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Sample records for directed network modules

  1. Centrality properties of directed module members in social networks

    NASA Astrophysics Data System (ADS)

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

    2008-08-01

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

  2. 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.

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

    PubMed

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

    2010-08-16

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

  4. 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.

  5. Transcranial Direct Current Stimulation Modulates Neuronal Networks in Attention Deficit Hyperactivity Disorder.

    PubMed

    Sotnikova, Anna; Soff, Cornelia; Tagliazucchi, Enzo; Becker, Katja; Siniatchkin, Michael

    2017-02-17

    Anodal transcranial direct current stimulation (tDCS) of the prefrontal cortex has been repeatedly shown to improve working memory (WM). Since patients with attention deficit hyperactivity disorder (ADHD) are characterized by both underactivation of the prefrontal cortex and deficits in WM, the modulation of prefrontal activity with tDCS in ADHD patients may increase their WM performance as well as improve the activation and connectivity of the WM network. In the present study, this hypothesis was tested using a double-blind sham-controlled experimental design. After randomization, sixteen adolescents with ADHD underwent either anodal tDCS over the left dorsolateral prefrontal cortex (DLPFC, 1 mA, 20 min) or sham stimulation with simultaneous fMRI during n-back WM task. Both in one-back and two-back conditions, tDCS led to a greater activation (compared with sham stimulation) of the left DLPFC (under the electrode), left premotor cortex, left supplementary motor cortex, and precuneus. The effects of tDCS were long-lasting and influenced resting state functional connectivity even 20 min after the stimulation, with patterns of strengthened DLPFC connectivity after tDCS outlining the WM network. In summary, anodal tDCS caused increased neuronal activation and connectivity, not only in the brain area under the stimulating electrode (i.e. left DLPFC) but also in other, more remote brain regions. Because of moderate behavioral effects of tDCS, the significance of this technique for ADHD treatment has to be investigated in further studies.

  6. A time domain approach to sensitivity analysis of direct detection optical FDMA networks with OOK modulation

    NASA Astrophysics Data System (ADS)

    Studer, John Anthony

    1995-03-01

    We derive the closed form expression for the probability of bit error in direct detection, dense wavelength division multiplexed (WDM) fiber optic systems employing on-off keying (OOK) as the modulation technique and single-cavity Fabry-Perot (FP) filters in the receiver as demultiplexers. The expression is derived in the time domain using the impulse response of the single-cavity Fabry-Perot filter and the complex baseband equivalent of the received dense WDM optical signal. The two are convolved to produce the FP filtered output signal s(t). We then integrate R(absolute value of s(t))(exp 2) over one bit period, where R is the responsivity (A/W) of the photodetector following the FP filter in the receiver structure. This integral is the deterministic X of the decision variable Y where Y = X + N. N is the postdetection thermal noise (amplifier generated), a zero mean Gaussian random variable with variance N(sub 0)T where N(sub 0) is the noise current spectral density (A(exp 2)/Hz). Both X and N are combined into an expression for probability of bit error. A limited case of the complete model is assumed, and probability of bit error graphs are generated.

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

    PubMed Central

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

    2015-01-01

    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

  8. 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.

  9. Reconfigurable intensity modulation and direct detection optical transceivers for variable-rate wavelength-division-multiplexing passive optical networks utilizing digital signal processing-based symbol mapper

    NASA Astrophysics Data System (ADS)

    Zhang, Zhiguo; Zhang, Bingbing; Chen, Yanxu; Chen, Xue

    2017-01-01

    Variable-rate intensity modulation and direct detection-based optical transceivers with software-controllable reconfigurability and transmission performance adaptability are experimentally demonstrated, utilizing M-QAM symbol mapping implemented in MATLAB® programs. A frequency division multiplexing-based symbol demapping and wavelength management method is proposed for the symbol demapper and tunable laser management used in colorless optical network unit.

  10. Cycle and flow trusses in directed networks

    NASA Astrophysics Data System (ADS)

    Takaguchi, Taro; Yoshida, Yuichi

    2016-11-01

    When we represent real-world systems as networks, the directions of links often convey valuable information. Finding module structures that respect link directions is one of the most important tasks for analysing directed networks. Although many notions of a directed module have been proposed, no consensus has been reached. This lack of consensus results partly because there might exist distinct types of modules in a single directed network, whereas most previous studies focused on an independent criterion for modules. To address this issue, we propose a generic notion of the so-called truss structures in directed networks. Our definition of truss is able to extract two distinct types of trusses, named the cycle truss and the flow truss, from a unified framework. By applying the method for finding trusses to empirical networks obtained from a wide range of research fields, we find that most real networks contain both cycle and flow trusses. In addition, the abundance of (and the overlap between) the two types of trusses may be useful to characterize module structures in a wide variety of empirical networks. Our findings shed light on the importance of simultaneously considering different types of modules in directed networks.

  11. Cycle and flow trusses in directed networks

    PubMed Central

    Yoshida, Yuichi

    2016-01-01

    When we represent real-world systems as networks, the directions of links often convey valuable information. Finding module structures that respect link directions is one of the most important tasks for analysing directed networks. Although many notions of a directed module have been proposed, no consensus has been reached. This lack of consensus results partly because there might exist distinct types of modules in a single directed network, whereas most previous studies focused on an independent criterion for modules. To address this issue, we propose a generic notion of the so-called truss structures in directed networks. Our definition of truss is able to extract two distinct types of trusses, named the cycle truss and the flow truss, from a unified framework. By applying the method for finding trusses to empirical networks obtained from a wide range of research fields, we find that most real networks contain both cycle and flow trusses. In addition, the abundance of (and the overlap between) the two types of trusses may be useful to characterize module structures in a wide variety of empirical networks. Our findings shed light on the importance of simultaneously considering different types of modules in directed networks. PMID:28018610

  12. 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.

  13. Breakdown of interdependent directed networks

    PubMed Central

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

    2016-01-01

    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. Network motifs modulate druggability of cellular targets

    PubMed Central

    Wu, Fan; Ma, Cong; Tan, Cheemeng

    2016-01-01

    Druggability refers to the capacity of a cellular target to be modulated by a small-molecule drug. To date, druggability is mainly studied by focusing on direct binding interactions between a drug and its target. However, druggability is impacted by cellular networks connected to a drug target. Here, we use computational approaches to reveal basic principles of network motifs that modulate druggability. Through quantitative analysis, we find that inhibiting self-positive feedback loop is a more robust and effective treatment strategy than inhibiting other regulations, and adding direct regulations to a drug-target generally reduces its druggability. The findings are explained through analytical solution of the motifs. Furthermore, we find that a consensus topology of highly druggable motifs consists of a negative feedback loop without any positive feedback loops, and consensus motifs with low druggability have multiple positive direct regulations and positive feedback loops. Based on the discovered principles, we predict potential genetic targets in Escherichia coli that have either high or low druggability based on their network context. Our work establishes the foundation toward identifying and predicting druggable targets based on their network topology. PMID:27824147

  15. A mean field neural network for hierarchical module placement

    NASA Technical Reports Server (NTRS)

    Unaltuna, M. Kemal; Pitchumani, Vijay

    1992-01-01

    This paper proposes a mean field neural network for the two-dimensional module placement problem. An efficient coding scheme with only O(N log N) neurons is employed where N is the number of modules. The neurons are evolved in groups of N in log N iteration steps such that the circuit is recursively partitioned in alternating vertical and horizontal directions. In our simulations, the network was able to find optimal solutions to all test problems with up to 128 modules.

  16. Graphlet characteristics in directed networks

    PubMed Central

    Trpevski, Igor; Dimitrova, Tamara; Boshkovski, Tommy; Stikov, Nikola; Kocarev, Ljupcho

    2016-01-01

    Graphlet analysis is part of network theory that does not depend on the choice of the network null model and can provide comprehensive description of the local network structure. Here, we propose a novel method for graphlet-based analysis of directed networks by computing first the signature vector for every vertex in the network and then the graphlet correlation matrix of the network. This analysis has been applied to brain effective connectivity networks by considering both direction and sign (inhibitory or excitatory) of the underlying directed (effective) connectivity. In particular, the signature vectors for brain regions and the graphlet correlation matrices of the brain effective network are computed for 40 healthy subjects and common dependencies are revealed. We found that the signature vectors (node, wedge, and triangle degrees) are dominant for the excitatory effective brain networks. Moreover, by considering only those correlations (or anti correlations) in the correlation matrix that are significant (>0.7 or <−0.7) and are presented in more than 60% of the subjects, we found that excitatory effective brain networks show stronger causal (measured with Granger causality) patterns (G-causes and G-effects) than inhibitory effective brain networks. PMID:27830769

  17. Graphlet characteristics in directed networks

    NASA Astrophysics Data System (ADS)

    Trpevski, Igor; Dimitrova, Tamara; Boshkovski, Tommy; Stikov, Nikola; Kocarev, Ljupcho

    2016-11-01

    Graphlet analysis is part of network theory that does not depend on the choice of the network null model and can provide comprehensive description of the local network structure. Here, we propose a novel method for graphlet-based analysis of directed networks by computing first the signature vector for every vertex in the network and then the graphlet correlation matrix of the network. This analysis has been applied to brain effective connectivity networks by considering both direction and sign (inhibitory or excitatory) of the underlying directed (effective) connectivity. In particular, the signature vectors for brain regions and the graphlet correlation matrices of the brain effective network are computed for 40 healthy subjects and common dependencies are revealed. We found that the signature vectors (node, wedge, and triangle degrees) are dominant for the excitatory effective brain networks. Moreover, by considering only those correlations (or anti correlations) in the correlation matrix that are significant (>0.7 or <‑0.7) and are presented in more than 60% of the subjects, we found that excitatory effective brain networks show stronger causal (measured with Granger causality) patterns (G-causes and G-effects) than inhibitory effective brain networks.

  18. Potential theory for directed networks.

    PubMed

    Zhang, Qian-Ming; Lü, Linyuan; Wang, Wen-Qiang; Zhu, Yu-Xiao; 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.

  19. 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.

  20. Identification of Topological Network Modules in Perturbed Protein Interaction Networks

    PubMed Central

    Sardiu, Mihaela E.; Gilmore, Joshua M.; Groppe, Brad; Florens, Laurence; Washburn, Michael P.

    2017-01-01

    Biological networks consist of functional modules, however detecting and characterizing such modules in networks remains challenging. Perturbing networks is one strategy for identifying modules. Here we used an advanced mathematical approach named topological data analysis (TDA) to interrogate two perturbed networks. In one, we disrupted the S. cerevisiae INO80 protein interaction network by isolating complexes after protein complex components were deleted from the genome. In the second, we reanalyzed previously published data demonstrating the disruption of the human Sin3 network with a histone deacetylase inhibitor. Here we show that disrupted networks contained topological network modules (TNMs) with shared properties that mapped onto distinct locations in networks. We define TMNs as proteins that occupy close network positions depending on their coordinates in a topological space. TNMs provide new insight into networks by capturing proteins from different categories including proteins within a complex, proteins with shared biological functions, and proteins disrupted across networks. PMID:28272416

  1. Identification of Topological Network Modules in Perturbed Protein Interaction Networks.

    PubMed

    Sardiu, Mihaela E; Gilmore, Joshua M; Groppe, Brad; Florens, Laurence; Washburn, Michael P

    2017-03-08

    Biological networks consist of functional modules, however detecting and characterizing such modules in networks remains challenging. Perturbing networks is one strategy for identifying modules. Here we used an advanced mathematical approach named topological data analysis (TDA) to interrogate two perturbed networks. In one, we disrupted the S. cerevisiae INO80 protein interaction network by isolating complexes after protein complex components were deleted from the genome. In the second, we reanalyzed previously published data demonstrating the disruption of the human Sin3 network with a histone deacetylase inhibitor. Here we show that disrupted networks contained topological network modules (TNMs) with shared properties that mapped onto distinct locations in networks. We define TMNs as proteins that occupy close network positions depending on their coordinates in a topological space. TNMs provide new insight into networks by capturing proteins from different categories including proteins within a complex, proteins with shared biological functions, and proteins disrupted across networks.

  2. Functional Module Analysis for Gene Coexpression Networks with Network Integration

    PubMed Central

    Zhang, Shuqin; Zhao, Hongyu

    2015-01-01

    Network has been a general tool for studying the complex interactions between different genes, proteins and other small molecules. Module as a fundamental property of many biological networks has been widely studied and many computational methods have been proposed to identify the modules in an individual network. However, in many cases a single network is insufficient for module analysis due to the noise in the data or the tuning of parameters when building the biological network. The availability of a large amount of biological networks makes network integration study possible. By integrating such networks, more informative modules for some specific disease can be derived from the networks constructed from different tissues, and consistent factors for different diseases can be inferred. In this paper, we have developed an effective method for module identification from multiple networks under different conditions. The problem is formulated as an optimization model, which combines the module identification in each individual network and alignment of the modules from different networks together. An approximation algorithm based on eigenvector computation is proposed. Our method outperforms the existing methods, especially when the underlying modules in multiple networks are different in simulation studies. We also applied our method to two groups of gene coexpression networks for humans, which include one for three different cancers, and one for three tissues from the morbidly obese patients. We identified 13 modules with 3 complete subgraphs, and 11 modules with 2 complete subgraphs, respectively. The modules were validated through Gene Ontology enrichment and KEGG pathway enrichment analysis. We also showed that the main functions of most modules for the corresponding disease have been addressed by other researchers, which may provide the theoretical basis for further studying the modules experimentally. PMID:26451826

  3. Direct Current Series Circuits: An Educational Module.

    ERIC Educational Resources Information Center

    Sturgess, Keith

    This module was developed as remedial material for physics students who have difficulty understanding concepts of circuits and calculating resistances, and voltage drops and currents. Lists of prerequisite skills and instructional objectives are followed by a pretest (with answers). Students are directed to the subject matter in the module based…

  4. Adaptive multidimensional modulation and multiplexing for next generation optical networks

    NASA Astrophysics Data System (ADS)

    Cvijetic, Milorad

    2015-01-01

    The overall spectral efficiency in optical transmission systems needs to be enhanced by employment of advanced modulation, multiplexing, and coding schemes, as well as the advanced detection techniques. In parallel, novel networking concepts with the griddles and elastic bandwidth allocation are needed to increase the network dynamics and flexibility. In this paper we discuss multidimensional modulation, multiplexing, and coding schemes, which are enablers not only of the information capacity increase, but also for the next generation elastic high-speed optical networking and outline possible future directions and application scenario in different networking segments.

  5. Dense module enumeration in biological networks

    NASA Astrophysics Data System (ADS)

    Tsuda, Koji; Georgii, Elisabeth

    2009-12-01

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

  6. OM300 Direction Drilling Module

    DOE Data Explorer

    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

  7. 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

  8. Modulation for emergent networks: serotonin and dopamine.

    PubMed

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

    2013-05-01

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

  9. 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

  10. Investigation of direct integrated optics modulators

    NASA Technical Reports Server (NTRS)

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

    1981-01-01

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

  11. Graphlet-based Characterization of Directed Networks

    NASA Astrophysics Data System (ADS)

    Sarajlić, Anida; Malod-Dognin, Noël; Yaveroğlu, Ömer Nebil; Pržulj, Nataša

    2016-10-01

    We are flooded with large-scale, dynamic, directed, networked data. Analyses requiring exact comparisons between networks are computationally intractable, so new methodologies are sought. To analyse directed networks, we extend graphlets (small induced sub-graphs) and their degrees to directed data. Using these directed graphlets, we generalise state-of-the-art network distance measures (RGF, GDDA and GCD) to directed networks and show their superiority for comparing directed networks. Also, we extend the canonical correlation analysis framework that enables uncovering the relationships between the wiring patterns around nodes in a directed network and their expert annotations. On directed World Trade Networks (WTNs), our methodology allows uncovering the core-broker-periphery structure of the WTN, predicting the economic attributes of a country, such as its gross domestic product, from its wiring patterns in the WTN for up-to ten years in the future. It does so by enabling us to track the dynamics of a country’s positioning in the WTN over years. On directed metabolic networks, our framework yields insights into preservation of enzyme function from the network wiring patterns rather than from sequence data. Overall, our methodology enables advanced analyses of directed networked data from any area of science, allowing domain-specific interpretation of a directed network’s topology.

  12. Graphlet-based Characterization of Directed Networks

    PubMed Central

    Sarajlić, Anida; Malod-Dognin, Noël; Yaveroğlu, Ömer Nebil; Pržulj, Nataša

    2016-01-01

    We are flooded with large-scale, dynamic, directed, networked data. Analyses requiring exact comparisons between networks are computationally intractable, so new methodologies are sought. To analyse directed networks, we extend graphlets (small induced sub-graphs) and their degrees to directed data. Using these directed graphlets, we generalise state-of-the-art network distance measures (RGF, GDDA and GCD) to directed networks and show their superiority for comparing directed networks. Also, we extend the canonical correlation analysis framework that enables uncovering the relationships between the wiring patterns around nodes in a directed network and their expert annotations. On directed World Trade Networks (WTNs), our methodology allows uncovering the core-broker-periphery structure of the WTN, predicting the economic attributes of a country, such as its gross domestic product, from its wiring patterns in the WTN for up-to ten years in the future. It does so by enabling us to track the dynamics of a country’s positioning in the WTN over years. On directed metabolic networks, our framework yields insights into preservation of enzyme function from the network wiring patterns rather than from sequence data. Overall, our methodology enables advanced analyses of directed networked data from any area of science, allowing domain-specific interpretation of a directed network’s topology. PMID:27734973

  13. Designed Proteins To Modulate Cellular Networks

    PubMed Central

    Cortajarena, Aitziber L.; Liu, Tina Y.; Hochstrasser, Mark; Regan, Lynne

    2012-01-01

    A major challenge of protein design is to create useful new proteins that interact specifically with biological targets in living cells. Such binding modules have many potential applications, including the targeted perturbation of protein networks. As a general approach to create such modules, we designed a library with approximately 109 different binding specificities based on a small 3-tetratricopeptide repeat (TPR) motif framework. We employed a novel strategy, based on split GFP reassembly, to screen the library for modules with the desired binding specificity. Using this approach, we identified modules that bind tightly and specifically to Dss1, a small human protein that interacts with the tumor suppressor protein BRCA2. We showed that these modules also bind the yeast homologue of Dss1, Sem1. Furthermore, we demonstrated that these modules inhibit Sem1 activity in yeast. This strategy will be generally applicable to make novel genetically encoded tools for systems/synthetic biology applications. PMID:20020775

  14. Adaptation to direction statistics modulates perceptual discrimination.

    PubMed

    Price, Nicholas S C; Prescott, Danielle L

    2012-06-22

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

  15. 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.

  16. Doppler modulation and Zeeman modulation: laser frequency stabilization without direct frequency modulation.

    PubMed

    Weis, A; Derler, S

    1988-07-01

    We discuss two methods (Zeeman modulation and Doppler modulation) for locking the frequency of a singlemode cw laser to an atomic absorption line. These methods do not require the laser frequency to be modulated directly. In the first scheme the absorption frequency of the atom is modulated via the Zeeman effect; in the second scheme the laser frequency is modulated indirectly via the Doppler effect in an atomic beam. We used the two methods successfully to lock two dye lasers to the transitions 6S((1/2)) ? 7S((1/2)) and 7S((1/2)) ? 15P(?) in atomic cesium.

  17. 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…

  18. 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.

  19. Directed network discovery with dynamic network modelling.

    PubMed

    Anzellotti, Stefano; Kliemann, Dorit; Jacoby, Nir; Saxe, Rebecca

    2017-02-16

    Cognitive tasks recruit multiple brain regions. Understanding how these regions influence each other (the network structure) is an important step to characterize the neural basis of cognitive processes. Often, limited evidence is available to restrict the range of hypotheses a priori, and techniques that sift efficiently through a large number of possible network structures are needed (network discovery). This article introduces a novel modelling technique for network discovery (Dynamic Network Modelling or DNM) that builds on ideas from Granger Causality and Dynamic Causal Modelling introducing three key changes: (1) efficient network discovery is implemented with statistical tests on the consistency of model parameters across participants, (2) the tests take into account the magnitude and sign of each influence, and (3) variance explained in independent data is used as an absolute (rather than relative) measure of the quality of the network model. In this article, we outline the functioning of DNM, we validate DNM in simulated data for which the ground truth is known, and we report an example of its application to the investigation of influences between regions during emotion recognition, revealing top-down influences from brain regions encoding abstract representations of emotions (medial prefrontal cortex and superior temporal sulcus) onto regions engaged in the perceptual analysis of facial expressions (occipital face area and fusiform face area) when participants are asked to switch between reporting the emotional valence and the age of a face.

  20. Caffeine modulates attention network function.

    PubMed

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

    2010-03-01

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

  1. Direct and indirect effects in causal networks

    NASA Astrophysics Data System (ADS)

    Krämer, Andreas

    2013-03-01

    Literature-derived networks of biomolecular interactions representing cause-effect relationships generally contain many indirect relationships where the actually observed causal effect results from a sequence of events represented in the same network. A statistical method is developed, based on an Ising-like spin model operating on the edges of the network, to distinguish between direct and indirect effects using only the network structure itself. This allows to identify paths representing likely causation mechanisms.

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

    PubMed

    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.

  3. 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.

  4. Sensor modules for wireless distributed sensor networks

    SciTech Connect

    Lee, A P; McConaghy, C F; Simon, J N; Benett, W; Jones, L; Trevino, J

    1999-02-22

    A national security need as well as environmental monitoring need exists for networks of sensors. The advantages of a network of sensors over a single sensor are improved range, sensitivity, directionality, and data readability. Depending upon the particular application, sensors can be acoustic, chemical, biological, thermal or inertial. A major desire in these sensor networks is to have the individual sensor and associated electronics small and low enough in power that the battery can also be small and of long life. Smaller, low power sensor nodes can allow more nodes per network. A typical network for security applications is depicted in Figure 1. Here a number of sensor nodes are deployed around a central hub node in a star configuration. In this scenario the hubs communicate with each other and ultimately relay information to a satellite. Future networks might follow this scenario or some other network architecture such as a hopping network where individual nodes communicate directly with each other. The focus of our research has been on development of the small low power nodes and less on the overall network topology. However, some consideration of the network must be given when designing the nodes and some consideration of the nodes must be given when designing the network. An individual sensor node contains not only the sensor but also the sensor interface electronics, analog to digital (A/D) converter, logic, RF communication link, antenna, and the battery. Future nodes will also contain some form of signal processing to allow more sophisticated network architectures. The FY98 goal for this project was to make a sensor node with a physical form factor of a 2 inch x 2 inch x 2 inch cube.

  5. 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.

  6. Cholinergic modulation of hippocampal network function

    PubMed Central

    Teles-Grilo Ruivo, Leonor M.; Mellor, Jack R.

    2013-01-01

    Cholinergic septohippocampal projections from the medial septal area to the hippocampus are proposed to have important roles in cognition by modulating properties of the hippocampal network. However, the precise spatial and temporal profile of acetylcholine release in the hippocampus remains unclear making it difficult to define specific roles for cholinergic transmission in hippocampal dependent behaviors. This is partly due to a lack of tools enabling specific intervention in, and recording of, cholinergic transmission. Here, we review the organization of septohippocampal cholinergic projections and hippocampal acetylcholine receptors as well as the role of cholinergic transmission in modulating cellular excitability, synaptic plasticity, and rhythmic network oscillations. We point to a number of open questions that remain unanswered and discuss the potential for recently developed techniques to provide a radical reappraisal of the function of cholinergic inputs to the hippocampus. PMID:23908628

  7. Doppler modulation and Zeeman modulation: laser frequency stabilization without direct frequency modulation

    SciTech Connect

    Weis, A.; Derler, S.

    1988-07-01

    We discuss two methods (Zeeman modulation and Doppler modulation) for locking the frequency of a single-mode cw laser to an atomic absorption line. These methods do not require the laser frequency to be modulated directly. In the first scheme the absorption frequency of the atom is modulated via the Zeeman effect; in the second scheme the laser frequency is modulated indirectly via the Doppler effect in an atomic beam. We used the two methods successfully to lock two dye lasers to the transitions 6S/sub 1/2/..-->..7S/sub 1/2/ and 7S/sub 1/2/..-->..15P/sub 3/2/ in atomic cesium.

  8. RNA Directed Modulation of Phenotypic Plasticity in Human Cells

    PubMed Central

    Burdach, Jon; Morris, Kevin V.

    2016-01-01

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

  9. RNA Directed Modulation of Phenotypic Plasticity in Human Cells.

    PubMed

    Trakman, Laura; Hewson, Chris; Burdach, Jon; Morris, Kevin V

    2016-01-01

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

  10. KIBRA Modulates Directional Migration of Podocytes

    PubMed Central

    Duning, Kerstin; Schurek, Eva-Maria; Schlüter, Marc; Bayer, Michael; Reinhardt, Hans-Christian; Schwab, Albrecht; Schaefer, Liliana; Benzing, Thomas; Schermer, Bernhard; Saleem, Moin A.; Huber, Tobias B.; Bachmann, Sebastian; Kremerskothen, Joachim; Weide, Thomas; Pavenstädt, Hermann

    2008-01-01

    Asymmetric delivery and distribution of macromolecules are essential for cell polarity and for cellular functions such as differentiation, division, and signaling. Injury of podocytes, which are polarized epithelial cells, changes the dynamics of the actin meshwork, resulting in foot process retraction and proteinuria. Although the spatiotemporal control of specific protein–protein interactions is crucial for the establishment of cell polarity, the mechanisms controlling polarity-dependent differentiation and division are incompletely understood. In this study, yeast two-hybrid screens were performed using a podocyte cDNA library and the polarity protein PATJ as bait. The protein KIBRA was identified as an interaction partner of PATJ and was localized to podocytes, tubular structures, and collecting ducts. The last four amino acids of KIBRA mediated binding to the eighth PDZ domain of PATJ. In addition, KIBRA directly bound to synaptopodin, an essential organizer of the podocyte cytoskeleton. Stable knockdown of KIBRA in immortalized podocytes impaired directed cell migration, suggesting that KIBRA modulates the motility of podocytes by linking polarity proteins and cytoskeleton-associated protein complexes. PMID:18596123

  11. Prisoner’s dilemma on directed networks

    NASA Astrophysics Data System (ADS)

    Ferreira, A. L.; Lipowski, A.; Pedro, T. B.; Santos, M.; Figueiredo, W.

    2016-12-01

    We study the prisoner’s dilemma model with a noisy imitation evolutionary dynamics on directed out-homogeneous and uncorrelated directed random networks. A heterogeneous pair mean-field approximation is presented showing good agreement with Monte Carlo simulations in the limit of weak selection (high noise) where we obtain analytical predictions for the critical temptations. We discuss the phase diagram as a function of temptation, intensity of noise and coordination number of the networks and we consider both the model with and without self-interaction. We compare our results with available results for non-directed lattices and networks.

  12. Hemispheric modulations of the attentional networks.

    PubMed

    Spagna, Alfredo; Martella, Diana; Fuentes, Luis J; Marotta, Andrea; Casagrande, Maria

    2016-10-01

    Although several recent studies investigated the hemispheric contributions to the attentional networks using the Attention Network Test (ANT), the role of the cerebral hemispheres in modulating the interaction among them remains unclear. In this study, two lateralized versions of this test (LANT) were used to investigate theal effects on the attentional networks under different conflict conditions. One version, the LANTI-A, presented arrows as target and flankers, while the other version, the LANTI-F, had fruits as target and flankers. Data collected from forty-seven participants confirmed well-known results on the efficiency and interactions among the attentional networks. Further, a left visual field advantage was found when a target occurred in an unattended location (e.g. invalid trials), only with the LANTI-F, but not with LANTI-A. The present study adds more evidence to the hemispheric asymmetry of the orienting of attention, and further reveals patterns of interactions between the attentional networks and the visual fields across different conflicting conditions, underlying the dynamic control of attention in complex environments.

  13. Dynamics-based centrality for directed networks

    NASA Astrophysics Data System (ADS)

    Masuda, Naoki; Kori, Hiroshi

    2010-11-01

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

  14. Temporal correlation coefficient for directed networks.

    PubMed

    Büttner, Kathrin; Salau, Jennifer; Krieter, Joachim

    2016-01-01

    Previous studies dealing with network theory focused mainly on the static aggregation of edges over specific time window lengths. Thus, most of the dynamic information gets lost. To assess the quality of such a static aggregation the temporal correlation coefficient can be calculated. It measures the overall possibility for an edge to persist between two consecutive snapshots. Up to now, this measure is only defined for undirected networks. Therefore, we introduce the adaption of the temporal correlation coefficient to directed networks. This new methodology enables the distinction between ingoing and outgoing edges. Besides a small example network presenting the single calculation steps, we also calculated the proposed measurements for a real pig trade network to emphasize the importance of considering the edge direction. The farm types at the beginning of the pork supply chain showed clearly higher values for the outgoing temporal correlation coefficient compared to the farm types at the end of the pork supply chain. These farm types showed higher values for the ingoing temporal correlation coefficient. The temporal correlation coefficient is a valuable tool to understand the structural dynamics of these systems, as it assesses the consistency of the edge configuration. The adaption of this measure for directed networks may help to preserve meaningful additional information about the investigated network that might get lost if the edge directions are ignored.

  15. 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.

  16. Data reliability in complex directed networks

    NASA Astrophysics Data System (ADS)

    Sanz, Joaquín; Cozzo, Emanuele; Moreno, Yamir

    2013-12-01

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

  17. Self-organized Collaboration Network Model Based on Module Emerging

    NASA Astrophysics Data System (ADS)

    Yang, Hongyong; Lu, Lan; Liu, Qiming

    Recently, the studies of the complex network have gone deep into many scientific fields, such as computer science, physics, mathematics, sociology, etc. These researches enrich the realization for complex network, and increase understands for the new characteristic of complex network. Based on the evolvement characteristic of the author collaboration in the scientific thesis, a self-organized network model of the scientific cooperation network is presented by module emerging. By applying the theoretical analysis, it is shown that this network model is a scale-free network, and the strength degree distribution and the module degree distribution of the network nodes have the same power law. In order to make sure the validity of the theoretical analysis for the network model, we create the computer simulation and demonstration collaboration network. By analyzing the data of the network, the results of the demonstration network and the computer simulation are consistent with that of the theoretical analysis of the model.

  18. 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.

  19. Design of a directed molecular network.

    PubMed

    Ashkenasy, Gonen; Jagasia, Reshma; Yadav, Maneesh; Ghadiri, M Reza

    2004-07-27

    An ability to rationally design complex networks from the bottom up can offer valuable quantitative model systems for use in gaining a deeper appreciation for the principles governing the self-organization and functional characteristics of complex systems. We report herein the de novo design, graph prediction, experimental analysis, and characterization of simple self-organized, nonlinear molecular networks. Our approach makes use of the sequence-dependent auto- and cross-catalytic functional characteristics of template-directed peptide fragment condensation reactions in neutral aqueous solutions. Starting with an array of 81 sequence similar 32-residue coiled-coil peptides, we estimated the relative stability difference between all plausible A(2)B-type coiled-coil ensembles and used this information to predict the auto- and cross-catalysis pathways and the resulting plausible network motif and connectivities. Similar to most complex systems, the generated graph displays clustered nodes with an overall hierarchical architecture. To test the validity of the design principles used, nine nodes composing a main segment of the graph were experimentally analyzed for their capacity in establishing the predicted network connectivity. The resulting self-organized chemical network is shown to display 25 directed edges in good agreement with the graph analysis estimations. Moreover, we show that by varying the system parameters (presence or absence of certain substrates or templates), its operating network motif can be altered, even to the extremes of turning pathways on or off. We suggest that this approach can be expanded for the construction of large-scale networks, offering a means to study and to understand better the emergent, collective behaviors of networks.

  20. Design of a directed molecular network

    PubMed Central

    Ashkenasy, Gonen; Jagasia, Reshma; Yadav, Maneesh; Ghadiri, M. Reza

    2004-01-01

    An ability to rationally design complex networks from the bottom up can offer valuable quantitative model systems for use in gaining a deeper appreciation for the principles governing the self-organization and functional characteristics of complex systems. We report herein the de novo design, graph prediction, experimental analysis, and characterization of simple self-organized, nonlinear molecular networks. Our approach makes use of the sequence-dependant auto- and cross-catalytic functional characteristics of template-directed peptide fragment condensation reactions in neutral aqueous solutions. Starting with an array of 81 sequence similar 32-residue coiled-coil peptides, we estimated the relative stability difference between all plausible A2B-type coiled-coil ensembles and used this information to predict the auto- and cross-catalysis pathways and the resulting plausible network motif and connectivities. Similar to most complex systems, the generated graph displays clustered nodes with an overall hierarchical architecture. To test the validity of the design principles used, nine nodes composing a main segment of the graph were experimentally analyzed for their capacity in establishing the predicted network connectivity. The resulting self-organized chemical network is shown to display 25 directed edges in good agreement with the graph analysis estimations. Moreover, we show that by varying the system parameters (presence or absence of certain substrates or templates), its operating network motif can be altered, even to the extremes of turning pathways on or off. We suggest that this approach can be expanded for the construction of large-scale networks, offering a means to study and to understand better the emergent, collective behaviors of networks. PMID:15256596

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

    NASA Astrophysics Data System (ADS)

    Guesmi, Latifa; Hraghi, Abir; Menif, Mourad

    2015-03-01

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

  2. Random walks in directed modular networks

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  3. Manipulating directed networks for better synchronization

    NASA Astrophysics Data System (ADS)

    Zeng, An; Lü, Linyuan; Zhou, Tao

    2012-08-01

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

  4. 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…

  5. Dynamic functional modules in co-expressed protein interaction networks of dilated cardiomyopathy

    PubMed Central

    2010-01-01

    Background Molecular networks represent the backbone of molecular activity within cells and provide opportunities for understanding the mechanism of diseases. While protein-protein interaction data constitute static network maps, integration of condition-specific co-expression information provides clues to the dynamic features of these networks. Dilated cardiomyopathy is a leading cause of heart failure. Although previous studies have identified putative biomarkers or therapeutic targets for heart failure, the underlying molecular mechanism of dilated cardiomyopathy remains unclear. Results We developed a network-based comparative analysis approach that integrates protein-protein interactions with gene expression profiles and biological function annotations to reveal dynamic functional modules under different biological states. We found that hub proteins in condition-specific co-expressed protein interaction networks tended to be differentially expressed between biological states. Applying this method to a cohort of heart failure patients, we identified two functional modules that significantly emerged from the interaction networks. The dynamics of these modules between normal and disease states further suggest a potential molecular model of dilated cardiomyopathy. Conclusions We propose a novel framework to analyze the interaction networks in different biological states. It successfully reveals network modules closely related to heart failure; more importantly, these network dynamics provide new insights into the cause of dilated cardiomyopathy. The revealed molecular modules might be used as potential drug targets and provide new directions for heart failure therapy. PMID:20950417

  6. Serotonin modulation of cortical neurons and networks

    PubMed Central

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

    2013-01-01

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

  7. Serotonin modulation of cortical neurons and networks.

    PubMed

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

    2013-01-01

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

  8. 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.

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

    PubMed

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

    2014-01-01

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

  10. 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

  11. 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.

  12. Genetic Modulation of Transcranial Direct Current Stimulation Effects on Cognition

    PubMed Central

    Wiegand, Ariane; Nieratschker, Vanessa; Plewnia, Christian

    2016-01-01

    High inter-individual variability substantially challenges the explanatory power of studies on the modulation of cognitive functions with transcranial direct current stimulation (tDCS). These differences in responsivity have been linked with a critical state-dependency of stimulation effects. In general, genetic diversity is a decisive biological basis of variations in neuronal network functioning. Therefore, it is most likely that inter-individual variability of tDCS-induced changes in cognitive functions is due to specific interactions between genetically determined network properties and the specific type of stimulation. In this context, predominantly the brain-derived neurotrophic factor (BDNF) Val66Met and the catechol-O-methyltransferase (COMT) Val108/158Met polymorphisms have been investigated. The studies on the interaction between the BDNF Val66Met polymorphism and the effect of brain stimulation indicate a critical but yet heterogeneous interaction. But up to now, data on the interplay between this polymorphism and tDCS on cognitive functioning are not available. However, recently, the functional Val(108/158)Met polymorphism in the COMT gene, that is particularly involved in the regulation of executive functions by means of the dopaminergic tone in frontal brain areas, has been demonstrated to specifically predict the effect of tDCS on cognitive control. Following an inverted U-shaped function, the high dopaminergic activity in Met allele homozygous individuals has been shown to be associated with a reduction of executive functioning by anodal tDCS to the prefrontal cortex. Consistently, Val homozygous individuals with lower dopaminergic tone show a clear reduction of response inhibition with cathodal tDCS. These findings exemplify the notion of a complex but neurophysiologically consistent interaction between genetically determined variations of neuronal activity and tDCS, particularly in the cognitive domain. Consequently, a systematic analysis and

  13. 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.

  14. 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

    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

  15. Models and average properties of scale-free directed networks

    NASA Astrophysics Data System (ADS)

    Bernhardsson, Sebastian; Minnhagen, Petter

    2006-08-01

    We extend the merging model for undirected networks by Kim [Eur. Phys. J. B 43, 369 (2004)] to directed networks and investigate the emerging scale-free networks. Two versions of the directed merging model, friendly and hostile merging, give rise to two distinct network types. We uncover that some nontrivial features of these two network types resemble two levels of a certain randomization/nonspecificity in the link reshuffling during network evolution. Furthermore, the same features show up, respectively, in metabolic networks and transcriptional networks. We introduce measures that single out the distinguishing features between the two prototype networks, as well as point out features that are beyond the prototypes.

  16. A core eating network and its modulations underlie diverse eating phenomena.

    PubMed

    Chen, Jing; Papies, Esther K; Barsalou, Lawrence W

    2016-12-01

    We propose that a core eating network and its modulations account for much of what is currently known about the neural activity underlying a wide range of eating phenomena in humans (excluding homeostasis and related phenomena). The core eating network is closely adapted from a network that Kaye, Fudge, and Paulus (2009) proposed to explain the neurocircuitry of eating, including a ventral reward pathway and a dorsal control pathway. In a review across multiple literatures that focuses on experiments using functional Magnetic Resonance Imaging (fMRI), we first show that neural responses to food cues, such as food pictures, utilize the same core eating network as eating. Consistent with the theoretical perspective of grounded cognition, food cues activate eating simulations that produce reward predictions about a perceived food and potentially motivate its consumption. Reviewing additional literatures, we then illustrate how various factors modulate the core eating network, increasing and/or decreasing activity in subsets of its neural areas. These modulating factors include food significance (palatability, hunger), body mass index (BMI, overweight/obesity), eating disorders (anorexia nervosa, bulimia nervosa, binge eating), and various eating goals (losing weight, hedonic pleasure, healthy living). By viewing all these phenomena as modulating a core eating network, it becomes possible to understand how they are related to one another within this common theoretical framework. Finally, we discuss future directions for better establishing the core eating network, its modulations, and their implications for behavior.

  17. Filter Bank Multicarrier (FBMC) for long-reach intensity modulated optical access networks

    NASA Astrophysics Data System (ADS)

    Saljoghei, Arsalan; Gutiérrez, Fernando A.; Perry, Philip; Barry, Liam P.

    2017-04-01

    Filter Bank Multi Carrier (FBMC) is a modulation scheme which has recently attracted significant interest in both wireless and optical communications. The interest in optical communications arises due to FBMC's capability to operate without a Cyclic Prefix (CP) and its high resilience to synchronisation errors. However, the operation of FBMC in optical access networks has not been extensively studied either in downstream or upstream. In this work we use experimental work to investigate the operation of FBMC in intensity modulated Passive Optical Networks (PONs) employing direct detection in conjunction with both direct and external modulation schemes. The data rates and propagation lengths employed here vary from 8.4 to 14.8 Gb/s and 0-75 km. The results suggest that by using FBMC it is possible to accomplish CP-Less transmission up to 75 km of SSMF in passive links using cost effective intensity modulation and detection schemes.

  18. 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.

  19. Directly modulated cable television transport systems using negative dispersion fiber

    NASA Astrophysics Data System (ADS)

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

    2005-03-01

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

  20. 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

  1. 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.

  2. Monthly modulation in dark matter direct-detection experiments

    SciTech Connect

    Britto, Vivian; Meyers, Joel E-mail: jmeyers@cita.utoronto.ca

    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.

  3. 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

  4. A developmental transcriptional network for maize defines coexpression modules.

    PubMed

    Downs, Gregory S; Bi, Yong-Mei; Colasanti, Joseph; Wu, Wenqing; Chen, Xi; Zhu, Tong; Rothstein, Steven J; Lukens, Lewis N

    2013-04-01

    Here, we present a genome-wide overview of transcriptional circuits in the agriculturally significant crop species maize (Zea mays). We examined transcript abundance data at 50 developmental stages, from embryogenesis to senescence, for 34,876 gene models and classified genes into 24 robust coexpression modules. Modules were strongly associated with tissue types and related biological processes. Sixteen of the 24 modules (67%) have preferential transcript abundance within specific tissues. One-third of modules had an absence of gene expression in specific tissues. Genes within a number of modules also correlated with the developmental age of tissues. Coexpression of genes is likely due to transcriptional control. For a number of modules, key genes involved in transcriptional control have expression profiles that mimic the expression profiles of module genes, although the expression of transcriptional control genes is not unusually representative of module gene expression. Known regulatory motifs are enriched in several modules. Finally, of the 13 network modules with more than 200 genes, three contain genes that are notably clustered (P < 0.05) within the genome. This work, based on a carefully selected set of major tissues representing diverse stages of maize development, demonstrates the remarkable power of transcript-level coexpression networks to identify underlying biological processes and their molecular components.

  5. 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.

  6. 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

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

    NASA Technical Reports Server (NTRS)

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

    1987-01-01

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

  8. 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.

  9. Learning biological networks: from modules to dynamics.

    PubMed

    Bonneau, Richard

    2008-11-01

    Learning regulatory networks from genomics data is an important problem with applications spanning all of biology and biomedicine. Functional genomics projects offer a cost-effective means of greatly expanding the completeness of our regulatory models, and for some prokaryotic organisms they offer a means of learning accurate models that incorporate the majority of the genome. There are, however, several reasons to believe that regulatory network inference is beyond our current reach, such as (i) the combinatorics of the problem, (ii) factors we can't (or don't often) collect genome-wide measurements for and (iii) dynamics that elude cost-effective experimental designs. Recent works have demonstrated the ability to reconstruct large fractions of prokaryotic regulatory networks from compendiums of genomics data; they have also demonstrated that these global regulatory models can be used to predict the dynamics of the transcriptome. We review an overall strategy for the reconstruction of global networks based on these results in microbial systems.

  10. Robust modulation classification techniques using cumulants and hierarchical neural networks

    NASA Astrophysics Data System (ADS)

    DeClouet, John A.; Naraghi-Pour, Mort

    2007-04-01

    The problem of automatic modulation classification is to identify the modulation type of a received signal from the signal parameters. Modulation classification has both military and civilian applications and has been the subject of intensive research for more than two decades. In this paper we use a hierarchical neural network in which the first network identifies the modulation class while a second set of networks identify the constellation size (order) of that modulation class. The set of features we use include normalized standard deviations of amplitude, phase and frequency, as well as the fourth and sixth order cumulants of the signal samples. Identifying the constellation size of quadrature amplitude modulation (QAM) has been particularly difficult in the past. In this paper we introduce two new approaches for computing the features of a QAM signal. The first uses the concatenated in- phase and quadrature components of the signal to compute the features. The second method maps the in-phase and quadrature components to the first quadrant of the constellation by calculating the absolute value of each separately. The mean of the resulting constellation points is then subtracted before calculating the features. Simulation results are presented for classification of several digital modulation schemes including FSK, PSK, ASK and QAM. Our results show that the proposed method significantly improves the classification error.

  11. Network-dependent modulation of brain activity during sleep.

    PubMed

    Watanabe, Takamitsu; Kan, Shigeyuki; Koike, Takahiko; Misaki, Masaya; Konishi, Seiki; Miyauchi, Satoru; Miyahsita, Yasushi; Masuda, Naoki

    2014-09-01

    Brain activity dynamically changes even during sleep. A line of neuroimaging studies has reported changes in functional connectivity and regional activity across different sleep stages such as slow-wave sleep (SWS) and rapid-eye-movement (REM) sleep. However, it remains unclear whether and how the large-scale network activity of human brains changes within a given sleep stage. Here, we investigated modulation of network activity within sleep stages by applying the pairwise maximum entropy model to brain activity obtained by functional magnetic resonance imaging from sleeping healthy subjects. We found that the brain activity of individual brain regions and functional interactions between pairs of regions significantly increased in the default-mode network during SWS and decreased during REM sleep. In contrast, the network activity of the fronto-parietal and sensory-motor networks showed the opposite pattern. Furthermore, in the three networks, the amount of the activity changes throughout REM sleep was negatively correlated with that throughout SWS. The present findings suggest that the brain activity is dynamically modulated even in a sleep stage and that the pattern of modulation depends on the type of the large-scale brain networks.

  12. Altered brain network modules induce helplessness in major depressive disorder

    PubMed Central

    Peng, Daihui; Shi, Feng; Shen, Ting; Peng, Ziwen; Zhang, Chen; Liu, Xiaohua; Qiu, Meihui; Liu, Jun; Jiang, Kaida; Shen, Dinggang

    2017-01-01

    Objective The abnormal brain functional connectivity (FC) has been assumed to be a pathophysiological aspect of major depressive disorder (MDD). However, it is poorly understood, regarding the underlying patterns of global FC network and their relationships with the clinical characteristics of MDD. Methods Resting-state functional magnetic resonance imaging data were acquired from 16 first episode, medication-naïve MDD patients and 16 healthy control subjects. The global FC network was constructed using 90 brain regions. The global topological patterns, e.g., small-worldness and modularity, and their relationships with depressive characteristics were investigated. Furthermore, the participant coefficient and module degree of MDD patients were measured to reflect the regional roles in module network, and the impairment of FC was examined by network based statistic. Results Small-world property was not altered in MDD. However, MDD patients exhibited 5 atypically reorganized modules compared to the controls. A positive relationship was also found among MDD patients between the intra-module I and helplessness factor evaluated via the Hamilton Depression Scale. Specifically, eight regions exhibited the abnormal participant coefficient or module degree, e.g., left superior orbital frontal cortex and right amygdala. The decreased FC was identified among the sub-network of 24 brain regions, e.g., frontal cortex, supplementary motor area, amygdala, thalamus, and hippocampus. Limitation The limited size of MDD samples precluded meaningful study of distinct clinical characteristics in relation to aberrant FC. Conclusions The results revealed altered patterns of brain module network at the global level in MDD patients, which might contribute to the feelings of helplessness. PMID:25033474

  13. Constructing module maps for integrated analysis of heterogeneous biological networks

    PubMed Central

    Amar, David; Shamir, Ron

    2014-01-01

    Improved methods for integrated analysis of heterogeneous large-scale omic data are direly needed. Here, we take a network-based approach to this challenge. Given two networks, representing different types of gene interactions, we construct a map of linked modules, where modules are genes strongly connected in the first network and links represent strong inter-module connections in the second. We develop novel algorithms that considerably outperform prior art on simulated and real data from three distinct domains. First, by analyzing protein–protein interactions and negative genetic interactions in yeast, we discover epistatic relations among protein complexes. Second, we analyze protein–protein interactions and DNA damage-specific positive genetic interactions in yeast and reveal functional rewiring among protein complexes, suggesting novel mechanisms of DNA damage response. Finally, using transcriptomes of non–small-cell lung cancer patients, we analyze networks of global co-expression and disease-dependent differential co-expression and identify a sharp drop in correlation between two modules of immune activation processes, with possible microRNA control. Our study demonstrates that module maps are a powerful tool for deeper analysis of heterogeneous high-throughput omic data. PMID:24497192

  14. 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

  15. 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.

  16. Methylphenidate Modulates Functional Network Connectivity to Enhance Attention

    PubMed Central

    Zhang, Sheng; Hsu, Wei-Ting; Scheinost, Dustin; Finn, Emily S.; Shen, Xilin; Constable, R. Todd; Li, Chiang-Shan R.; Chun, Marvin M.

    2016-01-01

    Recent work has demonstrated that human whole-brain functional connectivity patterns measured with fMRI contain information about cognitive abilities, including sustained attention. To derive behavioral predictions from connectivity patterns, our group developed a connectome-based predictive modeling (CPM) approach (Finn et al., 2015; Rosenberg et al., 2016). Previously using CPM, we defined a high-attention network, comprising connections positively correlated with performance on a sustained attention task, and a low-attention network, comprising connections negatively correlated with performance. Validating the networks as generalizable biomarkers of attention, models based on network strength at rest predicted attention-deficit/hyperactivity disorder (ADHD) symptoms in an independent group of individuals (Rosenberg et al., 2016). To investigate whether these networks play a causal role in attention, here we examined their strength in healthy adults given methylphenidate (Ritalin), a common ADHD treatment, compared with unmedicated controls. As predicted, individuals given methylphenidate showed patterns of connectivity associated with better sustained attention: higher high-attention and lower low-attention network strength than controls. There was significant overlap between the high-attention network and a network with greater strength in the methylphenidate group, and between the low-attention network and a network with greater strength in the control group. Network strength also predicted behavior on a stop-signal task, such that participants with higher go response rates showed higher high-attention and lower low-attention network strength. These results suggest that methylphenidate acts by modulating functional brain networks related to sustained attention, and that changing whole-brain connectivity patterns may help improve attention. SIGNIFICANCE STATEMENT Recent work identified a promising neuromarker of sustained attention based on whole

  17. Differential Space-Time Modulation for Wideband Wireless Networks

    DTIC Science & Technology

    2006-09-30

    modulation for wireless relay networks in Nakagami -m channels,” in Proceedings of the 2006 IEEE International Conference on Acoustic, Speech, and Signal... Nakagami -m fading channels," in Proceedings of the 6th IEEE International Workshop on Signal Processing Advances for Wireless Communications (SPAWC

  18. A neural network model of attention-modulated neurodynamics.

    PubMed

    Gu, Yuqiao; Liljenström, Hans

    2007-12-01

    Visual attention appears to modulate cortical neurodynamics and synchronization through various cholinergic mechanisms. In order to study these mechanisms, we have developed a neural network model of visual cortex area V4, based on psychophysical, anatomical and physiological data. With this model, we want to link selective visual information processing to neural circuits within V4, bottom-up sensory input pathways, top-down attention input pathways, and to cholinergic modulation from the prefrontal lobe. We investigate cellular and network mechanisms underlying some recent analytical results from visual attention experimental data. Our model can reproduce the experimental findings that attention to a stimulus causes increased gamma-frequency synchronization in the superficial layers. Computer simulations and STA power analysis also demonstrate different effects of the different cholinergic attention modulation action mechanisms.

  19. A neural network model of attention-modulated neurodynamics

    PubMed Central

    Gu, Yuqiao

    2007-01-01

    Visual attention appears to modulate cortical neurodynamics and synchronization through various cholinergic mechanisms. In order to study these mechanisms, we have developed a neural network model of visual cortex area V4, based on psychophysical, anatomical and physiological data. With this model, we want to link selective visual information processing to neural circuits within V4, bottom-up sensory input pathways, top-down attention input pathways, and to cholinergic modulation from the prefrontal lobe. We investigate cellular and network mechanisms underlying some recent analytical results from visual attention experimental data. Our model can reproduce the experimental findings that attention to a stimulus causes increased gamma-frequency synchronization in the superficial layers. Computer simulations and STA power analysis also demonstrate different effects of the different cholinergic attention modulation action mechanisms. PMID:19003498

  20. Transcriptional modules related to hepatocellular carcinoma survival: coexpression network analysis.

    PubMed

    Xu, Xinsen; Zhou, Yanyan; Miao, Runchen; Chen, Wei; Qu, Kai; Pang, Qing; Liu, Chang

    2016-06-01

    We performed weighted gene coexpression network analysis (WGCNA) to gain insights into the molecular aspects of hepatocellular carcinoma (HCC). Raw microarray datasets (including 488 samples) were downloaded from the Gene Expression Omnibus (GEO) website. Data were normalized using the RMA algorithm. We utilized the WGCNA to identify the coexpressed genes (modules) after non-specific filtering. Correlation and survival analyses were conducted using the modules, and gene ontology (GO) enrichment was applied to explore the possible mechanisms. Eight distinct modules were identified by the WGCNA. Pink and red modules were associated with liver function, whereas turquoise and black modules were inversely correlated with tumor staging. Poor outcomes were found in the low expression group in the turquoise module and in the high expression group in the red module. In addition, GO enrichment analysis suggested that inflammation, immune, virus-related, and interferon-mediated pathways were enriched in the turquoise module. Several potential biomarkers, such as cyclin-dependent kinase 1 (CDK1), topoisomerase 2α (TOP2A), and serpin peptidase inhibitor clade C (antithrombin) member 1 (SERPINC1), were also identified. In conclusion, gene signatures identified from the genome-based assays could contribute to HCC stratification. WGCNA was able to identify significant groups of genes associated with cancer prognosis.

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

    PubMed Central

    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

  2. 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

  3. Enabling Technologies for Direct Detection Optical Phase Modulation Formats

    NASA Astrophysics Data System (ADS)

    Xu, Xian

    Phase modulation formats are believed to be one of the key enabling techniques for next generation high speed long haul fiber-optic communication systems due to the following main advantages: (1) with a balanced detection, a better receiver sensitivity over conventional intensity modulation formats, e.g., a ˜3-dB sensitivity improvement using differential phase shift keying (DPSK) and a ˜1.3-dB sensitivity improvement using differential quadrature phase shift keying (DQPSK); (2) excellent robustness against fiber nonlinearities; (3) high spectrum efficiency when using multilevel phase modulation formats, such as DQPSK. As the information is encoded in the phase of the optical field, the phase modulation formats are sensitive to the phase-related impairments and the deterioration induced in the phase-intensity conversion. This consequently creates new challenging issues. The research objective of this thesis is to depict some of the challenging issues and provide possible solutions. The first challenge is the cross-phase modulation (XPM) penalty for the phase modulated channels co-propagating with the intensity modulated channels. The penalty comes from the pattern dependent intensity fluctuations of the neighboring intensity modulated channels being converted into phase noise in the phase modulation channels. We propose a model to theoretically analyze the XPM penalty dependence on the walk off effect. From this model, we suggest that using fibers with large local dispersion or intentionally introducing some residual dispersion per span would help mitigate the XPM penalty. The second challenge is the polarization dependent frequency shift (PDf) induced penalty during the phase-intensity conversion. The direct detection DPSK is usually demodulated in a Mach-Zehnder delay interferometer (DI). The polarization dependence of DI introduces a PDf causing a frequency offset between the laser's frequency and the transmissivity peak of DI, degrading the demodulated DPSK

  4. Modulations among the alerting, orienting and executive control networks.

    PubMed

    Callejas, Alicia; Lupiàñez, Juan; Funes, María Jesús; Tudela, Pío

    2005-11-01

    This paper reports a series of experiments that were carried out in order to study the attentional system. Three networks make up this system, and each of them specializes in particular processes. The executive control network specializes in control processes, such as conflict resolution or detection of errors; the orienting network directs the processing system to the source of input and enhances its processing; the alerting network prepares the system for a fast response by maintaining an adequate level of activation in the cognitive system. Recently, Fan and collaborators [J Cogn Neurosci 14(3):340-347, 2002] designed a task to measure the efficiency of each network. We modified Fan's task to test the influences among the networks. We found that the executive control network is inhibited by the alerting network, whereas the orienting network raises the efficiency of the executive control network (Experiment 1). We also found that the alerting network influences the orienting network by speeding up its time course function (Experiment 2). Results were replicated in a third experiment, proving the effects to be stable over time, participants and experimental context, and to be potentially important as a tool for neuropsychological assessment.

  5. 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

  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.

  8. Extending the Applicability of Graphlets to Directed Networks.

    PubMed

    Aparicio, David; Ribeiro, Pedro; Silva, Fernando

    2016-06-28

    With recent advances in high-throughput cell biology the amount of cellular biological data has grown drastically. Such data is often modeled as graphs (also called networks) and studying them can lead to new insights into molecule-level organization. A possible way to understand their structure is by analysing the smaller components that constitute them, namely network motifs and graphlets. Graphlets are particularly well suited to compare networks and to assess their level of similarity due to the rich topological information that they offer but are almost always used as small undirected graphs of up to five nodes, thus limiting their applicability in directed networks. However, a large set of interesting biological networks such as metabolic, cell signaling or transcriptional regulatory networks are intrinsically directional, and using metrics that ignore edge direction may gravely hinder information extraction. Our main purpose in this work is to extend the applicability of graphlets to directed networks by considering their edge direction, thus providing a powerful basis for the analysis of directed biological networks. We tested our approach on two network sets, one composed of synthetic graphs and another of real directed biological networks, and verified that they were more accurately grouped using directed graphlets than undirected graphlets. It is also evident that directed graphlets offer substantially more topological information than simple graph metrics such as degree distribution or reciprocity. However, enumerating graphlets in large networks is a computationally demanding task. Our implementation addresses this concern by using a state-of-the-art data structure, the g-trie, which is able to greatly reduce the necessary computation. We compared our tool to other state-of-the art methods and verified that it is the fastest general tool for graphlet counting.

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

    PubMed

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

    2015-10-16

    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.

  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. Acoustical Direction Finding with Time-Modulated Arrays.

    PubMed

    Clark, Ben; Flint, James A

    2016-12-11

    Time-Modulated Linear Arrays (TMLAs) offer useful efficiency savings over conventional phased arrays when applied in parameter estimation applications. The present paper considers the application of TMLAs to acoustic systems and proposes an algorithm for efficiently deriving the arrival angle of a signal. The proposed technique is applied in the frequency domain, where the signal and harmonic content is captured. Using a weighted average method on harmonic amplitudes and their respective main beam angles, it is possible to determine an estimate for the signal's direction of arrival. The method is demonstrated and evaluated using results from both numerical and practical implementations and performance data is provided. The use of Micro-Electromechanical Systems (MEMS) sensors allows time-modulation techniques to be applied at ultrasonic frequencies. Theoretical predictions for an array of five isotropic elements with half-wavelength spacing and 1000 data samples suggest an accuracy of ± 1 ∘ within an angular range of approximately ± 50 ∘ . In experiments of a 40 kHz five-element microphone array, a Direction of Arrival (DoA) estimation within ± 2 . 5 ∘ of the target signal is readily achieved inside a ± 45 ∘ range using a single switched input stage and a simple hardware setup.

  13. 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

  14. 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

    2015-12-16

    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.

  15. Acoustical Direction Finding with Time-Modulated Arrays

    PubMed Central

    Clark, Ben; Flint, James A.

    2016-01-01

    Time-Modulated Linear Arrays (TMLAs) offer useful efficiency savings over conventional phased arrays when applied in parameter estimation applications. The present paper considers the application of TMLAs to acoustic systems and proposes an algorithm for efficiently deriving the arrival angle of a signal. The proposed technique is applied in the frequency domain, where the signal and harmonic content is captured. Using a weighted average method on harmonic amplitudes and their respective main beam angles, it is possible to determine an estimate for the signal’s direction of arrival. The method is demonstrated and evaluated using results from both numerical and practical implementations and performance data is provided. The use of Micro-Electromechanical Systems (MEMS) sensors allows time-modulation techniques to be applied at ultrasonic frequencies. Theoretical predictions for an array of five isotropic elements with half-wavelength spacing and 1000 data samples suggest an accuracy of ±1∘ within an angular range of approximately ±50∘. In experiments of a 40 kHz five-element microphone array, a Direction of Arrival (DoA) estimation within ±2.5∘ of the target signal is readily achieved inside a ±45∘ range using a single switched input stage and a simple hardware setup. PMID:27973432

  16. A directed network of Greek and Roman mythology

    NASA Astrophysics Data System (ADS)

    Choi, Yeon-Mu; Kim, Hyun-Joo

    2007-08-01

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

  17. Detecting communities by asymmetric intimacy in directed-weighted network

    NASA Astrophysics Data System (ADS)

    Wang, Xingyuan; Qin, Xiaomeng

    Community detection and analysis have attracted wide public concerns over the recent years. Meanwhile, many related algorithms in complex networks have been proposed. However, most of them concentrate on undirected and unweighted networks. Concerning the significant theoretical value and potential application foreground for directed-weighted networks, in this paper, a novel hierarchical communities detection algorithm (termed as DCBAI) has been proposed on the basis of asymmetric intimacy between nodes. Community structures are effectively detected by node clustering algorithm in directed-weighted network, and a set of optimal communities are generated. In addition, a new and asymmetric parameter is adopted to measure the intimate relationship between nodes. We make some simulation using the proposed algorithm in real-world networks and artificial networks, and the result obtained proves that the parameter can describe the direct and indirect relationships between two nodes. Eventually, comparison with similar algorithms shows that our proposed algorithm has better performance.

  18. Chirp-based direct phase modulation of VCSELs for cost-effective transceivers.

    PubMed

    Altabas, Jose A; Izquierdo, David; Lazaro, Jose A; Garces, Ignacio

    2017-02-01

    A 2.5  Gb/s differential binary phase-shift keying (DPSK) transmitter based on direct phase modulation of a vertical cavity surface emitting lasers (VCSEL) using its own chirp is proposed. The VCSEL, which has a wavelength of 1539.84 nm, has been characterized both statically and dynamically. The sensitivity of a single photodiode heterodyne receiver using the proposed 2.5  Gb/s VCSEL transmitter is -39.5  dBm. Thus, this transmitter is an extremely cost-effective solution for future access networks.

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

    PubMed

    Foster, Joshua D; Dunford, Catherine; Sillar, Keith T; Miles, Gareth B

    2014-02-01

    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.

  20. Point Process Modeling for Directed Interaction Networks

    DTIC Science & Technology

    2011-10-01

    maximized via Newton’s method or a gradient- based optimization approach (Nocedal and Wright, 2006). These methods require one or both of the first two...Hand (2010). Bayesian anomaly detection methods for social networks. Ann. Appl. Statist. 4, 645–662. Jackson, M. O. (2008). Social and Economic...Washington Headquarters Services, Directorate for Information Operations and Reports, 1215 Jefferson Davis Highway, Suite 1204, Arlington VA, 22202-4302

  1. 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

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

    PubMed Central

    Pavan, Andrea; Skujevskis, Māris; 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

  3. Guide RNA functional modules direct Cas9 activity and orthogonality.

    PubMed

    Briner, Alexandra E; Donohoue, Paul D; Gomaa, Ahmed A; Selle, Kurt; Slorach, Euan M; Nye, Christopher H; Haurwitz, Rachel E; Beisel, Chase L; May, Andrew P; Barrangou, Rodolphe

    2014-10-23

    The RNA-guided Cas9 endonuclease specifically targets and cleaves DNA in a sequence-dependent manner and has been widely used for programmable genome editing. Cas9 activity is dependent on interactions with guide RNAs, and evolutionarily divergent Cas9 nucleases have been shown to work orthogonally. However, the molecular basis of selective Cas9:guide-RNA interactions is poorly understood. Here, we identify and characterize six conserved modules within native crRNA:tracrRNA duplexes and single guide RNAs (sgRNAs) that direct Cas9 endonuclease activity. We show the bulge and nexus are necessary for DNA cleavage and demonstrate that the nexus and hairpins are instrumental in defining orthogonality between systems. In contrast, the crRNA:tracrRNA complementary region can be modified or partially removed. Collectively, our results establish guide RNA features that drive DNA targeting by Cas9 and open new design and engineering avenues for CRISPR technologies.

  4. 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

  5. Optical modulation of astrocyte network using ultrashort pulsed laser

    NASA Astrophysics Data System (ADS)

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

    2012-03-01

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

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

    PubMed Central

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

    2016-01-01

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

  7. On Connectivity of Wireless Sensor Networks with Directional Antennas.

    PubMed

    Wang, Qiu; Dai, Hong-Ning; Zheng, Zibin; Imran, Muhammad; Vasilakos, Athanasios V

    2017-01-12

    In this paper, we investigate the network connectivity of wireless sensor networks with directional antennas. In particular, we establish a general framework to analyze the network connectivity while considering various antenna models and the channel randomness. Since existing directional antenna models have their pros and cons in the accuracy of reflecting realistic antennas and the computational complexity, we propose a new analytical directional antenna model called the iris model to balance the accuracy against the complexity. We conduct extensive simulations to evaluate the analytical framework. Our results show that our proposed analytical model on the network connectivity is accurate, and our iris antenna model can provide a better approximation to realistic directional antennas than other existing antenna models.

  8. On Connectivity of Wireless Sensor Networks with Directional Antennas

    PubMed Central

    Wang, Qiu; Dai, Hong-Ning; Zheng, Zibin; Imran, Muhammad; Vasilakos, Athanasios V.

    2017-01-01

    In this paper, we investigate the network connectivity of wireless sensor networks with directional antennas. In particular, we establish a general framework to analyze the network connectivity while considering various antenna models and the channel randomness. Since existing directional antenna models have their pros and cons in the accuracy of reflecting realistic antennas and the computational complexity, we propose a new analytical directional antenna model called the iris model to balance the accuracy against the complexity. We conduct extensive simulations to evaluate the analytical framework. Our results show that our proposed analytical model on the network connectivity is accurate, and our iris antenna model can provide a better approximation to realistic directional antennas than other existing antenna models. PMID:28085081

  9. Reconstructing direct and indirect interactions in networked public goods game

    NASA Astrophysics Data System (ADS)

    Han, Xiao; Shen, Zhesi; Wang, Wen-Xu; Lai, Ying-Cheng; Grebogi, Celso

    2016-07-01

    Network reconstruction is a fundamental problem for understanding many complex systems with unknown interaction structures. In many complex systems, there are indirect interactions between two individuals without immediate connection but with common neighbors. Despite recent advances in network reconstruction, we continue to lack an approach for reconstructing complex networks with indirect interactions. Here we introduce a two-step strategy to resolve the reconstruction problem, where in the first step, we recover both direct and indirect interactions by employing the Lasso to solve a sparse signal reconstruction problem, and in the second step, we use matrix transformation and optimization to distinguish between direct and indirect interactions. The network structure corresponding to direct interactions can be fully uncovered. We exploit the public goods game occurring on complex networks as a paradigm for characterizing indirect interactions and test our reconstruction approach. We find that high reconstruction accuracy can be achieved for both homogeneous and heterogeneous networks, and a number of empirical networks in spite of insufficient data measurement contaminated by noise. Although a general framework for reconstructing complex networks with arbitrary types of indirect interactions is yet lacking, our approach opens new routes to separate direct and indirect interactions in a representative complex system.

  10. Microtopography and flow modulate the direction of endothelial cell migration.

    PubMed

    Uttayarat, P; Chen, M; Li, M; Allen, F D; Composto, R J; Lelkes, P I

    2008-02-01

    The migration of vascular endothelial cells under flow can be modulated by the addition of chemical or mechanical stimuli. The aim of this study was to investigate how topographic cues derived from a substrate containing three-dimensional microtopography interact with fluid shear stress in directing endothelial cell migration. Subconfluent bovine aortic endothelial cells were seeded on fibronectin-coated poly(dimethylsiloxane) substrates patterned with a combinatorial array of parallel and orthogonal microgrooves ranging from 2 to 5 microm in width at a constant depth of 1 microm. During a 4-h time-lapse observation in the absence of flow, the majority of the prealigned cells migrated parallel to the grooves with the distribution of their focal adhesions (FAs) depending on the groove width. No change in this migratory pattern was observed after the cells were exposed to moderate shear stress (13.5 dyn/cm(2)), irrespective of groove direction with respect to flow. After 4-h exposure to high shear stress (58 dyn/cm(2)) parallel to the grooves, the cells continued to migrate in the direction of both grooves and flow. By contrast, when microgrooves were oriented perpendicular to flow, most cells migrated orthogonal to the grooves and downstream with flow. Despite the change in the migration direction of the cells under high shear stress, most FAs and actin microfilaments maintained their original alignment parallel to the grooves, suggesting that topographic cues were more effective than those derived from shear stress in guiding the orientation of cytoskeletal and adhesion proteins during the initial exposure to flow.

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

    SciTech Connect

    Hangauer, Andreas Nikodem, Michal; Wysocki, Gerard; Spinner, Georg

    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.

  12. Low cost direct modulation and coherent detection optical OFDM for metro applications

    NASA Astrophysics Data System (ADS)

    Sheffi, Nir; Sadot, Dan

    2011-01-01

    High speed transmission systems (> 10 Gb/s) for cost-sensitive applications such as metropolitan network have attracted extensive interest due to the explosive data traffic growth in such applications. Optical orthogonal frequency division multiplexing (OFDM) based on direct modulation and direct detection for single-mode fiber (SMF) and multi-mode fiber (MMF) without optical amplification and chromatic dispersion (CD) compensation was proposed. Recent research has also shown that optical OFDM can be used with electronic dispersion compensation using direct detection in SMF. However, laser frequency chirp has been identified as a key limiting factor of capacity-versus-reach performance. In this paper, we present a novel concept of low cost optical OFDM with direct modulation of distributed feedback (DFB) lasers and coherent detection at 51.4 Gb/s and 64 QAM. A comprehensive theoretical model of the proposed system is developed. The proposed optical OFDM system concept and performance is based upon using electronic precompensation of laser frequency response, and electronic post compensation of DFB laser frequency chirp and CD. A numerical simulation of the transmission performance of the aforementioned system is conducted using different fiber lengths (40 km, 60 km, 120 km) and chirp parameters, which shows its attractiveness for access and metro applications.

  13. A functional network module for Smith-Magenis syndrome.

    PubMed

    Girirajan, S; Truong, H T; Blanchard, C L; Elsea, S H

    2009-04-01

    Disorders with overlapping diagnostic features are grouped into a network module. Based on phenotypic similarities or differential diagnoses, it is possible to identify functional pathways leading to individual features. We generated a Smith-Magenis syndrome (SMS)-specific network module utilizing patient clinical data, text mining from the Online Mendelian Inheritance in Man database, and in vitro functional analysis. We tested our module by functional studies based on a hypothesis that RAI1 acts through phenotype-specific pathways involving several downstream genes, which are altered due to RAI1 haploinsufficiency. A preliminary genome-wide gene expression study was performed using microarrays on RAI1 haploinsufficient cells created by RNAi-based approximately 50% knockdown of RAI1 in HEK293T cells. The top dysregulated genes were involved in growth signaling and insulin sensitivity, neuronal differentiation, lipid biosynthesis and fat mobilization, circadian activity, behavior, renal, cardiovascular and skeletal development, gene expression, and cell-cycle regulation and recombination, reflecting the spectrum of clinical features observed in SMS. Validation using real-time quantitative reverse transcriptase polymerase chain reaction confirmed the gene expression profile of 75% of the selected genes analyzed in both HEK293T RAI1 knockdown cells and SMS lymphoblastoid cell lines. Overall, these data support a method for identifying genes and pathways responsible for individual clinical features in a complex disorder such as SMS.

  14. 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.

  15. 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

  16. 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

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

    PubMed Central

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

    2014-01-01

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

  18. Keratinocytes can modulate and directly initiate nociceptive responses

    PubMed Central

    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. DOI: http://dx.doi.org/10.7554/eLife.09674.001 PMID:26329459

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

    PubMed Central

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

    2016-01-01

    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

  20. 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.

  1. 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.

  2. Network deconvolution as a general method to distinguish direct dependencies in networks.

    PubMed

    Feizi, Soheil; Marbach, Daniel; Médard, Muriel; Kellis, Manolis

    2013-08-01

    Recognizing direct relationships between variables connected in a network is a pervasive problem in biological, social and information sciences as correlation-based networks contain numerous indirect relationships. Here we present a general method for inferring direct effects from an observed correlation matrix containing both direct and indirect effects. We formulate the problem as the inverse of network convolution, and introduce an algorithm that removes the combined effect of all indirect paths of arbitrary length in a closed-form solution by exploiting eigen-decomposition and infinite-series sums. We demonstrate the effectiveness of our approach in several network applications: distinguishing direct targets in gene expression regulatory networks; recognizing directly interacting amino-acid residues for protein structure prediction from sequence alignments; and distinguishing strong collaborations in co-authorship social networks using connectivity information alone. In addition to its theoretical impact as a foundational graph theoretic tool, our results suggest network deconvolution is widely applicable for computing direct dependencies in network science across diverse disciplines.

  3. The middleware architecture supports heterogeneous network systems for module-based personal robot system

    NASA Astrophysics Data System (ADS)

    Choo, Seongho; Li, Vitaly; Choi, Dong Hee; Jung, Gi Deck; Park, Hong Seong; Ryuh, Youngsun

    2005-12-01

    On developing the personal robot system presently, the internal architecture is every module those occupy separated functions are connected through heterogeneous network system. This module-based architecture supports specialization and division of labor at not only designing but also implementation, as an effect of this architecture, it can reduce developing times and costs for modules. Furthermore, because every module is connected among other modules through network systems, we can get easy integrations and synergy effect to apply advanced mutual functions by co-working some modules. In this architecture, one of the most important technologies is the network middleware that takes charge communications among each modules connected through heterogeneous networks systems. The network middleware acts as the human nerve system inside of personal robot system; it relays, transmits, and translates information appropriately between modules that are similar to human organizations. The network middleware supports various hardware platform, heterogeneous network systems (Ethernet, Wireless LAN, USB, IEEE 1394, CAN, CDMA-SMS, RS-232C). This paper discussed some mechanisms about our network middleware to intercommunication and routing among modules, methods for real-time data communication and fault-tolerant network service. There have designed and implemented a layered network middleware scheme, distributed routing management, network monitoring/notification technology on heterogeneous networks for these goals. The main theme is how to make routing information in our network middleware. Additionally, with this routing information table, we appended some features. Now we are designing, making a new version network middleware (we call 'OO M/W') that can support object-oriented operation, also are updating program sources itself for object-oriented architecture. It is lighter, faster, and can support more operation systems and heterogeneous network systems, but other general

  4. Mining Functional Modules in Heterogeneous Biological Networks Using Multiplex PageRank Approach

    PubMed Central

    Li, Jun; Zhao, Patrick X.

    2016-01-01

    Identification of functional modules/sub-networks in large-scale biological networks is one of the important research challenges in current bioinformatics and systems biology. Approaches have been developed to identify functional modules in single-class biological networks; however, methods for systematically and interactively mining multiple classes of heterogeneous biological networks are lacking. In this paper, we present a novel algorithm (called mPageRank) that utilizes the Multiplex PageRank approach to mine functional modules from two classes of biological networks. We demonstrate the capabilities of our approach by successfully mining functional biological modules through integrating expression-based gene-gene association networks and protein-protein interaction networks. We first compared the performance of our method with that of other methods using simulated data. We then applied our method to identify the cell division cycle related functional module and plant signaling defense-related functional module in the model plant Arabidopsis thaliana. Our results demonstrated that the mPageRank method is effective for mining sub-networks in both expression-based gene-gene association networks and protein-protein interaction networks, and has the potential to be adapted for the discovery of functional modules/sub-networks in other heterogeneous biological networks. The mPageRank executable program, source code, the datasets and results of the presented two case studies are publicly and freely available at http://plantgrn.noble.org/MPageRank/. PMID:27446133

  5. Directed disassembly of an interfacial rubisco protein network.

    PubMed

    Onaizi, Sagheer A; Malcolm, Andrew S; He, Lizhong; Middelberg, Anton P J

    2007-05-22

    We present the first study of the directed disassembly of a protein network at the air-water interface by the synergistic action of a surfactant and an enzyme. We seek to understand the fundamentals of protein network disassembly by using rubisco adsorbed at the air-water interface as a model. We propose that rubisco adsorption at the air-water interface results in the formation of a fishnet-like network of interconnected protein molecules, capable of transmitting lateral force. The mechanical properties of the rubisco network during assembly and disassembly at the air-water interface were characterized by direct measurement of laterally transmitted force through the protein network using the Cambridge interfacial tensiometer. We have shown that, when used individually, either 2 ppm of the surfactant, sodium dodecyl benzyl sulfonate (SDOBS), or 2 ppm of the enzyme, subtilisin A (SA), were insufficient to completely disassemble the rubisco network within 1 h of treatment. However, a combination of 2 ppm SDOBS and 2 ppm SA led to almost complete disassembly within 1 h. Increasing the concentration of SA in the mixture from 2 to 10 ppm, while keeping the SDOBS concentration constant, significantly decreased the time required to completely disassemble the rubisco network. Furthermore, the initial rate of network disassembly using formulations containing SDOBS was surprisingly insensitive to this increase in SA concentration. This study gives insight into the role of lateral interactions between protein molecules at interfaces in stabilizing interfacial protein networks and shows that surfactant and enzyme working in combination proves more effective at disrupting and mobilizing the interfacial protein network than the action of either agent alone.

  6. 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.

  7. UDOF direct improvement by modulating mask absorber thickness

    NASA Astrophysics Data System (ADS)

    Yu, Tuan-Yen; Lio, En Chuan; Chen, Po Tsang; Wei, Chih I.; Chen, Yi Ting; Peng, Ming Chun; Chou, William; Yu, Chun Chi

    2016-10-01

    As the process generation migrate to advanced and smaller dimension or pitch, the mask and resist 3D effects will impact the lithography focus common window severely because of both individual depth-of-focus (iDOF) range decrease and center mismatch. Furthermore, some chemical or thermal factors, such as PEB (Post Exposure Bake) also worsen the usable depth-of-focus (uDOF) performance. So the mismatch of thru-pitch iDOF center should be considered as a lithography process integration issue, and more complicated to partition the 3D effects induced by optical or chemical factors. In order to reduce the impact of 3D effects induced by both optical and chemical issues, and improve iDOF center mismatch, we would like to propose a mask absorber thickness offset approach, which is directly to compensate the iDOF center bias by adjusting mask absorber thickness, for iso, semi-iso or dense characteristics in line, space or via patterns to enlarge common process window, i.e uDOF, which intends to provide similar application as Flexwave[1] (ASML trademark). By the way, since mask absorber thickness offset approach is similar to focus tuning or change on wafer lithography process, it could be acted as the process tuning method of photoresist (PR) profile optimization locally, PR scum improvement in specific patterns or to modulate etching bias to meet process integration request. For mass production consideration, and available material, current att-PSM blank, quartz, MoSi with chrome layer as hard-mask in reticle process, will be implemented in this experiment, i.e. chrome will be kept remaining above partial thru-pitch patterns, and act as the absorber thickness bias in different patterns. And then, from the best focus offset of thru-pitch patterns, the iDOF center shifts could be directly corrected and to enlarge uDOF by increasing the overlap of iDOF. Finally, some negative tone development (NTD) result in line patterns will be demonstrated as well.

  8. Development of a synthetic gene network to modulate gene expression by mechanical forces

    PubMed Central

    Kis, Zoltán; Rodin, Tania; Zafar, Asma; Lai, Zhangxing; Freke, Grace; Fleck, Oliver; Del Rio Hernandez, Armando; Towhidi, Leila; Pedrigi, Ryan M.; Homma, Takayuki; Krams, Rob

    2016-01-01

    The majority of (mammalian) cells in our body are sensitive to mechanical forces, but little work has been done to develop assays to monitor mechanosensor activity. Furthermore, it is currently impossible to use mechanosensor activity to drive gene expression. To address these needs, we developed the first mammalian mechanosensitive synthetic gene network to monitor endothelial cell shear stress levels and directly modulate expression of an atheroprotective transcription factor by shear stress. The technique is highly modular, easily scalable and allows graded control of gene expression by mechanical stimuli in hard-to-transfect mammalian cells. We call this new approach mechanosyngenetics. To insert the gene network into a high proportion of cells, a hybrid transfection procedure was developed that involves electroporation, plasmids replication in mammalian cells, mammalian antibiotic selection, a second electroporation and gene network activation. This procedure takes 1 week and yielded over 60% of cells with a functional gene network. To test gene network functionality, we developed a flow setup that exposes cells to linearly increasing shear stress along the length of the flow channel floor. Activation of the gene network varied logarithmically as a function of shear stress magnitude. PMID:27404994

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

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

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

    PubMed

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

    2016-05-03

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

  11. Microarray and network-based identification of functional modules and pathways of active tuberculosis.

    PubMed

    Bian, Zhong-Rui; Yin, Juan; Sun, Wen; Lin, Dian-Jie

    2017-02-08

    Diagnose of active tuberculosis (TB) is challenging and treatment response is also difficult to efficiently monitor. The aim of this study was to use an integrated analysis of microarray and network-based method to the samples from publically available datasets to obtain a diagnostic module set and pathways in active TB. Towards this goal, background protein-protein interactions (PPI) network was generated based on global PPI information and gene expression data, following by identification of differential expression network (DEN) from the background PPI network. Then, ego genes were extracted according to the degree features in DEN. Next, module collection was conducted by ego gene expansion based on EgoNet algorithm. After that, differential expression of modules between active TB and controls was evaluated using random permutation test. Finally, biological significance of differential modules was detected by pathways enrichment analysis based on Reactome database, and Fisher's exact test was implemented to extract differential pathways for active TB. Totally, 47 ego genes and 47 candidate modules were identified from the DEN. By setting the cutoff-criteria of gene size >5 and classification accuracy ≥0.9, 7 ego modules (Module 4, Module 7, Module 9, Module 19, Module 25, Module 38 and Module 43) were extracted, and all of them had the statistical significance between active TB and controls. Then, Fisher's exact test was conducted to capture differential pathways for active TB. Interestingly, genes in Module 4, Module 25, Module 38, and Module 43 were enriched in the same pathway, formation of a pool of free 40S subunits. Significant pathway for Module 7 and Module 9 was eukaryotic translation termination, and for Module 19 was nonsense mediated decay enhanced by the exon junction complex (EJC). Accordingly, differential modules and pathways might be potential biomarkers for treating active TB, and provide valuable clues for better understanding of molecular

  12. 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.

  13. Analysis of dispersion compensation by chirped fiber grating in directly and externally modulated CATV systems

    NASA Astrophysics Data System (ADS)

    Ye, Qing; Liu, Feng; Qu, Ronghui; Fang, Zujie

    2007-12-01

    The dispersion compensation effect of the chirped fiber grating (CFG) is analyzed theoretically, and analytic expressions are derived for composite second-order (CSO) distortion in analog modulated sub-carrier multiplexed (AM-SCM) cable television (CATV) systems with externally and directly modulated transmitters. Simulations are given for the two kinds of modulations and for standard single mode fiber and non-zero dispersion shift fiber (NZDSF) systems. The results show that CFG could be used as a dispersion compensator in directly modulated systems, but its dispersion coefficient should be adjusted much more precisely than the externally modulated system. The requirements for the NZDSF system could be loosened much. It is proposed that directly modulated source may be used as a transmitter in CATV systems combined with tunable CFG dispersion compensator being adjusted precisely, which may be more cost-effective than externally modulation technology.

  14. 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.

  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. 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.

  17. Studying modulation on simultaneously activated SSVEP neural networks by a cognitive task.

    PubMed

    Wu, Zhenghua

    2014-01-01

    Since the discovery of steady-state visually evoked potential (SSVEP), it has been used in many fields. Numerous studies suggest that there exist three SSVEP neural networks in different frequency bands. An obvious phenomenon has been observed, that the amplitude and phase of SSVEP can be modulated by a cognitive task. Previous works have studied this modulation on separately activated SSVEP neural networks by a cognitive task. If two or more SSVEP neural networks are activated simultaneously in the process of a cognitive task, is the modulation on different SSVEP neural networks the same? In this study, two different SSVEP neural networks were activated simultaneously by two different frequency flickers, with a working memory task irrelevant to the flickers being conducted at the same time. The modulated SSVEP waves were compared with each other and to those only under one flicker in previous studies. The comparison results show that the cognitive task can modulate different SSVEP neural networks with a similar style.

  18. Magnetic eigenmaps for community detection in directed networks

    NASA Astrophysics Data System (ADS)

    Fanuel, Michaël; Alaíz, Carlos M.; Suykens, Johan A. K.

    2017-02-01

    Communities in directed networks have often been characterized as regions with a high density of links, or as sets of nodes with certain patterns of connection. Our approach for community detection combines the optimization of a quality function and a spectral clustering of a deformation of the combinatorial Laplacian, the so-called magnetic Laplacian. The eigenfunctions of the magnetic Laplacian, which we call magnetic eigenmaps, incorporate structural information. Hence, using the magnetic eigenmaps, dense communities including directed cycles can be revealed as well as "role" communities in networks with a running flow, usually discovered thanks to mixture models. Furthermore, in the spirit of the Markov stability method, an approach for studying communities at different energy levels in the network is put forward, based on a quantum mechanical system at finite temperature.

  19. 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 β/ν, γ/ν and 1/ν were calculated for several values of z.

  20. 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.

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

    PubMed

    Haruna, Taichi

    2013-11-01

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

  2. 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

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

    PubMed Central

    Knudstrup, Scott; Zochowski, Michal; Booth, Victoria

    2016-01-01

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

  4. Functional modules, structural topology, and optimal activity in metabolic networks.

    PubMed

    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

  5. Parietal transcranial direct current stimulation modulates primary motor cortex excitability.

    PubMed

    Rivera-Urbina, Guadalupe Nathzidy; Batsikadze, Giorgi; Molero-Chamizo, Andrés; Paulus, Walter; Kuo, Min-Fang; Nitsche, Michael A

    2015-03-01

    The posterior parietal cortex is part of the cortical network involved in motor learning and is structurally and functionally connected with the primary motor cortex (M1). Neuroplastic alterations of neuronal connectivity might be an important basis for learning processes. These have however not been explored for parieto-motor connections in humans by transcranial direct current stimulation (tDCS). Exploring tDCS effects on parieto-motor cortical connectivity might be functionally relevant, because tDCS has been shown to improve motor learning. We aimed to explore plastic alterations of parieto-motor cortical connections by tDCS in healthy humans. We measured neuroplastic changes of corticospinal excitability via motor evoked potentials (MEP) elicited by single-pulse transcranial magnetic stimulation (TMS) before and after tDCS over the left posterior parietal cortex (P3), and 3 cm posterior or lateral to P3, to explore the spatial specificity of the effects. Furthermore, short-interval intracortical inhibition/intracortical facilitation (SICI/ICF) over M1, and parieto-motor cortical connectivity were obtained before and after P3 tDCS. The results show polarity-dependent M1 excitability alterations primarily after P3 tDCS. Single-pulse TMS-elicited MEPs, M1 SICI/ICF at 5 and 7 ms and 10 and 15 ms interstimulus intervals (ISIs), and parieto-motor connectivity at 10 and 15 ms ISIs were all enhanced by anodal stimulation. Single pulse-TMS-elicited MEPs, and parieto-motor connectivity at 10 and 15 ms ISIs were reduced by cathodal tDCS. The respective corticospinal excitability alterations lasted for at least 120 min after stimulation. These results show an effect of remote stimulation of parietal areas on M1 excitability. The spatial specificity of the effects and the impact on parietal cortex-motor cortex connections suggest a relevant connectivity-driven effect.

  6. 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

  7. Metastability and Inter-Band Frequency Modulation in Networks of Oscillating Spiking Neuron Populations

    PubMed Central

    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

  8. Self-organizing task modules and explicit coordinate systems in a neural network model for 3-D saccades.

    PubMed

    Smith, M A; Crawford, J D

    2001-01-01

    The goal of this study was to train an artificial neural network to generate accurate saccades in Listing's plane and then determine how the hidden units performed the visuomotor transformation. A three-layer neural network was successfully trained, using back-prop, to take in oculocentric retinal error vectors and three-dimensional eye orientation and to generate the correct head-centric motor error vector within Listing's plane. Analysis of the hidden layer of trained networks showed that explicit representations of desired target direction and eye orientation were not employed. Instead, the hidden-layer units consistently divided themselves into four parallel modules: a dominant "vector-propagation" class (approximately 50% of units) with similar visual and motor tuning but negligible position sensitivity and three classes with specific spatial relations between position, visual, and motor tuning. Surprisingly, the vector-propagation units, and only these, formed a highly precise and consistent orthogonal coordinate system aligned with Listing's plane. Selective "lesions" confirmed that the vector-propagation module provided the main drive for saccade magnitude and direction, whereas a balance between activity in the other modules was required for the correct eye-position modulation. Thus, contrary to popular expectation, error-driven learning in itself was sufficient to produce a "neural" algorithm with discrete functional modules and explicit coordinate systems, much like those observed in the real saccade generator.

  9. Gene duplication models for directed networks with limits on growth

    NASA Astrophysics Data System (ADS)

    Enemark, Jakob; Sneppen, Kim

    2007-11-01

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

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

    SciTech Connect

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

    2014-10-12

    Transcranial direct current stimulation (tDCS) modulates glutamatergic neurotransmission and can be utilized as a novel treatment intervention for a multitude of populations. However, the exact mechanism by which tDCS modulates the brain's neural architecture, from the micro to macro scales, have yet to be investigated. In this paper, 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. Finally, 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.

  11. 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

  12. Modulation of physiological mirror activity with transcranial direct current stimulation over dorsal premotor cortex.

    PubMed

    Beaulé, Vincent; Tremblay, Sara; Lafleur, Louis-Philippe; Ferland, Marie C; Lepage, Jean-François; Théoret, Hugo

    2016-11-01

    Humans have a natural tendency towards symmetrical movements, which rely on a distributed cortical network that allows for complex unimanual movements. Studies on healthy humans using rTMS have shown that disruption of this network, and particularly the dorsal premotor cortex (dPMC), can result in increased physiological mirror movements. The aim of the present set of experiments was to further investigate the role of dPMC in restricting motor output to the contralateral hand and determine whether physiological mirror movements could be decreased in healthy individuals. Physiological mirror movements were assessed before and after transcranial direct current stimulation (tDCS) over right and left dPMC in three conditions: bilateral, unilateral left and unilateral right stimulation. Mirror EMG activity was assessed immediately before, 0, 10 and 20 min after tDCS. Results show that physiological mirroring increased significantly in the hand ipsilateral to cathodal stimulation during bilateral stimulation of the dPMC, 10 and 20 min after stimulation compared to baseline. There was no significant modulation of physiological mirroring in the hand ipsilateral to anodal stimulation in the bilateral condition or following unilateral anodal or unilateral cathodal stimulation. The present data further implicate the dPMC in the control of unimanual hand movements and show that physiological mirroring can be increased but not decreased with dPMC tDCS.

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

    PubMed

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

    2011-04-06

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

  14. Directed networks' different link formation mechanisms causing degree distribution distinction

    NASA Astrophysics Data System (ADS)

    Behfar, Stefan Kambiz; Turkina, Ekaterina; Cohendet, Patrick; Burger-Helmchen, Thierry

    2016-11-01

    Within undirected networks, scientists have shown much interest in presenting power-law features. For instance, Barabási and Albert (1999) claimed that a common property of many large networks is that vertex connectivity follows scale-free power-law distribution, and in another study Barabási et al. (2002) showed power law evolution in the social network of scientific collaboration. At the same time, Jiang et al. (2011) discussed deviation from power-law distribution; others indicated that size effect (Bagrow et al., 2008), information filtering mechanism (Mossa et al., 2002), and birth and death process (Shi et al., 2005) could account for this deviation. Within directed networks, many authors have considered that outlinks follow a similar mechanism of creation as inlinks' (Faloutsos et al., 1999; Krapivsky et al., 2001; Tanimoto, 2009) with link creation rate being the linear function of node degree, resulting in a power-law shape for both indegree and outdegree distribution. Some other authors have made an assumption that directed networks, such as scientific collaboration or citation, behave as undirected, resulting in a power-law degree distribution accordingly (Barabási et al., 2002). At the same time, we claim (1) Outlinks feature different degree distributions than inlinks; where different link formation mechanisms cause the distribution distinctions, (2) in/outdegree distribution distinction holds for different levels of system decomposition; therefore this distribution distinction is a property of directed networks. First, we emphasize in/outlink formation mechanisms as causal factors for distinction between indegree and outdegree distributions (where this distinction has already been noticed in Barker et al. (2010) and Baxter et al. (2006)) within a sample network of OSS projects as well as Java software corpus as a network. Second, we analyze whether this distribution distinction holds for different levels of system decomposition: open

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

    PubMed

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

    2013-01-01

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

  16. 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.

  17. Ising model simulation in directed lattices and networks

    NASA Astrophysics Data System (ADS)

    Lima, F. W. S.; Stauffer, D.

    2006-01-01

    On directed lattices, with half as many neighbours as in the usual undirected lattices, the Ising model does not seem to show a spontaneous magnetisation, at least for lower dimensions. Instead, the decay time for flipping of the magnetisation follows an Arrhenius law on the square and simple cubic lattice. On directed Barabási-Albert networks with two and seven neighbours selected by each added site, Metropolis and Glauber algorithms give similar results, while for Wolff cluster flipping the magnetisation decays exponentially with time.

  18. 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

  19. Phase transitions in Ising models on directed networks.

    PubMed

    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.

  20. 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.

  1. Nicotinic modulation of network and synaptic transmission in the immature hippocampus investigated with genetically modified mice

    PubMed Central

    Le Magueresse, Corentin; Safiulina, Victoria; Changeux, Jean-Pierre; Cherubini, Enrico

    2006-01-01

    The hippocampus, a key structure in learning and memory processes, receives a powerful cholinergic innervation from the septum and contains nicotinic acetylcholine receptors (nAChRs). Early in postnatal development, activation of nAChRs by nicotine or endogenous acetylcholine contributes to enhance synaptic signalling. Here, the patch-clamp technique was used to assess the contribution of α7 and β2-containing (α7* and β2*) nAChRs to nicotine-elicited modulation of GABAergic and glutamatergic activity at the network and single-cell level in the immature hippocampus of wild-type (WT), α7−/− and β2−/− mice. We found that α7* and β2* nAChRs were sufficient to modulate nicotine-induced increase in frequency of spontaneously occurring giant depolarizing potentials (GDPs), which are generated at the network level by the synergistic action of glutamate and depolarizing GABA, and thought to play a crucial role in neuronal wiring. However, α7* but not β2* receptors were essential in nicotine-induced increase of interictal discharge frequency recorded after postnatal day 3 in the presence of bicuculline, when GABA shifted from the depolarizing to the hyperpolarizing direction. To correlate these observations with nicotine-elicited changes in synaptic transmission, we recorded spontaneous GABAergic and glutamatergic postsynaptic currents in pyramidal cells and interneurons localized in stratum oriens, stratum pyramidale and stratum radiatum, in slices obtained from WT and knock-out animals. We found that early in postnatal life α7* and β2* nAChRs exert a fine regional modulation of GABAergic and glutamatergic transmission that underlies nicotine-elicited changes in network synchronization. PMID:16901939

  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

    2014-12-06

    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.

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

    DOE PAGES

    Hunter, Michael A.; Coffman, Brian A.; Gasparovic, Charles; ...

    2014-10-12

    Transcranial direct current stimulation (tDCS) modulates glutamatergic neurotransmission and can be utilized as a novel treatment intervention for a multitude of populations. However, the exact mechanism by which tDCS modulates the brain's neural architecture, from the micro to macro scales, have yet to be investigated. In this paper, 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 networksmore » 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. Finally, 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.« less

  5. 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.

  6. 60-GHz Millimeter-wave Over Fiber with Directly Modulated Dual-mode Laser Diode.

    PubMed

    Tsai, Cheng-Ting; Lin, Chi-Hsiang; Lin, Chun-Ting; Chi, Yu-Chieh; Lin, Gong-Ru

    2016-06-14

    A directly modulated dual-mode laser diode (DMLD) with third-order intermodulation distortion (IMD3) suppression is proposed for a 60-GHz millimeter-wave over fiber (MMWoF) architecture, enabling new fiber-wireless communication access to cover 4-km single-mode-fiber (SMF) and 3-m wireless 16-QAM OFDM transmissions. By dual-mode injection-locking, the throughput degradation of the DMLD is mitigated with saturation effect to reduce its threshold, IMD3 power and relative intensity noise to 7.7 mA, -85 dBm and -110.4 dBc/Hz, respectively, providing huge spurious-free dynamic range of 85.8 dB/Hz(2/3). This operation suppresses the noise floor of the DMLD carried QPSK-OFDM spectrum by 5 dB. The optical receiving power is optimized to restrict the power fading effect for improving the bit error rate to 1.9 × 10(-3 )and the receiving power penalty to 1.1 dB. Such DMLD based hybrid architecture for 60-GHz MMW fiber-wireless access can directly cover the current optical and wireless networks for next-generation indoor and short-reach mobile communications.

  7. 60-GHz Millimeter-wave Over Fiber with Directly Modulated Dual-mode Laser Diode

    PubMed Central

    Tsai, Cheng-Ting; Lin, Chi-Hsiang; Lin, Chun-Ting; Chi, Yu-Chieh; Lin, Gong-Ru

    2016-01-01

    A directly modulated dual-mode laser diode (DMLD) with third-order intermodulation distortion (IMD3) suppression is proposed for a 60-GHz millimeter-wave over fiber (MMWoF) architecture, enabling new fiber-wireless communication access to cover 4-km single-mode-fiber (SMF) and 3-m wireless 16-QAM OFDM transmissions. By dual-mode injection-locking, the throughput degradation of the DMLD is mitigated with saturation effect to reduce its threshold, IMD3 power and relative intensity noise to 7.7 mA, −85 dBm and −110.4 dBc/Hz, respectively, providing huge spurious-free dynamic range of 85.8 dB/Hz2/3. This operation suppresses the noise floor of the DMLD carried QPSK-OFDM spectrum by 5 dB. The optical receiving power is optimized to restrict the power fading effect for improving the bit error rate to 1.9 × 10−3 and the receiving power penalty to 1.1 dB. Such DMLD based hybrid architecture for 60-GHz MMW fiber-wireless access can directly cover the current optical and wireless networks for next-generation indoor and short-reach mobile communications. PMID:27297267

  8. 60-GHz Millimeter-wave Over Fiber with Directly Modulated Dual-mode Laser Diode

    NASA Astrophysics Data System (ADS)

    Tsai, Cheng-Ting; Lin, Chi-Hsiang; Lin, Chun-Ting; Chi, Yu-Chieh; Lin, Gong-Ru

    2016-06-01

    A directly modulated dual-mode laser diode (DMLD) with third-order intermodulation distortion (IMD3) suppression is proposed for a 60-GHz millimeter-wave over fiber (MMWoF) architecture, enabling new fiber-wireless communication access to cover 4-km single-mode-fiber (SMF) and 3-m wireless 16-QAM OFDM transmissions. By dual-mode injection-locking, the throughput degradation of the DMLD is mitigated with saturation effect to reduce its threshold, IMD3 power and relative intensity noise to 7.7 mA, ‑85 dBm and ‑110.4 dBc/Hz, respectively, providing huge spurious-free dynamic range of 85.8 dB/Hz2/3. This operation suppresses the noise floor of the DMLD carried QPSK-OFDM spectrum by 5 dB. The optical receiving power is optimized to restrict the power fading effect for improving the bit error rate to 1.9 × 10‑3 and the receiving power penalty to 1.1 dB. Such DMLD based hybrid architecture for 60-GHz MMW fiber-wireless access can directly cover the current optical and wireless networks for next-generation indoor and short-reach mobile communications.

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

    NASA Technical Reports Server (NTRS)

    Rippy, R. R.

    1975-01-01

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

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

    PubMed Central

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

    2013-01-01

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

  11. Facial Sketch Synthesis Using 2D Direct Combined Model-Based Face-Specific Markov Network.

    PubMed

    Tu, Ching-Ting; Chan, Yu-Hsien; Chen, Yi-Chung

    2016-08-01

    A facial sketch synthesis system is proposed, featuring a 2D direct combined model (2DDCM)-based face-specific Markov network. In contrast to the existing facial sketch synthesis systems, the proposed scheme aims to synthesize sketches, which reproduce the unique drawing style of a particular artist, where this drawing style is learned from a data set consisting of a large number of image/sketch pairwise training samples. The synthesis system comprises three modules, namely, a global module, a local module, and an enhancement module. The global module applies a 2DDCM approach to synthesize the global facial geometry and texture of the input image. The detailed texture is then added to the synthesized sketch in a local patch-based manner using a parametric 2DDCM model and a non-parametric Markov random field (MRF) network. Notably, the MRF approach gives the synthesized results an appearance more consistent with the drawing style of the training samples, while the 2DDCM approach enables the synthesis of outcomes with a more derivative style. As a result, the similarity between the synthesized sketches and the input images is greatly improved. Finally, a post-processing operation is performed to enhance the shadowed regions of the synthesized image by adding strong lines or curves to emphasize the lighting conditions. The experimental results confirm that the synthesized facial images are in good qualitative and quantitative agreement with the input images as well as the ground-truth sketches provided by the same artist. The representing power of the proposed framework is demonstrated by synthesizing facial sketches from input images with a wide variety of facial poses, lighting conditions, and races even when such images are not included in the training data set. Moreover, the practical applicability of the proposed framework is demonstrated by means of automatic facial recognition tests.

  12. 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

  13. Predicting Fault Prone Modules by the Dempster-Shafer Belief Networks

    PubMed Central

    Guo, Lan; Cukic, Bojan; Singh, Harshinder

    2015-01-01

    This paper describes a novel methodology for predicting fault prone modules. The methodology is based on Dempster-Shafer (D-S) belief networks. Our approach consists of three steps: First, building the Dempster-Shafer network by the induction algorithm; Second, selecting the predictors (attributes) by the logistic procedure; Third, feeding the predictors describing the modules of the current project into the inducted Dempster-Shafer network and identifying fault prone modules. We applied this methodology to a NASA dataset. The prediction accuracy of our methodology is higher than that achieved by logistic regression or discriminant analysis on the same dataset. PMID:26120284

  14. Uniform Sampling for Directed P2P Networks

    NASA Astrophysics Data System (ADS)

    Hall, Cyrus; Carzaniga, Antonio

    Selecting a random peer with uniform probability across a peer-to-peer (P2P) network is a fundamental function for unstructured search, data replication, and monitoring algorithms. Such uniform sampling is supported by several techniques. However, current techniques suffer from sample bias and limited applicability. In this paper, we present a sampling algorithm that achieves a desired uniformity while making essentially no assumptions about the underlying P2P network. This algorithm, called doubly stochastic converge (DSC), iteratively adjusts the probabilities of crossing each link in the network during a random walk, such that the resulting transition matrix is doubly stochastic. DSC is fully decentralized and is designed to work on both directed and undirected topologies, making it suitable for virtually any P2P network. Our simulations show that DSC converges quickly on a wide variety of topologies, and that the random walks needed for sampling are short for most topologies. In simulation studies with FreePastry, we show that DSC is resilient to high levels of churn, while incurring a minimal sample bias.

  15. Integrin-directed modulation of macrophage responses to biomaterials.

    PubMed

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

    2014-04-01

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

  16. Infant-Directed Speech Is Modulated by Infant Feedback

    ERIC Educational Resources Information Center

    Smith, Nicholas A.; Trainor, Laurel J.

    2008-01-01

    When mothers engage in infant-directed (ID) speech, their voices change in a number of characteristic ways, including adopting a higher overall pitch. Studies have examined these acoustical cues and have tested infants' preferences for ID speech. However, little is known about how these cues change with maternal sensitivity to infant feedback in…

  17. Quantitative Identification of Compound‐Dependent On‐Modules and Differential Allosteric Modules From Homologous Ischemic Networks

    PubMed Central

    Li, B; Liu, J; Zhang, YY; Wang, PQ; Yu, YN; Kang, RX; Wu, HL; Zhang, XX; Wang, YY

    2016-01-01

    Module‐based methods have made much progress in deconstructing biological networks. However, it is a great challenge to quantitatively compare the topological structural variations of modules (allosteric modules [AMs]) under different situations. A total of 23, 42, and 15 coexpression modules were identified in baicalin (BA), jasminoidin (JA), and ursodeoxycholic acid (UA) in a global anti‐ischemic mice network, respectively. Then, we integrated the methods of module‐based consensus ratio (MCR) and modified Zsummary module statistic to validate 12 BA, 22 JA, and 8 UA on‐modules based on comparing with vehicle. The MCRs for pairwise comparisons were 1.55% (BA vs. JA), 1.45% (BA vs. UA), and 1.27% (JA vs. UA), respectively. Five conserved allosteric modules (CAMs) and 17 unique allosteric modules (UAMs) were identified among these groups. In conclusion, module‐centric analysis may provide us a unique approach to understand multiple pharmacological mechanisms associated with differential phenotypes in the era of modular pharmacology. PMID:27758049

  18. Bridging the gap between modules in isolation and as part of networks: A systems framework for elucidating interaction and regulation of signalling modules

    NASA Astrophysics Data System (ADS)

    Menon, Govind; Krishnan, J.

    2016-07-01

    While signalling and biochemical modules have been the focus of numerous studies, they are typically studied in isolation, with no examination of the effects of the ambient network. In this paper we formulate and develop a systems framework, rooted in dynamical systems, to understand such effects, by studying the interaction of signalling modules. The modules we consider are (i) basic covalent modification, (ii) monostable switches, (iii) bistable switches, (iv) adaptive modules, and (v) oscillatory modules. We systematically examine the interaction of these modules by analyzing (a) sequential interaction without shared components, (b) sequential interaction with shared components, and (c) oblique interactions. Our studies reveal that the behaviour of a module in isolation may be substantially different from that in a network, and explicitly demonstrate how the behaviour of a given module, the characteristics of the ambient network, and the possibility of shared components can result in new effects. Our global approach illuminates different aspects of the structure and functioning of modules, revealing the importance of dynamical characteristics as well as biochemical features; this provides a methodological platform for investigating the complexity of natural modules shaped by evolution, elucidating the effects of ambient networks on a module in multiple cellular contexts, and highlighting the capabilities and constraints for engineering robust synthetic modules. Overall, such a systems framework provides a platform for bridging the gap between non-linear information processing modules, in isolation and as parts of networks, and a basis for understanding new aspects of natural and engineered cellular networks.

  19. Bridging the gap between modules in isolation and as part of networks: A systems framework for elucidating interaction and regulation of signalling modules.

    PubMed

    Menon, Govind; Krishnan, J

    2016-07-21

    While signalling and biochemical modules have been the focus of numerous studies, they are typically studied in isolation, with no examination of the effects of the ambient network. In this paper we formulate and develop a systems framework, rooted in dynamical systems, to understand such effects, by studying the interaction of signalling modules. The modules we consider are (i) basic covalent modification, (ii) monostable switches, (iii) bistable switches, (iv) adaptive modules, and (v) oscillatory modules. We systematically examine the interaction of these modules by analyzing (a) sequential interaction without shared components, (b) sequential interaction with shared components, and (c) oblique interactions. Our studies reveal that the behaviour of a module in isolation may be substantially different from that in a network, and explicitly demonstrate how the behaviour of a given module, the characteristics of the ambient network, and the possibility of shared components can result in new effects. Our global approach illuminates different aspects of the structure and functioning of modules, revealing the importance of dynamical characteristics as well as biochemical features; this provides a methodological platform for investigating the complexity of natural modules shaped by evolution, elucidating the effects of ambient networks on a module in multiple cellular contexts, and highlighting the capabilities and constraints for engineering robust synthetic modules. Overall, such a systems framework provides a platform for bridging the gap between non-linear information processing modules, in isolation and as parts of networks, and a basis for understanding new aspects of natural and engineered cellular networks.

  20. Module Anchored Network Inference: A Sequential Module-Based Approach to Novel Gene Network Construction from Genomic Expression Data on Human Disease Mechanism

    PubMed Central

    Keller, Susanna R.; Lee, Jae K.

    2017-01-01

    Different computational approaches have been examined and compared for inferring network relationships from time-series genomic data on human disease mechanisms under the recent Dialogue on Reverse Engineering Assessment and Methods (DREAM) challenge. Many of these approaches infer all possible relationships among all candidate genes, often resulting in extremely crowded candidate network relationships with many more False Positives than True Positives. To overcome this limitation, we introduce a novel approach, Module Anchored Network Inference (MANI), that constructs networks by analyzing sequentially small adjacent building blocks (modules). Using MANI, we inferred a 7-gene adipogenesis network based on time-series gene expression data during adipocyte differentiation. MANI was also applied to infer two 10-gene networks based on time-course perturbation datasets from DREAM3 and DREAM4 challenges. MANI well inferred and distinguished serial, parallel, and time-dependent gene interactions and network cascades in these applications showing a superior performance to other in silico network inference techniques for discovering and reconstructing gene network relationships. PMID:28197408

  1. Anodal transcranial direct current stimulation of the motor cortex induces opposite modulation of reciprocal inhibition in wrist extensor and flexor.

    PubMed

    Lackmy-Vallée, Alexandra; Klomjai, Wanalee; Bussel, Bernard; Katz, Rose; Roche, Nicolas

    2014-09-15

    Transcranial direct current stimulation (tDCS) is used as a noninvasive tool to modulate brain excitability in humans. Recently, several studies have demonstrated that tDCS applied over the motor cortex also modulates spinal neural network excitability and therefore can be used to explore the corticospinal control acting on spinal neurons. Previously, we showed that reciprocal inhibition directed to wrist flexor motoneurons is enhanced during contralateral anodal tDCS, but it is likely that the corticospinal control acting on spinal networks controlling wrist flexors and extensors is not similar. The primary aim of the study was to explore the effects of anodal tDCS on reciprocal inhibition directed to wrist extensor motoneurons. To further examine the supraspinal control acting on the reciprocal inhibition between wrist flexors and extensors, we also explored the effects of the tDCS applied to the ipsilateral hand motor area. In healthy volunteers, we tested the effects induced by sham and anodal tDCS on reciprocal inhibition pathways innervating wrist muscles. Reciprocal inhibition directed from flexor to extensor muscles and the reverse situation, i.e., reciprocal inhibition, directed from extensors to flexors were studied in parallel with the H reflex technique. Our main finding was that contralateral anodal tDCS induces opposing effects on reciprocal inhibition: it decreases reciprocal inhibition directed from flexors to extensors, but it increases reciprocal inhibition directed from extensors to flexors. The functional result of these opposite effects on reciprocal inhibition seems to favor wrist extension excitability, suggesting an asymmetric descending control onto the interneurons that mediate reciprocal inhibition.

  2. Transcriptionally Regulated Cell Adhesion Network Dictates Distal Tip Cell Directionality

    PubMed Central

    Wong, Ming-Ching; Kennedy, William P.; Schwarzbauer, Jean E.

    2015-01-01

    Background The mechanisms that govern directional changes in cell migration are poorly understood. The migratory paths of two distal tip cells (DTC) determine the U-shape of the C. elegans hermaphroditic gonad. The morphogenesis of this organ provides a model system to identify genes necessary for the DTCs to execute two stereotyped turns. Results Using candidate genes for RNAi knockdown in a DTC-specific strain, we identified two transcriptional regulators required for DTC turning: cbp-1, the CBP/p300 transcriptional coactivator homologue, and let-607, a CREBH transcription factor homologue. Further screening of potential target genes uncovered a network of integrin adhesion-related genes that have roles in turning and are dependent on cbp-1 and let-607 for expression. These genes include src-1/Src kinase, tln-1/talin, pat-2/α integrin and nmy-2, a nonmuscle myosin heavy chain. Conclusions Transcriptional regulation by means of cbp-1 and let-607 is crucial for determining directional changes during DTC migration. These regulators coordinate a gene network that is necessary for integrin-mediated adhesion. Overall, these results suggest that directional changes in cell migration rely on the precise gene regulation of adhesion. PMID:24811939

  3. Integrated module and gene-specific regulatory inference implicates upstream signaling networks.

    PubMed

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

    2013-01-01

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

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

    PubMed Central

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

    2013-01-01

    Regulatory networks that control gene expression are important in diverse biological contexts including stress response and development. Each gene's regulatory program is determined by module-level regulation (e.g. co-regulation via the same signaling system), as well as gene-specific determinants that can fine-tune expression. We present a novel approach, Modular regulatory network learning with per gene information (MERLIN), that infers regulatory programs for individual genes while probabilistically constraining these programs to reveal module-level organization of regulatory networks. Using edge-, regulator- and module-based comparisons of simulated networks of known ground truth, we find MERLIN reconstructs regulatory programs of individual genes as well or better than existing approaches of network reconstruction, while additionally identifying modular organization of the regulatory networks. We use MERLIN to dissect global transcriptional behavior in two biological contexts: yeast stress response and human embryonic stem cell differentiation. Regulatory modules inferred by MERLIN capture co-regulatory relationships between signaling proteins and downstream transcription factors thereby revealing the upstream signaling systems controlling transcriptional responses. The inferred networks are enriched for regulators with genetic or physical interactions, supporting the inference, and identify modules of functionally related genes bound by the same transcriptional regulators. Our method combines the strengths of per-gene and per-module methods to reveal new insights into transcriptional regulation in stress and development. PMID:24146602

  5. Silicon photonic Mach Zehnder modulators for next-generation short-reach optical communication networks

    NASA Astrophysics Data System (ADS)

    Lacava, C.; Liu, Z.; Thomson, D.; Ke, Li; Fedeli, J. M.; Richardson, D. J.; Reed, G. T.; Petropoulos, P.

    2016-02-01

    Communication traffic grows relentlessly in today's networks, and with ever more machines connected to the network, this trend is set to continue for the foreseeable future. It is widely accepted that increasingly faster communications are required at the point of the end users, and consequently optical transmission plays a progressively greater role even in short- and medium-reach networks. Silicon photonic technologies are becoming increasingly attractive for such networks, due to their potential for low cost, energetically efficient, high-speed optical components. A representative example is the silicon-based optical modulator, which has been actively studied. Researchers have demonstrated silicon modulators in different types of structures, such as ring resonators or slow light based devices. These approaches have shown remarkably good performance in terms of modulation efficiency, however their operation could be severely affected by temperature drifts or fabrication errors. Mach-Zehnder modulators (MZM), on the other hand, show good performance and resilience to different environmental conditions. In this paper we present a CMOS-compatible compact silicon MZM. We study the application of the modulator to short-reach interconnects by realizing data modulation using some relevant advanced modulation formats, such as 4-level Pulse Amplitude Modulation (PAM-4) and Discrete Multi-Tone (DMT) modulation and compare the performance of the different systems in transmission.

  6. Hybrid silicon plasmonic organic directional coupler-based modulator

    NASA Astrophysics Data System (ADS)

    Abdelatty, M. Y.; Zaki, A. O.; Swillam, M. A.

    2017-01-01

    An optical directional coupler (ODC)-based hybrid plasmonic waveguide is designed and demonstrated with a power splitting mechanism that can be tuned by applying an external electric field. The tuning mechanism takes the advantage of electro-optic properties of the embedded polymer layer. The ODC operates under 1550 nm telecommunication wavelength. A finite element method with a perfect matching layer, absorbing boundary condition, is taken up to simulate and analyze the ODC.

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

    PubMed Central

    Banga, Ajay K.

    2014-01-01

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

  8. Reconstructing network topology and coupling strengths in directed networks of discrete-time dynamics

    NASA Astrophysics Data System (ADS)

    Lai, Pik-Yin

    2017-02-01

    Reconstructing network connection topology and interaction strengths solely from measurement of the dynamics of the nodes is a challenging inverse problem of broad applicability in various areas of science and engineering. For a discrete-time step network under noises whose noise-free dynamics is stationary, we derive general analytic results relating the weighted connection matrix of the network to the correlation functions obtained from time-series measurements of the nodes for networks with one-dimensional intrinsic node dynamics. Information about the intrinsic node dynamics and the noise strengths acting on the nodes can also be obtained. Based on these results, we develop a scheme that can reconstruct the above information of the network using only the time-series measurements of node dynamics as input. Reconstruction formulas for higher-dimensional node dynamics are also derived and illustrated with a two-dimensional node dynamics network system. Furthermore, we extend our results and obtain a reconstruction scheme even for the cases when the noise-free dynamics is periodic. We demonstrate that our method can give accurate reconstruction results for weighted directed networks with linear or nonlinear node dynamics of various connection topologies, and with linear or nonlinear couplings.

  9. Goal-Directed and Habit-Like Modulations of Stimulus Processing during Reinforcement Learning.

    PubMed

    Luque, David; Beesley, Tom; Morris, Richard W; Jack, Bradley N; Griffiths, Oren; Whitford, Thomas J; Le Pelley, Mike E

    2017-03-15

    Recent research has shown that perceptual processing of stimuli previously associated with high-value rewards is automatically prioritized even when rewards are no longer available. It has been hypothesized that such reward-related modulation of stimulus salience is conceptually similar to an "attentional habit." Recording event-related potentials in humans during a reinforcement learning task, we show strong evidence in favor of this hypothesis. Resistance to outcome devaluation (the defining feature of a habit) was shown by the stimulus-locked P1 component, reflecting activity in the extrastriate visual cortex. Analysis at longer latencies revealed a positive component (corresponding to the P3b, from 550-700 ms) sensitive to outcome devaluation. Therefore, distinct spatiotemporal patterns of brain activity were observed corresponding to habitual and goal-directed processes. These results demonstrate that reinforcement learning engages both attentional habits and goal-directed processes in parallel. Consequences for brain and computational models of reinforcement learning are discussed.SIGNIFICANCE STATEMENT The human attentional network adapts to detect stimuli that predict important rewards. A recent hypothesis suggests that the visual cortex automatically prioritizes reward-related stimuli, driven by cached representations of reward value; that is, stimulus-response habits. Alternatively, the neural system may track the current value of the predicted outcome. Our results demonstrate for the first time that visual cortex activity is increased for reward-related stimuli even when the rewarding event is temporarily devalued. In contrast, longer-latency brain activity was specifically sensitive to transient changes in reward value. Therefore, we show that both habit-like attention and goal-directed processes occur in the same learning episode at different latencies. This result has important consequences for computational models of reinforcement learning.

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

    PubMed

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

    2006-12-01

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

  11. 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

  12. The second will be first: competition on directed networks

    PubMed Central

    Cencetti, Giulia; Bagnoli, Franco; Di Patti, Francesca; Fanelli, Duccio

    2016-01-01

    Multiple sinks competition is investigated for a walker diffusing on directed complex networks. The asymmetry of the imposed spatial support makes the system non transitive. As a consequence, it is always possible to identify a suitable location for the second absorbing sink that screens at most the flux of agents directed against the first trap, whose position has been preliminarily assigned. The degree of mutual competition between pairs of nodes is analytically quantified through apt indicators that build on the topological characteristics of the hosting graph. Moreover, the positioning of the second trap can be chosen so as to minimize, at the same time, the probability of being in turn shaded by a thirdly added trap. Supervised placing of absorbing traps on a asymmetric disordered and complex graph is hence possible, as follows a robust optimization protocol. This latter is here discussed and successfully tested against synthetic data. PMID:27271996

  13. 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.

  14. Investigation of the large-scale functional brain networks modulated by acupuncture.

    PubMed

    Feng, Yuanyuan; Bai, Lijun; Ren, Yanshuang; Wang, Hu; Liu, Zhenyu; Zhang, Wensheng; Tian, Jie

    2011-09-01

    Previous neuroimaging studies have primarily focused on the neural activities involving the acute effects of acupuncture. Considering that acupuncture can induce long-lasting effects, several researchers have begun to pay attention to the sustained effects of acupuncture on the resting brain. Most of these researchers adopted functional connectivity analysis based on one or a few preselected brain regions and demonstrated various function-guided brain networks underlying the specific effect of acupuncture. Few have investigated how these brain networks interacted at the whole-brain level. In this study, we sought to investigate the functional correlations throughout the entire brain following acupuncture at acupoint ST36 (ACUP) in comparison with acupuncture at nearby nonacupoint (SHAM). We divided the whole brain into 90 regions and constructed functional brain network for each condition. Then we examined the network hubs and identified statistically significant differences in functional correlations between the two conditions. Following ACUP, but not SHAM, the limbic/paralimbic regions such as the amygdala, hippocampus and anterior cingulate gyrus emerged as network hubs. For direct comparisons, increased correlations for ACUP compared to SHAM were primarily related with the limbic/paralimbic and subcortical regions such as the insula, amygdala, anterior cingulate gyrus, and thalamus, whereas decreased correlations were mainly related with the sensory and frontal cortex. The heterogeneous modulation patterns between the two conditions may relate to the functional specific modulatory effects of acupuncture. The preliminary findings may help us to better understand the long-lasting effects of acupuncture on the entire resting brain, as well as the neurophysiological mechanisms underlying acupuncture.

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

    PubMed

    Duan, Shiwei; Luo, Xuhong; Dong, Changzheng

    2013-12-01

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

  16. Distinguishing between direct and indirect directional couplings in large oscillator networks: Partial or non-partial phase analyses?

    NASA Astrophysics Data System (ADS)

    Rings, Thorsten; Lehnertz, Klaus

    2016-09-01

    We investigate the relative merit of phase-based methods for inferring directional couplings in complex networks of weakly interacting dynamical systems from multivariate time-series data. We compare the evolution map approach and its partialized extension to each other with respect to their ability to correctly infer the network topology in the presence of indirect directional couplings for various simulated experimental situations using coupled model systems. In addition, we investigate whether the partialized approach allows for additional or complementary indications of directional interactions in evolving epileptic brain networks using intracranial electroencephalographic recordings from an epilepsy patient. For such networks, both direct and indirect directional couplings can be expected, given the brain's connection structure and effects that may arise from limitations inherent to the recording technique. Our findings indicate that particularly in larger networks (number of nodes ≫10 ), the partialized approach does not provide information about directional couplings extending the information gained with the evolution map approach.

  17. Distinguishing between direct and indirect directional couplings in large oscillator networks: Partial or non-partial phase analyses?

    PubMed

    Rings, Thorsten; Lehnertz, Klaus

    2016-09-01

    We investigate the relative merit of phase-based methods for inferring directional couplings in complex networks of weakly interacting dynamical systems from multivariate time-series data. We compare the evolution map approach and its partialized extension to each other with respect to their ability to correctly infer the network topology in the presence of indirect directional couplings for various simulated experimental situations using coupled model systems. In addition, we investigate whether the partialized approach allows for additional or complementary indications of directional interactions in evolving epileptic brain networks using intracranial electroencephalographic recordings from an epilepsy patient. For such networks, both direct and indirect directional couplings can be expected, given the brain's connection structure and effects that may arise from limitations inherent to the recording technique. Our findings indicate that particularly in larger networks (number of nodes ≫10), the partialized approach does not provide information about directional couplings extending the information gained with the evolution map approach.

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

    PubMed

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

    2014-03-18

    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.

  19. 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

  20. Focused transcranial direct current stimulation (tDCS) over the dorsolateral prefrontal cortex modulates specific domains of self-regulation.

    PubMed

    Pripfl, Jürgen; Lamm, Claus

    2015-02-01

    Recent neuroscience theories suggest that different kinds of self-regulation may share a common psychobiological mechanism. However, empirical evidence for a domain general self-regulation mechanism is scarce. The aim of this study was to investigate whether focused anodal transcranial direct current stimulation (tDCS), facilitating the activity of the dorsolateral prefrontal cortex (dlPFC), acts on a domain general self-regulation mechanism and thus modulates both affective and appetitive self-regulation. Twenty smokers participated in this within-subject sham controlled study. Effects of anodal left, anodal right and sham tDCS over the dlPFC on affective picture appraisal and nicotine craving-cue appraisal were assessed. Anodal right tDCS over the dlPFC reduced negative affect in emotion appraisal, but neither modulated regulation of positive emotion appraisal nor of craving appraisal. Anodal left stimulation did not induce any significant effects. The results of our study show that domain specific self-regulation networks are at work in the prefrontal cortex. Focused tDCS modulation of this specific self-regulation network could probably be used during the first phase of nicotine abstinence, during which negative affect might easily result in relapse. These findings have implications for neuroscience models of self-regulation and are of relevance for the development of brain stimulation based treatment methods for neuropsychiatric disorders associated with self-regulation deficits.

  1. Using single side-band modulation for colorless OFDM-WDM access network to alleviate Rayleigh backscattering effects.

    PubMed

    Yeh, Chien-Hung; Chow, Chi-Wai

    2016-05-16

    In this investigation, we demonstrate a new colorless orthogonal-frequency-division-multiplexing (OFDM) wavelength-division-multiplexing passive optical network (WDM-PON) system with Rayleigh backscattering (RB) noise mitigation. Here, only a single laser source at the central office (CO) is needed to produce the downstream signal and distributed continuous-wave (CW) carrier, which will then be modulated at the optical networking unit (ONU) to produce the upstream signal. Single side-band (SSB) modulation is used to wavelength-shift the distributed CW carrier, which will be launched into a reflective semiconductor optical amplifier (RSOA) based ONU for directly modulation of 5.15 Gbps OFDM upstream signal. To avoid the radio-frequency (RF) power fading and chromatic fiber dispersion, the four-band OFDM modulation is proposed to generate a 40 Gbps downstream when a Mach-Zehnder modulator (MZM) with -0.7 chirp parameter is used. Hence, the RB circumvention can be centralized in the CO. Moreover, the signal performances of downstream and upstream are also studied and discussed in this measurement.

  2. Network based elucidation of drug response: from modulators to targets

    PubMed Central

    2013-01-01

    Network-based drug discovery aims at harnessing the power of networks to investigate the mechanism of action of existing drugs, or new molecules, in order to identify innovative therapeutic treatments. In this review, we describe some of the most recent advances in the field of network pharmacology, starting with approaches relying on computational models of transcriptional networks, then moving to protein and signaling network models and concluding with “drug networks”. These networks are derived from different sources of experimental data, or literature-based analysis, and provide a complementary view of drug mode of action. Molecular and drug networks are powerful integrated computational and experimental approaches that will likely speed up and improve the drug discovery process, once fully integrated into the academic and industrial drug discovery pipeline. PMID:24330611

  3. Transcutaneous spinal direct current stimulation modulates human corticospinal system excitability.

    PubMed

    Bocci, Tommaso; Marceglia, Sara; Vergari, Maurizio; Cognetto, Valeria; Cogiamanian, Filippo; Sartucci, Ferdinando; Priori, Alberto

    2015-07-01

    This study aimed to assess the effects of thoracic anodal and cathodal transcutaneous spinal direct current stimulation (tsDCS) on upper and lower limb corticospinal excitability. Although there have been studies assessing how thoracic tsDCS influences the spinal ascending tract and reflexes, none has assessed the effects of this technique over upper and lower limb corticomotor neuronal connections. In 14 healthy subjects we recorded motor evoked potentials (MEPs) elicited by transcranial magnetic stimulation (TMS) from abductor hallucis (AH) and hand abductor digiti minimi (ADM) muscles before (baseline) and at different time points (0 and 30 min) after anodal or cathodal tsDCS (2.5 mA, 20 min, T9-T11 level). In 8 of the 14 subjects we also tested the soleus H reflex and the F waves from AH and ADM before and after tsDCS. Both anodal and cathodal tsDCS left the upper limb MEPs and F wave unchanged. Conversely, while leaving lower limb H reflex unchanged, they oppositely affected lower limb MEPs: whereas anodal tsDCS increased resting motor threshold [(mean ± SE) 107.33 ± 3.3% increase immediately after tsDCS and 108.37 ± 3.2% increase 30 min after tsDCS compared with baseline] and had no effects on MEP area and latency, cathodal tsDCS increased MEP area (139.71 ± 12.9% increase immediately after tsDCS and 132.74 ± 22.0% increase 30 min after tsDCS compared with baseline) without affecting resting motor threshold and MEP latency. Our results show that tsDCS induces polarity-specific changes in corticospinal excitability that last for >30 min after tsDCS offset and selectively affect responses in lower limb muscles innervated by lumbar and sacral motor neurons.

  4. Transcutaneous spinal direct current stimulation modulates human corticospinal system excitability

    PubMed Central

    Bocci, Tommaso; Marceglia, Sara; Vergari, Maurizio; Cognetto, Valeria; Cogiamanian, Filippo; Sartucci, Ferdinando

    2015-01-01

    This study aimed to assess the effects of thoracic anodal and cathodal transcutaneous spinal direct current stimulation (tsDCS) on upper and lower limb corticospinal excitability. Although there have been studies assessing how thoracic tsDCS influences the spinal ascending tract and reflexes, none has assessed the effects of this technique over upper and lower limb corticomotor neuronal connections. In 14 healthy subjects we recorded motor evoked potentials (MEPs) elicited by transcranial magnetic stimulation (TMS) from abductor hallucis (AH) and hand abductor digiti minimi (ADM) muscles before (baseline) and at different time points (0 and 30 min) after anodal or cathodal tsDCS (2.5 mA, 20 min, T9–T11 level). In 8 of the 14 subjects we also tested the soleus H reflex and the F waves from AH and ADM before and after tsDCS. Both anodal and cathodal tsDCS left the upper limb MEPs and F wave unchanged. Conversely, while leaving lower limb H reflex unchanged, they oppositely affected lower limb MEPs: whereas anodal tsDCS increased resting motor threshold [(mean ± SE) 107.33 ± 3.3% increase immediately after tsDCS and 108.37 ± 3.2% increase 30 min after tsDCS compared with baseline] and had no effects on MEP area and latency, cathodal tsDCS increased MEP area (139.71 ± 12.9% increase immediately after tsDCS and 132.74 ± 22.0% increase 30 min after tsDCS compared with baseline) without affecting resting motor threshold and MEP latency. Our results show that tsDCS induces polarity-specific changes in corticospinal excitability that last for >30 min after tsDCS offset and selectively affect responses in lower limb muscles innervated by lumbar and sacral motor neurons. PMID:25925328

  5. Assessment of absolute added correlative coding in optical intensity modulation and direct detection channels

    NASA Astrophysics Data System (ADS)

    Dong-Nhat, Nguyen; Elsherif, Mohamed A.; Malekmohammadi, Amin

    2016-06-01

    The performance of absolute added correlative coding (AACC) modulation format with direct detection has been numerically and analytically reported, targeting metro data center interconnects. Hereby, the focus lies on the performance of the bit error rate, noise contributions, spectral efficiency, and chromatic dispersion tolerance. The signal space model of AACC, where the average electrical and optical power expressions are derived for the first time, is also delineated. The proposed modulation format was also compared to other well-known signaling, such as on-off-keying (OOK) and four-level pulse-amplitude modulation, at the same bit rate in a directly modulated vertical-cavity surface-emitting laser-based transmission system. The comparison results show a clear advantage of AACC in achieving longer fiber delivery distance due to the higher dispersion tolerance.

  6. Nonlinear impairment compensation for DFT-S OFDM signal transmission with directly modulated laser and direct detection

    NASA Astrophysics Data System (ADS)

    Gou, Pengqi; Wang, Kaihui; Qin, Chaoyi; Yu, Jianjun

    2017-03-01

    We experimentally demonstrate a 16-ary quadrature amplitude modulation (16QAM) DFT-spread optical orthogonal frequency division multiplexing (OFDM) transmission system utilizing a cost-effective directly modulated laser (DML) and direct detection. For 20-Gbaud 16QAM-OFDM signal, with the aid of nonlinear equalization (NLE) algorithm, we respectively provide 6.2-dB and 5.2-dB receiver sensitivity improvement under the hard-decision forward-error-correction (HD-FEC) threshold of 3.8×10-3 for the back-to-back (BTB) case and after transmission over 10-km standard single mode fiber (SSMF) case, related to only adopt post-equalization scheme. To our knowledge, this is the first time to use dynamic nonlinear equalizer (NLE) based on the summation of the square of the difference between samples in one IM/DD OFDM system with DML to mitigate nonlinear distortion.

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

    PubMed

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

    2015-02-18

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

  8. 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

    2015-12-09

    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.

  9. 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

  10. 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.

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

    PubMed

    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. Using directed phylogenetic networks to retrace species dispersal history.

    PubMed

    Layeghifard, Mehdi; Peres-Neto, Pedro R; Makarenkov, Vladimir

    2012-07-01

    Methods designed for inferring phylogenetic trees have been widely applied to reconstruct biogeographic history. Because traditional phylogenetic methods used in biogeographic reconstruction are based on trees rather than networks, they follow the strict assumption in which dispersal among geographical units have occurred on the basis of single dispersal routes across regions and are, therefore, incapable of modelling multiple alternative dispersal scenarios. The goal of this study is to describe a new method that allows for retracing species dispersal by means of directed phylogenetic networks obtained using a horizontal gene transfer (HGT) detection method as well as to draw parallels between the processes of HGT and biogeographic reconstruction. In our case study, we reconstructed the biogeographic history of the postglacial dispersal of freshwater fishes in the Ontario province of Canada. This case study demonstrated the utility and robustness of the new method, indicating that the most important events were south-to-north dispersal patterns, as one would expect, with secondary faunal interchange among regions. Finally, we showed how our method can be used to explore additional questions regarding the commonalities in dispersal history patterns and phylogenetic similarities among species.

  13. Reconstructing differentially co-expressed gene modules and regulatory networks of soybean cells

    PubMed Central

    2012-01-01

    Background Current experimental evidence indicates that functionally related genes show coordinated expression in order to perform their cellular functions. In this way, the cell transcriptional machinery can respond optimally to internal or external stimuli. This provides a research opportunity to identify and study co-expressed gene modules whose transcription is controlled by shared gene regulatory networks. Results We developed and integrated a set of computational methods of differential gene expression analysis, gene clustering, gene network inference, gene function prediction, and DNA motif identification to automatically identify differentially co-expressed gene modules, reconstruct their regulatory networks, and validate their correctness. We tested the methods using microarray data derived from soybean cells grown under various stress conditions. Our methods were able to identify 42 coherent gene modules within which average gene expression correlation coefficients are greater than 0.8 and reconstruct their putative regulatory networks. A total of 32 modules and their regulatory networks were further validated by the coherence of predicted gene functions and the consistency of putative transcription factor binding motifs. Approximately half of the 32 modules were partially supported by the literature, which demonstrates that the bioinformatic methods used can help elucidate the molecular responses of soybean cells upon various environmental stresses. Conclusions The bioinformatics methods and genome-wide data sources for gene expression, clustering, regulation, and function analysis were integrated seamlessly into one modular protocol to systematically analyze and infer modules and networks from only differential expression genes in soybean cells grown under stress conditions. Our approach appears to effectively reduce the complexity of the problem, and is sufficiently robust and accurate to generate a rather complete and detailed view of putative soybean

  14. Mode control and direct modulation for waveguide-coupled square microcavity lasers

    NASA Astrophysics Data System (ADS)

    Yang, Yue-De; Xiao, Zhi-Xiong; Weng, Hai-Zhong; Xiao, Jin-Long; Huang, Yong-Zhen

    2016-11-01

    Lasing mode control and direct modulation characteristics have been investigated for waveguide-coupled unidirectional-emission square microcavity lasers. A quasi-analytical model is introduced to analyze the mode field distributions and quality (Q) factors for the confined modes inside the square optical microcavities with directly coupled waveguide, where high-Q whispering-gallery-like (WG-like) modes are induced by the mode coupling between doubly-degenerate modes. AlGaInAs/InP waveguide-coupled unidirectional-emission square microcavity lasers are fabricated by using standard planar technology, and electrically-injected lasing is realized at room temperature. The lasing modes are controlled by properly designing the lasing cavity, output waveguide and injection pattern. Dual-transverse-mode lasing with a tunable wavelength interval from 0.25 to 0.39 nm is realized by using a spatially selective current injection to modulate the refractive index, as the mode field distributions of different transverse are spatially separated. The wavelength interval can be further increased to a few nanometers by reducing the cavity size and replacing the flat sidewalls with circular arcs. The field distributions of WG-like modes distribute uniformly in square microcavity, which avoid the burning-induced carrier diffusion in high-speed direct modulation. A small-signal modulation 3dB bandwidth exceeding 16 GHz, and an open eye diagram at 25 Gb/s are demonstrated for the high-speed direct modulated square microcavity laser.

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

    PubMed

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

    2015-07-15

    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 β1 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-3β, which leads to the activation of CRMP2, promoting microtubule growth. At the cellular level, the absence of ERI species impairs Ca(2+)-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.

  16. 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

  17. Directly executable formal models of middleware for MANET and Cloud Networking and Computing

    NASA Astrophysics Data System (ADS)

    Pashchenko, D. V.; Sadeq Jaafar, Mustafa; Zinkin, S. A.; Trokoz, D. A.; Pashchenko, T. U.; Sinev, M. P.

    2016-04-01

    The article considers some “directly executable” formal models that are suitable for the specification of computing and networking in the cloud environment and other networks which are similar to wireless networks MANET. These models can be easily programmed and implemented on computer networks.

  18. 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

  19. A network-based phenotype mapping approach to identify genes that modulate drug response phenotypes

    PubMed Central

    Cairns, Junmei; Ung, Choong Yong; da Rocha, Edroaldo Lummertz; Zhang, Cheng; Correia, Cristina; Weinshilboum, Richard; Wang, Liewei; Li, Hu

    2016-01-01

    To better address the problem of drug resistance during cancer chemotherapy and explore the possibility of manipulating drug response phenotypes, we developed a network-based phenotype mapping approach (P-Map) to identify gene candidates that upon perturbed can alter sensitivity to drugs. We used basal transcriptomics data from a panel of human lymphoblastoid cell lines (LCL) to infer drug response networks (DRNs) that are responsible for conferring response phenotypes for anthracycline and taxane, two common anticancer agents use in clinics. We further tested selected gene candidates that interact with phenotypic differentially expressed genes (PDEGs), which are up-regulated genes in LCL for a given class of drug response phenotype in triple-negative breast cancer (TNBC) cells. Our results indicate that it is possible to manipulate a drug response phenotype, from resistant to sensitive or vice versa, by perturbing gene candidates in DRNs and suggest plausible mechanisms regulating directionality of drug response sensitivity. More important, the current work highlights a new way to formulate systems-based therapeutic design: supplementing therapeutics that aim to target disease culprits with phenotypic modulators capable of altering DRN properties with the goal to re-sensitize resistant phenotypes. PMID:27841317

  20. Pitx2 modulates a Tbx5-dependent gene regulatory network to maintain atrial rhythm

    PubMed Central

    Nadadur, Rangarajan D.; Broman, Michael T.; Boukens, Bastiaan; Mazurek, Stefan R.; Yang, Xinan; van den Boogaard, Malou; Bekeny, Jenna; Gadek, Margaret; Ward, Tarsha; Zhang, Min; Qiao, Yun; Martin, James F.; Seidman, Christine E.; Seidman, Jon; Christoffels, Vincent; Efimov, Igor R.; McNally, Elizabeth M.; Weber, Christopher R.; Moskowitz, Ivan P.

    2017-01-01

    Cardiac rhythm is extremely robust, generating 2 billion contraction cycles during the average human life span. Transcriptional control of cardiac rhythm is poorly understood. We found that removal of the transcription factor gene Tbx5 from the adult mouse caused primary spontaneous and sustained atrial fibrillation (AF). Atrial cardiomyocytes from the Tbx5-mutant mice exhibited action potential abnormalities, including spontaneous depolarizations, which were rescued by chelating free calcium. We identified a multitiered transcriptional network that linked seven previously defined AF risk loci: TBX5 directly activated PITX2, and TBX5 and PITX2 antagonistically regulated membrane effector genes Scn5a, Gja1, Ryr2, Dsp, and Atp2a2. In addition, reduced Tbx5 dose by adult-specific haploinsufficiency caused decreased target gene expression, myocardial automaticity, and AF inducibility, which were all rescued by Pitx2 haploinsufficiency in mice. These results defined a transcriptional architecture for atrial rhythm control organized as an incoherent feed-forward loop, driven by TBX5 and modulated by PITX2. TBX5/PITX2 interplay provides tight control of atrial rhythm effector gene expression, and perturbation of the co-regulated network caused AF susceptibility. This work provides a model for the molecular mechanisms underpinning the genetic implication of multiple AF genome-wide association studies loci and will contribute to future efforts to stratify patients for AF risk by genotype. PMID:27582060

  1. 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.

  2. Social network modulation of reward-related signals.

    PubMed

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

    2012-06-27

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

  3. 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

  4. Hierarchical surface code for network quantum computing with modules of arbitrary size

    NASA Astrophysics Data System (ADS)

    Li, Ying; Benjamin, Simon C.

    2016-10-01

    The network paradigm for quantum computing involves interconnecting many modules to form a scalable machine. Typically it is assumed that the links between modules are prone to noise while operations within modules have a significantly higher fidelity. To optimize fault tolerance in such architectures we introduce a hierarchical generalization of the surface code: a small "patch" of the code exists within each module and constitutes a single effective qubit of the logic-level surface code. Errors primarily occur in a two-dimensional subspace, i.e., patch perimeters extruded over time, and the resulting noise threshold for intermodule links can exceed ˜10 % even in the absence of purification. Increasing the number of qubits within each module decreases the number of qubits necessary for encoding a logical qubit. But this advantage is relatively modest, and broadly speaking, a "fine-grained" network of small modules containing only about eight qubits is competitive in total qubit count versus a "course" network with modules containing many hundreds of qubits.

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

    NASA Technical Reports Server (NTRS)

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

    1991-01-01

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

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

    PubMed

    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.

  7. 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.

  8. 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. E-mail: gelmini@physics.ucla.edu

    2015-08-01

    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.

  9. Picosecond optical pulse generation at gigahertz rates by direct modulation of a semiconductor laser

    NASA Technical Reports Server (NTRS)

    Auyeung, J.

    1981-01-01

    We report the generation of picosecond pulses by the direct modulation of a buried heterostructure GaAlAs diode laser. Pulse width of 28 ps is achieved at a repetition frequency of 2.5 GHz. Pulse width dependence on the experimental parameters is described.

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

    NASA Technical Reports Server (NTRS)

    Levitt, B. K.

    1980-01-01

    The processing gain of a direct sequence spread spectrum system is approximately the ratio of the spreading code chip rate to the data rate. This paper provides a more accurate understanding of the performance of such systems as a function of the modulation scheme and jammer characteristics.

  11. Mapping the Structure of Directed Networks: Beyond the Bow-Tie Diagram

    NASA Astrophysics Data System (ADS)

    Timár, G.; Goltsev, A. V.; Dorogovtsev, S. N.; Mendes, J. F. F.

    2017-02-01

    We reveal a hierarchical, multilayer organization of finite components—i.e., tendrils and tubes—around the giant connected components in directed networks and propose efficient algorithms allowing one to uncover the entire organization of key real-world directed networks, such as the World Wide Web, the neural network of Caenorhabditis elegans, and others. With increasing damage, the giant components decrease in size while the number and size of tendril layers increase, enhancing the susceptibility of the networks to damage.

  12. 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.

  13. Deep brain stimulation mechanisms: the control of network activity via neurochemistry modulation.

    PubMed

    McIntyre, Cameron C; Anderson, Ross W

    2016-10-01

    Deep brain stimulation (DBS) has revolutionized the clinical care of late-stage Parkinson's disease and shows promise for improving the treatment of intractable neuropsychiatric disorders. However, after over 25 years of clinical experience, numerous questions still remain on the neurophysiological basis for the therapeutic mechanisms of action. At their fundamental core, the general purpose of electrical stimulation therapies in the nervous system are to use the applied electric field to manipulate the opening and closing of voltage-gated sodium channels on neurons, generate stimulation induced action potentials, and subsequently, control the release of neurotransmitters in targeted pathways. Historically, DBS mechanisms research has focused on characterizing the effects of stimulation on neurons and the resulting impact on neuronal network activity. However, when electrodes are placed within the central nervous system, glia are also being directly (and indirectly) influenced by the stimulation. Mounting evidence shows that non-neuronal tissue can play an important role in modulating the neurochemistry changes induced by DBS. The goal of this review is to evaluate how DBS effects on both neuronal and non-neuronal tissue can potentially work together to suppress oscillatory activity (and/or information transfer) between brain regions. These resulting effects of ~ 100 Hz electrical stimulation help explain how DBS can disrupt pathological network activity in the brain and generate therapeutic effects in patients. Deep brain stimulation is an effective clinical technology, but detailed therapeutic mechanisms remain undefined. This review provides an overview of the leading hypotheses, which focus on stimulation-induced disruption of network oscillations and integrates possible roles for non-neuronal tissue in explaining the clinical response to therapeutic stimulation. This article is part of a special issue on Parkinson disease.

  14. Altered directional connectivity between emotion network and motor network in Parkinson's disease with depression.

    PubMed

    Liang, Peipeng; Deshpande, Gopikrishna; Zhao, Sinan; Liu, Jiangtao; Hu, Xiaoping; Li, Kuncheng

    2016-07-01

    Depression is common in patients with Parkinson's disease (PD), which can make all the other symptoms of PD much worse. It is thus urgent to differentiate depressed PD (DPD) patients from non-depressed PD (NDPD).The purpose of the present study was to characterize alterations in directional brain connectivity unique to Parkinson's disease with depression, using resting state functional magnetic resonance imaging (rs-fMRI).Sixteen DPD patients, 20 NDPD patients, 17 patients with major depressive disorder (MDD) and 21 healthy control subjects (normal controls [NC]) underwent structural MRI and rs-fMRI scanning. Voxel-based morphometry and directional brain connectivity during resting-state were analyzed. Analysis of variance (ANOVA) and 2-sample t tests were used to compare each pair of groups, using sex, age, education level, structural atrophy, and/or HAMD, unified PD rating scale (UPDRS) as covariates.In contrast to NC, DPD showed significant gray matter (GM) volume abnormalities in some mid-line limbic regions including dorsomedial prefrontal cortex and precuneus, and sub-cortical regions including caudate and cerebellum. Relative to NC and MDD, both DPD and NDPD showed significantly increased directional connectivity from bilateral anterior insula and posterior orbitofrontal cortices to left inferior temporal cortex. As compared with NC, MDD and NDPD, alterations of directional connectivity in DPD were specifically observed in the pathway from bilateral anterior insula and posterior orbitofrontal cortices to right basal ganglia.Resting state directional connectivity alterations were observed between emotion network and motor network in DPD patients after controlling for age, sex, structural atrophy. Given that these alterations are unique to DPD, it may provide a potential differential biomarker for distinguishing DPD from NC, NDPD, and MDD.

  15. Altered directional connectivity between emotion network and motor network in Parkinson's disease with depression

    PubMed Central

    Liang, Peipeng; Deshpande, Gopikrishna; Zhao, Sinan; Liu, Jiangtao; Hu, Xiaoping; Li, Kuncheng

    2016-01-01

    Abstract Depression is common in patients with Parkinson's disease (PD), which can make all the other symptoms of PD much worse. It is thus urgent to differentiate depressed PD (DPD) patients from non-depressed PD (NDPD). The purpose of the present study was to characterize alterations in directional brain connectivity unique to Parkinson's disease with depression, using resting state functional magnetic resonance imaging (rs-fMRI). Sixteen DPD patients, 20 NDPD patients, 17 patients with major depressive disorder (MDD) and 21 healthy control subjects (normal controls [NC]) underwent structural MRI and rs-fMRI scanning. Voxel-based morphometry and directional brain connectivity during resting-state were analyzed. Analysis of variance (ANOVA) and 2-sample t tests were used to compare each pair of groups, using sex, age, education level, structural atrophy, and/or HAMD, unified PD rating scale (UPDRS) as covariates. In contrast to NC, DPD showed significant gray matter (GM) volume abnormalities in some mid-line limbic regions including dorsomedial prefrontal cortex and precuneus, and sub-cortical regions including caudate and cerebellum. Relative to NC and MDD, both DPD and NDPD showed significantly increased directional connectivity from bilateral anterior insula and posterior orbitofrontal cortices to left inferior temporal cortex. As compared with NC, MDD and NDPD, alterations of directional connectivity in DPD were specifically observed in the pathway from bilateral anterior insula and posterior orbitofrontal cortices to right basal ganglia. Resting state directional connectivity alterations were observed between emotion network and motor network in DPD patients after controlling for age, sex, structural atrophy. Given that these alterations are unique to DPD, it may provide a potential differential biomarker for distinguishing DPD from NC, NDPD, and MDD. PMID:27472694

  16. Direct Fabrication of 3D Metallic Networks and Their Performance.

    PubMed

    Ron, Racheli; Gachet, David; Rechav, Katya; Salomon, Adi

    2017-02-01

    Fabrication of macroscopic nanoporous metallic networks is challenging, because it demands fine structures at the nanoscale over a large-scale. A technique to form pure scalable networks is introduced. The networked-metals ("Netals") exhibit a strong interaction with light and indicate a large fraction of hot-electrons generation. These hot-electrons are available to derive photocatalytic processes.

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

    PubMed

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

    2016-02-24

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

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

    PubMed Central

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

    2016-01-01

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

  19. Modulating the Precision of Recurrent Bursts in Cultured Neural Networks

    NASA Astrophysics Data System (ADS)

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

    2012-03-01

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

  20. 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.

  1. 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.

  2. Specific directions of ultrasound propagation in double potassium tungstates for light modulation.

    PubMed

    Mazur, M M; Mazur, L I; Pozhar, V E

    2017-01-01

    Acousto-optical characteristics of double potassium tungstates are analyzed and specific directions for light modulation are found. First, an important subgroup of elasto-optic coefficients of KYb(WO4)2 and KLu(WO4)2 crystals are calculated with use of experimental data. It is revealed that with proper choice of ultrasound direction the acousto-optical figure-of-merit approximately 2 times exceeds the maximum value detected in previous experiments. Another unique direction is determined, which permits modulation of randomly polarized light. The elasto-optic characteristics of KYb(WO4)2 and KLu(WO4)2 crystals are compared to those of previously investigated materials of the same crystal group: KY(WO4)2, KGd(WO4)2.

  3. Reduced activity in functional networks during reward processing is modulated by abstinence in cocaine addicts.

    PubMed

    Costumero, Víctor; Bustamante, Juan Carlos; Rosell-Negre, Patricia; Fuentes, Paola; Llopis, Juan José; Ávila, César; Barrós-Loscertales, Alfonso

    2017-03-01

    Cocaine addiction is characterized by alterations in motivational and cognitive processes. Recent studies have shown that some alterations present in cocaine users may be related to the activity of large functional networks. The aim of this study was to investigate how these functional networks are modulated by non-drug rewarding stimuli in cocaine-dependent individuals. Twenty abstinent cocaine-dependent and 21 healthy matched male controls viewed erotic and neutral pictures while undergoing a functional magnetic resonance imaging scan. Group independent component analysis was then performed in order to investigate how functional networks were modulated by reward in cocaine addicts. The results showed that cocaine addicts, compared with healthy controls, displayed diminished modulation of the left frontoparietal network in response to erotic pictures, specifically when they were unpredicted. Additionally, a positive correlation between the length of cocaine abstinence and the modulation of the left frontoparietal network by unpredicted erotic images was found. In agreement with current addiction models, our results suggest that cocaine addiction contributes to reduce sensitivity to rewarding stimuli and that abstinence may mitigate this effect.

  4. Combining sequence and Gene Ontology for protein module detection in the Weighted Network.

    PubMed

    Yu, Yang; Liu, Jie; Feng, Nuan; Song, Bo; Zheng, Zeyu

    2017-01-07

    Studies of protein modules in a Protein-Protein Interaction (PPI) network contribute greatly to the understanding of biological mechanisms. With the development of computing science, computational approaches have played an important role in locating protein modules. In this paper, a new approach combining Gene Ontology and amino acid background frequency is introduced to detect the protein modules in the weighted PPI networks. The proposed approach mainly consists of three parts: the feature extraction, the weighted graph construction and the protein complex detection. Firstly, the topology-sequence information is utilized to present the feature of protein complex. Secondly, six types of the weighed graph are constructed by combining PPI network and Gene Ontology information. Lastly, protein complex algorithm is applied to the weighted graph, which locates the clusters based on three conditions, including density, network diameter and the included angle cosine. Experiments have been conducted on two protein complex benchmark sets for yeast and the results show that the approach is more effective compared to five typical algorithms with the performance of f-measure and precision. The combination of protein interaction network with sequence and gene ontology data is helpful to improve the performance and provide a optional method for protein module detection.

  5. Combining Sequence and Gene Ontology for Protein Module Detection in the Weighted Network.

    PubMed

    Yu, Yang; Liu, Jie; Feng, Nuan; Song, Bo; Zheng, Zeyu

    2016-10-29

    Studies of protein modules in a Protein-Protein Interaction (PPI) network contribute greatly to the understanding of biological mechanisms. With the development of computing science, computational approaches have played an important role in locating protein modules. In this paper, a new approach combining Gene Ontology and amino acid background frequency is introduced to detect the protein modules in the weighted PPI networks. The proposed approach mainly consists of three parts: the feature extraction, the weighted graph construction and the protein complex detection. Firstly, the topology-sequence information is utilized to present the feature of protein complex. Secondly, six types of the weighed graph are constructed by combining PPI network and Gene Ontology information. Lastly, protein complex algorithm is applied to the weighted graph, which locates the clusters based on three conditions, including density, network diameter and the included angle cosine. Experiments have been conducted on two protein complex benchmark sets for yeast and the results show that the approach is more effective compared to five typical algorithms with the performance of f-measure and precision. The combination of protein interaction network with sequence and gene ontology data is helpful to improve the performance and provide a optional method for protein module detection.

  6. The Limbic-Prefrontal Network Modulated by Electroacupuncture at CV4 and CV12

    PubMed Central

    Fang, Jiliang; Wang, Xiaoling; Liu, Hesheng; Wang, Yin; Zhou, Kehua; Hong, Yang; Liu, Jun; Wang, Lei; Xue, Chao; Song, Ming; Liu, Baoyan; Zhu, Bing

    2012-01-01

    fMRI studies showed that acupuncture could induce hemodynamic changes in brain networks. Many of these studies focused on whether specific acupoints could activate specific brain regions and were often limited to manual acupuncture at acupoints on the limbs. In this fMRI study, we investigated acupuncture's modulation effects on brain functional networks by electroacupuncture (EA) at acupoints on the midline of abdomen. Acupoints Guanyuan (CV4) and Zhongwan (CV12) were stimulated in 21 healthy volunteers. The needling sensations, brain activation, and functional connectivity were studied. We found that the limbic-prefrontal functional network was deactivated by EA at CV4 and CV12. More importantly, the local functional connectivity was significantly changed during EA stimulation, and the change persisted during the period after the stimulation. Although minor differences existed, both acupoints similarly modulated the limbic-prefrontal functional network, which is overlapped with the functional circuits associated with emotional and cognitive regulation. PMID:22291848

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

    PubMed

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

    2004-01-01

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

  8. 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

  9. An intensity modulation and coherent balanced detection intersatellite microwave photonic link using polarization direction control

    NASA Astrophysics Data System (ADS)

    Li, Xuan; Zhu, Zihang; Zhao, Shanghong; Li, Yongjun; Han, Lei; Zhao, Jing

    2014-03-01

    A simple approach for high loss intersatellite microwave photonic link with intensity modulation and coherent balanced detection is proposed. In the transmitter, the double sideband-suppressed carrier (DSB-SC) modulated optical signal and optical carrier (OC) are combined by employing a polarization combiner to chose and control the signals polarization directions, while in the receiver, they are selected respectively by using a polarization splitter for they have orthogonal polarization directions. The separated DSB-SC signal and OC put into balanced detectors and the coherent detection is realized without a local oscillator (LO). At the output, the fundamental signal is augmented and the third-order distortion is suppressed for the DSB-SC modulation, the second-order distortion is removed for the balanced detection and the noise is reduced for the polarization direction control. The signal to noise and distortion ratio (SNDR) can be optimized by adjusting the power of OC and modulation index. The simulation results show that, a SNDR higher than 30 dB can be obtained for the proposed method, which is in agreement with the theoretical analysis.

  10. 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.

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

    DOEpatents

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

    2010-02-09

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

  12. 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.

  13. Additive Functions in Boolean Models of Gene Regulatory Network Modules

    PubMed Central

    Darabos, Christian; Di Cunto, Ferdinando; Tomassini, Marco; Moore, Jason H.; Provero, Paolo; Giacobini, Mario

    2011-01-01

    Gene-on-gene regulations are key components of every living organism. Dynamical abstract models of genetic regulatory networks help explain the genome's evolvability and robustness. These properties can be attributed to the structural topology of the graph formed by genes, as vertices, and regulatory interactions, as edges. Moreover, the actual gene interaction of each gene is believed to play a key role in the stability of the structure. With advances in biology, some effort was deployed to develop update functions in Boolean models that include recent knowledge. We combine real-life gene interaction networks with novel update functions in a Boolean model. We use two sub-networks of biological organisms, the yeast cell-cycle and the mouse embryonic stem cell, as topological support for our system. On these structures, we substitute the original random update functions by a novel threshold-based dynamic function in which the promoting and repressing effect of each interaction is considered. We use a third real-life regulatory network, along with its inferred Boolean update functions to validate the proposed update function. Results of this validation hint to increased biological plausibility of the threshold-based function. To investigate the dynamical behavior of this new model, we visualized the phase transition between order and chaos into the critical regime using Derrida plots. We complement the qualitative nature of Derrida plots with an alternative measure, the criticality distance, that also allows to discriminate between regimes in a quantitative way. Simulation on both real-life genetic regulatory networks show that there exists a set of parameters that allows the systems to operate in the critical region. This new model includes experimentally derived biological information and recent discoveries, which makes it potentially useful to guide experimental research. The update function confers additional realism to the model, while reducing the complexity

  14. Additive functions in boolean models of gene regulatory network modules.

    PubMed

    Darabos, Christian; Di Cunto, Ferdinando; Tomassini, Marco; Moore, Jason H; Provero, Paolo; Giacobini, Mario

    2011-01-01

    Gene-on-gene regulations are key components of every living organism. Dynamical abstract models of genetic regulatory networks help explain the genome's evolvability and robustness. These properties can be attributed to the structural topology of the graph formed by genes, as vertices, and regulatory interactions, as edges. Moreover, the actual gene interaction of each gene is believed to play a key role in the stability of the structure. With advances in biology, some effort was deployed to develop update functions in boolean models that include recent knowledge. We combine real-life gene interaction networks with novel update functions in a boolean model. We use two sub-networks of biological organisms, the yeast cell-cycle and the mouse embryonic stem cell, as topological support for our system. On these structures, we substitute the original random update functions by a novel threshold-based dynamic function in which the promoting and repressing effect of each interaction is considered. We use a third real-life regulatory network, along with its inferred boolean update functions to validate the proposed update function. Results of this validation hint to increased biological plausibility of the threshold-based function. To investigate the dynamical behavior of this new model, we visualized the phase transition between order and chaos into the critical regime using Derrida plots. We complement the qualitative nature of Derrida plots with an alternative measure, the criticality distance, that also allows to discriminate between regimes in a quantitative way. Simulation on both real-life genetic regulatory networks show that there exists a set of parameters that allows the systems to operate in the critical region. This new model includes experimentally derived biological information and recent discoveries, which makes it potentially useful to guide experimental research. The update function confers additional realism to the model, while reducing the complexity

  15. Fuzzy Logic Module of Convolutional Neural Network for Handwritten Digits Recognition

    NASA Astrophysics Data System (ADS)

    Popko, E. A.; Weinstein, I. A.

    2016-08-01

    Optical character recognition is one of the important issues in the field of pattern recognition. This paper presents a method for recognizing handwritten digits based on the modeling of convolutional neural network. The integrated fuzzy logic module based on a structural approach was developed. Used system architecture adjusted the output of the neural network to improve quality of symbol identification. It was shown that proposed algorithm was flexible and high recognition rate of 99.23% was achieved.

  16. Modulator and VCSEL-MSM smart pixels for parallel pipeline networking and signal processing

    NASA Astrophysics Data System (ADS)

    Chen, C.-H.; Hoanca, Bogdan; Kuznia, C. B.; Pansatiankul, Dhawat E.; Zhang, Liping; Sawchuk, Alexander A.

    1999-07-01

    TRANslucent Smart Pixel Array (TRANSPAR) systems perform high performance parallel pipeline networking and signal processing based on optical propagation of 3D data packets. The TRANSPAR smart pixel devices use either self-electro- optic effect GaAs multiple quantum well modulators or CMOS- VCSEL-MSM (CMOS-Vertical Cavity Surface Emitting Laser- Metal-Semiconductor-Metal) technology. The data packets transfer among high throughput photonic network nodes using multiple access/collision detection or token-ring protocols.

  17. Modulation of Rhythmic Activity in Mammalian Spinal Networks Is Dependent on Excitability State

    PubMed Central

    2017-01-01

    Neuromodulators play an important role in activating rhythmically active motor networks; however, what remains unclear are the network interactions whereby neuromodulators recruit spinal motor networks to produce rhythmic activity. Evidence from invertebrate systems has demonstrated that the effect of neuromodulators depends on the pre-existing state of the network. We explored how network excitation state affects the ability of dopamine to evoke rhythmic locomotor activity in the neonatal mouse isolated spinal cord. We found that dopamine can evoke unique patterns of motor activity that are dependent on the excitability state of motor networks. Different patterns of motor activity ranging from tonic, nonrhythmic activity to multirhythmic, nonlocomotor activity to locomotor activity were produced by altering global motor network excitability through manipulations of the extracellular potassium and bath NMDA concentration. A similar effect was observed when network excitation was manipulated during an unstable multirhythm evoked by a low concentration (15 µm) of 5-HT, suggesting that our results are not neuromodulator specific. Our data show in vertebrate systems that modulation is a two-way street and that modulatory actions are largely influenced by the network state. The level of network excitation can account for variability between preparations and is an additional factor to be considered when circuit elements are removed from the network. PMID:28144626

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

    PubMed

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

    2014-06-16

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

  20. CHIMERA: Top-down model for hierarchical, overlapping and directed cluster structures in directed and weighted complex networks

    NASA Astrophysics Data System (ADS)

    Franke, R.

    2016-11-01

    In many networks discovered in biology, medicine, neuroscience and other disciplines special properties like a certain degree distribution and hierarchical cluster structure (also called communities) can be observed as general organizing principles. Detecting the cluster structure of an unknown network promises to identify functional subdivisions, hierarchy and interactions on a mesoscale. It is not trivial choosing an appropriate detection algorithm because there are multiple network, cluster and algorithmic properties to be considered. Edges can be weighted and/or directed, clusters overlap or build a hierarchy in several ways. Algorithms differ not only in runtime, memory requirements but also in allowed network and cluster properties. They are based on a specific definition of what a cluster is, too. On the one hand, a comprehensive network creation model is needed to build a large variety of benchmark networks with different reasonable structures to compare algorithms. On the other hand, if a cluster structure is already known, it is desirable to separate effects of this structure from other network properties. This can be done with null model networks that mimic an observed cluster structure to improve statistics on other network features. A third important application is the general study of properties in networks with different cluster structures, possibly evolving over time. Currently there are good benchmark and creation models available. But what is left is a precise sandbox model to build hierarchical, overlapping and directed clusters for undirected or directed, binary or weighted complex random networks on basis of a sophisticated blueprint. This gap shall be closed by the model CHIMERA (Cluster Hierarchy Interconnection Model for Evaluation, Research and Analysis) which will be introduced and described here for the first time.

  1. 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.

  2. 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.

  3. Expectancy constraints in degraded speech modulate the language comprehension network.

    PubMed

    Obleser, Jonas; Kotz, Sonja A

    2010-03-01

    In speech comprehension, the processing of auditory information and linguistic context are mutually dependent. This functional magnetic resonance imaging study examines how semantic expectancy ("cloze probability") in variably intelligible sentences ("noise vocoding") modulates the brain bases of comprehension. First, intelligibility-modulated activation along the superior temporal sulci (STS) was extended anteriorly and posteriorly in low-cloze sentences (e.g., "she weighs the flour") but restricted to a mid-superior temporal gyrus/STS area in more predictable high-cloze sentences (e.g., "she sifts the flour"). Second, the degree of left inferior frontal gyrus (IFG) (Brodmann's area 44) involvement in processing low-cloze constructions was proportional to increasing intelligibility. Left inferior parietal cortex (IPC; angular gyrus) activation accompanied successful speech comprehension that derived either from increased signal quality or from semantic facilitation. The results show that successful decoding of speech in auditory cortex areas regulates language-specific computation (left IFG and IPC). In return, semantic expectancy can constrain these speech-decoding processes, with fewer neural resources being allocated to highly predictable sentences. These findings offer an important contribution toward the understanding of the functional neuroanatomy in speech comprehension.

  4. 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

  5. Direct sensorimotor corticospinal modulation of dorsal horn neuronal C-fiber responses in the rat.

    PubMed

    Rojas-Piloni, Gerardo; Martínez-Lorenzana, Guadalupe; Condés-Lara, Miguel; Rodríguez-Jiménez, Javier

    2010-09-10

    Clinically, the stimulation of motor cortical areas has been used to alleviate certain pain conditions. However, the attempts to understand the mechanisms of cortical nociceptive modulation at the spinal cord level have yielded controversial results. The objectives of the present work were to: 1) determine the effects of activating and suppressing the activity of sensorimotor cortical neurons on the nociceptive electrophysiological responses of the segmental C-fibers, and 2) evaluate the contribution of direct and indirect corticospinal projections in segmental nociceptive modulation. By means of a bipolar matrix of stimulation electrodes we mapped the stimulation of cortical areas that modulate C-fiber evoked field potentials in the dorsal horn. In addition, suppressing the cortical activity by means of cortical spreading depression, we observed that the C-fiber evoked field potentials in the dorsal horn are facilitated when cortical activity is suppressed specifically in sensorimotor cortex. Moreover, the C-fiber evoked field potentials were inhibited during spontaneous activation of cortical projecting neurons. Furthermore, after a lesion of the pyramidal tract contralateral to the spinal cord recording sites, the cortical action was suppressed. Our results show that corticospinal tract fibers arising from the sensorimotor cortex modulate directly the nociceptive C-fiber evoked responses of the dorsal horn.

  6. 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

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

    SciTech Connect

    Nobile, Eugenio Del; Gelmini, Graciela B.; Witte, Samuel J. E-mail: gelmini@physics.ucla.edu

    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 E{sub R} 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 E{sub R} to v{sub min}, the minimum speed a dark matter particle must have to impart a fixed E{sub R} 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 v{sub min} 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.

  8. PDM-16QAM vector signal generation and detection based on intensity modulation and direct detection

    NASA Astrophysics Data System (ADS)

    Chen, Long; Yu, Jianjun; Li, Xinying

    2016-07-01

    We experimentally demonstrate a novel and simple method to generate and detect high speed polarization-division-multiplexing 16-ary quadrature-amplitude-modulation (PDM-16QAM) vector signal enabled by Mach-Zehnder modulator-based (MZM-based) optical-carrier-suppression (OCS) intensity modulation and direct detection. Due to the adoption of OCS intensity modulation, carrier beating can be avoided at the receiver, and thus polarization de-multiplexing can be implemented by digital-signal-processing-based (DSP-based) cascaded multi-modulus algorithm (CMMA) equalization instead of a polarization tracking system. The change of both amplitude and phase information due to the adoption of OCS modulation can be equalized by DSP-based amplitude and phase precoding at the transmitter. Up to 64-Gb/s PDM-16QAM vector signal is generated and detected after 2-km single-mode fiber-28 (SMF-28) or 20-km large-effective-area fiber (LEAF) transmission with a bit-error-ratio (BER) less than the hard-decision forward-error-correction (HD-FEC) threshold of 3.8×10-3.

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

    PubMed

    Masulli, Paolo; Villa, Alessandro E P

    2016-01-01

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

  10. 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.

  11. 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

  12. Attentional load modulates large-scale functional brain connectivity beyond the core attention networks.

    PubMed

    Alnæs, Dag; Kaufmann, Tobias; Richard, Geneviève; Duff, Eugene P; Sneve, Markus H; Endestad, Tor; Nordvik, Jan Egil; Andreassen, Ole A; Smith, Stephen M; Westlye, Lars T

    2015-04-01

    In line with the notion of a continuously active and dynamic brain, functional networks identified during rest correspond with those revealed by task-fMRI. Characterizing the dynamic cross-talk between these network nodes is key to understanding the successful implementation of effortful cognitive processing in healthy individuals and its breakdown in a variety of conditions involving aberrant brain biology and cognitive dysfunction. We employed advanced network modeling on fMRI data collected during a task involving sustained attentive tracking of objects at two load levels and during rest. Using multivariate techniques, we demonstrate that attentional load levels can be significantly discriminated, and from a resting-state condition, the accuracy approaches 100%, by means of estimates of between-node functional connectivity. Several network edges were modulated during task engagement: The dorsal attention network increased connectivity with a visual node, while decreasing connectivity with motor and sensory nodes. Also, we observed a decoupling between left and right hemisphere dorsal visual streams. These results support the notion of dynamic network reconfigurations based on attentional effort. No simple correspondence between node signal amplitude change and node connectivity modulations was found, thus network modeling provides novel information beyond what is revealed by conventional task-fMRI analysis. The current decoding of attentional states confirms that edge connectivity contains highly predictive information about the mental state of the individual, and the approach shows promise for the utilization in clinical contexts.

  13. Simplified polarization demultiplexing based on Stokes vector analysis for intensity-modulation direct-detection systems

    NASA Astrophysics Data System (ADS)

    Zhou, Xinyu; Yan, Lianshan; Chen, Zhiyu; Yi, Anlin; Pan, Yan; Jiang, Lin; Pan, Wei; Luo, Bin

    2016-10-01

    A simple and effective polarization demultiplexing method is proposed based on the improved Stokes vector analysis and digital signal processor algorithm for the intensity-modulation direct-detection optical communication systems. Such a scheme could significantly simplify optical receivers with low system cost. The experimental results demonstrate the feasibility of our proposed method and show that only 1- and 1.7-dB power penalties are measured for 10- and 25-km transmissions compared to back-to-back case.

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

    SciTech Connect

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

    2012-08-15

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

  15. 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.

  16. Ethanol modulation of gene networks: implications for alcoholism.

    PubMed

    Farris, Sean P; Miles, Michael F

    2012-01-01

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

  17. Using the Amino Acid Network to Modulate the Hydrolytic Activity of β-Glycosidases

    PubMed Central

    Souza, Diorge P.; Souza, Valquiria P.; Ikegami, Cecilia M.; Farah, Chuck S.; Marana, Sandro R.

    2016-01-01

    The active site residues in GH1 β-glycosidases are compartmentalized into 3 functional regions, involved in catalysis or binding of glycone and aglycone motifs from substrate. However, it still remains unclear how residues outside the active site modulate the enzymatic activity. To tackle this question, we solved the crystal structure of the GH1 β-glycosidase from Spodoptera frugiperda (Sfβgly) to systematically map its residue contact network and correlate effects of mutations within and outside the active site. External mutations neighbouring the functional residues involved in catalysis and glycone-binding are deleterious, whereas mutations neighbouring the aglycone-binding site are less detrimental or even beneficial. The large dataset of new and previously characterized Sfβgly mutants supports that external perturbations are coherently transmitted to active site residues possibly through contacts and specifically disturb functional regions they interact to, reproducing the effects observed for direct mutations of functional residues. This allowed us to suggest that positions related to the aglycone-binding site are preferential targets for introduction of mutations aiming to further improve the hydrolytic activity of β–glycosidases. PMID:27936116

  18. 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.

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

    NASA Astrophysics Data System (ADS)

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

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

  20. Shaping Embodied Neural Networks for Adaptive Goal-directed Behavior

    PubMed Central

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

    2008-01-01

    The acts of learning and memory are thought to emerge from the modifications of synaptic connections between neurons, as guided by sensory feedback during behavior. However, much is unknown about how such synaptic processes can sculpt and are sculpted by neuronal population dynamics and an interaction with the environment. Here, we embodied a simulated network, inspired by dissociated cortical neuronal cultures, with an artificial animal (an animat) through a sensory-motor loop consisting of structured stimuli, detailed activity metrics incorporating spatial information, and an adaptive training algorithm that takes advantage of spike timing dependent plasticity. By using our design, we demonstrated that the network was capable of learning associations between multiple sensory inputs and motor outputs, and the animat was able to adapt to a new sensory mapping to restore its goal behavior: move toward and stay within a user-defined area. We further showed that successful learning required proper selections of stimuli to encode sensory inputs and a variety of training stimuli with adaptive selection contingent on the animat's behavior. We also found that an individual network had the flexibility to achieve different multi-task goals, and the same goal behavior could be exhibited with different sets of network synaptic strengths. While lacking the characteristic layered structure of in vivo cortical tissue, the biologically inspired simulated networks could tune their activity in behaviorally relevant manners, demonstrating that leaky integrate-and-fire neural networks have an innate ability to process information. This closed-loop hybrid system is a useful tool to study the network properties intermediating synaptic plasticity and behavioral adaptation. The training algorithm provides a stepping stone towards designing future control systems, whether with artificial neural networks or biological animats themselves. PMID:18369432

  1. 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.

  2. 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

  3. 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.

  4. Dopamine modulation of transient potassium current evokes phase shifts in a central pattern generator network.

    PubMed

    Harris-Warrick, R M; Coniglio, L M; Barazangi, N; Guckenheimer, J; Gueron, S

    1995-01-01

    Bath application of dopamine modifies the rhythmic motor pattern generated by the 14 neuron pyloric network in the stomatogastric ganglion of the spiny lobster, Panulirus interruptus. Among other effects, dopamine excites many of the pyloric constrictor (PY) neurons to fire at high frequency and phase-advances the timing of their activity in the motor pattern. These responses arise in part from direct actions of dopamine to modulate the intrinsic electrophysiological properties of the PY cells, and can be studied in synaptically isolated neurons. The rate of rebound following a hyperpolarizing prestep and the spike frequency during a subsequent depolarization are both accelerated by dopamine. Based on theoretical simulations, Hartline (1979) suggested that the rate of postinhibitory rebound in stomatogastric neurons could vary with the amount of voltage-sensitive transient potassium current (IA). Consistent with this prediction, we found that dopamine evokes a net conductance decrease in synaptically isolated PY neurons. In voltage clamp, dopamine reduces IA, specifically by reducing the amplitude of the slowly inactivating component of the current and shifting its voltage activation curve in the depolarized direction. 4-Aminopyridine, a selective blocker of IA in stomatogastric neurons, mimics and occludes the effects of dopamine on isolated PY neurons. A conductance-based mathematical model of the PY neuron shows appropriate changes in activity upon quantitative modification of the IA parameters affected by dopamine. These results demonstrate that dopamine excites and phase-advances the PY neurons in the rhythmic pyloric motor pattern at least in part by reducing the transient K+ current, IA.

  5. Different Current Intensities of Anodal Transcranial Direct Current Stimulation Do Not Differentially Modulate Motor Cortex Plasticity

    PubMed Central

    Kidgell, Dawson J.; Daly, Robin M.; Young, Kayleigh; Lum, Jarrod; Tooley, Gregory; Jaberzadeh, Shapour; Zoghi, Maryam; Pearce, Alan J.

    2013-01-01

    Transcranial direct current stimulation (tDCS) is a noninvasive technique that modulates the excitability of neurons within the motor cortex (M1). Although the aftereffects of anodal tDCS on modulating cortical excitability have been described, there is limited data describing the outcomes of different tDCS intensities on intracortical circuits. To further elucidate the mechanisms underlying the aftereffects of M1 excitability following anodal tDCS, we used transcranial magnetic stimulation (TMS) to examine the effect of different intensities on cortical excitability and short-interval intracortical inhibition (SICI). Using a randomized, counterbalanced, crossover design, with a one-week wash-out period, 14 participants (6 females and 8 males, 22–45 years) were exposed to 10 minutes of anodal tDCS at 0.8, 1.0, and 1.2 mA. TMS was used to measure M1 excitability and SICI of the contralateral wrist extensor muscle at baseline, immediately after and 15 and 30 minutes following cessation of anodal tDCS. Cortical excitability increased, whilst SICI was reduced at all time points following anodal tDCS. Interestingly, there were no differences between the three intensities of anodal tDCS on modulating cortical excitability or SICI. These results suggest that the aftereffect of anodal tDCS on facilitating cortical excitability is due to the modulation of synaptic mechanisms associated with long-term potentiation and is not influenced by different tDCS intensities. PMID:23577272

  6. Different current intensities of anodal transcranial direct current stimulation do not differentially modulate motor cortex plasticity.

    PubMed

    Kidgell, Dawson J; Daly, Robin M; Young, Kayleigh; Lum, Jarrod; Tooley, Gregory; Jaberzadeh, Shapour; Zoghi, Maryam; Pearce, Alan J

    2013-01-01

    Transcranial direct current stimulation (tDCS) is a noninvasive technique that modulates the excitability of neurons within the motor cortex (M1). Although the aftereffects of anodal tDCS on modulating cortical excitability have been described, there is limited data describing the outcomes of different tDCS intensities on intracortical circuits. To further elucidate the mechanisms underlying the aftereffects of M1 excitability following anodal tDCS, we used transcranial magnetic stimulation (TMS) to examine the effect of different intensities on cortical excitability and short-interval intracortical inhibition (SICI). Using a randomized, counterbalanced, crossover design, with a one-week wash-out period, 14 participants (6 females and 8 males, 22-45 years) were exposed to 10 minutes of anodal tDCS at 0.8, 1.0, and 1.2 mA. TMS was used to measure M1 excitability and SICI of the contralateral wrist extensor muscle at baseline, immediately after and 15 and 30 minutes following cessation of anodal tDCS. Cortical excitability increased, whilst SICI was reduced at all time points following anodal tDCS. Interestingly, there were no differences between the three intensities of anodal tDCS on modulating cortical excitability or SICI. These results suggest that the aftereffect of anodal tDCS on facilitating cortical excitability is due to the modulation of synaptic mechanisms associated with long-term potentiation and is not influenced by different tDCS intensities.

  7. 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

    2015-05-04

    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.

  8. The vector modulation method to make precise measurements with directional sensors

    NASA Astrophysics Data System (ADS)

    Zhao, Y. S.; Lin, Y. R.; Deng, Z. L.

    2007-01-01

    The best plan to curtail measurement errors is to modulate the input signal before it enters a sensor. As far as linear directional sensors are concerned, VMM (the vector modulation method) can make the earliest modulation and appropriate demodulation to curtail measurement errors and then improve the precision of measurement. According to the modulation-demodulation principle and the linear system theory, especially the frequency-remaining character and the superposition theorem of linear systems, a precise response to the input signal will be resolved by means of demodulation. VMM curtails the main elements of errors, including quantization error and bias of a measurement system, along with bias, drift, noise and disturbance of sensors. Experiments measuring ERR (the Earth's rate of rotation) are presented, and a design for an experiment measuring gravitational acceleration with VMM is presented. The preliminary experiments have given positive support. VMM, which can remarkably get rid of errors, is much clearer in theory and easier to implement in engineering practice.

  9. 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.

  10. Integrating multiple sensory systems to modulate neural networks controlling posture

    PubMed Central

    Gerasimenko, Y.; Burdick, J.; Zhong, H.; Roy, R. R.; Edgerton, V. R.

    2015-01-01

    In this study we investigated the ability of sensory input to produce tonic responses in hindlimb muscles to facilitate standing in adult spinal rats and tested two hypotheses: 1) whether the spinal neural networks below a complete spinal cord transection can produce tonic reactions by activating different sensory inputs and 2) whether facilitation of tonic and rhythmic responses via activation of afferents and with spinal cord stimulation could engage similar neuronal mechanisms. We used a dynamically controlled platform to generate vibration during weight bearing, epidural stimulation (at spinal cord level S1), and/or tail pinching to determine the postural control responses that can be generated by the lumbosacral spinal cord. We observed that a combination of platform displacement, epidural stimulation, and tail pinching produces a cumulative effect that progressively enhances tonic responses in the hindlimbs. Tonic responses produced by epidural stimulation alone during standing were represented mainly by monosynaptic responses, whereas the combination of epidural stimulation and tail pinching during standing or epidural stimulation during stepping on a treadmill facilitated bilaterally both monosynaptic and polysynaptic responses. The results demonstrate that tonic muscle activity after complete spinal cord injury can be facilitated by activation of specific combinations of afferent inputs associated with load-bearing proprioception and cutaneous input in the presence of epidural stimulation and indicate that whether activation of tonic or rhythmic responses is generated depends on the specific combinations of sources and types of afferents activated in the hindlimb muscles. PMID:26445868

  11. ABC and IFC: Modules Detection Method for PPI Network

    PubMed Central

    Lei, Xiujuan; Tian, Jianfang

    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

  12. Integrating multiple sensory systems to modulate neural networks controlling posture.

    PubMed

    Lavrov, I; Gerasimenko, Y; Burdick, J; Zhong, H; Roy, R R; Edgerton, V R

    2015-12-01

    In this study we investigated the ability of sensory input to produce tonic responses in hindlimb muscles to facilitate standing in adult spinal rats and tested two hypotheses: 1) whether the spinal neural networks below a complete spinal cord transection can produce tonic reactions by activating different sensory inputs and 2) whether facilitation of tonic and rhythmic responses via activation of afferents and with spinal cord stimulation could engage similar neuronal mechanisms. We used a dynamically controlled platform to generate vibration during weight bearing, epidural stimulation (at spinal cord level S1), and/or tail pinching to determine the postural control responses that can be generated by the lumbosacral spinal cord. We observed that a combination of platform displacement, epidural stimulation, and tail pinching produces a cumulative effect that progressively enhances tonic responses in the hindlimbs. Tonic responses produced by epidural stimulation alone during standing were represented mainly by monosynaptic responses, whereas the combination of epidural stimulation and tail pinching during standing or epidural stimulation during stepping on a treadmill facilitated bilaterally both monosynaptic and polysynaptic responses. The results demonstrate that tonic muscle activity after complete spinal cord injury can be facilitated by activation of specific combinations of afferent inputs associated with load-bearing proprioception and cutaneous input in the presence of epidural stimulation and indicate that whether activation of tonic or rhythmic responses is generated depends on the specific combinations of sources and types of afferents activated in the hindlimb muscles.

  13. General relationship of global topology, local dynamics, and directionality in large-scale brain networks.

    PubMed

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

    2015-04-01

    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.

  14. How to estimate the signs' configuration in the directed signed social networks?

    NASA Astrophysics Data System (ADS)

    Guo, Long; Gao, Fujuan; Jiang, Jian

    2017-02-01

    Inspired by the ensemble theory in statistical mechanics, we introduce a reshuffling approach to empirical analyze signs' configuration in the directed signed social networks of Epinions and Slashdots. In our reshuffling approach, each negative link has the reshuffling probability prs to exchange its sign with another positive link chosen randomly. Many reshuffled networks with different signs' configuration are built under different prss. For each reshuffled network, the entropies of the self social status are calculated and the opinion formation of the majority-rule model is analyzed. We find that Souts reach their own minimum values and the order parameter |m* | reaches its maximum value in the networks of Epinions and Slashdots without the reshuffling operation. Namely, individuals share the homogeneous properties of self social status and dynamic status in the real directed signed social networks. Our present work provides some interesting tools and perspective to understand the signs' configuration in signed social networks, especially in the online affiliation networks.

  15. 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.

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

    PubMed Central

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

    2010-01-01

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

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

    PubMed

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

    2014-10-01

    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.

  18. Current-mode implementation of processing modules in ART-based neural networks

    NASA Astrophysics Data System (ADS)

    Lopez-Alcantud, Jose-Alejandro; Hauer, Hans; Diaz-Madrid, Jose-Angel; Ruiz-Merino, Ramon

    2003-04-01

    This paper describes implementation of neural network processing layers using basic current-mode operating modules. The research work has been focused on the implementation of neural networks based on the Adaptive Resonance Theory, developed by S. Grossberg and G.A. Carpenter. The ART-based neural network whose operating modules have been choosen for development is the one called MART, proposed by F. Delgado, because of its complex architecture, auto--adaptive self-learning process, able to discard unmeaningful cathegories. Our presentation starts introducing the behaviour of MART with an analysis of its structure. The development described by this research work is focused on the monochannel block included in the main signal processing part of the MART neural network. The description of the computing algorithm of the layers inside a monochannel block are also provided in order to show what operational current-mode modules are needed (multiplier, divider, square-rooter, adder, substractor, absolute value, maximum and minimum evaluator...). Descriptions at schematic and layout levels of all the processing layers are given. All of them have been designed using AMS 0.35 micron technology with a supply voltage of 3.3 volts. The modules are designed to deal with input currents in the range of 20 to 50 microamps, showing a lineal behaviour and an output error of less than 10%, which is good enough for neural signal processing systems. The maximum frecuency of operation is around 200 kHz. Simulation results are included to show that the operation performed by the hardware designed matches the behaviour described by the MART neural network. For testing purposes we show the design of a monochannel block hardware implementation restricted to five inputs and three cathegories.

  19. Microwave sidebands for laser cooling by direct modulation of a tapered amplifier

    NASA Astrophysics Data System (ADS)

    Mahnke, J.; Kulas, S.; Geisel, I.; Jöllenbeck, S.; Ertmer, W.; Klempt, C.

    2013-06-01

    Laser cooling of atoms usually necessitates several laser frequencies. Alkaline atoms, for example, are cooled by two lasers with a frequency difference in the gigahertz range. This gap cannot be closed with simple shifting techniques. Here, we present a method of generating sidebands at 6.6 GHz by modulating the current of a tapered amplifier, which is seeded by an unmodulated master laser. The sidebands enable trapping of 1.1 × 109 87Rb atoms in a chip-based magneto-optical trap. Compared to the direct modulation of the master laser, this method allows for an easy implementation, a fast adjustment over a wide frequency range, and the simultaneous extraction of unmodulated light for manipulation and detection. The low power consumption, small size, and applicability for multiple frequencies benefit a wide range of applications reaching from atom-based mobile sensors to the laser cooling of molecules.

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-12-22

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

  2. Facial Sketch Synthesis Using Two-dimensional Direct Combined Model-based Face-Specific Markov Network.

    PubMed

    Tu, Ching-Ting; Chan, Yu-Hsien; Chen, Yi-Chung

    2016-05-20

    A facial sketch synthesis system is proposed featuring a two-dimensional direct combined model (2DDCM)-based facespecific Markov network. In contrast to existing facial sketch synthesis systems, the proposed scheme aims to synthesize sketches which reproduce the unique drawing style of a particular artist, where this drawing style is learned from a dataset consisting of a large number of image/sketch pairwise training samples. The synthesis system comprises three modules, namely a global module, a local module, and an enhancement module. The global module applies a 2DDCM approach to synthesize the global facial geometry and texture of the input image. The detailed texture is then added to the synthesized sketch in a local patch-based manner using a parametric 2DDCM model and a non-parametric Markov random field (MRF) network. Notably, the MRF approach gives the synthesized results an appearance more consistent with the drawing style of the training samples, while the 2DDCM approach enables the synthesis of outcomes with a more derivative style. As a result, the similarity between the synthesized sketches and the input images is greatly improved. Finally, a post-processing operation is performed to enhance the shadowed regions of the synthesized image by adding strong lines or curves to emphasize the lighting conditions. The experimental results confirm that the synthesized facial images are in good qualitative and quantitative agreement with the input images as well as the ground-truth sketches provided by the same artist. The representing power of the proposed framework is demonstrated by synthesizing facial sketches from input images with a wide variety of facial poses, lighting conditions, and races even when such images are not included in the training dataset. Moreover, the practical applicability of the proposed framework is demonstrated by means of automatic facial recognition tests.

  3. 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.

  4. 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.

  5. 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

  6. Functional module search in protein networks based on semantic similarity improves the analysis of proteomics data.

    PubMed

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

    2014-07-01

    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.

  7. EEG Oscillations Are Modulated in Different Behavior-Related Networks during Rhythmic Finger Movements.

    PubMed

    Seeber, Martin; Scherer, Reinhold; Müller-Putz, Gernot R

    2016-11-16

    Sequencing and timing of body movements are essential to perform motoric tasks. In this study, we investigate the temporal relation between cortical oscillations and human motor behavior (i.e., rhythmic finger movements). High-density EEG recordings were used for source imaging based on individual anatomy. We separated sustained and movement phase-related EEG source amplitudes based on the actual finger movements recorded by a data glove. Sustained amplitude modulations in the contralateral hand area show decrease for α (10-12 Hz) and β (18-24 Hz), but increase for high γ (60-80 Hz) frequencies during the entire movement period. Additionally, we found movement phase-related amplitudes, which resembled the flexion and extension sequence of the fingers. Especially for faster movement cadences, movement phase-related amplitudes included high β (24-30 Hz) frequencies in prefrontal areas. Interestingly, the spectral profiles and source patterns of movement phase-related amplitudes differed from sustained activities, suggesting that they represent different frequency-specific large-scale networks. First, networks were signified by the sustained element, which statically modulate their synchrony levels during continuous movements. These networks may upregulate neuronal excitability in brain regions specific to the limb, in this study the right hand area. Second, movement phase-related networks, which modulate their synchrony in relation to the movement sequence. We suggest that these frequency-specific networks are associated with distinct functions, including top-down control, sensorimotor prediction, and integration. The separation of different large-scale networks, we applied in this work, improves the interpretation of EEG sources in relation to human motor behavior.

  8. Selective attention modulates high-frequency activity in the face-processing network.

    PubMed

    Müsch, Kathrin; Hamamé, Carlos M; Perrone-Bertolotti, Marcela; Minotti, Lorella; Kahane, Philippe; Engel, Andreas K; Lachaux, Jean-Philippe; Schneider, Till R

    2014-11-01

    Face processing depends on the orchestrated activity of a large-scale neuronal network. Its activity can be modulated by attention as a function of task demands. However, it remains largely unknown whether voluntary, endogenous attention and reflexive, exogenous attention to facial expressions equally affect all regions of the face-processing network, and whether such effects primarily modify the strength of the neuronal response, the latency, the duration, or the spectral characteristics. We exploited the good temporal and spatial resolution of intracranial electroencephalography (iEEG) and recorded from depth electrodes to uncover the fast dynamics of emotional face processing. We investigated frequency-specific responses and event-related potentials (ERP) in the ventral occipito-temporal cortex (VOTC), ventral temporal cortex (VTC), anterior insula, orbitofrontal cortex (OFC), and amygdala when facial expressions were task-relevant or task-irrelevant. All investigated regions of interest (ROI) were clearly modulated by task demands and exhibited stronger changes in stimulus-induced gamma band activity (50-150 Hz) when facial expressions were task-relevant. Observed latencies demonstrate that the activation is temporally coordinated across the network, rather than serially proceeding along a processing hierarchy. Early and sustained responses to task-relevant faces in VOTC and VTC corroborate their role for the core system of face processing, but they also occurred in the anterior insula. Strong attentional modulation in the OFC and amygdala (300 msec) suggests that the extended system of the face-processing network is only recruited if the task demands active face processing. Contrary to our expectation, we rarely observed differences between fearful and neutral faces. Our results demonstrate that activity in the face-processing network is susceptible to the deployment of selective attention. Moreover, we show that endogenous attention operates along the whole

  9. Acupuncture modulates resting state connectivity in default and sensorimotor brain networks.

    PubMed

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

    2008-06-01

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

  10. Modulation of temporally coherent brain networks estimated using ICA at rest and during cognitive tasks.

    PubMed

    Calhoun, Vince D; Kiehl, Kent A; Pearlson, Godfrey D

    2008-07-01

    Brain regions which exhibit temporally coherent fluctuations, have been increasingly studied using functional magnetic resonance imaging (fMRI). Such networks are often identified in the context of an fMRI scan collected during rest (and thus are called "resting state networks"); however, they are also present during (and modulated by) the performance of a cognitive task. In this article, we will refer to such networks as temporally coherent networks (TCNs). Although there is still some debate over the physiological source of these fluctuations, TCNs are being studied in a variety of ways. Recent studies have examined ways TCNs can be used to identify patterns associated with various brain disorders (e.g. schizophrenia, autism or Alzheimer's disease). Independent component analysis (ICA) is one method being used to identify TCNs. ICA is a data driven approach which is especially useful for decomposing activation during complex cognitive tasks where multiple operations occur simultaneously. In this article we review recent TCN studies with emphasis on those that use ICA. We also present new results showing that TCNs are robust, and can be consistently identified at rest and during performance of a cognitive task in healthy individuals and in patients with schizophrenia. In addition, multiple TCNs show temporal and spatial modulation during the cognitive task versus rest. In summary, TCNs show considerable promise as potential imaging biological markers of brain diseases, though each network needs to be studied in more detail.

  11. No Modulation of Visual Cortex Excitability by Transcranial Direct Current Stimulation.

    PubMed

    Brückner, Sabrina; Kammer, Thomas

    2016-01-01

    Measuring phosphene thresholds (PTs) is often used to investigate changes in the excitability of the human visual cortex through different brain stimulation methods like repetitive transcranial magnetic stimulation (rTMS) or transcranial direct current stimulation (tDCS). In several studies, PT increase or decrease has been shown after rTMS or tDCS application. Recently, using PT measurements we showed that the state of the neurons in the visual cortex after rTMS might have an influence on the modulatory effects of stimulation. In the present study we aimed to investigate whether visual cortex activity following stimulation influences the modulatory effects of tDCS as well. In a between-group design, anodal or cathodal tDCS was applied to the visual cortex twice per subject, with either high or low visual demand following stimulation. We observed no modulation of PT neither directly following both anodal and cathodal tDCS nor following the visual demand periods. We rather found high inter-individual variability in the response to tDCS, and intra-individual reliability in the direction of modulation was observed for cathodal tDCS only. Thus, our results do not confirm the modulatory effects of tDCS on visual cortex excitability published previously. Moreover, they support the confirmation that tDCS effects have little reliability on varied TMS outcome measurements.

  12. miR-25 modulates NSCLC cell radio-sensitivity through directly inhibiting BTG2 expression

    SciTech Connect

    He, Zhiwei Liu, Yi Xiao, Bing Qian, Xiaosen

    2015-02-13

    A large proportion of the NSCLC patients were insensitive to radiotherapy, but the exact mechanism is still unclear. This study explored the role of miR-25 in regulating sensitivity of NSCLC cells to ionizing radiation (IR) and its downstream targets. Based on measurement in tumor samples from NSCLC patients, this study found that miR-25 expression is upregulated in both NSCLC and radio-resistant NSCLC patients compared the healthy and radio-sensitive controls. In addition, BTG expression was found negatively correlated with miR-25a expression in the both tissues and cells. By applying luciferase reporter assay, we verified two putative binding sites between miR-25 and BTG2. Therefore, BTG2 is a directly target of miR-25 in NSCLC cancer. By applying loss-and-gain function analysis in NSCLC cell lines, we demonstrated that miR-25-BTG2 axis could directly regulated BTG2 expression and affect radiotherapy sensitivity of NSCLC cells. - Highlights: • miR-25 is upregulated, while BTG2 is downregulated in radioresistant NSCLC patients. • miR-25 modulates sensitivity to radiation induced apoptosis. • miR-25 directly targets BTG2 and suppresses its expression. • miR-25 modulates sensitivity to radiotherapy through inhibiting BTG2 expression.

  13. 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)

  14. Optimization of controllability and robustness of complex networks by edge directionality

    NASA Astrophysics Data System (ADS)

    Liang, Man; Jin, Suoqin; Wang, Dingjie; Zou, Xiufen

    2016-09-01

    Recently, controllability of complex networks has attracted enormous attention in various fields of science and engineering. How to optimize structural controllability has also become a significant issue. Previous studies have shown that an appropriate directional assignment can improve structural controllability; however, the evolution of the structural controllability of complex networks under attacks and cascading has always been ignored. To address this problem, this study proposes a new edge orientation method (NEOM) based on residual degree that changes the link direction while conserving topology and directionality. By comparing the results with those of previous methods in two random graph models and several realistic networks, our proposed approach is demonstrated to be an effective and competitive method for improving the structural controllability of complex networks. Moreover, numerical simulations show that our method is near-optimal in optimizing structural controllability. Strikingly, compared to the original network, our method maintains the structural controllability of the network under attacks and cascading, indicating that the NEOM can also enhance the robustness of controllability of networks. These results alter the view of the nature of controllability in complex networks, change the understanding of structural controllability and affect the design of network models to control such networks.

  15. 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

    2015-12-28

    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.

  16. Buckling-induced F-actin fragmentation modulates the contraction of active cytoskeletal networks.

    PubMed

    Li, Jing; Biel, Thomas; Lomada, Pranith; Yu, Qilin; Kim, Taeyoon

    2017-04-11

    Actomyosin contractility originating from interactions between F-actin and myosin facilitates various structural reorganizations of the actin cytoskeleton. Cross-linked actomyosin networks show a tendency to contract to single or multiple foci, which has been investigated extensively in numerous studies. Recently, it was suggested that suppression of F-actin buckling via an increase in bending rigidity significantly reduces network contraction. In this study, we demonstrate that networks may show the largest contraction at intermediate bending rigidity, not at the lowest rigidity, if filaments are severed by buckling arising from myosin activity as demonstrated in recent experiments; if filaments are very flexible, frequent severing events can severely deteriorate network connectivity, leading to the formation of multiple small foci and low network contraction. By contrast, if filaments are too stiff, the networks exhibit minimal contraction due to the inhibition of filament buckling. This study reveals that buckling-induced filament severing can modulate the contraction of active cytoskeletal networks, which has been neglected to date.

  17. Enhanced 10 Gb/s operations of directly modulated reflective semiconductor optical amplifiers without electronic equalization.

    PubMed

    Presi, M; Chiuchiarelli, A; Corsini, R; Choudury, P; Bottoni, F; Giorgi, L; Ciaramella, E

    2012-12-10

    We report enhanced 10 Gb/s operation of directly modulated bandwidth-limited reflective semiconductor optical amplifiers. By using a single suitable arrayed waveguide grating we achieve simultaneously WDM demultiplexing and optical equalization. Compared to previous approaches, the proposed system results significantly more tolerant to seeding wavelength drifts. This removes the need for wavelength lockers, additional electronic equalization or complex digital signal processing. Uniform C-band operations are obtained experimentally with < 2 dB power penalty within a wavelength drift of 10 GHz (which doubles the ITU-T standard recommendations).

  18. Vector radio-frequency optical signal generation based on one directly modulated laser

    NASA Astrophysics Data System (ADS)

    Wang, Yanyi; Xiao, Jiangnan; Chi, Nan; Yu, Jianjun

    2016-10-01

    We proposed single-sideband (SSB) quadrature phase-shift keying (QPSK) vector radio-frequency optical signal generation enabled by a single directly modulated laser without precoding technology, which can reduce the system cost and tolerate fiber dispersion. Based on our proposed scheme, we experimentally demonstrated 8-Gbaud SSB QPSK signals generation at 10 GHz, and the generated signals are transmitted over 50-km single-mode fiber without power penalty. Our experimental results show that an equal power SSB signal can tolerate fiber dispersion and have the highest receiver sensitivity.

  19. Laser direct writing of modulation-doped nanowire p/n junctions.

    PubMed

    Nam, Woongsik; Mitchell, James I; Xu, Xianfan

    2016-12-02

    We demonstrate a single-step, laser-based technique to fabricate axial modulation-doped silicon nanowires. Our method is based on laser-direct-write chemical vapor deposition and has the capability to fabricate nanowires as small as 60 nm, which is far below the diffraction limit of the laser wavelength of 395 nm, with precise control of nanowire position, length, and orientation. By switching dopant gases during nanowire writing, p-n junction nanowires are produced. The p-n junction nanowires are fabricated into multifinger devices with parallel metal contacts and electrically tested to demonstrate diode characteristics.

  20. Steganography in clustered-dot halftones using orientation modulation and modification of direct binary search

    NASA Astrophysics Data System (ADS)

    Chen, Yung-Yao; Hong, Sheng-Yi; Chen, Kai-Wen

    2015-03-01

    This paper proposes a novel message-embedded halftoning scheme that is based on orientation modulation (OM) encoding. To achieve high image quality, we employ a human visual system (HVS)-based error metric between the continuous-tone image and a data-embedded halftone, and integrate a modified direct binary search (DBS) framework into the proposed message-embedded halftoning method. The modified DBS framework ensures that the resulting data-embedded halftones have optimal image quality from the viewpoint of the HVS.

  1. 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

  2. Agreement Problems in Networks with Directed Graphs and Switching Topology

    DTIC Science & Technology

    2003-02-15

    C–3613. References [1] N. Biggs. Algebraic Graph Theory. Cambridge Tracks in Mathematics. Cambridge University Press , 1974. 15 [2] J. P. Desai, J. P...Springer, 2001. [9] R. A. Horn and C. R. Johnson. Matrix Analysis. Cambridge University Press , 1987. [10] A. Jadbabaie, J. Lin, and S. A. Morse...Networks of Dynamic Agents. Proc. of the American Control Conference, June 2003. [15] F. Paganini , J. Doyle, and S Low. Scalable laws for stable

  3. Connectomic Analysis of Brain Networks: Novel Techniques and Future Directions

    PubMed Central

    Cazemier, J. Leonie; Clascá, Francisco; Tiesinga, Paul H. E.

    2016-01-01

    Brain networks, localized or brain-wide, exist only at the cellular level, i.e., between specific pre- and post-synaptic neurons, which are connected through functionally diverse synapses located at specific points of their cell membranes. “Connectomics” is the emerging subfield of neuroanatomy explicitly aimed at elucidating the wiring of brain networks with cellular resolution and a quantified accuracy. Such data are indispensable for realistic modeling of brain circuitry and function. A connectomic analysis, therefore, needs to identify and measure the soma, dendrites, axonal path, and branching patterns together with the synapses and gap junctions of the neurons involved in any given brain circuit or network. However, because of the submicron caliber, 3D complexity, and high packing density of most such structures, as well as the fact that axons frequently extend over long distances to make synapses in remote brain regions, creating connectomic maps is technically challenging and requires multi-scale approaches, Such approaches involve the combination of the most sensitive cell labeling and analysis methods available, as well as the development of new ones able to resolve individual cells and synapses with increasing high-throughput. In this review, we provide an overview of recently introduced high-resolution methods, which researchers wanting to enter the field of connectomics may consider. It includes several molecular labeling tools, some of which specifically label synapses, and covers a number of novel imaging tools such as brain clearing protocols and microscopy approaches. Apart from describing the tools, we also provide an assessment of their qualities. The criteria we use assess the qualities that tools need in order to contribute to deciphering the key levels of circuit organization. We conclude with a brief future outlook for neuroanatomic research, computational methods, and network modeling, where we also point out several outstanding issues

  4. 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, H H H W

    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.

  5. Enhancing traffic capacity of scale-free networks by link-directed strategy

    NASA Astrophysics Data System (ADS)

    Ma, Jinlong; Han, Weizhan; Guo, Qing; Zhang, Shuai

    2016-08-01

    The transport efficiency of a network is strongly related to the underlying structure. In this paper, we propose an efficient strategy named high-betweenness-first (HBF) for the purpose of improving the traffic handling capacity of scale-free networks by limiting a fraction of undirected links to be unidirectional ones based on the links’ betweenness. Compared with the high-degree-first (HDF) strategy, the traffic capacity can be more significantly enhanced under the proposed link-directed strategy with the shortest path (SP) routing protocol. Simulation results in the Barabási-Albert (BA) model for scale-free networks show that the critical generating rate Rc which can evaluate the overall traffic capacity of a network system is larger after applying the HBF strategy, especially with nonrandom direction-determining rules. Because of the strongly improved traffic capacity, this work is helpful to design and optimize modern communication networks such as the software defined network.

  6. 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.

  7. Frequency interleaving towards spectrally efficient directly detected optical OFDM for next-generation optical access networks.

    PubMed

    Mehedy, Lenin; Bakaul, Masuduzzaman; Nirmalathas, Ampalavanapillai

    2010-10-25

    In this paper, we theoretically analyze and demonstrate that spectral efficiency of a conventional direct detection based optical OFDM system (DDO-OFDM) can be improved significantly using frequency interleaving of adjacent DDO-OFDM channels where OFDM signal band of one channel occupies the spectral gap of other channel and vice versa. We show that, at optimum operating condition, the proposed technique can effectively improve the spectral efficiency of the conventional DDO-OFDM system as much as 50%. We also show that such a frequency interleaved DDO-OFDM system, with a bit rate of 48 Gb/s within 25 GHz bandwidth, achieves sufficient power budget after transmission over 25 km single mode fiber to be used in next-generation time-division-multiplexed passive optical networks (TDM-PON). Moreover, by applying 64- quadrature amplitude modulation (QAM), the system can be further scaled up to 96 Gb/s with a power budget sufficient for 1:16 split TDM-PON.

  8. Enumeration of condition-dependent dense modules in protein interaction networks

    PubMed Central

    Georgii, Elisabeth; Dietmann, Sabine; Uno, Takeaki; Pagel, Philipp; Tsuda, Koji

    2009-01-01

    Motivation: Modern systems biology aims at understanding how the different molecular components of a biological cell interact. Often, cellular functions are performed by complexes consisting of many different proteins. The composition of these complexes may change according to the cellular environment, and one protein may be involved in several different processes. The automatic discovery of functional complexes from protein interaction data is challenging. While previous approaches use approximations to extract dense modules, our approach exactly solves the problem of dense module enumeration. Furthermore, constraints from additional information sources such as gene expression and phenotype data can be integrated, so we can systematically mine for dense modules with interesting profiles. Results: Given a weighted protein interaction network, our method discovers all protein sets that satisfy a user-defined minimum density threshold. We employ a reverse search strategy, which allows us to exploit the density criterion in an efficient way. Our experiments show that the novel approach is feasible and produces biologically meaningful results. In comparative validation studies using yeast data, the method achieved the best overall prediction performance with respect to confirmed complexes. Moreover, by enhancing the yeast network with phenotypic and phylogenetic profiles and the human network with tissue-specific expression data, we identified condition-dependent complex variants. Availability: A C++ implementation of the algorithm is available at http://www.kyb.tuebingen.mpg.de/~georgii/dme.html. Contact: koji.tsuda@tuebingen.mpg.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19213739

  9. Direct Inverse Control using an Artificial Neural Network for the Autonomous Hover of a Helicopter

    DTIC Science & Technology

    2014-10-05

    Inverse Control technique using an Artificial Neural Network to learn and then cancel out the Hover dynamics of the quadrotor UAV... Inverse Control , Neural Network , Flight Control , and UAV helicopter REPORT DOCUMENTATION PAGE 11. SPONSOR/MONITOR’S REPORT NUMBER(S) 10. SPONSOR...Helicopter. The goal of the project is to investigate the effectiveness of the Direct Inverse Control technique using an Artificial Neural Network to

  10. Finite-size effects on semi-directed Barabási-Albert networks

    NASA Astrophysics Data System (ADS)

    Radwan, M. A.; Sumour, Muneer A.; Elbitar, A. M.; Shabat, M. M.; Lima, F. W. S.

    2016-04-01

    In scale-free Barabási-Albert (BA) networks, we study the finite-size effect at different number m of neighbors. So, we investigate the effects of finite network size N for the recently developed semi-directed BA networks (SDBA1 and SDBA2) at fixed 2≤m≤300) and show and explain the gap in the distribution of the number k(i) of neighbors of the nodes i.

  11. 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

  12. Differential Modulation of Synaptic Strength and Timing Regulate Synaptic Efficacy in a Motor Network

    PubMed Central

    Brown, Jessica M.; Kvarta, Mark D.; Lu, Jay Y. J.; Schneider, Lauren R.; Nadim, Farzan; Harris-Warrick, Ronald M.

    2011-01-01

    Neuromodulators modify network output by altering neuronal firing properties and synaptic strength at multiple sites; however, the functional importance of each site is often unclear. We determined the importance of monoamine modulation of a single synapse for regulation of network cycle frequency in the oscillatory pyloric network of the lobster. The pacemaker kernel of the pyloric network receives only one chemical synaptic feedback, an inhibitory synapse from the lateral pyloric (LP) neuron to the pyloric dilator (PD) neurons, which can limit cycle frequency. We measured the effects of dopamine (DA), octopamine (Oct), and serotonin (5HT) on the strength of the LP→PD synapse and the ability of the modified synapse to regulate pyloric cycle frequency. DA and Oct strengthened, whereas 5HT weakened, LP→PD inhibition. Surprisingly, the DA-strengthened LP→PD synapse lost its ability to slow the pyloric oscillations, whereas the 5HT-weakened LP→PD synapse gained a greater influence on the oscillations. These results are explained by monoamine modulation of factors that determine the firing phase of the LP neuron in each cycle. DA acts via multiple mechanisms to phase-advance the LP neuron into the pacemaker's refractory period, where the strengthened synapse has little effect. In contrast, 5HT phase-delays LP activity into a region of greater pacemaker sensitivity to LP synaptic input. Only Oct enhanced LP regulation of cycle period simply by enhancing LP→PD synaptic strength. These results show that modulation of the strength and timing of a synaptic input can differentially affect the synapse's efficacy in the network. PMID:21047938

  13. Medium Access Control in Ad Hoc Networks With Omni-Directional and Directional Antennas

    DTIC Science & Technology

    2004-06-01

    49 3.3.2 The DTOR Scheme . . . . . . . . . . . . . . . . . . . . . . . . . . . 52 3.3.3 The MTOR Scheme...53 3.3 Calculation of various areas . . . . . . . . . . . . . . . . . . . . . . . . . . . 55 3.4 The MTOR scheme...directional or directional reception can be applied to this approach. When the former is used, we call it MTOR scheme (short for “mixed-directional

  14. Modulating contact angle hysteresis to direct fluid droplets along a homogenous surface.

    PubMed

    Luo, Mingxiang; Gupta, Rohini; Frechette, Joelle

    2012-02-01

    The shape and motion of drops on surfaces is governed by the balance between the driving and the pinning forces. Here we demonstrate control over the motion of droplets on an inclined surface by exerting control over the contact angle hysteresis. The external modulation of contact angle hysteresis is achieved through a voltage-induced local molecular reorganization within the surface film at the solid-liquid interface. We show that tuning contact angle hysteresis alone is sufficient to direct and deform drops when subjected to a constant external driving force, here gravity, in the absence of a pre-defined surface energy gradient or pattern. We also show that the observed stretching and contraction of the drops mimic the motion of an inchworm. Such reversible manipulation of the pinning forces could be an attractive means to direct drops, especially with the dominance of surface forces at micro-/nanoscale.

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

    PubMed

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

    2006-06-01

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

  16. Adaptive Modulation for DFIG and STATCOM With High-Voltage Direct Current Transmission.

    PubMed

    Tang, Yufei; He, Haibo; Ni, Zhen; Wen, Jinyu; Huang, Tingwen

    2016-08-01

    This paper develops an adaptive modulation approach for power system control based on the approximate/adaptive dynamic programming method, namely, the goal representation heuristic dynamic programming (GrHDP). In particular, we focus on the fault recovery problem of a doubly fed induction generator (DFIG)-based wind farm and a static synchronous compensator (STATCOM) with high-voltage direct current (HVDC) transmission. In this design, the online GrHDP-based controller provides three adaptive supplementary control signals to the DFIG controller, STATCOM controller, and HVDC rectifier controller, respectively. The mechanism is to observe the system states and their derivatives and then provides supplementary control to the plant according to the utility function. With the GrHDP design, the controller can adaptively develop an internal goal representation signal according to the observed power system states, therefore, to achieve more effective learning and modulating. Our control approach is validated on a wind power integrated benchmark system with two areas connected by HVDC transmission lines. Compared with the classical direct HDP and proportional integral control, our GrHDP approach demonstrates the improved transient stability under system faults. Moreover, experiments under different system operating conditions with signal transmission delays are also carried out to further verify the effectiveness and robustness of the proposed approach.

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

    SciTech Connect

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

    2003-08-01

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

  18. Effect of Sintering Temperature on Electrical Properties of Chip on Glass Module with Direct Printing Method

    NASA Astrophysics Data System (ADS)

    Lee, Young-Chul; Kim, Yongil; Jung, Seung-Boo

    2012-09-01

    In order to apply the direct printing method to the fabrication of chip on glass (COG) modules, we examined that the effect of the sintering temperature on the electrical properties of a COG module with direct printing method. Firstly, we fabricated an Ag conductive circuit on a glass substrate by the screen-printing method. To investigate its the effect on the electrical properties of the circuit, it was sintered at various temperatures, such as 150, 200, 250, and 300 °C for 30 min. Subsequently, we conducted Au electro-plating for the fabrication of a Si dummy chip. Finally, the flip-chip bonding process was conducted using anisotropic conductive film (ACF). The printed Ag circuits were well formed on the quartz substrate without any shorts or remarkable changes compared with the initial design. The electrical properties of the printed Ag circuits improved with increasing sintering temperature. The conductive particles in the ACF were well deformed in between the Au bumps and printed Ag pads after the bonding process. The four-point probe method was employed to measure the connection resistance of the joints constructed with the Au bumps on the Si chip and printed Ag circuit on the quartz substrate. The resistances of the interconnections drastically decreased with increasing sintering temperature, i.e., subsequently converged from 11.8 Ω to 7.36 mΩ.

  19. Membrane lipids tune synaptic transmission by direct modulation of presynaptic potassium channels.

    PubMed

    Carta, Mario; Lanore, Frederic; Rebola, Nelson; Szabo, Zsolt; Da Silva, Silvia Viana; Lourenço, Joana; Verraes, Agathe; Nadler, André; Schultz, Carsten; Blanchet, Christophe; Mulle, Christophe

    2014-02-19

    Voltage-gated potassium (Kv) channels are involved in action potential (AP) repolarization in excitable cells. Exogenous application of membrane-derived lipids, such as arachidonic acid (AA), regulates the gating of Kv channels. Whether membrane-derived lipids released under physiological conditions have an impact on neuronal coding through this mechanism is unknown. We show that AA released in an activity-dependent manner from postsynaptic hippocampal CA3 pyramidal cells acts as retrograde messenger, inducing a robust facilitation of mossy fiber (Mf) synaptic transmission over several minutes. AA acts by broadening presynaptic APs through the direct modulation of Kv channels. This form of short-term plasticity can be triggered when postsynaptic cell fires with physiologically relevant patterns and sets the threshold for the induction of the presynaptic form of long-term potentiation (LTP) at hippocampal Mf synapses. Hence, direct modulation of presynaptic Kv channels by activity-dependent release of lipids serves as a physiological mechanism for tuning synaptic transmission.

  20. Carboxylated and Uncarboxylated Forms of Osteocalcin Directly Modulate the Glucose Transport System and Inflammation in Adipocytes

    PubMed Central

    Hill, H. S.; Grams, J.; Walton, R. G.; Liu, J.; Moellering, D. R.; Garvey, W. T.

    2017-01-01

    Osteocalcin is secreted by osteoblasts and improves insulin sensitivity in vivo, although mechanisms remain unclear. We tested the hypothesis that osteocalcin directly modulates cell biology in insulin-targeted peripheral tissues. In L-6 myocytes, osteocalcin stimulated glucose transport both in the absence (basal) and presence of insulin. Similarly, in primary cultured adipocytes, both carboxylated and uncarboxylated osteocalcin increased basal and insulin-stimulated glucose transport as well as insulin sensitivity. Osteocalcin also increased basal and insulin-stimulated glucose oxidation, though there was no effect on fatty acid synthesis or lipolysis. In primary-cultured adipocytes, both forms of osteocalcin suppressed secretion of tumor necrosis factor alpha into the media; however, only carboxylated osteocalcin suppressed interleukin 6 release, and neither form of osteocalcin modulated monocyte chemoattractant protein-1 secretion. Both carboxylated and uncarboxylated osteocalcin increased secretion of adiponectin and the anti-inflammatory cytokine interleukin 10. In conclusion, both carboxylated and uncarboxylated osteocalcin directly increase glucose transport in adipocytes and muscle cells, while suppressing proinflammatory cytokine secretion and stimulating interleukin 10 and adiponectin release. Thus, these results provide a mechanism for the insulin-sensitizing effects of osteocalcin and help elucidate the role that bone plays in regulating systemic metabolism. PMID:24554534

  1. 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

  2. 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

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

    PubMed

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

    2014-01-01

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

  4. 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.

  5. Subthalamic stimulation modulates cortical motor network activity and synchronization in Parkinson's disease.

    PubMed

    Weiss, Daniel; Klotz, Rosa; Govindan, Rathinaswamy B; Scholten, Marlieke; Naros, Georgios; Ramos-Murguialday, Ander; Bunjes, Friedemann; Meisner, Christoph; Plewnia, Christian; Krüger, Rejko; Gharabaghi, Alireza

    2015-03-01

    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

  6. 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.

  7. 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.

  8. 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

  9. 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.

  10. Directed clustering coefficient as a measure of systemic risk in complex banking networks

    NASA Astrophysics Data System (ADS)

    Tabak, Benjamin M.; Takami, Marcelo; Rocha, Jadson M. C.; Cajueiro, Daniel O.; Souza, Sergio R. S.

    2014-01-01

    Recent literature has focused on the study of systemic risk in complex networks. It is clear now, after the crisis of 2008, that the aggregate behavior of the interaction among agents is not straightforward and it is very difficult to predict. Contributing to this debate, this paper shows that the directed clustering coefficient may be used as a measure of systemic risk in complex networks. Furthermore, using data from the Brazilian interbank network, we show that the directed clustering coefficient is negatively correlated with domestic interest rates.

  11. Co-expression network analyses identify functional modules associated with development and stress response in Gossypium arboreum

    PubMed Central

    You, Qi; Zhang, Liwei; Yi, Xin; Zhang, Kang; Yao, Dongxia; Zhang, Xueyan; Wang, Qianhua; Zhao, Xinhua; Ling, Yi; Xu, Wenying; Li, Fuguang; Su, Zhen

    2016-01-01

    Cotton is an economically important crop, essential for the agriculture and textile industries. Through integrating transcriptomic data, we discovered that multi-dimensional co-expression network analysis was powerful for predicting cotton gene functions and functional modules. Here, the recently available transcriptomic data on Gossypium arboreum, including data on multiple growth stages of tissues and stress treatment samples were applied to construct a co-expression network exploring multi-dimensional expression (development and stress) through multi-layered approaches. Based on differential gene expression and network analysis, a fibre development regulatory module of the gene GaKNL1 was found to regulate the second cell wall through repressing the activity of REVOLUTA, and a tissue-selective module of GaJAZ1a was examined in response to water stress. Moreover, comparative genomics analysis of the JAZ1-related regulatory module revealed high conservation across plant species. In addition, 1155 functional modules were identified through integrating the co-expression network, module classification and function enrichment tools, which cover functions such as metabolism, stress responses, and transcriptional regulation. In the end, an online platform was built for network analysis (http://structuralbiology.cau.edu.cn/arboreum), which could help to refine the annotation of cotton gene function and establish a data mining system to identify functional genes or modules with important agronomic traits. PMID:27922095

  12. A powerful weighted statistic for detecting group differences of directed biological networks

    PubMed Central

    Yuan, Zhongshang; Ji, Jiadong; Zhang, Xiaoshuai; Xu, Jing; Ma, Daoxin; Xue, Fuzhong

    2016-01-01

    Complex disease is largely determined by a number of biomolecules interwoven into networks, rather than a single biomolecule. Different physiological conditions such as cases and controls may manifest as different networks. Statistical comparison between biological networks can provide not only new insight into the disease mechanism but statistical guidance for drug development. However, the methods developed in previous studies are inadequate to capture the changes in both the nodes and edges, and often ignore the network structure. In this study, we present a powerful weighted statistical test for group differences of directed biological networks, which is independent of the network attributes and can capture the changes in both the nodes and edges, as well as simultaneously accounting for the network structure through putting more weights on the difference of nodes locating on relatively more important position. Simulation studies illustrate that this method had better performance than previous ones under various sample sizes and network structures. One application to GWAS of leprosy successfully identifies the specific gene interaction network contributing to leprosy. Another real data analysis significantly identifies a new biological network, which is related to acute myeloid leukemia. One potential network responsible for lung cancer has also been significantly detected. The source R code is available on our website. PMID:27686331

  13. A powerful weighted statistic for detecting group differences of directed biological networks.

    PubMed

    Yuan, Zhongshang; Ji, Jiadong; Zhang, Xiaoshuai; Xu, Jing; Ma, Daoxin; Xue, Fuzhong

    2016-09-30

    Complex disease is largely determined by a number of biomolecules interwoven into networks, rather than a single biomolecule. Different physiological conditions such as cases and controls may manifest as different networks. Statistical comparison between biological networks can provide not only new insight into the disease mechanism but statistical guidance for drug development. However, the methods developed in previous studies are inadequate to capture the changes in both the nodes and edges, and often ignore the network structure. In this study, we present a powerful weighted statistical test for group differences of directed biological networks, which is independent of the network attributes and can capture the changes in both the nodes and edges, as well as simultaneously accounting for the network structure through putting more weights on the difference of nodes locating on relatively more important position. Simulation studies illustrate that this method had better performance than previous ones under various sample sizes and network structures. One application to GWAS of leprosy successfully identifies the specific gene interaction network contributing to leprosy. Another real data analysis significantly identifies a new biological network, which is related to acute myeloid leukemia. One potential network responsible for lung cancer has also been significantly detected. The source R code is available on our website.

  14. 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.

  15. 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

  16. Constructivist Instructional Design and Development of a Networked Learning Skills (NICLS) Module for Continuing Professional Education Distance Learning.

    ERIC Educational Resources Information Center

    Nunes, J. M. Baptista; McPherson, M.; Rico, M.

    This paper proposes an instructional systems design (ISD) approach for the design and development of a basic Networked Information and Communication Literacy Skills (NICLS) module. It concentrates on the design and development of a NICLS core skills pre-module for the Master of Arts in Information Technology Management (MA ITM) program at the…

  17. 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.

  18. 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.

  19. Distributed Load Shedding over Directed Communication Networks with Time Delays

    SciTech Connect

    Yang, Tao; Wu, Di

    2016-07-25

    When generation is insufficient to support all loads under emergencies, effective and efficient load shedding needs to be deployed in order to maintain the supply-demand balance. This paper presents a distributed load shedding algorithm, which makes efficient decision based on the discovered global information. In the global information discovery process, each load only communicates with its neighboring load via directed communication links possibly with arbitrarily large but bounded time varying communication delays. We propose a novel distributed information discovery algorithm based on ratio consensus. Simulation results are used to validate the proposed method.

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

    PubMed Central

    2013-01-01

    Background With the continued proliferation of high-throughput biological experiments, there is a pressing need for tools to integrate the data produced in ways that produce biologically meaningful conclusions. Many microarray studies have analysed transcriptomic data from a pathway perspective, for instance by testing for KEGG pathway enrichment in sets of upregulated genes. However, the increasing availability of species-specific metabolic models provides the opportunity to analyse these data in a more objective, system-wide manner. Results Here we introduce ambient (Active Modules for Bipartite Networks), a simulated annealing approach to the discovery of metabolic subnetworks (modules) that are significantly affected by a given genetic or environmental change. The metabolic modules returned by ambient are connected parts of the bipartite network that change coherently between conditions, providing a more detailed view of metabolic changes than standard approaches based on pathway enrichment. Conclusions ambient is an effective and flexible tool for the analysis of high-throughput data in a metabolic context. The same approach can be applied to any system in which reactions (or metabolites) can be assigned a score based on some biological observation, without the limitation of predefined pathways. A Python implementation of ambient is available at http://www.theosysbio.bio.ic.ac.uk/ambient. PMID:23531303

  1. 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

  2. Optimization methods for locating lightning flashes using magnetic direction finding networks

    NASA Technical Reports Server (NTRS)

    Goodman, Steven J.

    1989-01-01

    Techniques for producing best point estimates of target position using direction finder bearing information are reviewed. The use of an algorithm that calculates the cloud-to-ground flash location given multiple bearings is illustrated and the position errors are described. This algorithm can be used to analyze direction finder network performance.

  3. 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.

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

    PubMed

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

    2012-04-01

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

  5. Enlightening discriminative network functional modules behind Principal Component Analysis separation in differential-omic science studies.

    PubMed

    Ciucci, Sara; Ge, Yan; Durán, Claudio; Palladini, Alessandra; Jiménez-Jiménez, Víctor; Martínez-Sánchez, Luisa María; Wang, Yuting; Sales, Susanne; Shevchenko, Andrej; Poser, Steven W; Herbig, Maik; Otto, Oliver; Androutsellis-Theotokis, Andreas; Guck, Jochen; Gerl, Mathias J; Cannistraci, Carlo Vittorio

    2017-03-13

    Omic science is rapidly growing and one of the most employed techniques to explore differential patterns in omic datasets is principal component analysis (PCA). However, a method to enlighten the network of omic features that mostly contribute to the sample separation obtained by PCA is missing. An alternative is to build correlation networks between univariately-selected significant omic features, but this neglects the multivariate unsupervised feature compression responsible for the PCA sample segregation. Biologists and medical researchers often prefer effective methods that offer an immediate interpretation to complicated algorithms that in principle promise an improvement but in practice are difficult to be applied and interpreted. Here we present PC-corr: a simple algorithm that associates to any PCA segregation a discriminative network of features. Such network can be inspected in search of functional modules useful in the definition of combinatorial and multiscale biomarkers from multifaceted omic data in systems and precision biomedicine. We offer proofs of PC-corr efficacy on lipidomic, metagenomic, developmental genomic, population genetic, cancer promoteromic and cancer stem-cell mechanomic data. Finally, PC-corr is a general functional network inference approach that can be easily adopted for big data exploration in computer science and analysis of complex systems in physics.

  6. Enlightening discriminative network functional modules behind Principal Component Analysis separation in differential-omic science studies

    PubMed Central

    Ciucci, Sara; Ge, Yan; Durán, Claudio; Palladini, Alessandra; Jiménez-Jiménez, Víctor; Martínez-Sánchez, Luisa María; Wang, Yuting; Sales, Susanne; Shevchenko, Andrej; Poser, Steven W.; Herbig, Maik; Otto, Oliver; Androutsellis-Theotokis, Andreas; Guck, Jochen; Gerl, Mathias J.; Cannistraci, Carlo Vittorio

    2017-01-01

    Omic science is rapidly growing and one of the most employed techniques to explore differential patterns in omic datasets is principal component analysis (PCA). However, a method to enlighten the network of omic features that mostly contribute to the sample separation obtained by PCA is missing. An alternative is to build correlation networks between univariately-selected significant omic features, but this neglects the multivariate unsupervised feature compression responsible for the PCA sample segregation. Biologists and medical researchers often prefer effective methods that offer an immediate interpretation to complicated algorithms that in principle promise an improvement but in practice are difficult to be applied and interpreted. Here we present PC-corr: a simple algorithm that associates to any PCA segregation a discriminative network of features. Such network can be inspected in search of functional modules useful in the definition of combinatorial and multiscale biomarkers from multifaceted omic data in systems and precision biomedicine. We offer proofs of PC-corr efficacy on lipidomic, metagenomic, developmental genomic, population genetic, cancer promoteromic and cancer stem-cell mechanomic data. Finally, PC-corr is a general functional network inference approach that can be easily adopted for big data exploration in computer science and analysis of complex systems in physics. PMID:28287094

  7. Common modulation of limbic network activation underlies musical emotions as they unfold.

    PubMed

    Singer, Neomi; Jacoby, Nori; Lin, Tamar; Raz, Gal; Shpigelman, Lavi; Gilam, Gadi; Granot, Roni Y; Hendler, Talma

    2016-11-01

    Music is a powerful means for communicating emotions among individuals. Here we reveal that this continuous stream of affective information is commonly represented in the brains of different listeners and that particular musical attributes mediate this link. We examined participants' brain responses to two naturalistic musical pieces using functional Magnetic Resonance imaging (fMRI). Following scanning, as participants listened to the musical pieces for a second time, they continuously indicated their emotional experience on scales of valence and arousal. These continuous reports were used along with a detailed annotation of the musical features, to predict a novel index of Dynamic Common Activation (DCA) derived from ten large-scale data-driven functional networks. We found an association between the unfolding music-induced emotionality and the DCA modulation within a vast network of limbic regions. The limbic-DCA modulation further corresponded with continuous changes in two temporal musical features: beat-strength and tempo. Remarkably, this "collective limbic sensitivity" to temporal features was found to mediate the link between limbic-DCA and the reported emotionality. An additional association with the emotional experience was found in a left fronto-parietal network, but only among a sub-group of participants with a high level of musical experience (>5years). These findings may indicate two processing-levels underlying the unfolding of common music emotionality; (1) a widely shared core-affective process that is confined to a limbic network and mediated by temporal regularities in music and (2) an experience based process that is rooted in a left fronto-parietal network that may involve functioning of the 'mirror-neuron system'.

  8. BinTree seeking: a novel approach to mine both bi-sparse and cohesive modules in protein interaction networks.

    PubMed

    Jiao, Qing-Ju; Zhang, Yan-Kai; Li, Lu-Ning; Shen, Hong-Bin

    2011-01-01

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

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

    SciTech Connect

    Zhu, Lun-Wu; 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.

  10. 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…

  11. Wireless Sensor Network Security Enhancement Using Directional Antennas: State of the Art and Research Challenges.

    PubMed

    Curiac, Daniel-Ioan

    2016-04-07

    Being often deployed in remote or hostile environments, wireless sensor networks are vulnerable to various types of security attacks. A possible solution to reduce the security risks is to use directional antennas instead of omnidirectional ones or in conjunction with them. Due to their increased complexity, higher costs and larger sizes, directional antennas are not traditionally used in wireless sensor networks, but recent technology trends may support this method. This paper surveys existing state of the art approaches in the field, offering a broad perspective of the future use of directional antennas in mitigating security risks, together with new challenges and open research issues.

  12. Wireless Sensor Network Security Enhancement Using Directional Antennas: State of the Art and Research Challenges

    PubMed Central

    Curiac, Daniel-Ioan

    2016-01-01

    Being often deployed in remote or hostile environments, wireless sensor networks are vulnerable to various types of security attacks. A possible solution to reduce the security risks is to use directional antennas instead of omnidirectional ones or in conjunction with them. Due to their increased complexity, higher costs and larger sizes, directional antennas are not traditionally used in wireless sensor networks, but recent technology trends may support this method. This paper surveys existing state of the art approaches in the field, offering a broad perspective of the future use of directional antennas in mitigating security risks, together with new challenges and open research issues. PMID:27070601

  13. Modulation of human auditory spatial scene analysis by transcranial direct current stimulation.

    PubMed

    Lewald, Jörg

    2016-04-01

    Localizing and selectively attending to the source of a sound of interest in a complex auditory environment is an important capacity of the human auditory system. The underlying neural mechanisms have, however, still not been clarified in detail. This issue was addressed by using bilateral bipolar-balanced transcranial direct current stimulation (tDCS) in combination with a task demanding free-field sound localization in the presence of multiple sound sources, thus providing a realistic simulation of the so-called "cocktail-party" situation. With left-anode/right-cathode, but not with right-anode/left-cathode, montage of bilateral electrodes, tDCS over superior temporal gyrus, including planum temporale and auditory cortices, was found to improve the accuracy of target localization in left hemispace. No effects were found for tDCS over inferior parietal lobule or with off-target active stimulation over somatosensory-motor cortex that was used to control for non-specific effects. Also, the absolute error in localization remained unaffected by tDCS, thus suggesting that general response precision was not modulated by brain polarization. This finding can be explained in the framework of a model assuming that brain polarization modulated the suppression of irrelevant sound sources, thus resulting in more effective spatial separation of the target from the interfering sound in the complex auditory scene.

  14. Analytical formulation of directly modulated OOFDM signals transmitted over an IM/DD dispersive link.

    PubMed

    Sánchez, C; Ortega, B; Wei, J L; Tang, J; Capmany, J

    2013-03-25

    We provide an analytical study on the propagation effects of a directly modulated OOFDM signal through a dispersive fiber and subsequent photo-detection. The analysis includes the effects of the laser operation point and the interplay between chromatic dispersion and laser chirp. The final expression allows to understand the physics behind the transmission of a multi-carrier signal in the presence of residual frequency modulation and the description of the induced intermodulation distortion gives us a detailed insight into the diferent intermodulation products which impair the recovered signal at the receiver-end side. Numerical comparisons between transmission simulations results and those provided by evaluating the expression obtained are carried out for different laser operation points. Results obtained by changing the fiber length, laser parameters and using single mode fiber with negative and positive dispersion are calculated in order to demonstrate the validity and versatility of the theory provided in this paper. Therefore, a novel analytical formulation is presented as a versatile tool for the description and study of IM/DD OOFDM systems with variable design parameters.

  15. Lasting modulation of in vitro oscillatory activity with weak direct current stimulation

    PubMed Central

    Bikson, Marom; Parra, Lucas C.

    2014-01-01

    Transcranial direct current stimulation (tDCS) is emerging as a versatile tool to affect brain function. While the acute neurophysiological effects of stimulation are well understood, little is know about the long-term effects. One hypothesis is that stimulation modulates ongoing neural activity, which then translates into lasting effects via physiological plasticity. Here we used carbachol-induced gamma oscillations in hippocampal rat slices to establish whether prolonged constant current stimulation has a lasting effect on endogenous neural activity. During 10 min of stimulation, the power and frequency of gamma oscillations, as well as multiunit activity, were modulated in a polarity specific manner. Remarkably, the effects on power and multiunit activity persisted for more than 10 min after stimulation terminated. Using a computational model we propose that altered synaptic efficacy in excitatory and inhibitory pathways could be the source of these lasting effects. Future experimental studies using this novel in vitro preparation may be able to confirm or refute the proposed hypothesis. PMID:25505103

  16. 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.

  17. Hybrid semiconductor-dielectric metamaterial modulation for switchable bi-directional THz absorbers

    NASA Astrophysics Data System (ADS)

    Le, Ly Nguyen; Thang, Nguyen Manh; Thuy, Le Minh; Tung, Nguyen Thanh

    2017-01-01

    There is an increasing interest for electromagnetic metamaterials that show mutable absorption properties with real-time and dynamic control. In this paper, we investigate a modulation of bi-directional metamaterial absorbers that is thermally switchable at terahertz frequencies. The metamaterial absorber is composed of symmetric hybrid semiconductor-dielectric cut-wire-pair structures, whose electromagnetic responses can be actively manipulated by utilizing an external heat source. As increasing the temperature of metamaterials from 300 to 350 K, we demonstrate that the magnetic resonance can be systematically blue-shifted and overlapped with the electric resonance, which is unaffectedly settled at about 0.8 THz. This superposition provides an effective mechanism to control the absorption intensity from 43% to nearly 95%. Finite integration simulation technique, standard retrieval method, and equivalent circuit model are employed to elaborate our idea.

  18. Bidirectional direct modulation CATV and phase remodulation radio-over-fiber transport systems.

    PubMed

    Tsai, Wen-Shing; Ma, Hsien-Li; Lu, Hai-Han; Lin, Ying-Pyng; Chen, Hung-Yi; Yan, Shr-Chi

    2010-12-06

    A bidirectional lightwave transport system employing direct modulation CATV and phase remodulation radio-over-fiber (ROF) signals in two-way transmission is proposed and experimentally demonstrated. To be the first system of reusing the phase of the transmitting lightwave with multi-carrier analog CATV signal, the transmission performances of CATV and ROF signals are investigated in bidirectional way, with the help of optical band-pass filters (OBPFs) at the receiving sites. Through a serious investigation, the transmitting light sources are successfully remodulated with RF signals for transmission. Brilliant transmission performances of composite second-order (CSO), composite triple-beat (CTB), and bit error rate (BER) were obtained; accompanied with acceptable carrier-to-noise ratio (CNR) value. This proposed system reveals a prominent one with economy and convenience to be installed.

  19. 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

    2015-07-29

    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.

  20. 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.

  1. Improved sequence learning with subthalamic nucleus deep brain stimulation: evidence for treatment-specific network modulation.

    PubMed

    Mure, Hideo; Tang, Chris C; Argyelan, Miklos; Ghilardi, Maria-Felice; Kaplitt, Michael G; Dhawan, Vijay; Eidelberg, David

    2012-02-22

    We used a network approach to study the effects of anti-parkinsonian treatment on motor sequence learning in humans. Eight Parkinson's disease (PD) patients with bilateral subthalamic nucleus (STN) deep brain stimulation underwent H(2)(15)O positron emission tomography (PET) imaging to measure regional cerebral blood flow (rCBF) while they performed kinematically matched sequence learning and movement tasks at baseline and during stimulation. Network analysis revealed a significant learning-related spatial covariance pattern characterized by consistent increases in subject expression during stimulation (p = 0.008, permutation test). The network was associated with increased activity in the lateral cerebellum, dorsal premotor cortex, and parahippocampal gyrus, with covarying reductions in the supplementary motor area (SMA) and orbitofrontal cortex. Stimulation-mediated increases in network activity correlated with concurrent improvement in learning performance (p < 0.02). To determine whether similar changes occurred during dopaminergic pharmacotherapy, we studied the subjects during an intravenous levodopa infusion titrated to achieve a motor response equivalent to stimulation. Despite consistent improvement in motor ratings during infusion, levodopa did not alter learning performance or network activity. Analysis of learning-related rCBF in network regions revealed improvement in baseline abnormalities with STN stimulation but not levodopa. These effects were most pronounced in the SMA. In this region, a consistent rCBF response to stimulation was observed across subjects and trials (p = 0.01), although the levodopa response was not significant. These findings link the cognitive treatment response in PD to changes in the activity of a specific cerebello-premotor cortical network. Selective modulation of overactive SMA-STN projection pathways may underlie the improvement in learning found with stimulation.

  2. 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 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.

  3. 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.

  4. 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

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

    PubMed

    Samura, Toshikazu; Hayashi, Hatsuo

    2012-09-01

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

  6. Directly Placed Restorative Materials: Review and Network Meta-analysis.

    PubMed

    Schwendicke, F; Göstemeyer, G; Blunck, U; Paris, S; Hsu, L-Y; Tu, Y-K

    2016-06-01

    For restoring cavitated dental lesions, whether carious or not, a large number of material combinations are available. We aimed to systematically review and synthesize data of comparative dental restorative trials. A systematic review was performed. Randomized controlled trials published between 2005 and 2015 were included that compared the survival of ≥2 restorative and/or adhesive materials (i.e., no need for restorative reintervention). Pairwise and Bayesian network meta-analyses were performed, with separate evaluations for cervical cavitated lesions and load-bearing posterior cavitated lesions in permanent and primary teeth. A total of 11,070 restorations (5,330 cervical, 5,740 load bearing) had been placed in 3,633 patients in the included trials. Thirty-six trials investigated restoration of cervical lesions (all in permanent teeth) and 36 of load-bearing lesions (8 in primary and 28 in permanent teeth). Resin-modified glass ionomer cements had the highest chance of survival in cervical cavitated lesions; composites or compomers placed via 2-step self-etch and 3-step etch-and-rinse adhesives were ranked next. Restorations placed with 2-step etch-and-rinse or 1-step self-etch adhesives performed worst. For load-bearing restorations, conventional composites had the highest probability of survival, while siloranes were found least suitable. Ambiguity remains regarding which adhesive strategy to use in load-bearing cavitated lesions. Most studies showed high risk of bias, and several comparisons were prone for publication bias. If prioritized for survival, resin-modified glass ionomer cements might be recommended to restore cervical lesions. For load-bearing ones, conventional or bulk fill composites seem most suitable. The available evidence is quantitatively and qualitatively insufficient for further recommendations, especially with regard to adhesive strategies in posterior load-bearing situations. Moreover, different material classifications might yield

  7. The Epidemic Spreading Model and the Direction of Information Flow in Brain Networks.

    PubMed

    Meier, J; Zhou, X; Hillebrand, A; Tewarie, P; Stam, C J; Mieghem, P Van

    2017-02-04

    The interplay between structural connections and emerging information flow in the human brain remains an open research problem. A recent study observed global patterns of directional information flow in empirical data using the measure of transfer entropy. For higher frequency bands, the overall direction of information flow was from posterior to anterior regions whereas an anterior-to-posterior pattern was observed in lower frequency bands. In this study, we applied a simple Susceptible-Infected-Susceptible (SIS) epidemic spreading model on the human connectome with the aim to reveal the topological properties of the structural network that give rise to these global patterns. We found that direct structural connections induced higher transfer entropy between two brain regions and that transfer entropy decreased with increasing distance between nodes (in terms of hops in the structural network). Applying the SIS model, we were able to confirm the empirically observed opposite information flow patterns and posterior hubs in the structural network seem to play a dominant role in the network dynamics. For small time scales, when these hubs acted as strong receivers of information, the global pattern of information flow was in the posterior-to-anterior direction and in the opposite direction when they were strong senders. Our analysis suggests that these global patterns of directional information flow are the result of an unequal spatial distribution of the structural degree between posterior and anterior regions and their directions seem to be linked to different time scales of the spreading process.

  8. Emerging subspecialties in neurology: deep brain stimulation and electrical neuro-network modulation.

    PubMed

    Hassan, Anhar; Okun, Michael S

    2013-01-29

    Deep brain stimulation (DBS) is a surgical therapy that involves the delivery of an electrical current to one or more brain targets. This technology has been rapidly expanding to address movement, neuropsychiatric, and other disorders. The evolution of DBS has created a niche for neurologists, both in the operating room and in the clinic. Since DBS is not always deep, not always brain, and not always simply stimulation, a more accurate term for this field may be electrical neuro-network modulation (ENM). Fellowships will likely in future years evolve their scope to include other technologies, and other nervous system regions beyond typical DBS therapy.

  9. Identification of a gene module associated with BMD through the integration of network analysis and genome-wide association data.

    PubMed

    Farber, Charles R

    2010-11-01

    Bone mineral density (BMD) is influenced by a complex network of gene interactions; therefore, elucidating the relationships between genes and how those genes, in turn, influence BMD is critical for developing a comprehensive understanding of osteoporosis. To investigate the role of transcriptional networks in the regulation of BMD, we performed a weighted gene coexpression network analysis (WGCNA) using microarray expression data on monocytes from young individuals with low or high BMD. WGCNA groups genes into modules based on patterns of gene coexpression. and our analysis identified 11 gene modules. We observed that the overall expression of one module (referred to as module 9) was significantly higher in the low-BMD group (p = .03). Module 9 was highly enriched for genes belonging to the immune system-related gene ontology (GO) category "response to virus" (p = 7.6 × 10(-11)). Using publically available genome-wide association study data, we independently validated the importance of module 9 by demonstrating that highly connected module 9 hubs were more likely, relative to less highly connected genes, to be genetically associated with BMD. This study highlights the advantages of systems-level analyses to uncover coexpression modules associated with bone mass and suggests that particular monocyte expression patterns may mediate differences in BMD.

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

    PubMed Central

    2011-01-01

    Background The incidence of congenital heart disease (CHD) is continuously increasing among infants born alive nowadays, making it one of the leading causes of infant morbidity worldwide. Various studies suggest that both genetic and environmental factors lead to CHD, and therefore identifying its candidate genes and disease-markers has been one of the central topics in CHD research. By using the high-throughput genomic data of CHD which are available recently, network-based methods provide powerful alternatives of systematic analysis of complex diseases and identification of dysfunctional modules and candidate disease genes. Results In this paper, by modeling the information flow from source disease genes to targets of differentially expressed genes via a context-specific protein-protein interaction network, we extracted dysfunctional modules which were then validated by various types of measurements and independent datasets. Network topology analysis of these modules revealed major and auxiliary pathways and cellular processes in CHD, demonstrating the biological usefulness of the identified modules. We also prioritized a list of candidate CHD genes from these modules using a guilt-by-association approach, which are well supported by various kinds of literature and experimental evidence. Conclusions We provided a network-based analysis to detect dysfunctional modules and disease genes of CHD by modeling the information transmission from source disease genes to targets of differentially expressed genes. Our method resulted in 12 modules from the constructed CHD subnetwork. We further identified and prioritized candidate disease genes of CHD from these dysfunctional modules. In conclusion, module analysis not only revealed several important findings with regard to the underlying molecular mechanisms of CHD, but also suggested the distinct network properties of causal disease genes which lead to identification of candidate CHD genes. PMID:22136190

  11. [Mechanism of action for deep brain stimulation and electrical neuro-network modulation (ENM)].

    PubMed

    Okun, Michael S; Oyama, Genko

    2013-01-01

    Deep brain stimulation (DBS) has become an important treatment option for carefully screened medication resistant neurological and neuropsychiatric disorders. DBS therapy is not always applied deep to the brain; does not have to be applied exclusively to the brain; and the mechanism for DBS is not simply stimulation of structures. The applications and target locations for DBS devices are rapidly expanding, with many new regions of the brain, spinal cord, peripheral nerves, and muscles now possibly accessed through this technology. We will review the idea of "electrical neuro-network modulation (ENM)"; discuss the importance of the complex neural networks underpinning the effects of DBS; discuss the expansion of brain targets; discuss the use of fiber based targets; and discuss the importance of tailoring DBS therapy to the symptom, rather than the disease.

  12. 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.

  13. 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

  14. Modulating Motor Learning through Transcranial Direct-Current Stimulation: An Integrative View

    PubMed Central

    Ammann, Claudia; Spampinato, Danny; Márquez-Ruiz, Javier

    2016-01-01

    Motor learning consists of the ability to improve motor actions through practice playing a major role in the acquisition of skills required for high-performance sports or motor function recovery after brain lesions. During the last decades, it has been reported that transcranial direct-current stimulation (tDCS), consisting in applying weak direct current through the scalp, is able of inducing polarity-specific changes in the excitability of cortical neurons. This low-cost, painless and well-tolerated portable technique has found a wide-spread use in the motor learning domain where it has been successfully applied to enhance motor learning in healthy individuals and for motor recovery after brain lesion as well as in pathological states associated to motor deficits. The main objective of this mini-review is to offer an integrative view about the potential use of tDCS for human motor learning modulation. Furthermore, we introduce the basic mechanisms underlying immediate and long-term effects associated to tDCS along with important considerations about its limitations and progression in recent years. PMID:28066300

  15. Direct and indirect ENSO modulation of winter temperature over the Asian–Pacific–American region

    PubMed Central

    Leung, Marco Y. T.; Zhou, Wen

    2016-01-01

    In this study, the direct and indirect atmospheric responses over the Asian–Pacific–American region to the El Niño–Southern Oscillation (ENSO) are documented. Since ENSO is likely to induce the northward displacement of the East Asian trough (NDEAT), some of the influence of ENSO on the Asian–Pacific–American region is possibly indirect and acts by inducing NDEAT. To separate corresponding influences of ENSO and NDEAT, partial regression is utilized. It is noted that temperature variations in the East Asian–Western Pacific region are controlled mainly by NDEAT. In contrast, ENSO demonstrates a weak direct relation to the temperature variation over the East Asian–Western Pacific region. This suggests that the influence of ENSO on this region is indirect, through modulation of NDEAT. On the other hand, temperature variation over the tropical eastern Pacific is dominated by ENSO forcing. Finally, temperature variation over the eastern North American–Western Pacific region is controlled by both ENSO and NDEAT. Nevertheless, their influences on temperature and circulation over this region tend to offset each other. This implies that temperature variation is controlled by their relative strengths. PMID:27821838

  16. Direct and indirect ENSO modulation of winter temperature over the Asian–Pacific–American region

    NASA Astrophysics Data System (ADS)

    Leung, Marco Y. T.; Zhou, Wen

    2016-11-01

    In this study, the direct and indirect atmospheric responses over the Asian–Pacific–American region to the El Niño–Southern Oscillation (ENSO) are documented. Since ENSO is likely to induce the northward displacement of the East Asian trough (NDEAT), some of the influence of ENSO on the Asian–Pacific–American region is possibly indirect and acts by inducing NDEAT. To separate corresponding influences of ENSO and NDEAT, partial regression is utilized. It is noted that temperature variations in the East Asian–Western Pacific region are controlled mainly by NDEAT. In contrast, ENSO demonstrates a weak direct relation to the temperature variation over the East Asian–Western Pacific region. This suggests that the influence of ENSO on this region is indirect, through modulation of NDEAT. On the other hand, temperature variation over the tropical eastern Pacific is dominated by ENSO forcing. Finally, temperature variation over the eastern North American–Western Pacific region is controlled by both ENSO and NDEAT. Nevertheless, their influences on temperature and circulation over this region tend to offset each other. This implies that temperature variation is controlled by their relative strengths.

  17. Combining segment generation with direct step-and-shoot optimization in intensity-modulated radiation therapy

    SciTech Connect

    Carlsson, Fredrik

    2008-09-15

    A method for generating a sequence of intensity-modulated radiation therapy step-and-shoot plans with increasing number of segments is presented. The objectives are to generate high-quality plans with few, large and regular segments, and to make the planning process more intuitive. The proposed method combines segment generation with direct step-and-shoot optimization, where leaf positions and segment weights are optimized simultaneously. The segment generation is based on a column generation approach. The method is evaluated on a test suite consisting of five head-and-neck cases and five prostate cases, planned for delivery with an Elekta SLi accelerator. The adjustment of segment shapes by direct step-and-shoot optimization improves the plan quality compared to using fixed segment shapes. The improvement in plan quality when adding segments is larger for plans with few segments. Eventually, adding more segments contributes very little to the plan quality, but increases the plan complexity. Thus, the method provides a tool for controlling the number of segments and, indirectly, the delivery time. This can support the planner in finding a sound trade-off between plan quality and treatment complexity.

  18. CO2 directly modulates connexin 26 by formation of carbamate bridges between subunits

    PubMed Central

    Meigh, Louise; Greenhalgh, Sophie A; Rodgers, Thomas L; Cann, Martin J; Roper, David I; Dale, Nicholas

    2013-01-01

    Homeostatic regulation of the partial pressure of CO2 (PCO2) is vital for life. Sensing of pH has been proposed as a sufficient proxy for determination of PCO2 and direct CO2-sensing largely discounted. Here we show that connexin 26 (Cx26) hemichannels, causally linked to respiratory chemosensitivity, are directly modulated by CO2. A ‘carbamylation motif’, present in CO2-sensitive connexins (Cx26, Cx30, Cx32) but absent from a CO2-insensitive connexin (Cx31), comprises Lys125 and four further amino acids that orient Lys125 towards Arg104 of the adjacent subunit of the connexin hexamer. Introducing the carbamylation motif into Cx31 created a mutant hemichannel (mCx31) that was opened by increases in PCO2. Mutation of the carbamylation motif in Cx26 and mCx31 destroyed CO2 sensitivity. Course-grained computational modelling of Cx26 demonstrated that the proposed carbamate bridge between Lys125 and Arg104 biases the hemichannel to the open state. Carbamylation of Cx26 introduces a new transduction principle for physiological sensing of CO2. DOI: http://dx.doi.org/10.7554/eLife.01213.001 PMID:24220509

  19. 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.

  20. CO₂directly modulates connexin 26 by formation of carbamate bridges between subunits.

    PubMed

    Meigh, Louise; Greenhalgh, Sophie A; Rodgers, Thomas L; Cann, Martin J; Roper, David I; Dale, Nicholas

    2013-11-12

    Homeostatic regulation of the partial pressure of CO2 (PCO2) is vital for life. Sensing of pH has been proposed as a sufficient proxy for determination of PCO2 and direct CO2-sensing largely discounted. Here we show that connexin 26 (Cx26) hemichannels, causally linked to respiratory chemosensitivity, are directly modulated by CO2. A 'carbamylation motif', present in CO2-sensitive connexins (Cx26, Cx30, Cx32) but absent from a CO2-insensitive connexin (Cx31), comprises Lys125 and four further amino acids that orient Lys125 towards Arg104 of the adjacent subunit of the connexin hexamer. Introducing the carbamylation motif into Cx31 created a mutant hemichannel (mCx31) that was opened by increases in PCO2. Mutation of the carbamylation motif in Cx26 and mCx31 destroyed CO2 sensitivity. Course-grained computational modelling of Cx26 demonstrated that the proposed carbamate bridge between Lys125 and Arg104 biases the hemichannel to the open state. Carbamylation of Cx26 introduces a new transduction principle for physiological sensing of CO2. DOI: http://dx.doi.org/10.7554/eLife.01213.001.

  1. Starch and alpha-glucan acting enzymes, modulating their properties by directed evolution.

    PubMed

    Kelly, Ronan M; Dijkhuizen, Lubbert; Leemhuis, Hans

    2009-03-25

    Starch is the major food reserve in plants and forms a large part of the daily calorie intake in the human diet. Industrially, starch has become a major raw material in the production of various products including bio-ethanol, coating and anti-staling agents. The complexity and diversity of these starch based industries and the demand for high quality end products through extensive starch processing, can only be met through the use of a broad range of starch and alpha-glucan modifying enzymes. The economic importance of these enzymes is such that the starch industry has grown to be the largest market for enzymes after the detergent industry. However, as the starch based industries expand and develop the demand for more efficient enzymes leading to lower production cost and higher quality products increases. This in turn stimulates interest in modifying the properties of existing starch and alpha-glucan acting enzymes through a variety of molecular evolution strategies. Within this review we examine and discuss the directed evolution strategies applied in the modulation of specific properties of starch and alpha-glucan acting enzymes and highlight the recent developments in the field of directed evolution techniques which are likely to be implemented in the future engineering of these enzymes.

  2. Inner composition alignment for inferring directed networks from short time series.

    PubMed

    Hempel, S; Koseska, A; Kurths, J; Nikoloski, Z

    2011-07-29

    Identifying causal links (couplings) is a fundamental problem that facilitates the understanding of emerging structures in complex networks. We propose and analyze inner composition alignment-a novel, permutation-based asymmetric association measure to detect regulatory links from very short time series, currently applied to gene expression. The measure can be used to infer the direction of couplings, detect indirect (superfluous) links, and account for autoregulation. Applications to the gene regulatory network of E. coli are presented.

  3. Transspinal direct current stimulation modulates migration and proliferation of adult newly born spinal cells in mice.

    PubMed

    Samaddar, Sreyashi; Vazquez, Kizzy; Ponkia, Dipen; Toruno, Pedro; Sahbani, Karim; Begum, Sultana; Abouelela, Ahmed; Mekhael, Wagdy; Ahmed, Zaghloul

    2017-02-01

    Direct current electrical fields have been shown to be a major factor in the regulation of cell proliferation, differentiation, migration, and survival, as well as in the maturation of dividing cells during development. During adulthood, spinal cord cells are continuously produced in both animals and humans, and they hold great potential for neural restoration following spinal cord injury. While the effects of direct current electrical fields on adult-born spinal cells cultured ex vivo have recently been reported, the effects of direct current electrical fields on adult-born spinal cells in vivo have not been characterized. Here, we provide convincing findings that a therapeutic form of transspinal direct current stimulation (tsDCS) affects the migration and proliferation of adult-born spinal cells in mice. Specifically, cathodal tsDCS attracted the adult-born spinal cells, while anodal tsDCS repulsed them. In addition, both tsDCS polarities caused a significant increase in cell number. Regarding the potential mechanisms involved, both cathodal and anodal tsDCS caused significant increases in expression of brain-derived neurotrophic factor, while expression of nerve growth factor increased and decreased, respectively. In the spinal cord, both anodal and cathodal tsDCS increased blood flow. Since blood flow and angiogenesis are associated with the proliferation of neural stem cells, increased blood flow may represent a major factor in the modulation of newly born spinal cells by tsDCS. Consequently, we propose that the method and novel findings presented in the current study have the potential to facilitate cellular, molecular, and/or bioengineering strategies to repair injured spinal cords.NEW & NOTEWORTHY Our results indicate that transspinal direct current stimulation (tsDCS) affects the migratory pattern and proliferation of adult newly born spinal cells, a cell population which has been implicated in learning and memory. In addition, our results suggest a

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

    PubMed

    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.

  5. 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

  6. 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.

  7. Externally induced frontoparietal synchronization modulates network dynamics and enhances working memory performance.

    PubMed

    Violante, Ines R; Li, Lucia M; Carmichael, David W; Lorenz, Romy; Leech, Robert; Hampshire, Adam; Rothwell, John C; Sharp, David J

    2017-03-14

    Cognitive functions such as working memory (WM) are emergent properties of large-scale network interactions. Synchronisation of oscillatory activity might contribute to WM by enabling the coordination of long-range processes. However, causal evidence for the way oscillatory activity shapes network dynamics and behavior in humans is limited. Here we applied transcranial alternating current stimulation (tACS) to exogenously modulate oscillatory activity in a right frontoparietal network that supports WM. Externally induced synchronization improved performance when cognitive demands were high. Simultaneously collected fMRI data reveals tACS effects dependent on the relative phase of the stimulation and the internal cognitive processing state. Specifically, synchronous tACS during the verbal WM task increased parietal activity, which correlated with behavioral performance. Furthermore, functional connectivity results indicate that the relative phase of frontoparietal stimulation influences information flow within the WM network. Overall, our findings demonstrate a link between behavioral performance in a demanding WM task and large-scale brain synchronization.

  8. 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).

  9. Confinement and diffusion modulate bistability and stochastic switching in a reaction network with positive feedback

    SciTech Connect

    Mlynarczyk, Paul J.; Pullen, Robert H.; Abel, Steven M.

    2016-01-07

    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.

  10. Externally induced frontoparietal synchronization modulates network dynamics and enhances working memory performance

    PubMed Central

    Violante, Ines R; Li, Lucia M; Carmichael, David W; Lorenz, Romy; Leech, Robert; Hampshire, Adam; Rothwell, John C; Sharp, David J

    2017-01-01

    Cognitive functions such as working memory (WM) are emergent properties of large-scale network interactions. Synchronisation of oscillatory activity might contribute to WM by enabling the coordination of long-range processes. However, causal evidence for the way oscillatory activity shapes network dynamics and behavior in humans is limited. Here we applied transcranial alternating current stimulation (tACS) to exogenously modulate oscillatory activity in a right frontoparietal network that supports WM. Externally induced synchronization improved performance when cognitive demands were high. Simultaneously collected fMRI data reveals tACS effects dependent on the relative phase of the stimulation and the internal cognitive processing state. Specifically, synchronous tACS during the verbal WM task increased parietal activity, which correlated with behavioral performance. Furthermore, functional connectivity results indicate that the relative phase of frontoparietal stimulation influences information flow within the WM network. Overall, our findings demonstrate a link between behavioral performance in a demanding WM task and large-scale brain synchronization. DOI: http://dx.doi.org/10.7554/eLife.22001.001 PMID:28288700

  11. Combining Partial Directed Coherence and Graph Theory to Analyse Effective Brain Networks of Different Mental Tasks

    PubMed Central

    Huang, Dengfeng; Ren, Aifeng; Shang, Jing; Lei, Qiao; Zhang, Yun; Yin, Zhongliang; Li, Jun; von Deneen, Karen M.; Huang, Liyu

    2016-01-01

    Purpose: The aim of this study is to qualify the network properties of the brain networks between two different mental tasks (play task or rest task) in a healthy population. Methods and Materials: EEG signals were recorded from 19 healthy subjects when performing different mental tasks. Partial directed coherence (PDC) analysis, based on Granger causality (GC), was used to assess the effective brain networks during the different mental tasks. Moreover, the network measures, including degree, degree distribution, local and global efficiency in delta, theta, alpha, and beta rhythms were calculated and analyzed. Results: The local efficiency is higher in the beta frequency and lower in the theta frequency during play task whereas the global efficiency is higher in the theta frequency and lower in the beta frequency in the rest task. Significance: This study reveals the network measures during different mental states and efficiency measures may be used as characteristic quantities for improvement in attentional performance. PMID:27242495

  12. Network diffusion-based analysis of high-throughput data for the detection of differentially enriched modules

    PubMed Central

    Bersanelli, Matteo; Mosca, Ettore; Remondini, Daniel; Castellani, Gastone; Milanesi, Luciano

    2016-01-01

    A relation exists between network proximity of molecular entities in interaction networks, functional similarity and association with diseases. The identification of network regions associated with biological functions and pathologies is a major goal in systems biology. We describe a network diffusion-based pipeline for the interpretation of different types of omics in the context of molecular interaction networks. We introduce the network smoothing index, a network-based quantity that allows to jointly quantify the amount of omics information in genes and in their network neighbourhood, using network diffusion to define network proximity. The approach is applicable to both descriptive and inferential statistics calculated on omics data. We also show that network resampling, applied to gene lists ranked by quantities derived from the network smoothing index, indicates the presence of significantly connected genes. As a proof of principle, we identified gene modules enriched in somatic mutations and transcriptional variations observed in samples of prostate adenocarcinoma (PRAD). In line with the local hypothesis, network smoothing index and network resampling underlined the existence of a connected component of genes harbouring molecular alterations in PRAD. PMID:27731320

  13. Synchronization of Coupled Reaction-Diffusion Neural Networks With Directed Topology via an Adaptive Approach.

    PubMed

    Zhang, Hao; Sheng, Yin; Zeng, Zhigang

    2017-03-15

    This paper investigates the synchronization issue of coupled reaction-diffusion neural networks with directed topology via an adaptive approach. Due to the complexity of the network structure and the presence of space variables, it is difficult to design proper adaptive strategies on coupling weights to accomplish the synchronous goal. Under the assumptions of two kinds of special network structures, that is, directed spanning path and directed spanning tree, some novel edge-based adaptive laws, which utilized the local information of node dynamics fully are designed on the coupling weights for reaching synchronization. By constructing appropriate energy function, and utilizing some analytical techniques, several sufficient conditions are given. Finally, some simulation examples are given to verify the effectiveness of the obtained theoretical results.

  14. 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.

  15. An analysis of the sectorial influence of CSI300 stocks within the directed network

    NASA Astrophysics Data System (ADS)

    Mai, Yong; Chen, Huan; Meng, Lei

    2014-02-01

    This paper uses the Partial Correlation Planar maximally filtered Graph (PCPG) method to construct a directed network for the constituent stocks underlying the China Securities Index 300 (CSI300). We also analyse the impact of individual stocks. We find that the CSI300 market is a scale-free network with a relatively small power law exponent. The volatility of the stock prices has significant impact on other stocks. In the sectorial network, the industrial sector is the most influential one over other sectors, the financial sector only has a modest influence, while the telecommunication services sector’s influence is marginal. In addition, such inter-sector influence displays quarterly stability.

  16. 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.

  17. The synthetic genetic network around PKC1 identifies novel modulators and components of protein kinase C signaling in Saccharomyces cerevisiae.

    PubMed

    Krause, Sue A; Xu, Hong; Gray, Joseph V

    2008-11-01

    Budding yeast Saccharomyces cerevisiae contains one protein kinase C (PKC) isozyme encoded by the essential gene PKC1. Pkc1 is activated by the small GTPase Rho1 and plays a central role in the cell wall integrity (CWI) signaling pathway. This pathway acts primarily to remodel the cell surface throughout the normal life cycle and upon various environmental stresses. The pathway is heavily branched, with multiple nonessential branches feeding into and out of the central essential Rho1-Pkc1 module. In an attempt to identify novel components and modifiers of CWI signaling, we determined the synthetic lethal genetic network around PKC1 by using dominant-negative synthetic genetic array analysis. The resulting mutants are hypersensitive to lowered Pkc1 activity. The corresponding 21 nonessential genes are closely related to CWI function: 14 behave in a chemical-genetic epistasis test as acting in the pathway, and 6 of these genes encode known components. Twelve of the 21 null mutants display elevated CWI reporter activity, consistent with the idea that the pathway is activated by and compensates for loss of the gene products. Four of the 21 mutants display low CWI reporter activity, consistent with the idea that the pathway is compromised in these mutants. One of the latter group of mutants lacks Ack1(Ydl203c), an uncharacterized SEL-1 domain-containing protein that we find modulates pathway activity. Epistasis analysis places Ack1 upstream of Pkc1 in the CWI pathway and dependent on the upstream Rho1 GTP exchange factors Rom2 and Tus1. Overall, the synthetic genetic network around PKC1 directly and efficiently identifies known and novel components of PKC signaling in yeast.

  18. 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.

  19. The Potential Role of Direct and Indirect Contacts on Infection Spread in Dairy Farm Networks

    PubMed Central

    Natalini, Silvano; Zarenghi, Luca; Ricchi, Matteo; Bolzoni, Luca

    2017-01-01

    Animals’ exchanges are considered the most effective route of between-farm infectious disease transmission. However, despite being often overlooked, the infection spread due to contaminated equipment, vehicles, or personnel proved to be important for several livestock epidemics. This study investigated the role of indirect contacts in a potential infection spread in the dairy farm network of the Province of Parma (Northern Italy). We built between-farm contact networks using data on cattle exchange (direct contacts), and on-farm visits by veterinarians (indirect contacts). We compared the features of the contact structures by using measures on static and temporal networks. We assessed the disease spreading potential of the direct and indirect network structures in the farm system by using data on the infection state of farms by paratuberculosis. Direct and indirect networks showed non-trivial differences with respect to connectivity, contact distribution, and super-spreaders identification. Furthermore, our analyses on paratuberculosis data suggested that the contributions of direct and indirect contacts on diseases spread are apparent at different spatial scales. Our results highlighted the potential role of indirect contacts in between-farm disease spread and underlined the need for a deeper understanding of these contacts to develop better strategies for prevention of livestock epidemics. PMID:28125610

  20. The Potential Role of Direct and Indirect Contacts on Infection Spread in Dairy Farm Networks.

    PubMed

    Rossi, Gianluigi; De Leo, Giulio A; Pongolini, Stefano; Natalini, Silvano; Zarenghi, Luca; Ricchi, Matteo; Bolzoni, Luca

    2017-01-01

    Animals' exchanges are considered the most effective route of between-farm infectious disease transmission. However, despite being often overlooked, the infection spread due to contaminated equipment, vehicles, or personnel proved to be important for several livestock epidemics. This study investigated the role of indirect contacts in a potential infection spread in the dairy farm network of the Province of Parma (Northern Italy). We built between-farm contact networks using data on cattle exchange (direct contacts), and on-farm visits by veterinarians (indirect contacts). We compared the features of the contact structures by using measures on static and temporal networks. We assessed the disease spreading potential of the direct and indirect network structures in the farm system by using data on the infection state of farms by paratuberculosis. Direct and indirect networks showed non-trivial differences with respect to connectivity, contact distribution, and super-spreaders identification. Furthermore, our analyses on paratuberculosis data suggested that the contributions of direct and indirect contacts on diseases spread are apparent at different spatial scales. Our results highlighted the potential role of indirect contacts in between-farm disease spread and underlined the need for a deeper understanding of these contacts to develop better strategies for prevention of livestock epidemics.

  1. On the relationship between deterministic and probabilistic directed Graphical models: from Bayesian networks to recursive neural networks.

    PubMed

    Baldi, Pierre; Rosen-Zvi, Michal

    2005-10-01

    Machine learning methods that can handle variable-size structured data such as sequences and graphs include Bayesian networks (BNs) and Recursive Neural Networks (RNNs). In both classes of models, the data is modeled using a set of observed and hidden variables associated with the nodes of a directed acyclic graph. In BNs, the conditional relationships between parent and child variables are probabilistic, whereas in RNNs they are deterministic and parameterized by neural networks. Here, we study the formal relationship between both classes of models and show that when the source nodes variables are observed, RNNs can be viewed as limits, both in distribution and probability, of BNs with local conditional distributions that have vanishing covariance matrices and converge to delta functions. Conditions for uniform convergence are also given together with an analysis of the behavior and exactness of Belief Propagation (BP) in 'deterministic' BNs. Implications for the design of mixed architectures and the corresponding inference algorithms are briefly discussed.

  2. 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.

  3. Evolution of egoism on semi-directed and undirected Barabási-Albert networks

    NASA Astrophysics Data System (ADS)

    Lima, F. W. S.

    2015-05-01

    Through Monte Carlo simulations, we study the evolution of the four strategies: Ethnocentric, altruistic, egoistic and cosmopolitan in one community of individuals. Interactions and reproduction among computational agents are simulated on undirected and semi-directed Barabási-Albert (BA) networks. We study the Hammond-Axelrod (HA) model on undirected and semi-directed BA networks for the asexual reproduction case. With a small modification in the traditional HA model, our simulations showed that egoism wins, differently from other results found in the literature where ethnocentric strategy is common. Here, mechanisms such as reciprocity are absent.

  4. Anti-inflammatory mechanism research of tanshinone II A by module-based network analysis.

    PubMed

    Zheng, Shichao; Ren, Zhenzhen; Zhang, Yanling; Qiao, Yanjiang

    2014-01-01

    Tanshinone IIA (Tan IIA) is one of the major fat-soluble ingredients in Salvia miltiorrhiza which has been widely used for various inflammatory conditions associated with cardiovascular and cerebrovascular disorders. However, the underlying anti-inflammatory mechanisms of Tan IIA are incompletely understood. The purpose of this study was to illuminate the anti-inflammatory mechanism of Tan IIA based on the protein interaction network (PIN) analysis. A PIN of Tan IIA was constructed with 281 nodes and 814 interactions and analyzed by gene ontology (GO) enrichment analysis based on Markov Cluster algorithm (MCL). Three modules were associated with anti-inflammatory actions. The most interesting finding of this study was that the anti-inflammatory effect of Tan IIA may be partly attributable to the mediate activation of TRAF2, TRAF3 and TRAF6, to inhibit the toll-like receptor signaling pathway and combine with AGER. Therefore, the module-based network analysis approach will be a new method for better understanding the anti-inflammatory mechanism of Tan IIA.

  5. Octopamine modulates activity of neural networks in the honey bee antennal lobe.

    PubMed

    Rein, Julia; Mustard, Julie A; Strauch, Martin; Smith, Brian H; Galizia, C Giovanni

    2013-11-01

    Neuronal plasticity allows an animal to respond to environmental changes by modulating its response to stimuli. In the honey bee (Apis mellifera), the biogenic amine octopamine plays a crucial role in appetitive odor learning, but little is known about how octopamine affects the brain. We investigated its effect in the antennal lobe, the first olfactory center in the brain, using calcium imaging to record background activity and odor responses before and after octopamine application. We show that octopamine increases background activity in olfactory output neurons, while reducing average calcium levels. Odor responses were modulated both upwards and downwards, with more odor response increases in glomeruli with negative or weak odor responses. Importantly, the octopamine effect was variable across glomeruli, odorants, odorant concentrations and animals, suggesting that the octopaminergic network is shaped by plasticity depending on an individual animal's history and possibly other factors. Using RNA interference, we show that the octopamine receptor AmOA1 (homolog of the Drosophila OAMB receptor) is involved in the octopamine effect. We propose a network model in which octopamine receptors are plastic in their density and located on a subpopulation of inhibitory neurons in a disinhibitory pathway. This would improve odor-coding of behaviorally relevant, previously experienced odors.

  6. Nano-rheology of hydrogels using direct drive force modulation atomic force microscopy†

    PubMed Central

    Nalam, Prathima C.; Gosvami, Nitya N.; Caporizzo, Matthew A.; Composto, Russell J.

    2016-01-01

    We present a magnetic force-based direct drive modulation method to measure local nano-rheological properties of soft materials across a broad frequency range (10 Hz to 2 kHz) using colloid-attached atomic force microscope (AFM) probes in liquid. The direct drive method enables artefact-free measurements over several decades of excitation frequency, and avoids the need to evaluate medium-induced hydrodynamic drag effects. The method was applied to measure the local mechanical properties of polyacrylamide hydrogels. The frequency-dependent storage stiffness, loss stiffness, and loss tangent (tan δ) were quantified for hydrogels having high and low crosslinking densities by measuring the amplitude and the phase response of the cantilever while the colloid was in contact with the hydrogel. The frequency bandwidth was further expanded to lower effective frequencies (0.1 Hz to 10 Hz) by obtaining force–displacement (FD) curves. Slow FD measurements showed a recoverable but highly hysteretic response, with the contact mechanical behaviour dependent on the loading direction: approach curves showed Hertzian behaviour while retraction curves fit the JKR contact mechanics model well into the adhesive regime, after which multiple detachment instabilities occurred. Using small amplitude dynamic modulation to explore faster rates, the load dependence of the storage stiffness transitioned from Hertzian to a dynamic punch-type (constant contact area) model, indicating significant influence of material dissipation coupled with adhesion. Using the appropriate contact model across the full frequency range measured, the storage moduli were found to remain nearly constant until an increase began near ∼100 Hz. The softer gels' storage modulus increased from 7.9 ± 0.4 to 14.5 ± 2.1 kPa (∼85%), and the stiffer gels' storage modulus increased from 16.3 ± 1.1 to 31.7 ± 5.0 kPa (∼95%). This increase at high frequencies may be attributed to a contribution from solvent

  7. Spectrally efficient terabit optical transmission with Nyquist 64-QAM half-cycle subcarrier modulation and direct detection.

    PubMed

    Zou, Kaiheng; Zhu, Yixiao; Zhang, Fan; Chen, Zhangyuan

    2016-06-15

    We demonstrate 1.728  Tb/s(16×108  Gb/s) direct-detection wavelength division multiplexing (WDM) transmission over 80 km standard single mode fiber (SSMF) with Nyquist 64-ary quadrature amplitude modulation (64-QAM) and half-cycle subcarrier modulation. Each channel carries single sideband 18 GBaud 64-QAM signal and the channel spacing is 27 GHz. Considering 20% soft-decision forward error correction and frame redundancy, a net spectral efficiency record of 3.25 b/s/Hz is achieved for 100 G single polarization direct-detection WDM transmission.

  8. 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

  9. Myths on Bi-direction Communication of Web 2.0 Based Social Networks: Is Social Network Truly Interactive?

    DTIC Science & Technology

    2011-03-10

    MAR 2012 2 . REPORT TYPE Final 3. DATES COVERED 01-03-2010 to 01-03-2012 4. TITLE AND SUBTITLE Myths on bi-direction communication of Web 2.0...publication • Search Engines, Portals, News • Business / Service App. interfaces • eBay, Amazone … • Social networks with many devices • Mobile phones...response Impact Analyser Figure 1 Social Interaction Monitoring 2 Status of Efforts 1) System Development We have studied web -monitoring

  10. Crustacean hyperglycemic hormones directly modulate the immune response of hemocytes in shrimp Litopenaeus vannamei.

    PubMed

    Wang, Lin; Chen, Hao; Xu, Jianchao; Xu, Qingsong; Wang, Mengqiang; Zhao, Depeng; Wang, Lingling; Song, Linsheng

    2017-03-01

    A robust immune response against invading pathogens is crucial for host to survive, which depends greatly on the well balance of metabolism. Increasing evidence has indicated that some metabolic hormones, such as insulin, could modulate immune responses directly. Crustacean hyperglycemic hormone (CHH) family is a group of ecdysozoans-specific peptide hormone involved in glucose metabolism and other biological events. In the present study, two members of CHH family (designated as LvCHH I and LvCHH II) in shrimp Litopenaeus vannamei with one and two crustacean neurohormone domains respectively were chosen to investigate their putative modulatory roles in both glucose metabolism and immune response. LvCHH I and LvCHH II were both expressed in the sinus gland and lamina ganglionalis of eyestalks and were significantly induced after white spot syndrome virus (WSSV) infection. Meanwhile, significant increases of hemolymph glucose levels were observed in shrimp at 12 and 24 h after WSSV infection while the glucose inside the hemocytes decreased at 6 h and then increased at 12 h. Gain-of-function of rLvCHHs was subsequently conducted in vivo by injecting the recombinant proteins (rLvCHH I and rLvCHH II). The hemolymph glucose increased significantly from 0.5 h to 3 h after the shrimps received an injection of rLvCHH I, while it decreased at 0.5 h and increased afterward at 3 h post rLvCHH II injection. At the meantime, significant decreases of reactive oxygen species level in hemocytes were observed at 3 h and 6 h post rLvCHH I injection, while it remained unchanged in rLvCHH II injection group. rLvCHH I and rLvCHH II could bind to the cytomembrane of primary shrimp hemocytes in vitro, and the expressions of superoxide dismutase and LvRelish increased when the hemocytes were incubated with rLvCHH I for 3 h. Meanwhile, the expression of antimicrobial peptides, crustin and penaeidin-4, were also induced by rLvCHH I and rLvCHH II. These results demonstrated that

  11. Analysis of SDWDM Ring Network and Enhancement Using Different Hybrid Optical Amplifiers and Modulation Formats

    NASA Astrophysics Data System (ADS)

    Anand, Vineet; Sharma, Anurag

    2016-09-01

    In this paper, performance enhancement of super-dense wavelength division multiplexing (SDWDM) optical add-drop multiplexer optical ring network for six nodes, 50 wavelengths having channel spacing of 0.2 nm for 300 km unidirectional nonlinear fiber is successfully demonstrated. The performance of the designed system is enhanced by comparing different modulation formats (non-return to zero (NRZ), return to zero (RZ), soliton, chirped return to zero (CRZ), carrier-suppressed RZ (CSRZ)) and hybrid amplifiers (Erbium-doped fiber amplifier (EDFA)-EDFA, semiconductor optical amplifier (SOA)-SOA, SOA, EDFA, EDFA-SOA) on the basis of eye diagram and bit error rate (BER). It has been observed that CRZ modulation format and EDFA-SOA shows the best results. It has been reported that EDFA-SOA/CRZ modulation format can achieve BER as better as e-13, which gives best performance. The effect of channel spacing on SDWDM system and performance degradation due to crosstalk is also evaluated.

  12. Module number of default mode network: inter-subject variability and effects of sleep deprivation.

    PubMed

    Wang, Yulin; Liu, Huan; Hitchman, Glenn; Lei, Xu

    2015-01-30

    Sleep deprivation have shown its great influence on the default mode network (DMN). The DMN is a core system in resting state brain activity. Recent studies have focused on its subsystems and multiple functions. However, the individual specific organization of the DMN is rarely investigated. As the effects of sleep deprivation (SD) on mood are well documented, a more interesting question is whether changes in the processing of emotional information due to sleep deprivation are related to any specific topological properties of the DMN. In this study, we proposed an index, module number of DMN (mnDMN), to measure the specific modular structure of the DMN for each individual. Our results showed that the DMN was generally split into two modules after SD, and the decreased functional connectivity between the two modules was related to a worsening of the participants׳ self-reported emotional state. Furthermore, the mnDMN was correlated with participants' rating scores of high valence pictures in the SD session, indicating that the mnDMN might reflect mood valuation in the human brain. Overall, our research reveals the diversity of the DMN, and may contribute towards a better understanding of the properties and functions of the DMN.

  13. A New High-Resolution Direction Finding Architecture Using Photonics and Neural Network Signal Processing for Miniature Air Vehicle Applications

    DTIC Science & Technology

    2015-09-01

    RESOLUTION DIRECTION FINDING ARCHITECTURE USING PHOTONICS AND NEURAL NETWORK SIGNAL PROCESSING FOR MINIATURE AIR VEHICLE APPLICATIONS by Robert...RESOLUTION DIRECTION FINDING ARCHITECTURE USING PHOTONICS AND NEURAL NETWORK SIGNAL PROCESSING FOR MINIATURE AIR VEHICLE APPLICATIONS 5. FUNDING...unlimited 12b. DISTRIBUTION CODE 13. ABSTRACT (maximum 200 words) This paper investigates the design of an interferometric direction finding receiver

  14. Stability Analysis for a Large-scale Space Power Network, International Space Station and Japanese Experiment Module

    NASA Astrophysics Data System (ADS)

    Komatsu, Masaaki; Arai, Satoaki

    The International Space Station (ISS), which is scheduled to start the operation fully in early 2000’s, is being developed and assembled on orbit since 1998 with international cooperation of the USA, Russia, Europe, Canada, and Japan. Japan participates in this ISS program and will provide the Japanese Experiment Module (JEM, named “Kibo") which will be attached to the ISS core. Japan Aerospace Exploration Agency (JAXA), which is responsible for the JEM system development and integration, has been developed JEM Electric Power System (JEM EPS) as part of the Space Station Electric Power System (EPS). The International Space Station Electric Power System is the world’s largest orbiting direct-current (DC) power system. The ISS electric power is generated by solar arrays, and distributed to the each module in 120 Vdc bus voltage rating. When designing a large-scale Space Power System using direct current (DC), special attention must be placed on the electrical stability and control of the system and individual load on the system. For a large-scale Space Power System, it is not feasible to design the entire system as a whole. Instead, the system can be defined in term of numerous small blocks, and each block then designed individually. The individual blocks are then integrated to form a complete system. The International Space Station (ISS) is one of good example for these issue and concerns as a large-scale Space Power System. This paper describes the approach of the stability analysis for a large-scale space power network.

  15. Random and directed walk-based top-(k) queries in wireless sensor networks.

    PubMed

    Fu, Jun-Song; Liu, Yun

    2015-05-26

    In wireless sensor networks, filter-based top-  query approaches are the state-of-the-art solutions and have been extensively researched in the literature, however, they are very sensitive to the network parameters, including the size of the network, dynamics of the sensors' readings and declines in the overall range of all the readings. In this work, a random walk-based top-  query approach called RWTQ and a directed walk-based top-  query approach called DWTQ are proposed. At the beginning of a top-  query, one or several tokens are sent to the specific node(s) in the network by the base station. Then, each token walks in the network independently to record and process the readings in a random or directed way. A strategy of choosing the "right" way in DWTQ is carefully designed for the token(s) to arrive at the high-value regions as soon as possible. When designing the walking strategy for DWTQ, the spatial correlations of the readings are also considered. Theoretical analysis and simulation results indicate that RWTQ and DWTQ both are very robust against these parameters discussed previously. In addition, DWTQ outperforms TAG, FILA and EXTOK in transmission cost, energy consumption and network lifetime.

  16. 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.

  17. Event-Triggered Distributed Average Consensus Over Directed Digital Networks With Limited Communication Bandwidth.

    PubMed

    Li, Huaqing; Chen, Guo; Huang, Tingwen; Dong, Zhaoyang; Zhu, Wei; Gao, Lan

    2016-12-01

    In this paper, we consider the event-triggered distributed average-consensus of discrete-time first-order multiagent systems with limited communication data rate and general directed network topology. In the framework of digital communication network, each agent has a real-valued state but can only exchange finite-bit binary symbolic data sequence with its neighborhood agents at each time step due to the digital communication channels with energy constraints. Novel event-triggered dynamic encoder and decoder for each agent are designed, based on which a distributed control algorithm is proposed. A scheme that selects the number of channel quantization level (number of bits) at each time step is developed, under which all the quantizers in the network are never saturated. The convergence rate of consensus is explicitly characterized, which is related to the scale of network, the maximum degree of nodes, the network structure, the scaling function, the quantization interval, the initial states of agents, the control gain and the event gain. It is also found that under the designed event-triggered protocol, by selecting suitable parameters, for any directed digital network containing a spanning tree, the distributed average consensus can be always achieved with an exponential convergence rate based on merely one bit information exchange between each pair of adjacent agents at each time step. Two simulation examples are provided to illustrate the feasibility of presented protocol and the correctness of the theoretical results.

  18. Weighted and directed interactions in evolving large-scale epileptic brain networks.

    PubMed

    Dickten, Henning; Porz, Stephan; Elger, Christian E; Lehnertz, Klaus

    2016-10-06

    Epilepsy can be regarded as a network phenomenon with functionally and/or structurally aberrant connections in the brain. Over the past years, concepts and methods from network theory substantially contributed to improve the characterization of structure and function of these epileptic networks and thus to advance understanding of the dynamical disease epilepsy. We extend this promising line of research and assess-with high spatial and temporal resolution and using complementary analysis approaches that capture different characteristics of the complex dynamics-both strength and direction of interactions in evolving large-scale epileptic brain networks of 35 patients that suffered from drug-resistant focal seizures with different anatomical onset locations. Despite this heterogeneity, we find that even during the seizure-free interval the seizure onset zone is a brain region that, when averaged over time, exerts strongest directed influences over other brain regions being part of a large-scale network. This crucial role, however, manifested by averaging on the population-sample level only - in more than one third of patients, strongest directed interactions can be observed between brain regions far off the seizure onset zone. This may guide new developments for individualized diagnosis, treatment and control.

  19. Weighted and directed interactions in evolving large-scale epileptic brain networks

    NASA Astrophysics Data System (ADS)

    Dickten, Henning; Porz, Stephan; Elger, Christian E.; Lehnertz, Klaus

    2016-10-01

    Epilepsy can be regarded as a network phenomenon with functionally and/or structurally aberrant connections in the brain. Over the past years, concepts and methods from network theory substantially contributed to improve the characterization of structure and function of these epileptic networks and thus to advance understanding of the dynamical disease epilepsy. We extend this promising line of research and assess—with high spatial and temporal resolution and using complementary analysis approaches that capture different characteristics of the complex dynamics—both strength and direction of interactions in evolving large-scale epileptic brain networks of 35 patients that suffered from drug-resistant focal seizures with different anatomical onset locations. Despite this heterogeneity, we find that even during the seizure-free interval the seizure onset zone is a brain region that, when averaged over time, exerts strongest directed influences over other brain regions being part of a large-scale network. This crucial role, however, manifested by averaging on the population-sample level only – in more than one third of patients, strongest directed interactions can be observed between brain regions far off the seizure onset zone. This may guide new developments for individualized diagnosis, treatment and control.

  20. Weighted and directed interactions in evolving large-scale epileptic brain networks

    PubMed Central

    Dickten, Henning; Porz, Stephan; Elger, Christian E.; Lehnertz, Klaus

    2016-01-01

    Epilepsy can be regarded as a network phenomenon with functionally and/or structurally aberrant connections in the brain. Over the past years, concepts and methods from network theory substantially contributed to improve the characterization of structure and function of these epileptic networks and thus to advance understanding of the dynamical disease epilepsy. We extend this promising line of research and assess—with high spatial and temporal resolution and using complementary analysis approaches that capture different characteristics of the complex dynamics—both strength and direction of interactions in evolving large-scale epileptic brain networks of 35 patients that suffered from drug-resistant focal seizures with different anatomical onset locations. Despite this heterogeneity, we find that even during the seizure-free interval the seizure onset zone is a brain region that, when averaged over time, exerts strongest directed influences over other brain regions being part of a large-scale network. This crucial role, however, manifested by averaging on the population-sample level only – in more than one third of patients, strongest directed interactions can be observed between brain regions far off the seizure onset zone. This may guide new developments for individualized diagnosis, treatment and control. PMID:27708381

  1. Transcranial direct-current stimulation modulates offline visual oscillatory activity: A magnetoencephalography study.

    PubMed

    Heinrichs-Graham, Elizabeth; McDermott, Timothy J; Mills, Mackenzie S; Coolidge, Nathan M; Wilson, Tony W

    2017-03-01

    Transcranial direct-current stimulation (tDCS) is a noninvasive neuromodulatory method that involves delivering low amplitude, direct current to specific regions of the brain. While a wealth of literature shows changes in behavior and cognition following tDCS administration, the underlying neuronal mechanisms remain largely unknown. Neuroimaging studies have generally used fMRI and shown only limited consensus to date, while the few electrophysiological studies have reported mostly null or counterintuitive findings. The goal of the current investigation was to quantify tDCS-induced alterations in the oscillatory dynamics of visual processing. To this end, we performed either active or sham tDCS using an occipital-frontal electrode configuration, and then recorded magnetoencephalography (MEG) offline during a visual entrainment task. Significant oscillatory responses were imaged in the time-frequency domain using beamforming, and the effects of tDCS on absolute and relative power were assessed. The results indicated significantly increased basal alpha levels in the occipital cortex following anodal tDCS, as well as reduced occipital synchronization at the second harmonic of the stimulus-flicker frequency relative to sham stimulation. In addition, we found reduced power in brain regions near the cathode (e.g., right inferior frontal gyrus [IFG]) following active tDCS, which was absent in the sham group. Taken together, these results suggest that anodal tDCS of the occipital cortices differentially modulates spontaneous and induced activity, and may interfere with the entrainment of neuronal populations by a visual-flicker stimulus. These findings also demonstrate the importance of electrode configuration on whole-brain dynamics, and highlight the deceptively complicated nature of tDCS in the context of neurophysiology.

  2. Liraglutide directly protects cardiomyocytes against reperfusion injury possibly via modulation of intracellular calcium homeostasis

    PubMed Central

    Hu, Shun-Ying; Zhang, Ying; Zhu, Ping-Jun; Zhou, Hao; Chen, Yun-Dai

    2017-01-01

    Background Liraglutide is glucagon-like peptide-1 receptor agonist for treating patients with type 2 diabetes mellitus. Our previous studies have demonstrated that liraglutide protects cardiac function through improving endothelial function in patients with acute myocardial infarction undergoing percutaneous coronary intervention. The present study will investigate whether liraglutide can perform direct protective effects on cardiomyocytes against reperfusion injury. Methods In vitro experiments were performed using H9C2 cells and neonatal rat ventricular cadiomyocytes undergoing simulative hypoxia/reoxygenation (H/R) induction. Cardiomyocytes apoptosis was detected by fluorescence TUNEL. Mitochondrial membrane potential (ΔΨm) and intracellular reactive oxygen species (ROS) was assessed by JC-1 and DHE, respectively. Fura-2/AM was used to measure intracellular Ca2+ concentration and calcium transient. Immunofluorescence staining was used to assess the expression level of sarcoplasmic reticulum Ca2+-ATPase (SERCA2a). In vivo experiments, myocardial apoptosis and expression of SERCA2a were detected by colorimetric TUNEL and by immunofluorescence staining, respectively. Results In vitro liraglutide inhibited cardiomyotes apoptosis against H/R. ΔΨm of cardiomyocytes was higher in liraglutide group than H/R group. H/R increased ROS production in H9C2 cells which was attenuated by liraglutide. Liraglutide significantly lowered Ca2+ overload and improved calcium transient compared with H/R group. Immunofluorescence staining results showed liraglutide promoted SERCA2a expression which was decreased in H/R group. In ischemia/reperfusion rat hearts, apoptosis was significantly attenuated and SERCA2a expression was increased by liraglutide compared with H/R group. Conclusions Liraglutide can directly protect cardiomyocytes against reperfusion injury which is possibly through modulation of intracellular calcium homeostasis. PMID:28270843

  3. 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) ha