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Sample records for directed network modules

  1. 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.

  2. 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.

  3. 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

  4. 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

  5. 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.

  6. 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

  7. 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.

  8. Extracellular vesicles modulate the glioblastoma microenvironment via a tumor suppression signaling network directed by miR-1.

    PubMed

    Bronisz, Agnieszka; Wang, Yan; Nowicki, Michal O; Peruzzi, Pierpaolo; Ansari, Khairul I; Ogawa, Daisuke; Balaj, Leonora; De Rienzo, Gianluca; Mineo, Marco; Nakano, Ichiro; Ostrowski, Michael C; Hochberg, Fred; Weissleder, Ralph; Lawler, Sean E; Chiocca, E Antonio; Godlewski, Jakub

    2014-02-01

    Extracellular vesicles have emerged as important mediators of intercellular communication in cancer, including by conveying tumor-promoting microRNAs between cells, but their regulation is poorly understood. In this study, we report the findings of a comparative microRNA profiling and functional analysis in human glioblastoma that identifies miR-1 as an orchestrator of extracellular vesicle function and glioblastoma growth and invasion. Ectopic expression of miR-1 in glioblastoma cells blocked in vivo growth, neovascularization, and invasiveness. These effects were associated with a role for miR-1 in intercellular communication in the microenvironment mediated by extracellular vesicles released by cancer stem-like glioblastoma cells. An extracellular vesicle-dependent phenotype defined by glioblastoma invasion, neurosphere growth, and endothelial tube formation was mitigated by loading miR-1 into glioblastoma-derived extracellular vesicles. Protein cargo in extracellular vesicles was characterized to learn how miR-1 directed extracellular vesicle function. The mRNA encoding Annexin A2 (ANXA2), one of the most abundant proteins in glioblastoma-derived extracellular vesicles, was found to be a direct target of miR-1 control. In addition, extracellular vesicle-derived miR-1 along with other ANXA2 extracellular vesicle networking partners targeted multiple pro-oncogenic signals in cells within the glioblastoma microenvironment. Together, our results showed how extracellular vesicle signaling promotes the malignant character of glioblastoma and how ectopic expression of miR-1 can mitigate this character, with possible implications for how to develop a unique miRNA-based therapy for glioblastoma management. PMID:24310399

  9. 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.

  10. 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.

  11. 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.

  12. 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 ? as the percentage of unidirectional links. The epidemic threshold ?(c) for the susceptible-infected-susceptible (SIS) epidemic is lower bounded by 1/?(1) in directed networks, where ?(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 ?. The effect of ? on the spectral radius ?(1), principal eigenvector x(1), spectral gap (?(1)-|?(2)|), and algebraic connectivity ?(N-1) is studied. Important findings are that the spectral radius ?(1) decreases with the directionality ?, whereas the spectral gap and the algebraic connectivity increase with the directionality ?. The extent of the decrease of the spectral radius depends on both the degree distribution and the degree-degree correlation ?(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

  13. 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

  14. Potential Theory for Directed Networks

    PubMed Central

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

    2013-01-01

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

  15. 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.

  16. Clustering in complex directed networks

    NASA Astrophysics Data System (ADS)

    Fagiolo, Giorgio

    2007-08-01

    Many empirical networks display an inherent tendency to cluster, i.e., to form circles of connected nodes. This feature is typically measured by the clustering coefficient (CC). The CC, originally introduced for binary, undirected graphs, has been recently generalized to weighted, undirected networks. Here we extend the CC to the case of (binary and weighted) directed networks and we compute its expected value for random graphs. We distinguish between CCs that count all directed triangles in the graph (independently of the direction of their edges) and CCs that only consider particular types of directed triangles (e.g., cycles). The main concepts are illustrated by employing empirical data on world-trade flows.

  17. 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

  18. 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

  19. 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

  20. 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

  1. Direct Imaging of Functional Networks

    PubMed Central

    2014-01-01

    Abstract In blood-oxygenation-level-dependent functional magnetic resonance imaging (fMRI), current methods typically acquire ?500,000 imaging voxels at each time point, and then use computer algorithms to reduce this data to the coefficients of a few hundred parcels or networks. This suggests that the amount of relevant information present in the fMRI signal is relatively small, and presents an opportunity to greatly improve the speed and signal to noise ratio (SNR) of the fMRI process. In this work, a theoretical framework is presented for calculating the coefficients of functional networks directly from highly undersampled fMRI data. Using predefined functional parcellations or networks and a compact k-space trajectory that samples data at optimal spatial scales, the problem of estimating network coefficients is reformulated to allow for direct least squares estimation, without Fourier encoding. By simulation, this approach is shown to allow for acceleration of the imaging process under ideal circumstances by nearly three orders of magnitude. PMID:25111798

  2. 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.

  3. PRESYNAPTIC NETWORKS. Single-cell-initiated monosynaptic tracing reveals layer-specific cortical network modules.

    PubMed

    Wertz, Adrian; Trenholm, Stuart; Yonehara, Keisuke; Hillier, Daniel; Raics, Zoltan; Leinweber, Marcus; Szalay, Gergely; Ghanem, Alexander; Keller, Georg; Rózsa, Balázs; Conzelmann, Karl-Klaus; Roska, Botond

    2015-07-01

    Individual cortical neurons can selectively respond to specific environmental features, such as visual motion or faces. How this relates to the selectivity of the presynaptic network across cortical layers remains unclear. We used single-cell-initiated, monosynaptically restricted retrograde transsynaptic tracing with rabies viruses expressing GCaMP6s to image, in vivo, the visual motion-evoked activity of individual layer 2/3 pyramidal neurons and their presynaptic networks across layers in mouse primary visual cortex. Neurons within each layer exhibited similar motion direction preferences, forming layer-specific functional modules. In one-third of the networks, the layer modules were locked to the direction preference of the postsynaptic neuron, whereas for other networks the direction preference varied by layer. Thus, there exist feature-locked and feature-variant cortical networks. PMID:26138975

  4. Coarse graining for synchronization in directed networks.

    PubMed

    Zeng, An; Lü, Linyuan

    2011-05-01

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

  5. Coarse graining for synchronization in directed networks

    NASA Astrophysics Data System (ADS)

    Zeng, An; Lü, Linyuan

    2011-05-01

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

  6. 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.

  7. 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…

  8. 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…

  9. 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.

  10. Directional Amplification using Josephson Ring Modulators

    NASA Astrophysics Data System (ADS)

    Hatridge, M.; Sliwa, K. M.; Narla, A.; Shankar, S.; Devoret, M. H.

    2015-03-01

    Quantum limited parametric amplifiers usually amplify in reflection, so that the input and output signals travel on the same physical port. Circulators and isolators are thus required both to separate input and output signals with minimal loss of signal-to-noise ratio and to avoid backward irradiation of the signal source. These devices are bulky, dissipative, and operate in large magnetic fields which make them incompatible with integration on chip. By interfering the non-reciprocal mixing processes present in Josephson Ring Modulators, directional amplification can be realized. The theory and performance of a novel directional amplifier will be presented. Work supported by: IARPA, ARO, and ONR.

  11. Network management, status and directions

    SciTech Connect

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

    1992-09-01

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

  12. Network management, status and directions

    SciTech Connect

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

    1992-09-01

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

  13. High Speed Direct Modulation of Semiconductor Lasers

    NASA Astrophysics Data System (ADS)

    Lippi, Gian-Luca; Dokhane, Nahed; Hachair, Xavier; Barland, Stephane; Tredicce, Jorge R.

    2002-12-01

    Direct modulation of the injected current still represents an attractive and inexpensive technique for encoding information in the output of a semiconductor laser. The growing requirements in volume of information to be transmitted and their conflict with the progressive, and rapid, degradation of the signal at high speeds have made this simple technical solution less and less attractive. A brief analysis of the sources of the problem is offered. A viable and inexpensive way of improving DM's performance is discussed. High quality signals are predicted at data transmission speeds that exceed by over an order of magnitude those obtainable with DM.

  14. Distributed pulse forming network for magnetic modulator

    NASA Astrophysics Data System (ADS)

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

    1984-05-01

    A pulse forming network with distributed inductance and capacitance is disclosed for use in a magnetic modulator. The magnetic modulator has a magnetic core with a primary winding and a secondary winding around it. The pulse forming network includes an inner winding of flattened wire around the magnetic core and connected to one end of the secondary winding for receiving an induced voltage. The pulse forming network also includes a metal foil shield around the inner winding, so that the induced voltage may be stored capacitively between the inner winding and the shield. When the magnetic core saturates, the impedance of the secondary winding drops, so that the pulse forming network discharges through a load. The shape of the pulse through the load is determined by the inductance of the inner winding and the capacitance between the inner winding and the shield. The number of turns per unit length of the inner winding, the spacing between the inner winding and the shield, and the dielectric constant of an insulating layer of material between the inner winding and the shield may all be modified to obtain a pulse forming network forming a desired pulse shape.

  15. Parsimonious Module Inference in Large Networks

    NASA Astrophysics Data System (ADS)

    Peixoto, Tiago P.

    2013-04-01

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

  16. 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.

  17. 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

  18. 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.

  19. Transmission line directional protection using neural networks and filtering algorithms

    NASA Astrophysics Data System (ADS)

    Sanaye-Pasand, Majid

    2000-02-01

    Power transmission lines are the vital links in power systems providing the essential continuity of service from generating plants to the end users. To maintain stability in a power system it is imperative that any fault in the transmission system be identified by protective relays and the faulted line be isolated from the network with minimal delay. Faults on transmission lines need to be detected, classified and cleared as fast as possible. Moreover, the fault direction should be identified. Development of different modules of a transmission line protective relaying system is outlined in this dissertation. Different modules such as fault direction identification, fault detection and phase selection modules are designed, implemented and tested. Neural network technique is employed to design the transmission line fault direction identification module. Different neural network structures are used and four different directional modules are proposed. A new high speed algorithm, based on impedance measurement is proposed for fault detection and phase selection. Adaptive features are also added to the proposed relaying modules to enable them to track the changing operation conditions of the system. Off-line studies are performed with the proposed relaying modules on a simulated power system model. The system is subjected to different types of disturbances while it is operating at different operating conditions, and the performance of the proposed modules is evaluated. The results obtained indicate that the proposed relaying modules perform rapidly and correctly for different system conditions. The relaying algorithm has been implemented on a digital signal processor board. Using a power system model consisting of a micro-alternator connected to a constant voltage system extensive experimental studies are conducted and the performance of the relaying algorithm is investigated. The performance of the proposed modules is investigated further using recorded fault data from a high voltage power system. In this way, the performance of the newly designed relaying modules can be further verified in a more realistic environment. Results using various recorded field data are presented. The results presented in this dissertation confirm the feasibility of the proposed relaying modules.

  20. 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.

  1. 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.

  2. 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.

  3. An effective method for network module extraction from microarray data

    PubMed Central

    2012-01-01

    Background The development of high-throughput Microarray technologies has provided various opportunities to systematically characterize diverse types of computational biological networks. Co-expression network have become popular in the analysis of microarray data, such as for detecting functional gene modules. Results This paper presents a method to build a co-expression network (CEN) and to detect network modules from the built network. We use an effective gene expression similarity measure called NMRS (Normalized mean residue similarity) to construct the CEN. We have tested our method on five publicly available benchmark microarray datasets. The network modules extracted by our algorithm have been biologically validated in terms of Q value and p value. Conclusions Our results show that the technique is capable of detecting biologically significant network modules from the co-expression network. Biologist can use this technique to find groups of genes with similar functionality based on their expression information. PMID:23320896

  4. 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.

  5. 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.

  6. 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%.

  7. 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.

  8. 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.

  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. 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.

  11. 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.

  12. 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.

  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 network’s 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. Direct modulation of lanthanide emission at sub-lifetime scales.

    PubMed

    Karaveli, Sinan; Weinstein, Aaron J; Zia, Rashid

    2013-05-01

    The long lifetime of lanthanide emitters can present a challenge for conventional pump-based modulation schemes, where the maximum switching speed is limited by the decay time of the excited state. However, spontaneous emission can also be controlled through the local optical environment. Here, we demonstrate a direct modulation scheme enabled by dynamic control of the local density of optical states (LDOS). Specifically, we exploit the LDOS differences between electric and magnetic dipole transitions near a metal mirror and demonstrate that rapid nanometer-scale mirror displacements can modulate the emission spectra of trivalent europium ions within their excited state lifetime. The dynamic LDOS modulation presented here can be readily extended to faster optical modulation schemes and applied to other long-lived emitters to control the direction, polarization, and spectrum of spontaneous emission at sublifetime scales. PMID:23597062

  16. 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

  17. 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.

  18. 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

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. Directed network topologies of smart grain sensors

    NASA Astrophysics Data System (ADS)

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

    2013-03-01

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

  4. 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.

  5. 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

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

    DOEpatents

    Miller, David Harold (San Pedro, CA); Korich, Mark D. (Chino Hills, CA); Ward, Terence G. (Redondo Beach, CA); Mann, Brooks S. (Redondo Beach, CA)

    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.

  7. Exploring molecular networks directly in the cell.

    PubMed

    Schubert, Walter

    2006-03-01

    The hierarchy of cell function comprises at least four distinct functional levels: genome, transcriptome, proteome, and toponome. The toponome is the entirety of all protein networks traced out directly as patterns on the single cell level in the natural environment of cells in situ (e.g. tissues). In this work a photonic microscopic robot technology (MELK) capable of tagging and imaging hundreds (and possibly thousands) of different molecular components (e.g. proteins) of morphologically-intact fixed cells and tissue have been developed. MELK data sets represent multidimensional vectors of the topologically determined arrangements of proteins within the cell. The data, assembled in a toponome dictionary of the cell, give rise to a new concept for target and drug lead discovery. PMID:16496422

  8. Monthly modulation in dark matter direct-detection experiments

    NASA Astrophysics Data System (ADS)

    Britto, Vivian; Meyers, Joel

    2015-11-01

    The signals in dark matter direct-detection experiments should exhibit modulation signatures due to the Earth's motion with respect to the Galactic dark matter halo. The annual and daily modulations, due to the Earth's revolution about the Sun and rotation about its own axis, have been explored previously. Monthly modulation is another such feature present in direct detection signals, and provides a nearly model-independent method of distinguishing dark matter signal events from background. We study here monthly modulations in detail for both WIMP and WISP dark matter searches, examining both the effect of the motion of the Earth about the Earth-Moon barycenter and the gravitational focusing due to the Moon. For WIMP searches, we calculate the monthly modulation of the count rate and show the effects are too small to be observed in the foreseeable future. For WISP dark matter experiments, we show that the photons generated by WISP to photon conversion have frequencies which undergo a monthly modulating shift which is detectable with current technology and which cannot in general be neglected in high resolution WISP searches.

  9. 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 ?out?3.0 and ?in?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.

  10. 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.

  11. Protein complexes and functional modules in molecular networks.

    PubMed

    Spirin, Victor; Mirny, Leonid A

    2003-10-14

    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. PMID:14517352

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

    NASA Astrophysics Data System (ADS)

    Kashany-Mizrahi, Inbal; Sadot, Dan

    2013-10-01

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

  13. 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

  14. Frequency modulation of large oscillatory neural networks.

    PubMed

    Wyffels, Francis; Li, Jiwen; Waegeman, Tim; Schrauwen, Benjamin; Jaeger, Herbert

    2014-04-01

    Dynamical systems which generate periodic signals are of interest as models of biological central pattern generators and in a number of robotic applications. A basic functionality that is required in both biological modelling and robotics is frequency modulation. This leads to the question of whether there are generic mechanisms to control the frequency of neural oscillators. Here we describe why this objective is of a different nature, and more difficult to achieve, than modulating other oscillation characteristics (like amplitude, offset, signal shape). We propose a generic way to solve this task which makes use of a simple linear controller. It rests on the insight that there is a bidirectional dependency between the frequency of an oscillation and geometric properties of the neural oscillator's phase portrait. By controlling the geometry of the neural state orbits, it is possible to control the frequency on the condition that the state space can be shaped such that it can be pushed easily to any frequency. PMID:24515094

  15. Module detection in complex networks using integer optimisation

    PubMed Central

    2010-01-01

    Background The detection of modules or community structure is widely used to reveal the underlying properties of complex networks in biology, as well as physical and social sciences. Since the adoption of modularity as a measure of network topological properties, several methodologies for the discovery of community structure based on modularity maximisation have been developed. However, satisfactory partitions of large graphs with modest computational resources are particularly challenging due to the NP-hard nature of the related optimisation problem. Furthermore, it has been suggested that optimising the modularity metric can reach a resolution limit whereby the algorithm fails to detect smaller communities than a specific size in large networks. Results We present a novel solution approach to identify community structure in large complex networks and address resolution limitations in module detection. The proposed algorithm employs modularity to express network community structure and it is based on mixed integer optimisation models. The solution procedure is extended through an iterative procedure to diminish effects that tend to agglomerate smaller modules (resolution limitations). Conclusions A comprehensive comparative analysis of methodologies for module detection based on modularity maximisation shows that our approach outperforms previously reported methods. Furthermore, in contrast to previous reports, we propose a strategy to handle resolution limitations in modularity maximisation. Overall, we illustrate ways to improve existing methodologies for community structure identification so as to increase its efficiency and applicability. PMID:21073720

  16. Analysis of linewidth and extinction ratio in directly modulated lasers for performance optimization in 10 Gbit/s CWDM systems

    NASA Astrophysics Data System (ADS)

    Campos, Carmina del Río; Horche, Paloma R.; Martin-Minguez, Alfredo

    2010-08-01

    Direct Modulation Lasers (DMLs) have attracted increased attention during the past few years because of their intrinsic simplicity and cost-effectiveness, especially when applied to WDM metro and access networks. However, the output power waveform from a directly modulated laser is not an exact replica of the modulation current and its instantaneous optical frequency varies with time depending on the changes in optical power and the extinction ratio (ER) (an effect also known as frequency chirp). In this work, using an Optical Communication System Design Software, we have studied a directly modulated WDM 10 Gb/s system which transmission performance depends strongly on DML characteristics; simulation results have provided supplementary details about the effects of DML type (adiabatic or transient chirp dominated) as well as the effects of the optical output power. These details can provide useful design guidelines for constructing a WDM metro network.

  17. 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

  18. 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.

  19. 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.

  20. Remote Synchronization Reveals Network Symmetries and Functional Modules

    NASA Astrophysics Data System (ADS)

    Nicosia, Vincenzo; Valencia, Miguel; Chavez, Mario; Díaz-Guilera, Albert; Latora, Vito

    2013-04-01

    We study a Kuramoto model in which the oscillators are associated with the nodes of a complex network and the interactions include a phase frustration, thus preventing full synchronization. The system organizes into a regime of remote synchronization where pairs of nodes with the same network symmetry are fully synchronized, despite their distance on the graph. We provide analytical arguments to explain this result, and we show how the frustration parameter affects the distribution of phases. An application to brain networks suggests that anatomical symmetry plays a role in neural synchronization by determining correlated functional modules across distant locations.

  1. 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

  2. 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

  3. 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

  4. 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.

  5. On-chip microwave photonic beamformer circuits operating with phase modulation and direct detection.

    PubMed

    Zhuang, Leimeng; Hoekman, Marcel; Taddei, Caterina; Leinse, Arne; Heideman, René G; Hulzinga, Adriaan; Verpoorte, Jaco; Oldenbeuving, Ruud M; van Dijk, Paulus W L; Boller, Klaus-J; Roeloffzen, Chris G H

    2014-07-14

    We propose and experimentally demonstrate the working principles of two novel microwave photonic (MWP) beamformer circuits operating with phase modulation (PM) and direct detection (DD). The proposed circuits incorporate two major signal processing functionalities, namely a broadband beamforming network employing ring resonator-based delay lines and an optical sideband manipulator that renders the circuit outputs equivalent to those of intensity-modulated MWP beamformers. These functionalities allow the system to employ low-circuit-complexity modulators and detectors, which brings significant benefits on the system construction cost and operation stability. The functionalities of the proposed MWP beamformer circuits were verified in experimental demonstrations performed on two sample circuits realized in Si(3)N(4)/SiO(2) waveguide technology. The measurements exhibit a 2 × 1 beamforming effect for an instantaneous RF transmission band of 3?7 GHz, which is, to our best knowledge, the first verification of on-chip MWP beamformer circuits operating with PM and DD. PMID:25090522

  6. 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

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

    PubMed

    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

  8. Search for Directed Networks by Different Random Walk Strategies

    NASA Astrophysics Data System (ADS)

    Zhu, Zi-Qi; Jin, Xiao-Ling; Huang, Zhi-Long

    2012-03-01

    A comparative study is carried out on the efficiency of five different random walk strategies searching on directed networks constructed based on several typical complex networks. Due to the difference in search efficiency of the strategies rooted in network clustering, the clustering coefficient in a random walker's eye on directed networks is defined and computed to be half of the corresponding undirected networks. The search processes are performed on the directed networks based on Erdös—Rényi model, Watts—Strogatz model, Barabási—Albert model and clustered scale-free network model. It is found that self-avoiding random walk strategy is the best search strategy for such directed networks. Compared to unrestricted random walk strategy, path-iteration-avoiding random walks can also make the search process much more efficient. However, no-triangle-loop and no-quadrangle-loop random walks do not improve the search efficiency as expected, which is different from those on undirected networks since the clustering coefficient of directed networks are smaller than that of undirected networks.

  9. 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

  10. 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.

  11. 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.

  12. 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 ? phase shift (?-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.

  13. Detecting modulated lasers in the battlefield and determining their direction

    NASA Astrophysics Data System (ADS)

    McAulay, Alastair D.

    2009-05-01

    Many different lasers are deployed in the battlefield for range finding, target designation, communications, dazzle, location of targets, munitions guidance, and destruction. Laser warning devices on military systems detect and identify lasers striking them in order to assess their threat level and plan avoidance or retaliation. Types of lasers and their characteristics are discussed: power, frequency, coherence, bandwidth, direction, pulse length and modulation. We describe three approaches for laser warning devices from which specific cases may be tailored: simultaneous estimation of direction and wavelength with a grating, wavefront direction only estimation for low light levels with lenses, absolute simultaneous wavelength only estimation with a Fizeau interferometer. We investigate the feasibility and compare the suitability of these approaches for different applications.

  14. 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

  15. Phase transitions for scaling of structural correlations in directed networks.

    PubMed

    van der Hoorn, Pim; Litvak, Nelly

    2015-08-01

    Analysis of degree-degree dependencies in complex networks, and their impact on processes on networks requires null models, i.e., models that generate uncorrelated scale-free networks. Most models to date, however, show structural negative dependencies, caused by finite size effects. We analyze the behavior of these structural negative degree-degree dependencies, using rank based correlation measures, in the directed erased configuration model. We obtain expressions for the scaling as a function of the exponents of the distributions. Moreover, we show that this scaling undergoes a phase transition, where one region exhibits scaling related to the natural cutoff of the network while another region has scaling similar to the structural cutoff for uncorrelated networks. By establishing the speed of convergence of these structural dependencies we are able to assess statistical significance of degree-degree dependencies on finite complex networks when compared to networks generated by the directed erased configuration model. PMID:26382450

  16. 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.

  17. 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

  18. 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

  19. DHCVIM: A direct heating containment vessel interactions module

    SciTech Connect

    Ginsberg, T.; Tutu, N.K.

    1987-01-01

    Models for prediction of direct containment heating phenomena as implemented in the DHCVIM computer module are described. The models were designed to treat thermal, chemical and hydrodynamic processes in the three regions of the Sandia National Laboratory Surtsey DCH test facility: the melt generator, cavity and vessel. The fundamental balance equations, along with constitutive relations are described. A combination of Eulerian treatment for the gas phase and Lagrangian treatment for the droplet phase is used in the modeling. Comparisons of calculations and DCH-1 test results are presented. Reasonable agreement is demonstrated for the vessel pressure rise, melt generator pressure decay and particle size distribution.

  20. 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

  1. 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

  2. Errorless and errorful learning modulated by transcranial direct current stimulation

    PubMed Central

    2011-01-01

    Background Errorless learning is advantageous over trial and error learning (errorful learning) as errors are avoided during learning resulting in increased memory performance. Errorful learning challenges the executive control system of memory processes as the erroneous items compete with the correct items during retrieval. The left dorsolateral prefrontal cortex (DLPFC) is a core region involved in this executive control system. Transcranial direct current stimulation (tDCS) can modify the excitability of underlying brain functioning. Results In a single blinded tDCS study one group of young healthy participants received anodal and another group cathodal tDCS of the left DLPFC each compared to sham stimulation. Participants had to learn words in an errorless and an errorful manner using a word stem completion paradigm. The results showed that errorless compared to errorful learning had a profound effect on the memory performance in terms of quality. Anodal stimulation of the left DLPFC did not modulate the memory performance following errorless or errorful learning. By contrast, cathodal stimulation hampered memory performance after errorful learning compared to sham, whereas there was no modulation after errorless learning. Conclusions Concluding, the study further supports the advantages of errorless learning over errorful learning. Moreover, cathodal stimulation of the left DLPFC hampered memory performance following the conflict-inducing errorful learning as compared to no modulation after errorless learning emphasizing the importance of the left DLPFC in executive control of memory. PMID:21781298

  3. 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

  4. Compression of Flow Can Reveal Overlapping-Module Organization in Networks

    NASA Astrophysics Data System (ADS)

    Viamontes Esquivel, Alcides; Rosvall, Martin

    2011-10-01

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

  5. 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

  6. Novel ?-Secretase Enzyme Modulators Directly Target Presenilin Protein*

    PubMed Central

    Ebke, Amelie; Luebbers, Thomas; Fukumori, Akio; Shirotani, Keiro; Haass, Christian; Baumann, Karlheinz; Steiner, Harald

    2011-01-01

    ?-Secretase is essential for the generation of the neurotoxic 42-amino acid amyloid ?-peptide (A?42). The aggregation-prone hydrophobic peptide, which is deposited in Alzheimer disease (AD) patient brain, is generated from a C-terminal fragment of the ?-amyloid precursor protein by an intramembrane cleavage of ?-secretase. Because A?42 is widely believed to trigger AD pathogenesis, ?-secretase is a key AD drug target. Unlike inhibitors of the enzyme, ?-secretase modulators (GSMs) selectively lower A?42 without interfering with the physiological function of ?-secretase. The molecular target(s) of GSMs and hence the mechanism of GSM action are not established. Here we demonstrate by using a biotinylated photocross-linkable derivative of highly potent novel second generation GSMs that ?-secretase is a direct target of GSMs. The GSM photoprobe specifically bound to the N-terminal fragment of presenilin, the catalytic subunit of ?-secretase, but not to other ?-secretase subunits. Binding was differentially competed by GSMs of diverse structural classes, indicating the existence of overlapping/multiple GSM binding sites or allosteric alteration of the photoprobe binding site. The ?-amyloid precursor protein C-terminal fragment previously implicated as the GSM binding site was not targeted by the compound. The identification of presenilin as the molecular target of GSMs directly establishes allosteric modulation of enzyme activity as a mechanism of GSM action and may contribute to the development of therapeutically active GSMs for the treatment of AD. PMID:21896486

  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. 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.

  10. 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

  11. 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

  12. 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.

  13. 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

  14. 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

  15. 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

  16. 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.

  17. Motion words selectively modulate direction discrimination sensitivity for threshold motion

    PubMed Central

    Pavan, Andrea; Skujevskis, M?ris; Baggio, Giosuè

    2013-01-01

    Can speech selectively modulate the sensitivity of a sensory system so that, in the presence of a suitable linguistic context, the discrimination of certain perceptual features becomes more or less likely? In this study, participants heard upward or downward motion words followed by a single visual field of random dots moving upwards or downwards. The time interval between the onsets of the auditory and the visual stimuli was varied parametrically. Motion direction could be either discriminable (suprathreshold motion) or non-discriminable (threshold motion). Participants had to judge whether the dots were moving upward or downward. Results show a double dissociation between discrimination sensitivity (d?) and reaction times depending on whether vertical motion was above or at threshold. With suprathreshold motion, responses were faster for congruent directions of words and dots, but sensitivity was equal across conditions. With threshold motion, sensitivity was higher for congruent directions of words and dots, but responses were equally fast across conditions. The observed differences in sensitivity and response times were largest when the dots appeared 450 ms after word onset, that is, consistently with electrophysiology, at the time the up/down semantics of the word had become available. These data suggest that word meanings can alter the balance between signal and noise within the visual system and affect the perception of low-level sensory features. PMID:23596407

  18. 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

  19. Both hand position and movement direction modulate visual attention

    PubMed Central

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

    2013-01-01

    The current study explored effects of continuous hand motion on the allocation of visual attention. A concurrent paradigm was used to combine visually concealed continuous hand movements with an attentionally demanding letter discrimination task. The letter probe appeared contingent upon the moving right hand passing through one of six positions. Discrimination responses were then collected via a keyboard press with the static left hand. Both the right hand's position and its movement direction systematically contributed to participants' visual sensitivity. Discrimination performance increased substantially when the right hand was distant from, but moving toward the visual probe location (replicating the far-hand effect, Festman et al., 2013). However, this effect disappeared when the probe appeared close to the static left hand, supporting the view that static and dynamic features of both hands combine in modulating pragmatic maps of attention. PMID:24098288

  20. 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

  1. Keratinocytes can modulate and directly initiate nociceptive responses.

    PubMed

    Baumbauer, Kyle M; DeBerry, Jennifer J; Adelman, Peter C; Miller, Richard H; Hachisuka, Junichi; Lee, Kuan Hsien; Ross, Sarah E; Koerber, H Richard; Davis, Brian M; Albers, Kathryn M

    2015-01-01

    How thermal, mechanical and chemical stimuli applied to the skin are transduced into signals transmitted by peripheral neurons to the CNS is an area of intense study. Several studies indicate that transduction mechanisms are intrinsic to cutaneous neurons and that epidermal keratinocytes only modulate this transduction. Using mice expressing channelrhodopsin (ChR2) in keratinocytes we show that blue light activation of the epidermis alone can produce action potentials (APs) in multiple types of cutaneous sensory neurons including SA1, A-HTMR, CM, CH, CMC, CMH and CMHC fiber types. In loss of function studies, yellow light stimulation of keratinocytes that express halorhodopsin reduced AP generation in response to naturalistic stimuli. These findings support the idea that intrinsic sensory transduction mechanisms in epidermal keratinocytes can directly elicit AP firing in nociceptive as well as tactile sensory afferents and suggest a significantly expanded role for the epidermis in sensory processing. PMID:26329459

  2. Enhancing complex network controllability by minimum link direction reversal

    NASA Astrophysics Data System (ADS)

    Hou, Lvlin; Lao, Songyang; Small, Michael; Xiao, Yandong

    2015-07-01

    Controllability of complex networks has recently become one of the most popular research fields, but the importance of link direction for controllability has not been systematically considered. We propose a method to enhance controllability of a directed network by changing the direction of a small fraction of links while keeping the total number of links unchanged. The main idea of the method is to find candidate links based on the matching path. Extensive numerical simulation on many modeled networks demonstrates that this method is effective. Furthermore, we find that the nodes linked to candidate links have a distinct character, which provide us with a strategy to improve the controllability based on the local structure. Since the whole topology of many real networks is not visible and we only get some local structure information, this strategy is potentially more practical compared to those that demand complete topology information.

  3. 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.

  4. Hierarchical Feedback Modules and Reaction Hubs in Cell Signaling Networks

    PubMed Central

    Xu, Jianfeng; Lan, Yueheng

    2015-01-01

    Despite much effort, identification of modular structures and study of their organizing and functional roles remain a formidable challenge in molecular systems biology, which, however, is essential in reaching a systematic understanding of large-scale cell regulation networks and hence gaining capacity of exerting effective interference to cell activity. Combining graph theoretic methods with available dynamics information, we successfully retrieved multiple feedback modules of three important signaling networks. These feedbacks are structurally arranged in a hierarchical way and dynamically produce layered temporal profiles of output signals. We found that global and local feedbacks act in very different ways and on distinct features of the information flow conveyed by signal transduction but work highly coordinately to implement specific biological functions. The redundancy embodied with multiple signal-relaying channels and feedback controls bestow great robustness and the reaction hubs seated at junctions of different paths announce their paramount importance through exquisite parameter management. The current investigation reveals intriguing general features of the organization of cell signaling networks and their relevance to biological function, which may find interesting applications in analysis, design and control of bio-networks. PMID:25951347

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. Modulating cognition using transcranial direct current stimulation of the cerebellum.

    PubMed

    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

  10. 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

  11. 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

  12. 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.

  13. 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

  14. Discriminating direct and indirect connectivities in biological networks.

    PubMed

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

    2015-10-13

    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

  15. 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

  16. 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 protein–protein 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

  17. 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

  18. Beyond Modules & Hubs: the potential of gene coexpression networks for investigating molecular mechanisms of complex brain disorders

    PubMed Central

    Gaiteri, Chris; Ding, Ying; French, Beverly; Tseng, George C.; Sibille, Etienne

    2013-01-01

    In a research environment dominated by reductionist approaches to brain disease mechanisms, gene network analysis provides a complementary framework in which to tackle the complex dysregulations that occur in neuropsychiatric and other neurological disorders. Gene-gene expression correlations are a common source of molecular networks because they can be extracted from high-dimensional disease data and encapsulate the activity of multiple regulatory systems. However, the analysis of gene coexpression patterns is often treated as a mechanistic black box, in which looming “hub genes” direct cellular networks, and where other features are obscured. By examining the biophysical bases of coexpression and gene regulatory changes that occur in disease, recent studies suggest it is possible to use coexpression networks as a multi-omic screening procedure to generate novel hypotheses for disease mechanisms. Because technical processing steps can affect the outcome and interpretation of coexpression networks, we examine the assumptions and alternatives to common patterns of coexpression analysis and discuss additional topics such as acceptable datasets for coexpression analysis, the robust identification of modules, disease-related prioritization of genes and molecular systems and network meta-analysis. To accelerate coexpression research beyond modules and hubs, we highlight some emerging directions for coexpression network research that are especially relevant to complex brain disease, including the centrality-lethality relationship, integration with machine learning approaches and network pharmacology. PMID:24320616

  19. 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

  20. 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

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

    PubMed

    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

  2. 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

  3. 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

    Bode, Nadine J; Debnath, Irina; Kuan, Lisa; Schulfer, Anjelique; Ty, Maureen; Pearson, Melanie M

    2015-06-01

    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

  4. 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

  5. Functional Modules, Structural Topology, and Optimal Activity in Metabolic Networks

    PubMed Central

    Resendis-Antonio, Osbaldo; Hernández, Magdalena; Mora, Yolanda; Encarnación, Sergio

    2012-01-01

    Modular organization in biological networks has been suggested as a natural mechanism by which a cell coordinates its metabolic strategies for evolving and responding to environmental perturbations. To understand how this occurs, there is a need for developing computational schemes that contribute to integration of genomic-scale information and assist investigators in formulating biological hypotheses in a quantitative and systematic fashion. In this work, we combined metabolome data and constraint-based modeling to elucidate the relationships among structural modules, functional organization, and the optimal metabolic phenotype of Rhizobium etli, a bacterium that fixes nitrogen in symbiosis with Phaseolus vulgaris. To experimentally characterize the metabolic phenotype of this microorganism, we obtained the metabolic profile of 220 metabolites at two physiological stages: under free-living conditions, and during nitrogen fixation with P. vulgaris. By integrating these data into a constraint-based model, we built a refined computational platform with the capability to survey the metabolic activity underlying nitrogen fixation in R. etli. Topological analysis of the metabolic reconstruction led us to identify modular structures with functional activities. Consistent with modular activity in metabolism, we found that most of the metabolites experimentally detected in each module simultaneously increased their relative abundances during nitrogen fixation. In this work, we explore the relationships among topology, biological function, and optimal activity in the metabolism of R. etli through an integrative analysis based on modeling and metabolome data. Our findings suggest that the metabolic activity during nitrogen fixation is supported by interacting structural modules that correlate with three functional classifications: nucleic acids, peptides, and lipids. More fundamentally, we supply evidence that such modular organization during functional nitrogen fixation is a robust property under different environmental conditions. PMID:23071431

  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. Majority-Vote on Directed BARABÁSI-ALBERT Networks

    NASA Astrophysics Data System (ADS)

    Lima, F. W. S.

    On directed Barabási-Albert networks with two and seven neighbours selected by each added site, the Ising model was seen not to show a spontaneous magnetisation. Instead, the decay time for flipping of the magnetisation followed an Arrhenius law for Metropolis and Glauber algorithms, but for Wolff cluster flipping the magnetisation decayed exponentially with time. On these networks the Majority-vote model with noise is now studied through Monte Carlo simulations. However, in this model, the order-disorder phase transition of the order parameter is well defined in this system. We calculate the value of the critical noise parameter qc for several values of connectivity z of the directed Barabási-Albert network. The critical exponentes ?/?, ?/? and 1/? were calculated for several values of z.

  8. Centrality in Directed Social Networks: A Game Theoretic Approach

    NASA Astrophysics Data System (ADS)

    González-Arangüena, E.; Manuel, C.; del Pozo, M.

    2010-09-01

    In this paper we define a family of centrality measures for directed social networks from a game theoretical point of view. We follow the line started with our previous work (Gómez et al.., 2003). Besides the definition, we obtain both, a characterization and an additive decomposition of the measures.

  9. 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

  10. 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.

  11. 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

  12. 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

  13. Unbiased degree-preserving randomization of directed binary networks.

    PubMed

    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. PMID:22680534

  14. 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.

  15. 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.

  16. 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

  17. 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

  18. 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

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

    PubMed

    Vukeli?, 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 ?-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 ?-band modulation could, however, be achieved in the BRI condition. This gain in controlling regional motor oscillations was accompanied by functional coupling of remote ?-band and ?-band activity in bilateral fronto-central regions and left parieto-occipital regions, respectively. The functional coupling of coherent ?-band oscillations correlated moreover with the skill of regional ?-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

  20. 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.

  1. 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.

  2. 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

  3. 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

  4. 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

  5. Moving Target Tracking through Distributed Clustering in Directional Sensor Networks

    PubMed Central

    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

  6. 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.

  7. 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

  8. 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.

  9. Phase transition in a directed traffic flow network.

    PubMed

    Mukherjee, G; Manna, S S

    2005-06-01

    The generic feature of traffic in a network of flowing electronic data packets is a phase transition from a stationary free-flow phase to a continuously growing congested nonstationary phase. In the most simple network of directed oriented square lattice we have been able to observe all crucial features of such flow systems having nontrivial critical behavior near the critical point of transition. The network here is in the shape of a square lattice and data packets are randomly posted with a rate rho at one side of the lattice. Each packet executes a directed diffusive motion toward the opposite boundary where it is delivered. Packets accumulated at a particular node form a queue and a maximum of m such packets randomly jump out of this node at every time step to its neighbors on a first-in-first-out basis. The phase transition occurs at rho(c) = m. The distribution of travel times through the system is found to have a log-normal behavior and the power spectrum of the load time series shows 1/f-like noise similar to the scenario of Internet traffic. PMID:16089821

  10. 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

  11. 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...

  12. Analytical approach to directed sandpile models on the Apollonian network

    NASA Astrophysics Data System (ADS)

    Vieira, André P.; Andrade, José S., Jr.; Herrmann, Hans J.; Andrade, Roberto F. S.

    2007-08-01

    We investigate a set of directed sandpile models on the Apollonian network, which are inspired by the work of Dhar and Ramaswamy [Phys. Rev. Lett. 63, 1659 (1989)] on Euclidian lattices. They are characterized by a single parameter q , which restricts the number of neighbors receiving grains from a toppling node. Due to the geometry of the network, two- and three-point correlation functions are amenable to exact treatment, leading to analytical results for avalanche distributions in the limit of an infinite system for q=1,2 . The exact recurrence expressions for the correlation functions are numerically iterated to obtain results for finite-size systems when larger values of q are considered. Finally, a detailed description of the local flux properties is provided by a multifractal scaling analysis.

  13. 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

  14. 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

  15. 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.

  16. 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

  17. Signal to Noise Ratios of Pulsed and Sinewave Modulated Direct Detection Lidar for IPDA Measurements

    NASA Technical Reports Server (NTRS)

    Sun, Xiaoli; Abshire, James B.

    2011-01-01

    The signal-to-noise ratios have been derived for IPDA lidar using a direct detection receiver for both pulsed and sinewave laser modulation techniques, and the results and laboratory measurements are presented

  18. 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

  19. 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.

  20. 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

  1. 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.

  2. Dynamic Brain Functional Connectivity Modulated by Resting-State Networks

    PubMed Central

    Di, Xin; Biswal, Bharat B.

    2014-01-01

    Studies of large-scale brain functional connectivity using the resting-state functional magnetic resonance imaging (fMRI) have advanced our understanding of human brain functions. Although the evidence of dynamic functional connectivity is accumulating, the variations of functional connectivity over time have not been well characterized. In the present study, we aimed to associate the variations of functional connectivity with the intrinsic activities of the resting-state networks during a single resting-state scan by comparing functional connectivity differences between when a network had higher and lower intrinsic activities. The activities of the salience network, default mode network (DMN), and motor network were associated with changes of resting-state functional connectivity. Higher activity of the salience network was accompanied by greater functional connectivity between the fronto-parietal regions and the DMN regions, and between the regions within the DMN. Higher DMN activity was associated with less connectivity between the regions within the DMN, and greater connectivity between the regions within the fronto-parietal network. Higher motor network activity was correlated with greater connectivity between the regions within the motor network, and smaller connectivity between the DMN regions and fronto-parietal regions, and between the DMN regions and the motor regions. In addition, the whole brain network modularity was positively correlated with the motor network activity, suggesting that the brain is more segregated as sub-systems when the motor network is intrinsically activated. Together, these results demonstrate the association between the resting-state connectivity variations and the intrinsic activities of specific networks, which can provide insights on the dynamic changes in large-scale brain connectivity and network configurations. PMID:25713839

  3. 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

  4. 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.

  5. Increasing Readiness for Self-Directed Learning: A Facilitator's Manual for Ten Self-Directed Learning Group Modules for Adults.

    ERIC Educational Resources Information Center

    Rutland, Adonna M.; Guglielmino, Lucy M.

    This manual was prepared for use by adult education teachers in facilitating a self-directed learning (SDL) group for students based on the modules described in the manual. The SDL group involves 10 sessions with specific objectives and activities for each session. Following an introduction, the manual is organized in five additional sections. The…

  6. 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

  7. 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.

  8. 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 NF?B 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

  9. An ELMO2-RhoG-ILK network modulates microtubule dynamics

    PubMed Central

    Jackson, Bradley C.; Ivanova, Iordanka A.; Dagnino, Lina

    2015-01-01

    ELMO2 belongs to a family of scaffold proteins involved in phagocytosis and cell motility. ELMO2 can simultaneously bind integrin-linked kinase (ILK) and RhoG, forming tripartite ERI complexes. These complexes are involved in promoting ?1 integrin–dependent directional migration in undifferentiated epidermal keratinocytes. ELMO2 and ILK have also separately been implicated in microtubule regulation at integrin-containing focal adhesions. During differentiation, epidermal keratinocytes cease to express integrins, but ERI complexes persist. Here we show an integrin-independent role of ERI complexes in modulation of microtubule dynamics in differentiated keratinocytes. Depletion of ERI complexes by inactivating the Ilk gene in these cells reduces microtubule growth and increases the frequency of catastrophe. Reciprocally, exogenous expression of ELMO2 or RhoG stabilizes microtubules, but only if ILK is also present. Mechanistically, activation of Rac1 downstream from ERI complexes mediates their effects on microtubule stability. In this pathway, Rac1 serves as a hub to modulate microtubule dynamics through two different routes: 1) phosphorylation and inactivation of the microtubule-destabilizing protein stathmin and 2) phosphorylation and inactivation of GSK-3?, which leads to the activation of CRMP2, promoting microtubule growth. At the cellular level, the absence of ERI species impairs Ca2+-mediated formation of adherens junctions, critical to maintaining mechanical integrity in the epidermis. Our findings support a key role for ERI species in integrin-independent stabilization of the microtubule network in differentiated keratinocytes. PMID:25995380

  10. 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

  11. 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.

  12. 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

  13. Task-Dependent Modulation of Effective Connectivity within the Default Mode Network.

    PubMed

    Li, Baojuan; Wang, Xiang; Yao, Shuqiao; Hu, Dewen; Friston, Karl

    2012-01-01

    The default mode network (DMN) has recently attracted widespread interest. Previous studies have found that task-related processing can induce deactivation and changes in the functional connectivity of this network. However, it remains unclear how tasks modulate the underlying effective connectivity within the DMN. Using recent advances in dynamic causal modeling (DCM), we investigated the modulatory effect of (gender judgment) task performance on directed connectivity within the DMN. Sixteen healthy subjects were scanned twice: at rest and while performing a gender judgment task. Group independent component analysis was used to identify independent spatial components. Four subject-specific regions of interest (ROIs) were defined according to the ensuing default mode component: the posterior cingulate cortex, the left lateral parietal cortex, the right lateral parietal cortex, and the medial prefrontal cortex. Effective connectivity among these regions was then characterized with stochastic DCM, revealing enhanced (extrinsic) between region connectivity within the DMN during task sessions - and a universal decrease in (intrinsic) self-inhibition - relative to resting sessions. These results suggest a distributed but systematic modulatory effect of cognitive and attentional set on the effective connectivity subtending the DMN: an effect that increases its sensitivity to inputs and may optimize distributed processing during task performance. PMID:22737141

  14. 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

  15. 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

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

    PubMed

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

    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

  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. A novel architecture of hybrid (WDM/TDM) passive optical networks with suitable modulation format

    NASA Astrophysics Data System (ADS)

    Goyal, Rakesh; Kaler, R. S.

    2012-12-01

    In this paper, we have analyzed the performance and feasibility of a hybrid wavelength division multiplexing/time division multiplexing passive optical network (WDM/TDM) PON system with 128 optical networks units (ONUs). In the proposed network, the triple play services (video, voice and data) are successfully transmitted to a distance of 28 km to all ONUs. In addition, we investigate and compare the proposed hybrid PON for suitability of various modulation formats for different distance. It has been observed that the most suitable data format for hybrid PON network is NRZ Rectangular.

  19. 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

  20. Direct and Propagated Effects of Small Molecules on Protein-Protein Interaction Networks.

    PubMed

    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

  1. 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

  2. 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

  3. 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.

  4. 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.

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

    NASA Astrophysics Data System (ADS)

    Tzeng, Shah-Jye

    2006-03-01

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

  6. Neural Networks For Demodulation Of Phase-Modulated Signals

    NASA Technical Reports Server (NTRS)

    Altes, Richard A.

    1995-01-01

    Hopfield neural networks proposed for demodulating quadrature phase-shift-keyed (QPSK) signals carrying digital information. Networks solve nonlinear integral equations prior demodulation circuits cannot solve. Consists of set of N operational amplifiers connected in parallel, with weighted feedback from output terminal of each amplifier to input terminals of other amplifiers. Used to solve signal processing problems. Implemented as analog very-large-scale integrated circuit that achieves rapid convergence. Alternatively, implemented as digital simulation of such circuit. Also used to improve phase estimation performance over that of phase-locked loop.

  7. Integrative multi-omics module network inference with Lemon-Tree.

    PubMed

    Bonnet, Eric; Calzone, Laurence; Michoel, Tom

    2015-02-01

    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

  8. 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

  9. Inference and Phase Transitions in the Detection of Modules in Sparse Networks

    NASA Astrophysics Data System (ADS)

    Decelle, Aurelien; Krzakala, Florent; Moore, Cristopher; Zdeborová, Lenka

    2011-08-01

    We present an asymptotically exact analysis of the problem of detecting communities in sparse random networks generated by stochastic block models. Using the cavity method of statistical physics and its relationship to belief propagation, we unveil a phase transition from a regime where we can infer the correct group assignments of the nodes to one where these groups are undetectable. Our approach yields an optimal inference algorithm for detecting modules, including both assortative and disassortative functional modules, assessing their significance, and learning the parameters of the underlying block model. Our algorithm is scalable and applicable to real-world networks, as long as they are well described by the block model.

  10. 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.

  11. Network analysis reveals that bacteria and fungi form modules that correlate independently with soil parameters.

    PubMed

    de Menezes, Alexandre B; Prendergast-Miller, Miranda T; Richardson, Alan E; Toscas, Peter; Farrell, Mark; Macdonald, Lynne M; Baker, Geoff; Wark, Tim; Thrall, Peter H

    2015-08-01

    Network and multivariate statistical analyses were performed to determine interactions between bacterial and fungal community terminal restriction length polymorphisms as well as soil properties in paired woodland and pasture sites. Canonical correspondence analysis (CCA) revealed that shifts in woodland community composition correlated with soil dissolved organic carbon, while changes in pasture community composition correlated with moisture, nitrogen and phosphorus. Weighted correlation network analysis detected two distinct microbial modules per land use. Bacterial and fungal ribotypes did not group separately, rather all modules comprised of both bacterial and fungal ribotypes. Woodland modules had a similar fungal?:?bacterial ribotype ratio, while in the pasture, one module was fungal dominated. There was no correspondence between pasture and woodland modules in their ribotype composition. The modules had different relationships to soil variables, and these contrasts were not detected without the use of network analysis. This study demonstrated that fungi and bacteria, components of the soil microbial communities usually treated as separate functional groups as in a CCA approach, were co-correlated and formed distinct associations in these adjacent habitats. Understanding these distinct modular associations may shed more light on their niche space in the soil environment, and allow a more realistic description of soil microbial ecology and function. PMID:25040229

  12. 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

  13. 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

  14. A terabit single-hop TDMA network with the spectrum-domain modulation

    NASA Astrophysics Data System (ADS)

    Smiljanic, Aleksandra; Kobayashi, Hisashi; Rhee, June-Koo

    1998-12-01

    In this paper, we propose a single-hop TDMA optical network with throughput of several Tb/s. This high throughput is achieved by combining spectrum encoding and fast demultiplexing. Fast packet switching is accomplished by using a rapidly tunable delay line. The frequency domain DPSK modulation is adopted, which provides 3 dB improvement over FD-OOK. Finally, we discuss a scalable protocol that can be employed in a network with a large number of channels and users.

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. Identifying functional modules in protein–protein interaction networks: an integrated exact approach

    PubMed Central

    Dittrich, Marcus T.; Klau, Gunnar W.; Rosenwald, Andreas; Dandekar, Thomas; Müller, Tobias

    2008-01-01

    Motivation: With the exponential growth of expression and protein–protein interaction (PPI) data, the frontier of research in systems biology shifts more and more to the integrated analysis of these large datasets. Of particular interest is the identification of functional modules in PPI networks, sharing common cellular function beyond the scope of classical pathways, by means of detecting differentially expressed regions in PPI networks. This requires on the one hand an adequate scoring of the nodes in the network to be identified and on the other hand the availability of an effective algorithm to find the maximally scoring network regions. Various heuristic approaches have been proposed in the literature. Results: Here we present the first exact solution for this problem, which is based on integer-linear programming and its connection to the well-known prize-collecting Steiner tree problem from Operations Research. Despite the NP-hardness of the underlying combinatorial problem, our method typically computes provably optimal subnetworks in large PPI networks in a few minutes. An essential ingredient of our approach is a scoring function defined on network nodes. We propose a new additive score with two desirable properties: (i) it is scalable by a statistically interpretable parameter and (ii) it allows a smooth integration of data from various sources. We apply our method to a well-established lymphoma microarray dataset in combination with associated survival data and the large interaction network of HPRD to identify functional modules by computing optimal-scoring subnetworks. In particular, we find a functional interaction module associated with proliferation over-expressed in the aggressive ABC subtype as well as modules derived from non-malignant by-stander cells. Availability: Our software is available freely for non-commercial purposes at http://www.planet-lisa.net. Contact: tobias.mueller@biozentrum.uni-wuerzburg.de PMID:18586718

  1. 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

  2. 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.

  3. 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.

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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.

  10. 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.

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

    DOEpatents

    Holmes, Michael Jerome (Thompson, ND); Ohrn, Theodore R. (Alliance, OH); Chen, Christopher Ming-Poh (Allentown, PA)

    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.

  12. Direct imaging of spatially modulated superfluid phases in atomic fermion systems.

    PubMed

    Mizushima, T; Machida, K; Ichioka, M

    2005-02-18

    It is proposed that the spatially modulated superfluid phase, or the Fulde-Ferrell-Larkin-Ovchinnikov state could be observed in resonant fermion atomic condensates which are realized recently. We examine optimal experimental setups to achieve it by solving the Bogoliubov-de Gennes equation for both idealized one-dimensional and realistic three-dimensional cases. The spontaneous modulation of this superfluid is shown to be directly imaged as the density profiles either by optical absorption or by Stern-Gerlach experiments. PMID:15783711

  13. 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

  14. 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.

  15. 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.

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

    PubMed

    Petersson, K M; Sandblom, J; Gisselgård, 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

  17. 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

  18. 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 ?m 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 2? range. The modulation transfer function was also measured.

  19. 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.

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

    PubMed

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

    2011-12-01

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

  1. Nonuniversality in Semi-Directed BARABÁSI-ALBERT Networks

    NASA Astrophysics Data System (ADS)

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

    2012-09-01

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

  2. A method for evaluating dynamic functional network connectivity and task-modulation: application to schizophrenia

    PubMed Central

    Sako?lu, Ünal; Pearlson, Godfrey D.; Kiehl, Kent A.; Wang, Y. Michelle; Michael, Andrew M.

    2010-01-01

    Objective In this paper, we develop a dynamic functional network connectivity (FNC) analysis approach using correlations between windowed time-courses of different brain networks (components) estimated via spatial independent component analysis (sICA). We apply the developed method to fMRI data to evaluate it and to study task-modulation of functional connections. Materials and methods We study the theoretical basis of the approach, perform a simulation analysis and apply it to fMRI data from schizophrenia patients (SP) and healthy controls (HC). Analyses on the fMRI data include: (a) group sICA to determine regions of significant task-related activity, (b) static and dynamic FNC analysis among these networks by using maximal lagged-correlation and time–frequency analysis, and (c) HC–SP group differences in functional network connections and in task-modulation of these connections. Results This new approach enables an assessment of task-modulation of connectivity and identifies meaningful inter-component linkages and differences between the two study groups during performance of an auditory oddball task (AOT). The static FNC results revealed that connectivities involving medial visual–frontal, medial temporal–medial visual, parietal–medial temporal, parietal–medial visual and medial temporal–anterior temporal were significantly greater in HC, whereas only the right lateral fronto-parietal (RLFP)–orbitofrontal connection was significantly greater in SP. The dynamic FNC revealed that task-modulation of motor–frontal, RLFP–medial temporal and posterior default mode (pDM)–parietal connections were significantly greater in SP, and task modulation of orbitofrontal–pDM and medial temporal–frontal connections were significantly greater in HC (all P < 0.05). Conclusion The task-modulation of dynamic FNC provided findings and differences between the two groups that are consistent with the existing hypothesis that schizophrenia patients show fewer segregated motor, sensory, cognitive functions and less default mode network activity when engaged with a task. Dynamic FNC, based on sICA, provided additional results which are different than, but complementary to, those of static FNC. For example, it revealed dynamic changes in default mode network connectivities with other regions which were significantly different in schizophrenia in terms of task-modulation, findings which were not possible to detect by static FNC. PMID:20162320

  3. 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

  4. Effect of gravitational focusing on annual modulation in dark-matter direct-detection experiments.

    PubMed

    Lee, Samuel K; Lisanti, Mariangela; Peter, Annika H G; Safdi, Benjamin R

    2014-01-10

    The scattering rate in dark-matter direct-detection experiments should modulate annually due to Earth's orbit around the Sun. The rate is typically thought to be extremized around June 1, when the relative velocity of Earth with respect to the dark-matter wind is maximal. We point out that gravitational focusing can alter this modulation phase. Unbound dark-matter particles are focused by the Sun's gravitational potential, affecting their phase-space density in the lab frame. Gravitational focusing can result in a significant overall shift in the annual-modulation phase, which is most relevant for dark matter with low scattering speeds. The induced phase shift for light O(10)??GeV dark matter may also be significant, depending on the threshold energy of the experiment. PMID:24483881

  5. Effect of Gravitational Focusing on Annual Modulation in Dark-Matter Direct-Detection Experiments

    NASA Astrophysics Data System (ADS)

    Lee, Samuel K.; Lisanti, Mariangela; Peter, Annika H. G.; Safdi, Benjamin R.

    2014-01-01

    The scattering rate in dark-matter direct-detection experiments should modulate annually due to Earth's orbit around the Sun. The rate is typically thought to be extremized around June 1, when the relative velocity of Earth with respect to the dark-matter wind is maximal. We point out that gravitational focusing can alter this modulation phase. Unbound dark-matter particles are focused by the Sun's gravitational potential, affecting their phase-space density in the lab frame. Gravitational focusing can result in a significant overall shift in the annual-modulation phase, which is most relevant for dark matter with low scattering speeds. The induced phase shift for light O(10) GeV dark matter may also be significant, depending on the threshold energy of the experiment.

  6. 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

  7. 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.

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

    PubMed Central

    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

  9. 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

  10. 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

  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. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. Rapid, time-division multiplexed, direct absorption- and wavelength modulation-spectroscopy.

    PubMed

    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

  20. 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.

  1. 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

  2. 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.

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. 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

  8. 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

  9. 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

  10. 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

  11. Functional Module Search in Protein Networks based on Semantic Similarity Improves the Analysis of Proteomics Data*

    PubMed Central

    Boyanova, Desislava; Nilla, Santosh; Klau, Gunnar W.; Dandekar, Thomas; Müller, Tobias; Dittrich, Marcus

    2014-01-01

    The continuously evolving field of proteomics produces increasing amounts of data while improving the quality of protein identifications. Albeit quantitative measurements are becoming more popular, many proteomic studies are still based on non-quantitative methods for protein identification. These studies result in potentially large sets of identified proteins, where the biological interpretation of proteins can be challenging. Systems biology develops innovative network-based methods, which allow an integrated analysis of these data. Here we present a novel approach, which combines prior knowledge of protein-protein interactions (PPI) with proteomics data using functional similarity measurements of interacting proteins. This integrated network analysis exactly identifies network modules with a maximal consistent functional similarity reflecting biological processes of the investigated cells. We validated our approach on small (H9N2 virus-infected gastric cells) and large (blood constituents) proteomic data sets. Using this novel algorithm, we identified characteristic functional modules in virus-infected cells, comprising key signaling proteins (e.g. the stress-related kinase RAF1) and demonstrate that this method allows a module-based functional characterization of cell types. Analysis of a large proteome data set of blood constituents resulted in clear separation of blood cells according to their developmental origin. A detailed investigation of the T-cell proteome further illustrates how the algorithm partitions large networks into functional subnetworks each representing specific cellular functions. These results demonstrate that the integrated network approach not only allows a detailed analysis of proteome networks but also yields a functional decomposition of complex proteomic data sets and thereby provides deeper insights into the underlying cellular processes of the investigated system. PMID:24807868

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

    PubMed

    Gonçalves, 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

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

    PubMed Central

    Gonçalves, 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

  14. Modulation of cerebello-cerebral resting state networks by site-specific stimulation.

    PubMed

    Rastogi, Anuj; Ghahremani, Ayda; Cash, Robin

    2015-10-01

    Converging evidence from neuroimaging and neuromodulation literature suggests that the cerebellum plays a broad role in motor as well as cognitive processes through its participation in resting-state networks. A recent study by Halko et al. (J Neurosci 34: 12049-12056, 2014) demonstrates, for the first time, the ability to modulate functional connectivity of some of these distinct resting-state networks using site-specific repetitive transcranial magnetic stimulation (rTMS) of the cerebellum. In this Neuro Forum, we discuss and critically analyze this study, emphasizing important findings, potential therapeutic relevance, and areas worthy of further inquiry. PMID:25673743

  15. 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.

  16. 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

  17. Identification of gene modules associated with drought response in rice by network-based analysis.

    PubMed

    Zhang, Lida; Yu, Shunwu; Zuo, Kaijing; Luo, Lijun; Tang, Kexuan

    2012-01-01

    Understanding the molecular mechanisms that underlie plant responses to drought stress is challenging due to the complex interplay of numerous different genes. Here, we used network-based gene clustering to uncover the relationships between drought-responsive genes from large microarray datasets. We identified 2,607 rice genes that showed significant changes in gene expression under drought stress; 1,392 genes were highly intercorrelated to form 15 gene modules. These drought-responsive gene modules are biologically plausible, with enrichments for genes in common functional categories, stress response changes, tissue-specific expression and transcription factor binding sites. We observed that a gene module (referred to as module 4) consisting of 134 genes was significantly associated with drought response in both drought-tolerant and drought-sensitive rice varieties. This module is enriched for genes involved in controlling the response of the plant to water and embryonic development, including a heat shock transcription factor as the key regulator in the expression of ABRE-containing genes. These results suggest that module 4 is highly conserved in the ABA-mediated drought response pathway in different rice varieties. Moreover, our study showed that many hub genes clustered in rice chromosomes had significant associations with QTLs for drought stress tolerance. The relationship between hub gene clusters and drought tolerance QTLs may provide a key to understand the genetic basis of drought tolerance in rice. PMID:22662107

  18. Sequential interrogation of multiple FBG sensors using LPG modulation and an artificial neural network

    NASA Astrophysics Data System (ADS)

    Basu, Mainak; Ghorai, S. K.

    2015-04-01

    Interrogating multiple fiber Bragg gratings (FBG) requires highly sensitive spectrum scanning equipment such as optical spectrum analyzers, tunable filters, acousto-optic tunable filters etc, which are expensive, bulky and time consuming. In this paper, we present a new approach for multiple FBG sensor interrogation using long-period gratings and an artificial neural network. The reflection spectra of the multiplexed FBGs are modulated by two long period gratings separately and the modulated optical intensities were detected by two photodetectors. The outputs of the detectors are then used as input in a previously trained artificial neural network to interrogate the FBG sensors. Simulations have been performed to determine the strain and wavelength shift using two and four sensors. The interrogation system has also been demonstrated experimentally for two sensors using simply supported beams in the range of 0-350??strain. The proposed interrogation scheme has been found to identify the perturbed FBG, and to determine strain and wavelength shift with reasonable accuracy.

  19. 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.

  20. 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

  1. Superconducting Network in Spatially Modulated Magnetic Field — Hofstadter-Type Problem in Checkerboard Field

    NASA Astrophysics Data System (ADS)

    Ito, Suguru; Ando, Masato; Katsumoto, Shingo; Iye, Yasuhiro

    1999-10-01

    The superconducting transition of a two-dimensional square network of Nb in a spatially modulated magnetic field, consisting of a uniform componentand a sign-alternating (checkerboard pattern) component, has been studied.Evolution of the Little-Parks oscillation pattern as a function of thecheckerboard field amplitude manifests some features of the low-energy envelopes of the corresponding Hofstadter butterfly-type diagrams.

  2. A wideband radiometer module for an unamplified direct detection scalable W-band imaging array

    NASA Astrophysics Data System (ADS)

    Schaffner, James H.; Lynch, Jonathan J.; Guinn, Keith V.; Schulman, Joel N.; Moyer, Harris P.; Bowen, Ross; Musni, Marcel

    2008-04-01

    A W-band unamplified direct detection radiometer module is described that provides a wideband response and is scalable to large arrays. The radiometer design is intended to provide sufficient sensitivity for millimeter wave imaging applications with a goal of 2K noise equivalent temperature difference (NETD) at a 30 Hz frame rate. This effort leverages previously reported device scaling to increase sensitivity. We present a radiometer module designed for 60 GHz RF bandwidth that utilizes HRL's antimonide-based backward tunnel diode. An impedance matching circuit with on- and off-chip elements, as well as ridged waveguide, provides a wideband match to the detectors. Modules were designed with two different microwave substrates: 125 micron thick quartz and 100 micron thick alumina. flip-chip bonding of the detectors is amenable to automated pick-and-place for high volume manufacturing. The modular nature of the array approach allows large arrays to be manufactured in a straightforward manner. We present the design approach along with both electromagnetic simulations and measured performance of the modules. This work was supported by phase II of DARPA's MIATA program.

  3. Layered ACO-OFDM for intensity-modulated direct-detection optical wireless transmission.

    PubMed

    Wang, Qi; Qian, Chen; Guo, Xuhan; Wang, Zhaocheng; Cunningham, David G; White, Ian H

    2015-05-01

    Layered asymmetrically clipped optical orthogonal frequency division multiplexing (ACO-OFDM) with high spectral efficiency is proposed in this paper for optical wireless transmission employing intensity modulation with direct detection. In contrast to the conventional ACO-OFDM, which only utilizes odd subcarriers for modulation, leading to an obvious spectral efficiency loss, in layered ACO-OFDM, the subcarriers are divided into different layers and modulated by different kinds of ACO-OFDM, which are combined for simultaneous transmission. In this way, more subcarriers are used for data transmission and the spectral efficiency is improved. An iterative receiver is also proposed for layered ACO-OFDM, where the negative clipping distortion of each layer is subtracted once it is detected so that the signals from different layers can be recovered. Theoretical analysis shows that the proposed scheme can improve the spectral efficiency by up to 2 times compared with conventional ACO-OFDM approaches with the same modulation order. Meanwhile, simulation results confirm a considerable signal-to-noise ratio gain over ACO-OFDM at the same spectral efficiency. PMID:25969323

  4. 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)

  5. Identification of Functional Modules by Integration of Multiple Data Sources Using a Bayesian Network Classifier

    PubMed Central

    Wang, Jinlian; Zuo, Yiming; Liu, Lun; Man, Yangao; Tadesse, Mahlet G.; Ressom, Habtom W

    2014-01-01

    Background Prediction of functional modules is indispensable for detecting protein deregulation in human complex diseases such as cancer. Bayesian network (BN) is one of the most commonly used models to integrate heterogeneous data from multiple sources such as protein domain, interactome, functional annotation, genome-wide gene expression, and the literature. Methods and Results In this paper, we present a BN classifier that is customized to: 1) increase the ability to integrate diverse information from different sources, 2) effectively predict protein-protein interactions, 3) infer aberrant networks with scale-free and small world properties, and 4) group molecules into functional modules or pathways based on the primary function and biological features. Application of this model on discovering protein biomarkers of hepatocelluar carcinoma (HCC) leads to the identification of functional modules that provide insights into the mechanism of the development and progression of HCC. These functional modules include cell cycle deregulation, increased angiogenesis (e.g., vascular endothelial growth factor, blood vessel morphogenesis), oxidative metabolic alterations, and aberrant activation of signaling pathways involved in cellular proliferation, survival, and differentiation. Conclusion The discoveries and conclusions derived from our customized BN classifier are consistent with previously published results. The proposed approach for determining BN structure facilitates the integration of heterogeneous data from multiple sources to elucidate the mechanisms of complex diseases. PMID:24736851

  6. 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.

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

    PubMed Central

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

    2004-01-01

    Background Cellular functions are coordinately carried out by groups of genes forming functional modules. Identifying such modules in the transcriptional regulatory network (TRN) of organisms is important for understanding the structure and function of these fundamental cellular networks and essential for the emerging modular biology. So far, the global connectivity structure of TRN has not been well studied and consequently not applied for the identification of functional modules. Moreover, network motifs such as feed forward loop are recently proposed to be basic building blocks of TRN. However, their relationship to functional modules is not clear. Results In this work we proposed a top-down approach to identify modules in the TRN of E. coli. By studying the global connectivity structure of the regulatory network, we first revealed a five-layer hierarchical structure in which all the regulatory relationships are downward. Based on this regulatory hierarchy, we developed a new method to decompose the regulatory network into functional modules and to identify global regulators governing multiple modules. As a result, 10 global regulators and 39 modules were identified and shown to have well defined functions. We then investigated the distribution and composition of the two basic network motifs (feed forward loop and bi-fan motif) in the hierarchical structure of TRN. We found that most of these network motifs include global regulators, indicating that these motifs are not basic building blocks of modules since modules should not contain global regulators. Conclusion The transcriptional regulatory network of E. coli possesses a multi-layer hierarchical modular structure without feedback regulation at transcription level. This hierarchical structure builds the basis for a new and simple decomposition method which is suitable for the identification of functional modules and global regulators in the transcriptional regulatory network of E. coli. Analysis of the distribution of feed forward loops and bi-fan motifs in the hierarchical structure suggests that these network motifs are not elementary building blocks of functional modules in the transcriptional regulatory network of E. coli. PMID:15603590

  8. 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

  9. 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.

  10. 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.

  11. Pinning Synchronization of Directed Networks With Switching Topologies: A Multiple Lyapunov Functions Approach.

    PubMed

    Wen, Guanghui; Yu, Wenwu; Hu, Guoqiang; Cao, Jinde; Yu, Xinghuo

    2015-12-01

    This paper studies the global pinning synchronization problem for a class of complex networks with switching directed topologies. The common assumption in the existing related literature that each possible network topology contains a directed spanning tree is removed in this paper. Using tools from M -matrix theory and stability analysis of the switched nonlinear systems, a new kind of network topology-dependent multiple Lyapunov functions is proposed for analyzing the synchronization behavior of the whole network. It is theoretically shown that the global pinning synchronization in switched complex networks can be ensured if some nodes are appropriately pinned and the coupling is carefully selected. Interesting issues of how many and which nodes should be pinned for possibly realizing global synchronization are further addressed. Finally, some numerical simulations on coupled neural networks are provided to verify the theoretical results. PMID:26595418

  12. 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

  13. 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.

  14. 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.

  15. 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

  16. Low-dispersion penalty directly modulated 1.55-um DFB lasers with complex coupled gratings

    NASA Astrophysics Data System (ADS)

    Ketelsen, Leonard J. P.; Eng, L.; Kim, Il; Grenko, J. A.; Sutryn, D.; Wessel, Thomas; Chakrabarti, U. K.; Coblentz, Debbie L.; Hartman, Robert L.

    1996-04-01

    Prior to the full maturation of electro-absorption modulated laser technology, directly modulated 1.55 micrometer distributed feedback lasers will continue to play a central role in long haul, high bit rate, optical communications systems. Maintaining a competitive advantage, however, requires that these devices be optimized for long fiber length transmission, high power, and low cost. In this talk we discuss the design elements needed to accomplish this. Focus is placed on factors leading to reduction of the linewidth enhancement factor, (alpha) . In particular, the role played by complex gratings is examined. We demonstrate typical cw (alpha) values of 1.65 can be achieved in a robust and manufacturable device. This device is shown to readily serve 2.5 Gb/s applications with span lengths of 200 km (approximately 3600 ps/nm).

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

    PubMed Central

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

    2013-01-01

    Disease-causing mutations usually change the interacting partners of mutant proteins. In this article, we propose that the biological consequences of mutation are directly related to the alteration of corresponding protein protein interaction networks (PPIN). Mutation of Huntingtin (HTT) which causes Huntington's disease (HD) and mutations to TP53 which is associated with different cancers are studied as two example cases. We construct the PPIN of wild type and mutant proteins separately and identify the structural modules of each of the networks. The functional role of these modules are then assessed by Gene Ontology (GO) enrichment analysis for biological processes (BPs). We find that a large number of significantly enriched () GO terms in mutant PPIN were absent in the wild type PPIN indicating the gain of BPs due to mutation. Similarly some of the GO terms enriched in wild type PPIN cease to exist in the modules of mutant PPIN, representing the loss. GO terms common in modules of mutant and wild type networks indicate both loss and gain of BPs. We further assign relevant biological function(s) to each module by classifying the enriched GO terms associated with it. It turns out that most of these biological functions in HTT networks are already known to be altered in HD and those of TP53 networks are altered in cancers. We argue that gain of BPs, and the corresponding biological functions, are due to new interacting partners acquired by mutant proteins. The methodology we adopt here could be applied to genetic diseases where mutations alter the ability of the protein to interact with other proteins. PMID:23741403

  18. 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 7–12 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

  19. 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

  20. 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

  1. Prototyping of optoelectronic clock distribution networks on multichip modules using silica glass waveguides and silicon microstructures

    NASA Astrophysics Data System (ADS)

    Koh, Seungug; Wu, Danjin

    1999-04-01

    The next generation giga-Hertz microprocessors require a high-speed clocking scheme with a robust and low-skew clock distribution network. The guided-wave optoelectronic clock distribution networks on multichip modules (MCMs) is believed to satisfy the high-speed clocking requirements by providing superior network bandwidth, low power consumption,and large fanout compared to the electrical interconnect counterpart. In this paper, we report a sixteen-fanout H-tree clock distribution network on MCMs, which utilizes silica glass waveguides and micromachined silicon microstructures. The proposed optoelectronic multichip modules (OE-MCMs) can be fabricated in a CMOS compatible batch process without modifying the conventional IC fabrication facilities and the OE-MCM assembly/packaging processes are simple and economical due to the arrays are characterized at wavelengths of 1310 nm and 1550 nm. The issues of system-level modeling and prototyping are also addressed by discussing VHDL/FD-BPM-based simulation tool: Optoelectronic System Simulator, such that OE-MCMs can be rapidly-designed and mass-produced through the design automation tools.

  2. Two cascaded SOAs used as intensity modulators for adaptively modulated optical OFDM signals in optical access networks.

    PubMed

    Hamié, Ali; Hamzé, Mohamad; Taki, Haidar; Makouk, Layaly; Sharaiha, Ammar; Alaeddine, Ali; Al Housseini, Ali; Giacoumidis, Elias; Tang, J M

    2014-06-30

    Detailed theoretical and numerical investigations of the transmission performance of adaptively modulated optical orthogonal frequency division multiplexed (AMOOFDM) signals are undertaken, for the first time, in optical amplification and chromatic dispersion (CD) compensation free single mode fiber (SMF) intensity-modulated and direct-detection (IMDD) systems using two cascaded semiconductor optical amplifiers in a counterpropagating configuration as an intensity modulator (TC-SOA-CC-IM). A theoretical model describing the characteristics of this configuration is developed. Extensive performance comparisons are also made between the TC-SOA-CC and the single SOA intensity modulators. It is shown that, the TC-SOA-CC reaches its strongly saturated region using a lower input optical power much faster than the single SOA resulting in significantly reduced effective carrier lifetime and thus wide TC-SOA-CC bandwidths. It is shown that at low input optical power, we can increase the signal line rate almost 115% which will be more than twice the transmission performance offered by single SOA. In addition, the TC-SOA-CC-IM is capable of supporting signal line rates higher than corresponding to the SOA-IM by using 10dB lower input optical powers. For long transmission distance, the TC-SOA-CC-IM has much stronger CD compensation capability compared to the SOA-IM. In addition the use of TC-SOA-CC-IM is more effective regarding the capability to benefit from the CD compensation for shorter distances starting at 60km SMF, whilst for the SOA-IM starting at 90km. PMID:24977835

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

    PubMed Central

    Hu, Zhenjun; Mellor, Joe; Wu, Jie; Yamada, Takuji; Holloway, Dustin; DeLisi, Charles

    2005-01-01

    VisANT is a web-based software framework for visualizing and analyzing many types of networks of biological interactions and associations. Networks are a useful computational tool for representing many types of biological data, such as biomolecular interactions, cellular pathways and functional modules. Given user-defined sets of interactions or groupings between genes or proteins, VisANT provides: (i) a visual interface for combining and annotating network data, (ii) supporting function and annotation data for different genomes from the Gene Ontology and KEGG databases and (iii) the statistical and analytical tools needed for extracting topological properties of the user-defined networks. Users can customize, modify, save and share network views with other users, and import basic network data representations from their own data sources, and from standard exchange formats such as PSI-MI and BioPAX. The software framework we employ also supports the development of more sophisticated visualization and analysis functions through its open API for Java-based plug-ins. VisANT is distributed freely via the web at and can also be downloaded for individual use. PMID:15980487

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

    NASA Astrophysics Data System (ADS)

    Ghani, Nasir

    1992-07-01

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

  5. 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.

  6. 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.

  7. 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

  8. 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

  9. 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.

  10. Techniques for high-speed direct modulation of quantum dot lasers

    NASA Astrophysics Data System (ADS)

    Li, Yan

    As a major component of optical transmitters, directly-modulated semiconductor lasers are widely used in today's fiber optical link systems by taking its advantage of their low cost, compact size and low power consumption. In this work, techniques to improve the high frequency modulation characteristics of semiconductor lasers with a low-dimensional active region medium, specifically quantum dots (QDs), are studied. These techniques include a p-doped active region in single-section QD lasers, the gain-lever effect in two-section lasers and the injection-locking technique. Firstly, the modulation performances of p-doped InAs/GaAs QD lasers were studied. Contrary to the theoretical predictions, the modulation efficiency and the highest relaxation frequency of 1.2-mm cavity length lasers decreasse monotonically with the p-doping level from 0.54 GHz/mA1/2 and 5.3 GHz (un-doped dots), to 0.46 GHz/mAl/2 and 3.6 GHz (40 holes/dot). Although the maximum ground state gain of the p-doped lasers is increases with p-type concentration, the undesired increase in internal losses induces stronger gain saturation and gain compression, thus degrading the high-speed performance. The degradation of the modulation performance of the p-doped device is also attributed to a higher gain compression factor due to the carrier heating effect. Secondly, the gain-lever effect is studied in two-section QD lasers in order to enhance the modulation efficiency and 3-dB bandwidth. An 8-dB modulation efficiency enhancement is achieved using the p-doped QD laser. Due to the stronger gain saturation with carrier density, it is found that un-doped QD devices show a more significant gain-lever effect over p-doped devices. A 20 dB enhancement of the modulation efficiency is demonstrated by the un-doped QD laser. A new modulation response equation is derived under the high photon density approximation, and a 1.7X 3-dB bandwidth improvement is theoretically predicted by the new model and realized in an un-doped QD gain-lever laser under extreme asymmetric pumping conditions. It is also demonstrated for the first time that the 3-dB bandwidth in gain-lever laser can be 3X higher than the relaxation frequency instead of 1.55X in typical single-section lasers. Finally, injection locking in QDash lasers was analyzed. By varying the power injection ratio and detuning, the modulation bandwidth of a 0.5-mm QDash Fabry-Perot slave laser by 4 times. By analyzing the curve fitted data, it was observed that the inverted gain-lever modulation response equation can approximate the injection-locking system in the Period 1, non-linear regime. Based on the gain-lever model, an analytical expression for the relaxation frequency of an injection-locked laser is derived, and the maximum achievable 3-dB bandwidth is predicted and verified experimentally.

  11. Novel Quantum Virtual Private Network Scheme for PON via Quantum Secure Direct Communication

    NASA Astrophysics Data System (ADS)

    Gong, Li-Hua; Liu, Ye; Zhou, Nan-Run

    2013-09-01

    Two quantum secure direct communication (QSDC) protocols with quantum identification (QI) based on passive optical network (PON) architecture are proposed. One QSDC protocol can be implemented between two different optical network units just with simple configurations of PON by optical line terminal when they are in the same virtual private network after optical line terminal performing QI to the optical network units in the given PON architecture. The other QSDC protocol is also implemented between any two legitimated users in the virtual private network but with considerable reduction of workload of the optical line terminal. The security analysis shows that the proposed QSDC schemes with quantum identification are unconditionally secure and allow the legitimate users to exchange their secret information efficiently and to realize a quantum virtual private network in the PON networks ultimately.

  12. 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

  13. 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.

  14. 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

  15. 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.

  16. Low-Intensity Electrical Stimulation Affects Network Dynamics by Modulating Population Rate and Spike Timing

    PubMed Central

    Reato, Davide; Rahman, Asif; Bikson, Marom; Parra, Lucas C.

    2012-01-01

    Clinical effects of transcranial electrical stimulation with weak currents are remarkable considering the low amplitude of the electric fields acting on the brain. Elucidating the processes by which small currents affect ongoing brain activity is of paramount importance for the rational design of noninvasive electrotherapeutic strategies and to determine the relevance of endogenous fields. We propose that in active neuronal networks, weak electrical fields induce small but coherent changes in the firing rate and timing of neuronal populations that can be magnified by dynamic network activity. Specifically, we show that carbachol-induced gamma oscillations (25–35 Hz) in rat hippocampal slices have an inherent rate-limiting dynamic and timing precision that govern susceptibility to low-frequency weak electric fields (<50 Hz; <10 V/m). This leads to a range of nonlinear responses, including the following: (1) asymmetric power modulation by DC fields resulting from balanced excitation and inhibition; (2) symmetric power modulation by lower frequency AC fields with a net-zero change in firing rate; and (3) half-harmonic oscillations for higher frequency AC fields resulting from increased spike timing precision. These underlying mechanisms were elucidated by slice experiments and a parsimonious computational network model of single-compartment spiking neurons responding to electric field stimulation with small incremental polarization. Intracellular recordings confirmed model predictions on neuronal timing and rate changes, as well as spike phase-entrainment resonance at 0.2 V/m. Finally, our data and mechanistic framework provide a functional role for endogenous electric fields, specifically illustrating that modulation of gamma oscillations during theta-modulated gamma activity can result from field effects alone. PMID:21068312

  17. 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

  18. 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

  19. 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

  20. 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

  1. 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

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

    PubMed

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

    2011-12-01

    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

  3. 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.

  4. 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

  5. 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

  6. 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.

  7. Direct white-light and a dual-channel barcode module from Pr(III)-MOF crystals.

    PubMed

    Du, Bin-Bin; Zhu, Yi-Xuan; Pan, Mei; Yue, Mei-Qin; Hou, Ya-Jun; Wu, Kai; Zhang, Lu-Yin; Chen, Ling; Yin, Shao-Yun; Fan, Ya-Nan; Su, Cheng-Yong

    2015-08-14

    Direct white-light emission and further a dual-channel readable barcode module in both visible and NIR region was established by single-component homo-metallic Pr(iii)-MOF crystals for the first time. PMID:26152399

  8. Molecular inspired models for prediction and control of directional FSO/RF wireless networks

    NASA Astrophysics Data System (ADS)

    Llorca, Jaime; Milner, Stuart D.; Davis, Christopher C.

    2010-08-01

    Directional wireless networks using FSO and RF transmissions provide wireless backbone support for mobile communications in dynamic environments. The heterogeneous and dynamic nature of such networks challenges their robustness and requires self-organization mechanisms to assure end-to-end broadband connectivity. We developed a framework based on the definition of a potential energy function to characterize robustness in communication networks and the study of first and second order variations of the potential energy to provide prediction and control strategies for network performance optimization. In this paper, we present non-convex molecular potentials such as the Morse Potential, used to describe the potential energy of bonds within molecules, for the characterization of communication links in the presence of physical constraints such as the power available at the network nodes. The inclusion of the Morse Potential translates into adaptive control strategies where forces on network nodes drive the release, retention or reconfiguration of communication links for network performance optimization. Simulation results show the effectiveness of our self-organized control mechanism, where the physical topology reorganizes to maximize the number of source to destination communicating pairs. Molecular Normal Mode Analysis (NMA) techniques for assessing network performance degradation in dynamic networks are also presented. Preliminary results show correlation between peaks in the eigenvalues of the Hessian of the network potential and network degradation.

  9. 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

  10. 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

  11. Reachability and recoverability of sink nodes in growing acyclic directed networks

    NASA Astrophysics Data System (ADS)

    Barbosa, Valmir C.

    2008-01-01

    We study the growth of networks from a set of isolated ground nodes by the addition of one new node per time step and also of a fixed number of directed edges leading from the new node to randomly selected nodes already in the network. A fixed-width time window is used so that, in general, only nodes that entered the network within the latest window may receive new incoming edges. The resulting directed network is acyclic at all times and allows some of the ground nodes, then called sinks, to be reached from some of the non-ground nodes. We regard such networks as representative of abstract systems of partially ordered constituents, for example in some of the domains related to technological evolution. Two properties of interest are the number of sinks that can be reached from a randomly chosen non-ground node (its reach) and, for a fixed sink, the number of nonoverlapping directed paths through which the sink can be reached, at a given time, from some of the latest nodes to have entered the network. We demonstrate, by means of simulations and also of analytic characterizations, that reaches are distributed according to a power law and that the desired directed paths are expected to occur in very small numbers, perhaps indicating that recovering sinks late in the process of network growth is strongly sensitive to accidental path disruptions.

  12. 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

  13. 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…

  14. 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…

  15. 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.

  16. Modulation of Cortical Activity by Transcranial Direct Current Stimulation in Patients with Affective Disorder

    PubMed Central

    Powell, Tamara Y.; Boonstra, Tjeerd W.; Martin, Donel M.; Loo, Colleen K.; Breakspear, Michael

    2014-01-01

    Transcranial direct current stimulation (tDCS) has been shown to have antidepressant efficacy in patients experiencing a major depressive episode, but little is known about the underlying neurophysiology. The purpose of our study was to investigate the acute effects of tDCS on cortical activity using electroencephalography (EEG) in patients with an affective disorder. Eighteen patients diagnosed with an affective disorder and experiencing a depressive episode participated in a sham-controlled study of tDCS, each receiving a session of active (2 mA for 20 minutes) and sham tDCS to the left dorsolateral prefrontal cortex (DLPFC). The effects of tDCS on EEG activity were assessed after each session using event-related potentials (ERP) and measurement of spectral activity during a visual working memory (VWM) task. We observed task and intervention dependent effects on both ERPs and task-related alpha and theta activity, where active compared to sham stimulation resulted in a significant reduction in the N2 amplitude and reduced theta activity over frontal areas during memory retrieval. In summary a single session of anodal tDCS stimulation to the left DLPFC during a major depressive episode resulted in modulated brain activity evident in task-related EEG. Effects on the N2 and frontal theta activity likely reflect modulated activity in the medial frontal cortex and hence indicate that the after-effects of tDCS extend beyond the direct focal effects to the left DLPFC. PMID:24914953

  17. Direct learning of sparse changes in Markov networks by density ratio estimation.

    PubMed

    Liu, Song; Quinn, John A; Gutmann, Michael U; Suzuki, Taiji; Sugiyama, Masashi

    2014-06-01

    We propose a new method for detecting changes in Markov network structure between two sets of samples. Instead of naively fitting two Markov network models separately to the two data sets and figuring out their difference, we directly learn the network structure change by estimating the ratio of Markov network models. This density-ratio formulation naturally allows us to introduce sparsity in the network structure change, which highly contributes to enhancing interpretability. Furthermore, computation of the normalization term, a critical bottleneck of the naive approach, can be remarkably mitigated. We also give the dual formulation of the optimization problem, which further reduces the computation cost for large-scale Markov networks. Through experiments, we demonstrate the usefulness of our method. PMID:24684449

  18. 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.

  19. 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

  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 2? phase change voltage to 22.8V at 1.55?m 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. DHCVIM - a direct heating containment vessel interactions module: applications to Sandia National Laboratories Surtsey experiments

    SciTech Connect

    Ginsberg, T.; Tutu, N.K.

    1987-01-01

    Direct containment heating is the mechanism of severe nuclear reactor accident containment loading that results from transfer of thermal and chemical energy from high-temperature, finely divided, molten core material to the containment atmosphere. The direct heating containment vessel interactions module (DHCVIM) has been developed at Brookhaven National Laboratory to model the mechanisms of containment loading resulting from the direct heating accident sequence. The calculational procedure is being used at present to model the Sandia National Laboratories one-tenth-scale Surtsey direct containment heating experiments. The objective of the code is to provide a test bed for detailed modeling of various aspects of the thermal, chemical, and hydrodynamic interactions that are expected to occur in three regions of a containment building: reactor cavity, intermediate subcompartments, and containment dome. Major emphasis is placed on the description of reactor cavity dynamics. This paper summarizes the modeling principles that are incorporated in DHCVIM and presents a prediction of the Surtsey Test DCH-2 that was made prior to execution of the experiment.

  2. DHCVIM: A direct heating containment vessel interactions module: Applications to Sandia National Laboratory Surtsey experiments

    SciTech Connect

    Ginsberg, T.; Tutu, N.K.

    1987-01-01

    Direct containment heating is the mechanism of severe nuclear reactor accident containment loading which results from transfer of thermal and chemical energy from high temperature, finely divided, molten core material to the containment atmosphere. The Direct Heating Containment Vessel Interactions Module, DHCVIM, has been developed at BNL to mechanistically model the mechanisms of containment loading resulting from the direct heating accident sequence. The calculational procedure is being used at present to model the Sandia National Laboratory 1/10th-scale Surtsey direct containment heating experiments. The objective of the code is to provide a test bed for detailed modeling of various aspects of the thermal, chemical and hydrodynamic interactions which are expected to occur in three regions of a containment building: reactor cavity, intermediate subcompartments and containment done. Major emphasis is placed, at present, on the description of reactor cavity dynamics. This paper summarizes the modeling principles which are incorporated in DHCVIM and presents a prediction of the Surtsey Test DCH-2 which was made prior to execution of the experiment.

  3. Modulation of effective connectivity in the default mode network at rest and during a memory task.

    PubMed

    Li, Xingfeng; Kehoe, Elizabeth G; McGinnity, Thomas Martin; Coyle, Damien; Bokde, Arun L W

    2015-02-01

    It is known that the default mode network (DMN) may be modulated by a cognitive task and by performance level. Changes in the DMN have been examined by investigating resting-state activation levels, but there have been very few studies examining the modulation of effective connectivity of the DMN during a task in healthy older subjects. In this study, the authors examined how effective connectivity changed in the DMN between rest and during a memory task. The authors also investigated whether there was any relationship between effective connectivity modulation in the DMN and memory performance, to establish whether variations in cognitive performance are related to neural network effective connectivity, either at rest or during task performance. Twenty-eight healthy older participants underwent a resting-state functional magnetic resonance imaging scan and an emotional face-name encoding task. Effective connectivity analyses were performed on the DMN to examine the effective connectivity modulation in these two different conditions. During the resting state, there was strong self-influence in the regions of the DMN, while the main regions with statistically significant cross-regional effective connectivity were the posterior cingulate cortex (PCC) and the hippocampus (HP). During the memory task, the self-influence effective connectivities remained statistically significant across the DMN, and there were statistically significant effective connectivities from the PCC, HP, amygdala (AM), and parahippocampal region to other DMN regions. The authors found that effective connectivities from PCC, HP, and AM (in both resting state and during task) were linearly correlated to memory performance. The results suggest that superior memory ability in this older cohort was associated with effective connectivity both at rest and during the memory task of three DMN regions, which are also known to be important for memory function. PMID:25390185

  4. 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

  5. Characterizing system dynamics with a weighted and directed network constructed from time series data

    SciTech Connect

    Sun, Xiaoran; School of Mathematics and Statistics, The University of Western Australia, Crawley WA 6009 ; Small, Michael; Zhao, Yi; Xue, Xiaoping

    2014-06-15

    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.

  6. 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.

  7. 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.

  8. 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

  9. 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

  10. 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

  11. 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.

  12. 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-?m 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.

  13. Comparison of IPDA lidar receiver sensitivity for coherent detection and for direct detection using sine-wave and pulsed modulation.

    PubMed

    Sun, Xiaoli; Abshire, James B

    2012-09-10

    We use theoretical models to compare the receiver signal to noise ratio (SNR) vs. average rate of detected signal photons for an integrated path differential absorption (IPDA) lidar using coherent detection with continuous wave (CW) lasers and direct detection with sine-wave and pulse modulations. The results show the coherent IPDA lidar has high receiver gain and narrow bandwidth to overcome the effects of detector circuit noise and background light, but the actual receiver performance can be limited by the coherent mixing efficiency, speckle and other factors. For direct detection, using sine-wave modulation allows the use of a low peak power laser transmitter and synchronous detection. The pulse modulation technique requires higher laser peak powers but is more efficient than sine-wave modulation in terms of average detected signal photon rate required to achieve a given receiver SNR. We also conducted experiments for the direct detection cases and the results agreed well with theory. PMID:23037252

  14. Generalised Sandpile Dynamics on Artificial and Real-World Directed Networks.

    PubMed

    Zachariou, Nicky; Expert, Paul; Takayasu, Misako; Christensen, Kim

    2015-01-01

    The main finding of this paper is a novel avalanche-size exponent ? ? 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 ? out of the two-dimensional directed sandpile universality class ? = 4/3, into the mean field universality class ? = 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

  15. 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

  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. 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. Hum Brain Mapp 37:381-394, 2016. © 2015 Wiley Periodicals, Inc. PMID:26512872

  18. Identification and evaluation of network modules for the prognosis of basal-like breast cancer

    PubMed Central

    Hallett, Robin M.; Cockburn, Jessica G.; Li, Brian; Dvorkin-Gheva, Anna; Hassell, John A.; Bane, Anita

    2015-01-01

    Purpose Basal-like breast cancer (BLBC) is a molecular subtype of breast cancer associated with poor clinical outcome, although some patients with BLBC experience long-term survival. Apart from nodal status, current clinical/histopathological variables show little capacity to identify BLBC patients at either high- or low-risk of disease recurrence. Accordingly, we sought to develop a network based genomic predictor for predicting the outcome of patients with BLBC. Experimental Design We performed network analysis on global gene expression profiling data of BLBCs, and identified BLBC network modules associated with AP-1 transcription, G-protein coupled receptors, and T-, B-, and NK-cells that are significant predictors of BLBC patient survival. Results In gene expression and tissue microarray (TMA) validation cohorts of 210 and 102 BLBC patients, respectively, the identified network modules were robustly associated with patient outcome. In the gene expression validation cohort, the Kaplan-Meier estimate for 10-year survival in the low-risk group was 90%, whereas in the high-risk group it was a 56%. In the TMA cohort, the Kaplan-Meier estimate for 10-year survival in the low-risk group was 98%, whereas in the high-risk group it was 71%. Conclusions The capacity to distinguish between patients with BLBC at high- or low-risk of recurrence at the time of diagnosis could permit timely intervention with more aggressive therapeutic regimens in those patients predicted to be high-risk, and to avoid such therapy in low-risk patients. PMID:25991675

  19. 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

  20. 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

  1. 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

  2. Pre-stimulus BOLD-network activation modulates EEG spectral activity during working memory retention

    PubMed Central

    Kottlow, Mara; Schlaepfer, Anthony; Baenninger, Anja; Michels, Lars; Brandeis, Daniel; Koenig, Thomas

    2015-01-01

    Working memory (WM) processes depend on our momentary mental state and therefore exhibit considerable fluctuations. Here, we investigate the interplay of task-preparatory and task-related brain activity as represented by pre-stimulus BOLD-fluctuations and spectral EEG from the retention periods of a visual WM task. Visual WM is used to maintain sensory information in the brain enabling the performance of cognitive operations and is associated with mental health. We tested 22 subjects simultaneously with EEG and fMRI while performing a visuo-verbal Sternberg task with two different loads, allowing for the temporal separation of preparation, encoding, retention and retrieval periods. Four temporally coherent networks (TCNs)—the default mode network (DMN), the dorsal attention, the right and the left WM network—were extracted from the continuous BOLD data by means of a group ICA. Subsequently, the modulatory effect of these networks' pre-stimulus activation upon retention-related EEG activity in the theta, alpha, and beta frequencies was analyzed. The obtained results are informative in the context of state-dependent information processing. We were able to replicate two well-known load-dependent effects: the frontal-midline theta increase during the task and the decrease of pre-stimulus DMN activity. As our main finding, these two measures seem to depend on each other as the significant negative correlations at frontal-midline channels suggested. Thus, suppressed pre-stimulus DMN levels facilitated later task related frontal midline theta increases. In general, based on previous findings that neuronal coupling in different frequency bands may underlie distinct functions in WM retention, our results suggest that processes reflected by spectral oscillations during retention seem not only to be “online” synchronized with activity in different attention-related networks but are also modulated by activity in these networks during preparation intervals. PMID:25999828

  3. 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

  4. 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.

  5. 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

  6. 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).

  7. 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

  8. 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

  9. 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.

  10. 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

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

    NASA Astrophysics Data System (ADS)

    Li, Jianping; Wakahara, Yasushi

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

  12. Direct innervation and modulation of orexin neurons by lateral hypothalamic LepRb neurons.

    PubMed

    Louis, Gwendolyn W; Leinninger, Gina M; Rhodes, Christopher J; Myers, Martin G

    2010-08-25

    Leptin, the adipose-derived hormonal signal of body energy stores, acts via the leptin receptor (LepRb) on neurons in multiple brain regions. We previously identified LepRb neurons in the lateral hypothalamic area (LHA), which are distinct from neighboring leptin-regulated melanin-concentrating hormone (MCH)- or orexin (OX)-expressing cells. Neither the direct synaptic targets of LHA LepRb neurons nor their potential role in the regulation of other LHA neurons has been determined, however. We thus generated several adenoviral and transgenic systems in which cre recombinase promotes the expression of the tracer, WGA (wheat germ agglutinin), and used these in combination with LepRb(cre) mice to determine the neuronal targets of LHA LepRb neurons. This analysis revealed that, although some LHA LepRb neurons project to dopamine neurons in the ventral tegmental area, LHA LepRb neurons also densely innervate the LHA where they directly synapse with OX, but not MCH, neurons. Indeed, few other LepRb neurons in the brain project to the OX-containing region of the mouse LHA, and direct leptin action via LHA LepRb neurons regulates gene expression in OX neurons. These findings thus reveal a major role for LHA leptin action in the modulation of OX neurons, suggesting the importance of LHA LepRb neurons in the regulation of OX signaling that is crucial to leptin action and metabolic control. PMID:20739548

  13. Direct acceleration of electrons by a circular polarized laser pulse with phase modulation

    NASA Astrophysics Data System (ADS)

    Zhu, Lun-Wu; Sheng, Zheng-Mao; Yu, M. Y.

    2013-11-01

    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.

  14. 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.

  15. ADAPTATION OF MAMMALIAN PHOTORECEPTORS TO BACKGROUND LIGHT: PUTATIVE ROLE FOR DIRECT MODULATION OF PHOSPHODIESTERASE

    PubMed Central

    Fain, Gordon L

    2011-01-01

    All sensory receptors adapt. As the mean level of light or sound or odor is altered, the sensitivity of the receptor is adjusted to permit the cell to function over as wide a range of ambient stimulation as possible. In a rod photoreceptor, adaptation to maintained background light produces a decrease (or “sag) in the response to the prolonged illumination, as well as an acceleration in response decay time and a Weber-Fechner-like decrease in sensitivity. Earlier work on salamander indicated that adaptation is controlled by the intracellular concentration of Ca2+. Three Ca2+-dependent mechanisms were subsequently identified, namely regulation of guanylyl cyclase, modulation of activated rhodopsin lifetime, and alteration of channel opening probability, with the contribution of the cyclase thought to be the most important. Later experiments on mouse that exploit the powerful techniques of molecular genetics have shown that cyclase does indeed play a significant role in mammalian rods, but that much of adaptation remains even when regulation of cyclase and both of the other proposed pathways have been genetically deleted. The identity of the missing mechanism or mechanisms is unclear, but recent speculation has focused on direct modulation of spontaneous and light-activated phosphodiesterase. PMID:21922272

  16. Parallel direct laser writing of micro-optical and photonic structures using spatial light modulator

    NASA Astrophysics Data System (ADS)

    Yang, Liang; El-Tamer, Ayman; Hinze, Ulf; Li, Jiawen; Hu, Yanlei; Huang, Wenhao; Chu, Jiaru; Chichkov, Boris N.

    2015-07-01

    Two-photon polymerization (2PP) is a powerful tool for direct laser writing of micro-optical and photonic structures due to its flexibility in 3D structuring and sub-micrometer resolution. However, it can be time consuming to fabricate arrays of micro-optical devices and complex photonic structures. In this study, we propose to use predefined patterns (PPs) for parallel 2PP processing. A PP contains a multiple focal spot pattern optimized for the fabrication of certain microstructures. PP can be created by holographic laser beam modulation with a spatial light modulator (SLM). The quantity and position of the multiple foci can be flexibly and precisely controlled by predesigned computer generated holograms (CGHs). With these specially designed PPs, parallel fabrication of arbitrary distributed microlens arrays and 3D photonic structures is demonstrated. This method significantly improves throughput and flexibility of the 2PP technique and can be used for mass production of functional devices in micro-optics and photonics.

  17. Unusual ferromagnetism in Ising and Potts model on semi-directed Barabási-Albert networks

    NASA Astrophysics Data System (ADS)

    Sumour, Muneer A.; Lima, F. W. S.

    2014-06-01

    We check the existence of a spontaneous magnetisation of Ising and Potts spins on semi-directed Barabasi-Albert networks by Monte Carlo simulations. We verify that the magnetisation for different temperatures T decays after a characteristic time ?( T), which we extrapolate to diverge at positive temperatures T c ( N) by a Vogel-Fulcher law, with T c ( N) increasing logarithmically with network size N.

  18. Direct-detection optical communication with color coded pulse position modulation signaling

    NASA Technical Reports Server (NTRS)

    Davidson, F.

    1985-01-01

    The performance characteristics of a direct-detection optical communication system which is based on a laser transmitter which produces single light pulses at selected nonoverlapping optical center frequencies are discussed. The signal format, called color coded pulse position modulation (CCPPM), uses more of the total available response bandwidth characteristics of the photodetector than does ordinary PPM signaling. The advantages of CCPPM signaling are obtained at the expense of an increased optical bandwidth of the transmitted signal and a more complicated transmitter and receiver structure. When the signal format is used in conjunction with block length Reed-Solomon codes, high data rates and reliable high-speed optical communications under conditions of optimal energy efficiency are obtained.

  19. Hybrid pulse position modulation/ultrashort-light-pulse code division multiple access for data networking

    NASA Astrophysics Data System (ADS)

    Marom, Daniel M.; Kim, Kwang S.; Milstein, Laurence B.; Fainman, Yeshaiahu

    2000-05-01

    Future data networks are required to support numerous high- capacity connections while providing simplified management and connectivity. To meet these requirements, we propose to utilize broadband ultrashort light pulses (ULP) in conjunction with pulse position modulation (PPM) as an efficient modulation format and code division multiple access (CDMA) for interference suppression. This networking format is operated asynchronously for simplified control, and requires minimal management for ensuring that the number of active users is below the limit at which multi-user interference generates excessive errors. The pulse positions can be detected at the receiver with high temporal resolution by utilizing a time-to-space conversion operating in real-time. The performance of the PPM/ULP-CDMA is found to depend on the following parameters: the ULP duration, the bandwidth of each spectral chip of the CDMA filter, and the ULP repetition time. We find that employing PPM improves the performance of the system relative to On-Off Keying. The performance can be further improved by increasing the number of PPM symbols, reducing the spectral chip bandwidth, and reducing the ratio of the pulse duration to repetition time. The performance analysis shows that the proposed system operates at a high bandwidth efficiency.

  20. Modules, networks and systems medicine for understanding disease and aiding diagnosis.

    PubMed

    Gustafsson, Mika; Nestor, Colm E; Zhang, Huan; Barabási, Albert-László; Baranzini, Sergio; Brunak, Sören; Chung, Kian Fan; Federoff, Howard J; Gavin, Anne-Claude; Meehan, Richard R; Picotti, Paola; Pujana, Miguel Àngel; Rajewsky, Nikolaus; Smith, Kenneth Gc; Sterk, Peter J; Villoslada, Pablo; Benson, Mikael

    2014-01-01

    Many common diseases, such as asthma, diabetes or obesity, involve altered interactions between thousands of genes. High-throughput techniques (omics) allow identification of such genes and their products, but functional understanding is a formidable challenge. Network-based analyses of omics data have identified modules of disease-associated genes that have been used to obtain both a systems level and a molecular understanding of disease mechanisms. For example, in allergy a module was used to find a novel candidate gene that was validated by functional and clinical studies. Such analyses play important roles in systems medicine. This is an emerging discipline that aims to gain a translational understanding of the complex mechanisms underlying common diseases. In this review, we will explain and provide examples of how network-based analyses of omics data, in combination with functional and clinical studies, are aiding our understanding of disease, as well as helping to prioritize diagnostic markers or therapeutic candidate genes. Such analyses involve significant problems and limitations, which will be discussed. We also highlight the steps needed for clinical implementation. PMID:25473422

  1. 10Gb/s direct modulation of widely tunable V-cavity-laser with chirp managed laser technology

    NASA Astrophysics Data System (ADS)

    Meng, Jianjun; Wang, Lei; He, Jian-Jun

    2015-03-01

    We report direct modulation results in a simple and compact widely tunable V-cavity laser. Chirp managed laser technology has been successfully applied to the V-cavity laser with an optical spectrum reshaping filter. The tunable V-cavity-laser employs a half-wave coupler to obtain single-mode operation with high side-mode suppression ratio and the Vernier effect to extend its tuning range. It does not require any grating structure and regrowth steps. In this experiment, we achieved single-electrode controlled wavelength tuning of about 18 channels at 100GHz spacing with a fixed temperature, and 32 channels using 2 temperature settings. Well-open eye diagrams with extinction ratio above 4.3dB in all channels are observed when the laser is directly modulated at 2.5Gb/s. Although the measured small-signal frequency response is only about 5.7GHz, more than 6.7dB extinction ratio under 10Gb/s modulation rate is achieved by using the chirp managed laser technology with an optical spectrum reshaping filter placed after the output of the laser to convert the frequency chirp accompanying the direct modulation to amplitude modulation. The advantages of compactness, fabrication simplicity, easy wavelength control algorithm, and simple direct modulation offer great potential for the chirped managed V-cavity laser to be used in low-cost WDM links.

  2. 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.

  3. 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.

  4. Optically heated ultra-fast-cycling gas chromatography module for separation of direct sampling and online monitoring applications.

    PubMed

    Fischer, Michael; Wohlfahrt, Sebastian; Varga, Janos; Matuschek, Georg; Saraji-Bozorgzad, Mohammad R; Denner, Thomas; Walte, Andreas; Zimmermann, Ralf

    2015-09-01

    This work describes an ultrafast-cycling gas chromatography module (fast-GC module) for direct-sampling gas chromatography/mass spectrometry (GC-MS). The sample can be introduced into the fast-GC module using a common GC injector or any GC × GC modulator. The new fast-GC module offers the possibility to conduct a complete temperature cycle within 30 s. Its thermal mass is minimized by using a specially developed home-built fused silica capillary column stack and a halogen lamp for heat generation, both placed inside a gold-coated quartz glass cylinder. A high airflow blower enables rapid cooling. The new device is highly flexible concerning the used separation column, the applied temperature program, and the integration into existing systems. An application of the fast-GC module is shown in this work by thermal analysis coupled to gas chromatography-mass spectrometry (TA-GC-MS). The continuously evolving gases of the TA are modulated by a liquid CO2 modulator. Because of the rapid cycling of the fast-GC module, it is possible to obtain the best separation while maintaining the online character of the TA. Restrictions in separation and retention time shifting, known from isothermal and normal ramped fast-GC systems, are overcome. PMID:26226397

  5. 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

  6. 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 ?m) 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-3? 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

  7. A target coverage scheduling scheme based on genetic algorithms in directional sensor networks.

    PubMed

    Gil, Joon-Min; Han, Youn-Hee

    2011-01-01

    As a promising tool for monitoring the physical world, directional sensor networks (DSNs) consisting of a large number of directional sensors are attracting increasing attention. As directional sensors in DSNs have limited battery power and restricted angles of sensing range, maximizing the network lifetime while monitoring all the targets in a given area remains a challenge. A major technique to conserve the energy of directional sensors is to use a node wake-up scheduling protocol by which some sensors remain active to provide sensing services, while the others are inactive to conserve their energy. In this paper, we first address a Maximum Set Covers for DSNs (MSCD) problem, which is known to be NP-complete, and present a greedy algorithm-based target coverage scheduling scheme that can solve this problem by heuristics. This scheme is used as a baseline for comparison. We then propose a target coverage scheduling scheme based on a genetic algorithm that can find the optimal cover sets to extend the network lifetime while monitoring all targets by the evolutionary global search technique. To verify and evaluate these schemes, we conducted simulations and showed that the schemes can contribute to extending the network lifetime. Simulation results indicated that the genetic algorithm-based scheduling scheme had better performance than the greedy algorithm-based scheme in terms of maximizing network lifetime. PMID:22319387

  8. Effects of ?-opioid receptor modulation on the hippocampal network activity of sharp wave and ripples

    PubMed Central

    Giannopoulos, Panagiotis; Papatheodoropoulos, Costas

    2013-01-01

    Background and Purpose Hippocampus-dependent memory involves the activity of sharp wave ripples (SWRs), which are thought to participate in the process of memory consolidation. The hippocampus contains high levels of endogenous opioids and of ?-opioid receptors (MORs). Here, we have assessed the role of MOR agonists in the modulation of SWRs. Experimental Approach Using recordings of extracellular potentials from the CA1 field of rat hippocampal slices, we examined the pharmacological actions of morphine, DAMGO and fentanyl on SWRs and on network excitability and paired-pulse inhibition. Key Results All three MOR agonists (1 nM–10 ?M) significantly increased the amplitude of sharp waves and the occurrence of SWR sequences, but reduced the initiation of episodes of SWRs. Fentanyl was most potent in producing these effects and morphine the least. Interestingly, although SWRs were reduced by relatively high concentrations (?100 nM) of all agonists, they were significantly enhanced by very low concentrations of morphine (5–10 nM). Morphine and DAMGO at moderate-to-high concentrations increased network excitability and reduced inhibition. Furthermore, DAMGO suppressed inhibition more readily than it increased excitation, whereas morphine suppressed inhibition only at high concentrations. These drug effects were reversed by the MOR antagonists naloxone and CTOP. Conclusions and Implications We found that the SWRs were significantly modulated by three MOR agonists and that the SWRs were very sensitive to subtle changes in the excitation/inhibition balance induced by MOR agonists. Such modulation might underlie the effects of these agonists on hippocampus-dependent memory. PMID:23043226

  9. 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.

  10. 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.

  11. Network-level effects of kinase inhibitors modulate TNF-?-induced apoptosis in the intestinal epithelium.

    PubMed

    Gierut, Jessica J; Wood, Levi B; Lau, Ken S; Lin, Yi-Jang; Genetti, Casie; Samatar, Ahmed A; Lauffenburger, Douglas A; Haigis, Kevin M

    2015-01-01

    Individual signaling pathways operate in the context of the broader signaling network. Thus, the response of a cell to signals from the environment is affected by the state of the signaling network, such as the clinically relevant example of whether some components in the network are inhibited. The cytokine tumor necrosis factor-? (TNF-?) promotes opposing cellular behaviors under different conditions; the outcome is influenced by the state of the network. For example, in the mouse intestinal epithelium, inhibition of the mitogen-activated protein kinase (MAPK) kinase MEK alters the timing of TNF-?-induced apoptosis. We investigated whether MAPK signaling directly influences TNF-?-induced apoptosis or whether network-level effects secondary to inhibition of the MAPK pathway alter the cellular response. We found that inhibitors of the MAPK kinase kinase Raf, MEK, or extracellular signal-regulated kinase (ERK) exerted distinct effects on the timing and magnitude of TNF-?-induced apoptosis in the mouse intestine. Furthermore, even different MEK inhibitors exerted distinct effects; one, CH5126766, potentiated TNF-?-induced apoptosis, and the others reduced cell death. Computational modeling and experimental perturbation identified the kinase Akt as the primary signaling node that enhanced apoptosis in the context of TNF-? signaling in the presence of CH5126766. Our work emphasizes the importance of integrated network signaling in specifying cellular behavior in response to experimental or therapeutic manipulation. More broadly, this study highlighted the importance of considering the network-level effects of pathway inhibitors and showed the distinct effects of inhibitors that share the same target. PMID:26671150

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

    PubMed

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

    2013-12-01

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

  13. 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

  14. 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

  15. 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 2? 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 1.55?m and 10.6 ?m, spatial light modulator in the MWIR (3~5?m) band, dynamic scene projectors for infrared seekers in the LWIR (8~12?m) 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 2? phase change at MWIR and response time less than 5 ms.

  16. 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.

  17. Modulating Bone Resorption and Bone Formation in Opposite Directions in the Treatment of Postmenopausal Osteoporosis.

    PubMed

    Appelman-Dijkstra, Natasha M; Papapoulos, Socrates E

    2015-07-01

    Bone remodeling, the fundamental process for bone renewal, is targeted by treatments of osteoporosis to correct the imbalance between bone resorption and bone formation and reduce the risk of fractures and associated clinical consequences. Currently available therapeutics affect bone resorption and bone formation in the same direction and either decrease (inhibitors of bone resorption) or increase (parathyroid hormone [PTH] peptides) bone remodeling. Studies of patients with rare bone diseases and genetically modified animal models demonstrated that bone resorption and bone formation may not necessarily be coupled, leading to identification of molecular targets in bone cells for the development of novel agents for the treatment of osteoporosis. Application of such agents to the treatment of women with low bone mass confirmed that bone resorption and bone formation can be modulated in different directions and so far two new classes of therapeutics for osteoporosis have been defined with distinct mechanisms of action. Such treatments, if combined with a favorable safety profile, will offer new therapeutic options and will improve the management of patients with osteoporosis. PMID:26056029

  18. 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

  19. AT1 receptors in the collecting duct directly modulate the concentration of urine.

    PubMed

    Stegbauer, Johannes; Gurley, Susan B; Sparks, Matthew A; Woznowski, Magdalena; Kohan, Donald E; Yan, Ming; Lehrich, Ruediger W; Coffman, Thomas M

    2011-12-01

    Mice lacking AT(1) angiotensin receptors have an impaired capacity to concentrate the urine, but the underlying mechanism is unknown. To determine whether direct actions of AT(1) receptors in epithelial cells of the collecting duct regulate water reabsorption, we used Cre-Loxp technology to specifically eliminate AT(1A) receptors from the collecting duct in mice (CD-KOs). Although levels of AT(1A) receptor mRNA in the inner medulla of CD-KO mice were significantly reduced, their kidneys appeared structurally normal. Under basal conditions, plasma and urine osmolalities and urine volumes were similar between CD-KO mice and controls. The increase in urine osmolality in response to water deprivation or vasopressin administration, however, was consistently attenuated in CD-KO mice. Similarly, levels of aquaporin-2 protein in inner and outer medulla after water deprivation were significantly lower in CD-KO mice compared with controls, despite its normal localization to the apical membrane. In summary, these results demonstrate that AT(1A) receptors in epithelial cells of the collecting duct directly modulate aquaporin-2 levels and contribute to the concentration of urine. PMID:22052052

  20. Shape-shifting 3D protein microstructures with programmable directionality via quantitative nanoscale stiffness modulation.

    PubMed

    Lee, Mian Rong; Phang, In Yee; Cui, Yan; Lee, Yih Hong; Ling, Xing Yi

    2015-02-11

    The ability to shape-shift in response to a stimulus increases an organism's survivability in nature. Similarly, man-made dynamic and responsive "smart" microtechnology is crucial for the advancement of human technology. Here, 10-30 ?m shape-changing 3D BSA protein hydrogel microstructures are fabricated with dynamic, quantitative, directional, and angle-resolved bending via two-photon photolithography. The controlled directional responsiveness is achieved by spatially controlling the cross-linking density of BSA at a nanometer lengthscale. Atomic force microscopy measurements of Young's moduli of structures indicate that increasing the laser writing distance at the z-axis from 100-500 nm decreases the modulus of the structure. Hence, through nanoscale modulation of the laser writing z-layer distance at the nanoscale, control over the cross-linking density is possible, allowing for the swelling extent of the microstructures to be quantified and controlled with high precision. This method of segmented moduli is applied within a single microstructure for the design of shape-shifting microstructures that exhibit stimulus-induced chirality, as well as for the fabrication of a free-standing 3D microtrap which is able to open and close in response to a pH change. PMID:25264141

  1. Direct-aperture optimization applied to selection of beam orientations in intensity-modulated radiation therapy

    NASA Astrophysics Data System (ADS)

    Bedford, J. L.; Webb, S.

    2007-01-01

    Direct-aperture optimization (DAO) was applied to iterative beam-orientation selection in intensity-modulated radiation therapy (IMRT), so as to ensure a realistic segmental treatment plan at each iteration. Nested optimization engines dealt separately with gantry angles, couch angles, collimator angles, segment shapes, segment weights and wedge angles. Each optimization engine performed a random search with successively narrowing step sizes. For optimization of segment shapes, the filtered backprojection (FBP) method was first used to determine desired fluence, the fluence map was segmented, and then constrained direct-aperture optimization was used thereafter. Segment shapes were fully optimized when a beam angle was perturbed, and minimally re-optimized otherwise. The algorithm was compared with a previously reported method using FBP alone at each orientation iteration. An example case consisting of a cylindrical phantom with a hemi-annular planning target volume (PTV) showed that for three-field plans, the method performed better than when using FBP alone, but for five or more fields, neither method provided much benefit over equally spaced beams. For a prostate case, improved bladder sparing was achieved through the use of the new algorithm. A plan for partial scalp treatment showed slightly improved PTV coverage and lower irradiated volume of brain with the new method compared to FBP alone. It is concluded that, although the method is computationally intensive and not suitable for searching large unconstrained regions of beam space, it can be used effectively in conjunction with prior class solutions to provide individually optimized IMRT treatment plans.

  2. 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

  3. 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.

  4. 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

  5. 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.

  6. 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

  7. Cello-oligomer-binding dynamics and directionality in family 4 carbohydrate-binding modules.

    PubMed

    Kognole, Abhishek A; Payne, Christina M

    2015-10-01

    Carbohydrate-binding modules (CBMs) play significant roles in modulating the function of cellulases, and understanding the protein-carbohydrate recognition mechanisms by which CBMs selectively bind substrate is critical to development of enhanced biomass conversion technology. CBMs exhibit a limited range of specificity and appear to bind polysaccharides in a directional fashion dictated by the position of the ring oxygen relative to the protein fold. The two family 4 CBMs of Cellulomonas fimi Cel9B (CfCBM4) are reported to preferentially bind cellulosic substrates. However, experimental evidence suggests that these CBMs may not exhibit a thermodynamic preference for a particular orientation. We use molecular dynamics (MD) and free energy calculations to investigate protein-carbohydrate recognition mechanisms in CfCBM4-1 and CfCBM4-2 and to elucidate preferential ligand-binding orientation. We evaluate four cellopentaose orientations including that of the crystal structure and three others suggested by nuclear magnetic resonance (NMR). These four orientations differ based on position of the ligand reducing end (RE) and pyranose ring orientations relative to the protein core. MD simulations indicate that the plausible orientations reduce to two conformations. Calculated ligand-binding free energy discerns each of the orientations is equally favorable. The calculated free energies are in excellent agreement with isothermal titration calorimetry measurements from the literature. MD simulations further reveal the approximate structural symmetry of the oligosaccharides relative to the amino acids along the binding cleft plays a role in the promiscuity of ligand binding. A survey of ligand-bound structures suggests this phenomenon may be characteristic of the broader class of proteins belonging to the ?-sandwich fold. PMID:26153106

  8. 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.

  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. 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.

  14. 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.

  15. Ising Model Spin S = 1 ON Directed BARABÁSI-ALBERT Networks

    NASA Astrophysics Data System (ADS)

    Lima, F. W. S.

    On directed Barabási-Albert networks with two and seven neighbours selected by each added site, the Ising model with spin S = 1/2 was seen not to show a spontaneous magnetisation. Instead, the decay time for flipping of the magnetisation followed an Arrhenius law for Metropolis and Glauber algorithms, but for Wolff cluster flipping the magnetisation decayed exponentially with time. On these networks the Ising model spin S = 1 is now studied through Monte Carlo simulations. However, in this model, the order-disorder phase transition is well defined in this system. We have obtained a first-order phase transition for values of connectivity m = 2 and m = 7 of the directed Barabási-Albert network.

  16. 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??) 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

  17. 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.

  18. 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.

  19. 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 ...

  20. Estimating the 3D Pore Size Distribution of Biopolymer Networks from Directionally Biased Data

    PubMed Central

    Lang, Nadine R.; Münster, Stefan; Metzner, Claus; Krauss, Patrick; Schürmann, Sebastian; Lange, Janina; Aifantis, Katerina E.; Friedrich, Oliver; Fabry, Ben

    2013-01-01

    The pore size of biopolymer networks governs their mechanical properties and strongly impacts the behavior of embedded cells. Confocal reflection microscopy and second harmonic generation microscopy are widely used to image biopolymer networks; however, both techniques fail to resolve vertically oriented fibers. Here, we describe how such directionally biased data can be used to estimate the network pore size. We first determine the distribution of distances from random points in the fluid phase to the nearest fiber. This distribution follows a Rayleigh distribution, regardless of isotropy and data bias, and is fully described by a single parameter—the characteristic pore size of the network. The bias of the pore size estimate due to the missing fibers can be corrected by multiplication with the square root of the visible network fraction. We experimentally verify the validity of this approach by comparing our estimates with data obtained using confocal fluorescence microscopy, which represents the full structure of the network. As an important application, we investigate the pore size dependence of collagen and fibrin networks on protein concentration. We find that the pore size decreases with the square root of the concentration, consistent with a total fiber length that scales linearly with concentration. PMID:24209841

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

    PubMed Central

    Zamora-López, Gorka; Zhou, Changsong; Kurths, Jürgen

    2009-01-01

    Sensory stimuli entering the nervous system follow particular paths of processing, typically separated (segregated) from the paths of other modal information. However, sensory perception, awareness and cognition emerge from the combination of information (integration). The corticocortical networks of cats and macaque monkeys display three prominent characteristics: (i) modular organisation (facilitating the segregation), (ii) abundant alternative processing paths and (iii) the presence of highly connected hubs. Here, we study in detail the organisation and potential function of the cortical hubs by graph analysis and information theoretical methods. We find that the cortical hubs form a spatially delocalised, but topologically central module with the capacity to integrate multisensory information in a collaborative manner. With this, we resolve the underlying anatomical substrate that supports the simultaneous capacity of the cortex to segregate and to integrate multisensory information. PMID:20428515

  2. 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

  3. 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

  4. Acupuncture Modulates the Functional Connectivity of the Default Mode Network in Stroke Patients

    PubMed Central

    Zhang, Yong; Li, Kuangshi; Ren, Yi; Cui, Fangyuan; Xie, Zijing; Shin, Jae-Young; Tan, Zhongjian; Tang, Lixin; Bai, Lijun; Zou, Yihuai

    2014-01-01

    Abundant evidence from previous fMRI studies on acupuncture has revealed significant modulatory effects at widespread brain regions. However, few reports on the modulation to the default mode network (DMN) of stroke patients have been investigated in the field of acupuncture. To study the modulatory effects of acupuncture on the DMN of stroke patients, eight right hemispheric infarction and stable ischemic stroke patients and ten healthy subjects were recruited to undergo resting state fMRI scanning before and after acupuncture stimulation. Functional connectivity analysis was applied with the bilateral posterior cingulate cortices chosen as the seed regions. The main finding demonstrated that the interregional interactions between the ACC and PCC especially enhanced after acupuncture at GB34 in stroke patients, compared with healthy controls. The results indicated that the possible mechanisms of the modulatory effects of acupuncture on the DMN of stroke patients could be interpreted in terms of cognitive ability and motor function recovery. PMID:24734113

  5. 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

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

    PubMed Central

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

    2012-01-01

    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

  7. Inference of directed climate networks: role of instability of causality estimation methods

    NASA Astrophysics Data System (ADS)

    Hlinka, Jaroslav; Hartman, David; Vejmelka, Martin; Paluš, Milan

    2013-04-01

    Climate data are increasingly analyzed by complex network analysis methods, including graph-theoretical approaches [1]. For such analysis, links between localized nodes of climate network are typically quantified by some statistical measures of dependence (connectivity) between measured variables of interest. To obtain information on the directionality of the interactions in the networks, a wide range of methods exists. These can be broadly divided into linear and nonlinear methods, with some of the latter having the theoretical advantage of being model-free, and principally a generalization of the former [2]. However, as a trade-off, this generality comes together with lower accuracy - in particular if the system was close to linear. In an overall stationary system, this may potentially lead to higher variability in the nonlinear network estimates. Therefore, with the same control of false alarms, this may lead to lower sensitivity for detection of real changes in the network structure. These problems are discussed on the example of daily SAT and SLP data from the NCEP/NCAR reanalysis dataset. We first reduce the dimensionality of data using PCA with VARIMAX rotation to detect several dozens of components that together explain most of the data variability. We further construct directed climate networks applying a selection of most widely used methods - variants of linear Granger causality and conditional mutual information. Finally, we assess the stability of the detected directed climate networks by computing them in sliding time windows. To understand the origin of the observed instabilities and their range, we also apply the same procedure to two types of surrogate data: either with non-stationarity in network structure removed, or imposed in a controlled way. In general, the linear methods show stable results in terms of overall similarity of directed climate networks inferred. For instance, for different decades of SAT data, the Spearman correlation of edge weights in the networks is ~ 0.6. The networks constructed using nonlinear measures were in general less stable both in real data and stationarized surrogates. Interestingly, when the nonlinear method parameters are optimized with respect to temporal stability of the networks, the networks seem to converge close to those detected by linear Granger causality. This provides further evidence for the hypothesis of overall sparsity and weakness of nonlinear coupling in climate networks on this spatial and temporal scale [3] and sufficient support for the use of linear methods in this context, unless specific clearly detectable nonlinear phenomena are targeted. Acknowledgement: This study is supported by the Czech Science Foundation, Project No. P103/11/J068. [1] Boccaletti, S.; Latora, V.; Moreno, Y.; Chavez, M. & Hwang, D. U.: Complex networks: Structure and dynamics, Physics Reports, 2006, 424, 175-308 [2] Barnett, L.; Barrett, A. B. & Seth, A. K.: Granger Causality and Transfer Entropy Are Equivalent for Gaussian Variables, Physical Review Letters, 2009, 103, 238701 [3] Hlinka, J.; Hartman, D.; Vejmelka, M.; Novotná, D.; Paluš, M.: Non-linear dependence and teleconnections in climate data: sources, relevance, nonstationarity, submitted preprint (http://arxiv.org/abs/1211.6688)

  8. Integrated CMOS system and thermally actuated optical switch for wavelength modulation/lock in communication network

    NASA Astrophysics Data System (ADS)

    Liou, J. C.; Tseng, F. G.

    2009-12-01

    The advancement of communication technology and growth of internet traffic have continuously driven the fast evolution of networks. Compared to the traditional optoelectronic switch, all-optical switch provides high throughput, rich routing functionalities, and excellent flexibility for rapid signal exchange in fiber optical network. Among various all-optical switches, thermal actuated ring switch provides the advantages of high accuracy, easy actuation, and reasonable switching speed. However, when scale up, thermal ring switch may encounter issues related to fabrication error, non-accurate wavelength response, and large terminal numbers in the control circuit. In this research, we propose the employment of an integrated CMOS control circuit to compensate the fabrication error and tune as well as lock the wavelength in a thermal-actuated ring-type optical switch through a frequency modulation scheme. Additional functionalities can also be added in this circuit by tailoring externally the roundtrip loss or coupling constants of the ring. The design concept can be easily scaled up for large array optical switch system without much change in the terminal numbers thanks to the three-dimensional hierarchy of control circuit design, which effectively reduces the terminal numbers into the cubic root of the total control unit numbers. The integrated circuit has been designed, simulated, as well as fabricated, and demonstrated a decent performance with free spectral range (FSR) equal to 1.5 nm at 1534 nm and very accurate wavelength modulation to 0.3 nm within 0.01 nm fluctuation for thermal actuated ring type optical switch.

  9. 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

  10. Abnormal dopaminergic modulation of striato-cortical networks underlies levodopa-induced dyskinesias in humans

    PubMed Central

    Haagensen, Brian N.; Christensen, Mark S.; Madsen, Kristoffer H.; Rowe, James B.; Løkkegaard, Annemette; Siebner, Hartwig R.

    2015-01-01

    Dopaminergic signalling in the striatum contributes to reinforcement of actions and motivational enhancement of motor vigour. Parkinson's disease leads to progressive dopaminergic denervation of the striatum, impairing the function of cortico-basal ganglia networks. While levodopa therapy alleviates basal ganglia dysfunction in Parkinson's disease, it often elicits involuntary movements, referred to as levodopa-induced peak-of-dose dyskinesias. Here, we used a novel pharmacodynamic neuroimaging approach to identify the changes in cortico-basal ganglia connectivity that herald the emergence of levodopa-induced dyskinesias. Twenty-six patients with Parkinson's disease (age range: 51–84 years; 11 females) received a single dose of levodopa and then performed a task in which they had to produce or suppress a movement in response to visual cues. Task-related activity was continuously mapped with functional magnetic resonance imaging. Dynamic causal modelling was applied to assess levodopa-induced modulation of effective connectivity between the pre-supplementary motor area, primary motor cortex and putamen when patients suppressed a motor response. Bayesian model selection revealed that patients who later developed levodopa-induced dyskinesias, but not patients without dyskinesias, showed a linear increase in connectivity between the putamen and primary motor cortex after levodopa intake during movement suppression. Individual dyskinesia severity was predicted by levodopa-induced modulation of striato-cortical feedback connections from putamen to the pre-supplementary motor area (Pcorrected = 0.020) and primary motor cortex (Pcorrected = 0.044), but not feed-forward connections from the cortex to the putamen. Our results identify for the first time, aberrant dopaminergic modulation of striatal-cortical connectivity as a neural signature of levodopa-induced dyskinesias in humans. We argue that excessive striato-cortical connectivity in response to levodopa produces an aberrant reinforcement signal producing an abnormal motor drive that ultimately triggers involuntary movements. PMID:25882651

  11. Abnormal dopaminergic modulation of striato-cortical networks underlies levodopa-induced dyskinesias in humans.

    PubMed

    Herz, Damian M; Haagensen, Brian N; Christensen, Mark S; Madsen, Kristoffer H; Rowe, James B; Løkkegaard, Annemette; Siebner, Hartwig R

    2015-06-01

    Dopaminergic signalling in the striatum contributes to reinforcement of actions and motivational enhancement of motor vigour. Parkinson's disease leads to progressive dopaminergic denervation of the striatum, impairing the function of cortico-basal ganglia networks. While levodopa therapy alleviates basal ganglia dysfunction in Parkinson's disease, it often elicits involuntary movements, referred to as levodopa-induced peak-of-dose dyskinesias. Here, we used a novel pharmacodynamic neuroimaging approach to identify the changes in cortico-basal ganglia connectivity that herald the emergence of levodopa-induced dyskinesias. Twenty-six patients with Parkinson's disease (age range: 51-84 years; 11 females) received a single dose of levodopa and then performed a task in which they had to produce or suppress a movement in response to visual cues. Task-related activity was continuously mapped with functional magnetic resonance imaging. Dynamic causal modelling was applied to assess levodopa-induced modulation of effective connectivity between the pre-supplementary motor area, primary motor cortex and putamen when patients suppressed a motor response. Bayesian model selection revealed that patients who later developed levodopa-induced dyskinesias, but not patients without dyskinesias, showed a linear increase in connectivity between the putamen and primary motor cortex after levodopa intake during movement suppression. Individual dyskinesia severity was predicted by levodopa-induced modulation of striato-cortical feedback connections from putamen to the pre-supplementary motor area (Pcorrected = 0.020) and primary motor cortex (Pcorrected = 0.044), but not feed-forward connections from the cortex to the putamen. Our results identify for the first time, aberrant dopaminergic modulation of striatal-cortical connectivity as a neural signature of levodopa-induced dyskinesias in humans. We argue that excessive striato-cortical connectivity in response to levodopa produces an aberrant reinforcement signal producing an abnormal motor drive that ultimately triggers involuntary movements. PMID:25882651

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

    PubMed Central

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

    2013-01-01

    Motor system neural networks are activated during movement imagery, observation and execution, with a neural signature characterized by suppression of the Mu rhythm. In order to investigate the origin of this neurophysiological marker, we tested whether transcranial direct current stimulation (tDCS) modifies Mu rhythm oscillations during tasks involving observation and imagery of biological and non-biological movements. We applied tDCS (anodal, cathodal, and sham) in 21 male participants (mean age 23.8 ± 3.06), over the left M1 with a current of 2 mA for 20 min. Following this, we recorded the EEG at C3, C4, and Cz and surrounding C3 and C4 electrodes. Analyses of C3 and C4 showed significant effects for biological vs. non-biological movement (p = 0.005), and differential hemisphere effects according to the type of stimulation (p = 0.04) and type of movement (p = 0.02). Analyses of surrounding electrodes revealed significant interaction effects considering type of stimulation and imagery or observation of biological or non-biological movement (p = 0.03). The main findings of this study were (1) Mu desynchronization during biological movement of the hand region in the contralateral hemisphere after sham tDCS; (2) polarity-dependent modulation effects of tDCS on the Mu rhythm, i.e., anodal tDCS led to Mu synchronization while cathodal tDCS led to Mu desynchronization during movement observation and imagery (3) specific focal and opposite inter-hemispheric effects, i.e., contrary effects for the surrounding electrodes during imagery condition and also for inter-hemispheric electrodes (C3 vs. C4). These findings provide insights into the cortical oscillations during movement observation and imagery. Furthermore, it shows that tDCS can be highly focal when guided by a behavioral task. PMID:23761755

  13. Direct-aperture optimization applied to selection of beam orientations in intensity-modulated radiation therapy.

    PubMed

    Bedford, J L; Webb, S

    2007-01-21

    Direct-aperture optimization (DAO) was applied to iterative beam-orientation selection in intensity-modulated radiation therapy (IMRT), so as to ensure a realistic segmental treatment plan at each iteration. Nested optimization engines dealt separately with gantry angles, couch angles, collimator angles, segment shapes, segment weights and wedge angles. Each optimization engine performed a random search with successively narrowing step sizes. For optimization of segment shapes, the filtered backprojection (FBP) method was first used to determine desired fluence, the fluence map was segmented, and then constrained direct-aperture optimization was used thereafter. Segment shapes were fully optimized when a beam angle was perturbed, and minimally re-optimized otherwise. The algorithm was compared with a previously reported method using FBP alone at each orientation iteration. An example case consisting of a cylindrical phantom with a hemi-annular planning target volume (PTV) showed that for three-field plans, the method performed better than when using FBP alone, but for five or more fields, neither method provided much benefit over equally spaced beams. For a prostate case, improved bladder sparing was achieved through the use of the new algorithm. A plan for partial scalp treatment showed slightly improved PTV coverage and lower irradiated volume of brain with the new method compared to FBP alone. It is concluded that, although the method is computationally intensive and not suitable for searching large unconstrained regions of beam space, it can be used effectively in conjunction with prior class solutions to provide individually optimized IMRT treatment plans. PMID:17202628

  14. Attitudes towards Social Networking and Sharing Behaviors among Consumers of Direct-to-Consumer Personal Genomics

    PubMed Central

    Lee, Sandra Soo-Jin; Vernez, Simone L.; Ormond, K.E.; Granovetter, Mark

    2013-01-01

    Little is known about how consumers of direct-to-consumer personal genetic services share personal genetic risk information. In an age of ubiquitous online networking and rapid development of social networking tools, understanding how consumers share personal genetic risk assessments is critical in the development of appropriate and effective policies. This exploratory study investigates how consumers share personal genetic information and attitudes towards social networking behaviors. Methods: Adult participants aged 23 to 72 years old who purchased direct-to-consumer genetic testing from a personal genomics company were administered a web-based survey regarding their sharing activities and social networking behaviors related to their personal genetic test results. Results: 80 participants completed the survey; of those, 45% shared results on Facebook and 50.9% reported meeting or reconnecting with more than 10 other individuals through the sharing of their personal genetic information. For help interpreting test results, 70.4% turned to Internet websites and online sources, compared to 22.7% who consulted their healthcare providers. Amongst participants, 51.8% reported that they believe the privacy of their personal genetic information would be breached in the future. Conclusion: Consumers actively utilize online social networking tools to help them share and interpret their personal genetic information. These findings suggest a need for careful consideration of policy recommendations in light of the current ambiguity of regulation and oversight of consumer initiated sharing activities. PMID:25562728

  15. Dopaminergic modulation of positive expectations for goal-directed action: evidence from Parkinson’s disease

    PubMed Central

    Wolpe, Noham; Nombela, Cristina; Rowe, James B.

    2015-01-01

    Parkinson’s disease (PD) impairs the control of movement and cognition, including the planning of action and its consequences. This provides the opportunity to study the dopaminergic influences on the perception and awareness of action. Here we examined the perception of the outcome of a goal-directed action made by medicated patients with PD. A visuomotor task probed the integration of sensorimotor signals with the positive expectations of outcomes (Self priors), which in healthy adults bias perception toward success in proportion to trait optimism. We tested the hypotheses that (i) the priors on the perception of the consequences of one’s own actions differ between patients and age- and sex-matched controls, and (ii) that these priors are modulated by the levodopa dose equivalent (LDEs) in patients. There was no overall difference between patients and controls in the perceptual priors used. However, the precision of patient priors was inversely related to their LDE. Patients with high LDE showed more accurate priors, representing predictions that were closer to the true distribution of performance. Such accuracy has previously been demonstrated when observing the actions of others, suggesting abnormal awareness of action in these patients. These results confirm a link between dopamine and the positive expectation of the outcome of one’s own actions, and may have implications for the management of PD. PMID:26500582

  16. Dopaminergic modulation of positive expectations for goal-directed action: evidence from Parkinson's disease.

    PubMed

    Wolpe, Noham; Nombela, Cristina; Rowe, James B

    2015-01-01

    Parkinson's disease (PD) impairs the control of movement and cognition, including the planning of action and its consequences. This provides the opportunity to study the dopaminergic influences on the perception and awareness of action. Here we examined the perception of the outcome of a goal-directed action made by medicated patients with PD. A visuomotor task probed the integration of sensorimotor signals with the positive expectations of outcomes (Self priors), which in healthy adults bias perception toward success in proportion to trait optimism. We tested the hypotheses that (i) the priors on the perception of the consequences of one's own actions differ between patients and age- and sex-matched controls, and (ii) that these priors are modulated by the levodopa dose equivalent (LDEs) in patients. There was no overall difference between patients and controls in the perceptual priors used. However, the precision of patient priors was inversely related to their LDE. Patients with high LDE showed more accurate priors, representing predictions that were closer to the true distribution of performance. Such accuracy has previously been demonstrated when observing the actions of others, suggesting abnormal awareness of action in these patients. These results confirm a link between dopamine and the positive expectation of the outcome of one's own actions, and may have implications for the management of PD. PMID:26500582

  17. Modulation of Cortical Inhibitory Circuits after Cathodal Transcranial Direct Current Stimulation over the Primary Motor Cortex

    PubMed Central

    Sasaki, Ryoki; Miyaguchi, Shota; Kotan, Shinichi; Kojima, Sho; Kirimoto, Hikari; Onishi, Hideaki

    2016-01-01

    Here, we aimed to evaluate whether cathodal transcranial direct current stimulation (tDCS) over the primary motor cortex (M1) and primary somatosensory cortex (S1) can modulate cortical inhibitory circuits. Sixteen healthy subjects participated in this study. Cathodal tDCS was positioned over the left M1 (M1 cathodal) or left S1 (S1 cathodal) with an intensity of 1 mA for 10 min. Sham tDCS was applied for 10 min over the left M1 (sham). Motor evoked potentials (MEPs) elicited by transcranial magnetic stimulation (TMS) were recorded from the right abductor pollicis brevis (APB) muscle before the intervention (pre) and 10 and 30 min after the intervention (post 1 and post 2, respectively). Cortical inhibitory circuits were evaluated using short-interval intracortical inhibition (SICI) and short-latency afferent inhibition (SAI). M1 cathodal decreased single-pulse MEP amplitudes at post 1 and decreased SAI at post 1 and post 2; however, SICI did not exhibit any change. S1 cathodal and sham did not show any changes in MEP amplitudes at any of the three time points. These results demonstrated that cathodal tDCS over the M1 not only decreases the M1 excitability but also affects the cortical inhibitory circuits related to SAI. PMID:26869909

  18. FILAMENTOUS FLOWER Is a Direct Target of JAZ3 and Modulates Responses to Jasmonate.

    PubMed

    Boter, Marta; Golz, John F; Giménez-Ibañez, Selena; Fernandez-Barbero, Gemma; Franco-Zorrilla, José M; Solano, Roberto

    2015-11-01

    The plant hormone jasmonate (JA) plays an important role in regulating growth, development, and immunity. Activation of the JA-signaling pathway is based on the hormone-triggered ubiquitination and removal of transcriptional repressors (JASMONATE-ZIM DOMAIN [JAZ] proteins) by an SCF receptor complex (SCF(COI1)/JAZ). This removal allows the rapid activation of transcription factors (TFs) triggering a multitude of downstream responses. Identification of TFs bound by the JAZ proteins is essential to better understand how the JA-signaling pathway modulates and integrates different responses. In this study, we found that the JAZ3 repressor physically interacts with the YABBY (YAB) family transcription factor FILAMENTOUS FLOWER (FIL)/YAB1. In Arabidopsis thaliana, FIL regulates developmental processes such as axial patterning and growth of lateral organs, shoot apical meristem activity, and inflorescence phyllotaxy. Phenotypic analysis of JA-regulated responses in loss- and gain-of-function FIL lines suggested that YABs function as transcriptional activators of JA-triggered responses. Moreover, we show that MYB75, a component of the WD-repeat/bHLH/MYB complex regulating anthocyanin production, is a direct transcriptional target of FIL. We propose that JAZ3 interacts with YABs to attenuate their transcriptional function. Upon perception of JA signal, degradation of JAZ3 by the SCF(COI1) complex releases YABs to activate a subset of JA-regulated genes in leaves leading to anthocyanin accumulation, chlorophyll loss, and reduced bacterial defense. PMID:26530088

  19. GABA signalling modulates plant growth by directly regulating the activity of plant-specific anion transporters

    PubMed Central

    Ramesh, Sunita A.; Tyerman, Stephen D.; Xu, Bo; Bose, Jayakumar; Kaur, Satwinder; Conn, Vanessa; Domingos, Patricia; Ullah, Sana; Wege, Stefanie; Shabala, Sergey; Feijó, José A.; Ryan, Peter R.; Gillham, Matthew

    2015-01-01

    The non-protein amino acid, gamma-aminobutyric acid (GABA) rapidly accumulates in plant tissues in response to biotic and abiotic stress, and regulates plant growth. Until now it was not known whether GABA exerts its effects in plants through the regulation of carbon metabolism or via an unidentified signalling pathway. Here, we demonstrate that anion flux through plant aluminium-activated malate transporter (ALMT) proteins is activated by anions and negatively regulated by GABA. Site-directed mutagenesis of selected amino acids within ALMT proteins abolishes GABA efficacy but does not alter other transport properties. GABA modulation of ALMT activity results in altered root growth and altered root tolerance to alkaline pH, acid pH and aluminium ions. We propose that GABA exerts its multiple physiological effects in plants via ALMT, including the regulation of pollen tube and root growth, and that GABA can finally be considered a legitimate signalling molecule in both the plant and animal kingdoms. PMID:26219411

  20. Transcranial direct current stimulation over posterior parietal cortex modulates visuospatial localization

    PubMed Central

    Wright, Jessica M.; Krekelberg, Bart

    2014-01-01

    Visual localization is based on the complex interplay of bottom-up and top-down processing. Based on previous work, the posterior parietal cortex (PPC) is assumed to play an essential role in this interplay. In this study, we investigated the causal role of the PPC in visual localization. Specifically, our goal was to determine whether modulation of the PPC via transcranial direct current stimulation (tDCS) could induce visual mislocalization similar to that induced by an exogenous attentional cue (Wright, Morris, & Krekelberg, 2011). We placed one stimulation electrode over the right PPC and the other over the left PPC (dual tDCS) and varied the polarity of the stimulation. We found that this manipulation altered visual localization; this supports the causal involvement of the PPC in visual localization. Notably, mislocalization was more rightward when the cathode was placed over the right PPC than when the anode was placed over the right PPC. This mislocalization was found within a few minutes of stimulation onset, it dissipated during stimulation, but then resurfaced after stimulation offset and lasted for another 10–15 min. On the assumption that excitability is reduced beneath the cathode and increased beneath the anode, these findings support the view that each hemisphere biases processing to the contralateral hemifield and that the balance of activation between the hemispheres contributes to position perception (Kinsbourne, 1977; Szczepanski, Konen, & Kastner, 2010). PMID:25104830

  1. GABA signalling modulates plant growth by directly regulating the activity of plant-specific anion transporters.

    PubMed

    Ramesh, Sunita A; Tyerman, Stephen D; Xu, Bo; Bose, Jayakumar; Kaur, Satwinder; Conn, Vanessa; Domingos, Patricia; Ullah, Sana; Wege, Stefanie; Shabala, Sergey; Feijó, José A; Ryan, Peter R; Gilliham, Matthew; Gillham, Matthew

    2015-01-01

    The non-protein amino acid, gamma-aminobutyric acid (GABA) rapidly accumulates in plant tissues in response to biotic and abiotic stress, and regulates plant growth. Until now it was not known whether GABA exerts its effects in plants through the regulation of carbon metabolism or via an unidentified signalling pathway. Here, we demonstrate that anion flux through plant aluminium-activated malate transporter (ALMT) proteins is activated by anions and negatively regulated by GABA. Site-directed mutagenesis of selected amino acids within ALMT proteins abolishes GABA efficacy but does not alter other transport properties. GABA modulation of ALMT activity results in altered root growth and altered root tolerance to alkaline pH, acid pH and aluminium ions. We propose that GABA exerts its multiple physiological effects in plants via ALMT, including the regulation of pollen tube and root growth, and that GABA can finally be considered a legitimate signalling molecule in both the plant and animal kingdoms. PMID:26219411

  2. Direction/location estimation and modulation detection for RF sources using steerable 3D IIR digital beam filters

    NASA Astrophysics Data System (ADS)

    Udayanga, Nilan; Madanayake, Arjuna; Wijenayake, Chamith

    2014-05-01

    A planar antenna array based feature detection scheme is proposed to estimate the directional, location and modulation information pertaining to radio sources in a cognitive radio environment. The proposed system employs multiple direction estimation stations and a fusion station. Planar antenna arrays and three-dimensional (3-D) infinite impulse response (IIR) digital filters are employed to perform volume scanning of the radio environment, leading to a spatial power profile, which is subjected to peak detection in order to estimate the direction of arrival corresponding to each source. Cyclosationay feature detection is then performed along each direction to estimate the frequency and modulation information. Two simulation examples are provided to verify the feasibility of the proposed approach.

  3. Engineering a Blood Vessel Network Module for Body-on-a-Chip Applications.

    PubMed

    Ryu, Hyunryul; Oh, Soojung; Lee, Hyun Jae; Lee, Jin Young; Lee, Hae Kwang; Jeon, Noo Li

    2015-06-01

    The blood circulatory system links all organs from one to another to support and maintain each organ's functions consistently. Therefore, blood vessels have been considered as a vital unit. Engineering perfusable functional blood vessels in vitro has been challenging due to difficulties in designing the connection between rigid macroscale tubes and fragile microscale ones. Here, we propose a generalizable method to engineer a "long" perfusable blood vessel network. To form millimeter-scale vessels, fibroblasts were co-cultured with human umbilical vein endothelial cells (HUVECs) in close proximity. In contrast to previous works, in which all cells were permanently placed within the device, we developed a novel method to culture paracrine factor secreting fibroblasts on an O-ring-shaped guide that can be transferred in and out. This approach affords flexibility in co-culture, where the effects of secreted factors can be decoupled. Using this, blood vessels with length up to 2 mm were successfully produced in a reproducible manner (>90%). Because the vessels form a perfusable network within the channel, simple links to inlets and outlets of the device allowed connections to the outside world. The robust and reproducible formation of in vitro engineered vessels can be used as a module to link various organ components as parts of future body-on-a-chip applications. PMID:25532526

  4. Emotional reactivity to threat modulates activity in mentalizing network during aggression.

    PubMed

    Beyer, Frederike; Münte, Thomas F; Erdmann, Christian; Krämer, Ulrike M

    2014-10-01

    Aggression is a common response to provocation, albeit with considerable interindividual differences. In this fMRI study, we investigated emotional reactivity to threat as possible link between provocation and aggression, as well as the neural correlates of this relationship. We hypothesized that emotional reactivity, measured as fear potentiation (FP) of the startle response, would be negatively associated with aggressive behavior and would modulate neural activity during an aggressive interaction. In 30 healthy female participants, FP was measured as the difference between blink amplitudes while watching threatening vs neutral pictures. Participants subsequently engaged in a variant of the Taylor Aggression Paradigm (TAP), while being scanned. During the TAP, participants selected a punishment level for either a highly provoking or a nonprovoking opponent. There was no difference in aggressive behavior between participants high and low in FP. However, we found a negative correlation between FP and the neural provocation effect in several regions of a network previously associated with mentalizing including the medial prefrontal cortex, precuneus and the temporo-parietal junction. Independently of the FP variability, aggressive behavior correlated with the provocation effect on activity in the caudate nucleus. Our results indicate that during a provocative confrontation, high emotional reactivity to threat suppresses recruitment of the mentalizing network. PMID:23986265

  5. Pattern-specific synaptic mechanisms in a multifunctional network. II. Intrinsic modulation by metabotropic glutamate receptors.

    PubMed

    Lieske, Steven P; Ramirez, Jan-Marino

    2006-03-01

    The in vitro respiratory network contained in the transverse brain stem slice of mice simultaneously generates fast (approximately 15 min(-1)) and slow ( approximately 0.5 min(-1)) rhythmic activities corresponding to fictive eupnea ("normal" breathing) and fictive sighs. We show that these two activity patterns are differentially controlled through the modulatory actions of metabotropic glutamate receptors (mGluRs). Sighs were selectively inhibited by agonists of the group III mGluRs according to a pharmacological profile most consistent with activation of mGluR8. Sighs were also blocked by the supposedly inactive L-isomer of the widely used N-methyl-D-aspartate (NMDA) receptor antagonist 2-amino-5-phosphonopentanoic acid (L-AP5, 5 microM), an effect that was abolished in the presence of group III mGluR antagonists. Excitatory postsynaptic potentials (EPSPs) were recorded in pre-Bötzinger Complex neurons after stimulation of the contralateral ventral respiratory group (VRG); evoked EPSP amplitude was variably reduced after bath application of the group III agonist L-serine-O-phosphate (L-SOP), with an average reduction of 15%. Therefore although group III mGluRs do play a role in regulating synapse strength, this seems to be only a minor factor in the regulation of synapses made by midline-crossing axons. Intrinsic modulation of the respiratory central pattern generator by mGluRs appears to be an essential component of the multifunctionality that characterizes this network. PMID:16492945

  6. Modulation of EEG functional connectivity networks in subjects undergoing repetitive transcranial magnetic stimulation.

    PubMed

    Shafi, Mouhsin M; Brandon Westover, M; Oberman, Lindsay; Cash, Sydney S; Pascual-Leone, Alvaro

    2014-01-01

    Transcranial magnetic stimulation (TMS) is a noninvasive brain stimulation technique that utilizes magnetic fluxes to alter cortical activity. Continuous theta-burst repetitive TMS (cTBS) results in long-lasting decreases in indices of cortical excitability, and alterations in performance of behavioral tasks. We investigated the effects of cTBS on cortical function via functional connectivity and graph theoretical analysis of EEG data. Thirty-one channel resting-state EEG recordings were obtained before and after 40 s of cTBS stimulation to the left primary motor cortex. Functional connectivity between nodes was assessed in multiple frequency bands using lagged max-covariance, and subsequently thresholded to construct undirected graphs. After cTBS, we find widespread decreases in functional connectivity in the alpha band. There are also simultaneous increases in functional connectivity in the high-beta bands, especially amongst anterior and interhemispheric connections. The analysis of the undirected graphs reveals that interhemispheric and interregional connections are more likely to be modulated after cTBS than local connections. There is also a shift in the topology of network connectivity, with an increase in the clustering coefficient after cTBS in the beta bands, and a decrease in clustering and increase in path length in the alpha band, with the alpha-band connectivity primarily decreased near the site of stimulation. cTBS produces widespread alterations in cortical functional connectivity, with resulting shifts in cortical network topology. PMID:23471637

  7. Modulation of EEG Functional Connectivity Networks in Subjects Undergoing Repetitive Transcranial Magnetic Stimulation

    PubMed Central

    Shafi, Mouhsin M.; Westover, M. Brandon; Oberman, Lindsay; Cash, Sydney S.; Pascual-Leone, Alvaro

    2014-01-01

    Transcranial magnetic stimulation (TMS) is a noninvasive brain stimulation technique that utilizes magnetic fluxes to alter cortical activity. Continuous theta-burst repetitive TMS (cTBS) results in long-lasting decreases in indices of cortical excitability, and alterations in performance of behavioral tasks. We investigated the effects of cTBS on cortical function via functional connectivity and graph theoretical analysis of EEG data. Thirty-one channel resting-state EEG recordings were obtained before and after 40 s of cTBS stimulation to the left primary motor cortex. Functional connectivity between nodes was assessed in multiple frequency bands using lagged max-covariance, and subsequently thresholded to construct undirected graphs. After cTBS, we find widespread decreases in functional connectivity in the alpha band. There are also simultaneous increases in functional connectivity in the high-beta bands, especially amongst anterior and interhemispheric connections. The analysis of the undirected graphs reveals that interhemispheric and interregional connections are more likely to be modulated after cTBS than local connections. There is also a shift in the topology of network connectivity, with an increase in the clustering coefficient after cTBS in the beta bands, and a decrease in clustering and increase in path length in the alpha band, with the alpha-band connectivity primarily decreased near the site of stimulation. cTBS produces widespread alterations in cortical functional connectivity, with resulting shifts in cortical network topology. PMID:23471637

  8. 28 Gb/s direct modulation heterogeneously integrated C-band InP/SOI DFB laser.

    PubMed

    Abbasi, Amin; Verbist, Jochem; Van Kerrebrouck, Joris; Lelarge, Francois; Duan, Guang-Hua; Yin, Xin; Bauwelinck, Johan; Roelkens, Gunther; Morthier, Geert

    2015-10-01

    We demonstrate direct modulation of a heterogeneously integrated C-band DFB laser on SOI at 28 Gb/s with a 2 dB extinction ratio. This is the highest direct modulation bitrate so far reported for a membrane laser coupled to an SOI waveguide. The laser operates single mode with 6 mW output power at 100 mA bias current. The 3 dB modulation bandwidth is 15 GHz. Transmission experiments using a 2 km non zero dispersion shifted single mode fiber were performed at 28 Gb/s bitrate using a 2(7)-1 NRZ-PRBS pattern resulting in a 1 dB power penalty. PMID:26480161

  9. Extracting directed information flow networks: An application to genetics and semantics

    NASA Astrophysics Data System (ADS)

    Masucci, A. P.; Kalampokis, A.; Eguíluz, V. M.; Hernández-García, E.

    2011-02-01

    We introduce a general method to infer the directional information flow between populations whose elements are described by n-dimensional vectors of symbolic attributes. The method is based on the Jensen-Shannon divergence and on the Shannon entropy and has a wide range of application. We show here the results of two applications: first we extract the network of genetic flow between meadows of the seagrass Poseidonia oceanica, where the meadow elements are specified by sets of microsatellite markers, and then we extract the semantic flow network from a set of Wikipedia pages, showing the semantic channels between different areas of knowledge.

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

    PubMed Central

    2010-01-01

    Background Soybean (Glycine max [L] Merr.) seed isoflavones have long been considered a desirable trait to target in selection programs for their contribution to human health and plant defense systems. However, attempts to modify seed isoflavone contents have not always produced the expected results because their genetic basis is polygenic and complex. Undoubtedly, the extreme variability that seed isoflavones display over environments has obscured our understanding of the genetics involved. Results In this study, a mapping population of RILs with three replicates was analyzed in four different environments (two locations over two years). We found a total of thirty-five main-effect genomic regions and many epistatic interactions controlling genistein, daidzein, glycitein and total isoflavone accumulation in seeds. The use of distinct environments permitted detection of a great number of environment-modulated and minor-effect QTL. Our findings suggest that isoflavone seed concentration is controlled by a complex network of multiple minor-effect loci interconnected by a dense epistatic map of interactions. The magnitude and significance of the effects of many of the nodes and connections in the network varied depending on the environmental conditions. In an attempt to unravel the genetic architecture underlying the traits studied, we searched on a genome-wide scale for genomic regions homologous to the most important identified isoflavone biosynthetic genes. We identified putative candidate genes for several of the main-effect and epistatic QTL and for QTL reported by other groups. Conclusions To better understand the underlying genetics of isoflavone accumulation, we performed a large scale analysis to identify genomic regions associated with isoflavone concentrations. We not only identified a number of such regions, but also found that they can interact with one another and with the environment to form a complex adaptable network controlling seed isoflavone levels. We also found putative candidate genes in several regions and overall we advanced the knowledge of the genetics underlying isoflavone synthesis. PMID:20540761

  11. Modulation of direct pathway striatal projection neurons by muscarinic M₄-type receptors.

    PubMed

    Hernández-Flores, Teresa; Hernández-González, Omar; Pérez-Ramírez, María B; Lara-González, Esther; Arias-García, Mario A; Duhne, Mariana; Pérez-Burgos, Azucena; Prieto, G Aleph; Figueroa, Alejandra; Galarraga, Elvira; Bargas, José

    2015-02-01

    Models of basal ganglia (BG) function posit a dynamic balance between two classes of striatal projection neurons (SPNs): direct pathway neurons (dSPNs) that facilitate movements, and indirect pathway neurons (iSPNs) that repress movement execution. Two main modulatory transmitters regulate the output of these neurons: dopamine (DA) and acetylcholine (ACh). dSPNs express D1-type DA, M1-and M4-type ACh receptors, while iSPNs express D2-type DA and M1-type ACh receptors. Actions of M1-, D1-, and D2-receptors have been extensively reported, but we still ignore most actions of muscarinic M4-type receptors. Here, we used whole-cell recordings in acutely dissociated neurons, pharmacological tools such as mamba-toxins, and BAC D(1 or 2)-eGFP transgenic mice to show that activation of M4-type receptors with bath applied muscarine enhances Ca(2+)-currents through CaV1-channels in dSPNs and not in iSPNs. This action increases excitability of dSPNs after both direct current injection and synaptically driven stimulation. The increases in Ca(2+)-current and excitability were blocked specifically by mamba toxin-3, suggesting mediation via M4-type receptors. M4-receptor activation also increased network activity of dSPNs but not of iSPNs as seen with calcium-imaging techniques. Moreover, actions of D1-type and M4-type receptors may add to produce a larger enhancement of excitability of dSPNs or, paradoxically, oppose each other depending on the order of their activation. Possible implications of these findings are discussed. PMID:25290553

  12. Right hemisphere dominance directly predicts both baseline V1 cortical excitability and the degree of top-down modulation exerted over low-level brain structures.

    PubMed

    Arshad, Q; Siddiqui, S; Ramachandran, S; Goga, U; Bonsu, A; Patel, M; Roberts, R E; Nigmatullina, Y; Malhotra, P; Bronstein, A M

    2015-12-17

    Right hemisphere dominance for visuo-spatial attention is characteristically observed in most right-handed individuals. This dominance has been attributed to both an anatomically larger right fronto-parietal network and the existence of asymmetric parietal interhemispheric connections. Previously it has been demonstrated that interhemispheric conflict, which induces left hemisphere inhibition, results in the modulation of both (i) the excitability of the early visual cortex (V1) and (ii) the brainstem-mediated vestibular-ocular reflex (VOR) via top-down control mechanisms. However to date, it remains unknown whether the degree of an individual's right hemisphere dominance for visuospatial function can influence, (i) the baseline excitability of the visual cortex and (ii) the extent to which the right hemisphere can exert top-down modulation. We directly tested this by correlating line bisection error (or pseudoneglect), taken as a measure of right hemisphere dominance, with both (i) visual cortical excitability measured using phosphene perception elicited via single-pulse occipital trans-cranial magnetic stimulation (TMS) and (ii) the degree of trans-cranial direct current stimulation (tDCS)-mediated VOR suppression, following left hemisphere inhibition. We found that those individuals with greater right hemisphere dominance had a less excitable early visual cortex at baseline and demonstrated a greater degree of vestibular nystagmus suppression following left hemisphere cathodal tDCS. To conclude, our results provide the first demonstration that individual differences in right hemisphere dominance can directly predict both the baseline excitability of low-level brain structures and the degree of top-down modulation exerted over them. PMID:26518461

  13. Right hemisphere dominance directly predicts both baseline V1 cortical excitability and the degree of top-down modulation exerted over low-level brain structures

    PubMed Central

    Arshad, Q.; Siddiqui, S.; Ramachandran, S.; Goga, U.; Bonsu, A.; Patel, M.; Roberts, R.E.; Nigmatullina, Y.; Malhotra, P.; Bronstein, A.M.

    2015-01-01

    Right hemisphere dominance for visuo-spatial attention is characteristically observed in most right-handed individuals. This dominance has been attributed to both an anatomically larger right fronto-parietal network and the existence of asymmetric parietal interhemispheric connections. Previously it has been demonstrated that interhemispheric conflict, which induces left hemisphere inhibition, results in the modulation of both (i) the excitability of the early visual cortex (V1) and (ii) the brainstem-mediated vestibular–ocular reflex (VOR) via top-down control mechanisms. However to date, it remains unknown whether the degree of an individual’s right hemisphere dominance for visuospatial function can influence, (i) the baseline excitability of the visual cortex and (ii) the extent to which the right hemisphere can exert top-down modulation. We directly tested this by correlating line bisection error (or pseudoneglect), taken as a measure of right hemisphere dominance, with both (i) visual cortical excitability measured using phosphene perception elicited via single-pulse occipital trans-cranial magnetic stimulation (TMS) and (ii) the degree of trans-cranial direct current stimulation (tDCS)-mediated VOR suppression, following left hemisphere inhibition. We found that those individuals with greater right hemisphere dominance had a less excitable early visual cortex at baseline and demonstrated a greater degree of vestibular nystagmus suppression following left hemisphere cathodal tDCS. To conclude, our results provide the first demonstration that individual differences in right hemisphere dominance can directly predict both the baseline excitability of low-level brain structures and the degree of top-down modulation exerted over them. PMID:26518461

  14. Modulating activity in the orbitofrontal cortex changes trustees' cooperation: A transcranial direct current stimulation study.

    PubMed

    Wang, Guangrong; Li, Jianbiao; Yin, Xile; Li, Shuaiqi; Wei, Mengxing

    2016-04-15

    Trust is one of the most important factors in human society, as it pervades almost all domains of the society. The trusting behavior of trustors is dependent on the belief about the cooperative (reciprocal) level of trustees. Thence what are the motives underlying the cooperative behavior? An important explanation is that guilt aversion can motivate cooperative behavior. The right orbitofrontal cortex (OFC) is the guilt-specific region, while there is little understanding on the causal effect of this network. We explored the causal effect of the OFC on cooperative behavior using transcranial direct current stimulation (tDCS). Sixty participants played the trust game as trustees, and they received either anodal tDCS over the right OFC and simultaneously cathodal electrode over the right dorsolateral prefrontal cortex (DLPFC), or sham stimulation. Experimental results showed that participants as trustees transferred back more money in the tDCS treatment than sham stimulation. This suggests that the activity of the right OFC has causal effects on cooperative behavior. PMID:26808605

  15. Vibrio parahaemolyticus thermostable direct hemolysin modulates cytoskeletal organization and calcium homeostasis in intestinal cultured cells.

    PubMed

    Fabbri, A; Falzano, L; Frank, C; Donelli, G; Matarrese, P; Raimondi, F; Fasano, A; Fiorentini, C

    1999-03-01

    Vibrio parahaemolyticus is a marine bacterium known to be the leading cause of seafood gastroenteritis worldwide. A 46-kDa homodimer protein secreted by this microorganism, the thermostable direct hemolysin (TDH), is considered a major virulence factor involved in bacterial pathogenesis since a high percentage of strains of clinical origin are positive for TDH production. TDH is a pore-forming toxin, and its most extensively studied effect is the ability to cause hemolysis of erythrocytes from different mammalian species. Moreover, TDH induces in a variety of cells cytotoxic effects consisting mainly of cell degeneration which often leads to loss of viability. In this work, we examined the cellular changes induced by TDH in monolayers of IEC-6 cells (derived from the rat crypt small intestine), which represent a useful cell model for studying toxins from enteric bacteria. In experimental conditions allowing cell survival, TDH induces a rapid transient increase in intracellular calcium as well as a significant though reversible decreased rate of progression through the cell cycle. The morphological changes seem to be dependent on the organization of the microtubular network, which appears to be the preferential cytoskeletal element involved in the cellular response to the toxin. PMID:10024554

  16. Experimental investigation of dynamic impairment-aware bi-directional lightpath provisioning in GMPLS-enabled optical networks

    NASA Astrophysics Data System (ADS)

    Liu, Lei; Tsuritani, Takehiro; Morita, Itsuro

    2011-12-01

    The lightpaths within a wavelength switched optical network (WSON) are usually bi-directional, with a same route and a same wavelength which are allocated for both directions from the viewpoint of optical network operation. On the other hand, the introduction of generalized multi-protocol label switching (GMPLS) as a network control plane is expected to bring more intelligence and to provision the end-to-end lightpath in a cost-efficient manner. In this paper, we experimentally demonstrate and evaluate dynamic provisioning of bidirectional lightpaths in GMPLS controlled optical networks, considering the wavelength continuity constraint and the physical impairment constraint on both directions.

  17. Self-organizing path integration using a linked continuous attractor and competitive network: path integration of head direction.

    PubMed

    Stringer, Simon M; Rolls, Edmund T

    2006-12-01

    A key issue is how networks in the brain learn to perform path integration, that is update a represented position using a velocity signal. Using head direction cells as an example, we show that a competitive network could self-organize to learn to respond to combinations of head direction and angular head rotation velocity. These combination cells can then be used to drive a continuous attractor network to the next head direction based on the incoming rotation signal. An associative synaptic modification rule with a short term memory trace enables preceding combination cell activity during training to be associated with the next position in the continuous attractor network. The network accounts for the presence of neurons found in the brain that respond to combinations of head direction and angular head rotation velocity. Analogous networks in the hippocampal system could self-organize to perform path integration of place and spatial view representations. PMID:17162462

  18. A Study of an Optical Lunar Surface Communications Network with High Bandwidth Direct to Earth Link

    NASA Technical Reports Server (NTRS)

    Wilson, K.; Biswas, A.; Schoolcraft, J.

    2011-01-01

    Analyzed optical DTE (direct to earth) and lunar relay satellite link analyses, greater than 200 Mbps downlink to 1-m Earth receiver and greater than 1 Mbps uplink achieved with mobile 5-cm lunar transceiver, greater than 1Gbps downlink and greater than 10 Mpbs uplink achieved with 10-cm stationary lunar transceiver, MITLL (MIT Lincoln Laboratory) 2013 LLCD (Lunar Laser Communications Demonstration) plans to demonstrate 622 Mbps downlink with 20 Mbps uplink between lunar orbiter and ground station; Identified top five technology challenges to deploying lunar optical network, Performed preliminary experiments on two of challenges: (i) lunar dust removal and (ii)DTN over optical carrier, Exploring opportunities to evaluate DTN (delay-tolerant networking) over optical link in a multi-node network e.g. Desert RATS.

  19. W-band RoF transmission based on optical multi-carrier generation by cascading one directly-modulated DFB laser and one phase modulator

    NASA Astrophysics Data System (ADS)

    Li, Xinying; Yu, Jianjun

    2015-06-01

    We experimentally demonstrate that, adopting an optical multi-carrier source based on cascaded directly-modulated distributed-feedback laser (DML) and phase modulator (PM), any pair of subcarriers spaced by 100 GHz selected from the generated optical subcarriers can be used to generate 100-GHz millimeter-wave (mm-wave) frequency based on remote heterodyning technique, and thus realize 3.125-Gb/s on-off-keying (OOK) signal transmission over a radio-over-fiber (RoF) system at W-band. After 20-km large-effective-area fiber (LEAF) transmission and 2-m wireless delivery, the bit-error ratio (BER) of 1×10-9 can be attained when the two selected subcarriers spaced by 100 GHz are simultaneously modulated before remote heterodyning. 1.5-dB power penalty at the BER of 1×10-9 is caused by 2-m wireless delivery while almost no penalty is caused by 20-km LEAF transmission. However, because of different path lengths and the quite wide linewidth of the DML, the 3.125-Gb/s OOK signal after the same RoF transmission cannot be recovered when the two selected subcarriers are separated into two different optical paths and only one of them is modulated before remote heterodyning.

  20. Stitching together Multiple Data Dimensions Reveals Interacting Metabolomic and Transcriptomic Networks That Modulate Cell Regulation

    PubMed Central

    Dombek, Kenneth M.; Xu, Ethan Y.; Vu, Heather; Tu, Zhidong; Brem, Rachel B.; Bumgarner, Roger E.; Schadt, Eric E.

    2012-01-01

    Cells employ multiple levels of regulation, including transcriptional and translational regulation, that drive core biological processes and enable cells to respond to genetic and environmental changes. Small-molecule metabolites are one category of critical cellular intermediates that can influence as well as be a target of cellular regulations. Because metabolites represent the direct output of protein-mediated cellular processes, endogenous metabolite concentrations can closely reflect cellular physiological states, especially when integrated with other molecular-profiling data. Here we develop and apply a network reconstruction approach that simultaneously integrates six different types of data: endogenous metabolite concentration, RNA expression, DNA variation, DNA–protein binding, protein–metabolite interaction, and protein–protein interaction data, to construct probabilistic causal networks that elucidate the complexity of cell regulation in a segregating yeast population. Because many of the metabolites are found to be under strong genetic control, we were able to employ a causal regulator detection algorithm to identify causal regulators of the resulting network that elucidated the mechanisms by which variations in their sequence affect gene expression and metabolite concentrations. We examined all four expression quantitative trait loci (eQTL) hot spots with colocalized metabolite QTLs, two of which recapitulated known biological processes, while the other two elucidated novel putative biological mechanisms for the eQTL hot spots. PMID:22509135

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

  2. Goal-Directed Modulation of Neural Memory Patterns: Implications for fMRI-Based Memory Detection.

    PubMed

    Uncapher, Melina R; Boyd-Meredith, J Tyler; Chow, Tiffany E; Rissman, Jesse; Wagner, Anthony D

    2015-06-01

    Remembering a past event elicits distributed neural patterns that can be distinguished from patterns elicited when encountering novel information. These differing patterns can be decoded with relatively high diagnostic accuracy for individual memories using multivoxel pattern analysis (MVPA) of fMRI data. Brain-based memory detection--if valid and reliable--would have clear utility beyond the domain of cognitive neuroscience, in the realm of law, marketing, and beyond. However, a significant boundary condition on memory decoding validity may be the deployment of "countermeasures": strategies used to mask memory signals. Here we tested the vulnerability of fMRI-based memory detection to countermeasures, using a paradigm that bears resemblance to eyewitness identification. Participants were scanned while performing two tasks on previously studied and novel faces: (1) a standard recognition memory task; and (2) a task wherein they attempted to conceal their true memory state. Univariate analyses revealed that participants were able to strategically modulate neural responses, averaged across trials, in regions implicated in memory retrieval, including the hippocampus and angular gyrus. Moreover, regions associated with goal-directed shifts of attention and thought substitution supported memory concealment, and those associated with memory generation supported novelty concealment. Critically, whereas MVPA enabled reliable classification of memory states when participants reported memory truthfully, the ability to decode memory on individual trials was compromised, even reversing, during attempts to conceal memory. Together, these findings demonstrate that strategic goal states can be deployed to mask memory-related neural patterns and foil memory decoding technology, placing a significant boundary condition on their real-world utility. PMID:26041920

  3. Direct and Indirect Influence of Altruistic Behavior in a Social Network.

    PubMed

    Liu, Pei-Pei; Safin, Vasiliy; Yang, Barry; Luhmann, Christian C

    2015-01-01

    Prior research has suggested that recipients of generosity behave more generously themselves (a direct social influence). In contrast, there is conflicting evidence about the existence of indirect influence (i.e., whether interacting with a recipient of generosity causes one to behave more generously), casting doubt on the possibility that altruistic behavior can cascade through social networks. The current study investigated how far selfish and generous behavior can be transmitted through social networks and the cognitive mechanisms that underlie such transmission. Participants played a sequence of public goods games comprising a chain network. This network is advantageous because it permits only a single, unambiguous path of influence. Furthermore, we experimentally manipulated the behavior of the first link in the chain to be either generous or selfish. Results revealed the presence of direct social influence, but no evidence for indirect influence. Results also showed that selfish behavior exerted a substantially greater influence than generous behavior. Finally, expectations about future partners' behavior strongly mediated the observed social influence, suggesting an adaptive basis for such influence. PMID:26469066

  4. Direct and Indirect Influence of Altruistic Behavior in a Social Network

    PubMed Central

    Liu, Pei-Pei; Safin, Vasiliy; Yang, Barry; Luhmann, Christian C.

    2015-01-01

    Prior research has suggested that recipients of generosity behave more generously themselves (a direct social influence). In contrast, there is conflicting evidence about the existence of indirect influence (i.e., whether interacting with a recipient of generosity causes one to behave more generously), casting doubt on the possibility that altruistic behavior can cascade through social networks. The current study investigated how far selfish and generous behavior can be transmitted through social networks and the cognitive mechanisms that underlie such transmission. Participants played a sequence of public goods games comprising a chain network. This network is advantageous because it permits only a single, unambiguous path of influence. Furthermore, we experimentally manipulated the behavior of the first link in the chain to be either generous or selfish. Results revealed the presence of direct social influence, but no evidence for indirect influence. Results also showed that selfish behavior exerted a substantially greater influence than generous behavior. Finally, expectations about future partners’ behavior strongly mediated the observed social influence, suggesting an adaptive basis for such influence. PMID:26469066

  5. Organocatalysis by Networks of Cooperative Hydrogen Bonds: Enantioselective Direct Mannich Addition to Preformed Arylideneureas.

    PubMed

    Lillo, Victor J; Mansilla, Javier; Saá, José M

    2016-03-18

    The concept of noncovalent organocatalysis by means of networks of cooperative hydrogen bonds (NCHB organocatalysis) has been explored. Arylideneureas were chosen as ideal substrates because of their powerful donor-acceptor properties. We have examined their uncatalyzed, direct Mannich reaction with acetoacetates in comparison with that catalyzed by a number of salan derivatives capable of providing a network of cooperative hydrogen bonds. Catalyst D [(R,R)-N,N'-bis(salicyl)cyclohexane-1,2-diamine] was found to drive the above direct Mannich reaction in an enantioselective manner, thereby allowing the synthesis of several Biginelli dihydropyrimidinones with high enantioselectivity. DFT calculations (B3LYP-D-PCM/6-31+G*//B3LYP/6-31+G*) revealed that the NCHB organocatalyst lowers the energy barrier of the reaction. The NCHB organocatalysts appear to function as biomimetic catalysts. PMID:26918408

  6. Prediction of the anti-inflammatory mechanisms of curcumin by module-based protein interaction network analysis

    PubMed Central

    Gan, Yanxiong; Zheng, Shichao; Baak, Jan P.A.; Zhao, Silei; Zheng, Yongfeng; Luo, Nini; Liao, Wan; Fu, Chaomei

    2015-01-01

    Curcumin, the medically active component from Curcuma longa (Turmeric), is widely used to treat inflammatory diseases. Protein interaction network (PIN) analysis was used to predict its mechanisms of molecular action. Targets of curcumin were obtained based on ChEMBL and STITCH databases. Protein–protein interactions (PPIs) were extracted from the String database. The PIN of curcumin was constructed by Cytoscape and the function modules identified by gene ontology (GO) enrichment analysis based on molecular complex detection (MCODE). A PIN of curcumin with 482 nodes and 1688 interactions was constructed, which has scale-free, small world and modular properties. Based on analysis of these function modules, the mechanism of curcumin is proposed. Two modules were found to be intimately associated with inflammation. With function modules analysis, the anti-inflammatory effects of curcumin were related to SMAD, ERG and mediation by the TLR family. TLR9 may be a potential target of curcumin to treat inflammation. PMID:26713275

  7. Prediction of the anti-inflammatory mechanisms of curcumin by module-based protein interaction network analysis.

    PubMed

    Gan, Yanxiong; Zheng, Shichao; Baak, Jan P A; Zhao, Silei; Zheng, Yongfeng; Luo, Nini; Liao, Wan; Fu, Chaomei

    2015-11-01

    Curcumin, the medically active component from Curcuma longa (Turmeric), is widely used to treat inflammatory diseases. Protein interaction network (PIN) analysis was used to predict its mechanisms of molecular action. Targets of curcumin were obtained based on ChEMBL and STITCH databases. Protein-protein interactions (PPIs) were extracted from the String database. The PIN of curcumin was constructed by Cytoscape and the function modules identified by gene ontology (GO) enrichment analysis based on molecular complex detection (MCODE). A PIN of curcumin with 482 nodes and 1688 interactions was constructed, which has scale-free, small world and modular properties. Based on analysis of these function modules, the mechanism of curcumin is proposed. Two modules were found to be intimately associated with inflammation. With function modules analysis, the anti-inflammatory effects of curcumin were related to SMAD, ERG and mediation by the TLR family. TLR9 may be a potential target of curcumin to treat inflammation. PMID:26713275

  8. Asymmetric friction of non-motor MAPs can lead to their directional motion in active microtubule networks

    PubMed Central

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

    2014-01-01

    Summary 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 non-motor MAPs (NuMA, PRC1, and EB1) required for cell division. We find that frictional forces increase non-linearly with MAP velocity across microtubules and depend on filament polarity, with NuMA’s friction being lower when moving towards minus-ends, EB1’s lower towards plus-ends, and PRC1 exhibiting no directional preference. Mathematical models predict, and experiments confirm, that MAPs with asymmetric friction can move directionally within active microtubule pairs they crosslink. Our findings reveal how non-motor 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

  9. Modulation of resting state functional connectivity of the motor network by transcranial pulsed current stimulation.

    PubMed

    Sours, Chandler; Alon, Gad; Roys, Steve; Gullapalli, Rao P

    2014-04-01

    The effects of transcranial pulsed current stimulation (tPCS) on resting state functional connectivity (rs-FC) within the motor network were investigated. Eleven healthy participants received one magnetic resonance imaging (MRI) session with three resting state functional MRI (rs-fMRI) scans, one before stimulation (PRE-STIM) to collect baseline measures, one during stimulation (STIM), and one after 13?min of stimulation (POST-STIM). Rs-FC measures during the STIM and POST-STIM conditions were compared to the PRE-STIM baseline. Regions of interest for the rs-FC analysis were extracted from the significantly activated clusters obtained during a finger tapping motor paradigm and included the right primary motor cortex (R M1), left primary motor cortex (L M1), supplemental motor area (SMA), and cerebellum (Cer). The main findings were reduced rs-FC between the left M1 and surrounding motor cortex, and increased rs-FC between the left M1 and left thalamus during stimulation, but increased rs-FC between the Cer and right insula after stimulations. Bivariate measures of connectivity demonstrate reduced strength of connectivity for the whole network average (p=0.044) and reduced diversity of connectivity for the network average during stimulation (p=0.024). During the POST-STIM condition, the trend of reduced diversity for the network average was statistically weaker (p=0.071). In conclusion, while many of the findings are comparable to previous reports using simultaneous transcranial direct current stimulation (tDCS) and fMRI acquisition, we also demonstrate additional changes in connectivity patterns that are induced by tPCS. PMID:24593667

  10. Nonlinear distortion evaluation in a directly modulated distributed feedback laser diode-based fiber-optic cable television transport system

    NASA Astrophysics Data System (ADS)

    Li, Chung-Yi; Ying, Cheng-Ling; Lin, Chun-Yu; Chu, Chien-An

    2015-12-01

    This study evaluated a directly modulated distributed feedback (DFB) laser diode (LD) for cable TV systems with respect to carrier-to-nonlinear distortion of LDs. The second-order distortion-to-carrier ratio is found to be proportional to that of the second-order coefficient-to-first-order coefficient of the DFB laser diode driving current and to the optical modulation index (OMI). Furthermore, the third-order distortion-to-carrier ratio is proportional to that of the third-order coefficient-to-first-order coefficient of the DFB laser diode driving current, and to the OMI2.

  11. Lightning Radio Source Retrieval Using Advanced Lightning Direction Finder (ALDF) Networks

    NASA Technical Reports Server (NTRS)

    Koshak, William J.; Blakeslee, Richard J.; Bailey, J. C.

    1998-01-01

    A linear algebraic solution is provided for the problem of retrieving the location and time of occurrence of lightning ground strikes from an Advanced Lightning Direction Finder (ALDF) network. The ALDF network measures field strength, magnetic bearing and arrival time of lightning radio emissions. Solutions for the plane (i.e., no Earth curvature) are provided that implement all of tile measurements mentioned above. Tests of the retrieval method are provided using computer-simulated data sets. We also introduce a quadratic planar solution that is useful when only three arrival time measurements are available. The algebra of the quadratic root results are examined in detail to clarify what portions of the analysis region lead to fundamental ambiguities in source location. Complex root results are shown to be associated with the presence of measurement errors when the lightning source lies near an outer sensor baseline of the ALDF network. In the absence of measurement errors, quadratic root degeneracy (no source location ambiguity) is shown to exist exactly on the outer sensor baselines for arbitrary non-collinear network geometries. The accuracy of the quadratic planar method is tested with computer generated data sets. The results are generally better than those obtained from the three station linear planar method when bearing errors are about 2 deg. We also note some of the advantages and disadvantages of these methods over the nonlinear method of chi(sup 2) minimization employed by the National Lightning Detection Network (NLDN) and discussed in Cummins et al.(1993, 1995, 1998).

  12. Hypoxia-Ischemia Disrupts Directed Interactions within Neonatal Prefrontal-Hippocampal Networks

    PubMed Central

    Brockmann, Marco D.; Kukovic, Maja; Schönfeld, Michael; Sedlacik, Jan; Hanganu-Opatz, Ileana L.

    2013-01-01

    Due to improved survival rates and outcome of human infants experiencing a hypoxic-ischemic episode, cognitive dysfunctions have become prominent. They might result from abnormal communication within prefrontal-hippocampal networks, as synchrony and directed interactions between the prefrontal cortex and hippocampus account for mnemonic and executive performance. Here, we elucidate the structural and functional impact of hypoxic-ischemic events on developing prefrontal-hippocampal networks in an immature rat model of injury. The magnitude of infarction, cell loss and astrogliosis revealed that an early hypoxic-ischemic episode had either a severe or a mild/moderate outcome. Without affecting the gross morphology, hypoxia-ischemia with mild/moderate outcome diminished prefrontal neuronal firing and gamma network entrainment. This dysfunction resulted from decreased coupling synchrony within prefrontal-hippocampal networks and disruption of hippocampal theta drive. Thus, early hypoxia-ischemia may alter the functional maturation of neuronal networks involved in cognitive processing by disturbing the communication between the neonatal prefrontal cortex and hippocampus. PMID:24376636

  13. Integration of offshore wind farms through high voltage direct current networks

    NASA Astrophysics Data System (ADS)

    Livermore, Luke

    The integration of offshore wind farms through Multi Terminal DC (MTDC) networks into the GB network was investigated. The ability of Voltage Source Converter (VSC) High Voltage Direct Current (HVDC) to damp Subsynchronous Resonance (SSR) and ride through onshore AC faults was studied. Due to increased levels of wind generation in Scotland, substantial onshore and offshore reinforcements to the GB transmission network are proposed. Possible inland reinforcements include the use of series compensation through fixed capacitors. This potentially can lead to SSR. Offshore reinforcements are proposed by two HVDC links. In addition to its primary functions of bulk power transmission, a HVDC link can be used to provide damping against SSR, and this function has been modelled. Simulation studies have been carried out in PSCAD. In addition, a real-time hardware-in-the-loop HVDC test rig has been used to implement and validate the proposed damping scheme on an experimental platform. When faults occur within AC onshore networks, offshore MTDC networks are vulnerable to DC overvoltages, potentially damaging the DC plant and cables. Power reduction and power dissipation control systems were investigated to ride through onshore AC faults. These methods do not require dedicated fast communication systems. Simulations and laboratory experiments are carried out to evaluate the control systems, with the results from the two platforms compared..

  14. Health system tests CRM data base. Community Health Network uses direct mail to boost physicians.

    PubMed

    Botvin, Judith D

    2003-01-01

    A six-month pilot patient retention project for Community Health Network (CHN), Indianapolis, ran from July 2002 to January 2003. It was a direct mail campaign on behalf of some members of the group practices owned by CHN, designed to test the use of the system's CRM database. Patients of the physicians received personal, dynamically-generated cards reminding them to schedule appointments and tests. Each mailing cost $1.76, including production and mailing. PMID:12645315

  15. Eukaryotic Chemotaxis: A Network of Signaling Pathways Controls Motility, Directional Sensing, and Polarity

    PubMed Central

    Swaney, Kristen F.; Huang, Chuan-Hsiang; Devreotes, Peter N.

    2015-01-01

    Chemotaxis, the directed migration of cells in chemical gradients, is a vital process in normal physiology and in the pathogenesis of many diseases. Chemotactic cells display motility, directional sensing, and polarity. Motility refers to the random extension of pseudopodia, which may be driven by spontaneous actin waves that propagate through the cytoskeleton. Directional sensing is mediated by a system that detects temporal and spatial stimuli and biases motility toward the gradient. Polarity gives cells morphologically and functionally distinct leading and lagging edges by relocating proteins or their activities selectively to the poles. By exploiting the genetic advantages of Dictyostelium, investigators are working out the complex network of interactions between the proteins that have been implicated in the chemotactic processes of motility, directional sensing, and polarity. PMID:20192768

  16. Daily modulation and gravitational focusing in direct dark matter search experiments

    NASA Astrophysics Data System (ADS)

    Kouvaris, Chris; Nielsen, Niklas G.

    2015-10-01

    We study the effect of gravitational focusing of the Earth on dark matter. We find that the effect can produce a detectable diurnal modulation in the dark matter signal for part of the parameter space which for high dark matter masses is larger than the diurnal modulation induced by the fluctuations in the flux of dark matter particles due to the rotation of the Earth around its own axis. The two sources of diurnal modulation have different phases and can be distinguished from each other. We demonstrate that the diurnal modulation can potentially check the self-consistency of experiments that observe annual modulated signals that can be attributed to dark matter. Failing to discover a daily varying signal can result conclusively in the falsification of the hypothesis that the annual modulation is due to dark matter. We also suggest that null result experiments should check for a daily modulation of their rejected background signal with specific phases. A potential discovery could mean that dark matter collisions have been vetoed out.

  17. Optical Access Architecture Designs Based on WDM-Direct toward New Generation Networks

    NASA Astrophysics Data System (ADS)

    Miyazawa, Takaya; Harai, Hiroaki

    We present our proposed designs of optical access architecture based on WDM technology toward new-generation networks for two types of topologies: Single-star (SS) and passive-double-star (PDS). We adopt the concept of WDM-direct which links multiple wavelengths to each optical network unit (ONU). Our proposed architecture based on WDM-direct can achieve more than 10Gbps access per ONU. Moreover, our architecture can provide not only conventional bandwidth-shared services but also bandwidth-guaranteed services requiring more than 10Gbps bandwidth by establishing end-to-end lightpaths directly to each ONU, and thus meet high requirements of QoS in new-generation networks. Firstly, we show our proposed designs of SS-type architecture, and experimentally demonstrate the system. We confirm that the optical line terminal (OLT) successfully switches between packet/lightpath data transmissions for each ONU. In addition, we measure and evaluate optical power loss in upstream/downstream transmissions between the OLT and ONUs. Secondly, we show our proposed designs of PDS-type architecture, and theoretically analyze and evaluate the bit-rate capacity of the system.

  18. Nitric Oxide-Mediated Modulation of Central Network Dynamics during Olfactory Perception.

    PubMed

    Watanabe, Satoshi; Takanashi, Fumihito; Ishida, Kohei; Kobayashi, Suguru; Kitamura, Yoshiichiro; Hamasaki, Yuuta; Saito, Minoru

    2015-01-01

    Nitric oxide (NO) modulates the dynamics of central olfactory networks and has been implicated in olfactory processing including learning. Land mollusks have a specialized olfactory lobe in the brain called the procerebral (PC) lobe. The PC lobe produces ongoing local field potential (LFP) oscillation, which is modulated by olfactory stimulation. We hypothesized that NO should be released in the PC lobe in response to olfactory stimulation, and to prove this, we applied an NO electrode to the PC lobe of the land slug Limax in an isolated tentacle-brain preparation. Olfactory stimulation applied to the olfactory epithelium transiently increased the NO concentration in the PC lobe, and this was blocked by the NO synthase inhibitor L-NAME at 3.7 mM. L-NAME at this concentration did not block the ongoing LFP oscillation, but did block the frequency increase during olfactory stimulation. Olfactory stimulation also enhanced spatial synchronicity of activity, and this response was also blocked by L-NAME. Single electrical stimulation of the superior tentacle nerve (STN) mimicked the effects of olfactory stimulation on LFP frequency and synchronicity, and both of these effects were blocked by L-NAME. L-NAME did not block synaptic transmission from the STN to the nonbursting (NB)-type PC lobe neurons, which presumably produce NO in an activity-dependent manner. Previous behavioral experiments have revealed impairment of olfactory discrimination after L-NAME injection. The recording conditions in the present work likely reproduce the in vivo brain state in those behavioral experiments. We speculate that the dynamical effects of NO released during olfactory perception underlie precise odor representation and memory formation in the brain, presumably through regulation of NB neuron activity. PMID:26360020

  19. Nitric Oxide-Mediated Modulation of Central Network Dynamics during Olfactory Perception

    PubMed Central

    Kobayashi, Suguru; Kitamura, Yoshiichiro; Hamasaki, Yuuta; Saito, Minoru

    2015-01-01

    Nitric oxide (NO) modulates the dynamics of central olfactory networks and has been implicated in olfactory processing including learning. Land mollusks have a specialized olfactory lobe in the brain called the procerebral (PC) lobe. The PC lobe produces ongoing local field potential (LFP) oscillation, which is modulated by olfactory stimulation. We hypothesized that NO should be released in the PC lobe in response to olfactory stimulation, and to prove this, we applied an NO electrode to the PC lobe of the land slug Limax in an isolated tentacle-brain preparation. Olfactory stimulation applied to the olfactory epithelium transiently increased the NO concentration in the PC lobe, and this was blocked by the NO synthase inhibitor L-NAME at 3.7 mM. L-NAME at this concentration did not block the ongoing LFP oscillation, but did block the frequency increase during olfactory stimulation. Olfactory stimulation also enhanced spatial synchronicity of activity, and this response was also blocked by L-NAME. Single electrical stimulation of the superior tentacle nerve (STN) mimicked the effects of olfactory stimulation on LFP frequency and synchronicity, and both of these effects were blocked by L-NAME. L-NAME did not block synaptic transmission from the STN to the nonbursting (NB)-type PC lobe neurons, which presumably produce NO in an activity-dependent manner. Previous behavioral experiments have revealed impairment of olfactory discrimination after L-NAME injection. The recording conditions in the present work likely reproduce the in vivo brain state in those behavioral experiments. We speculate that the dynamical effects of NO released during olfactory perception underlie precise odor representation and memory formation in the brain, presumably through regulation of NB neuron activity. PMID:26360020

  20. GABAergic and glycinergic inputs modulate rhythmogenic mechanisms in the lamprey respiratory network