs, even for the most challenging targets. We also discuss how interfering with one PPI can propagate changes through the broader web of interactions. Through this analysis, it is becoming clear that a combination of direct and propagated effects on PPI networks is ultimately how small molecules re-shape biology. PMID:26380257

  17. Stress-response balance drives the evolution of a network module and its host genome

    PubMed Central

    González, Caleb; Ray, Joe Christian J; Manhart, Michael; Adams, Rhys M; Nevozhay, Dmitry; Morozov, Alexandre V; Balázsi, Gábor

    2015-01-01

    Stress response genes and their regulators form networks that underlie drug resistance. These networks often have an inherent tradeoff: their expression is costly in the absence of stress, but beneficial in stress. They can quickly emerge in the genomes of infectious microbes and cancer cells, protecting them from treatment. Yet, the evolution of stress resistance networks is not well understood. Here, we use a two-component synthetic gene circuit integrated into the budding yeast genome to model experimentally the adaptation of a stress response module and its host genome in three different scenarios. In agreement with computational predictions, we find that: (i) intra-module mutations target and eliminate the module if it confers only cost without any benefit to the cell; (ii) intra- and extra-module mutations jointly activate the module if it is potentially beneficial and confers no cost; and (iii) a few specific mutations repeatedly fine-tune the module's noisy response if it has excessive costs and/or insufficient benefits. Overall, these findings reveal how the timing and mechanisms of stress response network evolution depend on the environment. PMID:26324468

  18. Stress-response balance drives the evolution of a network module and its host genome.

    PubMed

    Gonzlez, Caleb; Ray, Joe Christian J; Manhart, Michael; Adams, Rhys M; Nevozhay, Dmitry; Morozov, Alexandre V; Balzsi, Gbor

    2015-08-01

    Stress response genes and their regulators form networks that underlie drug resistance. These networks often have an inherent tradeoff: their expression is costly in the absence of stress, but beneficial in stress. They can quickly emerge in the genomes of infectious microbes and cancer cells, protecting them from treatment. Yet, the evolution of stress resistance networks is not well understood. Here, we use a two-component synthetic gene circuit integrated into the budding yeast genome to model experimentally the adaptation of a stress response module and its host genome in three different scenarios. In agreement with computational predictions, we find that: (i) intra-module mutations target and eliminate the module if it confers only cost without any benefit to the cell; (ii) intra- and extra-module mutations jointly activate the module if it is potentially beneficial and confers no cost; and (iii) a few specific mutations repeatedly fine-tune the module's noisy response if it has excessive costs and/or insufficient benefits. Overall, these findings reveal how the timing and mechanisms of stress response network evolution depend on the environment. PMID:26324468

  19. Facilitation of Visual Perception in Head Direction: Visual Attention Modulation Based on Head Direction

    PubMed Central

    Nakashima, Ryoichi; Shioiri, Satoshi

    2015-01-01

    People usually see things using frontal viewing, and avoid lateral viewing (or eccentric gaze) where the directions of the head and eyes are largely different. Lateral viewing interferes with attentive visual search performance, probably because the head is directed away from the target and/or because the head and eyes are misaligned. In this study, we examined which of these factors is the primary one for interference by conducting a visual identification experiment where a target was presented in the peripheral visual field. The critical manipulation was the participants’ head direction and fixation position: the head was directed to the fixation location, the target position, or the opposite side of the fixation. The performance was highest when the head was directed to the target position even when there was misalignment of the head and eye, suggesting that visual perception can be influenced by both head direction and fixation position. PMID:25919316

  20. Normal aging modulates prefrontoparietal networks underlying multiple memory processes.

    PubMed

    Sambataro, Fabio; Safrin, Martin; Lemaitre, Herve S; Steele, Sonya U; Das, Saumitra B; Callicott, Joseph H; Weinberger, Daniel R; Mattay, Venkata S

    2012-12-01

    A functional decline of brain regions underlying memory processing represents a hallmark of cognitive aging. Although a rich literature documents age-related differences in several memory domains, the effect of aging on networks that underlie multiple memory processes has been relatively unexplored. Here we used functional magnetic resonance imaging during working memory and incidental episodic encoding memory to investigate patterns of age-related differences in activity and functional covariance patterns common across multiple memory domains. Relative to younger subjects, older subjects showed increased activation in left dorso-lateral prefrontal cortex along with decreased deactivation in the posterior cingulate. Older subjects showed greater functional covariance during both memory tasks in a set of regions that included a positive prefronto-parietal-occipital network as well as a negative network that spanned the default mode regions. These findings suggest that the memory process-invariant recruitment of brain regions within prefronto-parietal-occipital network increases with aging. Our results are in line with the dedifferentiation hypothesis of neurocognitive aging, thereby suggesting a decreased specialization of the brain networks supporting different memory networks. PMID:22909094

  1. Hypnotic modulation of resting state fMRI default mode and extrinsic network connectivity.

    PubMed

    Demertzi, A; Soddu, A; Faymonville, M-E; Bahri, M A; Gosseries, O; Vanhaudenhuyse, A; Phillips, C; Maquet, P; Noirhomme, Q; Luxen, A; Laureys, S

    2011-01-01

    Resting state fMRI (functional magnetic resonance imaging) acquisitions are characterized by low-frequency spontaneous activity in a default mode network (encompassing medial brain areas and linked to self-related processes) and an anticorrelated "extrinsic" system (encompassing lateral frontoparietal areas and modulated via external sensory stimulation). In order to better determine the functional contribution of these networks to conscious awareness, we here sought to transiently modulate their relationship by means of hypnosis. We used independent component analysis (ICA) on resting state fMRI acquisitions during normal wakefulness, under hypnotic state, and during a control condition of autobiographical mental imagery. As compared to mental imagery, hypnosis-induced modulation of resting state fMRI networks resulted in a reduced "extrinsic" lateral frontoparietal cortical connectivity, possibly reflecting a decreased sensory awareness. The default mode network showed an increased connectivity in bilateral angular and middle frontal gyri, whereas its posterior midline and parahippocampal structures decreased their connectivity during hypnosis, supposedly related to an altered "self" awareness and posthypnotic amnesia. In our view, fMRI resting state studies of physiological (e.g., sleep or hypnosis), pharmacological (e.g., sedation or anesthesia), and pathological modulation (e.g., coma or related states) of "intrinsic" default mode and anticorrelated "extrinsic" sensory networks, and their interaction with other cerebral networks, will further improve our understanding of the neural correlates of subjective awareness. PMID:21854971

  2. Hybrid electro-optic plasmonic modulators based on directional coupler switches

    NASA Astrophysics Data System (ADS)

    Zografopoulos, Dimitrios C.; Swillam, Mohamed A.; Shahada, Lamees A.; Beccherelli, Romeo

    2016-04-01

    By breaking the diffraction limit, plasmonics enable the miniaturization of integrated optical signal processing units in a platform compatible with traditional CMOS technology. In such architectures, modulators and switches are essential elements for fast and low-power optical signal processing. This work presents the design of a CMOS-compatible hybrid plasmonic modulator based on directional couplers enhanced with a layer of electro-optic polymer. The modulator shows very broad operating window with low crosstalk values and very small footprint with respect to similar couplers and switches of the silicon photonics platform.

  3. Direct Conversion of Free Space Millimeter Waves to Optical Domain by Plasmonic Modulator Antenna

    PubMed Central

    2015-01-01

    A scheme for the direct conversion of millimeter and THz waves to optical signals is introduced. The compact device consists of a plasmonic phase modulator that is seamlessly cointegrated with an antenna. Neither high-speed electronics nor electronic amplification is required to drive the modulator. A built-in enhancement of the electric field by a factor of 35 000 enables the direct conversion of millimeter-wave signals to the optical domain. This high enhancement is obtained via a resonant antenna that is directly coupled to an optical field by means of a plasmonic modulator. The suggested concept provides a simple and cost-efficient alternative solution to conventional schemes where millimeter-wave signals are first converted to the electrical domain before being up-converted to the optical domain. PMID:26570995

  4. Direct Conversion of Free Space Millimeter Waves to Optical Domain by Plasmonic Modulator Antenna.

    PubMed

    Salamin, Yannick; Heni, Wolfgang; Haffner, Christian; Fedoryshyn, Yuriy; Hoessbacher, Claudia; Bonjour, Romain; Zahner, Marco; Hillerkuss, David; Leuchtmann, Pascal; Elder, Delwin L; Dalton, Larry R; Hafner, Christian; Leuthold, Juerg

    2015-12-01

    A scheme for the direct conversion of millimeter and THz waves to optical signals is introduced. The compact device consists of a plasmonic phase modulator that is seamlessly cointegrated with an antenna. Neither high-speed electronics nor electronic amplification is required to drive the modulator. A built-in enhancement of the electric field by a factor of 35,000 enables the direct conversion of millimeter-wave signals to the optical domain. This high enhancement is obtained via a resonant antenna that is directly coupled to an optical field by means of a plasmonic modulator. The suggested concept provides a simple and cost-efficient alternative solution to conventional schemes where millimeter-wave signals are first converted to the electrical domain before being up-converted to the optical domain. PMID:26570995

  5. Investigations on beam-shape transformation by direct inscribing an index modulation pattern on optical fiber surface

    NASA Astrophysics Data System (ADS)

    Liao, Tongqing; Zhao, QiDa; Li, ShuHong

    2008-11-01

    End surface grating by direct inscribing an index modulation pattern on optical waveguide surface to control amplitude and direction of the diffracted light is fabricated. Direct inscribing an index modulation pattern by femto-laser is simple, agile and the pattern is steady and durable. We control power and direction of diffracting orders by inscribing different modulation patterns and the controllability may well offer opportunities for various kinds of applications such as beam splitter, beam deflector, and beam shape controller.

  6. The segment polarity network is a robust developmental module

    NASA Astrophysics Data System (ADS)

    von Dassow, George; Meir, Eli; Munro, Edwin M.; Odell, Garrett M.

    2000-07-01

    All insects possess homologous segments, but segment specification differs radically among insect orders. In Drosophila, maternal morphogens control the patterned activation of gap genes, which encode transcriptional regulators that shape the patterned expression of pair-rule genes. This patterning cascade takes place before cellularization. Pair-rule gene products subsequently `imprint' segment polarity genes with reiterated patterns, thus defining the primordial segments. This mechanism must be greatly modified in insect groups in which many segments emerge only after cellularization. In beetles and parasitic wasps, for instance, pair-rule homologues are expressed in patterns consistent with roles during segmentation, but these patterns emerge within cellular fields. In contrast, although in locusts pair-rule homologues may not control segmentation, some segment polarity genes and their interactions are conserved. Perhaps segmentation is modular, with each module autonomously expressing a characteristic intrinsic behaviour in response to transient stimuli. If so, evolution could rearrange inputs to modules without changing their intrinsic behaviours. Here we suggest, using computer simulations, that the Drosophila segment polarity genes constitute such a module, and that this module is resistant to variations in the kinetic constants that govern its behaviour.

  7. Temporal modulation of collective cell behavior controls vascular network topology

    PubMed Central

    Kur, Esther; Kim, Jiha; Tata, Aleksandra; Comin, Cesar H; Harrington, Kyle I; Costa, Luciano da F; Bentley, Katie; Gu, Chenghua

    2016-01-01

    Vascular network density determines the amount of oxygen and nutrients delivered to host tissues, but how the vast diversity of densities is generated is unknown. Reiterations of endothelial-tip-cell selection, sprout extension and anastomosis are the basis for vascular network generation, a process governed by the VEGF/Notch feedback loop. Here, we find that temporal regulation of this feedback loop, a previously unexplored dimension, is the key mechanism to determine vascular density. Iterating between computational modeling and in vivo live imaging, we demonstrate that the rate of tip-cell selection determines the length of linear sprout extension at the expense of branching, dictating network density. We provide the first example of a host tissue-derived signal (Semaphorin3E-Plexin-D1) that accelerates tip cell selection rate, yielding a dense network. We propose that temporal regulation of this critical, iterative aspect of network formation could be a general mechanism, and additional temporal regulators may exist to sculpt vascular topology. DOI: http://dx.doi.org/10.7554/eLife.13212.001 PMID:26910011

  8. Normal aging modulates prefrontoparietal networks underlying multiple memory processes

    PubMed Central

    Sambataro, Fabio; Safrin, Martin; Lemaitre, Herve S.; Steele, Sonya U.; Das, Saumitra B.; Callicott, Joseph H; Weinberger, Daniel R.; Mattay, Venkata S.

    2012-01-01

    Functional decline of brain regions underlying memory processing represents a hallmark of cognitive aging. Although a rich literature documents age-related differences in several memory domains, the effect of aging on networks that underlie multiple memory processes has been relatively unexplored. Here we used functional magnetic resonance imaging during working memory and incidental episodic encoding memory to investigate patterns of age-related differences in activity and functional covariance patterns common across multiple memory domains. Relative to younger subjects, older subjects showed increased activation in left dorso-lateral prefrontal cortex along with decreased deactivation in the posterior cingulate. Older subjects showed greater functional covariance during both memory tasks in a set of regions that included a positive prefronto-parietal-occipital networkas well as a negative network that spanned the default mode regions. These findings suggest that the memory process-invariant recruitment of brain regions within prefronto-parietal-occipital network increases with aging.Our results are in line with the dedifferentiation hypothesis of neurocognitive aging, thereby suggesting a decreased specialization of the brain networks supporting different memory networks. PMID:22909094

  9. Intensity modulation and direct detection quantum key distribution based on quantum noise

    NASA Astrophysics Data System (ADS)

    Ikuta, Takuya; Inoue, Kyo

    2016-01-01

    Quantum key distribution (QKD) has been studied for achieving perfectly secure cryptography based on quantum mechanics. This paper presents a novel QKD scheme that is based on an intensity-modulation and direct-detection system. Two slightly intensity-modulated pulses are sent from a transmitter, and a receiver determines key bits from the directly detected intensity. We analyzed the system performance for two typical eavesdropping methods, a beam splitting attack and an intercept-resend attack, with an assumption that the transmitting and receiving devices are fully trusted. Our brief analysis showed that short- or middle-range QKD systems are achievable with a simple setup.

  10. A phase-modulated direct-detection fiber optical CATV transport system

    NASA Astrophysics Data System (ADS)

    Chen, Chia-Yi; Lu, Hai-Han; Lin, Chun-Yu; Wu, Kuan-Hung; Jhang, Tai-Wei; Ying, Cheng-Ling

    2014-05-01

    A fiber optical CATV transport system based on phase modulation (PM) and direct-detection schemes to reduce noise and distortion induced by systems is proposed and experimentally demonstrated. The architecture of the proposed systems is simplified by the fiber-dispersion-induced PM-to-intensity modulation (IM) conversion technique. As a result, the optical signal is detected directly by a photodiode (PD), without using the sophisticated and expensive delay interferometer (DI). Impressive performances 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 single-mode fiber (SMF) transport.

  11. Integrative Multi-omics Module Network Inference with Lemon-Tree

    PubMed Central

    Bonnet, Eric; Calzone, Laurence; Michoel, Tom

    2015-01-01

    Module network inference is an established statistical method to reconstruct co-expression modules and their upstream regulatory programs from integrated multi-omics datasets measuring the activity levels of various cellular components across different individuals, experimental conditions or time points of a dynamic process. We have developed Lemon-Tree, an open-source, platform-independent, modular, extensible software package implementing state-of-the-art ensemble methods for module network inference. We benchmarked Lemon-Tree using large-scale tumor datasets and showed that Lemon-Tree algorithms compare favorably with state-of-the-art module network inference software. We also analyzed a large dataset of somatic copy-number alterations and gene expression levels measured in glioblastoma samples from The Cancer Genome Atlas and found that Lemon-Tree correctly identifies known glioblastoma oncogenes and tumor suppressors as master regulators in the inferred module network. Novel candidate driver genes predicted by Lemon-Tree were validated using tumor pathway and survival analyses. Lemon-Tree is available from http://lemon-tree.googlecode.com under the GNU General Public License version 2.0. PMID:25679508

  12. Topological interactive analysis of power system and its communication module: A complex network approach

    NASA Astrophysics Data System (ADS)

    Hu, Jianqiang; Yu, Jie; Cao, Jinde; Ni, Ming; Yu, Wenjie

    2014-12-01

    Power system and its communication system, which can be called a cyber-physical system, are interconnected and interdependent on each other. This paper considers the interaction problem between power system and its communication module from the perspective of the topological structure. Firstly, some structural properties and centrality measures of complex networks are briefly reviewed. Furthermore, novel interactive measures are proposed to describe the interactive system in terms of topologies. Finally, based on these metrics, the statistical properties and the interactive relationships of the main power system and its communication module (abstracted as two complex heterogeneous networks) of one province in China are investigated.

  13. Differential network analysis reveals the genome-wide landscape of estrogen receptor modulation in hormonal cancers.

    PubMed

    Hsiao, Tzu-Hung; Chiu, Yu-Chiao; Hsu, Pei-Yin; Lu, Tzu-Pin; Lai, Liang-Chuan; Tsai, Mong-Hsun; Huang, Tim H-M; Chuang, Eric Y; Chen, Yidong

    2016-01-01

    Several mutual information (MI)-based algorithms have been developed to identify dynamic gene-gene and function-function interactions governed by key modulators (genes, proteins, etc.). Due to intensive computation, however, these methods rely heavily on prior knowledge and are limited in genome-wide analysis. We present the modulated gene/gene set interaction (MAGIC) analysis to systematically identify genome-wide modulation of interaction networks. Based on a novel statistical test employing conjugate Fisher transformations of correlation coefficients, MAGIC features fast computation and adaption to variations of clinical cohorts. In simulated datasets MAGIC achieved greatly improved computation efficiency and overall superior performance than the MI-based method. We applied MAGIC to construct the estrogen receptor (ER) modulated gene and gene set (representing biological function) interaction networks in breast cancer. Several novel interaction hubs and functional interactions were discovered. ER+ dependent interaction between TGFβ and NFκB was further shown to be associated with patient survival. The findings were verified in independent datasets. Using MAGIC, we also assessed the essential roles of ER modulation in another hormonal cancer, ovarian cancer. Overall, MAGIC is a systematic framework for comprehensively identifying and constructing the modulated interaction networks in a whole-genome landscape. MATLAB implementation of MAGIC is available for academic uses at https://github.com/chiuyc/MAGIC. PMID:26972162

  14. Differential network analysis reveals the genome-wide landscape of estrogen receptor modulation in hormonal cancers

    PubMed Central

    Hsiao, Tzu-Hung; Chiu, Yu-Chiao; Hsu, Pei-Yin; Lu, Tzu-Pin; Lai, Liang-Chuan; Tsai, Mong-Hsun; Huang, Tim H.-M.; Chuang, Eric Y.; Chen, Yidong

    2016-01-01

    Several mutual information (MI)-based algorithms have been developed to identify dynamic gene-gene and function-function interactions governed by key modulators (genes, proteins, etc.). Due to intensive computation, however, these methods rely heavily on prior knowledge and are limited in genome-wide analysis. We present the modulated gene/gene set interaction (MAGIC) analysis to systematically identify genome-wide modulation of interaction networks. Based on a novel statistical test employing conjugate Fisher transformations of correlation coefficients, MAGIC features fast computation and adaption to variations of clinical cohorts. In simulated datasets MAGIC achieved greatly improved computation efficiency and overall superior performance than the MI-based method. We applied MAGIC to construct the estrogen receptor (ER) modulated gene and gene set (representing biological function) interaction networks in breast cancer. Several novel interaction hubs and functional interactions were discovered. ER+ dependent interaction between TGFβ and NFκB was further shown to be associated with patient survival. The findings were verified in independent datasets. Using MAGIC, we also assessed the essential roles of ER modulation in another hormonal cancer, ovarian cancer. Overall, MAGIC is a systematic framework for comprehensively identifying and constructing the modulated interaction networks in a whole-genome landscape. MATLAB implementation of MAGIC is available for academic uses at https://github.com/chiuyc/MAGIC. PMID:26972162

  15. Mining functional modules in genetic networks with decomposable graphical models.

    PubMed

    Dejori, Mathäus; Schwaighofer, Anton; Tresp, Volker; Stetter, Martin

    2004-01-01

    In recent years, graphical models have become an increasingly important tool for the structural analysis of genome-wide expression profiles at the systems level. Here we present a new graphical modelling technique, which is based on decomposable graphical models, and apply it to a set of gene expression profiles from acute lymphoblastic leukemia (ALL). The new method explains probabilistic dependencies of expression levels in terms of the concerted action of underlying genetic functional modules, which are represented as so-called "cliques" in the graph. In addition, the method uses continuous-valued (instead of discretized) expression levels, and makes no particular assumption about their probability distribution. We show that the method successfully groups members of known functional modules to cliques. Our method allows the evaluation of the importance of genes for global cellular functions based on both link count and the clique membership count. PMID:15268775

  16. Silicon electro-optic modulator based on an ITO-integrated tunable directional coupler

    NASA Astrophysics Data System (ADS)

    Kim, Jin-Soo; Kim, Jin Tae

    2016-02-01

    Indium-tin-oxide (ITO) has attracted great attention because of its electrically-induced epsilon-near-zero (ENZ) characteristics, which has allowed us to develop electro-absorption optical modulators. As an extended application of ITO in a silicon optical modulator, we propose a silicon electro-optic modulator based on an ITO-integrated tunable directional coupler. An ITO block placed at the center of the two-core silicon directional coupler plays a key role in attenuating the optical power of the guided modes. Strong confinement of the optical field at the ENZ layer of ITO with the nonzero imaginary part of ITO’s permittivity let the guiding light experience high absorption as it propagates along the directional coupler. Numerical simulations reveal that the highest modulation depth of 5 dB is achievable at the ENZ region of ITO at a 1.55 μm wavelength. We can modulate the optical signals on an entire C-band ranging from a 1.530 to 1.565 μm wavelength with an on/off extinction ratio of larger than 4.6 dB.

  17. A compact frequency domain fluorometer with a directly modulated deuterium light source

    NASA Astrophysics Data System (ADS)

    Morgan, C. G.; Hua, Y.; Mitchell, A. K.; Murray, J. G.; Boardman, A. D.

    1996-01-01

    A phase fluorometer based on a low-cost and versatile high-frequency modulated light source and a fast gain-modulated photomultiplier is described. The apparatus is particularly well-suited to high-sensitivity frequency-domain fluorescence measurements requiring ultraviolet excitation. The system is very compact since it features a directly modulated light source, a miniature photomultiplier tube, and an rf synthesizer on a PC board. Equipped with a suitable fiber optic probe sensor, the device has potential as a portable unit for a wide range of remote sensing applications. The lamp can be modulated at frequencies up to 120 MHz and the phase fluorometer has been tested at up to 70 MHz with a range of fluorescent lifetime standards containing quinine sulfate quenched with sodium chloride.

  18. Quantitative orientation-independent DIC microscope with fast switching shear direction and bias modulation

    PubMed Central

    Shribak, Michael

    2013-01-01

    We describe quantitative orientation-independent differential interference contrast (OI-DIC) microscope, which allows the bias retardation to be modulated and shear directions to be switched rapidly without any mechanically moving. The shear direction is switched by regular liquid crystal cell sandwiched between two standard DIC prisms. Another liquid crystal cell modulates the bias. Techniques for measuring parameters of DIC prisms and calibrating the bias are shown. Two sets of raw DIC images with the orthogonal shear directions are captured within a second. Then the quantitative image of optical path gradient distribution within a thin optical section is computed. The gradient data are used to obtain quantitative distribution of optical path, which represents refractive index gradient or height distribution. Computing enhanced regular DIC images with any desired shear direction is also possible. PMID:23595339

  19. Morphology effect on the light scattering and dynamic response of polymer network liquid crystal phase modulator.

    PubMed

    Xiangjie, Zhao; Cangli, Liu; Jiazhu, Duan; Jiancheng, Zeng; Dayong, Zhang; Yongquan, Luo

    2014-06-16

    Polymer network liquid crystal (PNLC) was one of the most potential liquid crystal for submillisecond response phase modulation, which was possible to be applied in submillisecond response phase only spatial light modulator. But until now the light scattering when liquid crystal director was reoriented by external electric field limited its phase modulation application. Dynamic response of phase change when high voltage was applied was also not elucidated. The mechanism that determines the light scattering was studied by analyzing the polymer network morphology by SEM method. Samples were prepared by varying the polymerization temperature, UV curing intensity and polymerization time. The morphology effect on the dynamic response of phase change was studied, in which high voltage was usually applied and electro-striction effect was often induced. The experimental results indicate that the polymer network morphology was mainly characterized by cross linked single fibrils, cross linked fibril bundles or even both. Although the formation of fibril bundle usually induced large light scattering, such a polymer network could endure higher voltage. In contrast, although the formation of cross linked single fibrils induced small light scattering, such a polymer network cannot endure higher voltage. There is a tradeoff between the light scattering and high voltage endurance. The electro-optical properties such as threshold voltage and response time were taken to verify our conclusion. For future application, the monomer molecular structure, the liquid crystal solvent and the polymerization conditions should be optimized to generate optimal polymer network morphology. PMID:24977571

  20. Convective stability in the Rayleigh-Benard and directional solidification problems - High-frequency gravity modulation

    NASA Technical Reports Server (NTRS)

    Wheeler, A. A.; Mcfadden, G. B.; Murray, B. T.; Coriell, S. R.

    1991-01-01

    The effect of vertical, sinusoidal, time-dependent gravitational acceleration on the onset of solutal convection during directional solidification is analyzed in the limit of large modulation frequency. When the unmodulated state is unstable, the modulation amplitude required to stabilize the system is determined by the method of averaging. When the unmodulated state is stable, resonant modes of instability occur at large modulation amplitude. These are analyzed using matched asymptotic expansions to elucidate the boundary-layer structure for both the Rayleigh-Benard and directional solidification configurations. Based on these analyses, a thorough examination of the dependence of the stability criteria on the unmodulated Rayleigh number, Schmidt number, and distribution coefficient, is carried out.

  1. A digital receiver module with direct data acquisition for magnetic resonance imaging systems

    NASA Astrophysics Data System (ADS)

    Tang, Weinan; Sun, Hongyu; Wang, Weimin

    2012-10-01

    A digital receiver module for magnetic resonance imaging (MRI) with detailed hardware implementations is presented. The module is based on a direct sampling scheme using the latest mixed-signal circuit design techniques. A single field-programmable gate array chip is employed to perform software-based digital down conversion for radio frequency signals. The modular architecture of the receiver allows multiple acquisition channels to be implemented on a highly integrated printed circuit board. To maintain the phase coherence of the receiver and the exciter in the context of direct sampling, an effective phase synchronization method was proposed to achieve a phase deviation as small as 0.09. The performance of the described receiver module was verified in the experiments for both low- and high-field (0.5 T and 1.5 T) MRI scanners and was compared to a modern commercial MRI receiver system.

  2. Gravitational focusing and substructure effects on the rate modulation in direct dark matter searches

    SciTech Connect

    Nobile, Eugenio Del; Gelmini, Graciela B.; Witte, Samuel J.

    2015-08-21

    We study how gravitational focusing (GF) of dark matter by the Sun affects the annual and biannual modulation of the expected signal in non-directional direct dark matter searches, in the presence of dark matter substructure in the local dark halo. We consider the Sagittarius stream and a possible dark disk, and show that GF suppresses some, but not all, of the distinguishing features that would characterize substructure of the dark halo were GF neglected.

  3. Amyloid beta modulation of neuronal network activity in vitro.

    PubMed

    Charkhkar, Hamid; Meyyappan, Susheela; Matveeva, Evgenia; Moll, Jonathan R; McHail, Daniel G; Peixoto, Nathalia; Cliff, Richard O; Pancrazio, Joseph J

    2015-12-10

    In vitro assays offer a means of screening potential therapeutics and accelerating the drug development process. Here, we utilized neuronal cultures on planar microelectrode arrays (MEA) as a functional assay to assess the neurotoxicity of amyloid-β 1-42 (Aβ42), a biomolecule implicated in the Alzheimer׳s disease (AD). In this approach, neurons harvested from embryonic mice were seeded on the substrate-integrated microelectrode arrays. The cultured neurons form a spontaneously active network, and the spiking activity as a functional endpoint could be detected via the MEA. Aβ42 oligomer, but not monomer, significantly reduced network spike rate. In addition, we demonstrated that the ionotropic glutamate receptors, NMDA and AMPA/kainate, play a role in the effects of Aβ42 on neuronal activity in vitro. To examine the utility of the MEA-based assay for AD drug discovery, we tested two model therapeutics for AD, methylene blue (MB) and memantine. Our results show an almost full recovery in the activity within 24h after administration of Aβ42 in the cultures pre-treated with either MB or memantine. Our findings suggest that cultured neuronal networks may be a useful platform in screening potential therapeutics for Aβ induced changes in neurological function. PMID:26453830

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

    NASA Technical Reports Server (NTRS)

    Levitt, B. K.

    1980-01-01

    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.

  5. Observation of a time modulated muon flux in the direction of Cygnus X-3

    NASA Astrophysics Data System (ADS)

    Battistoni, G.; Bellotti, E.; Bloise, C.; Bologna, G.; Campana, P.; Castagnoli, C.; Castellina, A.; Chiarella, V.; Ciocio, A.; Cundy, D.; D'Ettorre-Piazzoli, B.; Fiorini, E.; Galeotti, P.; Iarocci, E.; Liguori, C.; Mannocchi, G.; Murtas, G.; Negri, P.; Nicoletti, G.; Picchi, P.; Price, M.; Pullia, A.; Ragazzi, S.; Rollier, M.; Saavedra, O.; Satta, L.; Serri, P.; Vernetto, S.; Zanotti, L.

    1985-06-01

    The analysis of angular and phase distribution is reported for high energy muons recorded in the NUSEX nucleon decay detector, located in the Mont Blanc tunnel at a depth of about 5000 hg of standard rock. Evidence is found for a signal correlated to the direction and time modulation of Cygnus X-3.

  6. Directed Network Motifs in Alzheimer’s Disease and Mild Cognitive Impairment

    PubMed Central

    Friedman, Eric J.; Young, Karl; Tremper, Graham; Liang, Jason; Landsberg, Adam S.; Schuff, Norbert

    2015-01-01

    Directed network motifs are the building blocks of complex networks, such as human brain networks, and capture deep connectivity information that is not contained in standard network measures. In this paper we present the first application of directed network motifs in vivo to human brain networks, utilizing recently developed directed progression networks which are built upon rates of cortical thickness changes between brain regions. This is in contrast to previous studies which have relied on simulations and in vitro analysis of non-human brains. We show that frequencies of specific directed network motifs can be used to distinguish between patients with Alzheimer’s disease (AD) and normal control (NC) subjects. Especially interesting from a clinical standpoint, these motif frequencies can also distinguish between subjects with mild cognitive impairment who remained stable over three years (MCI) and those who converted to AD (CONV). Furthermore, we find that the entropy of the distribution of directed network motifs increased from MCI to CONV to AD, implying that the distribution of pathology is more structured in MCI but becomes less so as it progresses to CONV and further to AD. Thus, directed network motifs frequencies and distributional properties provide new insights into the progression of Alzheimer’s disease as well as new imaging markers for distinguishing between normal controls, stable mild cognitive impairment, MCI converters and Alzheimer’s disease. PMID:25879535

  7. Digital quadrature amplitude modulation with optimized non-rectangular constellations for 100 Gb/s transmission by a directly-modulated laser.

    PubMed

    Ling, William A; Lyubomirsky, Ilya; Solgaard, Olav

    2014-05-01

    We study the performance of novel quadrature amplitude modulation (QAM) constellations for 100 Gb/s transmission by a directly-modulated laser. Due to the strong nonlinearity of a directly-modulated laser, rectangular constellations suffer a large penalty from their regular spacing between symbols. We present a method for synthesizing irregular constellations which position symbols more efficiently. We will demonstrate the improved performance of these novel constellations over the conventional rectangular constellation as well as the superior performance achievable with digital QAM compared to optimally bit-loaded discrete-multitone modulation. PMID:24921784

  8. The topology of the directed clique complex as a network invariant.

    PubMed

    Masulli, Paolo; Villa, Alessandro E P

    2016-01-01

    We introduce new algebro-topological invariants of directed networks, based on the topological construction of the directed clique complex. The shape of the underlying directed graph is encoded in a way that can be studied mathematically to obtain network invariants such as the Euler characteristic and the Betti numbers. Two different cases illustrate the application of the Euler characteristic. We investigate how the evolution of a Boolean recurrent artificial neural network is influenced by its topology in a dynamics involving pruning and strengthening of the connections, and to show that the topological features of the directed clique complex influence the dynamical evolution of the network. The second application considers the directed clique complex in a broader framework, to define an invariant of directed networks, the network degree invariant, which is constructed by computing the topological invariant on a sequence of sub-networks filtered by the minimum in- or out-degree of the nodes. The application of the Euler characteristic presented here can be extended to any directed network and provides a new method for the assessment of specific functional features associated with the network topology. PMID:27047714

  9. New evidence of corticospinal network modulation induced by motor imagery.

    PubMed

    Grosprêtre, Sidney; Lebon, Florent; Papaxanthis, Charalambos; Martin, Alain

    2016-03-01

    Motor imagery (MI) is the mental simulation of movement, without the corresponding muscle contraction. Whereas the activation of cortical motor areas during MI is established, the involvement of spinal structures is still under debate. We used original and complementary techniques to probe the influence of MI on spinal structures. Amplitude of motor-evoked potentials (MEPs), cervico-medullary-evoked potentials (CMEPs), and Hoffmann (H)-reflexes of the flexor carpi radialis (FCR) muscle and of the triceps surae muscles was measured in young, healthy subjects at rest and during MI. Participants were asked to imagine maximal voluntary contraction of the wrist and ankle, while the targeted limb was fixed (static condition). We confirmed previous studies with an increase of FCR MEPs during MI compared with rest. Interestingly, CMEPs, but not H-reflexes, also increased during MI, revealing a possible activation of subcortical structures. Then, to investigate the effect of MI on the spinal network, we used two techniques: 1) passive lengthening of the targeted muscle via an isokinetic dynamometer and 2) conditioning of H-reflexes with stimulation of the antagonistic nerve. Both techniques activate spinal inhibitory presynaptic circuitry, reducing the H-reflex amplitude at rest. In contrast, no reduction of H-reflex amplitude was observed during MI. These findings suggest that MI has modulatory effects on the spinal neuronal network. Specifically, the activation of low-threshold spinal structures during specific conditions (lengthening and H-reflex conditioning) highlights the possible generation of subliminal cortical output during MI. PMID:26719089

  10. Ethanol Modulation of Gene Networks: Implications for Alcoholism

    PubMed Central

    Farris, Sean P.; Miles, Michael F.

    2011-01-01

    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. PMID:21536129

  11. Social status modulates neural activity in the mentalizing network

    PubMed Central

    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.

    2013-01-01

    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

  12. CAN-DOO: The Climate Action Network through Direct Observations and Outreach

    NASA Astrophysics Data System (ADS)

    Taubman, B.; Sherman, J. P.; Perry, L. B.; Markham, J.; Kelly, G.

    2011-12-01

    The urgency of climate change demands a greater understanding of our climate system, not only by the leaders of today, but by the scientists, policy makers, and citizens of tomorrow. Unfortunately, a large segment of the population currently possesses inadequate knowledge of climate science. In direct response to a need for greater scientific literacy with respect to climate science, researchers from Appalachian State University's Appalachian Atmospheric Interdisciplinary Research (AppalAIR) group, with support from NASA, have developed CAN-DOO: the Climate Action Network through Direct Observations and Outreach. CAN-DOO addresses climate science literacy by 1) Developing the infrastructure for sustaining and expanding public outreach through long-term climate measurements capable of complementing existing NASA measurements, 2) Enhancing public awareness of climate science and NASA's role in advancing our understanding of the Earth System, and 3) Introducing Science, Technology, Engineering, and Mathematics principles to homeschooled, public school, and Appalachian State University students through applied climate science activities. Project partners include the Grandfather Mountain Stewardship Foundation, Pisgah Astronomical Research Institute, and local elementary schools. In partnership with Grandfather Mountain, climate science awareness is promoted through citizen science activities, interactive public displays, and staff training. CAN-DOO engages students by involving them in the entire scientific investigative process as applied to climate science. We introduce local elementary and middle school students, homeschooled students throughout North Carolina, and undergraduate students in a new Global Climate Change course and select other courses at Appalachian State University to instrument assembly, measurement techniques, data collection, hypothesis testing, and drawing conclusions. Results are placed in the proper context via comparisons with other student data products, local research-grade measurements, and NASA measurements. Several educational modules have been developed that address specific topics in climate science. The modules are scalable and have been successfully implemented at levels ranging from 2nd grade through first-year graduate as well as with citizen science groups. They also can be applied in user-desired segments to a variety of Earth Science units. In this paper, we will introduce the project activities and present results from the first year of observations and outreach, with a special emphasis on two of the developed modules, the surface energy balance and aerosol optical depth module.

  13. Age-dependent modulation of the somatosensory network upon eye closure.

    PubMed

    Brodoehl, Stefan; Klingner, Carsten; Witte, Otto W

    2016-02-01

    Eye closure even in complete darkness can improve somatosensory perception by switching the brain to a uni-sensory processing mode. This causes an increased information flow between the thalamus and the somatosensory cortex while decreasing modulation by the visual cortex. Previous work suggests that these modulations are age-dependent and that the benefit in somatosensory performance due to eye closing diminishes with age. The cause of this age-dependency and to what extent somatosensory processing is involved remains unclear. Therefore, we intended to characterize the underlying age-dependent modifications in the interaction and connectivity of different sensory networks caused by eye closure. We performed functional MR-imaging with tactile stimulation of the right hand under the conditions of opened and closed eyes in healthy young and elderly participants. Conditional Granger causality analysis was performed to assess the somatosensory and visual networks, including the thalamus. Independent of age, eye closure improved the information transfer from the thalamus to and within the somatosensory cortex. However, beyond that, we found an age-dependent recruitment strategy. Whereas young participants were characterized by an optimized information flow within the relays of the somatosensory network, elderly participants revealed a stronger modulatory influence of the visual network upon the somatosensory cortex. Our results demonstrate that the modulation of the somatosensory and visual networks by eye closure diminishes with age and that the dominance of the visual system is more pronounced in the aging brain. PMID:26546882

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

    SciTech Connect

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

    2012-08-15

    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.

  15. Integration of turbo-generator modules in digital transient network analyzer

    SciTech Connect

    Guo, Y.; Ooi, B.T.; Lee, H.C. . Dept. of Electrical Engineering)

    1994-05-01

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2012-08-01

    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.

  17. A hybrid graph-theoretic method for mining overlapping functional modules in large sparse protein interaction networks.

    PubMed

    Zhang, Shihua; Liu, Hong-Wei; Ning, Xue-Mei; Zhang, Xiang-Sun

    2009-01-01

    Modular architecture, which encompasses groups of genes/proteins involved in elementary biological functional units, is a basic form of the organisation of interacting proteins. Here, we propose a method that combines the Line Graph Transformation (LGT) and clique percolation-clustering algorithm to detect network modules, which may overlap each other in large sparse PPI networks. The resulting modules by the present method show a high coverage among yeast, fly, and worm PPI networks, respectively. Our analysis of the yeast PPI network suggests that most of these modules have well-biological significance in context of protein localisation, function annotation, and protein complexes. PMID:19432377

  18. MORAL ENHANCEMENT VIA DIRECT EMOTION MODULATION: A REPLY TO JOHN HARRIS

    PubMed Central

    Douglas, Thomas

    2013-01-01

    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

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

    PubMed

    Douglas, Thomas

    2013-03-01

    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

  20. Pupil size directly modulates the feedforward response in human primary visual cortex independently of attention.

    PubMed

    Bombeke, Klaas; Duthoo, Wout; Mueller, Sven C; Hopf, Jens-Max; Boehler, C Nico

    2016-02-15

    Controversy revolves around the question of whether psychological factors like attention and emotion can influence the initial feedforward response in primary visual cortex (V1). Although traditionally, the electrophysiological correlate of this response in humans (the C1 component) has been found to be unaltered by psychological influences, a number of recent studies have described attentional and emotional modulations. Yet, research into psychological effects on the feedforward V1 response has neglected possible direct contributions of concomitant pupil-size modulations, which are known to also occur under various conditions of attentional load and emotional state. Here we tested the hypothesis that such pupil-size differences themselves directly affect the feedforward V1 response. We report data from two complementary experiments, in which we used procedures that modulate pupil size without differences in attentional load or emotion while simultaneously recording pupil-size and EEG data. Our results confirm that pupil size indeed directly influences the feedforward V1 response, showing an inverse relationship between pupil size and early V1 activity. While it is unclear in how far this effect represents a functionally-relevant adaptation, it identifies pupil-size differences as an important modulating factor of the feedforward response of V1 and could hence represent a confounding variable in research investigating the neural influence of psychological factors on early visual processing. PMID:26658931

  1. Direct experimental observation of periodic intensity modulation along a straight hollow-core optical waveguide

    SciTech Connect

    Pfeifer, T.; Downer, M. C.

    2007-05-15

    We report the direct observation of periodic intensity modulation of a laser pulse propagating in a hollow-core waveguide. A series of equally spaced plasma sparks along the gas-filled capillary is produced. This effect can be explained by the beating of different fiber modes, which are excited by controlling the size of the focal spot at the capillary entrance. As compared with an artificial modulated waveguide structure, our presented approach represents an easier and more flexible quasi-phase-matching scheme for nonlinear-optical frequency conversion.

  2. Ion transport membrane module and vessel system with directed internal gas flow

    DOEpatents

    Holmes, Michael Jerome; Ohrn, Theodore R.; Chen, Christopher Ming-Poh

    2010-02-09

    An ion transport membrane system comprising (a) a pressure vessel having an interior, an inlet adapted to introduce gas into the interior of the vessel, an outlet adapted to withdraw gas from the interior of the vessel, and an axis; (b) a plurality of planar ion transport membrane modules disposed in the interior of the pressure vessel and arranged in series, each membrane module comprising mixed metal oxide ceramic material and having an interior region and an exterior region; and (c) one or more gas flow control partitions disposed in the interior of the pressure vessel and adapted to change a direction of gas flow within the vessel.

  3. Sliding mode pulse-width modulation technique for direct torque controlled induction motor drive

    NASA Astrophysics Data System (ADS)

    Bounadja, M.; Belarbi, A. W.; Belmadani, B.

    2010-05-01

    This paper presents a novel pulse-width modulation technique based sliding mode approach for direct torque control of an induction machine drive. Methodology begins with a sliding mode control of machine's torque and stator flux to generate the reference voltage vector and to reduce parameters sensitivity. Then, the switching control of the three-phase inverter is developed using sliding mode concept to make the system tracking reference voltage inputs. The main features of the proposed methodologies are the high tracking accuracy and the much easier implementation compared to the space vector modulation. Simulations are carried out to confirm the effectiveness of proposed control algorithms.

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

    NASA Astrophysics Data System (ADS)

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

    2010-05-01

    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 α 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.

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

    PubMed

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

    2010-05-01

    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 α 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. PMID:20866299

  6. A metro-access integrated network with all-optical virtual private network function using DPSK/ASK modulation format

    NASA Astrophysics Data System (ADS)

    Tian, Yue; Leng, Lufeng; Su, Yikai

    2008-11-01

    All-optical virtual private network (VPN), which offers dedicated optical channels to connect users within a VPN group, is considered a promising approach to efficient internetworking with low latency and enhanced security implemented in the physical layer. On the other hand, time-division multiplexed (TDM) / wavelength-division multiplexed (WDM) network architecture based on a feeder-ring with access-tree topology, is considered a pragmatic migration scenario from current TDM-PONs to future WDM-PONs and a potential convergence scheme for access and metropolitan networks, due to its efficiently shared hardware and bandwidth resources. All-optical VPN internetworking in such a metro-access integrated structure is expected to cover a wider service area and therefore is highly desirable. In this paper, we present a TDM/WDM metro-access integrated network supporting all-optical VPN internetworking among ONUs in different sub- PONs based on orthogonal differential-phase-shift keying (DPSK) / amplitude-shift keying (ASK) modulation format. In each ONU, no laser but a single Mach-Zehnder modulator (MZM) is needed for the upstream and VPN signal generation, which is cost-effective. Experiments and simulations are performed to verify its feasibility as a potential solution to the future access service.

  7. Cortical spreading depression and central pain networks in trigeminal nuclei modulation: time for an integrated migraine pathogenesis perspective.

    PubMed

    De Simone, R; Ranieri, A; Montella, S; Bonavita, V

    2013-05-01

    The role of the cortical spreading depression (CSD)-dependent trigeminovascular activation in migraine etiopathogenesis, long considered paradigmatic, has remained substantially unproven in humans. The parallel advancement of functional neuroimaging techniques promoted the extensive exploration of the brain networks involved in pain processing in search of a possible central migraine generator. However, despite initial enthusiasms, it has not been possible to clarify whether the functional central "markers" of pain observed in primary headaches could be considered as causative or just the neural correlates of the ongoing pain. Nonetheless, our knowledge on the complex interactions between CSD, neurogenic inflammation, peripheral trigeminovascular input, central cortico-trigeminal nuclei direct modulation and pain processing and limbic system networks has enormously grown, allowing the reconceptualisation of migraine from a neurovascular to a pure neurolimbic pain disorder, therefore relocating it in the much broader frame of the brain and whole organism homeostatic control. In this work, the available evidences currently supporting the relevance of CSD, of peripheral trigeminovascular input and of direct cortico-trigeminal nuclei modulation in migraine pathogenesis are reviewed in the light of a possible integrated migraine etiopathogenetic perspective. PMID:23695046

  8. Dynamics of neuromodulatory feedback determines frequency modulation in a reduced respiratory network: a computational study.

    PubMed

    Toporikova, Natalia; Butera, Robert J

    2013-02-01

    Neuromodulators, such as amines and neuropeptides, alter the activity of neurons and neuronal networks. In this work, we investigate how neuromodulators, which activate G(q)-protein second messenger systems, can modulate the bursting frequency of neurons in a critical portion of the respiratory neural network, the pre-Bötzinger complex (preBötC). These neurons are a vital part of the ponto-medullary neuronal network, which generates a stable respiratory rhythm whose frequency is regulated by neuromodulator release from the nearby Raphe nucleus. Using a simulated 50-cell network of excitatory preBötC neurons with a heterogeneous distribution of persistent sodium conductance and Ca(2+), we determined conditions for frequency modulation in such a network by simulating interaction between Raphe and preBötC nuclei. We found that the positive feedback between the Raphe excitability and preBötC activity induces frequency modulation in the preBötC neurons. In addition, the frequency of the respiratory rhythm can be regulated via phasic release of excitatory neuromodulators from the Raphe nucleus. We predict that the application of a G(q) antagonist will eliminate this frequency modulation by the Raphe and keep the network frequency constant and low. In contrast, application of a G(q) agonist will result in a high frequency for all levels of Raphe stimulation. Our modeling results also suggest that high [K(+)] requirement in respiratory brain slice experiments may serve as a compensatory mechanism for low neuromodulatory tone. PMID:23202052

  9. Learning related modulation of functional retrieval networks in man.

    PubMed

    Petersson, K M; Sandblom, J; Gisselgrd, J; Ingvar, M

    2001-07-01

    The medial temporal lobe has been implicated in studies of episodic memory tasks involving spatio-temporal context and object-location conjunctions. We have previously demonstrated that an increased level of practice in a free-recall task parallels a decrease in the functional activity of several brain regions, including the medial temporal lobe, the prefrontal, the anterior cingulate, the anterior insular, and the posterior parietal cortices, that in concert demonstrate a move from elaborate controlled processing towards a higher degree of automaticity. Here we report data from two experiments that extend these initial observations. We used a similar experimental approach but probed for effects of retrieval paradigms and stimulus material. In the first experiment we investigated practice related changes during recognition of object-location conjunctions and in the second during free-recall of pseudo-words. Learning in a neural network is a dynamic consequence of information processing and network plasticity. The present and previous PET results indicate that practice can induce a learning related functional restructuring of information processing. Different adaptive processes likely subserve the functional re-organisation observed. These may in part be related to different demands for attentional and working memory processing. It appears that the role(s) of the prefrontal cortex and the medial temporal lobe in memory retrieval are complex, perhaps reflecting several different interacting processes or cognitive components. We suggest that an integrative interactive perspective on the role of the prefrontal and medial temporal lobe is necessary for an understanding of the processing significance of these regions in learning and memory. It appears necessary to develop elaborated and explicit computational models for prefrontal and medial temporal functions in order to derive detailed empirical predictions, and in combination with an efficient use and development of functional neuroimaging approaches, to further the understanding of the processing significance of these regions in memory. PMID:11501735

  10. Acoustic richness modulates the neural networks supporting intelligible speech processing.

    PubMed

    Lee, Yune-Sang; Min, Nam Eun; Wingfield, Arthur; Grossman, Murray; Peelle, Jonathan E

    2016-03-01

    The information contained in a sensory signal plays a critical role in determining what neural processes are engaged. Here we used interleaved silent steady-state (ISSS) functional magnetic resonance imaging (fMRI) to explore how human listeners cope with different degrees of acoustic richness during auditory sentence comprehension. Twenty-six healthy young adults underwent scanning while hearing sentences that varied in acoustic richness (high vs. low spectral detail) and syntactic complexity (subject-relative vs. object-relative center-embedded clause structures). We manipulated acoustic richness by presenting the stimuli as unprocessed full-spectrum speech, or noise-vocoded with 24 channels. Importantly, although the vocoded sentences were spectrally impoverished, all sentences were highly intelligible. These manipulations allowed us to test how intelligible speech processing was affected by orthogonal linguistic and acoustic demands. Acoustically rich speech showed stronger activation than acoustically less-detailed speech in a bilateral temporoparietal network with more pronounced activity in the right hemisphere. By contrast, listening to sentences with greater syntactic complexity resulted in increased activation of a left-lateralized network including left posterior lateral temporal cortex, left inferior frontal gyrus, and left dorsolateral prefrontal cortex. Significant interactions between acoustic richness and syntactic complexity occurred in left supramarginal gyrus, right superior temporal gyrus, and right inferior frontal gyrus, indicating that the regions recruited for syntactic challenge differed as a function of acoustic properties of the speech. Our findings suggest that the neural systems involved in speech perception are finely tuned to the type of information available, and that reducing the richness of the acoustic signal dramatically alters the brain's response to spoken language, even when intelligibility is high. PMID:26723103

  11. Directional MAC Approach for Wireless Body Area Networks

    PubMed Central

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

    2011-01-01

    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. PMID:22346602

  12. Directional MAC approach for wireless body area networks.

    PubMed

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

    2011-01-01

    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. PMID:22346602

  13. Characterization of submillisecond response optical addressing phase modulator based on low light scattering polymer network liquid crystal

    SciTech Connect

    Xiangjie, Zhao E-mail: zxjdouble@gmail.com; Cangli, Liu; Jiazhu, Duan; Dayong, Zhang; Yongquan, Luo

    2015-01-07

    Optically addressed conventional nematic liquid crystal spatial light modulator has attracted wide research interests. But the slow response speed limited its further application. In this paper, polymer network liquid crystal (PNLC) was proposed to replace the conventional nematic liquid crystal to enhance the response time to the order of submillisecond. The maximum light scattering of the employed PNLC was suppressed to be less than 2% at 1.064 μm by optimizing polymerization conditions and selecting large viscosity liquid crystal as solvent. The occurrence of phase ripple phenomenon due to electron diffusion and drift in photoconductor was found to deteriorate the phase modulation effect of the optical addressed PNLC phase modulator. The wavelength effect and AC voltage frequency effect on the on state dynamic response of phase change was investigated by experimental methods. These effects were interpreted by electron diffusion and drift theory based on the assumption that free electron was inhomogeneously distributed in accordance with the writing beam intensity distribution along the incident direction. The experimental results indicated that the phase ripple could be suppressed by optimizing the wavelength of the writing beam and the driving AC voltage frequency when varying the writing beam intensity to generate phase change in 2π range. The modulation transfer function was also measured.

  14. Characterization of submillisecond response optical addressing phase modulator based on low light scattering polymer network liquid crystal

    NASA Astrophysics Data System (ADS)

    Xiangjie, Zhao; Cangli, Liu; Jiazhu, Duan; Dayong, Zhang; Yongquan, Luo

    2015-01-01

    Optically addressed conventional nematic liquid crystal spatial light modulator has attracted wide research interests. But the slow response speed limited its further application. In this paper, polymer network liquid crystal (PNLC) was proposed to replace the conventional nematic liquid crystal to enhance the response time to the order of submillisecond. The maximum light scattering of the employed PNLC was suppressed to be less than 2% at 1.064 μm by optimizing polymerization conditions and selecting large viscosity liquid crystal as solvent. The occurrence of phase ripple phenomenon due to electron diffusion and drift in photoconductor was found to deteriorate the phase modulation effect of the optical addressed PNLC phase modulator. The wavelength effect and AC voltage frequency effect on the on state dynamic response of phase change was investigated by experimental methods. These effects were interpreted by electron diffusion and drift theory based on the assumption that free electron was inhomogeneously distributed in accordance with the writing beam intensity distribution along the incident direction. The experimental results indicated that the phase ripple could be suppressed by optimizing the wavelength of the writing beam and the driving AC voltage frequency when varying the writing beam intensity to generate phase change in 2π range. The modulation transfer function was also measured.

  15. Asymmetric friction of nonmotor MAPs can lead to their directional motion in active microtubule networks.

    PubMed

    Forth, Scott; Hsia, Kuo-Chiang; Shimamoto, Yuta; Kapoor, Tarun M

    2014-04-10

    Diverse cellular processes require microtubules to be organized into distinct structures, such as asters or bundles. Within these dynamic motifs, microtubule-associated proteins (MAPs) are frequently under load, but how force modulates these proteins' function is poorly understood. Here, we combine optical trapping with TIRF-based microscopy to measure the force dependence of microtubule interaction for three nonmotor MAPs (NuMA, PRC1, and EB1) required for cell division. We find that frictional forces increase nonlinearly with MAP velocity across microtubules and depend on filament polarity, with NuMA's friction being lower when moving toward minus ends, EB1's lower toward plus ends, and PRC1's exhibiting no directional preference. Mathematical models predict, and experiments confirm, that MAPs with asymmetric friction can move directionally within actively moving microtubule pairs they crosslink. Our findings reveal how nonmotor MAPs can generate frictional resistance in dynamic cytoskeletal networks via micromechanical adaptations whose anisotropy may be optimized for MAP localization and function within cellular structures. PMID:24725408

  16. How Transcranial Direct Current Stimulation Can Modulate Implicit Motor Sequence Learning and Consolidation: A Brief Review.

    PubMed

    Savic, Branislav; Meier, Beat

    2016-01-01

    The purpose of this review is to investigate how transcranial direct current stimulation (tDCS) can modulate implicit motor sequence learning and consolidation. So far, most of the studies have focused on the modulating effect of tDCS for explicit motor learning. Here, we focus explicitly on implicit motor sequence learning and consolidation in order to improve our understanding about the potential of tDCS to affect this kind of unconscious learning. Specifically, we concentrate on studies with the serial reaction time task (SRTT), the classical paradigm for measuring implicit motor sequence learning. The influence of tDCS has been investigated for the primary motor cortex, the premotor cortex, the prefrontal cortex, and the cerebellum. The results indicate that tDCS above the primary motor cortex gives raise to the most consistent modulating effects for both implicit motor sequence learning and consolidation. PMID:26903837

  17. How Transcranial Direct Current Stimulation Can Modulate Implicit Motor Sequence Learning and Consolidation: A Brief Review

    PubMed Central

    Savic, Branislav; Meier, Beat

    2016-01-01

    The purpose of this review is to investigate how transcranial direct current stimulation (tDCS) can modulate implicit motor sequence learning and consolidation. So far, most of the studies have focused on the modulating effect of tDCS for explicit motor learning. Here, we focus explicitly on implicit motor sequence learning and consolidation in order to improve our understanding about the potential of tDCS to affect this kind of unconscious learning. Specifically, we concentrate on studies with the serial reaction time task (SRTT), the classical paradigm for measuring implicit motor sequence learning. The influence of tDCS has been investigated for the primary motor cortex, the premotor cortex, the prefrontal cortex, and the cerebellum. The results indicate that tDCS above the primary motor cortex gives raise to the most consistent modulating effects for both implicit motor sequence learning and consolidation. PMID:26903837

  18. Protein kinase A directly phosphorylates metabotropic glutamate receptor 5 to modulate its function.

    PubMed

    Uematsu, Ken; Heiman, Myriam; Zelenina, Marina; Padovan, Júlio; Chait, Brian T; Aperia, Anita; Nishi, Akinori; Greengard, Paul

    2015-03-01

    Metabotropic glutamate receptor 5 (mGluR5) regulates excitatory post-synaptic signaling in the central nervous system (CNS) and is implicated in various CNS disorders. Protein kinase A (PKA) signaling is known to play a critical role in neuropsychiatric disorders such as Parkinson's disease, schizophrenia, and addiction. Dopamine signaling is known to modulate the properties of mGluR5 in a cAMP- and PKA-dependent manner, suggesting that mGluR5 may be a direct target for PKA. Our study identifies mGluR5 at Ser870 as a direct substrate for PKA phosphorylation and demonstrates that this phosphorylation plays a critical role in the PKA-mediated modulation of mGluR5 functions such as extracellular signal-regulated kinase phosphorylation and intracellular Ca(2+) oscillations. The identification of the molecular mechanism by which PKA signaling modulates mGluR5-mediated cellular responses contributes to the understanding of the interaction between dopaminergic and glutamatergic neuronal signaling. We identified serine residue 870 (S870) in metabotropic glutamate receptor 5 (mGluR5) as a direct substrate for protein kinase A (PKA). The phosphorylation of this site regulates the ability of mGluR5 to induce extracellular signal-regulated kinase (ERK) phosphorylation and intracellular Ca(2+) oscillations. This study provides a direct molecular mechanism by which PKA signaling interacts with glutamate neurotransmission. PMID:25639954

  19. A portable inspection system to estimate direct glare of various LED modules

    NASA Astrophysics Data System (ADS)

    Chen, Po-Li; Liao, Chun-Hsiang; Li, Hung-Chung; Jou, Shyh-Jye; Chen, Han-Ting; Lin, Yu-Hsin; Tang, Yu-Hsiang; Peng, Wei-Jei; Kuo, Hui-Jean; Sun, Pei-Li; Lee, Tsung-Xian

    2015-07-01

    Glare is caused by both direct and indirect light sources and discomfort glare produces visual discomfort, annoyance, or loss in visual performance and visibility. Direct glare is caused by light sources in the field of view whereas reflected glare is caused by bright reflections from polished or glossy surfaces that are reflected toward an individual. To improve visual comfort of our living environment, a portable inspection system to estimate direct glare of various commercial LED modules with the range of color temperature from 3100 K to 5300 K was developed in this study. The system utilized HDR images to obtain the illumination distribution of LED modules and was first calibrated for brightness and chromaticity and corrected with flat field, dark-corner and curvature by the installed algorithm. The index of direct glare was then automatically estimated after image capturing, and the operator can recognize the performance of LED modules and the possible effects on human being once the index was out of expecting range. In the future, we expect that the quick-response smart inspection system can be applied in several new fields and market, such as home energy diagnostics, environmental lighting and UGR monitoring and popularize it in several new fields.

  20. Modulation of spontaneous alpha brain rhythms using low-intensity transcranial direct-current stimulation.

    PubMed

    Spitoni, Grazia F; Cimmino, Rocco L; Bozzacchi, Chiara; Pizzamiglio, Luigi; Di Russo, Francesco

    2013-01-01

    Transcranial direct-current stimulation (tDCS) is a form of neurostimulation in which a constant, low current is delivered directly to the brain area of interest by small electrodes. The overall aim of this study was to examine and monitor the modulation of brain activity by electroencephalogram (EEG) in the frequency domain during tDCS in the resting state. To this end, we considered the modulation of spontaneous EEG to be a marker of the perturbation that was induced through the direct current (1.5 mA for 15 min). In all conditions (anodal, cathodal, and sham), an active electrode was placed over the right posterior parietal cortex, and a reference electrode was placed on the ipsilateral deltoid muscle. The EEG was recorded using a 64-channel system. The effect of tDCS was limited to the alpha rhythm, and the anodal stimulation significantly affected the alpha rhythm, whereas the cathodal stimulation did not elicit any modifications. Further, we observed modulation of alpha activity in areas that were stimulated directly through tDCS and in anterior noncontiguous areas. Finally, the anodal effect peaked 7.5 min after stimulation and decreased gradually over time. Our study demonstrates that in the resting brain, monocephalic anodal tDCS over posterior parietal areas alters ongoing brain activity, specifically in the alpha band rhythm. Our data can be used to fine-tune tDCS protocols in neurorehabilitation settings. PMID:24027517

  1. Dopamine: a parallel pathway for the modulation of spinal locomotor networks

    PubMed Central

    Sharples, Simon A.; Koblinger, Kathrin; Humphreys, Jennifer M.; Whelan, Patrick J.

    2014-01-01

    The spinal cord contains networks of neurons that can produce locomotor patterns. To readily respond to environmental conditions, these networks must be flexible yet at the same time robust. Neuromodulators play a key role in contributing to network flexibility in a variety of invertebrate and vertebrate networks. For example, neuromodulators contribute to altering intrinsic properties and synaptic weights that, in extreme cases, can lead to neurons switching between networks. Here we focus on the role of dopamine in the control of stepping networks in the spinal cord. We first review the role of dopamine in modulating rhythmic activity in the stomatogastric ganglion (STG) and the leech, since work from these preparations provides a foundation to understand its role in vertebrate systems. We then move to a discussion of dopamine’s role in modulation of swimming in aquatic species such as the larval xenopus, lamprey and zebrafish. The control of terrestrial walking in vertebrates by dopamine is less studied and we review current evidence in mammals with a focus on rodent species. We discuss data suggesting that the source of dopamine within the spinal cord is mainly from the A11 area of the diencephalon, and then turn to a discussion of dopamine’s role in modulating walking patterns from both in vivo and in vitro preparations. Similar to the descending serotonergic system, the dopaminergic system may serve as a potential target to promote recovery of locomotor function following spinal cord injury (SCI); evidence suggests that dopaminergic agonists can promote recovery of function following SCI. We discuss pharmacogenetic and optogenetic approaches that could be deployed in SCI and their potential tractability. Throughout the review we draw parallels with both noradrenergic and serotonergic modulatory effects on spinal cord networks. In all likelihood, a complementary monoaminergic enhancement strategy should be deployed following SCI. PMID:24982614

  2. Dopamine: a parallel pathway for the modulation of spinal locomotor networks.

    PubMed

    Sharples, Simon A; Koblinger, Kathrin; Humphreys, Jennifer M; Whelan, Patrick J

    2014-01-01

    The spinal cord contains networks of neurons that can produce locomotor patterns. To readily respond to environmental conditions, these networks must be flexible yet at the same time robust. Neuromodulators play a key role in contributing to network flexibility in a variety of invertebrate and vertebrate networks. For example, neuromodulators contribute to altering intrinsic properties and synaptic weights that, in extreme cases, can lead to neurons switching between networks. Here we focus on the role of dopamine in the control of stepping networks in the spinal cord. We first review the role of dopamine in modulating rhythmic activity in the stomatogastric ganglion (STG) and the leech, since work from these preparations provides a foundation to understand its role in vertebrate systems. We then move to a discussion of dopamine's role in modulation of swimming in aquatic species such as the larval xenopus, lamprey and zebrafish. The control of terrestrial walking in vertebrates by dopamine is less studied and we review current evidence in mammals with a focus on rodent species. We discuss data suggesting that the source of dopamine within the spinal cord is mainly from the A11 area of the diencephalon, and then turn to a discussion of dopamine's role in modulating walking patterns from both in vivo and in vitro preparations. Similar to the descending serotonergic system, the dopaminergic system may serve as a potential target to promote recovery of locomotor function following spinal cord injury (SCI); evidence suggests that dopaminergic agonists can promote recovery of function following SCI. We discuss pharmacogenetic and optogenetic approaches that could be deployed in SCI and their potential tractability. Throughout the review we draw parallels with both noradrenergic and serotonergic modulatory effects on spinal cord networks. In all likelihood, a complementary monoaminergic enhancement strategy should be deployed following SCI. PMID:24982614

  3. Global analysis of the human pathophenotypic similarity gene network merges disease module components.

    PubMed

    Reyes-Palomares, Armando; Rodríguez-López, Rocío; Ranea, Juan A G; Sánchez Jiménez, Francisca; Medina, Miguel Angel

    2013-01-01

    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. PMID:23437198

  4. Discrimination of direction in fast frequency-modulated tones by rats.

    PubMed

    Gaese, Bernhard H; King, Isabella; Felsheim, Christian; Ostwald, Joachim; von der Behrens, Wolfger

    2006-03-01

    Fast frequency modulations (FM) are an essential part of species-specific auditory signals in animals as well as in human speech. Major parameters characterizing non-periodic frequency modulations are the direction of frequency change in the FM sweep (upward/downward) and the sweep speed, i.e., the speed of frequency change. While it is well established that both parameters are represented in the mammalian central auditory pathway, their importance at the perceptual level in animals is unclear. We determined the ability of rats to discriminate between upward and downward modulated FM-tones as a function of sweep speed in a two-alternative-forced-choice-paradigm. Directional discrimination in logarithmic FM-sweeps was reduced with increasing sweep speed between 20 and 1,000 octaves/s following a psychometric function. Average threshold sweep speed for FM directional discrimination was 96 octaves/s. This upper limit of perceptual FM discrimination fits well the upper limit of preferred sweep speeds in auditory neurons and the upper limit of neuronal direction selectivity in the rat auditory cortex and midbrain, as it is found in the literature. Influences of additional stimulus parameters on FM discrimination were determined using an adaptive testing-procedure for efficient threshold estimation based on a maximum likelihood approach. Directional discrimination improved with extended FM sweep range between two and five octaves. Discrimination performance declined with increasing lower frequency boundary of FM sweeps, showing an especially strong deterioration when the boundary was raised from 2 to 4 kHz. This deterioration corresponds to a frequency-dependent decline in direction selectivity of FM-encoding neurons in the rat auditory cortex, as described in the literature. Taken together, by investigating directional discrimination of FM sweeps in the rat we found characteristics at the perceptual level that can be related to several aspects of FM encoding in the central auditory pathway. PMID:16411160

  5. Discrimination of Direction in Fast Frequency-Modulated Tones by Rats

    PubMed Central

    King, Isabella; Felsheim, Christian; Ostwald, Joachim; von der Behrens, Wolfger

    2006-01-01

    Fast frequency modulations (FM) are an essential part of species-specific auditory signals in animals as well as in human speech. Major parameters characterizing non-periodic frequency modulations are the direction of frequency change in the FM sweep (upward/downward) and the sweep speed, i.e., the speed of frequency change. While it is well established that both parameters are represented in the mammalian central auditory pathway, their importance at the perceptual level in animals is unclear. We determined the ability of rats to discriminate between upward and downward modulated FM-tones as a function of sweep speed in a two-alternative-forced-choice-paradigm. Directional discrimination in logarithmic FM-sweeps was reduced with increasing sweep speed between 20 and 1,000 octaves/s following a psychometric function. Average threshold sweep speed for FM directional discrimination was 96 octaves/s. This upper limit of perceptual FM discrimination fits well the upper limit of preferred sweep speeds in auditory neurons and the upper limit of neuronal direction selectivity in the rat auditory cortex and midbrain, as it is found in the literature. Influences of additional stimulus parameters on FM discrimination were determined using an adaptive testing-procedure for efficient threshold estimation based on a maximum likelihood approach. Directional discrimination improved with extended FM sweep range between two and five octaves. Discrimination performance declined with increasing lower frequency boundary of FM sweeps, showing an especially strong deterioration when the boundary was raised from 2 to 4 kHz. This deterioration corresponds to a frequency-dependent decline in direction selectivity of FM-encoding neurons in the rat auditory cortex, as described in the literature. Taken together, by investigating directional discrimination of FM sweeps in the rat we found characteristics at the perceptual level that can be related to several aspects of FM encoding in the central auditory pathway. PMID:16411160

  6. ABC and IFC: modules detection method for PPI network.

    PubMed

    Lei, Xiujuan; Wu, Fang-Xiang; Tian, Jianfang; Zhao, Jie

    2014-01-01

    Many clustering algorithms are unable to solve the clustering problem of protein-protein interaction (PPI) networks effectively. A novel clustering model which combines the optimization mechanism of artificial bee colony (ABC) with the fuzzy membership matrix is proposed in this paper. The proposed ABC-IFC clustering model contains two parts: searching for the optimum cluster centers using ABC mechanism and forming clusters using intuitionistic fuzzy clustering (IFC) method. Firstly, the cluster centers are set randomly and the initial clustering results are obtained by using fuzzy membership matrix. Then the cluster centers are updated through different functions of bees in ABC algorithm; then the clustering result is obtained through IFC method based on the new optimized cluster center. To illustrate its performance, the ABC-IFC method is compared with the traditional fuzzy C-means clustering and IFC method. The experimental results on MIPS dataset show that the proposed ABC-IFC method not only gets improved in terms of several commonly used evaluation criteria such as precision, recall, and P value, but also obtains a better clustering result. PMID:24991575

  7. Phenology Across the LTER Network: Initial Findings, Future Directions

    NASA Astrophysics Data System (ADS)

    Henebry, G. M.

    2007-12-01

    Phenology is, in the words of Aldo Leopold, a "horizontal science" that cuts across and binds together multiple biological disciplines. It is a far-reaching but poorly understood aspect of the environmental sciences. Phenological research has been a component of the Long Term Ecological Research (LTER) Network at several sites over the years. However, it has not received the attention or resources to bring it to the forefront as an effective theme for interdisciplinary and cross-site synthesis. With the recent establishment of the USA National Phenology Network (USA-NPN), it is appropriate to assess the status of phenological knowledge across the LTER Network. A workshop funded by the LTER Network Office took place at the Sevilleta Field Station during February 26 to March 2, 2007. From the workshop three main products emerged: (1) an inventory of LTER phenology datasets, (2) establishment of a website to facilitate information interchange, and (3) a white paper recommending next steps for the LTER Network to engage the USA-NPN. This poster relates the findings and recommendations of the workshop, including a summary of phenologically explicit and phenologically implicit LTER datasets and illustrations of how the climatic envelopes described by simple weather variables can provide context for phenological comparisons within and across sites.

  8. Network discovery pipeline elucidates conserved time-of-day-specific cis-regulatory modules.

    PubMed

    Michael, Todd P; Mockler, Todd C; Breton, Ghislain; McEntee, Connor; Byer, Amanda; Trout, Jonathan D; Hazen, Samuel P; Shen, Rongkun; Priest, Henry D; Sullivan, Christopher M; Givan, Scott A; Yanovsky, Marcelo; Hong, Fangxin; Kay, Steve A; Chory, Joanne

    2008-02-01

    Correct daily phasing of transcription confers an adaptive advantage to almost all organisms, including higher plants. In this study, we describe a hypothesis-driven network discovery pipeline that identifies biologically relevant patterns in genome-scale data. To demonstrate its utility, we analyzed a comprehensive matrix of time courses interrogating the nuclear transcriptome of Arabidopsis thaliana plants grown under different thermocycles, photocycles, and circadian conditions. We show that 89% of Arabidopsis transcripts cycle in at least one condition and that most genes have peak expression at a particular time of day, which shifts depending on the environment. Thermocycles alone can drive at least half of all transcripts critical for synchronizing internal processes such as cell cycle and protein synthesis. We identified at least three distinct transcription modules controlling phase-specific expression, including a new midnight specific module, PBX/TBX/SBX. We validated the network discovery pipeline, as well as the midnight specific module, by demonstrating that the PBX element was sufficient to drive diurnal and circadian condition-dependent expression. Moreover, we show that the three transcription modules are conserved across Arabidopsis, poplar, and rice. These results confirm the complex interplay between thermocycles, photocycles, and the circadian clock on the daily transcription program, and provide a comprehensive view of the conserved genomic targets for a transcriptional network key to successful adaptation. PMID:18248097

  9. Network Discovery Pipeline Elucidates Conserved Time-of-Day–Specific cis-Regulatory Modules

    PubMed Central

    McEntee, Connor; Byer, Amanda; Trout, Jonathan D; Hazen, Samuel P; Shen, Rongkun; Priest, Henry D; Sullivan, Christopher M; Givan, Scott A; Yanovsky, Marcelo; Hong, Fangxin; Kay, Steve A; Chory, Joanne

    2008-01-01

    Correct daily phasing of transcription confers an adaptive advantage to almost all organisms, including higher plants. In this study, we describe a hypothesis-driven network discovery pipeline that identifies biologically relevant patterns in genome-scale data. To demonstrate its utility, we analyzed a comprehensive matrix of time courses interrogating the nuclear transcriptome of Arabidopsis thaliana plants grown under different thermocycles, photocycles, and circadian conditions. We show that 89% of Arabidopsis transcripts cycle in at least one condition and that most genes have peak expression at a particular time of day, which shifts depending on the environment. Thermocycles alone can drive at least half of all transcripts critical for synchronizing internal processes such as cell cycle and protein synthesis. We identified at least three distinct transcription modules controlling phase-specific expression, including a new midnight specific module, PBX/TBX/SBX. We validated the network discovery pipeline, as well as the midnight specific module, by demonstrating that the PBX element was sufficient to drive diurnal and circadian condition-dependent expression. Moreover, we show that the three transcription modules are conserved across Arabidopsis, poplar, and rice. These results confirm the complex interplay between thermocycles, photocycles, and the circadian clock on the daily transcription program, and provide a comprehensive view of the conserved genomic targets for a transcriptional network key to successful adaptation. PMID:18248097

  10. Co-expression network analysis identifies transcriptional modules in the mouse liver.

    PubMed

    Liu, Wei; Ye, Hua

    2014-10-01

    The mouse liver transcriptome has been extensively studied but little is known about the global hepatic gene network of the mouse under normal physiological conditions. Understanding this will help reveal the transcriptional organization of the liver and elucidate its functional complexity. Here, weighted gene co-expression network analysis (WGCNA) was carried out to explore gene co-expression networks using large-scale microarray data from normal mouse livers. A total of 7,203 genes were parsed into 16 gene modules associated with protein catabolism, RNA processing, muscle contraction, transcriptional regulation, oxidation reduction, sterol biosynthesis, translation, fatty acid metabolism, immune response and others. The modules were organized into higher order co-expression groups. Hub genes in each module were found to be critical for module function. In sum, the analyses revealed the gene modular map of the mouse liver under normal physiological condition. These results provide a systems-level framework to help understand the complexity of the mouse liver at the molecular level, and should be beneficial in annotating uncharacterized genes. PMID:24816893

  11. Frequency Modulation of Directly Imaged Exoplanets: Geometric Effect as a Probe of Planetary Obliquity

    NASA Astrophysics Data System (ADS)

    Kawahara, Hajime

    2016-05-01

    We consider the time–frequency analysis of a scattered light curve of a directly imaged exoplanet. We show that the geometric effect due to planetary obliquity and orbital inclination induce the frequency modulation of the apparent diurnal periodicity. We construct a model of the frequency modulation and compare it with the instantaneous frequency extracted from the pseudo-Wigner distribution of simulated light curves of a cloudless Earth. The model provides good agreement with the simulated modulation factor, even for the light curve with Gaussian noise comparable to the signal. Notably, the shape of the instantaneous frequency is sensitive to the difference between the prograde, retrograde, and pole-on spin rotations. While our technique requires the albedo map to be static, it does not need to solve the albedo map of the planet. The time–frequency analysis is complementary to other methods which utilize the amplitude modulation. This paper demonstrates the importance of the frequency domain of the photometric variability for the characterization of directly imaged exoplanets in future research.

  12. Rapid, Time-Division Multiplexed, Direct Absorption- and Wavelength Modulation-Spectroscopy

    PubMed Central

    Klein, Alexander; Witzel, Oliver; Ebert, Volker

    2014-01-01

    We present a tunable diode laser spectrometer with a novel, rapid time multiplexed direct absorption- and wavelength modulation-spectroscopy operation mode. The new technique allows enhancing the precision and dynamic range of a tunable diode laser absorption spectrometer without sacrificing accuracy. The spectroscopic technique combines the benefits of absolute concentration measurements using calibration-free direct tunable diode laser absorption spectroscopy (dTDLAS) with the enhanced noise rejection of wavelength modulation spectroscopy (WMS). In this work we demonstrate for the first time a 125 Hz time division multiplexed (TDM-dTDLAS-WMS) spectroscopic scheme by alternating the modulation of a DFB-laser between a triangle-ramp (dTDLAS) and an additional 20 kHz sinusoidal modulation (WMS). The absolute concentration measurement via the dTDLAS-technique allows one to simultaneously calibrate the normalized 2f/1f-signal of the WMS-technique. A dTDLAS/WMS-spectrometer at 1.37 μm for H2O detection was built for experimental validation of the multiplexing scheme over a concentration range from 50 to 3000 ppmV (0.1 MPa, 293 K). A precision of 190 ppbV was achieved with an absorption length of 12.7 cm and an averaging time of two seconds. Our results show a five-fold improvement in precision over the entire concentration range and a significantly decreased averaging time of the spectrometer. PMID:25405508

  13. Prospects for detection of target-dependent annual modulation in direct dark matter searches

    NASA Astrophysics Data System (ADS)

    Del Nobile, Eugenio; Gelmini, Graciela B.; Witte, Samuel J.

    2016-02-01

    Earth's rotation about the Sun produces an annual modulation in the expected scattering rate at direct dark matter detection experiments. The annual modulation as a function of the recoil energy ER imparted by the dark matter particle to a target nucleus is expected to vary depending on the detector material. However, for most interactions a change of variables from ER to vmin, the minimum speed a dark matter particle must have to impart a fixed ER to a target nucleus, produces an annual modulation independent of the target element. We recently showed that if the dark matter-nucleus cross section contains a non-factorizable target and dark matter velocity dependence, the annual modulation as a function of vmin can be target dependent. Here we examine more extensively the necessary conditions for target-dependent modulation, its observability in present-day experiments, and the extent to which putative signals could identify a dark matter-nucleus differential cross section with a non-factorizable dependence on the dark matter velocity.

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

    PubMed

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

    2013-10-01

    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 β-BaB₂O₄ crystal, where a 4 times enhancement in green power is observed compared to cw operation. PMID:24104250

  15. Wireless Multimedia Sensor Networks: current trends and future directions.

    PubMed

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

    2010-01-01

    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

  16. Wireless Multimedia Sensor Networks: Current Trends and Future Directions

    PubMed Central

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

    2010-01-01

    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

  17. General Relationship of Global Topology, Local Dynamics, and Directionality in Large-Scale Brain Networks

    PubMed Central

    Moon, Joon-Young; Lee, UnCheol; Blain-Moraes, Stefanie; Mashour, George A.

    2015-01-01

    The balance of global integration and functional specialization is a critical feature of efficient brain networks, but the relationship of global topology, local node dynamics and information flow across networks has yet to be identified. One critical step in elucidating this relationship is the identification of governing principles underlying the directionality of interactions between nodes. Here, we demonstrate such principles through analytical solutions based on the phase lead/lag relationships of general oscillator models in networks. We confirm analytical results with computational simulations using general model networks and anatomical brain networks, as well as high-density electroencephalography collected from humans in the conscious and anesthetized states. Analytical, computational, and empirical results demonstrate that network nodes with more connections (i.e., higher degrees) have larger amplitudes and are directional targets (phase lag) rather than sources (phase lead). The relationship of node degree and directionality therefore appears to be a fundamental property of networks, with direct applicability to brain function. These results provide a foundation for a principled understanding of information transfer across networks and also demonstrate that changes in directionality patterns across states of human consciousness are driven by alterations of brain network topology. PMID:25874700

  18. Finding pathway-modulating genes from a novel Ontology Fingerprint-derived gene network

    PubMed Central

    Qin, Tingting; Matmati, Nabil; Tsoi, Lam C.; Mohanty, Bidyut K.; Gao, Nan; Tang, Jijun; Lawson, Andrew B.; Hannun, Yusuf A.; Zheng, W. Jim

    2014-01-01

    To enhance our knowledge regarding biological pathway regulation, we took an integrated approach, using the biomedical literature, ontologies, network analyses and experimental investigation to infer novel genes that could modulate biological pathways. We first constructed a novel gene network via a pairwise comparison of all yeast genes’ Ontology Fingerprints—a set of Gene Ontology terms overrepresented in the PubMed abstracts linked to a gene along with those terms’ corresponding enrichment P-values. The network was further refined using a Bayesian hierarchical model to identify novel genes that could potentially influence the pathway activities. We applied this method to the sphingolipid pathway in yeast and found that many top-ranked genes indeed displayed altered sphingolipid pathway functions, initially measured by their sensitivity to myriocin, an inhibitor of de novo sphingolipid biosynthesis. Further experiments confirmed the modulation of the sphingolipid pathway by one of these genes, PFA4, encoding a palmitoyl transferase. Comparative analysis showed that few of these novel genes could be discovered by other existing methods. Our novel gene network provides a unique and comprehensive resource to study pathway modulations and systems biology in general. PMID:25063300

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

    SciTech Connect

    2012-01-30

    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.

  20. Writing and erasing of temporal cavity solitons by direct phase modulation of the cavity driving field.

    PubMed

    Jang, Jae K; Erkintalo, Miro; Murdoch, Stuart G; Coen, Stéphane

    2015-10-15

    Temporal cavity solitons (CSs) are persisting pulses of light that can manifest themselves in continuously driven passive resonators, such as macroscopic fiber ring cavities and monolithic microresonators. Experiments so far have demonstrated two techniques for their excitation, yet both possess drawbacks in the form of system complexity or lack of control over soliton positioning. Here we experimentally demonstrate a new CS writing scheme that alleviates these deficiencies. Specifically, we show that temporal CSs can be excited at arbitrary positions through direct phase modulation of the cavity driving field, and that this technique also allows existing CSs to be selectively erased. Our results constitute the first experimental demonstration of temporal CS excitation via direct phase modulation, as well as their selective erasure (by any means). These advances reduce the complexity of CS excitation and could lead to controlled pulse generation in monolithic microresonators. PMID:26469612

  1. Tunable photonic microwave generation by directly modulating a dual-wavelength amplified feedback laser

    NASA Astrophysics Data System (ADS)

    Yu, Liqiang; Lu, Dan; Sun, Yu; Zhao, Lingjuan

    2015-06-01

    A compact and simple approach to realizing tunable high-frequency photonic microwave using a directly-modulated dual-wavelength amplified feedback laser (AFL) diode is demonstrated. By directly modulating the AFL at the 1/2 sub-harmonic frequency of its fundamental mode spacing, frequency-doubled microwave is generated. At a low RF driven power of 2.8 dBm, tunable microwave outputs ranging from 15 GHz to 33 GHz are obtained with 2-GHz locking range. The phase noise and frequency stability of the generated microwave signal are also investigated. The proposed scheme requires much lower RF driven power and can be a viable choice for situations where high power and high frequency RF signal is not available.

  2. Ultrasound-modulated optical tomography: direct recovery of elasticity distribution from experimentally measured intensity autocorrelation.

    PubMed

    Mohanan, K P; Nandakumaran, A K; Roy, D; Vasu, R M

    2015-05-01

    Based on an ultrasound-modulated optical tomography experiment, a direct, quantitative recovery of Young's modulus (E) is achieved from the modulation depth (M) in the intensity autocorrelation. The number of detector locations is limited to two in orthogonal directions, reducing the complexity of the data gathering step whilst ensuring against an impoverishment of the measurement, by employing ultrasound frequency as a parameter to vary during data collection. The M and E are related via two partial differential equations. The first one connects M to the amplitude of vibration of the scattering centers in the focal volume and the other, this amplitude to E. A (composite) sensitivity matrix is arrived at mapping the variation of M with that of E and used in a (barely regularized) Gauss-Newton algorithm to iteratively recover E. The reconstruction results showing the variation of E are presented. PMID:26366922

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

    NASA Astrophysics Data System (ADS)

    Su, Xiao-hui; Xu, Shu-Ping

    2013-03-01

    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.

  4. Electrophysiological properties of rostral ventrolateral medulla presympathetic neurons modulated by the respiratory network in rats.

    PubMed

    Moraes, Davi J A; da Silva, Melina P; Bonagamba, Leni G H; Mecawi, André S; Zoccal, Daniel B; Antunes-Rodrigues, José; Varanda, Wamberto A; Machado, Benedito H

    2013-12-01

    The respiratory pattern generator modulates the sympathetic outflow, the strength of which is enhanced by challenges produced by hypoxia. This coupling is due to the respiratory-modulated presympathetic neurons in the rostral ventrolateral medulla (RVLM), but the underlining electrophysiological mechanisms remain unclear. For a better understanding of the neural substrates responsible for generation of this respiratory-sympathetic coupling, we combined immunofluorescence, single cell qRT-pCR, and electrophysiological recordings of the RVLM presympathetic neurons in in situ preparations from normal rats and rats submitted to a metabolic challenge produced by chronic intermittent hypoxia (CIH). Our results show that the spinally projected cathecholaminergic C1 and non-C1 respiratory-modulated RVLM presympathetic neurons constitute a heterogeneous neuronal population regarding the intrinsic electrophysiological properties, respiratory synaptic inputs, and expression of ionic currents, albeit all neurons presented persistent sodium current-dependent intrinsic pacemaker properties after synaptic blockade. A specific subpopulation of non-C1 respiratory-modulated RVLM presympathetic neurons presented enhanced excitatory synaptic inputs from the respiratory network after CIH. This phenomenon may contribute to the increased sympathetic activity observed in CIH rats. We conclude that the different respiratory-modulated RVLM presympathetic neurons contribute to the central generation of respiratory-sympathetic coupling as part of a complex neuronal network, which in response to the challenges produced by CIH contribute to respiratory-related increase in the sympathetic activity. PMID:24305818

  5. Optical vector network analyzer with improved accuracy based on polarization modulation and polarization pulling.

    PubMed

    Li, Wei; Liu, Jian Guo; Zhu, Ning Hua

    2015-04-15

    We report a novel optical vector network analyzer (OVNA) with improved accuracy based on polarization modulation and stimulated Brillouin scattering (SBS) assisted polarization pulling. The beating between adjacent higher-order optical sidebands which are generated because of the nonlinearity of an electro-optic modulator (EOM) introduces considerable error to the OVNA. In our scheme, the measurement error is significantly reduced by removing the even-order optical sidebands using polarization discrimination. The proposed approach is theoretically analyzed and experimentally verified. The experimental results show that the accuracy of the OVNA is greatly improved compared to a conventional OVNA. PMID:25872046

  6. Implementing direct, spatially isolated problems on transputer networks

    NASA Technical Reports Server (NTRS)

    Ellis, Graham K.

    1988-01-01

    Parametric studies were performed on transputer networks of up to 40 processors to determine how to implement and maximize the performance of the solution of problems where no processor-to-processor data transfer is required for the problem solution (spatially isolated). Two types of problems are investigated a computationally intensive problem where the solution required the transmission of 160 bytes of data through the parallel network, and a communication intensive example that required the transmission of 3 Mbytes of data through the network. This data consists of solutions being sent back to the host processor and not intermediate results for another processor to work on. Studies were performed on both integer and floating-point transputers. The latter features an on-chip floating-point math unit and offers approximately an order of magnitude performance increase over the integer transputer on real valued computations. The results indicate that a minimum amount of work is required on each node per communication to achieve high network speedups (efficiencies). The floating-point processor requires approximately an order of magnitude more work per communication than the integer processor because of the floating-point unit's increased computing capacity.

  7. A Sphere Phantom Approach to Measure Directional Modulation Transfer Functions for Tomosynthesis Imaging Systems.

    PubMed

    Lee, Changwoo; Baek, Jongduk

    2016-03-01

    We propose a sphere phantom approach to measure spatially varying directional modulation transfer functions (MTFs) for tomosynthesis imaging systems. Since the reconstructed tomosynthesis images contain significant artifacts, traditional background detrending techniques may not be effective to estimate the background trends accurately, which is essential to acquire sphere only data. A background detrending technique optimized for local volumes with different cone angles is presented. To measure directional MTFs, we calculate plane integrals of ideal sphere phantom and sphere only data. To minimize the effects of the high level of noise in tomosynthesis images, Richardson-Lucy deconvolution with Tikhonov-Miller is used to estimate directional plane spread function (PlSF). Then, directional MTFs are calculated by taking the modulus of the Fourier transform of the directional PlSFs. The measured directional MTFs are compared with the ideal directional MTFs calculated from a simulated point object. Our results show that the proposed method reliably measures directional MTFs along any desired directions, especially near low frequency regions. PMID:26571519

  8. Inherent directionality explains the lack of feedback loops in empirical networks.

    PubMed

    Domínguez-García, Virginia; Pigolotti, Simone; Muñoz, Miguel A

    2014-01-01

    We explore the hypothesis that the relative abundance of feedback loops in many empirical complex networks is severely reduced owing to the presence of an inherent global directionality. Aimed at quantifying this idea, we propose a simple probabilistic model in which a free parameter γ controls the degree of inherent directionality. Upon strengthening such directionality, the model predicts a drastic reduction in the fraction of loops which are also feedback loops. To test this prediction, we extensively enumerated loops and feedback loops in many empirical biological, ecological and socio-technological directed networks. We show that, in almost all cases, empirical networks have a much smaller fraction of feedback loops than network randomizations. Quite remarkably, this empirical finding is quantitatively reproduced, for all loop lengths, by our model by fitting its only parameter γ. Moreover, the fitted value of γ correlates quite well with another direct measurement of network directionality, performed by means of a novel algorithm. We conclude that the existence of an inherent network directionality provides a parsimonious quantitative explanation for the observed lack of feedback loops in empirical networks. PMID:25531727

  9. Inherent directionality explains the lack of feedback loops in empirical networks

    PubMed Central

    Domínguez-García, Virginia; Pigolotti, Simone; Muñoz, Miguel A.

    2014-01-01

    We explore the hypothesis that the relative abundance of feedback loops in many empirical complex networks is severely reduced owing to the presence of an inherent global directionality. Aimed at quantifying this idea, we propose a simple probabilistic model in which a free parameter γ controls the degree of inherent directionality. Upon strengthening such directionality, the model predicts a drastic reduction in the fraction of loops which are also feedback loops. To test this prediction, we extensively enumerated loops and feedback loops in many empirical biological, ecological and socio-technological directed networks. We show that, in almost all cases, empirical networks have a much smaller fraction of feedback loops than network randomizations. Quite remarkably, this empirical finding is quantitatively reproduced, for all loop lengths, by our model by fitting its only parameter γ. Moreover, the fitted value of γ correlates quite well with another direct measurement of network directionality, performed by means of a novel algorithm. We conclude that the existence of an inherent network directionality provides a parsimonious quantitative explanation for the observed lack of feedback loops in empirical networks. PMID:25531727

  10. Regulatory Snapshots: integrative mining of regulatory modules from expression time series and regulatory networks.

    PubMed

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

    2012-01-01

    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. PMID:22563474

  11. Optimizing Environmental Monitoring Networks with Direction-Dependent Distance Thresholds.

    ERIC Educational Resources Information Center

    Hudak, Paul F.

    1993-01-01

    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)

  12. EgoNet: identification of human disease ego-network modules

    PubMed Central

    2014-01-01

    Background Mining novel biomarkers from gene expression profiles for accurate disease classification is challenging due to small sample size and high noise in gene expression measurements. Several studies have proposed integrated analyses of microarray data and protein-protein interaction (PPI) networks to find diagnostic subnetwork markers. However, the neighborhood relationship among network member genes has not been fully considered by those methods, leaving many potential gene markers unidentified. The main idea of this study is to take full advantage of the biological observation that genes associated with the same or similar diseases commonly reside in the same neighborhood of molecular networks. Results We present EgoNet, a novel method based on egocentric network-analysis techniques, to exhaustively search and prioritize disease subnetworks and gene markers from a large-scale biological network. When applied to a triple-negative breast cancer (TNBC) microarray dataset, the top selected modules contain both known gene markers in TNBC and novel candidates, such as RAD51 and DOK1, which play a central role in their respective ego-networks by connecting many differentially expressed genes. Conclusions Our results suggest that EgoNet, which is based on the ego network concept, allows the identification of novel biomarkers and provides a deeper understanding of their roles in complex diseases. PMID:24773628

  13. Gene Networks in the Wild: Identifying Transcriptional Modules that Mediate Coral Resistance to Experimental Heat Stress.

    PubMed

    Rose, Noah H; Seneca, Francois O; Palumbi, Stephen R

    2016-01-01

    Organisms respond to environmental variation partly through changes in gene expression, which underlie both homeostatic and acclimatory responses to environmental stress. In some cases, so many genes change in expression in response to different influences that understanding expression patterns for all these individual genes becomes difficult. To reduce this problem, we use a systems genetics approach to show that variation in the expression of thousands of genes of reef-building corals can be explained as variation in the expression of a small number of coexpressed "modules." Modules were often enriched for specific cellular functions and varied predictably among individuals, experimental treatments, and physiological state. We describe two transcriptional modules for which expression levels immediately after heat stress predict bleaching a day later. One of these early "bleaching modules" is enriched for sequence-specific DNA-binding proteins, particularly E26 transformation-specific (ETS)-family transcription factors. The other module is enriched for extracellular matrix proteins. These classes of bleaching response genes are clear in the modular gene expression analysis we conduct but are much more difficult to discern in single gene analyses. Furthermore, the ETS-family module shows repeated differences in expression among coral colonies grown in the same common garden environment, suggesting a heritable genetic or epigenetic basis for these expression polymorphisms. This finding suggests that these corals harbor high levels of gene-network variation, which could facilitate rapid evolution in the face of environmental change. PMID:26710855

  14. Clinical relevance of cyclic GMP modulators: A translational success story of network pharmacology.

    PubMed

    Oettrich, J M; Dao, V T; Frijhoff, J; Kleikers, Pwm; Casas, A I; Hobbs, A J; Schmidt, Hhhw

    2016-04-01

    Therapies that modulate cyclic guanosine-3'-5'-monophosphate (cGMP) have emerged as one of the most successful areas in recent drug discovery and clinical pharmacology. Historically, their focus has been on cardiovascular disease phenotypes; however, cGMP's relevance is likely to go beyond this rather limited organ-based set of indications. Moreover, the multitude of targets and their apparent interchangeability is a proof-of-concept of network pharmacology. PMID:26765222

  15. Detection of type 2 diabetes related modules and genes based on epigenetic networks

    PubMed Central

    2014-01-01

    Background Type 2 diabetes (T2D) is one of the most common chronic metabolic diseases characterized by insulin resistance and the decrease of insulin secretion. Genetic variation can only explain part of the heritability of T2D, so there need new methods to detect the susceptibility genes of the disease. Epigenetics could establish the interface between the environmental factor and the T2D Pathological mechanism. Results Based on the network theory and by combining epigenetic characteristics with human interactome, the weighted human DNA methylation network (WMPN) was constructed, and a T2D-related subnetwork (TMSN) was obtained through T2D-related differentially methylated genes. It is found that TMSN had a T2D specific network structure that non-fatal metabolic disease causing genes were often located in the topological and functional periphery of network. Combined with chromatin modifications, the weighted chromatin modification network (WCPN) was built, and a T2D-related chromatin modification pattern subnetwork was obtained by the TMSN gene set. TCSN had a densely connected network community, indicating that TMSN and TCSN could represent a collection of T2D-related epigenetic dysregulated sub-pathways. Using the cumulative hypergeometric test, 24 interplay modules of DNA methylation and chromatin modifications were identified. By the analysis of gene expression in human T2D islet tissue, it is found that there existed genes with the variant expression level caused by the aberrant DNA methylation and (or) chromatin modifications, which might affect and promote the development of T2D. Conclusions Here we have detected the potential interplay modules of DNA methylation and chromatin modifications for T2D. The study of T2D epigenetic networks provides a new way for understanding the pathogenic mechanism of T2D caused by epigenetic disorders. PMID:24565181

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

    PubMed Central

    Reyes-Palomares, Armando; Rodríguez-López, Rocío; Ranea, Juan A. G.; Jiménez, Francisca Sánchez; Medina, Miguel Angel

    2013-01-01

    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. PMID:23437198

  17. Protein kinase A directly phosphorylates metabotropic glutamate receptor 5 to modulate its function

    PubMed Central

    Uematsu, Ken; Heiman, Myriam; Zelenina, Marina; Padovan, Júlio; Chait, Brian T.; Aperia, Anita; Nishi, Akinori; Greengard, Paul

    2015-01-01

    Metabotropic glutamate receptor 5 (mGluR5) regulates excitatory postsynaptic signaling in the central nervous system (CNS) and is implicated in various CNS disorders. Protein kinase A (PKA) signaling is known to play a critical role in neuropsychiatric disorders such as Parkinson’s disease, schizophrenia and addiction. Dopamine signaling is known to modulate the properties of mGluR5 in a cAMP- and PKA-dependent manner, suggesting that mGluR5 may be a direct target for PKA. Our study identifies mGluR5 at Ser870 as a direct substrate for PKA phosphorylation and demonstrates that this phosphorylation plays a critical role in the PKA-mediated modulation of mGluR5 functions such as extracellular signal-regulated kinase (ERK) phosphorylation and intracellular Ca2+ oscillations. The identification of the molecular mechanism by which PKA signaling modulates mGluR5-mediated cellular responses contributes to the understanding of the interaction between dopaminergic and glutamatergic neuronal signaling. PMID:25639954

  18. A 50-kW Module Power Station of Directly Solar-Pumped Iodine Laser

    NASA Technical Reports Server (NTRS)

    Choi, S. H.; Lee, J. H.; Meador, W. E.; Conway, E. J.

    1997-01-01

    The conceptual design of a 50 kW Directly Solar-Pumped Iodine Laser (DSPIL) module was developed for a space-based power station which transmits its coherent-beam power to users such as the moon, Martian rovers, or other satellites with large (greater than 25 kW) electric power requirements. Integration of multiple modules would provide an amount of power that exceeds the power of a single module by combining and directing the coherent beams to the user's receiver. The model developed for the DSPIL system conservatively predicts the laser output power (50 kW) that appears much less than the laser output (93 kW) obtained from the gain volume ratio extrapolation of experimental data. The difference in laser outputs may be attributed to reflector configurations adopted in both design and experiment. Even though the photon absorption by multiple reflections in experimental cavity setup was more efficient, the maximum secondary absorption amounts to be only 24.7 percent of the primary. However, the gain volume ratio shows 86 percent more power output than theoretical estimation that is roughly 60 percent more than the contribution by the secondary absorption. Such a difference indicates that the theoretical model adopted in the study underestimates the overall performance of the DSPIL. This fact may tolerate more flexible and radical selection of design parameters than used in this design study. The design achieves an overall specific power of approximately 5 W/kg and total mass of 10 metric tons.

  19. A 50-kW module power station of directly solar-pumped iodine laser

    SciTech Connect

    Choi, S.H.; Lee, J.H.; Meador, W.E.; Conway, E.J.

    1997-11-01

    The conceptual design of a 50 kW directly solar-pumped iodine laser (DSPIL) module was developed for a space-based power station which transmits its coherent-beam power to users such as the moon, Martian rovers, or other satellites with large (>25 kW) electric power requirements. Integration of multiple modules would provide an amount of power that exceeds the power of a single module by combining and directing the coherent beams to the user`s receiver. The model developed for the DSPIL system conservatively predicts the laser output power (50 kW) that appears much less than the laser output (93 kW) obtained from the gain volume ratio extrapolation of experimental data. The difference in laser outputs may be attributed to reflector configurations adopted in both design and experiment. Even though the photon absorption by multiple reflections in experimental cavity setup was more efficient, the maximum secondary absorption amounts to be only 24.7 percent of the primary. However, the gain volume ratio shows 86 percent more power output than theoretical estimation that is roughly 60 percent more than the contribution by the secondary absorption. Such a difference indicates that the theoretical model adopted in the study underestimates the overall performance of the DSPIL. This fact may tolerate more flexible and radical selection of design parameters than used in this design study. The design achieves an overall specific power of approximately 5 W/kg and total mass of 10 metric tons.

  20. Robust modulation formats recognition technique using wavelet transform for high speed optical networks

    NASA Astrophysics Data System (ADS)

    Guesmi, Latifa; Hraghi, Abir; Menif, Mourad

    2015-09-01

    There is a need, for high speed optical communication networks, in the monitoring process, to determine the modulation format type of a received signal. In this paper, we present a new achievement of modulation format recognition technique, where we proposed the use of wavelet transform of the detected signal in conjunction with the artificial neural network (ANN) algorithm. Besides, wavelet transform is one of the most popular candidates of the time-frequency transformations, where the wavelets are generated from a basic wavelet function by dilations and translations. We proved that this technique is capable of recognizing the multi-carriers modulation scheme with high accuracy under different transmission impairments such as chromatic dispersion (CD), differential group delay (DGD) and accumulated amplified spontaneous emission (ASE) noise with different ranges. Both the theoretical analysis and the simulation results showed that the wavelet transform not only can be used for modulation identification of optical communication signals, but also has a better classification accuracies under appropriate OSNR (optical signal-to-noise ratio) values.

  1. The Myth of Spatial Reuse with Directional Antennas in Indoor Wireless Networks

    NASA Astrophysics Data System (ADS)

    Lakshmanan, Sriram; Sundaresan, Karthikeyan; Rangarajan, Sampath; Sivakumar, Raghupathy

    Interference among co-channel users is a fundamental problem in wireless networks, which prevents nearby links from operating concurrently. Directional antennas allow the radiation patterns of wireless transmitters to be shaped to form directed beams. Conventionally, such beams are assumed to improve the spatial reuse (i.e. concurrency) in indoor wireless networks. In this paper, we use experiments in an indoor office setting of Wifi Access points equipped with directional antennas, to study their potential for interference mitigation and spatial reuse. In contrast to conventional wisdom, we observe that the interference mitigation benefits of directional antennas are minimal. On analyzing our experimental traces we observe that directional links do not reduce interference to nearby links due to the lack of signal confinement due to indoor multipath fading. We then use the insights derived from our study to develop an alternative approach that provides better interference reduction in indoor networks compared to directional links.

  2. Early appraisal of the fixation probability in directed networks

    NASA Astrophysics Data System (ADS)

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

    2010-10-01

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2009-12-01

    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.

  4. Technical evaluation of a USSC Integrated/Direct Mount PV Roofing Module system at NREL

    SciTech Connect

    Strand, T.; Hansen, R.; Mrig, L.

    1995-05-01

    The results of a 16 month technical evaluation performed on a nominal 1 kW{sub ac} utility-interconnect amorphous silicon PV system deployed at the National Renewable Energy Laboratory`s PV outdoor test site are given here. The system employs 64 prototype United Solar Systems Corp. Integrated/Direct Mount PV Roofing Modules mounted on simulated attic/roof structures. In this paper we show that the PV array fill factor has been relatively stable with respect to time and that the seasonal variations in performance can be largely attributed to seasonal variations in current. We also show that in determining the summer and winter ac power output, the summation of the manufacturer-supplied module peak powers at STC for a similarly located and configured a-Si PV array should be derated by factors of approximately of 0.83 and 0.78 for summer and winter operation, respectively.

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

    PubMed

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

    2010-01-01

    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

  6. Technical evaluation of a USSC Integrated/Direct Mount PV Roofing Module system at NREL

    NASA Astrophysics Data System (ADS)

    Strand, Troy; Hansen, Robert; Mrig, Laxmi

    1995-05-01

    The results of a 16 month technical evaluation performed on a nominal 1 kW(sub ac) utility-interconnect amorphous silicon PV system deployed at the National Renewable Energy Laboratory's PV outdoor test site are given here. The system employs 64 prototype United Solar Systems Corp. Integrated/Direct Mount PV Roofing Modules mounted on simulated attic/roof structures. In this paper we show that the PV array fill factor has been relatively stable with respect to time and that the seasonal variations in performance can be largely attributed to seasonal variations in current. We also show that in determining the summer and winter ac power output, the summation of the manufacturer-supplied module peak powers at STC for a similarly located and configured a-Si PV array should be derated by factors of approximately of 0.83 and 0.78 for summer and winter operation, respectively.

  7. Direct and wavelength modulation spectroscopy using a cw external cavity quantum cascade laser

    NASA Astrophysics Data System (ADS)

    Hancock, G.; van Helden, J. H.; Peverall, R.; Ritchie, G. A. D.; Walker, R. J.

    2009-05-01

    A continuous wave external cavity quantum cascade laser (EC-QCL) operating between 1872 and 1958 cm-1 has been used to make rotationally resolved measurements in the fundamental band of nitric oxide at 140 mTorr, and the ν2 band of water at atmospheric pressure. These measurements demonstrate the advantages of wide tunability and high resolution of the EC-QCL system. From direct absorption spectroscopy on nitric oxide a laser bandwidth of 20 MHz has been deduced and a sensitivity of 8.4×10-4 cm-1 Hz-1/2 was achieved. Wavelength modulation spectroscopy using current modulation enhances the sensitivity by a factor of 23 to 3.7×10-5 cm-1 Hz-1/2.

  8. Effect of serotonin modulating pharmacotherapies on body mass index and dysglycaemia among children and adolescents: a systematic review and network meta-analysis protocol

    PubMed Central

    Al Khalifah, Reem A; De Long, Nicole E; Florez, Ivan D; Mbuagbaw, Lawrence; Morrison, Katherine M

    2016-01-01

    Introduction Serotonin-modulating medications are commonly prescribed for mental health issues. Currently, there is limited consensus on weight gain and dysglycaemia development among children using these medications. The objective of this study is to review and synthesise all the available evidence on serotonin-modulating medications and their effects on body mass index (BMI), weight and glycaemic control. Methods and analysis We will conduct a systematic review of all randomised controlled trials evaluating the use of serotonin-modulating medications in the treatment of children 2–17 years with mental health conditions. The outcome measures are BMI, weight and dysglycaemia. We will perform literature searches through Ovid Medline, Ovid Embase, PsycINFO and grey literature resources. Two reviewers from the team will independently screen titles and abstracts, assess the eligibility of full-text trials, extract information from eligible trials and assess the risk of bias and quality of the evidence. Results of this review will be summarised narratively and quantitatively as appropriate. We will perform a multiple treatment comparison using network meta-analysis to estimate the pooled direct, indirect and network estimate for all serotonin-modulating medications on outcomes if adequate data are available. Ethics and dissemination Serotonin-modulating medications are widely prescribed for children with mental health diseases and are also used off-label. This network meta-analysis will be the first to assess serotonin modulating antidepressants and their effects on weight and glycaemic control. We anticipate that our results will help physicians and patients make more informed choices while considering the side effect profile. We will disseminate the results of the systematic review and network meta-analysis through peer-reviewed journals. PROSPERO registration number CRD42015024367. PMID:26983945

  9. Community structure detection for overlapping modules through mathematical programming in protein interaction networks.

    PubMed

    Bennett, Laura; Kittas, Aristotelis; Liu, Songsong; Papageorgiou, Lazaros G; Tsoka, Sophia

    2014-01-01

    Community structure detection has proven to be important in revealing the underlying properties of complex networks. The standard problem, where a partition of disjoint communities is sought, has been continually adapted to offer more realistic models of interactions in these systems. Here, a two-step procedure is outlined for exploring the concept of overlapping communities. First, a hard partition is detected by employing existing methodologies. We then propose a novel mixed integer non linear programming (MINLP) model, known as OverMod, which transforms disjoint communities to overlapping. The procedure is evaluated through its application to protein-protein interaction (PPI) networks of the rat, E. coli, yeast and human organisms. Connector nodes of hard partitions exhibit topological and functional properties indicative of their suitability as candidates for multiple module membership. OverMod identifies two types of connector nodes, inter and intra-connector, each with their own particular characteristics pertaining to their topological and functional role in the organisation of the network. Inter-connector proteins are shown to be highly conserved proteins participating in pathways that control essential cellular processes, such as proliferation, differentiation and apoptosis and their differences with intra-connectors is highlighted. Many of these proteins are shown to possess multiple roles of distinct nature through their participation in different network modules, setting them apart from proteins that are simply 'hubs', i.e. proteins with many interaction partners but with a more specific biochemical role. PMID:25412367

  10. Unilateral deafness in children affects development of multi-modal modulation and default mode networks

    PubMed Central

    Schmithorst, Vincent J.; Plante, Elena; Holland, Scott

    2014-01-01

    Monaural auditory input due to congenital or acquired unilateral hearing loss (UHL) may have neurobiological effects on the developing brain. Using functional magnetic resonance imaging (fMRI), we investigated the effect of UHL on the development of functional brain networks used for cross-modal processing. Children ages 712 with moderate or greater unilateral hearing loss of sensorineural origin (UHL-SN; N = 21) and normal-hearing controls (N = 23) performed an fMRI-compatible adaptation of the Token Test involving listening to a sentence such as touched the small green circle and the large blue square and simultaneously viewing an arrow touching colored shapes on a video. Children with right or severe-to-profound UHL-SN displayed smaller activation in a region encompassing the right inferior temporal, middle temporal, and middle occipital gyrus (BA 19/37/39), evidencing differences due to monaural hearing in cross-modal modulation of the visual processing pathway. Children with UHL-SN displayed increased activation in the left posterior superior temporal gyrus, likely the result either of more effortful low-level processing of auditory stimuli or differences in cross-modal modulation of the auditory processing pathway. Additionally, children with UHL-SN displayed reduced deactivation of anterior and posterior regions of the default mode network. Results suggest that monaural hearing affects the development of brain networks related to cross-modal sensory processing and the regulation of the default network during processing of spoken language. PMID:24723873

  11. Matrix stiffness modulates formation and activity of neuronal networks of controlled architectures.

    PubMed

    Lantoine, Joséphine; Grevesse, Thomas; Villers, Agnès; Delhaye, Geoffrey; Mestdagh, Camille; Versaevel, Marie; Mohammed, Danahe; Bruyère, Céline; Alaimo, Laura; Lacour, Stéphanie P; Ris, Laurence; Gabriele, Sylvain

    2016-05-01

    The ability to construct easily in vitro networks of primary neurons organized with imposed topologies is required for neural tissue engineering as well as for the development of neuronal interfaces with desirable characteristics. However, accumulating evidence suggests that the mechanical properties of the culture matrix can modulate important neuronal functions such as growth, extension, branching and activity. Here we designed robust and reproducible laminin-polylysine grid micropatterns on cell culture substrates that have similar biochemical properties but a 100-fold difference in Young's modulus to investigate the role of the matrix rigidity on the formation and activity of cortical neuronal networks. We found that cell bodies of primary cortical neurons gradually accumulate in circular islands, whereas axonal extensions spread on linear tracks to connect circular islands. Our findings indicate that migration of cortical neurons is enhanced on soft substrates, leading to a faster formation of neuronal networks. Furthermore, the pre-synaptic density was two times higher on stiff substrates and consistently the number of action potentials and miniature synaptic currents was enhanced on stiff substrates. Taken together, our results provide compelling evidence to indicate that matrix stiffness is a key parameter to modulate the growth dynamics, synaptic density and electrophysiological activity of cortical neuronal networks, thus providing useful information on scaffold design for neural tissue engineering. PMID:26946402

  12. Community Structure Detection for Overlapping Modules through Mathematical Programming in Protein Interaction Networks

    PubMed Central

    Bennett, Laura; Kittas, Aristotelis; Liu, Songsong; Papageorgiou, Lazaros G.; Tsoka, Sophia

    2014-01-01

    Community structure detection has proven to be important in revealing the underlying properties of complex networks. The standard problem, where a partition of disjoint communities is sought, has been continually adapted to offer more realistic models of interactions in these systems. Here, a two-step procedure is outlined for exploring the concept of overlapping communities. First, a hard partition is detected by employing existing methodologies. We then propose a novel mixed integer non linear programming (MINLP) model, known as OverMod, which transforms disjoint communities to overlapping. The procedure is evaluated through its application to protein-protein interaction (PPI) networks of the rat, E. coli, yeast and human organisms. Connector nodes of hard partitions exhibit topological and functional properties indicative of their suitability as candidates for multiple module membership. OverMod identifies two types of connector nodes, inter and intra-connector, each with their own particular characteristics pertaining to their topological and functional role in the organisation of the network. Inter-connector proteins are shown to be highly conserved proteins participating in pathways that control essential cellular processes, such as proliferation, differentiation and apoptosis and their differences with intra-connectors is highlighted. Many of these proteins are shown to possess multiple roles of distinct nature through their participation in different network modules, setting them apart from proteins that are simply ‘hubs’, i.e. proteins with many interaction partners but with a more specific biochemical role. PMID:25412367

  13. Linguistic complex networks: Rationale, application, interpretation, and directions. Reply to comments on "Approaching human language with complex networks"

    NASA Astrophysics Data System (ADS)

    Cong, Jin; Liu, Haitao

    2014-12-01

    Amid the enthusiasm for real-world networks of the new millennium, the enquiry into linguistic networks is flourishing not only as a productive branch of the new networks science but also as a promising approach to linguistic research. Although the complex network approach constitutes a potential opportunity to make linguistics a science, the world of linguistics seems unprepared to embrace it. For one thing, linguistics has been largely unaffected by quantitative methods. Those who are accustomed to qualitative linguistic methods may find it hard to appreciate the application of quantitative properties of language such as frequency and length, not to mention quantitative properties of language modeled as networks. With this in mind, in our review [1] we restrict ourselves to the basics of complex networks and the new insights into human language with the application of complex networks. For another, while breaking new grounds and posing new challenges for linguistics, the complex network approach to human language as a new tradition of linguistic research is faced with challenges and unsolved issues of its own. It is no surprise that the comments on our review, especially their skepticism and suggestions, focus on various different aspects of the complex network approach to human language. We are grateful to all the insightful and penetrating comments, which, together with our review, mark a significant impetus to linguistic research from the complex network approach. In this reply, we would like to address four major issues of the complex network approach to human language, namely, a) its theoretical rationale, b) its application in linguistic research, c) interpretation of the results, and d) directions of future research.

  14. Direct detection of RDX vapor using a conjugated polymer network.

    PubMed

    Gopalakrishnan, Deepti; Dichtel, William R

    2013-06-01

    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

  15. Evolutionary developmental transcriptomics reveals a gene network module regulating interspecific diversity in plant leaf shape

    PubMed Central

    Ichihashi, Yasunori; Aguilar-Martínez, José Antonio; Farhi, Moran; Chitwood, Daniel H.; Kumar, Ravi; Millon, Lee V.; Peng, Jie; Maloof, Julin N.; Sinha, Neelima R.

    2014-01-01

    Despite a long-standing interest in the genetic basis of morphological diversity, the molecular mechanisms that give rise to developmental variation are incompletely understood. Here, we use comparative transcriptomics coupled with the construction of gene coexpression networks to predict a gene regulatory network (GRN) for leaf development in tomato and two related wild species with strikingly different leaf morphologies. The core network in the leaf developmental GRN contains regulators of leaf morphology that function in global cell proliferation with peripheral gene network modules (GNMs). The BLADE-ON-PETIOLE (BOP) transcription factor in one GNM controls the core network by altering effective concentration of the KNOTTED-like HOMEOBOX gene product. Comparative network analysis and experimental perturbations of BOP levels suggest that variation in BOP expression could explain the diversity in leaf complexity among these species through dynamic rewiring of interactions in the GRN. The peripheral location of the BOP-containing GNM in the leaf developmental GRN and the phenotypic mimics of evolutionary diversity caused by alteration in BOP levels identify a key role for this GNM in canalizing the leaf morphospace by modifying the maturation schedule of leaves to create morphological diversity. PMID:24927584

  16. Direct leaf trajectory optimization for volumetric modulated arc therapy planning with sliding window delivery

    SciTech Connect

    Papp, Dávid Unkelbach, Jan

    2014-01-15

    Purpose: The authors propose a novel optimization model for volumetric modulated arc therapy (VMAT) planning that directly optimizes deliverable leaf trajectories in the treatment plan optimization problem, and eliminates the need for a separate arc-sequencing step. Methods: In this model, a 360° arc is divided into a given number of arc segments in which the leaves move unidirectionally. This facilitates an algorithm that determines the optimal piecewise linear leaf trajectories for each arc segment, which are deliverable in a given treatment time. Multileaf collimator constraints, including maximum leaf speed and interdigitation, are accounted for explicitly. The algorithm is customized to allow for VMAT delivery using constant gantry speed and dose rate, however, the algorithm generalizes to variable gantry speed if beneficial. Results: The authors demonstrate the method for three different tumor sites: a head-and-neck case, a prostate case, and a paraspinal case. The authors first obtain a reference plan for intensity modulated radiotherapy (IMRT) using fluence map optimization and 20 intensity-modulated fields in equally spaced beam directions, which is beyond the standard of care. Modeling the typical clinical setup for the treatment sites considered, IMRT plans using seven or nine beams are also computed. Subsequently, VMAT plans are optimized by dividing the 360° arc into 20 corresponding arc segments. Assuming typical machine parameters (a dose rate of 600 MU/min, and a maximum leaf speed of 3 cm/s), it is demonstrated that the optimized VMAT plans with 2–3 min delivery time are of noticeably better quality than the 7–9 beam IMRT plans. The VMAT plan quality approaches the quality of the 20-beam IMRT benchmark plan for delivery times between 3 and 4 min. Conclusions: The results indicate that high quality treatments can be delivered in a single arc with 20 arc segments if sufficient time is allowed for modulation in each segment.

  17. Transcranial Direct Current Stimulation Modulates Neuronal Activity and Learning in Pilot Training

    PubMed Central

    Choe, Jaehoon; Coffman, Brian A.; Bergstedt, Dylan T.; Ziegler, Matthias D.; Phillips, Matthew E.

    2016-01-01

    Skill acquisition requires distributed learning both within (online) and across (offline) days to consolidate experiences into newly learned abilities. In particular, piloting an aircraft requires skills developed from extensive training and practice. Here, we tested the hypothesis that transcranial direct current stimulation (tDCS) can modulate neuronal function to improve skill learning and performance during flight simulator training of aircraft landing procedures. Thirty-two right-handed participants consented to participate in four consecutive daily sessions of flight simulation training and received sham or anodal high-definition-tDCS to the right dorsolateral prefrontal cortex (DLPFC) or left motor cortex (M1) in a randomized, double-blind experiment. Continuous electroencephalography (EEG) and functional near infrared spectroscopy (fNIRS) were collected during flight simulation, n-back working memory, and resting-state assessments. tDCS of the right DLPFC increased midline-frontal theta-band activity in flight and n-back working memory training, confirming tDCS-related modulation of brain processes involved in executive function. This modulation corresponded to a significantly different online and offline learning rates for working memory accuracy and decreased inter-subject behavioral variability in flight and n-back tasks in the DLPFC stimulation group. Additionally, tDCS of left M1 increased parietal alpha power during flight tasks and tDCS to the right DLPFC increased midline frontal theta-band power during n-back and flight tasks. These results demonstrate a modulation of group variance in skill acquisition through an increasing in learned skill consistency in cognitive and real-world tasks with tDCS. Further, tDCS performance improvements corresponded to changes in electrophysiological and blood-oxygenation activity of the DLPFC and motor cortices, providing a stronger link between modulated neuronal function and behavior. PMID:26903841

  18. Transcranial Direct Current Stimulation Modulates Neuronal Activity and Learning in Pilot Training.

    PubMed

    Choe, Jaehoon; Coffman, Brian A; Bergstedt, Dylan T; Ziegler, Matthias D; Phillips, Matthew E

    2016-01-01

    Skill acquisition requires distributed learning both within (online) and across (offline) days to consolidate experiences into newly learned abilities. In particular, piloting an aircraft requires skills developed from extensive training and practice. Here, we tested the hypothesis that transcranial direct current stimulation (tDCS) can modulate neuronal function to improve skill learning and performance during flight simulator training of aircraft landing procedures. Thirty-two right-handed participants consented to participate in four consecutive daily sessions of flight simulation training and received sham or anodal high-definition-tDCS to the right dorsolateral prefrontal cortex (DLPFC) or left motor cortex (M1) in a randomized, double-blind experiment. Continuous electroencephalography (EEG) and functional near infrared spectroscopy (fNIRS) were collected during flight simulation, n-back working memory, and resting-state assessments. tDCS of the right DLPFC increased midline-frontal theta-band activity in flight and n-back working memory training, confirming tDCS-related modulation of brain processes involved in executive function. This modulation corresponded to a significantly different online and offline learning rates for working memory accuracy and decreased inter-subject behavioral variability in flight and n-back tasks in the DLPFC stimulation group. Additionally, tDCS of left M1 increased parietal alpha power during flight tasks and tDCS to the right DLPFC increased midline frontal theta-band power during n-back and flight tasks. These results demonstrate a modulation of group variance in skill acquisition through an increasing in learned skill consistency in cognitive and real-world tasks with tDCS. Further, tDCS performance improvements corresponded to changes in electrophysiological and blood-oxygenation activity of the DLPFC and motor cortices, providing a stronger link between modulated neuronal function and behavior. PMID:26903841

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

    PubMed Central

    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

    2011-01-01

    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

  20. Random networks of cross-linked directed polymers.

    PubMed

    Ulrich, Stephan; Zippelius, Annette; Benetatos, Panayotis

    2010-02-01

    We explore the effect of random permanent cross-links on a system of directed polymers confined between two planes with their end points free to slide on them. We treat the cross-links as quenched disorder and we use a semimicroscopic replica field theory to study the structure and elasticity of this system. Upon increasing the cross-link density, we get a continuous gelation transition signaled by the emergence of a finite in-plane localization length. The distribution of localization length turns out to depend on the height along the preferred direction of the directed polymers. The gelation transition also gives rise to a finite in-plane shear modulus which we calculate and turns out to be universal, i.e., independent of the energy and length scales of the polymers and the cross-links. Using a symmetry argument, we show that cross-links of negligible extent along the preferred axis of the directed polymers do not cause any renormalization to the tilt modulus of the uncross-linked system. PMID:20365585

  1. Acupuncture induce the different modulation patterns of the default mode network: an fMRI study

    NASA Astrophysics Data System (ADS)

    Liu, Peng; Qin, Wei; Tian, Jie; Zhang, Yi

    2009-02-01

    According to Traditional Chinese Medicine (TCM) theory and certain clinical treatment reports, the sustained effects of acupuncture indeed exist, which may last several minutes or hours. Furthermore, increased attention has fallen on the sustained effects of acupuncture. Recently, it is reported that the sustained acupuncture effects may alter the default mode network (DMN). It raises interesting questions: whether the modulations of acupuncture effects to the DMN are still detected at other acupoints and whether the modulation patterns are different induced by different acupoints. In the present study, we wanted to investigate the questions. An experiment fMRI design was carried out on 36 subjects with the electroacupuncture stimulation (EAS) at the three acupoints: Guangming (GB37), Kunlun (BL60) and Jiaoxin (KI8) on the left leg. The data sets were analyzed by a data driven method named independent component analysis (ICA). The results indicated that the three acupoints stimulations may modulate the DMN. Moreover, the modulation patterns were distinct. We suggest the different modulation patterns on the DMN may attribute to the distinct functional effects of acupoints.

  2. Gene Networks in the Wild: Identifying Transcriptional Modules that Mediate Coral Resistance to Experimental Heat Stress

    PubMed Central

    Rose, Noah H.; Seneca, Francois O.; Palumbi, Stephen R.

    2016-01-01

    Organisms respond to environmental variation partly through changes in gene expression, which underlie both homeostatic and acclimatory responses to environmental stress. In some cases, so many genes change in expression in response to different influences that understanding expression patterns for all these individual genes becomes difficult. To reduce this problem, we use a systems genetics approach to show that variation in the expression of thousands of genes of reef-building corals can be explained as variation in the expression of a small number of coexpressed “modules.” Modules were often enriched for specific cellular functions and varied predictably among individuals, experimental treatments, and physiological state. We describe two transcriptional modules for which expression levels immediately after heat stress predict bleaching a day later. One of these early “bleaching modules” is enriched for sequence-specific DNA-binding proteins, particularly E26 transformation-specific (ETS)-family transcription factors. The other module is enriched for extracellular matrix proteins. These classes of bleaching response genes are clear in the modular gene expression analysis we conduct but are much more difficult to discern in single gene analyses. Furthermore, the ETS-family module shows repeated differences in expression among coral colonies grown in the same common garden environment, suggesting a heritable genetic or epigenetic basis for these expression polymorphisms. This finding suggests that these corals harbor high levels of gene-network variation, which could facilitate rapid evolution in the face of environmental change. PMID:26710855

  3. miR-25 modulates NSCLC cell radio-sensitivity through directly inhibiting BTG2 expression

    SciTech Connect

    He, Zhiwei Liu, Yi Xiao, Bing Qian, Xiaosen

    2015-02-13

    A large proportion of the NSCLC patients were insensitive to radiotherapy, but the exact mechanism is still unclear. This study explored the role of miR-25 in regulating sensitivity of NSCLC cells to ionizing radiation (IR) and its downstream targets. Based on measurement in tumor samples from NSCLC patients, this study found that miR-25 expression is upregulated in both NSCLC and radio-resistant NSCLC patients compared the healthy and radio-sensitive controls. In addition, BTG expression was found negatively correlated with miR-25a expression in the both tissues and cells. By applying luciferase reporter assay, we verified two putative binding sites between miR-25 and BTG2. Therefore, BTG2 is a directly target of miR-25 in NSCLC cancer. By applying loss-and-gain function analysis in NSCLC cell lines, we demonstrated that miR-25-BTG2 axis could directly regulated BTG2 expression and affect radiotherapy sensitivity of NSCLC cells. - Highlights: • miR-25 is upregulated, while BTG2 is downregulated in radioresistant NSCLC patients. • miR-25 modulates sensitivity to radiation induced apoptosis. • miR-25 directly targets BTG2 and suppresses its expression. • miR-25 modulates sensitivity to radiotherapy through inhibiting BTG2 expression.

  4. Moral judgment modulation by disgust is bi-directionally moderated by individual sensitivity.

    PubMed

    Ong, How Hwee; Mullette-Gillman, O'Dhaniel A; Kwok, Kenneth; Lim, Julian

    2014-01-01

    Modern theories of moral judgment predict that both conscious reasoning and unconscious emotional influences affect the way people decide about right and wrong. In a series of experiments, we tested the effect of subliminal and conscious priming of disgust facial expressions on moral dilemmas. "Trolley-car"-type scenarios were used, with subjects rating how acceptable they found the utilitarian course of action to be. On average, subliminal priming of disgust facial expressions resulted in higher rates of utilitarian judgments compared to neutral facial expressions. Further, in replication, we found that individual change in moral acceptability ratings due to disgust priming was modulated by individual sensitivity to disgust, revealing a bi-directional function. Our second replication extended this result to show that the function held for both subliminally and consciously presented stimuli. Combined across these experiments, we show a reliable bi-directional function, with presentation of disgust expression primes to individuals with higher disgust sensitivity resulting in more utilitarian judgments (i.e., number-based) and presentations to individuals with lower sensitivity resulting in more deontological judgments (i.e., rules-based). Our results may reconcile previous conflicting reports of disgust modulation of moral judgment by modeling how individual sensitivity to disgust determines the direction and degree of this effect. PMID:24639665

  5. Directional Bias and Pheromone for Discovery and Coverage on Networks

    SciTech Connect

    Fink, Glenn A.; Berenhaut, Kenneth S.; Oehmen, Christopher S.

    2012-09-11

    Natural multi-agent systems often rely on “correlated random walks” (random walks that are biased toward a current heading) to distribute their agents over a space (e.g., for foraging, search, etc.). Our contribution involves creation of a new movement and pheromone model that applies the concept of heading bias in random walks to a multi-agent, digital-ants system designed for cyber-security monitoring. We examine the relative performance effects of both pheromone and heading bias on speed of discovery of a target and search-area coverage in a two-dimensional network layout. We found that heading bias was unexpectedly helpful in reducing search time and that it was more influential than pheromone for improving coverage. We conclude that while pheromone is very important for rapid discovery, heading bias can also greatly improve both performance metrics.

  6. Directed clustering coefficient as a measure of systemic risk in complex banking networks

    NASA Astrophysics Data System (ADS)

    Tabak, Benjamin M.; Takami, Marcelo; Rocha, Jadson M. C.; Cajueiro, Daniel O.; Souza, Sergio R. S.

    2014-01-01

    Recent literature has focused on the study of systemic risk in complex networks. It is clear now, after the crisis of 2008, that the aggregate behavior of the interaction among agents is not straightforward and it is very difficult to predict. Contributing to this debate, this paper shows that the directed clustering coefficient may be used as a measure of systemic risk in complex networks. Furthermore, using data from the Brazilian interbank network, we show that the directed clustering coefficient is negatively correlated with domestic interest rates.

  7. A complex task? Direct modulation of transcription factors with small molecules

    PubMed Central

    Koehler, Angela N.

    2010-01-01

    Transcription factors with aberrant activity in disease are promising yet untested targets for therapeutic development, particularly in oncology. Directly inhibiting or activating the function of a transcription factor requires specific disruption or recruitment of protein-protein or protein-DNA interactions. The discovery or design of small molecules that specifically modulate these interactions has thus far proven to be a significant challenge and the protein class is often perceived to be ‘undruggable.’ This review will summarize recent progress in the development of small-molecule probes of transcription factors and provide evidence to challenge the notion that this important protein class is chemically intractable. PMID:20395165

  8. Directly modulated and fully tunable hybrid silicon lasers for future generation of coherent colorless ONU.

    PubMed

    de Valicourt, G; Le Liepvre, A; Vacondio, F; Simonneau, C; Lamponi, M; Jany, C; Accard, A; Lelarge, F; Make, D; Poingt, F; Duan, G H; Fedeli, J-M; Messaoudene, S; Bordel, D; Lorcy, L; Antona, J-C; Bigo, S

    2012-12-10

    We propose and demonstrate asymmetric 10 Gbit/s upstream--100 Gbit/s downstream per wavelength colorless WDM/TDM PON using a novel hybrid-silicon chip integrating two tunable lasers. The first laser is directly modulated in burst mode for upstream transmission over up to 25 km of standard single mode fiber and error free transmission over 4 channels across the C-band is demonstrated. The second tunable laser is successfully used as local oscillator in a coherent receiver across the C-band simultaneously operating with the presence of 80 downstream co-channels. PMID:23262901

  9. Steganography in clustered-dot halftones using orientation modulation and modification of direct binary search

    NASA Astrophysics Data System (ADS)

    Chen, Yung-Yao; Hong, Sheng-Yi; Chen, Kai-Wen

    2015-03-01

    This paper proposes a novel message-embedded halftoning scheme that is based on orientation modulation (OM) encoding. To achieve high image quality, we employ a human visual system (HVS)-based error metric between the continuous-tone image and a data-embedded halftone, and integrate a modified direct binary search (DBS) framework into the proposed message-embedded halftoning method. The modified DBS framework ensures that the resulting data-embedded halftones have optimal image quality from the viewpoint of the HVS.

  10. Gain modulation of synaptic inputs by network state in auditory cortex in vivo.

    PubMed

    Reig, Ramon; Zerlaut, Yann; Vergara, Ramiro; Destexhe, Alain; Sanchez-Vives, Maria V

    2015-02-11

    The cortical network recurrent circuitry generates spontaneous activity organized into Up (active) and Down (quiescent) states during slow-wave sleep or anesthesia. These different states of cortical activation gain modulate synaptic transmission. However, the reported modulation that Up states impose on synaptic inputs is disparate in the literature, including both increases and decreases of responsiveness. Here, we tested the hypothesis that such disparate observations may depend on the intensity of the stimulation. By means of intracellular recordings, we studied synaptic transmission during Up and Down states in rat auditory cortex in vivo. Synaptic potentials were evoked either by auditory or electrical (thalamocortical, intracortical) stimulation while randomly varying the intensity of the stimulus. Synaptic potentials evoked by the same stimulus intensity were compared in Up/Down states. Up states had a scaling effect on the stimulus-evoked synaptic responses: the amplitude of weaker responses was potentiated whereas that of larger responses was maintained or decreased with respect to the amplitude during Down states. We used a computational model to explore the potential mechanisms explaining this nontrivial stimulus-response relationship. During Up/Down states, there is different excitability in the network and the neuronal conductance varies. We demonstrate that the competition between presynaptic recruitment and the changing conductance might be the central mechanism explaining the experimentally observed stimulus-response relationships. We conclude that the effect that cortical network activation has on synaptic transmission is not constant but contingent on the strength of the stimulation, with a larger modulation for stimuli involving both thalamic and cortical networks. PMID:25673859

  11. Criticality of forcing directions on the fragmentation and resilience of grid networks.

    PubMed

    Abundo, Cheryl; Monterola, Christopher; Legara, Erika Fille

    2014-01-01

    A general framework for probing the dynamic evolution of spatial networks comprised of nodes applying force amongst each other is presented. Aside from the already reported magnitude of forces and elongation thresholds, we show that preservation of links in a network is also crucially dependent on how nodes are connected and how edges are directed. We demonstrate that the time it takes for the networks to reach its equilibrium network structure follows a robust power law relationship consistent with Basquin's law with an exponent that can be tuned by changing only the force directions. Further, we illustrate that networks with different connection structures, node positions and edge directions have different Basquin's exponent which can be used to distinguish spatial directed networks from each other. Using an extensive waiting time simulation that spans up to over 16 orders of magnitude, we establish that the presence of memory combined with the scale-free bursty dynamics of edge breaking at the micro level leads to the evident macroscopic power law distribution of network lifetime. PMID:25160061

  12. Identifying core gene modules in glioblastoma based on multilayer factor-mediated dysfunctional regulatory networks through integrating multi-dimensional genomic data

    PubMed Central

    Ping, Yanyan; Deng, Yulan; Wang, Li; Zhang, Hongyi; Zhang, Yong; Xu, Chaohan; Zhao, Hongying; Fan, Huihui; Yu, Fulong; Xiao, Yun; Li, Xia

    2015-01-01

    The driver genetic aberrations collectively regulate core cellular processes underlying cancer development. However, identifying the modules of driver genetic alterations and characterizing their functional mechanisms are still major challenges for cancer studies. Here, we developed an integrative multi-omics method CMDD to identify the driver modules and their affecting dysregulated genes through characterizing genetic alteration-induced dysregulated networks. Applied to glioblastoma (GBM), the CMDD identified a core gene module of 17 genes, including seven known GBM drivers, and their dysregulated genes. The module showed significant association with shorter survival of GBM. When classifying driver genes in the module into two gene sets according to their genetic alteration patterns, we found that one gene set directly participated in the glioma pathway, while the other indirectly regulated the glioma pathway, mostly, via their dysregulated genes. Both of the two gene sets were significant contributors to survival and helpful for classifying GBM subtypes, suggesting their critical roles in GBM pathogenesis. Also, by applying the CMDD to other six cancers, we identified some novel core modules associated with overall survival of patients. Together, these results demonstrate integrative multi-omics data can identify driver modules and uncover their dysregulated genes, which is useful for interpreting cancer genome. PMID:25653168

  13. Test particle simulation of direct laser acceleration in a density-modulated plasma waveguide

    SciTech Connect

    Lin, M.-W.; Jovanovic, I.

    2012-11-15

    Direct laser acceleration (DLA) of electrons by the use of the intense axial electric field of an ultrafast radially polarized laser pulse is a promising technique for future compact accelerators. Density-modulated plasma waveguides can be implemented for guiding the propagation of the laser pulse to extend the acceleration distance and for the quasi-phase-matching between the accelerated electrons and the laser pulse. A test particle model is developed to study the optimal axial density modulation structure of plasma waveguides for laser pulses to efficiently accelerate co-propagating electrons. A simple analytical approach is also presented, which can be used to estimate the energy gain in DLA. The analytical model is validated by the test particle simulation. The effect of injection phase and acceleration of electrons injected at various radial positions are studied. The results indicate that a positively chirped density modulation of the waveguide structure is required to accelerate electron with low initial energies, and can be effectively optimized. A wider tolerance on the injection phase and radial distance from the waveguide axis exists for electrons injected with a higher initial energy.

  14. Frequency tunable optoelectronic oscillator based on a directly modulated DFB semiconductor laser under optical injection.

    PubMed

    Wang, Peng; Xiong, Jintian; Zhang, Tingting; Chen, Dalei; Xiang, Peng; Zheng, Jilin; Zhang, Yunshan; Li, Ruoming; Huang, Long; Pu, Tao; Chen, Xiangfei

    2015-08-10

    A frequency tunable optoelectronic oscillator based on a directly modulated distributed-feedback (DFB) semiconductor laser under optical injection is proposed and experimentally demonstrated. Through optical injection, the relaxation oscillation frequency of the DFB laser is enhanced and its high modulation efficiency can enable the loop oscillation with a RF threshold gain of less than 20 dB. The DFB laser is a commercial semiconductor laser with a package of 10 GHz, and its packaging limitation can be overcome by optical injection. In our scheme, neither a high-speed external modulator nor an electrical bandpass filter is required, making the system simple and low-cost. Microwave signals with a frequency tuning range from 5.98 to 15.22 GHz are generated by adjusting the injection ratio and frequency detuning between the master and slave lasers. The phase noise of the generated 9.75 GHz microwave signal is measured to be -104.8 dBc/Hz @ 10 kHz frequency offset. PMID:26367899

  15. Human perception of visual stimuli modulated by direction of linear polarization.

    PubMed

    Misson, Gary P; Timmerman, Brenda H; Bryanston-Cross, Peter J

    2015-10-01

    This study explores both theoretically and experimentally the human perception of polarized light beyond that currently established. The radial analyser theory of Haidinger's phenomenon (HP) is used to predict the effect of observing visual stimuli comprising patterned zones characterized by orthogonal planes of linear polarization (linear polarization direction fields, LPD-fields). Any pattern can be represented as an LPD-field including optotypes and geometric forms. Simulated percepts differ from the original patterns although edges are mostly preserved. In edge-rich images a cross of attenuating contrast spanning the field of view is predicted. The mathematical model is verified experimentally using a liquid crystal display (LCD)-based polarization modulator imaged through a tangential (azimuthal) analyser with properties complementary to a radial analyser. The LCD device is then used in vivo to elicit perceptual responses in human subjects. Normal humans are found to readily detect spatially and temporally modulated isoluminant spatially-isochromatic, highly polarized LPD stimuli. Most subjects match the stimuli to corresponding images of theoretically predicted percepts. In particular edge perception and the presence of the contrast cross was confirmed. Unlike HP, static patterned LPD stimuli are perceived without difficulty. The simplest manifestation of human polarization perception is HP which is the fundamental element of an open set of stimulus-dependent percepts. This study demonstrates that humans have the ability to perceive and identify visual pattern stimuli defined solely by polarization state modulation. PMID:26291073

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

    PubMed Central

    MILLS, STEPHEN L.; XIA, XIAO-BO; HOSHI, HIDEO; FIRTH, SALLY I.; RICE, MARGARET E.; FRISHMAN, LAURA J.; MARSHAK, DAVID W.

    2008-01-01

    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 α 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 D1 dopamine receptor, while the gap junctions between ganglion cells were closed via stimulation of a D2 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 α ganglion cell/amacrine cell network is differentially modulated with changing levels of dopamine. PMID:17711603

  17. Plastic modulation of PTSD resting-state networks by EEG neurofeedback

    PubMed Central

    Kluetsch, Rosemarie C.; Ros, Tomas; Théberge, Jean; Frewen, Paul A.; Calhoun, Vince D.; Schmahl, Christian; Jetly, Rakesh; Lanius, Ruth A.

    2015-01-01

    Objective Electroencephalographic (EEG) neurofeedback training has been shown to produce plastic modulations in salience network and default mode network functional connectivity in healthy individuals. In this study, we investigated whether a single session of neurofeedback training aimed at the voluntary reduction of alpha rhythm (8–12 Hz) amplitude would be related to differences in EEG network oscillations, functional MRI (fMRI) connectivity, and subjective measures of state anxiety and arousal in a group of individuals with PTSD. Method 21 individuals with PTSD related to childhood abuse underwent 30 minutes of EEG neurofeedback training preceded and followed by a resting-state fMRI scan. Results Alpha desynchronizing neurofeedback was associated with decreased alpha amplitude during training, followed by a significant increase (‘rebound’) in resting-state alpha synchronization. This rebound was linked to increased calmness, greater salience network connectivity with the right insula, and enhanced default mode network connectivity with bilateral posterior cingulate, right middle frontal gyrus, and left medial prefrontal cortex. Conclusion Our study represents a first step in elucidating the potential neurobehavioral mechanisms mediating the effects of neurofeedback treatment on regulatory systems in PTSD. Moreover, it documents for the first time a spontaneous EEG ‘rebound’ after neurofeedback, pointing to homeostatic/compensatory mechanisms operating in the brain. PMID:24266644

  18. Identifying progression related disease risk modules based on the human subcellular signaling networks.

    PubMed

    Xie, Ruiqiang; Huang, Hao; Li, Wan; Chen, Binbin; Jiang, Jing; He, Yuehan; Lv, Junjie; ma, Bo; Zhou, Yanyan; Feng, Chenchen; Chen, Lina; He, Weiming

    2014-12-01

    Many studies have shown that the structure and dynamics of the human signaling network are disturbed in complex diseases such as coronary artery disease, and gene expression profiles can distinguish variations in diseases since they can accurately reflect the status of cells. Integration of subcellular localization and the human signaling network holds promise for providing insight into human diseases. In this study, we performed a novel algorithm to identify progression-related-disease-risk modules (PRDRMs) among patients of different disease states within eleven subcellular sub-networks from a human signaling network. The functional annotation and literature retrieval showed that the PRDRMs were strongly associated with disease pathogenesis. The results indicated that the PRDRM expression values as classification features had a good classification performance to distinguish patients of different disease states. Our approach compared with the method PageRank had a better classification performance. The identification of the PRDRMs in response to the dynamic gene expression change could facilitate our understanding of the pathological basis of complex diseases. Our strategy could provide new insights into the potential use of prognostic biomarkers and the effective guidance of clinical therapy from the human subcellular signaling network perspective. PMID:25315201

  19. Modulation of Cortical Oscillations by Low-Frequency Direct Cortical Stimulation Is State-Dependent.

    PubMed

    Alagapan, Sankaraleengam; Schmidt, Stephen L; Lefebvre, Jérémie; Hadar, Eldad; Shin, Hae Won; Frӧhlich, Flavio

    2016-03-01

    Cortical oscillations play a fundamental role in organizing large-scale functional brain networks. Noninvasive brain stimulation with temporally patterned waveforms such as repetitive transcranial magnetic stimulation (rTMS) and transcranial alternating current stimulation (tACS) have been proposed to modulate these oscillations. Thus, these stimulation modalities represent promising new approaches for the treatment of psychiatric illnesses in which these oscillations are impaired. However, the mechanism by which periodic brain stimulation alters endogenous oscillation dynamics is debated and appears to depend on brain state. Here, we demonstrate with a static model and a neural oscillator model that recurrent excitation in the thalamo-cortical circuit, together with recruitment of cortico-cortical connections, can explain the enhancement of oscillations by brain stimulation as a function of brain state. We then performed concurrent invasive recording and stimulation of the human cortical surface to elucidate the response of cortical oscillations to periodic stimulation and support the findings from the computational models. We found that (1) stimulation enhanced the targeted oscillation power, (2) this enhancement outlasted stimulation, and (3) the effect of stimulation depended on behavioral state. Together, our results show successful target engagement of oscillations by periodic brain stimulation and highlight the role of nonlinear interaction between endogenous network oscillations and stimulation. These mechanistic insights will contribute to the design of adaptive, more targeted stimulation paradigms. PMID:27023427

  20. Modulation of Cortical Oscillations by Low-Frequency Direct Cortical Stimulation Is State-Dependent

    PubMed Central

    Alagapan, Sankaraleengam; Schmidt, Stephen L.; Lefebvre, Jérémie; Hadar, Eldad; Shin, Hae Won; Frӧhlich, Flavio

    2016-01-01

    Cortical oscillations play a fundamental role in organizing large-scale functional brain networks. Noninvasive brain stimulation with temporally patterned waveforms such as repetitive transcranial magnetic stimulation (rTMS) and transcranial alternating current stimulation (tACS) have been proposed to modulate these oscillations. Thus, these stimulation modalities represent promising new approaches for the treatment of psychiatric illnesses in which these oscillations are impaired. However, the mechanism by which periodic brain stimulation alters endogenous oscillation dynamics is debated and appears to depend on brain state. Here, we demonstrate with a static model and a neural oscillator model that recurrent excitation in the thalamo-cortical circuit, together with recruitment of cortico-cortical connections, can explain the enhancement of oscillations by brain stimulation as a function of brain state. We then performed concurrent invasive recording and stimulation of the human cortical surface to elucidate the response of cortical oscillations to periodic stimulation and support the findings from the computational models. We found that (1) stimulation enhanced the targeted oscillation power, (2) this enhancement outlasted stimulation, and (3) the effect of stimulation depended on behavioral state. Together, our results show successful target engagement of oscillations by periodic brain stimulation and highlight the role of nonlinear interaction between endogenous network oscillations and stimulation. These mechanistic insights will contribute to the design of adaptive, more targeted stimulation paradigms. PMID:27023427

  1. The anticonvulsant stiripentol acts directly on the GABAA receptor as a positive allosteric modulator

    PubMed Central

    Fisher, Janet L.

    2009-01-01

    SUMMARY Stiripentol(STP) has been used as co-therapy for treatment of epilepsy for many years. Its mechanism of action has long been considered to be indirect, as it inhibits the enzymes responsible for metabolism of other anticonvulsant agents. However, a recent report suggested that STP might also act at the neuronal level, increasing inhibitory GABAergic neurotransmission. We examined the effect of STP on the functional properties of recombinant GABAA receptors (GABARs) and found that it was a positive allosteric modulator of these ion channels. Its activity showed some dependence on subunit composition, with greater potentiation of α3-containing receptors and reduced potentiation when the β1 or ε subunits were present. STP caused a leftward shift in the GABA concentration-response relationship, but did not increase the peak response of the receptors to a maximal GABA concentration. Although STP shares some functional characteristics with the neurosteroids, its activity was not inhibited by a neurosteroid site antagonist and was unaffected by a mutation in the α3 subunit that reduced positive modulation by neurosteroids. The differential effect of STP on β1- and β2/β3-containing receptors was not altered by mutations within the second transmembrane domain that affect modulation by loreclezole. These findings suggest that STP acts as a direct allosteric modulator of the GABAR at a site distinct from many commonly used anti-convulsant, sedative and anxiolytic drugs. Its higher activity at α3-containing receptors as well as its activity at δ-containing receptors may provide a unique opportunity to target selected populations of GABARs. PMID:18585399

  2. Molecular Correlates of Cortical Network Modulation by Long-Term Sensory Experience in the Adult Rat Barrel Cortex

    ERIC Educational Resources Information Center

    Valls, Astrid; Granic, Ivica; De Weerd, Peter; Martens, Gerard J. M.

    2014-01-01

    Modulation of cortical network connectivity is crucial for an adaptive response to experience. In the rat barrel cortex, long-term sensory stimulation induces cortical network modifications and neuronal response changes of which the molecular basis is unknown. Here, we show that long-term somatosensory stimulation by enriched environment

  3. Molecular Correlates of Cortical Network Modulation by Long-Term Sensory Experience in the Adult Rat Barrel Cortex

    ERIC Educational Resources Information Center

    Vallès, Astrid; Granic, Ivica; De Weerd, Peter; Martens, Gerard J. M.

    2014-01-01

    Modulation of cortical network connectivity is crucial for an adaptive response to experience. In the rat barrel cortex, long-term sensory stimulation induces cortical network modifications and neuronal response changes of which the molecular basis is unknown. Here, we show that long-term somatosensory stimulation by enriched environment…

  4. Effects of Edge Directions on the Structural Controllability of Complex Networks

    PubMed Central

    Xiao, Yandong; Lao, Songyang; Hou, Lvlin; Small, Michael; Bai, Liang

    2015-01-01

    Recent advances indicate that assigning or reversing edge direction can significantly improve the structural controllability of complex networks. For directed networks, approaching the optimal structural controllability can be achieved by detecting and reversing certain “inappropriate” edge directions. However, the existence of multiple sets of “inappropriate” edge directions suggests that different edges have different effects on optimal controllability—that is, different combinations of edges can be reversed to achieve the same structural controllability. Therefore, we classify edges into three categories based on their direction: critical, redundant and intermittent. We then investigate the effects of changing these edge directions on network controllability, and demonstrate that the existence of more critical edge directions implies not only a lower cost of modifying inappropriate edges but also better controllability. Motivated by this finding, we present a simple edge orientation method aimed at producing more critical edge directions—utilizing only local information—which achieves near optimal controllability. Furthermore, we explore the effects of edge direction on the controllability of several real networks. PMID:26281042

  5. Fiber-Optic Transceiver Module for High-Speed Intrasatellite Networks

    NASA Astrophysics Data System (ADS)

    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

    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.

  6. Bi-directional modulation of somatosensory mismatch negativity with transcranial direct current stimulation: an event related potential study.

    PubMed

    Chen, Jui-Cheng; Hämmerer, Dorothea; D'Ostilio, Kevin; Casula, Elias P; Marshall, Louise; Tsai, Chon-Haw; Rothwell, John C; Edwards, Mark J

    2014-02-15

    Appropriate orientation towards potentially salient novel environmental stimuli requires a system capable of detecting change in the sensorium. Mismatch negativity (MMN), an evoked potential calculated by subtracting the response to a standard repeated stimulus and a rare 'oddball' stimulus, is proposed as such a change detection mechanism. It is most widely studied in the auditory domain, but here we chose to explore the mechanism of somatosensory MMN, and specifically its dependence on the cerebellum. We recorded event-related potentials (ERPs) evoked in response to auditory and sensory stimuli from 10 healthy subjects before and after anodal, cathodal and sham transcranial direct current stimulation (tDCS) of the right cerebellar hemisphere. There was a significant increase in peak amplitude of somatosensory MMN after anodal tDCS (F(1,9) = 8.98, P < 0.02, mean difference anodal pre-post: -1.02 μV) and a significant reduction in peak amplitude of somatosensory MMN after cathodal tDCS (F(1,9) = 7.15, P < 0.03, mean difference cathodal pre-post: 0.65 μV). The amplitude of auditory MMN was unchanged by tDCS. These results reveal the capability of tDCS to cause bidirectional modulation of somatosensory MMN and the dependence of somatosensory MMN on the cerebellum. PMID:24366257

  7. Performance of motor imagery brain-computer interface based on anodal transcranial direct current stimulation modulation.

    PubMed

    Wei, Pengfei; He, Wei; Zhou, Yi; Wang, Liping

    2013-05-01

    Voluntarily modulating neural activity plays a key role in brain-computer interface (BCI). In general, the self-regulated neural activation patterns are used in the current BCI systems involving the repetitive trainings with feedback for an attempt to achieve a high-quality control performance. With the limitation posed by the training procedure in most BCI studies, the present work aims to investigate whether directly modulating the neural activity by using an external method could facilitate the BCI control. We designed an experimental paradigm that combines anodal transcranial direct current stimulation (tDCS) with a motor imagery (MI)-based feedback EEG BCI system. Thirty-two young and healthy human subjects were randomly assigned to the real and sham stimulation groups to evaluate the effect of tDCS-induced EEG pattern changes on BCI classification accuracy. Results showed that the anodal tDCS obviously induces sensorimotor rhythm (SMR)-related event-related desynchronization (ERD) pattern changes in the upper-mu (10-14 Hz) and beta (14-26 Hz) rhythm components. Both the online and offline BCI classification results demonstrate that the enhancing ERD patterns could conditionally improve BCI performance. This pilot study suggests that the tDCS is a promising method to help the users to develop reliable BCI control strategy in a relatively short time. PMID:23475381

  8. Wireless Sensor Network Security Enhancement Using Directional Antennas: State of the Art and Research Challenges

    PubMed Central

    Curiac, Daniel-Ioan

    2016-01-01

    Being often deployed in remote or hostile environments, wireless sensor networks are vulnerable to various types of security attacks. A possible solution to reduce the security risks is to use directional antennas instead of omnidirectional ones or in conjunction with them. Due to their increased complexity, higher costs and larger sizes, directional antennas are not traditionally used in wireless sensor networks, but recent technology trends may support this method. This paper surveys existing state of the art approaches in the field, offering a broad perspective of the future use of directional antennas in mitigating security risks, together with new challenges and open research issues. PMID:27070601

  9. Wireless Sensor Network Security Enhancement Using Directional Antennas: State of the Art and Research Challenges.

    PubMed

    Curiac, Daniel-Ioan

    2016-01-01

    Being often deployed in remote or hostile environments, wireless sensor networks are vulnerable to various types of security attacks. A possible solution to reduce the security risks is to use directional antennas instead of omnidirectional ones or in conjunction with them. Due to their increased complexity, higher costs and larger sizes, directional antennas are not traditionally used in wireless sensor networks, but recent technology trends may support this method. This paper surveys existing state of the art approaches in the field, offering a broad perspective of the future use of directional antennas in mitigating security risks, together with new challenges and open research issues. PMID:27070601

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

    PubMed Central

    Sänger, Johanna; Müller, Viktor; Lindenberger, Ulman

    2013-01-01

    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

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

    PubMed

    Sänger, Johanna; Müller, Viktor; Lindenberger, Ulman

    2013-01-01

    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

  12. A method for modeling and analysis of directed weighted accident causation network (DWACN)

    NASA Astrophysics Data System (ADS)

    Zhou, Jin; Xu, Weixiang; Guo, Xin; Ding, Jing

    2015-11-01

    Using complex network theory to analyze accidents is effective to understand the causes of accidents in complex systems. In this paper, a novel method is proposed to establish directed weighted accident causation network (DWACN) for the Rail Accident Investigation Branch (RAIB) in the UK, which is based on complex network and using event chains of accidents. DWACN is composed of 109 nodes which denote causal factors and 260 directed weighted edges which represent complex interrelationships among factors. The statistical properties of directed weighted complex network are applied to reveal the critical factors, the key event chains and the important classes in DWACN. Analysis results demonstrate that DWACN has characteristics of small-world networks with short average path length and high weighted clustering coefficient, and display the properties of scale-free networks captured by that the cumulative degree distribution follows an exponential function. This modeling and analysis method can assist us to discover the latent rules of accidents and feature of faults propagation to reduce accidents. This paper is further development on the research of accident analysis methods using complex network.

  13. Characterizing system dynamics with a weighted and directed network constructed from time series data

    NASA Astrophysics Data System (ADS)

    Sun, Xiaoran; Small, Michael; Zhao, Yi; Xue, Xiaoping

    2014-06-01

    In this work, we propose a novel method to transform a time series into a weighted and directed network. For a given time series, we first generate a set of segments via a sliding window, and then use a doubly symbolic scheme to characterize every windowed segment by combining absolute amplitude information with an ordinal pattern characterization. Based on this construction, a network can be directly constructed from the given time series: segments corresponding to different symbol-pairs are mapped to network nodes and the temporal succession between nodes is represented by directed links. With this conversion, dynamics underlying the time series has been encoded into the network structure. We illustrate the potential of our networks with a well-studied dynamical model as a benchmark example. Results show that network measures for characterizing global properties can detect the dynamical transitions in the underlying system. Moreover, we employ a random walk algorithm to sample loops in our networks, and find that time series with different dynamics exhibits distinct cycle structure. That is, the relative prevalence of loops with different lengths can be used to identify the underlying dynamics.

  14. An Experimental Wireless Mesh Network Node Based on AVR ATmega16 Microcontroller and RFM12B Radio Module

    NASA Astrophysics Data System (ADS)

    Olejnik, Remigiusz

    The paper describes a simple node designed to act as part of an experimental wireless mesh network. The node is based on Atmel AVR ATmega16 microcontroller and Hope Microelectronics RFM12B radio module. Along with technical details of the node, the network layer (addressing scheme and routing algorithms) is presented. Fundamental principles on wireless mesh networks are also presented. Experimental results summarize the paper and prove limited usability of the project.

  15. Directly Placed Restorative Materials: Review and Network Meta-analysis.

    PubMed

    Schwendicke, F; Göstemeyer, G; Blunck, U; Paris, S; Hsu, L-Y; Tu, Y-K

    2016-06-01

    For restoring cavitated dental lesions, whether carious or not, a large number of material combinations are available. We aimed to systematically review and synthesize data of comparative dental restorative trials. A systematic review was performed. Randomized controlled trials published between 2005 and 2015 were included that compared the survival of ≥2 restorative and/or adhesive materials (i.e., no need for restorative reintervention). Pairwise and Bayesian network meta-analyses were performed, with separate evaluations for cervical cavitated lesions and load-bearing posterior cavitated lesions in permanent and primary teeth. A total of 11,070 restorations (5,330 cervical, 5,740 load bearing) had been placed in 3,633 patients in the included trials. Thirty-six trials investigated restoration of cervical lesions (all in permanent teeth) and 36 of load-bearing lesions (8 in primary and 28 in permanent teeth). Resin-modified glass ionomer cements had the highest chance of survival in cervical cavitated lesions; composites or compomers placed via 2-step self-etch and 3-step etch-and-rinse adhesives were ranked next. Restorations placed with 2-step etch-and-rinse or 1-step self-etch adhesives performed worst. For load-bearing restorations, conventional composites had the highest probability of survival, while siloranes were found least suitable. Ambiguity remains regarding which adhesive strategy to use in load-bearing cavitated lesions. Most studies showed high risk of bias, and several comparisons were prone for publication bias. If prioritized for survival, resin-modified glass ionomer cements might be recommended to restore cervical lesions. For load-bearing ones, conventional or bulk fill composites seem most suitable. The available evidence is quantitatively and qualitatively insufficient for further recommendations, especially with regard to adhesive strategies in posterior load-bearing situations. Moreover, different material classifications might yield different findings on the same materials. Future trials should aim for sufficient power, longer follow-up times, and high internal validity to prove or refute differences between certain material combinations. An agreed material classification for future syntheses is desirable. PMID:26912220

  16. Gene network coherence based on prior knowledge using direct and indirect relationships.

    PubMed

    Gómez-Vela, Francisco; Lagares, José Antonio; Díaz-Díaz, Norberto

    2015-06-01

    Gene networks (GNs) have become one of the most important approaches for modeling biological processes. They are very useful to understand the different complex biological processes that may occur in living organisms. Currently, one of the biggest challenge in any study related with GN is to assure the quality of these GNs. In this sense, recent works use artificial data sets or a direct comparison with prior biological knowledge. However, these approaches are not entirely accurate as they only take into account direct gene-gene interactions for validation, leaving aside the weak (indirect) relationships. We propose a new measure, named gene network coherence (GNC), to rate the coherence of an input network according to different biological databases. In this sense, the measure considers not only the direct gene-gene relationships but also the indirect ones to perform a complete and fairer evaluation of the input network. Hence, our approach is able to use the whole information stored in the networks. A GNC JAVA-based implementation is available at: http://fgomezvela.github.io/GNC/. The results achieved in this work show that GNC outperforms the classical approaches for assessing GNs by means of three different experiments using different biological databases and input networks. According to the results, we can conclude that the proposed measure, which considers the inherent information stored in the direct and indirect gene-gene relationships, offers a new robust solution to the problem of GNs biological validation. PMID:25935118

  17. Generalised Sandpile Dynamics on Artificial and Real-World Directed Networks

    PubMed Central

    Zachariou, Nicky; Expert, Paul; Takayasu, Misako; Christensen, Kim

    2015-01-01

    The main finding of this paper is a novel avalanche-size exponent τ ≈ 1.87 when the generalised sandpile dynamics evolves on the real-world Japanese inter-firm network. The topology of this network is non-layered and directed, displaying the typical bow tie structure found in real-world directed networks, with cycles and triangles. We show that one can move from a strictly layered regular lattice to a more fluid structure of the inter-firm network in a few simple steps. Relaxing the regular lattice structure by introducing an interlayer distribution for the interactions, forces the scaling exponent of the avalanche-size probability density function τ out of the two-dimensional directed sandpile universality class τ = 4/3, into the mean field universality class τ = 3/2. Numerical investigation shows that these two classes are the only that exist on the directed sandpile, regardless of the underlying topology, as long as it is strictly layered. Randomly adding a small proportion of links connecting non adjacent layers in an otherwise layered network takes the system out of the mean field regime to produce non-trivial avalanche-size probability density function. Although these do not display proper scaling, they closely reproduce the behaviour observed on the Japanese inter-firm network. PMID:26606143

  18. ACC-FMD: ant colony clustering for functional module detection in protein-protein interaction networks.

    PubMed

    Ji, Junzhong; Liu, Hongxin; Zhang, Aidong; Liu, Zhijun; Liu, Chunnian

    2015-01-01

    Mining functional modules in Protein-Protein Interaction (PPI) networks is a very important research for revealing the structure-functionality relationships in biological processes. More recently, some swarm intelligence algorithms have been successfully applied in the field. This paper presents a new nature-inspired approach, ACC-FMD, which is based on ant colony clustering to detect functional modules. First, some proteins with the higher clustering coefficients are, respectively, selected as ant seed nodes. And then, the picking and dropping operations based on ant probabilistic models are developed and employed to assign proteins into the corresponding clusters represented by seeds. Finally, the best clustering result in each generation is used to perform the information transmission by updating the similarly function. Experimental results on some benchmarked datasets show that ACC-FMD outperforms the CFinder and MCODE algorithms and has comparative performance with the MINE, COACH, DPClus and Core algorithms in terms of the general evaluation metrics. PMID:26333266

  19. Serotonin in the modulation of neural plasticity and networks: implications for neurodevelopmental disorders.

    PubMed

    Lesch, Klaus-Peter; Waider, Jonas

    2012-10-01

    Serotonin (5-HT) shapes brain networks during development and modulates a wide spectrum of essential neuronal functions ranging from perception and cognitive appraisal to emotional responses in the mature brain. Deficits in 5-HT-moderated synaptic signaling fundamentally impact the pathophysiology and long-term outcome of neurodevelopmental disorders. Our understanding of how 5-HT-dependent modulation of circuit configuration influences social cognition and emotional learning has been enhanced by recent insight into the molecular and cellular mechanisms of synapse formation and plasticity. In this review, we discuss emerging concepts as to how defects in synaptic plasticity impact our biosocial brain and how recent findings regarding 5-HT's role in brain development and function provide insight into the cellular and physiological basis of neurodevelopmental disorders. PMID:23040814

  20. Low voltage polymer network liquid crystal for infrared spatial light modulators.

    PubMed

    Peng, Fenglin; Xu, Daming; Chen, Haiwei; Wu, Shin-Tson

    2015-02-01

    We report a low-voltage and fast-response polymer network liquid crystal (PNLC) infrared phase modulator. To optimize device performance, we propose a physical model to understand the curing temperature effect on average domain size. Good agreement between model and experiment is obtained. By optimizing the UV curing temperature and employing a large dielectric anisotropy LC host, we have lowered the 2π phase change voltage to 22.8V at 1.55μm wavelength while keeping response time at about 1 ms. Widespread application of such a PNLC integrated into a high resolution liquid-crystal-on-silicon (LCoS) for infrared spatial light modulator is foreseeable. PMID:25836103

  1. Motor system modulation for movement direction and rotation angle during motor imagery.

    PubMed

    Pizzolato, F; Fiorio, M; Cesari, P

    2012-08-30

    Transcranial magnetic stimulation (TMS) studies have shown that the motor system is facilitated when we imagine performing motor actions. However, it is not clear whether the individual's motor system modulates bilaterally and selectively for task parameters, such as movement direction and amplitude. To investigate this issue, we applied single-pulse TMS over the left and right primary motor cortex (M1) of healthy subjects, who had to imagine grasping and rotating a clock hour hand, having a starting position at noon, towards four different times: 2, 5, 7 and 10 o'clock. Rotations could be in clockwise (2 and 5 o'clock) or counter-clockwise (7 and 10 o'clock) directions and could require small (2 and 10 o'clock) or large (5 and 7 o'clock) rotation angle. TMS motor-evoked potentials were recorded for three muscles, and movements were imagined with the right and left hands. Results showed that during motor imagery a mirroring pattern was present between the right and the left motor cortices, showing selective activation of the hand-intrinsic muscles spatially close to the direction of the imagined movement. Overall a higher activation for large and a lower activation for small rotation angle were found, but no selective muscle activity was present within the hand-intrinsic muscles for this parameter. Following these results we propose that during action imagination an internally coded covariance between movement parameters is present with a muscle-specific activation for movement direction. PMID:22634508

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

    PubMed

    Samura, Toshikazu; Hayashi, Hatsuo

    2012-09-01

    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

  3. Plasmonic modulator utilizing three parallel metal-dielectric-metal waveguide directional coupler and elasto-optic effects

    NASA Astrophysics Data System (ADS)

    Dwivedi, Ram Prakash; Lee, Hyun-Shik; Song, Jun-Hwa; An, Shinmo; Lee, El-Hang

    2011-03-01

    We report, for the first time, on the design of a plasmonic modulator working on the principle of the elasto-optic effects in a directional coupling structure, utilizing three parallel metal-dielectric-metal waveguides. We propose to achieve the active switching of the power propagation using the elasto-optic effect and optimize the extinction ratio of the optical modulation. The device is characterized and numerically analyzed using the finite-element-method at the wavelengths of 1.55 μm. For the modulator length of 2.33 μm, the extinction ratio of the modulation is nearly 14 dB, and the calculated attenuation loss is 4.5 dB. The calculated driving voltage is 4.8 V for the given modulator. The effect of the applied voltage on the modulation is also analyzed.

  4. A low voltage submillisecond-response polymer network liquid crystal spatial light modulator

    NASA Astrophysics Data System (ADS)

    Sun, Jie; Wu, Shin-Tson; Haseba, Yasuhiro

    2014-01-01

    We report a low voltage and highly transparent polymer network liquid crystal (PNLC) with submillisecond response time. By employing a large dielectric anisotropy LC host JC-BP07N, we have lowered the V2π voltage to 23 V at λ = 514 nm. This will enable PNLC to be integrated with a high resolution liquid-crystal-on-silicon spatial light modulator, in which the maximum voltage is 24 V. A simple model correlating PNLC performance with its host LC is proposed and validated experimentally. By optimizing the domain size, we can achieve V2π < 15 V with some compromises in scattering and response time.

  5. Rapid decision threshold modulation by reward rate in a neural network

    PubMed Central

    Simen, Patrick; Cohen, Jonathan D.; Holmes, Philip

    2006-01-01

    Optimal performance in two-alternative, free response decision making tasks can be achieved by the drift-diffusion model of decision making - which can be implemented in a neural network - as long as the threshold parameter of that model can be adapted to different task conditions. Evidence exists that people seek to maximize reward in such tasks by modulating response thresholds. However, few models have been proposed for threshold adaptation, and none have been implemented using neurally plausible mechanisms. Here we propose a neural network that adapts thresholds in order to maximize reward rate. The model makes predictions regarding optimal performance and provides a benchmark against which actual performance can be compared, as well as testable predictions about the way in which reward rate may be encoded by neural mechanisms. PMID:16987636

  6. A systematic method to identify modulation of transcriptional regulation via chromatin activity reveals regulatory network during mESC differentiation.

    PubMed

    Duren, Zhana; Wang, Yong

    2016-01-01

    Chromatin regulators (CRs) are crucial for connecting the chromatin level and transcriptome level by modulating chromatin structures, establishing, and maintaining epigenetic modifications. We present a systematic method to identify MOdulation of transcriptional regulation via CHromatin Activity (MOCHA) from gene expression data and demonstrate its advantage in associating CRs to their chromatin localization and understand CRs' function. We first re-construct the CRs modulation network by integrating the correlation and conditional correlation concepts. Then we quantify the chromatin activity as hidden variable in network by integrating the upstream and downstream information. We applied MOCHA to systematically explore the interplay of CRs, TFs, and target genes in mouse embryonic stem cells (ESC). As a result, MOCHA identified 420 chromatin regulators with modulation preference, including Pou5f1 and Eed. We found that BAF complex, NuRD complex, and polycomb-group proteins, regulate the delicate balance between pluripotency and differentiation by modulating key TFs including Klf4, Tcf3, and Max; NuRD complex members Mbd3 and Hdac1 may modulate Klf4 to achieve its dual functional roles in pluripotent and differentiation stages;Imprinted gene H19 and Igf2 are modulated by DNA methylation, histone acetylation, and insulator CTCF. Finally, we analyzed CR's combinational modulation pattern by constructing a CR-CR interaction network. PMID:26949222

  7. A systematic method to identify modulation of transcriptional regulation via chromatin activity reveals regulatory network during mESC differentiation

    PubMed Central

    Duren, Zhana; Wang, Yong

    2016-01-01

    Chromatin regulators (CRs) are crucial for connecting the chromatin level and transcriptome level by modulating chromatin structures, establishing, and maintaining epigenetic modifications. We present a systematic method to identify MOdulation of transcriptional regulation via CHromatin Activity (MOCHA) from gene expression data and demonstrate its advantage in associating CRs to their chromatin localization and understand CRs’ function. We first re-construct the CRs modulation network by integrating the correlation and conditional correlation concepts. Then we quantify the chromatin activity as hidden variable in network by integrating the upstream and downstream information. We applied MOCHA to systematically explore the interplay of CRs, TFs, and target genes in mouse embryonic stem cells (ESC). As a result, MOCHA identified 420 chromatin regulators with modulation preference, including Pou5f1 and Eed. We found that BAF complex, NuRD complex, and polycomb-group proteins, regulate the delicate balance between pluripotency and differentiation by modulating key TFs including Klf4, Tcf3, and Max; NuRD complex members Mbd3 and Hdac1 may modulate Klf4 to achieve its dual functional roles in pluripotent and differentiation stages;Imprinted gene H19 and Igf2 are modulated by DNA methylation, histone acetylation, and insulator CTCF. Finally, we analyzed CR’s combinational modulation pattern by constructing a CR-CR interaction network. PMID:26949222

  8. 25 Gbit/s differential phase-shift-keying signal generation using directly modulated quantum-dot semiconductor optical amplifiers

    SciTech Connect

    Zeghuzi, A. Schmeckebier, H.; Stubenrauch, M.; Bimberg, D.; Meuer, C.; Schubert, C.; Bunge, C.-A.

    2015-05-25

    Error-free generation of 25-Gbit/s differential phase-shift keying (DPSK) signals via direct modulation of InAs quantum-dot (QD) based semiconductor optical amplifiers (SOAs) is experimentally demonstrated with an input power level of −5 dBm. The QD SOAs emit in the 1.3-μm wavelength range and provide a small-signal fiber-to-fiber gain of 8 dB. Furthermore, error-free DPSK modulation is achieved for constant optical input power levels from 3 dBm down to only −11 dBm for a bit rate of 20 Gbit/s. Direct phase modulation of QD SOAs via current changes is thus demonstrated to be much faster than direct gain modulation.

  9. 25 Gbit/s differential phase-shift-keying signal generation using directly modulated quantum-dot semiconductor optical amplifiers

    NASA Astrophysics Data System (ADS)

    Zeghuzi, A.; Schmeckebier, H.; Stubenrauch, M.; Meuer, C.; Schubert, C.; Bunge, C.-A.; Bimberg, D.

    2015-05-01

    Error-free generation of 25-Gbit/s differential phase-shift keying (DPSK) signals via direct modulation of InAs quantum-dot (QD) based semiconductor optical amplifiers (SOAs) is experimentally demonstrated with an input power level of -5 dBm. The QD SOAs emit in the 1.3-μm wavelength range and provide a small-signal fiber-to-fiber gain of 8 dB. Furthermore, error-free DPSK modulation is achieved for constant optical input power levels from 3 dBm down to only -11 dBm for a bit rate of 20 Gbit/s. Direct phase modulation of QD SOAs via current changes is thus demonstrated to be much faster than direct gain modulation.

  10. Water distribution system vulnerability analysis using weighted and directed network models

    NASA Astrophysics Data System (ADS)

    Yazdani, Alireza; Jeffrey, Paul

    2012-06-01

    The reliability and robustness against failures of networked water distribution systems are central tenets of water supply system design and operation. The ability of such networks to continue to supply water when components are damaged or fail is dependent on the connectivity of the network and the role and location of the individual components. This paper employs a set of advanced network analysis techniques to study the connectivity of water distribution systems, its relationship with system robustness, and susceptibility to damage. Water distribution systems are modeled as weighted and directed networks by using the physical and hydraulic attributes of system components. A selection of descriptive measurements is utilized to quantify the structural properties of benchmark systems at both local (component) and global (network) scales. Moreover, a novel measure of component criticality, the demand-adjusted entropic degree, is proposed to support identification of critical nodes and their ranking according to failure impacts. The application and value of this metric is demonstrated through two case study networks in the USA and UK. Discussion focuses on the potential for gradual evolution of abstract graph-based tools and techniques to more practical network analysis methods, where a theoretical framework for the analysis of robustness and vulnerability of water distribution networks to better support planning and management decisions is presented.

  11. Low frequency steady-state brain responses modulate large scale functional networks in a frequency-specific means.

    PubMed

    Wang, Yi-Feng; Long, Zhiliang; Cui, Qian; Liu, Feng; Jing, Xiu-Juan; Chen, Heng; Guo, Xiao-Nan; Yan, Jin H; Chen, Hua-Fu

    2016-01-01

    Neural oscillations are essential for brain functions. Research has suggested that the frequency of neural oscillations is lower for more integrative and remote communications. In this vein, some resting-state studies have suggested that large scale networks function in the very low frequency range (<1 Hz). However, it is difficult to determine the frequency characteristics of brain networks because both resting-state studies and conventional frequency tagging approaches cannot simultaneously capture multiple large scale networks in controllable cognitive activities. In this preliminary study, we aimed to examine whether large scale networks can be modulated by task-induced low frequency steady-state brain responses (lfSSBRs) in a frequency-specific pattern. In a revised attention network test, the lfSSBRs were evoked in the triple network system and sensory-motor system, indicating that large scale networks can be modulated in a frequency tagging way. Furthermore, the inter- and intranetwork synchronizations as well as coherence were increased at the fundamental frequency and the first harmonic rather than at other frequency bands, indicating a frequency-specific modulation of information communication. However, there was no difference among attention conditions, indicating that lfSSBRs modulate the general attention state much stronger than distinguishing attention conditions. This study provides insights into the advantage and mechanism of lfSSBRs. More importantly, it paves a new way to investigate frequency-specific large scale brain activities. PMID:26512872

  12. Road traffic: A case study of flow and path-dependency in weighted directed networks

    NASA Astrophysics Data System (ADS)

    Bono, Flavio; Gutiérrez, Eugenio; Poljansek, Karmen

    2010-11-01

    How much can we tell about flows through networks just from their topological properties? Whereas flow distributions of river basins, trees or cardiovascular systems come naturally to mind, more complex topologies are not so immediate, especially if the network is large and heterogeneously directed. Our study is motivated by the question of how the distribution of path-dependent trails in directed networks is correlated to the distribution of network flows. As an example we have studied the path-dependencies in closed trails in four metropolitan areas in England and the USA and computed their global and spatial correlations with measured traffic flows. We have found that the heterogeneous distribution of traffic intensity is mirrored by the distribution of agglomerate path-dependency and that high traffic roads are packed along corridors at short-to-medium trail lengths from the ensemble of nodes.

  13. Catechol-O-Methyltransferase Valine158Methionine Polymorphism Modulates Brain Networks Underlying Working Memory Across Adulthood

    PubMed Central

    Sambataro, Fabio; Reed, Jeff D.; Murty, Vishnu P.; Das, Saumitra; Tan, Hao Yang; Callicott, Joseph H.; Weinberger, Daniel R.; Mattay, Venkata S.

    2010-01-01

    Background Cognitive abilities decline with age with large individual variability. Genetic variations have been suggested to be an important source for some of this heterogeneity. Among these variations, those related to the dopaminergic system, particularly the valine158methionine polymorphism in catechol-O-methyltransferase (COMTval158met), have been implicated in modulating age-related changes in executive function. Methods We studied 75 subjects (age 21–90 years) using functional neuroimaging while they performed a low-level working memory (WM) task to explore the effects of aging, of the COMTval158met polymorphism, and their interactions on the physiological patterns of interconnected cortical activity engaged by WM. Results Our results show that val homozygotes and older subjects showed increased activity in dorsolateral prefrontal cortex (DLPFC) and decreased activity in ventrolateral prefrontal cortex (VLPFC) relative to met homozygotes and younger subjects, respectively. Interestingly, there were also independent effects of the COMTval158met polymorphism and age on the strength of connectivity between brain regions within the left prefrontal-parietal network; val homozygotes and older subjects showed greater connectivity between the DLPFC and other brain regions within the network and met homozygotes showed greater connectivity between the VLPFC and other brain regions within the network. Furthermore, the greater functional connectivity strength of DLPFC in val homozygotes relative to met homozygotes was much more pronounced in older adults Conclusions Our findings suggest that the COMTval158met polymorphism modulates both the activity and functional connectivity of brain regions within WM networks and most importantly that this effect is exaggerated with increasing age, contributing to the variability in age-related decline in executive cognition. PMID:19539269

  14. Extrasynaptic Neurotransmission in the Modulation of Brain Function. Focus on the Striatal Neuronal–Glial Networks

    PubMed Central

    Fuxe, Kjell; Borroto-Escuela, Dasiel O.; Romero-Fernandez, Wilber; Diaz-Cabiale, Zaida; Rivera, Alicia; Ferraro, Luca; Tanganelli, Sergio; Tarakanov, Alexander O.; Garriga, Pere; Narváez, José Angel; Ciruela, Francisco; Guescini, Michele; Agnati, Luigi F.

    2012-01-01

    Extrasynaptic neurotransmission is an important short distance form of volume transmission (VT) and describes the extracellular diffusion of transmitters and modulators after synaptic spillover or extrasynaptic release in the local circuit regions binding to and activating mainly extrasynaptic neuronal and glial receptors in the neuroglial networks of the brain. Receptor-receptor interactions in G protein-coupled receptor (GPCR) heteromers play a major role, on dendritic spines and nerve terminals including glutamate synapses, in the integrative processes of the extrasynaptic signaling. Heteromeric complexes between GPCR and ion-channel receptors play a special role in the integration of the synaptic and extrasynaptic signals. Changes in extracellular concentrations of the classical synaptic neurotransmitters glutamate and GABA found with microdialysis is likely an expression of the activity of the neuron-astrocyte unit of the brain and can be used as an index of VT-mediated actions of these two neurotransmitters in the brain. Thus, the activity of neurons may be functionally linked to the activity of astrocytes, which may release glutamate and GABA to the extracellular space where extrasynaptic glutamate and GABA receptors do exist. Wiring transmission (WT) and VT are fundamental properties of all neurons of the CNS but the balance between WT and VT varies from one nerve cell population to the other. The focus is on the striatal cellular networks, and the WT and VT and their integration via receptor heteromers are described in the GABA projection neurons, the glutamate, dopamine, 5-hydroxytryptamine (5-HT) and histamine striatal afferents, the cholinergic interneurons, and different types of GABA interneurons. In addition, the role in these networks of VT signaling of the energy-dependent modulator adenosine and of endocannabinoids mainly formed in the striatal projection neurons will be underlined to understand the communication in the striatal cellular networks. PMID:22675301

  15. Multiple monoaminergic modulation of posturo-locomotor network activity in the newborn rat spinal cord

    PubMed Central

    Beliez, Lauriane; Barrière, Gregory; Bertrand, Sandrine S.; Cazalets, Jean-René

    2014-01-01

    Studies devoted to understanding locomotor control have mainly addressed the functioning of the neural circuits controlling leg movements and relatively little is known of the operation of networks that activate trunk muscles in coordination with limb movements. The aim of the present work was (1) to identify the exogenous neurotransmitter cocktail that most strongly activates postural thoracic circuitry; (2) to investigate how the biogenic amines serotonin (5-HT), dopamine (DA), and noradrenaline (NA) modulate the coordination between limb and axial motor networks. Experiments were carried out on in vitro isolated spinal cord preparations from newborn rats. We recorded from ventral roots to monitor hindlimb locomotor and axial postural network activity. Each combination of the three amines with excitatory amino acids (EAAs) elicited coordinated rhythmic motor activity at all segmental levels with specific characteristics. The variability in cycle period was similar with 5-HT and DA while it was significantly higher with NA. DA elicited motor bursts of smaller amplitude in thoracic segments compared to 5-HT and NA, while both DA and NA elicited motor bursts of higher amplitude than 5-HT in the lumbar and sacral segments. The amines modulated the phase relationships of bursts in various segments with respect to the reference lumbar segment. At the thoracic level there was a phase lag between all recorded segments in the presence of 5-HT, while DA and NA elicited synchronous bursting. At the sacral level, 5-HT and DA induced an intersegmental phase shift while relationships became phase-locked with NA. Various combinations of EAAs with two or even all three amines elicited rhythmic motor output that was more variable than with one amine alone. Our results provide new data on the coordinating processes between spinal cord networks, demonstrating that each amine has a characteristic “signature” regarding its specific effect on intersegmental phase relationships. PMID:25177275

  16. A Functionally Conserved Gene Regulatory Network Module Governing Olfactory Neuron Diversity

    PubMed Central

    Okuwa, Sumie; Maciejewski, Abigail; Brandt, Alicia T.; Reinhold, Dominik; Jones, Corbin D.; Volkan, Pelin Cayirlioglu

    2016-01-01

    Sensory neuron diversity is required for organisms to decipher complex environmental cues. In Drosophila, the olfactory environment is detected by 50 different olfactory receptor neuron (ORN) classes that are clustered in combinations within distinct sensilla subtypes. Each sensilla subtype houses stereotypically clustered 1–4 ORN identities that arise through asymmetric divisions from a single multipotent sensory organ precursor (SOP). How each class of SOPs acquires a unique differentiation potential that accounts for ORN diversity is unknown. Previously, we reported a critical component of SOP diversification program, Rotund (Rn), increases ORN diversity by generating novel developmental trajectories from existing precursors within each independent sensilla type lineages. Here, we show that Rn, along with BarH1/H2 (Bar), Bric-à-brac (Bab), Apterous (Ap) and Dachshund (Dac), constitutes a transcription factor (TF) network that patterns the developing olfactory tissue. This network was previously shown to pattern the segmentation of the leg, which suggests that this network is functionally conserved. In antennal imaginal discs, precursors with diverse ORN differentiation potentials are selected from concentric rings defined by unique combinations of these TFs along the proximodistal axis of the developing antennal disc. The combinatorial code that demarcates each precursor field is set up by cross-regulatory interactions among different factors within the network. Modifications of this network lead to predictable changes in the diversity of sensilla subtypes and ORN pools. In light of our data, we propose a molecular map that defines each unique SOP fate. Our results highlight the importance of the early prepatterning gene regulatory network as a modulator of SOP and terminally differentiated ORN diversity. Finally, our model illustrates how conserved developmental strategies are used to generate neuronal diversity. PMID:26765103

  17. A Functionally Conserved Gene Regulatory Network Module Governing Olfactory Neuron Diversity.

    PubMed

    Li, Qingyun; Barish, Scott; Okuwa, Sumie; Maciejewski, Abigail; Brandt, Alicia T; Reinhold, Dominik; Jones, Corbin D; Volkan, Pelin Cayirlioglu

    2016-01-01

    Sensory neuron diversity is required for organisms to decipher complex environmental cues. In Drosophila, the olfactory environment is detected by 50 different olfactory receptor neuron (ORN) classes that are clustered in combinations within distinct sensilla subtypes. Each sensilla subtype houses stereotypically clustered 1-4 ORN identities that arise through asymmetric divisions from a single multipotent sensory organ precursor (SOP). How each class of SOPs acquires a unique differentiation potential that accounts for ORN diversity is unknown. Previously, we reported a critical component of SOP diversification program, Rotund (Rn), increases ORN diversity by generating novel developmental trajectories from existing precursors within each independent sensilla type lineages. Here, we show that Rn, along with BarH1/H2 (Bar), Bric-à-brac (Bab), Apterous (Ap) and Dachshund (Dac), constitutes a transcription factor (TF) network that patterns the developing olfactory tissue. This network was previously shown to pattern the segmentation of the leg, which suggests that this network is functionally conserved. In antennal imaginal discs, precursors with diverse ORN differentiation potentials are selected from concentric rings defined by unique combinations of these TFs along the proximodistal axis of the developing antennal disc. The combinatorial code that demarcates each precursor field is set up by cross-regulatory interactions among different factors within the network. Modifications of this network lead to predictable changes in the diversity of sensilla subtypes and ORN pools. In light of our data, we propose a molecular map that defines each unique SOP fate. Our results highlight the importance of the early prepatterning gene regulatory network as a modulator of SOP and terminally differentiated ORN diversity. Finally, our model illustrates how conserved developmental strategies are used to generate neuronal diversity. PMID:26765103

  18. Confinement and diffusion modulate bistability and stochastic switching in a reaction network with positive feedback.

    PubMed

    Mlynarczyk, Paul J; Pullen, Robert H; Abel, Steven M

    2016-01-01

    Positive feedback is a common feature in signal transduction networks and can lead to phenomena such as bistability and signal propagation by domain growth. Physical features of the cellular environment, such as spatial confinement and the mobility of proteins, play important but inadequately understood roles in shaping the behavior of signaling networks. Here, we use stochastic, spatially resolved kinetic Monte Carlo simulations to explore a positive feedback network as a function of system size, system shape, and mobility of molecules. We show that these physical properties can markedly alter characteristics of bistability and stochastic switching when compared with well-mixed simulations. Notably, systems of equal volume but different shapes can exhibit qualitatively different behaviors under otherwise identical conditions. We show that stochastic switching to a state maintained by positive feedback occurs by cluster formation and growth. Additionally, the frequency at which switching occurs depends nontrivially on the diffusion coefficient, which can promote or suppress switching relative to the well-mixed limit. Taken together, the results provide a framework for understanding how confinement and protein mobility influence emergent features of the positive feedback network by modulating molecular concentrations, diffusion-influenced rate parameters, and spatiotemporal correlations between molecules. PMID:26747820

  19. Confinement and diffusion modulate bistability and stochastic switching in a reaction network with positive feedback

    NASA Astrophysics Data System (ADS)

    Mlynarczyk, Paul J.; Pullen, Robert H.; Abel, Steven M.

    2016-01-01

    Positive feedback is a common feature in signal transduction networks and can lead to phenomena such as bistability and signal propagation by domain growth. Physical features of the cellular environment, such as spatial confinement and the mobility of proteins, play important but inadequately understood roles in shaping the behavior of signaling networks. Here, we use stochastic, spatially resolved kinetic Monte Carlo simulations to explore a positive feedback network as a function of system size, system shape, and mobility of molecules. We show that these physical properties can markedly alter characteristics of bistability and stochastic switching when compared with well-mixed simulations. Notably, systems of equal volume but different shapes can exhibit qualitatively different behaviors under otherwise identical conditions. We show that stochastic switching to a state maintained by positive feedback occurs by cluster formation and growth. Additionally, the frequency at which switching occurs depends nontrivially on the diffusion coefficient, which can promote or suppress switching relative to the well-mixed limit. Taken together, the results provide a framework for understanding how confinement and protein mobility influence emergent features of the positive feedback network by modulating molecular concentrations, diffusion-influenced rate parameters, and spatiotemporal correlations between molecules.

  20. Electro-acupuncture at different acupoints modulating the relative specific brain functional network

    NASA Astrophysics Data System (ADS)

    Fang, Jiliang; Wang, Xiaoling; Wang, Yin; Liu, Hesheng; Hong, Yang; Liu, Jun; Zhou, Kehua; Wang, Lei; Xue, Chao; Song, Ming; Liu, Baoyan; Zhu, Bing

    2010-11-01

    Objective: The specific brain effects of acupoint are important scientific concern in acupuncture. However, previous acupuncture fMRI studies focused on acupoints in muscle layer on the limb. Therefore, researches on acupoints within connective tissue at trunk are warranted. Material and Methods: Brain effects of acupuncture on abdomen at acupoints Guanyuan (CV4) and Zhongwan (CV12) were tested using fMRI on 21 healthy volunteers. The data acquisition was performed at resting state, during needle retention, electroacupuncture (EA) and post-EA resting state. Needling sensations were rated after every electroacupuncture (EA) procedure. The needling sensations and the brain functional activity and connectivity were compared between CV4 and CV12 using SPSS, SPM2 and the local and remote connectivity maps. Results and conclusion: EA at CV4 and CV12 induced apparent deactivation effects in the limbic-paralimbic-neocortical network. The default mode of the brain was modified by needle retention and EA, respectively. The functional brain network was significantly changed post EA. However, the minor differences existed between these two acupoints. The results demonstrated similarity between functional brain network mode of acupuncture modulation and functional circuits of emotional and cognitive regulation. Acupuncture may produce analgesia, anti-anxiety and anti-depression via the limbic-paralimbic-neocortical network (LPNN).

  1. Protein thermal denaturation is modulated by central residues in the protein structure network.

    PubMed

    Souza, Valquiria P; Ikegami, Cecília M; Arantes, Guilherme M; Marana, Sandro R

    2016-03-01

    Network structural analysis, known as residue interaction networks or graphs (RIN or RIG, respectively) or protein structural networks or graphs (PSN or PSG, respectively), comprises a useful tool for detecting important residues for protein function, stability, folding and allostery. In RIN, the tertiary structure is represented by a network in which residues (nodes) are connected by interactions (edges). Such structural networks have consistently presented a few central residues that are important for shortening the pathways linking any two residues in a protein structure. To experimentally demonstrate that central residues effectively participate in protein properties, mutations were directed to seven central residues of the β-glucosidase Sfβgly (β-d-glucoside glucohydrolase; EC 3.2.1.21). These mutations reduced the thermal stability of the enzyme, as evaluated by changes in transition temperature (Tm ) and the denaturation rate at 45 °C. Moreover, mutations directed to the vicinity of a central residue also caused significant decreases in the Tm of Sfβgly and clearly increased the unfolding rate constant at 45 °C. However, mutations at noncentral residues or at surrounding residues did not affect the thermal stability of Sfβgly. Therefore, the data reported in the present study suggest that the perturbation of the central residues reduced the stability of the native structure of Sfβgly. These results are in agreement with previous findings showing that networks are robust, whereas attacks on central nodes cause network failure. Finally, the present study demonstrates that central residues underlie the functional properties of proteins. PMID:26785700

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

    PubMed

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

    2013-01-01

    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

  3. Direct Correlation between Nonrandom Ion Hopping and Network Structure in Ion-Conducting Borophosphate Glasses

    NASA Astrophysics Data System (ADS)

    Zielniok, D.; Eckert, H.; Cramer, C.

    2008-01-01

    We present temperature-dependent conductivity spectra of sodium borophosphate glasses with a varying borate/phosphate ratio but a constant sodium oxide content which can be mapped into time-dependent mean square displacements. For the first time, we show that characteristic lengths of ion transport derived thereof are directly linked to features of network structure, viz., the number of boron oxide tetrahedra. Our results also shed light on the mixed network former effect.

  4. Combining Partial Directed Coherence and Graph Theory to Analyse Effective Brain Networks of Different Mental Tasks

    PubMed Central

    Huang, Dengfeng; Ren, Aifeng; Shang, Jing; Lei, Qiao; Zhang, Yun; Yin, Zhongliang; Li, Jun; von Deneen, Karen M.; Huang, Liyu

    2016-01-01

    Purpose: The aim of this study is to qualify the network properties of the brain networks between two different mental tasks (play task or rest task) in a healthy population. Methods and Materials: EEG signals were recorded from 19 healthy subjects when performing different mental tasks. Partial directed coherence (PDC) analysis, based on Granger causality (GC), was used to assess the effective brain networks during the different mental tasks. Moreover, the network measures, including degree, degree distribution, local and global efficiency in delta, theta, alpha, and beta rhythms were calculated and analyzed. Results: The local efficiency is higher in the beta frequency and lower in the theta frequency during play task whereas the global efficiency is higher in the theta frequency and lower in the beta frequency in the rest task. Significance: This study reveals the network measures during different mental states and efficiency measures may be used as characteristic quantities for improvement in attentional performance.

  5. Elimination of cross-modulation distortion in a radio frequency-amplified intensity-modulation direct-detection analog photonic link

    NASA Astrophysics Data System (ADS)

    Liang, Xiaodong; Yin, Feifei; Dai, Yitang; Li, Jianqiang; Xu, Kun

    2016-03-01

    By cascading two standard Mach-Zehnder modulators (MZMs), we propose and demonstrate a scheme to effectively eliminate the cross-modulation distortion (XMD), which results from the out-of-band interference in multicarrier intensity-modulation direct-detection (IMDD) analog photonic links. When the bias angle of the cascaded modulator is specifically designed, the XMDs, both from the photonic link itself and from the nonlinear electrical amplifiers, are well suppressed. Our proposal is theoretically analyzed, and the performance of the cascading system is experimentally demonstrated. A suppression ratio of more than 30 dB is achieved by the cascading scheme. By using the high-performance pre- and postamplifiers, the measured link gain and noise figure are improved by 62 and 32 dB, respectively.

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

    PubMed Central

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

    2012-01-01

    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. PMID:22429242

  7. Modulation of amplitude and latency of motor evoked potential by direction of transcranial magnetic stimulation

    NASA Astrophysics Data System (ADS)

    Sato, Aya; Torii, Tetsuya; Iwahashi, Masakuni; Itoh, Yuji; Iramina, Keiji

    2014-05-01

    The present study analyzed the effects of monophasic magnetic stimulation to the motor cortex. The effects of magnetic stimulation were evaluated by analyzing the motor evoked potentials (MEPs). The amplitude and latency of MEPs on the abductor pollicis brevis muscle were used to evaluate the effects of repetitive magnetic stimulation. A figure eight-shaped flat coil was used to stimulate the region over the primary motor cortex. The intensity of magnetic stimulation was 120% of the resting motor threshold, and the frequency of magnetic stimulation was 0.1 Hz. In addition, the direction of the current in the brain was posterior-anterior (PA) or anterior-posterior (AP). The latency of MEP was compared with PA and AP on initial magnetic stimulation. The results demonstrated that a stimulus in the AP direction increased the latency of the MEP by approximately 2.5 ms. MEP amplitude was also compared with PA and AP during 60 magnetic stimulations. The results showed that a stimulus in the PA direction gradually increased the amplitude of the MEP. However, a stimulus in the AP direction did not modulate the MEP amplitude. The average MEP amplitude induced from every 10 magnetic pulses was normalized by the average amplitude of the first 10 stimuli. These results demonstrated that the normalized MEP amplitude increased up to approximately 150%. In terms of pyramidal neuron indirect waves (I waves), magnetic stimulation inducing current flowing backward to the anterior preferentially elicited an I1 wave, and current flowing forward to the posterior elicited an I3 wave. It has been reported that the latency of the I3 wave is approximately 2.5 ms longer than the I1 wave elicitation, so the resulting difference in latency may be caused by this phenomenon. It has also been reported that there is no alteration of MEP amplitude at a frequency of 0.1 Hz. However, this study suggested that the modulation of MEP amplitude depends on stimulation strength and stimulation direction.

  8. Transcranial direct current stimulation of the posterior parietal cortex modulates arithmetic learning.

    PubMed

    Grabner, Roland H; Rütsche, Bruno; Ruff, Christian C; Hauser, Tobias U

    2015-07-01

    The successful acquisition of arithmetic skills is an essential step in the development of mathematical competencies and has been associated with neural activity in the left posterior parietal cortex (PPC). It is unclear, however, whether this brain region plays a causal role in arithmetic skill acquisition and whether arithmetic learning can be modulated by means of non-invasive brain stimulation of this key region. In the present study we addressed these questions by applying transcranial direct current stimulation (tDCS) over the left PPC during a short-term training that simulates the typical path of arithmetic skill acquisition (specifically the transition from effortful procedural to memory-based problem-solving strategies). Sixty participants received either anodal, cathodal or sham tDCS while practising complex multiplication and subtraction problems. The stability of the stimulation-induced learning effects was assessed in a follow-up test 24 h after the training. Learning progress was modulated by tDCS. Cathodal tDCS (compared with sham) decreased learning rates during training and resulted in poorer performance which lasted over 24 h after stimulation. Anodal tDCS showed an operation-specific improvement for subtraction learning. Our findings extend previous studies by demonstrating that the left PPC is causally involved in arithmetic learning (and not only in arithmetic performance) and that even a short-term tDCS application can modulate the success of arithmetic knowledge acquisition. Moreover, our finding of operation-specific anodal stimulation effects suggests that the enhancing effects of tDCS on learning can selectively affect just one of several cognitive processes mediated by the stimulated area. PMID:25970697

  9. Direct current stimulation over the human sensorimotor cortex modulates the brain's hemodynamic response to tactile stimulation.

    PubMed

    Wang, Ye; Hao, Ying; Zhou, Junhong; Fried, Peter J; Wang, Xiaoying; Zhang, Jue; Fang, Jing; Pascual-Leone, Alvaro; Manor, Brad

    2015-08-01

    Tactile stimuli produce afferent signals that activate specific regions of the cerebral cortex. Noninvasive transcranial direct current stimulation (tDCS) effectively modulates cortical excitability. We therefore hypothesised that a single session of tDCS targeting the sensory cortices would alter the cortical response to tactile stimuli. This hypothesis was tested with a block-design functional magnetic resonance imaging protocol designed to quantify the blood oxygen level-dependent response to controlled sinusoidal pressure stimulation applied to the right foot sole, as compared with rest, in 16 healthy young adults. Following sham tDCS, right foot sole stimulation was associated with activation bilaterally within the precentral cortex, postcentral cortex, middle and superior frontal gyri, temporal lobe (subgyral) and cingulate gyrus. Activation was also observed in the left insula, middle temporal lobe, superior parietal lobule, supramarginal gyrus and thalamus, as well as the right inferior parietal lobule and claustrum (false discovery rate corrected, P < 0.05). To explore the regional effects of tDCS, brain regions related to somatosensory processing, and cortical areas underneath each tDCS electrode, were chosen as regions of interest. Real tDCS, as compared with sham tDCS, increased the percent signal change associated with foot stimulation relative to rest in the left posterior paracentral lobule. These results indicate that tDCS acutely modulated the cortical responsiveness to controlled foot pressure stimuli in healthy adults. Further study is warranted, in both healthy individuals and patients with sensory impairments, to link tDCS-induced modulation of the cortical response to tactile stimuli with changes in somatosensory perception. PMID:25989209

  10. Spontaneous formation of InGaN nanowall network directly on Si

    SciTech Connect

    Soto Rodriguez, P. E. D.; Kumar, Praveen; Gomez, V. J.; Alvi, N. H.; Calleja, E.; Noetzel, R.

    2013-04-29

    We present the study on epitaxial growth of an InGaN nanowall network directly on Si by plasma-assisted molecular beam epitaxy. Scanning electron microscopy, high-resolution X-ray diffraction, and transmission electron microscopy together with energy-dispersive X-ray analysis infer the crystalline nature of the InGaN nanowall network, oriented along the C-axis, with In composition ranging from pure GaN to 40%. Room temperature photoluminescence is observed, indicating good optical quality. The nanowall network is highly in-plane electrically conductive.

  11. Brain network dynamics characterization in epileptic seizures. Joint directed graph and pairwise synchronization measures

    NASA Astrophysics Data System (ADS)

    Rodrigues, A. C.; Machado, B. S.; Florence, G.; Hamad, A. P.; Sakamoto, A. C.; Fujita, A.; Baccalá, L. A.; Amaro, E.; Sameshima, K.

    2014-12-01

    Here we propose and evaluate a new approach to analyse multichannel mesial temporal lobe epilepsy EEG data from eight patients through complex network and synchronization theories. The method employs a Granger causality test to infer the directed connectivity graphs and a wavelet transform based phase synchronization measure whose characteristics allow studying dynamical transitions during epileptic seizures. We present a new combined graph measure that quantifies the level of network hub formation, called network hub out-degree, which closely reflects the level of synchronization observed during the ictus.

  12. Learning partially directed functional networks from meta-analysis imaging data

    PubMed Central

    Neumann, Jane; Fox, Peter T.; Turner, Robert; Lohmann, Gabriele

    2009-01-01

    We propose a new exploratory method for the discovery of partially directed functional networks from fMRI meta-analysis data. The method performs structure learning of Bayesian networks in search of directed probabilistic dependencies between brain regions. Learning is based on the co-activation of brain regions observed across several independent imaging experiments. In a series of simulations, we first demonstrate the reliability of the method. We then present the application of our approach in an extensive meta-analysis including several thousand activation coordinates from more than 500 imaging studies. Results show that our method is able to automatically infer Bayesian networks that capture both directed and undirected probabilistic dependencies between a number of brain regions, including regions that are frequently observed in motor-related and cognitive control tasks. PMID:19815079

  13. Direct reconstitution of plasma membrane lipids and proteins in nanotube-vesicle networks.

    PubMed

    Bauer, Brigitte; Davidson, Max; Orwar, Owe

    2006-10-24

    We demonstrate here that nanotube-vesicle networks can be constructed directly from plasma membranes of cultured cells. We used a combination of dithiothreitol (DTT) and formaldehyde to produce micron-sized plasma membrane vesicles that were subsequently shaped into networks using micromanipulation methods previously used on purely synthetic systems. Only a single cell is required to derive material sufficient to build a small network. This protocol covers the advantages of reconstitution in vesicles, such as full control over the solution environment, while keeping the proteins in their original surroundings with the proper orientation. Furthermore, control of membrane protein and lipid content in the networks is achievable by employing different cell types, for example, by overexpression of a desired protein or the use of specialized cell-types as sources for rare proteins and lipids. In general, the method provides simple accessibility for functional studies of plasma membrane constituents. Specifically, it provides a direct means to functionalize nanotube-vesicle networks with desired proteins and lipids for studies of transport activity both across membranes (protein-mediated) and across nanotubes (diffusion), and substrate conversion down to the single-molecule limit. Nanotube-vesicle networks can adopt different geometries and topologies and undergo shape changes at will, providing a flexible system for changing the physical and chemical environment around, for example, a membrane protein. Furthermore, the method offers unique possibilities for extracting membrane and protein material for nanotechnological sensor and analytical devices based on lipid membrane networks. PMID:17042549

  14. CINCINNATA in Antirrhinum majus directly modulates genes involved in cytokinin and auxin signaling.

    PubMed

    Das Gupta, Mainak; Aggarwal, Pooja; Nath, Utpal

    2014-12-01

    Mutations in the CINCINNATA (CIN) gene in Antirrhinum majus and its orthologs in Arabidopsis result in crinkly leaves as a result of excess growth towards the leaf margin. CIN homologs code for TCP (TEOSINTE-BRANCHED 1, CYCLOIDEA, PROLIFERATING CELL FACTOR 1 AND 2) transcription factors and are expressed in a broad zone in a growing leaf distal to the proliferation zone where they accelerate cell maturation. Although a few TCP targets are known, the functional basis of CIN-mediated leaf morphogenesis remains unclear. We compared the global transcription profiles of wild-type and the cin mutant of A. majus to identify the targets of CIN. We cloned and studied the direct targets using RNA in situ hybridization, DNA-protein interaction, chromatin immunoprecipitation and reporter gene analysis. Many of the genes involved in the auxin and cytokinin signaling pathways showed altered expression in the cin mutant. Further, we showed that CIN binds to genomic regions and directly promotes the transcription of a cytokinin receptor homolog HISTIDINE KINASE 4 (AmHK4) and an IAA3/SHY2 (INDOLE-3-ACETIC ACID INDUCIBLE 3/SHORT HYPOCOTYL 2) homolog in A. majus. Our results suggest that CIN limits excess cell proliferation and maintains the flatness of the leaf surface by directly modulating the hormone pathways involved in patterning cell proliferation and differentiation during leaf growth. PMID:25109749

  15. Direct acceleration of electrons by a circular polarized laser pulse with phase modulation

    SciTech Connect

    Zhu, Lun-Wu; Department of Science, Zhejiang University of Science and Technology, Hangzhou 310023 ; Sheng, Zheng-Mao; Yu, M. Y.

    2013-11-15

    Electron acceleration by transversely echelon phase-modulated (EPM) circularly polarized (CP) intense laser pulse is investigated. Solution of the relativistic electron equations of motion shows that the CP EPM light wave structure can disrupt the harmonic response of a trapped electron not only in the transverse direction but also in the direction of laser propagation. In each laser cycle, there can be a net gain in the electron's transverse momentum, which is promptly converted into the forward direction by the Lorentz force. As a result, the electron can be trapped and accelerated in the favorable phase of the laser for a rather long time. Its momentum gain then accumulates and can eventually reach high levels. It is also found that with the CP EPM laser, the net acceleration of the electron is not sensitive to its initial position and velocity relative to the phase of the laser fields, so that such a laser can also be useful for accelerating thermal electron bunches to high energies.

  16. Modulation of human auditory spatial scene analysis by transcranial direct current stimulation.

    PubMed

    Lewald, Jörg

    2016-04-01

    Localizing and selectively attending to the source of a sound of interest in a complex auditory environment is an important capacity of the human auditory system. The underlying neural mechanisms have, however, still not been clarified in detail. This issue was addressed by using bilateral bipolar-balanced transcranial direct current stimulation (tDCS) in combination with a task demanding free-field sound localization in the presence of multiple sound sources, thus providing a realistic simulation of the so-called "cocktail-party" situation. With left-anode/right-cathode, but not with right-anode/left-cathode, montage of bilateral electrodes, tDCS over superior temporal gyrus, including planum temporale and auditory cortices, was found to improve the accuracy of target localization in left hemispace. No effects were found for tDCS over inferior parietal lobule or with off-target active stimulation over somatosensory-motor cortex that was used to control for non-specific effects. Also, the absolute error in localization remained unaffected by tDCS, thus suggesting that general response precision was not modulated by brain polarization. This finding can be explained in the framework of a model assuming that brain polarization modulated the suppression of irrelevant sound sources, thus resulting in more effective spatial separation of the target from the interfering sound in the complex auditory scene. PMID:26825012

  17. Transcranial direct current stimulation of the prefrontal cortex: a means to modulate fear memories.

    PubMed

    Mungee, Aditya; Kazzer, Philipp; Feeser, Melanie; Nitsche, Michael A; Schiller, Daniela; Bajbouj, Malek

    2014-05-01

    Targeting memory processes by noninvasive interventions is a potential gateway to modulate fear memories as shown by animal and human studies in recent years. Modulation of fear memories by noninvasive brain stimulation techniques might be an attractive approach, which, however, has not been examined so far. We investigated the effect of transcranial direct current stimulation (tDCS) applied to the right dorsolateral prefrontal cortex and left supraorbital region on fear memories in humans. Seventy-four young, healthy individuals were assigned randomly to two groups, which underwent fear conditioning with mild electric stimuli paired with a visual stimulus. Twenty-four hours later, both groups were shown a reminder of the conditioned fearful stimulus. Shortly thereafter, they received either tDCS (right prefrontal--anodal, left supraorbital--cathodal) for 20 min at 1 mA current intensity or sham stimulation. A day later, fear responses of both groups were compared by monitoring skin conductance. On day 3, during fear response assessment, the tDCS group had a significantly (P<0.05) higher mean skin conductance in comparison with the sham group. These results suggest that tDCS (right prefrontal--anodal, left supraorbital--cathodal) enhanced fear memories, possibly by influencing the prefrontal cortex-amygdala circuit underlying the memory for fear. PMID:24384505

  18. Directly modulated laser-based optical radio frequency self-interference cancellation system

    NASA Astrophysics Data System (ADS)

    Zhang, Shaojie; Xiao, Shilin; Zhang, Yunhao; Feng, Hanlin; Zhang, Lu; Zhou, Zhao

    2016-02-01

    We propose a microwave photonics system for radio frequency self-interference cancellation using optical techniques. With a simple structure, this system employs two low-cost directly modulated lasers and a balanced photodetector to subtract the strong self-interference signal from a corrupted received signal. For commonly used wireless applications, 40-dB cancellation within 900-MHz band and 33-dB cancellation within 2.4-GHz band are experimentally obtained, both over 400-MHz bandwidth. Moreover, for ultra-wideband cancellation, this system achieves more than 27-dB cancellation over 6-GHz bandwidth. The experimental results show good recovery of the weak signal of interest buried by strong self-interference after the cancellation.

  19. Technical evaluation of a USSC integrated/direct mount PV roofing module system at NREL

    NASA Astrophysics Data System (ADS)

    Strand, T.; Hansen, R.; Mrig, L.

    1996-01-01

    The results of a 16 month technical evaluation performed on a nominal 1 kWac utility-interconnect amorphous silicon PV system deployed at the National Renewable Energy Laboratory's PV outdoor test site are given here. The system employs 64 prototype United Solar Systems Corp. Integrated/Direct Mount PV Roofing Molecules mounted on simulated attic/roof structures. In this paper we show that the PV array fill factor has been relatively stable with respect to time and that the seasonal variations in performance can be largely attributed to seasonal variations in current. We also show that in determining the summer and winter ac power output, the summation of the manufacturer-supplied module peak powers at STC for a similarly located and configured a-Si PV array should be derated by factors of approximately of 0.83 and 0.78 for summer and winter operation, respectively.

  20. Emergence of complex computational structures from chaotic neural networks through reward-modulated Hebbian learning.

    PubMed

    Hoerzer, Gregor M; Legenstein, Robert; Maass, Wolfgang

    2014-03-01

    This paper addresses the question how generic microcircuits of neurons in different parts of the cortex can attain and maintain different computational specializations. We show that if stochastic variations in the dynamics of local microcircuits are correlated with signals related to functional improvements of the brain (e.g. in the control of behavior), the computational operation of these microcircuits can become optimized for specific tasks such as the generation of specific periodic signals and task-dependent routing of information. Furthermore, we show that working memory can autonomously emerge through reward-modulated Hebbian learning, if needed for specific tasks. Altogether, our results suggest that reward-modulated synaptic plasticity can not only optimize the network parameters for specific computational tasks, but also initiate a functional rewiring that re-programs microcircuits, thereby generating diverse computational functions in different generic cortical microcircuits. On a more general level, this work provides a new perspective for a standard model for computations in generic cortical microcircuits (liquid computing model). It shows that the arguably most problematic assumption of this model, the postulate of a teacher that trains neural readouts through supervised learning, can be eliminated. We show that generic networks of neurons can learn numerous biologically relevant computations through trial and error. PMID:23146969

  1. Direct patterning of carbon nanotube network devices by selective vacuum filtration

    NASA Astrophysics Data System (ADS)

    Lim, Chaehyun; Min, Dong-Hun; Lee, Seung-Beck

    2007-12-01

    We report on a method which allows direct patterning of density controlled carbon nanotube network (NTN) devices during network formation. By lithographically patterning photoresist on the filter membrane, the nanotubes in suspension were guided to the exposed pattern areas of the filter surface during vacuum filtration allowing in situ device formation. The NTNs were transferred to an elastomer substrate by directly curing polydimethylsiloxane on its surface. We compared electrical characteristics of NTN patterns fabricated simultaneously using this method and found that the different NTNs with equal nanotube density showed reproducible characteristics.

  2. Positive cloud-to-ground lightning detection by a direction-finder network

    NASA Technical Reports Server (NTRS)

    Macgorman, Donald R.; Taylor, William L.

    1989-01-01

    Consideration is given to the ability of an automatic direction-finder network to identify cloud-to-ground flashes that effectively lower positive charge to the ground (+CG flashes). Records from an extremely low frequency system are examined to determine whether or not 340 +CG flashes detected by the network have coincident waveforms characteristic of +CG flashes. It is found that false detection in the system is negligible for +CG flashes with range-normalized amplitudes of at least 50 direction-finder units. Also, it is shown that no more than about 15 percent of the +CG flashes detected by the system at smaller amplitudes are false detections.

  3. Evolution of egoism on semi-directed and undirected Barabási-Albert networks

    NASA Astrophysics Data System (ADS)

    Lima, F. W. S.

    2015-05-01

    Through Monte Carlo simulations, we study the evolution of the four strategies: Ethnocentric, altruistic, egoistic and cosmopolitan in one community of individuals. Interactions and reproduction among computational agents are simulated on undirected and semi-directed Barabási-Albert (BA) networks. We study the Hammond-Axelrod (HA) model on undirected and semi-directed BA networks for the asexual reproduction case. With a small modification in the traditional HA model, our simulations showed that egoism wins, differently from other results found in the literature where ethnocentric strategy is common. Here, mechanisms such as reciprocity are absent.

  4. Subthalamic stimulation modulates cortical motor network activity and synchronization in Parkinson’s disease

    PubMed Central

    Klotz, Rosa; Govindan, Rathinaswamy B.; Scholten, Marlieke; Naros, Georgios; Ramos-Murguialday, Ander; Bunjes, Friedemann; Meisner, Christoph; Plewnia, Christian; Krüger, Rejko

    2015-01-01

    Dynamic modulations of large-scale network activity and synchronization are inherent to a broad spectrum of cognitive processes and are disturbed in neuropsychiatric conditions including Parkinson’s disease. Here, we set out to address the motor network activity and synchronization in Parkinson’s disease and its modulation with subthalamic stimulation. To this end, 20 patients with idiopathic Parkinson’s disease with subthalamic nucleus stimulation were analysed on externally cued right hand finger movements with 1.5-s interstimulus interval. Simultaneous recordings were obtained from electromyography on antagonistic muscles (right flexor digitorum and extensor digitorum) together with 64-channel electroencephalography. Time-frequency event-related spectral perturbations were assessed to determine cortical and muscular activity. Next, cross-spectra in the time-frequency domain were analysed to explore the cortico-cortical synchronization. The time-frequency modulations enabled us to select a time-frequency range relevant for motor processing. On these time-frequency windows, we developed an extension of the phase synchronization index to quantify the global cortico-cortical synchronization and to obtain topographic differentiations of distinct electrode sites with respect to their contributions to the global phase synchronization index. The spectral measures were used to predict clinical and reaction time outcome using regression analysis. We found that movement-related desynchronization of cortical activity in the upper alpha and beta range was significantly facilitated with ‘stimulation on’ compared to ‘stimulation off’ on electrodes over the bilateral parietal, sensorimotor, premotor, supplementary-motor, and prefrontal areas, including the bilateral inferior prefrontal areas. These spectral modulations enabled us to predict both clinical and reaction time improvement from subthalamic stimulation. With ‘stimulation on’, interhemispheric cortico-cortical coherence in the beta band was significantly attenuated over the bilateral sensorimotor areas. Similarly, the global cortico-cortical phase synchronization was attenuated, and the topographic differentiation revealed stronger desynchronization over the (ipsilateral) right-hemispheric prefrontal, premotor and sensorimotor areas compared to ‘stimulation off’. We further demonstrated that the cortico-cortical phase synchronization was largely dominated by genuine neuronal coupling. The clinical improvement with ‘stimulation on’ compared to ‘stimulation off’ could be predicted from this cortical decoupling with multiple regressions, and the reduction of synchronization over the right prefrontal area showed a linear univariate correlation with clinical improvement. Our study demonstrates wide-spread activity and synchronization modulations of the cortical motor network, and highlights subthalamic stimulation as a network-modulating therapy. Accordingly, subthalamic stimulation may release bilateral cortical computational resources by facilitating movement-related desynchronization. Moreover, the subthalamic nucleus is critical to balance inhibitory and facilitatory cortical players within the motor program. PMID:25558877

  5. Estradiol rapidly modulates spinogenesis in hippocampal dentate gyrus: Involvement of kinase networks.

    PubMed

    Hojo, Yasushi; Munetomo, Arisa; Mukai, Hideo; Ikeda, Muneki; Sato, Rei; Hatanaka, Yusuke; Murakami, Gen; Komatsuzaki, Yoshimasa; Kimoto, Tetsuya; Kawato, Suguru

    2015-08-01

    This article is part of a Special Issue "Estradiol and cognition". Estradiol (E2) is locally synthesized within the hippocampus and the gonads. Rapid modulation of hippocampal synaptic plasticity by E2 is essential for synaptic regulation. The molecular mechanisms of modulation through the synaptic estrogen receptor (ER) and its downstream signaling, however, are largely unknown in the dentate gyrus (DG). We investigated the E2-induced modulation of dendritic spines in male adult rat hippocampal slices by imaging Lucifer Yellow-injected DG granule cells. Treatments with 1 nM E2 increased the density of spines by approximately 1.4-fold within 2h. Spine head diameter analysis showed that the density of middle-head spines (0.4-0.5 μm) was significantly increased. The E2-induced spine density increase was suppressed by blocking Erk MAPK, PKA, PKC and LIMK. These suppressive effects by kinase inhibitors are not non-specific ones because the GSK-3β antagonist did not inhibit E2-induced spine increase. The ER antagonist ICI 182,780 also blocked the E2-induced spine increase. Taken together, these results suggest that E2 rapidly increases the density of spines through kinase networks that are driven by synaptic ER. PMID:26122288

  6. Bandwidth provisioning in infrastructure-based wireless networks employing directional antennas

    SciTech Connect

    Hasiviswanthan, Shiva; Zhao, Bo; Vasudevan, Sudarshan; Yrgaonkar, Bhuvan

    2009-01-01

    Motivated by the widespread proliferation of wireless networks employing directional antennas, we study the problem of provisioning bandwidth in such networks. Given a set of subscribers and one or more access points possessing directional antennas, we formalize the problem of orienting these antennas in two fundamental settings: (1) subscriber-centric, where the objective is to fairly allocate bandwidth among the subscribers and (2) provider-centric, where the objective is to maximize the revenue generated by satisfying the bandwidth requirements of subscribers. For both the problems, we first design algorithms for a network with only one access point working under the assumption that the number of antennas does not exceed the number of noninterfering channels. Using the well-regarded lexicographic max-min fair allocation as the objective for a subscriber-centric network, we present an optimum dynamic programming algorithm. For a provider-centric network, the allocation problem turns out to be NP-hard. We present a greedy heuristic based algorithm that guarantees almost half of the optimum revenue. We later enhance both these algorithms to operate in more general networks with multiple access points and no restrictions on the relative numbers of antennas and channels. A simulation-based evaluation using OPNET demonstrates the efficacy of our approaches and provides us further in insights into these problems.

  7. Random and directed walk-based top-(k) queries in wireless sensor networks.

    PubMed

    Fu, Jun-Song; Liu, Yun

    2015-01-01

    In wireless sensor networks, filter-based top-  query approaches are the state-of-the-art solutions and have been extensively researched in the literature, however, they are very sensitive to the network parameters, including the size of the network, dynamics of the sensors' readings and declines in the overall range of all the readings. In this work, a random walk-based top-  query approach called RWTQ and a directed walk-based top-  query approach called DWTQ are proposed. At the beginning of a top-  query, one or several tokens are sent to the specific node(s) in the network by the base station. Then, each token walks in the network independently to record and process the readings in a random or directed way. A strategy of choosing the "right" way in DWTQ is carefully designed for the token(s) to arrive at the high-value regions as soon as possible. When designing the walking strategy for DWTQ, the spatial correlations of the readings are also considered. Theoretical analysis and simulation results indicate that RWTQ and DWTQ both are very robust against these parameters discussed previously. In addition, DWTQ outperforms TAG, FILA and EXTOK in transmission cost, energy consumption and network lifetime. PMID:26016914

  8. Random and Directed Walk-Based Top-k Queries in Wireless Sensor Networks

    PubMed Central

    Fu, Jun-Song; Liu, Yun

    2015-01-01

    In wireless sensor networks, filter-based top-k query approaches are the state-of-the-art solutions and have been extensively researched in the literature, however, they are very sensitive to the network parameters, including the size of the network, dynamics of the sensors’ readings and declines in the overall range of all the readings. In this work, a random walk-based top-k query approach called RWTQ and a directed walk-based top-k query approach called DWTQ are proposed. At the beginning of a top-k query, one or several tokens are sent to the specific node(s) in the network by the base station. Then, each token walks in the network independently to record and process the readings in a random or directed way. A strategy of choosing the “right” way in DWTQ is carefully designed for the token(s) to arrive at the high-value regions as soon as possible. When designing the walking strategy for DWTQ, the spatial correlations of the readings are also considered. Theoretical analysis and simulation results indicate that RWTQ and DWTQ both are very robust against these parameters discussed previously. In addition, DWTQ outperforms TAG, FILA and EXTOK in transmission cost, energy consumption and network lifetime. PMID:26016914

  9. Susceptible-infected-susceptible model on quenched directed scale-free networks

    NASA Astrophysics Data System (ADS)

    Kwon, Sungchul; Kim, Jin Min

    2014-08-01

    The critical behavior of the susceptible-infected-susceptible model is investigated on quenched directed scale-free networks with the in-degree (k) distribution {{P}_{\\text{in}}}\\left(k\\right)\\sim {{k}^{-{{\\gamma}_{\\text{in}}}}} and the out-degree (ℓ) distribution, {{P}_{\\text{out}}}\\left(\\ell \\right)\\sim {{\\ell}^{-{{\\gamma}_{\\text{out}}}}} . The correlation of each node is controlled. In the model, an infected individual becomes healthy with unit rate and infects all healthy neighbors with rate λ. On quenched undirected networks with degree distribution P(q) ˜ q-γ, the system is always in an endemic state for any γ, so the critical threshold λc is always zero. Heterogeneous mean-field theory fails to predict the behavior of the quenched undirected networks. However, for quenched directed networks, we show via Monte Carlo simulations that the critical behavior of the directed quenched networks is well described by heterogeneous mean-field theory.

  10. Learning modulation of odor representations: new findings from Arc-indexed networks

    PubMed Central

    Yuan, Qi; Harley, Carolyn W.

    2014-01-01

    We first review our understanding of odor representations in rodent olfactory bulb (OB) and anterior piriform cortex (APC). We then consider learning-induced representation changes. Finally we describe the perspective on network representations gained from examining Arc-indexed odor networks of awake rats. Arc-indexed networks are sparse and distributed, consistent with current views. However Arc provides representations of repeated odors. Arc-indexed repeated odor representations are quite variable. Sparse representations are assumed to be compact and reliable memory codes. Arc suggests this is not necessarily the case. The variability seen is consistent with electrophysiology in awake animals and may reflect top-down cortical modulation of context. Arc-indexing shows that distinct odors share larger than predicted neuron pools. These may be low-threshold neuronal subsets. Learning’s effect on Arc-indexed representations is to increase the stable or overlapping component of rewarded odor representations. This component can decrease for similar odors when their discrimination is rewarded. The learning effects seen are supported by electrophysiology, but mechanisms remain to be elucidated. PMID:25565958

  11. Disruption of structural covariance networks for language in autism is modulated by verbal ability.

    PubMed

    Sharda, Megha; Khundrakpam, Budhachandra S; Evans, Alan C; Singh, Nandini C

    2016-03-01

    The presence of widespread speech and language deficits is a core feature of autism spectrum disorders (ASD). These impairments have often been attributed to altered connections between brain regions. Recent developments in anatomical correlation-based approaches to map structural covariance offer an effective way of studying such connections in vivo. In this study, we employed such a structural covariance network (SCN)-based approach to investigate the integrity of anatomical networks in fronto-temporal brain regions of twenty children with ASD compared to an age and gender-matched control group of twenty-two children. Our findings reflected large-scale disruption of inter and intrahemispheric covariance in left frontal SCNs in the ASD group compared to controls, but no differences in right fronto-temporal SCNs. Interhemispheric covariance in left-seeded networks was further found to be modulated by verbal ability of the participants irrespective of autism diagnosis, suggesting that language function might be related to the strength of interhemispheric structural covariance between frontal regions. Additionally, regional cortical thickening was observed in right frontal and left posterior regions, which was predicted by decreasing symptom severity and increasing verbal ability in ASD. These findings unify reports of regional differences in cortical morphology in ASD. They also suggest that reduced left hemisphere asymmetry and increased frontal growth may not only reflect neurodevelopmental aberrations but also compensatory mechanisms. PMID:25445842

  12. All-optical virtual private network system in OFDM based long-reach PON using RSOA re-modulation technique

    NASA Astrophysics Data System (ADS)

    Kim, Chang-Hun; Jung, Sang-Min; Kang, Su-Min; Han, Sang-Kook

    2015-01-01

    We propose an all-optical virtual private network (VPN) system in an orthogonal frequency division multiplexing (OFDM) based long reach PON (LR-PON). In the optical access network field, technologies based on fundamental upstream (U/S) and downstream (D/S) have been actively researched to accommodate explosion of data capacity. However, data transmission among the end users which is arisen from cloud computing, file-sharing and interactive game takes a large weight inside of internet traffic. Moreover, this traffic is predicted to increase more if Internet of Things (IoT) services are activated. In a conventional PON, VPN data is transmitted through ONU-OLT-ONU via U/S and D/S carriers. It leads to waste of bandwidth and energy due to O-E-O conversion in the OLT and round-trip propagation between OLT and remote node (RN). Also, it causes inevitable load to the OLT for electrical buffer, scheduling and routing. The network inefficiency becomes more critical in a LR-PON which has been researched as an effort to reduce CAPEX and OPEX through metro-access consolidation. In the proposed system, the VPN data is separated from conventional U/S and re-modulated on the D/S carrier by using RSOA in the ONUs to avoid bandwidth consumption of U/S and D/S unlike in previously reported system. Moreover, the transmitted VPN data is re-directed to the ONUs by wavelength selective reflector device in the RN without passing through the OLT. Experimental demonstration for the VPN communication system in an OFDM based LR-PON has been verified.

  13. Performance improvement of 10 Gb/s direct modulation OFDM by optical injection using monolithically integrated Discrete Mode lasers.

    PubMed

    Browning, C; Shi, K; Latkowski, S; Anandarajah, P M; Smyth, F; Cardiff, B; Phelan, R; Barry, L P

    2011-12-12

    Performance improvement of a directly modulated 10 Gb/s OFDM system by optical injection of monolithically integrated lasers is shown experimentally over differing fibre lengths. The modulation and optical injection is performed using monolithically integrated Discrete Mode lasers. It is shown that optical injection with this device reduces third order inter-modulation distortion by up to 10dB and this results in an improvement in system performance from above a forward error correction BER threshold of 1 × 10(-3) to significantly below it. PMID:22274032

  14. Fast-response IR spatial light modulators with a polymer network liquid crystal

    NASA Astrophysics Data System (ADS)

    Peng, Fenglin; Chen, Haiwei; Tripathi, Suvagata; Twieg, Robert J.; Wu, Shin-Tson

    2015-03-01

    Liquid crystals (LC) have widespread applications for amplitude modulation (e.g. flat panel displays) and phase modulation (e.g. beam steering). For phase modulation, a 2π phase modulo is required. To extend the electro-optic application into infrared region (MWIR and LWIR), several key technical challenges have to be overcome: 1. low absorption loss, 2. high birefringence, 3. low operation voltage, and 4. fast response time. After three decades of extensive development, an increasing number of IR devices adopting LC technology have been demonstrated, such as liquid crystal waveguide, laser beam steering at 1.55μm and 10.6 μm, spatial light modulator in the MWIR (3~5μm) band, dynamic scene projectors for infrared seekers in the LWIR (8~12μm) band. However, several fundamental molecular vibration bands and overtones exist in the MWIR and LWIR regions, which contribute to high absorption coefficient and hinder its widespread application. Therefore, the inherent absorption loss becomes a major concern for IR devices. To suppress IR absorption, several approaches have been investigated: 1) Employing thin cell gap by choosing a high birefringence liquid crystal mixture; 2) Shifting the absorption bands outside the spectral region of interest by deuteration, fluorination and chlorination; 3) Reducing the overlap vibration bands by using shorter alkyl chain compounds. In this paper, we report some chlorinated LC compounds and mixtures with a low absorption loss in the near infrared and MWIR regions. To achieve fast response time, we have demonstrated a polymer network liquid crystal with 2π phase change at MWIR and response time less than 5 ms.

  15. Direct current stimulation of the left temporoparietal junction modulates dynamic humor appreciation.

    PubMed

    Slaby, Isabella; Holmes, Amanda; Moran, Joseph M; Eddy, Marianna D; Mahoney, Caroline R; Taylor, Holly A; Brunyé, Tad T

    2015-11-11

    The aim of this study was to evaluate the influence of transcranial direct current stimulation targeting the left temporoparietal junction (TPJ) on humor appreciation during a dynamic video rating task. In a within-participants design, we targeted the left TPJ with anodal, cathodal, or no transcranial direct current stimulation, centered at electrode site C3 using a 4×1 targeted stimulation montage. During stimulation, participants dynamically rated a series of six stand-up comedy videos for perceived humor. We measured event-related (time-locked to crowd laughter) modulation of humor ratings as a function of stimulation condition. Results showed decreases in rated humor during anodal (vs. cathodal or none) stimulation; this pattern was evident for the majority of videos and was only partially predicted by individual differences in humor style. We discuss the possibility that upregulation of neural circuits involved in the theory of mind and empathizing with others may reduce appreciation of aggressive humor. In conclusion, the present data show that neuromodulation of the TPJ can alter the mental processes underlying humor appreciation, suggesting critical involvement of this cortical region in detecting, comprehending, and appreciating humor. PMID:26351965

  16. DIRECT MODULATION OF THE PROTEIN KINASE A CATALYTIC SUBUNIT α BY GROWTH FACTOR RECEPTOR TYROSINE KINASES

    PubMed Central

    Caldwell, George B.; Howe, Alan K.; Nickl, Christian K.; Dostmann, Wolfgang R.; Ballif, Bryan A.; Deming, Paula B.

    2011-01-01

    The cyclic-AMP-dependent protein kinase A (PKA) regulates processes such as cell proliferation and migration following activation of growth factor receptor tyrosine kinases (RTKs), yet the signaling mechanisms that link PKA with growth factor receptors remain largely undefined. Here we report that RTKs can directly modulate the function of the catalytic subunit of PKA (PKA-C) through post-translational modification. In vitro kinase assays revealed that both the epidermal growth factor and platelet derived growth factor receptors (EGFR and PDGFR, respectively) tyrosine phosphorylate PKA-C. Mass spectrometry identified tyrosine 330 (Y330) as a receptor-mediated phosphorylation site and mutation of Y330 to phenylalanine (Y330F) all but abolished the RTK-mediated phosphorylation of PKA-C in vitro. Y330 resides within a conserved region at the C-terminal tail of PKA-C that allosterically regulates enzymatic activity. Therefore, the effect of phosphorylation at Y330 on the activity of PKA-C was investigated. The Km for a peptide substrate was markedly decreased when PKA-C subunits were tyrosine phosphorylated by the receptors as compared to un-phosphorylated controls. Importantly, tyrosine-phosphorylated PKA-C subunits were detected in cells stimulated with EGF, PDGF and FGF2 and in fibroblasts undergoing PDGF-mediated chemotaxis. These results demonstrate a direct, functional interaction between RTKs and PKA-C and identify tyrosine phosphorylation as a novel mechansim for regulating PKA activity. PMID:21866565

  17. Opinion formation driven by PageRank node influence on directed networks

    NASA Astrophysics Data System (ADS)

    Eom, Young-Ho; Shepelyansky, Dima L.

    2015-10-01

    We study a two states opinion formation model driven by PageRank node influence and report an extensive numerical study on how PageRank affects collective opinion formations in large-scale empirical directed networks. In our model the opinion of a node can be updated by the sum of its neighbor nodes' opinions weighted by the node influence of the neighbor nodes at each step. We consider PageRank probability and its sublinear power as node influence measures and investigate evolution of opinion under various conditions. First, we observe that all networks reach steady state opinion after a certain relaxation time. This time scale is decreasing with the heterogeneity of node influence in the networks. Second, we find that our model shows consensus and non-consensus behavior in steady state depending on types of networks: Web graph, citation network of physics articles, and LiveJournal social network show non-consensus behavior while Wikipedia article network shows consensus behavior. Third, we find that a more heterogeneous influence distribution leads to a more uniform opinion state in the cases of Web graph, Wikipedia, and Livejournal. However, the opposite behavior is observed in the citation network. Finally we identify that a small number of influential nodes can impose their own opinion on significant fraction of other nodes in all considered networks. Our study shows that the effects of heterogeneity of node influence on opinion formation can be significant and suggests further investigations on the interplay between node influence and collective opinion in networks.

  18. Analysis of weblike network structures of directed graphs for chemical reactions in methane plasmas

    NASA Astrophysics Data System (ADS)

    Sakai, Osamu; Nobuto, Kyosuke; Miyagi, Shigeyuki; Tachibana, Kunihide

    2015-10-01

    Chemical reactions of molecular gases like methane are so complicated that a chart of decomposed and/or synthesized species originating from molecules in plasma resembles a weblike network in which we write down species and reactions among them. Here we consider properties of the network structures of chemical reactions in methane plasmas. In the network, atoms/molecules/radical species are assumed to form nodes and chemical reactions correspond to directed edges in the terminology of graph theory. Investigation of the centrality index reveals importance of CH3 in the global chemical reaction, and difference of an index for each radical species between cases with and without electrons clarifies that the electrons are at an influential position to tighten the network structure.

  19. Evolution of ethnocentrism on undirected and directed Barabási-Albert networks

    NASA Astrophysics Data System (ADS)

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

    2009-12-01

    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.

  20. Identifying Influential Nodes in Large-Scale Directed Networks: The Role of Clustering

    PubMed Central

    Chen, Duan-Bing; Gao, Hui; Lü, Linyuan; Zhou, Tao

    2013-01-01

    Identifying influential nodes in very large-scale directed networks is a big challenge relevant to disparate applications, such as accelerating information propagation, controlling rumors and diseases, designing search engines, and understanding hierarchical organization of social and biological networks. Known methods range from node centralities, such as degree, closeness and betweenness, to diffusion-based processes, like PageRank and LeaderRank. Some of these methods already take into account the influences of a node’s neighbors but do not directly make use of the interactions among it’s neighbors. Local clustering is known to have negative impacts on the information spreading. We further show empirically that it also plays a negative role in generating local connections. Inspired by these facts, we propose a local ranking algorithm named ClusterRank, which takes into account not only the number of neighbors and the neighbors’ influences, but also the clustering coefficient. Subject to the susceptible-infected-recovered (SIR) spreading model with constant infectivity, experimental results on two directed networks, a social network extracted from delicious.com and a large-scale short-message communication network, demonstrate that the ClusterRank outperforms some benchmark algorithms such as PageRank and LeaderRank. Furthermore, ClusterRank can also be applied to undirected networks where the superiority of ClusterRank is significant compared with degree centrality and k-core decomposition. In addition, ClusterRank, only making use of local information, is much more efficient than global methods: It takes only 191 seconds for a network with about nodes, more than 15 times faster than PageRank. PMID:24204833

  1. Identifying influential nodes in large-scale directed networks: the role of clustering.

    PubMed

    Chen, Duan-Bing; Gao, Hui; Lü, Linyuan; Zhou, Tao

    2013-01-01

    Identifying influential nodes in very large-scale directed networks is a big challenge relevant to disparate applications, such as accelerating information propagation, controlling rumors and diseases, designing search engines, and understanding hierarchical organization of social and biological networks. Known methods range from node centralities, such as degree, closeness and betweenness, to diffusion-based processes, like PageRank and LeaderRank. Some of these methods already take into account the influences of a node's neighbors but do not directly make use of the interactions among it's neighbors. Local clustering is known to have negative impacts on the information spreading. We further show empirically that it also plays a negative role in generating local connections. Inspired by these facts, we propose a local ranking algorithm named ClusterRank, which takes into account not only the number of neighbors and the neighbors' influences, but also the clustering coefficient. Subject to the susceptible-infected-recovered (SIR) spreading model with constant infectivity, experimental results on two directed networks, a social network extracted from delicious.com and a large-scale short-message communication network, demonstrate that the ClusterRank outperforms some benchmark algorithms such as PageRank and LeaderRank. Furthermore, ClusterRank can also be applied to undirected networks where the superiority of ClusterRank is significant compared with degree centrality and k-core decomposition. In addition, ClusterRank, only making use of local information, is much more efficient than global methods: It takes only 191 seconds for a network with about [Formula: see text] nodes, more than 15 times faster than PageRank. PMID:24204833

  2. Controllability analysis of the directed human protein interaction network identifies disease genes and drug targets.

    PubMed

    Vinayagam, Arunachalam; Gibson, Travis E; Lee, Ho-Joon; Yilmazel, Bahar; Roesel, Charles; Hu, Yanhui; Kwon, Young; Sharma, Amitabh; Liu, Yang-Yu; Perrimon, Norbert; Barabási, Albert-László

    2016-05-01

    The protein-protein interaction (PPI) network is crucial for cellular information processing and decision-making. With suitable inputs, PPI networks drive the cells to diverse functional outcomes such as cell proliferation or cell death. Here, we characterize the structural controllability of a large directed human PPI network comprising 6,339 proteins and 34,813 interactions. This network allows us to classify proteins as "indispensable," "neutral," or "dispensable," which correlates to increasing, no effect, or decreasing the number of driver nodes in the network upon removal of that protein. We find that 21% of the proteins in the PPI network are indispensable. Interestingly, these indispensable proteins are the primary targets of disease-causing mutations, human viruses, and drugs, suggesting that altering a network's control property is critical for the transition between healthy and disease states. Furthermore, analyzing copy number alterations data from 1,547 cancer patients reveals that 56 genes that are frequently amplified or deleted in nine different cancers are indispensable. Among the 56 genes, 46 of them have not been previously associated with cancer. This suggests that controllability analysis is very useful in identifying novel disease genes and potential drug targets. PMID:27091990

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

    NASA Astrophysics Data System (ADS)

    Kazantzidis, Matheos

    2006-05-01

    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.

  4. Global epidemic invasion thresholds in directed cattle subpopulation networks having source, sink, and transit nodes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Through the characterization of a metapopulation cattle disease model on a directed network having source, transit, and sink nodes, we derive two global epidemic invasion thresholds. The first threshold defines the conditions necessary for an epidemic to successfully spread at the global scale. The ...

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

    SciTech Connect

    Struckmeyer, R.

    1997-03-01

    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.

  6. NRC TLD Direct Radiation Monitoring Network progress report, October--December 1994. Volume 14, No. 4

    SciTech Connect

    Struckmeyer, R.

    1995-03-01

    This report presents the results of the NRC Direct Radiation Monitoring Network for the fourth quarter of 1994. It provides the ambient radiation levels measured in the vicinity of 75 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.

  7. Direct frequency modulation of vapor phase transported distributed feedback semiconductor lasers

    SciTech Connect

    Vodhanel, R.S.; Cheung, N.K.; Koch, T.L.

    1986-04-14

    The frequency modulation (FM) due to injection current modulation of vapor phase transported distributed feedback (VPT DFB) semiconductor lasers is measured as a function of modulation frequency from 10 kHz to 1 GHz. A large frequency modulation response of 350 MHz/mA is obtained for the modulation frequency range of 10 to 1000 MHz. Demodulation of optical frequency shift keying (FSK) at 560 Mb/s is demonstrated, indicating that frequency modulation due to thermal modulation does not pose a significant limitation at this bit rate or higher. The large FM response together with modulation bandwidths up to 8 GHz makes the VPT DFB laser an attractive source for high bit rate optical FSK transmission.

  8. Non-coplanar beam direction optimization for intensity-modulated radiotherapy.

    PubMed

    Meedt, G; Alber, M; Nüsslin, F

    2003-09-21

    An algorithm for the optimization of the direction of intensity-modulated beams is presented. Although the global optimum dose distribution cannot be predicted, usually a large number of equivalent beam configurations exists. This degeneracy facilitates beam direction optimization (BDO) through a number of possible approximations and because the target set of good beam configurations is very large. Usually, the target volume is accessible through a finite number of paths of little resistance, which are defined by the properties of the objective function and the global optimum dose distribution. Since these paths can be occupied by a finite number of beams, it is reasonable to assume that a minimum number of beams for a configuration that is degenerate to the global optimum exists. Efficiency of the BDO will be characterized by detecting this degeneracy threshold. Beam configurations are altered by adding and deleting beams. A fast exhaustive (up to 3500 non-coplanar orientations) search finds beam directions that improve a configuration. Redundant beams of a configuration can be identified by a fast criterion based on second-order derivative information of the objective function. This offers a fast means of iteratively substituting redundant beams from a configuration. Inferior stationary states can be evaded by adding more beams than the desired number to the current configuration, followed by the subsequent cancellation of superfluous beams. The significance of BDO is examined in a coplanar and a non-coplanar test case. The existence of a threshold number for the minimum configuration and its dependence on the complexity of the problem are shown. BDO outperforms manual configurations and equispaced coplanar beam arrangements in both example cases. PMID:14529207

  9. Simple Gifts: The Education of the Gifted, Talented, and Creative. Learning Modules for Directed Study Sequences.

    ERIC Educational Resources Information Center

    Wisconsin Univ., Madison. Univ. Extension.

    Twelve modules are presented for the education of gifted and talented students. Modules include a brief introduction; list of objectives; overview of the content; and suggestions for core, application, and quest (further study) activities. The modules focus on the following topics: definitions of giftedness; history of their educational treatment;…

  10. Not seeing or feeling is still believing: conscious and non-conscious pain modulation after direct and observational learning

    PubMed Central

    Egorova, Natalia; Park, Joel; Orr, Scott P.; Kirsch, Irving; Gollub, Randy L.; Kong, Jian

    2015-01-01

    Our experience with the world is shaped not only directly through personal exposure but also indirectly through observing others and learning from their experiences. Using a conditioning paradigm, we investigated how directly and observationally learned information can affect pain perception, both consciously and non-consciously. Differences between direct and observed cues were manifest in higher pain ratings and larger skin conductance responses to directly experienced cues. However, the pain modulation effects produced by conditioning were of comparable magnitude for direct and observational learning. These results suggest that social observation can induce positive and negative pain modulation. Importantly, the fact that cues learned by observation and activated non-consciously still produced a robust conditioning effect that withstood extinction highlights the role of indirect exposure in placebo and nocebo effects. PMID:26578164

  11. SU-C-16A-03: Direction Modulated Brachytherapy for HDR Treatment of Cervical Cancer

    SciTech Connect

    Han, D; Webster, M; Scanderbeg, D; Yashar, C; Choi, D; Song, B; Song, W; Devic, S; Ravi, A

    2014-06-15

    Purpose: To investigate a new Directional Modulated Brachytherapy (DMBT) intra-uterine tandem using various 192-Ir after-loaders. Methods: Dose distributions from the 192-Ir sources were modulated using a 6.3mm diameter tungsten shield (18.0g/cm3). The source moved along 6 longitudinal grooves, each 1.3mm in diameter, evenly spaced along periphery of the shield, The tungsten rod was enclosqed by 0.5mm thick Delrin (1.41g/cc). Monte Carlo N particle (MCNPX) was used to calculate dose distributions. 51million particles were calculated on 504 cores of a supercomputer. Fifteen different patients originally treated with a traditional tandem-and-ovoid applicator, with 5 fractions each, (15 patients X 5 fxs = 75 plans) were re-planned with the DMBT applicator combined with traditional ovoids, on an in-house developed HDR brachytherapy planning platform, which used intensity modulated planning capabilities using a constrained gradient optimization algorithm. For all plans the prescription dose was 6 Gy and they were normalized to match the clinical treated V100. Results: Generally, the DMBT plan quality was a remarkable improvement from conventional T and O plans because of the anisotropic dose distribution of DMBT. The largest difference was to the bladder which had a 0.59±0.87 Gy (8.5±28.7%) reduction in dose. This was because of the the horseshoe shape (U-shape) of the bladder. The dose reduction to rectum and sigmoid were 0.48±0.55 Gy (21.1±27.2%) and 0.10±0.38 Gy (40.6±214.9%), respectively. The D90 to the HRCTV was 6.55±0.96 Gy (conventional T and O) and 6.59±1.06 Gy (DMBT). Conclusion: For image guided adaptive brachytherapy, greater flexibility of radiation intensity is essential and DMBT can be the solution.

  12. Network-State Modulation of Power-Law Frequency-Scaling in Visual Cortical Neurons

    PubMed Central

    Béhuret, Sébastien; Baudot, Pierre; Yger, Pierre; Bal, Thierry; Destexhe, Alain; Frégnac, Yves

    2009-01-01

    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 Vm 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 Vm 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

  13. Nano-rheology of hydrogels using direct drive force modulation atomic force microscopy†

    PubMed Central

    Nalam, Prathima C.; Gosvami, Nitya N.; Caporizzo, Matthew A.; Composto, Russell J.

    2016-01-01

    We present a magnetic force-based direct drive modulation method to measure local nano-rheological properties of soft materials across a broad frequency range (10 Hz to 2 kHz) using colloid-attached atomic force microscope (AFM) probes in liquid. The direct drive method enables artefact-free measurements over several decades of excitation frequency, and avoids the need to evaluate medium-induced hydrodynamic drag effects. The method was applied to measure the local mechanical properties of polyacrylamide hydrogels. The frequency-dependent storage stiffness, loss stiffness, and loss tangent (tan δ) were quantified for hydrogels having high and low crosslinking densities by measuring the amplitude and the phase response of the cantilever while the colloid was in contact with the hydrogel. The frequency bandwidth was further expanded to lower effective frequencies (0.1 Hz to 10 Hz) by obtaining force–displacement (FD) curves. Slow FD measurements showed a recoverable but highly hysteretic response, with the contact mechanical behaviour dependent on the loading direction: approach curves showed Hertzian behaviour while retraction curves fit the JKR contact mechanics model well into the adhesive regime, after which multiple detachment instabilities occurred. Using small amplitude dynamic modulation to explore faster rates, the load dependence of the storage stiffness transitioned from Hertzian to a dynamic punch-type (constant contact area) model, indicating significant influence of material dissipation coupled with adhesion. Using the appropriate contact model across the full frequency range measured, the storage moduli were found to remain nearly constant until an increase began near ∼100 Hz. The softer gels' storage modulus increased from 7.9 ± 0.4 to 14.5 ± 2.1 kPa (∼85%), and the stiffer gels' storage modulus increased from 16.3 ± 1.1 to 31.7 ± 5.0 kPa (∼95%). This increase at high frequencies may be attributed to a contribution from solvent confinement in the hydrogel (poroelasticity). The storage moduli measured by both macro-rheometry and AFM FD curves were comparable to those measured using the modulation method at their overlapping frequencies (10–25 Hz). In all cases, care was taken to ensure the contact mechanics models were applied within the important limit of small relative deformations. This study thus highlights possible transitions in the probe–material contact mechanical behaviour for soft matter, especially when the applied strain rates and the material relaxation rates become comparable. In particular, at low frequencies, the modulus follows Hertzian contact mechanics, while at high frequencies adhesive contact is well represented by punch-like behaviour. More generally, use of the Hertz model on hydrogels at high loading rates, at high strains, or during the retraction portion of FD curves, leads to significant errors in the calculated moduli. PMID:26337502

  14. Nano-rheology of hydrogels using direct drive force modulation atomic force microscopy.

    PubMed

    Nalam, Prathima C; Gosvami, Nitya N; Caporizzo, Matthew A; Composto, Russell J; Carpick, Robert W

    2015-11-01

    We present a magnetic force-based direct drive modulation method to measure local nano-rheological properties of soft materials across a broad frequency range (10 Hz to 2 kHz) using colloid-attached atomic force microscope (AFM) probes in liquid. The direct drive method enables artefact-free measurements over several decades of excitation frequency, and avoids the need to evaluate medium-induced hydrodynamic drag effects. The method was applied to measure the local mechanical properties of polyacrylamide hydrogels. The frequency-dependent storage stiffness, loss stiffness, and loss tangent (tan δ) were quantified for hydrogels having high and low crosslinking densities by measuring the amplitude and the phase response of the cantilever while the colloid was in contact with the hydrogel. The frequency bandwidth was further expanded to lower effective frequencies (0.1 Hz to 10 Hz) by obtaining force-displacement (FD) curves. Slow FD measurements showed a recoverable but highly hysteretic response, with the contact mechanical behaviour dependent on the loading direction: approach curves showed Hertzian behaviour while retraction curves fit the JKR contact mechanics model well into the adhesive regime, after which multiple detachment instabilities occurred. Using small amplitude dynamic modulation to explore faster rates, the load dependence of the storage stiffness transitioned from Hertzian to a dynamic punch-type (constant contact area) model, indicating significant influence of material dissipation coupled with adhesion. Using the appropriate contact model across the full frequency range measured, the storage moduli were found to remain nearly constant until an increase began near ∼100 Hz. The softer gels' storage modulus increased from 7.9 ± 0.4 to 14.5 ± 2.1 kPa (∼85%), and the stiffer gels' storage modulus increased from 16.3 ± 1.1 to 31.7 ± 5.0 kPa (∼95%). This increase at high frequencies may be attributed to a contribution from solvent confinement in the hydrogel (poroelasticity). The storage moduli measured by both macro-rheometry and AFM FD curves were comparable to those measured using the modulation method at their overlapping frequencies (10-25 Hz). In all cases, care was taken to ensure the contact mechanics models were applied within the important limit of small relative deformations. This study thus highlights possible transitions in the probe-material contact mechanical behaviour for soft matter, especially when the applied strain rates and the material relaxation rates become comparable. In particular, at low frequencies, the modulus follows Hertzian contact mechanics, while at high frequencies adhesive contact is well represented by punch-like behaviour. More generally, use of the Hertz model on hydrogels at high loading rates, at high strains, or during the retraction portion of FD curves, leads to significant errors in the calculated moduli. PMID:26337502

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

    PubMed Central

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

    2011-01-01

    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. PMID:21695124

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

    PubMed

    Kumanyika, S

    2013-10-01

    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

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

    SciTech Connect

    Gubin, Vladimir P; Morshnev, Sergey K; Starostin, Nikolay I; Chamorovsky, Yury K; Sazonov, Aleksandr I; Przhiyalkovskii, Ya V; Boev, A I

    2011-09-30

    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.

  18. A network module-based method for identifying cancer prognostic signatures.

    PubMed

    Wu, Guanming; Stein, Lincoln

    2012-01-01

    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. PMID:23228031

  19. Astrocytes modulate neural network activity by Ca²+-dependent uptake of extracellular K+.

    PubMed

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

    2012-04-01

    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. PMID:22472648

  20. Flexible establishment of functional brain networks supports attentional modulation of unconscious cognition.

    PubMed

    Ulrich, Martin; Adams, Sarah C; Kiefer, Markus

    2014-11-01

    In classical theories of attention, unconscious automatic processes are thought to be independent of higher-level attentional influences. Here, we propose that unconscious processing depends on attentional enhancement of task-congruent processing pathways implemented by a dynamic modulation of the functional communication between brain regions. Using functional magnetic resonance imaging, we tested our model with a subliminally primed lexical decision task preceded by an induction task preparing either a semantic or a perceptual task set. Subliminal semantic priming was significantly greater after semantic compared to perceptual induction in ventral occipito-temporal (vOT) and inferior frontal cortex, brain areas known to be involved in semantic processing. The functional connectivity pattern of vOT varied depending on the induction task and successfully predicted the magnitude of behavioral and neural priming. Together, these findings support the proposal that dynamic establishment of functional networks by task sets is an important mechanism in the attentional control of unconscious processing. PMID:24954512