Science.gov

Sample records for links signaling network

  1. Novel links in the plant TOR kinase signaling network.

    PubMed

    Xiong, Yan; Sheen, Jen

    2015-12-01

    Nutrient and energy sensing and signaling mechanisms constitute the most ancient and fundamental regulatory networks to control growth and development in all life forms. The target of rapamycin (TOR) protein kinase is modulated by diverse nutrient, energy, hormone and stress inputs and plays a central role in regulating cell proliferation, growth, metabolism and stress responses from yeasts to plants and animals. Recent chemical, genetic, genomic and metabolomic analyses have enabled significant progress toward molecular understanding of the TOR signaling network in multicellular plants. This review discusses the applications of new chemical tools to probe plant TOR functions and highlights recent findings and predictions on TOR-mediate biological processes. Special focus is placed on novel and evolutionarily conserved TOR kinase effectors as positive and negative signaling regulators that control transcription, translation and metabolism to support cell proliferation, growth and maintenance from embryogenesis to senescence in the plant system. PMID:26476687

  2. New mechanistic links between sugar and hormone signalling networks.

    PubMed

    Ljung, Karin; Nemhauser, Jennifer L; Perata, Pierdomenico

    2015-06-01

    Plant growth and development must be coordinated with metabolism, notably with the efficiency of photosynthesis and the uptake of nutrients. This coordination requires local connections between hormonal response and metabolic state, as well as long-distance connections between shoot and root tissues. Recently, several molecular mechanisms have been proposed to explain the integration of sugar signalling with hormone pathways. In this work, DELLA and PIF proteins have emerged as hubs in sugar-hormone cross-regulation networks. PMID:26037392

  3. SignaLink 2 – a signaling pathway resource with multi-layered regulatory networks

    PubMed Central

    2013-01-01

    Background Signaling networks in eukaryotes are made up of upstream and downstream subnetworks. The upstream subnetwork contains the intertwined network of signaling pathways, while the downstream regulatory part contains transcription factors and their binding sites on the DNA as well as microRNAs and their mRNA targets. Currently, most signaling and regulatory databases contain only a subsection of this network, making comprehensive analyses highly time-consuming and dependent on specific data handling expertise. The need for detailed mapping of signaling systems is also supported by the fact that several drug development failures were caused by undiscovered cross-talk or regulatory effects of drug targets. We previously created a uniformly curated signaling pathway resource, SignaLink, to facilitate the analysis of pathway cross-talks. Here, we present SignaLink 2, which significantly extends the coverage and applications of its predecessor. Description We developed a novel concept to integrate and utilize different subsections (i.e., layers) of the signaling network. The multi-layered (onion-like) database structure is made up of signaling pathways, their pathway regulators (e.g., scaffold and endocytotic proteins) and modifier enzymes (e.g., phosphatases, ubiquitin ligases), as well as transcriptional and post-transcriptional regulators of all of these components. The user-friendly website allows the interactive exploration of how each signaling protein is regulated. The customizable download page enables the analysis of any user-specified part of the signaling network. Compared to other signaling resources, distinctive features of SignaLink 2 are the following: 1) it involves experimental data not only from humans but from two invertebrate model organisms, C. elegans and D. melanogaster; 2) combines manual curation with large-scale datasets; 3) provides confidence scores for each interaction; 4) operates a customizable download page with multiple file formats

  4. Choline-releasing glycerophosphodiesterase EDI3 links the tumor metabolome to signaling network activities.

    PubMed

    Marchan, Rosemarie; Lesjak, Michaela S; Stewart, Joanna D; Winter, Roland; Seeliger, Janine; Hengstler, Jan G

    2012-12-15

    Recently, EDI3 was identified as a key factor for choline metabolism that controls tumor cell migration and is associated with metastasis in endometrial carcinomas. EDI3 cleaves glycerophosphocholine (GPC) to form choline and glycerol-3-phosphate (G3P). Choline is then further metabolized to phosphatidylcholine (PtdC), the major lipid in membranes and a key player in membrane-mediated cell signaling. The second product, G3P, is a precursor molecule for several lipids with central roles in signaling, for example lysophosphatidic acid (LPA), phosphatidic acid (PA) and diacylglycerol (DAG). LPA activates intracellular signaling pathways by binding to specific LPA receptors, including membrane-bound G protein-coupled receptors and the intracellular nuclear receptor, PPARγ. Conversely, PA and DAG mediate signaling by acting as lipid anchors that bind and activate several signaling proteins. For example, binding of GTPases and PKC to PA and DAG, respectively, increases the activation of signaling networks, mediating processes such as migration, adhesion, proliferation or anti-apoptosis-all relevant for tumor development. We present a concept by which EDI3 either directly generates signaling molecules or provides "membrane anchors" for downstream signaling factors. As a result, EDI3 links choline metabolism to signaling activities resulting in a more malignant phenotype. PMID:23114620

  5. PIPELINES AS COMMUNICATION NETWORK LINKS

    SciTech Connect

    Kelvin T. Erickson; Ann Miller; E. Keith Stanek; C.H. Wu; Shari Dunn-Norman

    2005-03-14

    This report presents the results of an investigation into two methods of using the natural gas pipeline as a communication medium. The work addressed the need to develop secure system monitoring and control techniques between the field and control centers and to robotic devices in the pipeline. In the first method, the pipeline was treated as a microwave waveguide. In the second method, the pipe was treated as a leaky feeder or a multi-ground neutral and the signal was directly injected onto the metal pipe. These methods were tested on existing pipeline loops at UMR and Batelle. The results reported in this report indicate the feasibility of both methods. In addition, a few suitable communication link protocols for this network were analyzed.

  6. Covalently linked organic networks

    NASA Astrophysics Data System (ADS)

    Tsotsalas, Manuel; Addicoat, Matthew

    2015-02-01

    In this review, we intend to give an overview of the synthesis of well-defined covalently-bound organic network materials such as covalent organic frameworks (COFs), conjugated microporous frameworks (CMPs) and other “ideal polymer networks” and discuss the different approaches in their synthesis and their potential applications. In addition we will describe the common computational approaches and highlight recent achievements in the computational study of their structure and properties. For further information the interested reader is referred to several excellent and more detailed reviews dealing with the synthesis [Dawson 2012; Ding 2013; Feng 2012] and computational aspects [Han 2009; Colón 2014] of the materials presented here.

  7. Multiplexing and networking through fiber optic links for SCADA systems

    SciTech Connect

    Damsker, D.

    1982-07-01

    The Supervisory Control and Data Acquisition (SCADA) systems of the future might consist of local computer networks tied together through long haul links, using a packet-switching technique. This paper assesses fiber optic link characteristics as potential components of SCADA systems. Essentially, a fiber optic link is constrained to a simplex communication from transmitter to receiver. Such a simplex link is analyzed for its capability to convey baseband signaling and time-, frequency-, and spectral-division multiplexing. The combination of a microcomputer and a simplex fiber optic link is a building block for several configurations of local computer networks. Such a building block is called the Universal Intelligent Optical Communication Link (UIOCL). The paper examines prospective optical networking techniques and evaluates several optical couplers for various network configurations as well as for full- and halfduplex communications. The feasibility of long haul fiber optic links and networks is considered further in the paper.

  8. LinkMind: link optimization in swarming mobile sensor networks.

    PubMed

    Ngo, Trung Dung

    2011-01-01

    A swarming mobile sensor network is comprised of a swarm of wirelessly connected mobile robots equipped with various sensors. Such a network can be applied in an uncertain environment for services such as cooperative navigation and exploration, object identification and information gathering. One of the most advantageous properties of the swarming wireless sensor network is that mobile nodes can work cooperatively to organize an ad-hoc network and optimize the network link capacity to maximize the transmission of gathered data from a source to a target. This paper describes a new method of link optimization of swarming mobile sensor networks. The new method is based on combination of the artificial potential force guaranteeing connectivities of the mobile sensor nodes and the max-flow min-cut theorem of graph theory ensuring optimization of the network link capacity. The developed algorithm is demonstrated and evaluated in simulation. PMID:22164070

  9. LinkMind: Link Optimization in Swarming Mobile Sensor Networks

    PubMed Central

    Ngo, Trung Dung

    2011-01-01

    A swarming mobile sensor network is comprised of a swarm of wirelessly connected mobile robots equipped with various sensors. Such a network can be applied in an uncertain environment for services such as cooperative navigation and exploration, object identification and information gathering. One of the most advantageous properties of the swarming wireless sensor network is that mobile nodes can work cooperatively to organize an ad-hoc network and optimize the network link capacity to maximize the transmission of gathered data from a source to a target. This paper describes a new method of link optimization of swarming mobile sensor networks. The new method is based on combination of the artificial potential force guaranteeing connectivities of the mobile sensor nodes and the max-flow min-cut theorem of graph theory ensuring optimization of the network link capacity. The developed algorithm is demonstrated and evaluated in simulation. PMID:22164070

  10. Growing Networks with Positive and Negative Links

    NASA Astrophysics Data System (ADS)

    Dech, Corynne; Antwi, Shadrack; Shaw, Leah

    Scale-free networks grown via preferential attachment have been used to model real-world networks such as the Internet, citation networks, and social networks. Here we investigate signed scale-free networks where an edge represents a positive or negative connection. We present analytic results and simulation for a growing signed network model. We compare the signed network to an unsigned scale-free network. We discuss several options for preferential attachment in a signed network that could be further adapted to model the accumulation of links over time in real-world signed networks.

  11. Link prediction in complex networks: A survey

    NASA Astrophysics Data System (ADS)

    Lü, Linyuan; Zhou, Tao

    2011-03-01

    Link prediction in complex networks has attracted increasing attention from both physical and computer science communities. The algorithms can be used to extract missing information, identify spurious interactions, evaluate network evolving mechanisms, and so on. This article summaries recent progress about link prediction algorithms, emphasizing on the contributions from physical perspectives and approaches, such as the random-walk-based methods and the maximum likelihood methods. We also introduce three typical applications: reconstruction of networks, evaluation of network evolving mechanism and classification of partially labeled networks. Finally, we introduce some applications and outline future challenges of link prediction algorithms.

  12. Interplant signalling through hyphal networks.

    PubMed

    Johnson, David; Gilbert, Lucy

    2015-03-01

    Mycorrhizal fungi can form common mycelial networks (CMNs) that interconnect plants. Here, we provide an insight into recent findings demonstrating that CMNs can be conduits for interplant signalling, influencing defence against insect herbivores and foliar necrotrophic fungi. A likely mechanism is direct transfer of signalling molecules within hyphae. However, electrical signals, which can be induced by wounding, may also enable signalling over relatively long distances, because the biophysical constraints imposed by liquid transport in hyphae and interaction with soil are relieved. We do not yet understand the ecological, evolutionary and agronomic implications of interplant signalling via CMNs. Identifying the mechanism of interplant signalling will help to address these gaps. PMID:25421970

  13. SIGNALING NETWORKS IN PALATE DEVELOPMENT

    PubMed Central

    Lane, Jamie; Kaartinen, Vesa

    2014-01-01

    Palatogenesis, the formation of the palate, is a dynamic process that is regulated by a complex series of context-dependent morphogenetic signaling events. Many genes involved in palatogenesis have been discovered through the use of genetically-manipulated mouse models as well as from human genetic studies, but the roles of these genes and their products in signaling networks regulating palatogenesis are still poorly known. In this review, we give a brief overview on palatogenesis and introduce key signaling cascades leading to formation of the intact palate. Moreover, we review conceptual differences between pathway biology and network biology and discuss how some of the recent technological advances in conjunction with mouse genetic models have contributed to our understanding of signaling networks regulating palate growth and fusion. PMID:24644145

  14. Cross-linked structure of network evolution

    NASA Astrophysics Data System (ADS)

    Bassett, Danielle S.; Wymbs, Nicholas F.; Porter, Mason A.; Mucha, Peter J.; Grafton, Scott T.

    2014-03-01

    We study the temporal co-variation of network co-evolution via the cross-link structure of networks, for which we take advantage of the formalism of hypergraphs to map cross-link structures back to network nodes. We investigate two sets of temporal network data in detail. In a network of coupled nonlinear oscillators, hyperedges that consist of network edges with temporally co-varying weights uncover the driving co-evolution patterns of edge weight dynamics both within and between oscillator communities. In the human brain, networks that represent temporal changes in brain activity during learning exhibit early co-evolution that then settles down with practice. Subsequent decreases in hyperedge size are consistent with emergence of an autonomous subgraph whose dynamics no longer depends on other parts of the network. Our results on real and synthetic networks give a poignant demonstration of the ability of cross-link structure to uncover unexpected co-evolution attributes in both real and synthetic dynamical systems. This, in turn, illustrates the utility of analyzing cross-links for investigating the structure of temporal networks.

  15. Cross-linked structure of network evolution

    SciTech Connect

    Bassett, Danielle S.; Wymbs, Nicholas F.; Grafton, Scott T.; Porter, Mason A.; Mucha, Peter J.

    2014-03-15

    We study the temporal co-variation of network co-evolution via the cross-link structure of networks, for which we take advantage of the formalism of hypergraphs to map cross-link structures back to network nodes. We investigate two sets of temporal network data in detail. In a network of coupled nonlinear oscillators, hyperedges that consist of network edges with temporally co-varying weights uncover the driving co-evolution patterns of edge weight dynamics both within and between oscillator communities. In the human brain, networks that represent temporal changes in brain activity during learning exhibit early co-evolution that then settles down with practice. Subsequent decreases in hyperedge size are consistent with emergence of an autonomous subgraph whose dynamics no longer depends on other parts of the network. Our results on real and synthetic networks give a poignant demonstration of the ability of cross-link structure to uncover unexpected co-evolution attributes in both real and synthetic dynamical systems. This, in turn, illustrates the utility of analyzing cross-links for investigating the structure of temporal networks.

  16. TLR-signaling Networks

    PubMed Central

    Brown, J.; Wang, H.; Hajishengallis, G.N.; Martin, M.

    2011-01-01

    Toll-like receptors play a critical role in innate immunity by detecting invading pathogens. The ability of TLRs to engage different intracellular signaling molecules and cross-talk with other regulatory pathways is an important factor in shaping the type, magnitude, and duration of the inflammatory response. The present review will cover the fundamental signaling pathways utilized by TLRs and how these pathways regulate the innate immune response to pathogens. Abbreviations: TLR, Toll-like receptor; PRR, pattern recognition receptor; PAMP, pathogen-associated molecular pattern; LPS, lipopolysaccharide; APC, antigen-presenting cell; IL, interleukin; TIR, Toll/IL-1R homology; MyD88, myeloid differentiation factor 88; IFN, interferon; TRIF, TIR-domain-containing adapter-inducing interferon-β; IRAK, IL-1R-associated kinase; TAK1, TGF-β-activated kinase; TAB1, TAK1-binding protein; NF-κB, nuclear factor kappa-light-chain-enhancer of activated B-cells; MAPK, mitogen-activated protein kinase; NLR, NOD-like receptors; LRR, leucine-rich repeats; DC, dendritic cell; PI3K, phosphoinositide 3-kinases; GSK3, glycogen synthase kinase-3; mTOR, mammalian target of rapamycin; DAF, decay-accelerating factor; IKK, IκB kinase; IRF, interferon regulatory factors; TBK1, TANK-binding kinase 1; CARD, caspase activation and recruitment domain; PYD, pyrin N-terminal homology domain; ATF, activating transcription factor; and PTEN, phosphatase and tensin homolog. PMID:20940366

  17. Toward link predictability of complex networks

    PubMed Central

    Lü, Linyuan; Pan, Liming; Zhou, Tao; Zhang, Yi-Cheng; Stanley, H. Eugene

    2015-01-01

    The organization of real networks usually embodies both regularities and irregularities, and, in principle, the former can be modeled. The extent to which the formation of a network can be explained coincides with our ability to predict missing links. To understand network organization, we should be able to estimate link predictability. We assume that the regularity of a network is reflected in the consistency of structural features before and after a random removal of a small set of links. Based on the perturbation of the adjacency matrix, we propose a universal structural consistency index that is free of prior knowledge of network organization. Extensive experiments on disparate real-world networks demonstrate that (i) structural consistency is a good estimation of link predictability and (ii) a derivative algorithm outperforms state-of-the-art link prediction methods in both accuracy and robustness. This analysis has further applications in evaluating link prediction algorithms and monitoring sudden changes in evolving network mechanisms. It will provide unique fundamental insights into the above-mentioned academic research fields, and will foster the development of advanced information filtering technologies of interest to information technology practitioners. PMID:25659742

  18. Toward link predictability of complex networks.

    PubMed

    Lü, Linyuan; Pan, Liming; Zhou, Tao; Zhang, Yi-Cheng; Stanley, H Eugene

    2015-02-24

    The organization of real networks usually embodies both regularities and irregularities, and, in principle, the former can be modeled. The extent to which the formation of a network can be explained coincides with our ability to predict missing links. To understand network organization, we should be able to estimate link predictability. We assume that the regularity of a network is reflected in the consistency of structural features before and after a random removal of a small set of links. Based on the perturbation of the adjacency matrix, we propose a universal structural consistency index that is free of prior knowledge of network organization. Extensive experiments on disparate real-world networks demonstrate that (i) structural consistency is a good estimation of link predictability and (ii) a derivative algorithm outperforms state-of-the-art link prediction methods in both accuracy and robustness. This analysis has further applications in evaluating link prediction algorithms and monitoring sudden changes in evolving network mechanisms. It will provide unique fundamental insights into the above-mentioned academic research fields, and will foster the development of advanced information filtering technologies of interest to information technology practitioners. PMID:25659742

  19. Influence of reciprocal links in social networks.

    PubMed

    Zhu, Yu-Xiao; Zhang, Xiao-Guang; Sun, Gui-Quan; Tang, Ming; Zhou, Tao; Zhang, Zi-Ke

    2014-01-01

    How does reciprocal links affect the function of real social network? Does reciprocal link and non-reciprocal link play the same role? Previous researches haven't displayed a clear picture to us until now according to the best of our knowledge. Motivated by this, in this paper, we empirically study the influence of reciprocal links in two representative real datasets, Sina Weibo and Douban. Our results demonstrate that the reciprocal links play a more important role than non-reciprocal ones in information diffusion process. In particular, not only coverage but also the speed of the information diffusion can be significantly enhanced by considering the reciprocal effect. We give some possible explanations from the perspectives of network connectivity and efficiency. This work may shed some light on the in-depth understanding and application of the reciprocal effect in directed online social networks. PMID:25072242

  20. Influence of Reciprocal Links in Social Networks

    PubMed Central

    Zhu, Yu-Xiao; Zhang, Xiao-Guang; Sun, Gui-Quan; Tang, Ming; Zhou, Tao; Zhang, Zi-Ke

    2014-01-01

    How does reciprocal links affect the function of real social network? Does reciprocal link and non-reciprocal link play the same role? Previous researches haven't displayed a clear picture to us until now according to the best of our knowledge. Motivated by this, in this paper, we empirically study the influence of reciprocal links in two representative real datasets, Sina Weibo and Douban. Our results demonstrate that the reciprocal links play a more important role than non-reciprocal ones in information diffusion process. In particular, not only coverage but also the speed of the information diffusion can be significantly enhanced by considering the reciprocal effect. We give some possible explanations from the perspectives of network connectivity and efficiency. This work may shed some light on the in-depth understanding and application of the reciprocal effect in directed online social networks. PMID:25072242

  1. Hierarchical link clustering algorithm in networks

    NASA Astrophysics Data System (ADS)

    Bodlaj, Jernej; Batagelj, Vladimir

    2015-06-01

    Hierarchical network clustering is an approach to find tightly and internally connected clusters (groups or communities) of nodes in a network based on its structure. Instead of nodes, it is possible to cluster links of the network. The sets of nodes belonging to clusters of links can overlap. While overlapping clusters of nodes are not always expected, they are natural in many applications. Using appropriate dissimilarity measures, we can complement the clustering strategy to consider, for example, the semantic meaning of links or nodes based on their properties. We propose a new hierarchical link clustering algorithm which in comparison to existing algorithms considers node and/or link properties (descriptions, attributes) of the input network alongside its structure using monotonic dissimilarity measures. The algorithm determines communities that form connected subnetworks (relational constraint) containing locally similar nodes with respect to their description. It is only implicitly based on the corresponding line graph of the input network, thus reducing its space and time complexities. We investigate both complexities analytically and statistically. Using provided dissimilarity measures, our algorithm can, in addition to the general overlapping community structure of input networks, uncover also related subregions inside these communities in a form of hierarchy. We demonstrate this ability on real-world and artificial network examples.

  2. Hierarchical link clustering algorithm in networks.

    PubMed

    Bodlaj, Jernej; Batagelj, Vladimir

    2015-06-01

    Hierarchical network clustering is an approach to find tightly and internally connected clusters (groups or communities) of nodes in a network based on its structure. Instead of nodes, it is possible to cluster links of the network. The sets of nodes belonging to clusters of links can overlap. While overlapping clusters of nodes are not always expected, they are natural in many applications. Using appropriate dissimilarity measures, we can complement the clustering strategy to consider, for example, the semantic meaning of links or nodes based on their properties. We propose a new hierarchical link clustering algorithm which in comparison to existing algorithms considers node and/or link properties (descriptions, attributes) of the input network alongside its structure using monotonic dissimilarity measures. The algorithm determines communities that form connected subnetworks (relational constraint) containing locally similar nodes with respect to their description. It is only implicitly based on the corresponding line graph of the input network, thus reducing its space and time complexities. We investigate both complexities analytically and statistically. Using provided dissimilarity measures, our algorithm can, in addition to the general overlapping community structure of input networks, uncover also related subregions inside these communities in a form of hierarchy. We demonstrate this ability on real-world and artificial network examples. PMID:26172761

  3. Bounded link prediction in very large networks

    NASA Astrophysics Data System (ADS)

    Cui, Wei; Pu, Cunlai; Xu, Zhongqi; Cai, Shimin; Yang, Jian; Michaelson, Andrew

    2016-09-01

    Evaluating link prediction methods is a hard task in very large complex networks due to the prohibitive computational cost. However, if we consider the lower bound of node pairs' similarity scores, this task can be greatly optimized. In this paper, we study CN index in the bounded link prediction framework, which is applicable to enormous heterogeneous networks. Specifically, we propose a fast algorithm based on the parallel computing scheme to obtain all node pairs with CN values larger than the lower bound. Furthermore, we propose a general measurement, called self-predictability, to quantify the performance of similarity indices in link prediction, which can also indicate the link predictability of networks with respect to given similarity indices.

  4. Porous Cross-Linked Polyimide Networks

    NASA Technical Reports Server (NTRS)

    Meador, Mary Ann B. (Inventor); Guo, Haiquan (Inventor)

    2015-01-01

    Porous cross-linked polyimide networks are provided. The networks comprise an anhydride end-capped polyamic acid oligomer. The oligomer (i) comprises a repeating unit of a dianhydride and a diamine and terminal anhydride groups, (ii) has an average degree of polymerization of 10 to 50, (iii) has been cross-linked via a cross-linking agent, comprising three or more amine groups, at a balanced stoichiometry of the amine groups to the terminal anhydride groups, and (iv) has been chemically imidized to yield the porous cross-linked polyimide network. Also provided are porous cross-linked polyimide aerogels comprising a cross-linked and imidized anhydride end-capped polyamic acid oligomer, wherein the oligomer comprises a repeating unit of a dianhydride and a diamine, and the aerogel has a density of 0.10 to 0.333 g/cm.sup.3 and a Young's modulus of 1.7 to 102 MPa. Also provided are thin films comprising aerogels, and methods of making porous cross-linked polyimide networks.

  5. Retrograde signaling: Organelles go networking.

    PubMed

    Kleine, Tatjana; Leister, Dario

    2016-08-01

    The term retrograde signaling refers to the fact that chloroplasts and mitochondria utilize specific signaling molecules to convey information on their developmental and physiological states to the nucleus and modulate the expression of nuclear genes accordingly. Signals emanating from plastids have been associated with two main networks: 'Biogenic control' is active during early stages of chloroplast development, while 'operational' control functions in response to environmental fluctuations. Early work focused on the former and its major players, the GUN proteins. However, our view of retrograde signaling has since been extended and revised. Elements of several 'operational' signaling circuits have come to light, including metabolites, signaling cascades in the cytosol and transcription factors. Here, we review recent advances in the identification and characterization of retrograde signaling components. We place particular emphasis on the strategies employed to define signaling components, spanning the entire spectrum of genetic screens, metabolite profiling and bioinformatics. This article is part of a Special Issue entitled 'EBEC 2016: 19th European Bioenergetics Conference, Riva del Garda, Italy, July 2-6, 2016', edited by Prof. Paolo Bernardi. PMID:26997501

  6. Full-duplex RoF link with broadband mm-wave signal in W-band based on WDM-PON access network with optical mm-wave local oscillator broadcasting

    NASA Astrophysics Data System (ADS)

    Ma, Jianxin; Zhang, Ruijiao; Li, Yanjie; Zhang, Qi; Yu, Jianguo

    2015-02-01

    A novel full-duplex link with an optical mm-wave local oscillator broadcasting for broadband millimeter (mm)-wave wireless access in W-band is proposed based on the WDM-PON-RoF. In our scheme, a universal optical mm-wave local oscillator in W-band is distributed over the whole network to up-convert the downlink IF optical signal, which not only improves the spectrum efficiency by reducing the bandwidth requirement of each downlink, but also decreases the degradation caused by the fiber chromatic dispersion. Moreover, since the incoherently down-converted uplink signal is modulated on the reused blank optical carrier extracted from the downlink signal, the base stations (BSs) need no optical source, and so its structure is simplified. The numerical simulation results agree well with the theoretical analysis and show that the proposed full-duplex link for the W-band wireless access based on WDM-PON-RoF maintains good performance with cost effective implement.

  7. Visualizing Transmedia Networks: Links, Paths and Peripheries

    ERIC Educational Resources Information Center

    Ruppel, Marc Nathaniel

    2012-01-01

    'Visualizing Transmedia Networks: Links, Paths and Peripheries' examines the increasingly complex rhetorical intersections between narrative and media ("old" and "new") in the creation of transmedia fictions, loosely defined as multisensory and multimodal stories told extensively across a diverse media set. In order…

  8. Percolation of networks with directed dependency links

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  9. Dopamine D1 signaling organizes network dynamics underlying working memory

    PubMed Central

    Roffman, Joshua L.; Tanner, Alexandra S.; Eryilmaz, Hamdi; Rodriguez-Thompson, Anais; Silverstein, Noah J.; Ho, New Fei; Nitenson, Adam Z.; Chonde, Daniel B.; Greve, Douglas N.; Abi-Dargham, Anissa; Buckner, Randy L.; Manoach, Dara S.; Rosen, Bruce R.; Hooker, Jacob M.; Catana, Ciprian

    2016-01-01

    Local prefrontal dopamine signaling supports working memory by tuning pyramidal neurons to task-relevant stimuli. Enabled by simultaneous positron emission tomography–magnetic resonance imaging (PET-MRI), we determined whether neuromodulatory effects of dopamine scale to the level of cortical networks and coordinate their interplay during working memory. Among network territories, mean cortical D1 receptor densities differed substantially but were strongly interrelated, suggesting cross-network regulation. Indeed, mean cortical D1 density predicted working memory–emergent decoupling of the frontoparietal and default networks, which respectively manage task-related and internal stimuli. In contrast, striatal D1 predicted opposing effects within these two networks but no between-network effects. These findings specifically link cortical dopamine signaling to network crosstalk that redirects cognitive resources to working memory, echoing neuromodulatory effects of D1 signaling on the level of cortical microcircuits. PMID:27386561

  10. Link-quality measurement and reporting in wireless sensor networks.

    PubMed

    Chehri, Abdellah; Jeon, Gwanggil; Choi, Byoungjo

    2013-01-01

    Wireless Sensor networks (WSNs) are created by small hardware devices that possess the necessary functionalities to measure and exchange a variety of environmental data in their deployment setting. In this paper, we discuss the experiments in deploying a testbed as a first step towards creating a fully functional heterogeneous wireless network-based underground monitoring system. The system is mainly composed of mobile and static ZigBee nodes, which are deployed on the underground mine galleries for measuring ambient temperature. In addition, we describe the measured results of link characteristics such as received signal strength, latency and throughput for different scenarios. PMID:23459389

  11. Link-Quality Measurement and Reporting in Wireless Sensor Networks

    PubMed Central

    Chehri, Abdellah; Jeon, Gwanggil; Choi, Byoungjo

    2013-01-01

    Wireless Sensor networks (WSNs) are created by small hardware devices that possess the necessary functionalities to measure and exchange a variety of environmental data in their deployment setting. In this paper, we discuss the experiments in deploying a testbed as a first step towards creating a fully functional heterogeneous wireless network-based underground monitoring system. The system is mainly composed of mobile and static ZigBee nodes, which are deployed on the underground mine galleries for measuring ambient temperature. In addition, we describe the measured results of link characteristics such as received signal strength, latency and throughput for different scenarios. PMID:23459389

  12. Nonlinear elasticity of cross-linked networks

    NASA Astrophysics Data System (ADS)

    John, Karin; Caillerie, Denis; Peyla, Philippe; Raoult, Annie; Misbah, Chaouqi

    2013-04-01

    Cross-linked semiflexible polymer networks are omnipresent in living cells. Typical examples are actin networks in the cytoplasm of eukaryotic cells, which play an essential role in cell motility, and the spectrin network, a key element in maintaining the integrity of erythrocytes in the blood circulatory system. We introduce a simple mechanical network model at the length scale of the typical mesh size and derive a continuous constitutive law relating the stress to deformation. The continuous constitutive law is found to be generically nonlinear even if the microscopic law at the scale of the mesh size is linear. The nonlinear bulk mechanical properties are in good agreement with the experimental data for semiflexible polymer networks, i.e., the network stiffens and exhibits a negative normal stress in response to a volume-conserving shear deformation, whereby the normal stress is of the same order as the shear stress. Furthermore, it shows a strain localization behavior in response to an uniaxial compression. Within the same model we find a hierarchy of constitutive laws depending on the degree of nonlinearities retained in the final equation. The presented theory provides a basis for the continuum description of polymer networks such as actin or spectrin in complex geometries and it can be easily coupled to growth problems, as they occur, for example, in modeling actin-driven motility.

  13. Feedback to distal dendrites links fMRI signals to neural receptive fields in a spiking network model of the visual cortex.

    PubMed

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

    2015-07-01

    The blood oxygenation level-dependent (BOLD) response has been strongly associated with neuronal activity in the brain. However, some neuronal tuning properties are consistently different from the BOLD response. We studied the spatial extent of neural and hemodynamic responses in the primary visual cortex, where the BOLD responses spread and interact over much longer distances than the small receptive fields of individual neurons would predict. Our model shows that a feedforward-feedback loop between V1 and a higher visual area can account for the observed spread of the BOLD response. In particular, anisotropic landing of inputs to compartmental neurons were necessary to account for the BOLD signal spread, while retaining realistic spiking responses. Our work shows that simple dendrites can separate tuning at the synapses and at the action potential output, thus bridging the BOLD signal to the neural receptive fields with high fidelity. PMID:25925319

  14. A comparative analysis of network robustness against different link attacks

    NASA Astrophysics Data System (ADS)

    Duan, Boping; Liu, Jing; Zhou, Mingxing; Ma, Liangliang

    2016-04-01

    Recently, the study of optimizing network robustness has attracted increasing attentions, and the constraint that every node's degree cannot be changed is considered. Although this constraint maintains the node degree distribution consistently in order to reserve the structure of networks, it makes the network structure be lack of flexibility since many network structure always transform in the modern society. Given this consideration, in this paper, we analyze the robustness of networks through setting a new constraint; that is, only the number of edges should be unchanged. Then, we use the link-robustness index (Rl) as the measure of the network robustness against either random failures or intentional attacks, and make a comparative analysis of network robustness against different types of link attacks. Moreover, we use four types of networks as initial networks, namely scale-free networks, random networks, regular networks, and small-world networks. The experimental results show that the values of robustness measures for the optimized networks starting from different initial networks are similar under different link attacks, but the network topologies may be different. That is to say, networks with different topologies may have similar robustness in terms of the robustness measures. We also find that the optimized networks obtained by one link attack may not robust against other link attacks, sometimes, even weaker than the original networks. Therefore, before building networks, it is better to study which type of link attacks may happen.

  15. Enhanced photoacoustic signal from DNA assembled gold nanoparticle networks

    NASA Astrophysics Data System (ADS)

    Buchkremer, A.; Beckmann, M. F.; Linn, M.; Ruff, J.; Rosencrantz, R. R.; von Plessen, G.; Schmitz, G.; Simon, U.

    2014-12-01

    We report an experimental finding of photoacoustic signal enhancement from finite sized DNA-gold nanoparticle networks. We synthesized DNA-functionalized hollow and solid gold nanospheres (AuNS) to form finite sized networks, which were characterized by means of optical extinction spectroscopy, dynamic light scattering, and scanning electron microscopy in transmission mode. It is shown that the signal amplification scales with network size for networks comprising either hollow or solid AuNS as well as networks consisting of both types of nanoparticles. The laser intensities applied in our multispectral setup (λ = 650 nm, 850 nm, 905 nm) were low enough to maintain the structural integrity of the networks. This reflects that the binding and recognition properties of the temperature-sensitive cross-linking DNA-molecules are retained.

  16. Improving interdependent networks robustness by adding connectivity links

    NASA Astrophysics Data System (ADS)

    Ji, Xingpei; Wang, Bo; Liu, Dichen; Chen, Guo; Tang, Fei; Wei, Daqian; Tu, Lian

    2016-02-01

    Compared with a single and isolated network, interdependent networks have two types of links: connectivity link and dependency link. This paper aims to improve the robustness of interdependent networks by adding connectivity links. Firstly, interdependent networks failure model and four frequently used link addition strategies are briefly reviewed. Furthermore, by defining inter degree-degree difference, two novel link addition strategies are proposed. Finally, we verify the effectiveness of our proposed link addition strategies by comparing with the current link addition strategies in three different network models. The simulation results show that, given the number of added links, link allocation strategies have great effects on the robustness of interdependent networks, i.e., the double-network link allocation strategy is superior to single-network link allocation strategy. Link addition strategies proposed in this paper excel the current strategies, especially for BA interdependent networks. Moreover, our work can provide guidance on how to allocate limited resources to an existing interdependent networks system and optimize its topology to avoid the potential cascade failures.

  17. Optimal Prediction by Cellular Signaling Networks

    NASA Astrophysics Data System (ADS)

    Becker, Nils B.; Mugler, Andrew; ten Wolde, Pieter Rein

    2015-12-01

    Living cells can enhance their fitness by anticipating environmental change. We study how accurately linear signaling networks in cells can predict future signals. We find that maximal predictive power results from a combination of input-noise suppression, linear extrapolation, and selective readout of correlated past signal values. Single-layer networks generate exponential response kernels, which suffice to predict Markovian signals optimally. Multilayer networks allow oscillatory kernels that can optimally predict non-Markovian signals. At low noise, these kernels exploit the signal derivative for extrapolation, while at high noise, they capitalize on signal values in the past that are strongly correlated with the future signal. We show how the common motifs of negative feedback and incoherent feed-forward can implement these optimal response functions. Simulations reveal that E. coli can reliably predict concentration changes for chemotaxis, and that the integration time of its response kernel arises from a trade-off between rapid response and noise suppression.

  18. Analysis and logical modeling of biological signaling transduction networks

    NASA Astrophysics Data System (ADS)

    Sun, Zhongyao

    The study of network theory and its application span across a multitude of seemingly disparate fields of science and technology: computer science, biology, social science, linguistics, etc. It is the intrinsic similarities embedded in the entities and the way they interact with one another in these systems that link them together. In this dissertation, I present from both the aspect of theoretical analysis and the aspect of application three projects, which primarily focus on signal transduction networks in biology. In these projects, I assembled a network model through extensively perusing literature, performed model-based simulations and validation, analyzed network topology, and proposed a novel network measure. The application of network modeling to the system of stomatal opening in plants revealed a fundamental question about the process that has been left unanswered in decades. The novel measure of the redundancy of signal transduction networks with Boolean dynamics by calculating its maximum node-independent elementary signaling mode set accurately predicts the effect of single node knockout in such signaling processes. The three projects as an organic whole advance the understanding of a real system as well as the behavior of such network models, giving me an opportunity to take a glimpse at the dazzling facets of the immense world of network science.

  19. Cascaded multiplexed optical link on a telecommunication network for frequency dissemination.

    PubMed

    Lopez, Olivier; Haboucha, Adil; Kéfélian, Fabien; Jiang, Haifeng; Chanteau, Bruno; Roncin, Vincent; Chardonnet, Christian; Amy-Klein, Anne; Santarelli, Giorgio

    2010-08-01

    We demonstrate a cascaded optical link for ultrastable frequency dissemination comprised of two compensated links of 150 km and a repeater station. Each link includes 114 km of Internet fiber simultaneously carrying data traffic through a dense wavelength division multiplexing technology, and passes through two routing centers of the telecommunication network. The optical reference signal is inserted in and extracted from the communication network using bidirectional optical add-drop multiplexers. The repeater station operates autonomously ensuring noise compensation on the two links and the ultra-stable signal optical regeneration. The compensated link shows a fractional frequency instability of 3 x 10(-15) at one second measurement time and 5 x 10(-20) at 20 hours. This work paves the way to a wide dissemination of ultra-stable optical clock signals between distant laboratories via the Internet network. PMID:20721077

  20. Ubiquitousness of link-density and link-pattern communities in real-world networks

    NASA Astrophysics Data System (ADS)

    Šubelj, L.; Bajec, M.

    2012-01-01

    Community structure appears to be an intrinsic property of many complex real-world networks. However, recent work shows that real-world networks reveal even more sophisticated modules than classical cohesive (link-density) communities. In particular, networks can also be naturally partitioned according to similar patterns of connectedness among the nodes, revealing link-pattern communities. We here propose a propagation based algorithm that can extract both link-density and link-pattern communities, without any prior knowledge of the true structure. The algorithm was first validated on different classes of synthetic benchmark networks with community structure, and also on random networks. We have further applied the algorithm to different social, information, technological and biological networks, where it indeed reveals meaningful (composites of) link-density and link-pattern communities. The results thus seem to imply that, similarly as link-density counterparts, link-pattern communities appear ubiquitous in nature and design.

  1. Identification of hybrid node and link communities in complex networks

    NASA Astrophysics Data System (ADS)

    He, Dongxiao; Jin, Di; Chen, Zheng; Zhang, Weixiong

    2015-03-01

    Identifying communities in complex networks is an effective means for analyzing complex systems, with applications in diverse areas such as social science, engineering, biology and medicine. Finding communities of nodes and finding communities of links are two popular schemes for network analysis. These schemes, however, have inherent drawbacks and are inadequate to capture complex organizational structures in real networks. We introduce a new scheme and an effective approach for identifying complex mixture structures of node and link communities, called hybrid node-link communities. A central piece of our approach is a probabilistic model that accommodates node, link and hybrid node-link communities. Our extensive experiments on various real-world networks, including a large protein-protein interaction network and a large network of semantically associated words, illustrated that the scheme for hybrid communities is superior in revealing network characteristics. Moreover, the new approach outperformed the existing methods for finding node or link communities separately.

  2. Accelerating coordination in temporal networks by engineering the link order

    PubMed Central

    Masuda, Naoki

    2016-01-01

    Social dynamics on a network may be accelerated or decelerated depending on which pairs of individuals in the network communicate early and which pairs do later. The order with which the links in a given network are sequentially used, which we call the link order, may be a strong determinant of dynamical behaviour on networks, potentially adding a new dimension to effects of temporal networks relative to static networks. Here we study the effect of the link order on linear coordination (i.e., synchronisation) dynamics. We show that the coordination speed considerably depends on specific orders of links. In addition, applying each single link for a long time to ensure strong pairwise coordination before moving to a next pair of individuals does not often enhance coordination of the entire network. We also implement a simple greedy algorithm to optimise the link order in favour of fast coordination. PMID:26916093

  3. Accelerating coordination in temporal networks by engineering the link order

    NASA Astrophysics Data System (ADS)

    Masuda, Naoki

    2016-02-01

    Social dynamics on a network may be accelerated or decelerated depending on which pairs of individuals in the network communicate early and which pairs do later. The order with which the links in a given network are sequentially used, which we call the link order, may be a strong determinant of dynamical behaviour on networks, potentially adding a new dimension to effects of temporal networks relative to static networks. Here we study the effect of the link order on linear coordination (i.e., synchronisation) dynamics. We show that the coordination speed considerably depends on specific orders of links. In addition, applying each single link for a long time to ensure strong pairwise coordination before moving to a next pair of individuals does not often enhance coordination of the entire network. We also implement a simple greedy algorithm to optimise the link order in favour of fast coordination.

  4. Identification of hybrid node and link communities in complex networks

    PubMed Central

    He, Dongxiao; Jin, Di; Chen, Zheng; Zhang, Weixiong

    2015-01-01

    Identifying communities in complex networks is an effective means for analyzing complex systems, with applications in diverse areas such as social science, engineering, biology and medicine. Finding communities of nodes and finding communities of links are two popular schemes for network analysis. These schemes, however, have inherent drawbacks and are inadequate to capture complex organizational structures in real networks. We introduce a new scheme and an effective approach for identifying complex mixture structures of node and link communities, called hybrid node-link communities. A central piece of our approach is a probabilistic model that accommodates node, link and hybrid node-link communities. Our extensive experiments on various real-world networks, including a large protein-protein interaction network and a large network of semantically associated words, illustrated that the scheme for hybrid communities is superior in revealing network characteristics. Moreover, the new approach outperformed the existing methods for finding node or link communities separately. PMID:25728010

  5. Eph/ephrin signaling: networks

    PubMed Central

    Arvanitis, Dina; Davy, Alice

    2008-01-01

    Bidirectional signaling has emerged as an important signature by which Ephs and ephrins control biological functions. Eph/ephrin signaling participates in a wide spectrum of developmental processes, and cross-regulation with other communication pathways lies at the heart of the complexity underlying their function in vivo. Here, we review in vitro and in vivo data describing molecular, functional, and genetic interactions between Eph/ephrin and other cell surface signaling pathways. The complexity of Eph/ephrin function is discussed in terms of the pathways that regulate Eph/ephrin signaling and also the pathways that are regulated by Eph/ephrin signaling. PMID:18281458

  6. Utility-Based Link Recommendation in Social Networks

    ERIC Educational Resources Information Center

    Li, Zhepeng

    2013-01-01

    Link recommendation, which suggests links to connect currently unlinked users, is a key functionality offered by major online social networking platforms. Salient examples of link recommendation include "people you may know"' on Facebook and "who to follow" on Twitter. A social networking platform has two types of stakeholder:…

  7. Optimum waiting time for acquisition of return link PN signals

    NASA Technical Reports Server (NTRS)

    Kolata, W.

    1982-01-01

    The subject of this paper is a model that takes into account the effect that acquisition of a PN signal on the forward link has on the acquisition of a PN signal on the return link. The model is used to determine how long the start of the PN search on the return link should be delayed in order to minimize the combined acquisition time (delay + acquisition time) as a function of desired acquisition probability. It is assumed that the return link a-priori epoch uncertainty information is available. Software has been developed that models the return link PN receiver and incorporates in it the effect of forward link PN acquisition statistics in assessing performance.

  8. Robust bidirectional links for photonic quantum networks

    PubMed Central

    Xu, Jin-Shi; Yung, Man-Hong; Xu, Xiao-Ye; Tang, Jian-Shun; Li, Chuan-Feng; Guo, Guang-Can

    2016-01-01

    Optical fibers are widely used as one of the main tools for transmitting not only classical but also quantum information. We propose and report an experimental realization of a promising method for creating robust bidirectional quantum communication links through paired optical polarization-maintaining fibers. Many limitations of existing protocols can be avoided with the proposed method. In particular, the path and polarization degrees of freedom are combined to deterministically create a photonic decoherence-free subspace without the need for any ancillary photon. This method is input state–independent, robust against dephasing noise, postselection-free, and applicable bidirectionally. To rigorously quantify the amount of quantum information transferred, the optical fibers are analyzed with the tools developed in quantum communication theory. These results not only suggest a practical means for protecting quantum information sent through optical quantum networks but also potentially provide a new physical platform for enriching the structure of the quantum communication theory. PMID:26824069

  9. Robust bidirectional links for photonic quantum networks.

    PubMed

    Xu, Jin-Shi; Yung, Man-Hong; Xu, Xiao-Ye; Tang, Jian-Shun; Li, Chuan-Feng; Guo, Guang-Can

    2016-01-01

    Optical fibers are widely used as one of the main tools for transmitting not only classical but also quantum information. We propose and report an experimental realization of a promising method for creating robust bidirectional quantum communication links through paired optical polarization-maintaining fibers. Many limitations of existing protocols can be avoided with the proposed method. In particular, the path and polarization degrees of freedom are combined to deterministically create a photonic decoherence-free subspace without the need for any ancillary photon. This method is input state-independent, robust against dephasing noise, postselection-free, and applicable bidirectionally. To rigorously quantify the amount of quantum information transferred, the optical fibers are analyzed with the tools developed in quantum communication theory. These results not only suggest a practical means for protecting quantum information sent through optical quantum networks but also potentially provide a new physical platform for enriching the structure of the quantum communication theory. PMID:26824069

  10. Signaling in Pollen Tube Growth: Crosstalk, Feedback, and Missing Links

    PubMed Central

    Guan, Yuefeng

    2013-01-01

    Pollen tubes elongate rapidly at their tips through highly polarized cell growth known as tip growth. Tip growth requires intensive exocytosis at the tip, which is supported by a dynamic cytoskeleton and vesicle trafficking. Several signaling pathways have been demonstrated to coordinate pollen tube growth by regulating cellular activities such as actin dynamics, exocytosis, and endocytosis. These signaling pathways crosstalk to form a signaling network that coordinates the cellular processes required for tip growth. The homeostasis of key signaling molecules is critical for the proper elongation of the pollen tube tip, and is commonly fine-tuned by positive and negative regulations. In addition to the major signaling pathways, emerging evidence implies the roles of other signals in the regulation of pollen tube growth. Here we review and discuss how these signaling networks modulate the rapid growth of pollen tubes. PMID:23873928

  11. Design and Analysis of Underwater Acoustic Networks with Reflected Links

    NASA Astrophysics Data System (ADS)

    Emokpae, Lloyd

    Underwater acoustic networks (UWANs) have applications in environmental state monitoring, oceanic profile measurements, leak detection in oil fields, distributed surveillance, and navigation. For these applications, sets of nodes are employed to collaboratively monitor an area of interest and track certain events or phenomena. In addition, it is common to find autonomous underwater vehicles (AUVs) acting as mobile sensor nodes that perform search-and-rescue missions, reconnaissance in combat zones, and coastal patrol. These AUVs are to work cooperatively to achieve a desired goal and thus need to be able to, in an ad-hoc manner, establish and sustain communication links in order to ensure some desired level of quality of service. Therefore, each node is required to adapt to environmental changes and be able to overcome broken communication links caused by external noise affecting the communication channel due to node mobility. In addition, since radio waves are quickly absorbed in the water medium, it is common for most underwater applications to rely on acoustic (or sound) rather than radio channels for mid-to-long range communications. However, acoustic channels pose multiple challenging issues, most notably the high transmission delay due to slow signal propagation and the limited channel bandwidth due to high frequency attenuation. Moreover, the inhomogeneous property of the water medium affects the sound speed profile while the signal surface and bottom reflections leads to multipath effects. In this dissertation, we address these networking challenges by developing protocols that take into consideration the underwater physical layer dynamics. We begin by introducing a novel surface-based reflection scheme (SBR), which takes advantage of the multipath effects of the acoustic channel. SBR works by using reflections from the water surface, and bottom, to establish non-line-of-sight (NLOS) communication links. SBR makes it possible to incorporate both line

  12. Protein modules and signalling networks

    NASA Astrophysics Data System (ADS)

    Pawson, Tony

    1995-02-01

    Communication between cells assumes particular importance in multicellular organisms. The growth, migration and differentiation of cells in the embryo, and their organization into specific tissues, depend on signals transmitted from one cell to another. In the adult, cell signalling orchestrates normal cellular behaviour and responses to wounding and infection. The consequences of breakdowns in this signalling underlie cancer, diabetes and disorders of the immune and cardiovascular systems. Conserved protein domains that act as key regulatory participants in many of these different signalling pathways are highlighted.

  13. Advanced signaling technologies for high-speed digital fiber-optic links.

    PubMed

    Stark, Andrew J; Isautier, Pierre; Pan, Jie; Pavan, Sriharsha Kota; Filer, Mark; Tibuleac, Sorin; Lingle, Robert; de Salvo, Richard; Ralph, Stephen E

    2014-09-01

    We summarize the most recent research of the Georgia Tech Terabit Optical Networking Consortium and the state-of-the-art in fiber telecommunications. These results comprise high-capacity single-mode fiber systems with digital coherent receivers and shorter-reach multimode fiber links with vertical cavity surface emitting lasers. We strongly emphasize the capabilities that sophisticated digital signal processing and electronics add to these fiber-based data transport links. PMID:25321383

  14. Lewis Information Network (LINK): Background and overview

    NASA Technical Reports Server (NTRS)

    Schulte, Roger R.

    1987-01-01

    The NASA Lewis Research Center supports many research facilities with many isolated buildings, including wind tunnels, test cells, and research laboratories. These facilities are all located on a 350 acre campus adjacent to the Cleveland Hopkins Airport. The function of NASA-Lewis is to do basic and applied research in all areas of aeronautics, fluid mechanics, materials and structures, space propulsion, and energy systems. These functions require a great variety of remote high speed, high volume data communications for computing and interactive graphic capabilities. In addition, new requirements for local distribution of intercenter video teleconferencing and data communications via satellite have developed. To address these and future communications requirements for the next 15 yrs, a project team was organized to design and implement a new high speed communication system that would handle both data and video information in a common lab-wide Local Area Network. The project team selected cable television broadband coaxial cable technology as the communications medium and first installation of in-ground cable began in the summer of 1980. The Lewis Information Network (LINK) became operational in August 1982 and has become the backbone of all data communications and video.

  15. Correlations between Community Structure and Link Formation in Complex Networks

    PubMed Central

    Liu, Zhen; He, Jia-Lin; Kapoor, Komal; Srivastava, Jaideep

    2013-01-01

    Background Links in complex networks commonly represent specific ties between pairs of nodes, such as protein-protein interactions in biological networks or friendships in social networks. However, understanding the mechanism of link formation in complex networks is a long standing challenge for network analysis and data mining. Methodology/Principal Findings Links in complex networks have a tendency to cluster locally and form so-called communities. This widely existed phenomenon reflects some underlying mechanism of link formation. To study the correlations between community structure and link formation, we present a general computational framework including a theory for network partitioning and link probability estimation. Our approach enables us to accurately identify missing links in partially observed networks in an efficient way. The links having high connection likelihoods in the communities reveal that links are formed preferentially to create cliques and accordingly promote the clustering level of the communities. The experimental results verify that such a mechanism can be well captured by our approach. Conclusions/Significance Our findings provide a new insight into understanding how links are created in the communities. The computational framework opens a wide range of possibilities to develop new approaches and applications, such as community detection and missing link prediction. PMID:24039818

  16. Critical Links and Nonlocal Rerouting in Complex Supply Networks

    NASA Astrophysics Data System (ADS)

    Witthaut, Dirk; Rohden, Martin; Zhang, Xiaozhu; Hallerberg, Sarah; Timme, Marc

    2016-04-01

    Link failures repeatedly induce large-scale outages in power grids and other supply networks. Yet, it is still not well understood which links are particularly prone to inducing such outages. Here we analyze how the nature and location of each link impact the network's capability to maintain a stable supply. We propose two criteria to identify critical links on the basis of the topology and the load distribution of the network prior to link failure. They are determined via a link's redundant capacity and a renormalized linear response theory we derive. These criteria outperform the critical link prediction based on local measures such as loads. The results not only further our understanding of the physics of supply networks in general. As both criteria are available before any outage from the state of normal operation, they may also help real-time monitoring of grid operation, employing countermeasures and support network planning and design.

  17. Critical Links and Nonlocal Rerouting in Complex Supply Networks.

    PubMed

    Witthaut, Dirk; Rohden, Martin; Zhang, Xiaozhu; Hallerberg, Sarah; Timme, Marc

    2016-04-01

    Link failures repeatedly induce large-scale outages in power grids and other supply networks. Yet, it is still not well understood which links are particularly prone to inducing such outages. Here we analyze how the nature and location of each link impact the network's capability to maintain a stable supply. We propose two criteria to identify critical links on the basis of the topology and the load distribution of the network prior to link failure. They are determined via a link's redundant capacity and a renormalized linear response theory we derive. These criteria outperform the critical link prediction based on local measures such as loads. The results not only further our understanding of the physics of supply networks in general. As both criteria are available before any outage from the state of normal operation, they may also help real-time monitoring of grid operation, employing countermeasures and support network planning and design. PMID:27082006

  18. Automated modelling of signal transduction networks

    PubMed Central

    2002-01-01

    Background Intracellular signal transduction is achieved by networks of proteins and small molecules that transmit information from the cell surface to the nucleus, where they ultimately effect transcriptional changes. Understanding the mechanisms cells use to accomplish this important process requires a detailed molecular description of the networks involved. Results We have developed a computational approach for generating static models of signal transduction networks which utilizes protein-interaction maps generated from large-scale two-hybrid screens and expression profiles from DNA microarrays. Networks are determined entirely by integrating protein-protein interaction data with microarray expression data, without prior knowledge of any pathway intermediates. In effect, this is equivalent to extracting subnetworks of the protein interaction dataset whose members have the most correlated expression profiles. Conclusion We show that our technique accurately reconstructs MAP Kinase signaling networks in Saccharomyces cerevisiae. This approach should enhance our ability to model signaling networks and to discover new components of known networks. More generally, it provides a method for synthesizing molecular data, either individual transcript abundance measurements or pairwise protein interactions, into higher level structures, such as pathways and networks. PMID:12413400

  19. Computational Modeling of Mammalian Signaling Networks

    PubMed Central

    Hughey, Jacob J; Lee, Timothy K; Covert, Markus W

    2011-01-01

    One of the most exciting developments in signal transduction research has been the proliferation of studies in which a biological discovery was initiated by computational modeling. Here we review the major efforts that enable such studies. First, we describe the experimental technologies that are generally used to identify the molecular components and interactions in, and dynamic behavior exhibited by, a network of interest. Next, we review the mathematical approaches that are used to model signaling network behavior. Finally, we focus on three specific instances of “model-driven discovery”: cases in which computational modeling of a signaling network has led to new insights which have been verified experimentally. Signal transduction networks are the bridge between the extraordinarily complex extracellular environment and a carefully orchestrated cellular response. These networks are largely composed of proteins which can interact, move to specific cellular locations, or be modified or degraded. The integration of these events often leads to the activation or inactivation of transcription factors, which then induce or repress the expression of thousands of genes. Because of this critical role in translating environmental cues to cellular behaviors, malfunctioning signaling networks can lead to a variety of pathologies. One example is cancer, in which many of the key genes found to be involved in cancer onset and development are components of signaling pathways [1, 2]. A detailed understanding of the cellular signaling networks underlying such diseases would likely be extremely useful in developing new treatments. However, the complexity of signaling networks is such that their integrated functions cannot be determined without computational simulation. In recent years, mathematical modeling of signal transduction has led to some exciting new findings and biological discoveries. Here, we review the work that has enabled computational modeling of mammalian

  20. Optimal search strategies on complex multi-linked networks

    PubMed Central

    Di Patti, Francesca; Fanelli, Duccio; Piazza, Francesco

    2015-01-01

    In this paper we consider the problem of optimal search strategies on multi-linked networks, i.e. graphs whose nodes are endowed with several independent sets of links. We focus preliminarily on agents randomly hopping along the links of a graph, with the additional possibility of performing non-local hops to randomly chosen nodes with a given probability. We show that an optimal combination of the two jump rules exists that maximises the efficiency of target search, the optimum reflecting the topology of the network. We then generalize our results to multi-linked networks with an arbitrary number of mutually interfering link sets. PMID:25950716

  1. Retrieval algorithm for rainfall mapping from microwave links in a cellular communication network

    NASA Astrophysics Data System (ADS)

    Overeem, Aart; Uijlenhoet, Remko; Leijnse, Hidde

    2016-04-01

    Microwave links in commercial cellular communication networks hold a promise for areal rainfall monitoring and could complement rainfall estimates from ground-based weather radars, rain gauges, and satellites. It has been shown that country-wide rainfall maps can be derived from the signal attenuations of microwave links in such a network. We present a rainfall retrieval algorithm, which is employed to obtain rainfall maps from microwave links in a cellular communication network. We compare these rainfall maps to gauge-adjusted radar rainfall maps. The microwave link data set, as well as the developed code, a package in the open source scripting language "R", are freely available at GitHub (https://github.com/overeem11/RAINLINK). The purpose of this presentation is to promote rainfall mapping utilizing microwave links from cellular communication networks as an alternative or complementary means for continental-scale rainfall monitoring.

  2. Local degree blocking model for link prediction in complex networks.

    PubMed

    Liu, Zhen; Dong, Weike; Fu, Yan

    2015-01-01

    Recovering and reconstructing networks by accurately identifying missing and unreliable links is a vital task in the domain of network analysis and mining. In this article, by studying a specific local structure, namely, a degree block having a node and its all immediate neighbors, we find it contains important statistical features of link formation for complex networks. We therefore propose a parameter-free local blocking (LB) predictor to quantitatively detect link formation in given networks via local link density calculations. The promising experimental results performed on six real-world networks suggest that the new index can outperform other traditional local similarity-based methods on most of tested networks. After further analyzing the scores' correlations between LB and two other methods, we find that LB index simultaneously captures the features of both PA index and short-path-based index, which empirically verifies that LB index is a multiple-mechanism-driven link predictor. PMID:25637926

  3. Linked in: immunologic membrane nanotube networks.

    PubMed

    Zaccard, C R; Rinaldo, C R; Mailliard, R B

    2016-07-01

    Membrane nanotubes, also termed tunneling nanotubes, are F-actin-based structures that can form direct cytoplasmic connections and support rapid communication between distant cells. These nanoscale conduits have been observed in diverse cell types, including immune, neuronal, stromal, cancer, and stem cells. Until recently, little was known about the mechanisms involved in membrane nanotube development in myeloid origin APCs or how membrane nanotube networks support their ability to bridge innate and adaptive immunity. New research has provided insight into the modes of induction and regulation of the immune process of "reticulation" or the development of multicellular membrane nanotube networks in dendritic cells. Preprogramming by acute type 1 inflammatory mediators at their immature stage licenses mature type 1-polarized dendritic cells to reticulate upon subsequent interaction with CD40 ligand-expressing CD4(+) Th cells. Dendritic cell reticulation can support direct antigen transfer for amplification of specific T cell responses and can be positively or negatively regulated by signals from distinct Th cell subsets. Membrane nanotubes not only enhance the ability of immature dendritic cells to sense pathogens and rapidly mobilize nearby antigen-presenting cells in the peripheral tissues but also likely support communication of pathogen-related information from mature migratory dendritic cells to resident dendritic cells in lymph nodes. Therefore, the reticulation process facilitates a coordinated multicellular response for the efficient initiation of cell-mediated adaptive immune responses. Herein, we discuss studies focused on the molecular mechanisms of membrane nanotube formation, structure, and function in the context of immunity and how pathogens, such as HIV-1, may use dendritic cell reticulation to circumvent host defenses. PMID:26931578

  4. Wideband link-budget analysis for undersea acoustic signaling

    NASA Astrophysics Data System (ADS)

    Rice, Joseph A.; Hansen, Joseph T.

    2002-11-01

    Link-budget analysis is commonly applied to satellite and wireless communications for estimating the signal-to-noise ratio (SNR) at the receiver. Link-budget analysis considers transmitter power, transmitter antenna gain, channel losses, channel noise, and receiver antenna gain. For underwater signaling, the terms of the sonar equation readily translate to a formulation of the link budget. However, the strong frequency dependence of underwater acoustic propagation requires special consideration, and is represented as an intermediate result called the channel SNR. The channel SNR includes ambient-noise and transmission-loss components. Several acoustic communication and navigation problems are addressed through wideband link-budget analyses. [Work sponsored by ONR 321.

  5. Mixed-method Exploration of Social Network Links to Participation

    PubMed Central

    Kreider, Consuelo M.; Bendixen, Roxanna M.; Mann, William C.; Young, Mary Ellen; McCarty, Christopher

    2015-01-01

    The people who regularly interact with an adolescent form that youth's social network, which may impact participation. We investigated the relationship of social networks to participation using personal network analysis and individual interviews. The sample included 36 youth, age 11 – 16 years. Nineteen had diagnoses of learning disability, attention disorder, or high-functioning autism and 17 were typically developing. Network analysis yielded 10 network variables, of which 8 measured network composition and 2 measured network structure, with significant links to at least one measure of participation using the Children's Assessment of Participation and Enjoyment (CAPE). Interviews from youth in the clinical group yielded description of strategies used to negotiate social interactions, as well as processes and reasoning used to remain engaged within social networks. Findings contribute to understanding the ways social networks are linked to youth participation and suggest the potential of social network factors for predicting rehabilitation outcomes. PMID:26594737

  6. Enhancing complex network controllability by minimum link direction reversal

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

  7. Adenylate Kinase and AMP Signaling Networks: Metabolic Monitoring, Signal Communication and Body Energy Sensing

    PubMed Central

    Dzeja, Petras; Terzic, Andre

    2009-01-01

    Adenylate kinase and downstream AMP signaling is an integrated metabolic monitoring system which reads the cellular energy state in order to tune and report signals to metabolic sensors. A network of adenylate kinase isoforms (AK1-AK7) are distributed throughout intracellular compartments, interstitial space and body fluids to regulate energetic and metabolic signaling circuits, securing efficient cell energy economy, signal communication and stress response. The dynamics of adenylate kinase-catalyzed phosphotransfer regulates multiple intracellular and extracellular energy-dependent and nucleotide signaling processes, including excitation-contraction coupling, hormone secretion, cell and ciliary motility, nuclear transport, energetics of cell cycle, DNA synthesis and repair, and developmental programming. Metabolomic analyses indicate that cellular, interstitial and blood AMP levels are potential metabolic signals associated with vital functions including body energy sensing, sleep, hibernation and food intake. Either low or excess AMP signaling has been linked to human disease such as diabetes, obesity and hypertrophic cardiomyopathy. Recent studies indicate that derangements in adenylate kinase-mediated energetic signaling due to mutations in AK1, AK2 or AK7 isoforms are associated with hemolytic anemia, reticular dysgenesis and ciliary dyskinesia. Moreover, hormonal, food and antidiabetic drug actions are frequently coupled to alterations of cellular AMP levels and associated signaling. Thus, by monitoring energy state and generating and distributing AMP metabolic signals adenylate kinase represents a unique hub within the cellular homeostatic network. PMID:19468337

  8. Robust classification of salient links in complex networks.

    PubMed

    Grady, Daniel; Thiemann, Christian; Brockmann, Dirk

    2012-01-01

    Complex networks in natural, social and technological systems generically exhibit an abundance of rich information. Extracting meaningful structural features from data is one of the most challenging tasks in network theory. Many methods and concepts have been proposed to address this problem such as centrality statistics, motifs, community clusters and backbones, but such schemes typically rely on external and arbitrary parameters. It is unknown whether generic networks permit the classification of elements without external intervention. Here we show that link salience is a robust approach to classifying network elements based on a consensus estimate of all nodes. A wide range of empirical networks exhibit a natural, network-implicit classification of links into qualitatively distinct groups, and the salient skeletons have generic statistical properties. Salience also predicts essential features of contagion phenomena on networks, and points towards a better understanding of universal features in empirical networks that are masked by their complexity. PMID:22643891

  9. Robust classification of salient links in complex networks

    NASA Astrophysics Data System (ADS)

    Grady, Daniel; Thiemann, Christian; Brockmann, Dirk

    2012-05-01

    Complex networks in natural, social and technological systems generically exhibit an abundance of rich information. Extracting meaningful structural features from data is one of the most challenging tasks in network theory. Many methods and concepts have been proposed to address this problem such as centrality statistics, motifs, community clusters and backbones, but such schemes typically rely on external and arbitrary parameters. It is unknown whether generic networks permit the classification of elements without external intervention. Here we show that link salience is a robust approach to classifying network elements based on a consensus estimate of all nodes. A wide range of empirical networks exhibit a natural, network-implicit classification of links into qualitatively distinct groups, and the salient skeletons have generic statistical properties. Salience also predicts essential features of contagion phenomena on networks, and points towards a better understanding of universal features in empirical networks that are masked by their complexity.

  10. Linking cortical network synchrony and excitability

    PubMed Central

    Meisel, Christian

    2016-01-01

    ABSTRACT Theoretical approaches based on dynamical systems theory can provide useful frameworks to guide experiments and analysis techniques when investigating cortical network activity. The notion of phase transitions between qualitatively different kinds of network dynamics has been such a framework inspiring novel approaches to neurophysiological data analysis over the recent years. One particular intriguing hypothesis has been that cortical networks reside in the vicinity of a phase transition. Although the final verdict on this hypothesis is still out, trying to understand cortex dynamics from this viewpoint has recently led to interesting insights on cortical network function with relevance for clinical practice. PMID:27065159

  11. Percolation in networks composed of connectivity and dependency links

    NASA Astrophysics Data System (ADS)

    Bashan, Amir; Parshani, Roni; Havlin, Shlomo

    2011-05-01

    Networks composed from both connectivity and dependency links were found to be more vulnerable compared to classical networks with only connectivity links. Their percolation transition is usually of a first order compared to the second-order transition found in classical networks. We analytically analyze the effect of different distributions of dependencies links on the robustness of networks. For a random Erdös-Rényi (ER) network with average degree k that is divided into dependency clusters of size s, the fraction of nodes that belong to the giant component P∞ is given by P∞=ps-1[1-exp(-kpP∞)]s, where 1-p is the initial fraction of removed nodes. Our general result coincides with the known Erdös-Rényi equation for random networks for s=1. For networks with Poissonian distribution of dependency links we find that P∞ is given by P∞=fk,p(P∞)e(-1)[pfk,p(P∞)-1], where fk,p(P∞)≡1-exp(-kpP∞) and is the mean value of the size of dependency clusters. For networks with Gaussian distribution of dependency links we show how the average and width of the distribution affect the robustness of the networks.

  12. Link Prediction in Complex Networks: A Mutual Information Perspective

    PubMed Central

    Tan, Fei; Xia, Yongxiang; Zhu, Boyao

    2014-01-01

    Topological properties of networks are widely applied to study the link-prediction problem recently. Common Neighbors, for example, is a natural yet efficient framework. Many variants of Common Neighbors have been thus proposed to further boost the discriminative resolution of candidate links. In this paper, we reexamine the role of network topology in predicting missing links from the perspective of information theory, and present a practical approach based on the mutual information of network structures. It not only can improve the prediction accuracy substantially, but also experiences reasonable computing complexity. PMID:25207920

  13. Auxiliary and Autonomous Proteoglycan Signaling Networks

    PubMed Central

    Elfenbein, Arye; Simons, Michael

    2013-01-01

    signal transduction, and present unique challenges to the study of their indispensable roles within cell signaling networks. PMID:20816202

  14. PACRG, a protein linked to ciliary motility, mediates cellular signaling.

    PubMed

    Loucks, Catrina M; Bialas, Nathan J; Dekkers, Martijn P J; Walker, Denise S; Grundy, Laura J; Li, Chunmei; Inglis, P Nick; Kida, Katarzyna; Schafer, William R; Blacque, Oliver E; Jansen, Gert; Leroux, Michel R

    2016-07-01

    Cilia are microtubule-based organelles that project from nearly all mammalian cell types. Motile cilia generate fluid flow, whereas nonmotile (primary) cilia are required for sensory physiology and modulate various signal transduction pathways. Here we investigate the nonmotile ciliary signaling roles of parkin coregulated gene (PACRG), a protein linked to ciliary motility. PACRG is associated with the protofilament ribbon, a structure believed to dictate the regular arrangement of motility-associated ciliary components. Roles for protofilament ribbon-associated proteins in nonmotile cilia and cellular signaling have not been investigated. We show that PACRG localizes to a small subset of nonmotile cilia in Caenorhabditis elegans, suggesting an evolutionary adaptation for mediating specific sensory/signaling functions. We find that it influences a learning behavior known as gustatory plasticity, in which it is functionally coupled to heterotrimeric G-protein signaling. We also demonstrate that PACRG promotes longevity in C. elegans by acting upstream of the lifespan-promoting FOXO transcription factor DAF-16 and likely upstream of insulin/IGF signaling. Our findings establish previously unrecognized sensory/signaling functions for PACRG and point to a role for this protein in promoting longevity. Furthermore, our work suggests additional ciliary motility-signaling connections, since EFHC1 (EF-hand containing 1), a potential PACRG interaction partner similarly associated with the protofilament ribbon and ciliary motility, also positively regulates lifespan. PMID:27193298

  15. A new mutually reinforcing network node and link ranking algorithm

    PubMed Central

    Wang, Zhenghua; Dueñas-Osorio, Leonardo; Padgett, Jamie E.

    2015-01-01

    This study proposes a novel Normalized Wide network Ranking algorithm (NWRank) that has the advantage of ranking nodes and links of a network simultaneously. This algorithm combines the mutual reinforcement feature of Hypertext Induced Topic Selection (HITS) and the weight normalization feature of PageRank. Relative weights are assigned to links based on the degree of the adjacent neighbors and the Betweenness Centrality instead of assigning the same weight to every link as assumed in PageRank. Numerical experiment results show that NWRank performs consistently better than HITS, PageRank, eigenvector centrality, and edge betweenness from the perspective of network connectivity and approximate network flow, which is also supported by comparisons with the expensive N-1 benchmark removal criteria based on network efficiency. Furthermore, it can avoid some problems, such as the Tightly Knit Community effect, which exists in HITS. NWRank provides a new inexpensive way to rank nodes and links of a network, which has practical applications, particularly to prioritize resource allocation for upgrade of hierarchical and distributed networks, as well as to support decision making in the design of networks, where node and link importance depend on a balance of local and global integrity. PMID:26492958

  16. Cross-Linked Fiber Network Embedded in Elastic Matrix

    PubMed Central

    Zhang, L.; Lake, S.P.; Barocas, V.H.; Shephard, M.S.; Picu, R.C.

    2013-01-01

    The mechanical behavior of a three-dimensional cross-linked fiber network embedded in matrix is studied in this work. The network is composed from linear elastic fibers which store energy only in the axial deformation mode, while the matrix is also isotropic and linear elastic. Such systems are encountered in a broad range of applications, from tissue to consumer products. As the matrix modulus increases, the network is constrained to deform more affinely. This leads to internal forces acting between the network and the matrix, which produce strong stress concentration at the network cross-links. This interaction increases the apparent modulus of the network and decreases the apparent modulus of the matrix. A model is developed to predict the effective modulus of the composite and its predictions are compared with numerical data for a variety of networks. PMID:24089623

  17. Master Regulators in Plant Glucose Signaling Networks

    PubMed Central

    Sheen, Jen

    2014-01-01

    The daily life of photosynthetic plants revolves around sugar production, transport, storage and utilization, and the complex sugar metabolic and signaling networks integrate internal regulators and environmental cues to govern and sustain plant growth and survival. Although diverse sugar signals have emerged as pivotal regulators from embryogenesis to senescence, glucose is the most ancient and conserved regulatory signal that controls gene and protein expression, cell-cycle progression, central and secondary metabolism, as well as growth and developmental programs. Glucose signals are perceived and transduced by two principal mechanisms: direct sensing through glucose sensors and indirect sensing via a variety of energy and metabolite sensors. This review focuses on the comparative and functional analyses of three glucose-modulated master regulators in Arabidopsis thaliana, the hexokinase1 (HXK1) glucose sensor, the energy sensor kinases KIN10/KIN11 inactivated by glucose, and the glucose-activated target of rapamycin (TOR) kinase. These regulators are evolutionarily conserved, but have evolved universal and unique regulatory wiring and functions in plants and animals. They form protein complexes with multiple partners as regulators or effectors to serve distinct functions in different subcellular locales and organs, and play integrative and complementary roles from cellular signaling and metabolism to development in the plant glucose signaling networks. PMID:25530701

  18. Targeted attack on networks coupled by connectivity and dependency links

    NASA Astrophysics Data System (ADS)

    Du, Ruijin; Dong, Gaogao; Tian, Lixin; Liu, Runran

    2016-05-01

    Coupled systems used to increase capacity were shown beneficial as long as it does not open pathways to cascades. Previous studies on the robustness of coupled networks except for interdependent networks are almost the cases of random attack. Many challenges remain exist in targeted-attack problem of coupled networks. Since nodes within coupled networks show different functions for each network, this paper both analytically and numerically analyzed the robustness of coupled networks under three types of targeted attacking strategies, including attacking on nodes by considering internal and external degree, internal degree only, and external degree only. For coupled network with both interdependent and interconnected links, all degree distributions of intra- and inter-connectivity links are Poissonian, we find the system undergoes from second to first order phase transition as coupling strength q increases. The fraction of nodes in the giant component P∞ at stable state, the critical phase transition threshold pc (first order threshold pcI and second order threshold pcII), and the critical point (pc ,qc) separating the first and second order phase transitions are analytically obtained for three types of attacking strategies with attacking probability parameter α = 0 , 1. We also find the system becomes more vulnerable as the average degree of intra-links k ¯ or inter-links K ¯ decreases. Therefore, the minimum average degrees k¯min and K¯min to maintain the system stable are obtained for the case of α = 0 , 1. Moreover, we discussed three typical cases of coupled networks, interdependent networks (K ¯ = 0), interacting networks (q = 0) and bipartite network (k = 0, q = 0), the analytical expressions of P∞, pc and (pc ,qc) (only for interdependent) are given respectively. Besides, we study the equivalence relations between interdependent networks and coupled networks with connectivity and dependency links for the same pc. The results imply that we can

  19. Retrieval algorithm for rainfall mapping from microwave links in a cellular communication network

    NASA Astrophysics Data System (ADS)

    Overeem, A.; Leijnse, H.; Uijlenhoet, R.

    2015-08-01

    Microwave links in commercial cellular communication networks hold a promise for areal rainfall monitoring and could complement rainfall estimates from ground-based weather radars, rain gauges, and satellites. It has been shown that country-wide rainfall maps can be derived from the signal attenuations of microwave links in such a network. Here we give a detailed description of the employed rainfall retrieval algorithm and provide the corresponding code. Moreover, the code (in the scripting language "R") is made available including a data set of commercial microwave links. The purpose of this paper is to promote rainfall monitoring utilizing microwave links from cellular communication networks as an alternative or complementary means for global, continental-scale rainfall monitoring.

  20. Retrieval algorithm for rainfall mapping from microwave links in a cellular communication network

    NASA Astrophysics Data System (ADS)

    Overeem, Aart; Leijnse, Hidde; Uijlenhoet, Remko

    2016-06-01

    Microwave links in commercial cellular communication networks hold a promise for areal rainfall monitoring and could complement rainfall estimates from ground-based weather radars, rain gauges, and satellites. It has been shown that country-wide (≈ 35 500 km2) 15 min rainfall maps can be derived from the signal attenuations of approximately 2400 microwave links in such a network. Here we give a detailed description of the employed rainfall retrieval algorithm. Moreover, the documented, modular, and user-friendly code (a package in the scripting language "R") is made available, including a 2-day data set of approximately 2600 commercial microwave links from the Netherlands. The purpose of this paper is to promote rainfall mapping utilising microwave links from cellular communication networks as an alternative or complementary means for continental-scale rainfall monitoring.

  1. International Datacasting's Aquarius and I/LINK networks

    NASA Astrophysics Data System (ADS)

    Noppe, Susan M.

    Many communications applications are surfacing which cannot be implemented on traditional equipment. Many corporations are demanding private, dedicated inter-branch data networks while others require high speed data links to remote locations. This paper presents two International Datacasting Corporation networks designed to provide such capabilities: Aquarius and I/LINK. Aquarius is a high speed point to multi-point satellite network which provides an interface compatible with the X.25 equipment used by most North American companies. I/LINK is a satellite network designed to connect private corporate networks of primary access integrated, switched data network (ISDN) services. Each island would contain equipment such as telephones, PC LANs, document image processing systems, FAX, electronic mail, and audio/video conferencing facilities. I/LINK will connect earthbound, primary access ISDN systems with a satellite transmission service. The I/LINK design eliminates the double hop delay factor in voice transmission. I/LINK stations will communicate with each other via a Ku-band geosynchronous satellite. It will permit use of very small aperture terminal satellite communications stations employing small (1.8 to 2.4 m) antennas.

  2. Link Prediction in Weighted Networks: A Weighted Mutual Information Model

    PubMed Central

    Zhu, Boyao; Xia, Yongxiang

    2016-01-01

    The link-prediction problem is an open issue in data mining and knowledge discovery, which attracts researchers from disparate scientific communities. A wealth of methods have been proposed to deal with this problem. Among these approaches, most are applied in unweighted networks, with only a few taking the weights of links into consideration. In this paper, we present a weighted model for undirected and weighted networks based on the mutual information of local network structures, where link weights are applied to further enhance the distinguishable extent of candidate links. Empirical experiments are conducted on four weighted networks, and results show that the proposed method can provide more accurate predictions than not only traditional unweighted indices but also typical weighted indices. Furthermore, some in-depth discussions on the effects of weak ties in link prediction as well as the potential to predict link weights are also given. This work may shed light on the design of algorithms for link prediction in weighted networks. PMID:26849659

  3. Random links enhance the sensitivity of networks to heterogeneity

    NASA Astrophysics Data System (ADS)

    Deep Rungta, Pranay; Sinha, Sudeshna

    2015-12-01

    In this work we investigate the dynamics of networks of bistable elements with varying degrees of randomness in connections, considering both static random links and time-varying random links. We explore how the presence of a few dissimilar elements affects the collective features of this system, and find that a network with random links is hyper-sensitive to heterogeneity. Namely, counter-intuitively, even a small number of distinct elements manages to drastically influence the collective dynamics of the network, with the mean-field swinging to the steady state of the minority elements. We find that the transition in the collective field gets sharper as the fraction of random links increases, for both static and time-varying links. We also demonstrate that networks where the links are switched more frequently, synchronize faster. Lastly, we show that as global bias tends to a critical value, even a single different element manages to drag the entire system to the natural stable state of the minority element. So it is evident that when coupling connections are random, a network with even a very small number of links per node, has the ability to become ultra-sensitive to heterogeneity.

  4. Link Prediction in Weighted Networks: A Weighted Mutual Information Model.

    PubMed

    Zhu, Boyao; Xia, Yongxiang

    2016-01-01

    The link-prediction problem is an open issue in data mining and knowledge discovery, which attracts researchers from disparate scientific communities. A wealth of methods have been proposed to deal with this problem. Among these approaches, most are applied in unweighted networks, with only a few taking the weights of links into consideration. In this paper, we present a weighted model for undirected and weighted networks based on the mutual information of local network structures, where link weights are applied to further enhance the distinguishable extent of candidate links. Empirical experiments are conducted on four weighted networks, and results show that the proposed method can provide more accurate predictions than not only traditional unweighted indices but also typical weighted indices. Furthermore, some in-depth discussions on the effects of weak ties in link prediction as well as the potential to predict link weights are also given. This work may shed light on the design of algorithms for link prediction in weighted networks. PMID:26849659

  5. Signal dispersion within a hippocampal neural network

    NASA Technical Reports Server (NTRS)

    Horowitz, J. M.; Mates, J. W. B.

    1975-01-01

    A model network is described, representing two neural populations coupled so that one population is inhibited by activity it excites in the other. Parameters and operations within the model represent EPSPs, IPSPs, neural thresholds, conduction delays, background activity and spatial and temporal dispersion of signals passing from one population to the other. Simulations of single-shock and pulse-train driving of the network are presented for various parameter values. Neuronal events from 100 to 300 msec following stimulation are given special consideration in model calculations.

  6. Computation of signal delays in RC networks

    NASA Technical Reports Server (NTRS)

    Hidalgo, Juan Carlos; Narendran, Paliath; Chaiken, Seth

    1993-01-01

    A model for signal delay computation in RC networks is presented. The strength of the paradigm is its generality and simplicity. The definition of delay is applicable to RC meshes with potential resistive attenuating paths to ground. The algorithms can also be applied to undriven circuits (static charge sharing) and circuits with initial charge. To compute the delays, each node in the network is explored locally to derive a system of sparse linear equations. The solutions of the system are delay values based on the Elmore time constant at each point in the circuit.

  7. Computation of signal delays in RC networks

    NASA Astrophysics Data System (ADS)

    Hidalgo, Juan Carlos; Narendran, Paliath; Chaiken, Seth

    A model for signal delay computation in RC networks is presented. The strength of the paradigm is its generality and simplicity. The definition of delay is applicable to RC meshes with potential resistive attenuating paths to ground. The algorithms can also be applied to undriven circuits (static charge sharing) and circuits with initial charge. To compute the delays, each node in the network is explored locally to derive a system of sparse linear equations. The solutions of the system are delay values based on the Elmore time constant at each point in the circuit.

  8. Link prediction in the network of global virtual water trade

    NASA Astrophysics Data System (ADS)

    Tuninetti, Marta; Tamea, Stefania; Laio, Francesco; Ridolfi, Luca

    2016-04-01

    Through the international food-trade, water resources are 'virtually' transferred from the country of production to the country of consumption. The international food-trade, thus, implies a network of virtual water flows from exporting to importing countries (i.e., nodes). Given the dynamical behavior of the network, where food-trade relations (i.e., links) are created and dismissed every year, link prediction becomes a challenge. In this study, we propose a novel methodology for link prediction in the virtual water network. The model aims at identifying the main factors (among 17 different variables) driving the creation of a food-trade relation between any two countries, along the period between 1986 and 2011. Furthermore, the model can be exploited to investigate the network configuration in the future, under different possible (climatic and demographic) scenarios. The model grounds the existence of a link between any two nodes on the link weight (i.e., the virtual water flow): a link exists when the nodes exchange a minimum (fixed) volume of virtual water. Starting from a set of potential links between any two nodes, we fit the associated virtual water flows (both the real and the null ones) by means of multivariate linear regressions. Then, links with estimated flows higher than a minimum value (i.e., threshold) are considered active-links, while the others are non-active ones. The discrimination between active and non-active links through the threshold introduces an error (called link-prediction error) because some real links are lost (i.e., missed links) and some non-existing links (i.e., spurious links) are inevitably introduced in the network. The major drivers are those significantly minimizing the link-prediction error. Once the structure of the unweighted virtual water network is known, we apply, again, linear regressions to assess the major factors driving the fluxes traded along (modelled) active-links. Results indicate that, on the one hand

  9. CrossRef: A Collaborative Linking Network.

    ERIC Educational Resources Information Center

    Pentz, Ed

    2001-01-01

    CrossRef was created to make broad-based linking efficient and scalable across a wide range of primary publishers, secondary publishers, abstracting and indexing services, and libraries. CrossRef runs a system that enables publishers to assign Digital Object Identifiers (DOIs) to articles and collects standardized metadata so the identifiers can…

  10. Network worlds : from link analysis to virtual places.

    SciTech Connect

    Joslyn, C.

    2002-01-01

    Significant progress is being made in knowledge systems through recent advances in the science of very large networks. Attention is now turning in many quarters to the potential impact on counter-terrorism methods. After reviewing some of these advances, we will discuss the difference between such 'network analytic' approaches, which focus on large, homogeneous graph strucures, and what we are calling 'link analytic' approaches, which focus on somewhat smaller graphs with heterogeneous link types. We use this venue to begin the process of rigorously defining link analysis methods, especially the concept of chaining of views of multidimensional databases. We conclude with some speculation on potential connections to virtual world architectures.

  11. Link Investigation of IEEE 802.15.4 Wireless Sensor Networks in Forests.

    PubMed

    Ding, Xingjian; Sun, Guodong; Yang, Gaoxiang; Shang, Xinna

    2016-01-01

    Wireless sensor networks are expected to automatically monitor the ecological evolution and wildlife habits in forests. Low-power links (transceivers) are often adopted in wireless sensor network applications, in order to save the precious sensor energy and then achieve long-term, unattended monitoring. Recent research has presented some performance characteristics of such low-power wireless links under laboratory or outdoor scenarios with less obstacles, and they have found that low-power wireless links are unreliable and prone to be affected by the target environment. However, there is still less understanding about how well the low-power wireless link performs in real-world forests and to what extent the complex in-forest surrounding environments affect the link performances. In this paper, we empirically evaluate the low-power links of wireless sensors in three typical different forest environments. Our experiment investigates the performance of the link layer compatible with the IEEE 802.15.4 standard and analyzes the variation patterns of the packet reception ratio (PRR), the received signal strength indicator (RSSI) and the link quality indicator (LQI) under diverse experimental settings. Some observations of this study are inconsistent with or even contradict prior results that are achieved in open fields or relatively clean environments and thus, provide new insights both into effectively evaluating the low-power wireless links and into efficiently deploying wireless sensor network systems in forest environments. PMID:27355957

  12. Link Investigation of IEEE 802.15.4 Wireless Sensor Networks in Forests

    PubMed Central

    Ding, Xingjian; Sun, Guodong; Yang, Gaoxiang; Shang, Xinna

    2016-01-01

    Wireless sensor networks are expected to automatically monitor the ecological evolution and wildlife habits in forests. Low-power links (transceivers) are often adopted in wireless sensor network applications, in order to save the precious sensor energy and then achieve long-term, unattended monitoring. Recent research has presented some performance characteristics of such low-power wireless links under laboratory or outdoor scenarios with less obstacles, and they have found that low-power wireless links are unreliable and prone to be affected by the target environment. However, there is still less understanding about how well the low-power wireless link performs in real-world forests and to what extent the complex in-forest surrounding environments affect the link performances. In this paper, we empirically evaluate the low-power links of wireless sensors in three typical different forest environments. Our experiment investigates the performance of the link layer compatible with the IEEE 802.15.4 standard and analyzes the variation patterns of the packet reception ratio (PRR), the received signal strength indicator (RSSI) and the link quality indicator (LQI) under diverse experimental settings. Some observations of this study are inconsistent with or even contradict prior results that are achieved in open fields or relatively clean environments and thus, provide new insights both into effectively evaluating the low-power wireless links and into efficiently deploying wireless sensor network systems in forest environments. PMID:27355957

  13. Community detection in networks with positive and negative links

    NASA Astrophysics Data System (ADS)

    Traag, V. A.; Bruggeman, Jeroen

    2009-09-01

    Detecting communities in complex networks accurately is a prime challenge, preceding further analyses of network characteristics and dynamics. Until now, community detection took into account only positively valued links, while many actual networks also feature negative links. We extend an existing Potts model to incorporate negative links as well, resulting in a method similar to the clustering of signed graphs, as dealt with in social balance theory, but more general. To illustrate our method, we applied it to a network of international alliances and disputes. Using data from 1993-2001, it turns out that the world can be divided into six power blocs similar to Huntington’s civilizations, with some notable exceptions.

  14. Numeric simulation of plant signaling networks.

    PubMed

    Genoud, T; Trevino Santa Cruz, M B; Métraux, J P

    2001-08-01

    Plants have evolved an intricate signaling apparatus that integrates relevant information and allows an optimal response to environmental conditions. For instance, the coordination of defense responses against pathogens involves sophisticated molecular detection and communication systems. Multiple protection strategies may be deployed differentially by the plant according to the nature of the invading organism. These responses are also influenced by the environment, metabolism, and developmental stage of the plant. Though the cellular signaling processes traditionally have been described as linear sequences of events, it is now evident that they may be represented more accurately as network-like structures. The emerging paradigm can be represented readily with the use of Boolean language. This digital (numeric) formalism allows an accurate qualitative description of the signal transduction processes, and a dynamic representation through computer simulation. Moreover, it provides the required power to process the increasing amount of information emerging from the fields of genomics and proteomics, and from the use of new technologies such as microarray analysis. In this review, we have used the Boolean language to represent and analyze part of the signaling network of disease resistance in Arabidopsis. PMID:11500542

  15. Numeric Simulation of Plant Signaling Networks1

    PubMed Central

    Genoud, Thierry; Trevino Santa Cruz, Marcela B.; Métraux, Jean-Pierre

    2001-01-01

    Plants have evolved an intricate signaling apparatus that integrates relevant information and allows an optimal response to environmental conditions. For instance, the coordination of defense responses against pathogens involves sophisticated molecular detection and communication systems. Multiple protection strategies may be deployed differentially by the plant according to the nature of the invading organism. These responses are also influenced by the environment, metabolism, and developmental stage of the plant. Though the cellular signaling processes traditionally have been described as linear sequences of events, it is now evident that they may be represented more accurately as network-like structures. The emerging paradigm can be represented readily with the use of Boolean language. This digital (numeric) formalism allows an accurate qualitative description of the signal transduction processes, and a dynamic representation through computer simulation. Moreover, it provides the required power to process the increasing amount of information emerging from the fields of genomics and proteomics, and from the use of new technologies such as microarray analysis. In this review, we have used the Boolean language to represent and analyze part of the signaling network of disease resistance in Arabidopsis. PMID:11500542

  16. ATR promotes cilia signalling: links to developmental impacts.

    PubMed

    Stiff, Tom; Casar Tena, Teresa; O'Driscoll, Mark; Jeggo, Penny A; Philipp, Melanie

    2016-04-15

    Mutations in ATR(ataxia telangiectasia and RAD3-related) cause Seckel syndrome (ATR-SS), a microcephalic primordial dwarfism disorder. Hitherto, the clinical manifestation of ATR deficiency has been attributed to its canonical role in DNA damage response signalling following replication fork stalling/collapse. Here, we show that ATR regulates cilia-dependent signalling in a manner that can be uncoupled from its function during replication. ATR-depleted or patient-derived ATR-SS cells form cilia of slightly reduced length but are dramatically impaired in cilia-dependent signalling functions, including growth factor and Sonic hedgehog signalling. To better understand the developmental impact of ATR loss of function, we also used zebrafish as a model. Zebrafish embryos depleted of Atr resembled ATR-SS morphology, showed a modest but statistically significant reduction in cilia length and other morphological features indicative of cilia dysfunction. Additionally, they displayed defects in left-right asymmetry including ambiguous expression of southpaw, incorrectly looped hearts and randomized localization of internal organs including the pancreas, features typically conferred by cilia dysfunction. Our findings reveal a novel role for ATR in cilia signalling distinct from its canonical function during replication and strengthen emerging links between cilia function and development. PMID:26908596

  17. ATR promotes cilia signalling: links to developmental impacts

    PubMed Central

    Stiff, Tom; Casar Tena, Teresa; O'Driscoll, Mark; Jeggo, Penny A.; Philipp, Melanie

    2016-01-01

    Mutations in ATR (ataxia telangiectasia and RAD3-related) cause Seckel syndrome (ATR-SS), a microcephalic primordial dwarfism disorder. Hitherto, the clinical manifestation of ATR deficiency has been attributed to its canonical role in DNA damage response signalling following replication fork stalling/collapse. Here, we show that ATR regulates cilia-dependent signalling in a manner that can be uncoupled from its function during replication. ATR-depleted or patient-derived ATR-SS cells form cilia of slightly reduced length but are dramatically impaired in cilia-dependent signalling functions, including growth factor and Sonic hedgehog signalling. To better understand the developmental impact of ATR loss of function, we also used zebrafish as a model. Zebrafish embryos depleted of Atr resembled ATR-SS morphology, showed a modest but statistically significant reduction in cilia length and other morphological features indicative of cilia dysfunction. Additionally, they displayed defects in left-right asymmetry including ambiguous expression of southpaw, incorrectly looped hearts and randomized localization of internal organs including the pancreas, features typically conferred by cilia dysfunction. Our findings reveal a novel role for ATR in cilia signalling distinct from its canonical function during replication and strengthen emerging links between cilia function and development. PMID:26908596

  18. Link-Prediction Enhanced Consensus Clustering for Complex Networks

    PubMed Central

    Burgess, Matthew; Adar, Eytan; Cafarella, Michael

    2016-01-01

    Many real networks that are collected or inferred from data are incomplete due to missing edges. Missing edges can be inherent to the dataset (Facebook friend links will never be complete) or the result of sampling (one may only have access to a portion of the data). The consequence is that downstream analyses that “consume” the network will often yield less accurate results than if the edges were complete. Community detection algorithms, in particular, often suffer when critical intra-community edges are missing. We propose a novel consensus clustering algorithm to enhance community detection on incomplete networks. Our framework utilizes existing community detection algorithms that process networks imputed by our link prediction based sampling algorithm and merges their multiple partitions into a final consensus output. On average our method boosts performance of existing algorithms by 7% on artificial data and 17% on ego networks collected from Facebook. PMID:27203750

  19. Optimization of an avionic VCSEL-based optical link through large signal characterization

    NASA Astrophysics Data System (ADS)

    Ly, Khadijetou S.; Rissons, A.; Gambardella, E.; Mollier, J.-C.

    2008-04-01

    Optical communication systems have been widely preferred for network communications, especially for Datacoms Local Area Network links. The optical technology is an excellent candidate for on-board systems due to the potential weight saving and EMC immunity. According to the short length of the link and a cost saving, Vertical Cavity Surface Emitting Laser (VCSEL) and multimode fiber are the best solution for gigabit systems. In this context, we propose a modeling of 850nm VCSEL based on the rate equations analysis to predict the optical interconnect performances (jitter, bit error rate). Our aim is to define the operation conditions of VCSEL under large signal modulation in order to maximize the Extinction Ratio (current I OFF below threshold) without affecting link performances. The VCSEL model is developed to provide large signal modulation response. Biasing below threshold causes stochastic turn-on delay. Fluctuations of this delay occur, due to the spontaneous emission. This leads to additional turn-on jitter. These stochastic effects are included in the model by adding the Langevin photon and electron noise sources. The VCSEL behavior under high-speed modulation is studied to observe the transient response and extract the resonance frequency, overshoot and turn-on delay. The associated jitter is evaluated with the standard deviation of the turn-on delay probability density function. Simulations of stochastic and deterministic jitters are realized under different conditions of modulation (OFF current levels). Comparing simulations with measurement results carried out on VCSEL and a short haul gigabit link validates the approach.

  20. Detection of the dominant direction of information flow and feedback links in densely interconnected regulatory networks

    PubMed Central

    Ispolatov, Iaroslav; Maslov, Sergei

    2008-01-01

    Background Finding the dominant direction of flow of information in densely interconnected regulatory or signaling networks is required in many applications in computational biology and neuroscience. This is achieved by first identifying and removing links which close up feedback loops in the original network and hierarchically arranging nodes in the remaining network. In mathematical language this corresponds to a problem of making a graph acyclic by removing as few links as possible and thus altering the original graph in the least possible way. The exact solution of this problem requires enumeration of all cycles and combinations of removed links, which, as an NP-hard problem, is computationally prohibitive even for modest-size networks. Results We introduce and compare two approximate numerical algorithms for solving this problem: the probabilistic one based on a simulated annealing of the hierarchical layout of the network which minimizes the number of "backward" links going from lower to higher hierarchical levels, and the deterministic, "greedy" algorithm that sequentially cuts the links that participate in the largest number of feedback cycles. We find that the annealing algorithm outperforms the deterministic one in terms of speed, memory requirement, and the actual number of removed links. To further improve a visual perception of the layout produced by the annealing algorithm, we perform an additional minimization of the length of hierarchical links while keeping the number of anti-hierarchical links at their minimum. The annealing algorithm is then tested on several examples of regulatory and signaling networks/pathways operating in human cells. Conclusion The proposed annealing algorithm is powerful enough to performs often optimal layouts of protein networks in whole organisms, consisting of around ~104 nodes and ~105 links, while the applicability of the greedy algorithm is limited to individual pathways with ~100 vertices. The considered examples

  1. Detecting link failures in complex network processes using remote monitoring

    NASA Astrophysics Data System (ADS)

    Dhal, R.; Abad Torres, J.; Roy, S.

    2015-11-01

    We study whether local structural changes in a complex network can be distinguished from passive remote time-course measurements of the network's dynamics. Specifically the detection of link failures in a network synchronization process from noisy measurements at a single network component is considered. By phrasing the detection task as a Maximum A Posteriori Probability hypothesis testing problem, we are able to obtain conditions under which the detection is (1) improved over the a priori and (2) asymptotically perfect, in terms of the network spectrum and graph. We find that, in the case where the detector has knowledge of the network's state, perfect detection is possible under general connectivity conditions regardless of the measurement location. When the detector does not have state knowledge, a remote signature permits improved but not perfect detection, under the same connectivity conditions. At its essence, detectability is achieved because of the close connection between a network's topology, its eigenvalues and local response characteristics.

  2. Acoustic signal propagation characterization of conduit networks

    NASA Astrophysics Data System (ADS)

    Khan, Muhammad Safeer

    Analysis of acoustic signal propagation in conduit networks has been an important area of research in acoustics. One major aspect of analyzing conduit networks as acoustic channels is that a propagating signal suffers frequency dependent attenuation due to thermo-viscous boundary layer effects and the presence of impedance mismatches such as side branches. The signal attenuation due to side branches is strongly influenced by their numbers and dimensions such as diameter and length. Newly developed applications for condition based monitoring of underground conduit networks involve measurement of acoustic signal attenuation through tests in the field. In many cases the exact installation layout of the field measurement location may not be accessible or actual installation may differ from the documented layout. The lack of exact knowledge of numbers and lengths of side branches, therefore, introduces uncertainty in the measurements of attenuation and contributes to the random variable error between measured results and those predicted from theoretical models. There are other random processes in and around conduit networks in the field that also affect the propagation of an acoustic signal. These random processes include but are not limited to the presence of strong temperature and humidity gradients within the conduits, blockages of variable sizes and types, effects of aging such as cracks, bends, sags and holes, ambient noise variations and presence of variable layer of water. It is reasonable to consider that the random processes contributing to the error in the measured attenuation are independent and arbitrarily distributed. The error, contributed by a large number of independent sources of arbitrary probability distributions, is best described by an approximately normal probability distribution in accordance with the central limit theorem. Using an analytical approach to model the attenuating effect of each of the random variable sources can be very complex and

  3. Gene Network Analysis of Glucose Linked Signaling Pathways and Their Role in Human Hepatocellular Carcinoma Cell Growth and Survival in HuH7 and HepG2 Cell Lines

    PubMed Central

    Berger, Emmanuelle; Vega, Nathalie; Weiss-Gayet, Michèle; Géloën, Alain

    2015-01-01

    Cancer progression may be affected by metabolism. In this study, we aimed to analyze the effect of glucose on the proliferation and/or survival of human hepatocellular carcinoma (HCC) cells. Human gene datasets regulated by glucose were compared to gene datasets either dysregulated in HCC or regulated by other signaling pathways. Significant numbers of common genes suggested putative involvement in transcriptional regulations by glucose. Real-time proliferation assays using high (4.5 g/L) versus low (1 g/L) glucose on two human HCC cell lines and specific inhibitors of selected pathways were used for experimental validations. High glucose promoted HuH7 cell proliferation but not that of HepG2 cell line. Gene network analyses suggest that gene transcription by glucose could be mediated at 92% through ChREBP in HepG2 cells, compared to 40% in either other human cells or rodent healthy liver, with alteration of LKB1 (serine/threonine kinase 11) and NOX (NADPH oxidases) signaling pathways and loss of transcriptional regulation of PPARGC1A (peroxisome-proliferator activated receptors gamma coactivator 1) target genes by high glucose. Both PPARA and PPARGC1A regulate transcription of genes commonly regulated by glycolysis, by the antidiabetic agent metformin and by NOX, suggesting their major interplay in the control of HCC progression. PMID:26380295

  4. The Hippo signal transduction network for exercise physiologists.

    PubMed

    Gabriel, Brendan M; Hamilton, D Lee; Tremblay, Annie M; Wackerhage, Henning

    2016-05-15

    The ubiquitous transcriptional coactivators Yap (gene symbol Yap1) and Taz (gene symbol Wwtr1) regulate gene expression mainly by coactivating the Tead transcription factors. Being at the center of the Hippo signaling network, Yap and Taz are regulated by the Hippo kinase cassette and additionally by a plethora of exercise-associated signals and signaling modules. These include mechanotransduction, the AKT-mTORC1 network, the SMAD transcription factors, hypoxia, glucose homeostasis, AMPK, adrenaline/epinephrine and angiotensin II through G protein-coupled receptors, and IL-6. Consequently, exercise should alter Hippo signaling in several organs to mediate at least some aspects of the organ-specific adaptations to exercise. Indeed, Tead1 overexpression in muscle fibers has been shown to promote a fast-to-slow fiber type switch, whereas Yap in muscle fibers and cardiomyocytes promotes skeletal muscle hypertrophy and cardiomyocyte adaptations, respectively. Finally, genome-wide association studies in humans have linked the Hippo pathway members LATS2, TEAD1, YAP1, VGLL2, VGLL3, and VGLL4 to body height, which is a key factor in sports. PMID:26940657

  5. The organization of strong links in complex networks

    NASA Astrophysics Data System (ADS)

    Pajevic, Sinisa; Plenz, Dietmar

    2012-05-01

    Many complex systems reveal a small-world topology, which allows simultaneously local and global efficiency in the interaction between system constituents. Here, we report the results of a comprehensive study that investigates the relation between the clustering properties in such small-world systems and the strength of interactions between its constituents, quantified by the link weight. For brain, gene, social and language networks, we find a local integrative weight organization in which strong links preferentially occur between nodes with overlapping neighbourhoods; we relate this to global robustness of the clustering to removal of the weakest links. Furthermore, we identify local learning rules that establish integrative networks and improve network traffic in response to past traffic failures. Our findings identify a general organization for complex systems that strikes a balance between efficient local and global communication in their strong interactions, while allowing for robust, exploratory development of weak interactions.

  6. A supramolecular cross-linked conjugated polymer network for multiple fluorescent sensing.

    PubMed

    Ji, Xiaofan; Yao, Yong; Li, Jinying; Yan, Xuzhou; Huang, Feihe

    2013-01-01

    A supramolecular cross-linked network was fabricated and demonstrated to act as a multiple fluorescent sensor. It was constructed from a fluorescent conjugated polymer and a bisammonium salt cross-linker driven by dibenzo[24]crown-8/secondary ammonium salt host-guest interactions. Compared with the conjugated polymer, the network has weak fluorescence due to the aggregation of polymer chains. Thanks to the multiple stimuli-responsiveness of host-guest interactions, the fluorescence intensity of the system can be enhanced by four types of signals, including potassium cation, chloride anion, pH increase, and heating. Hence, the network can serve as a cation sensor, an anion sensor, a pH sensor, and a temperature sensor. It can be used in both solution and thin film. Interestingly, exposure of a film made from this supramolecular cross-linked network to ammonia leads to an increase of fluorescence, making it a good candidate for gas detection. PMID:23259828

  7. Cascaded optical fiber link using the internet network for remote clocks comparison

    NASA Astrophysics Data System (ADS)

    Chiodo, Nicola; Quintin, Nicolas; Stefani, Fabio; Wiotte, Fabrice; Camisard, Emilie; Chardonnet, Christian; Santarelli, Giorgio; Amy-Klein, Anne; Pottie, Paul-Eric; Lopez, Olivier

    2015-12-01

    We report a cascaded optical link of 1100 km for ultra-stable frequency distribution over an Internet fiber network. The link is composed of four spans for which the propagation noise is actively compensated. The robustness and the performance of the link are ensured by five fully automated optoelectronic stations, two of them at the link ends, and three deployed on the field and connecting the spans. This device coherently regenerates the optical signal with the heterodyne optical phase locking of a low-noise laser diode. Optical detection of the beat-note signals for the laser lock and the link noise compensation are obtained with stable and low-noise fibered optical interferometer. We show 3.5 days of continuous operation of the noise-compensated 4-span cascaded link leading to fractional frequency instability of 4x10-16 at 1-s measurement time and 1x10-19 at 2000 s. This cascaded link was extended to 1480-km with the same performance. This work is a significant step towards a sustainable wide area ultra-stable optical frequency distribution and comparison network at a very high level of performance.

  8. Early-warning signals of topological collapse in interbank networks.

    PubMed

    Squartini, Tiziano; van Lelyveld, Iman; Garlaschelli, Diego

    2013-01-01

    The financial crisis clearly illustrated the importance of characterizing the level of 'systemic' risk associated with an entire credit network, rather than with single institutions. However, the interplay between financial distress and topological changes is still poorly understood. Here we analyze the quarterly interbank exposures among Dutch banks over the period 1998-2008, ending with the crisis. After controlling for the link density, many topological properties display an abrupt change in 2008, providing a clear - but unpredictable - signature of the crisis. By contrast, if the heterogeneity of banks' connectivity is controlled for, the same properties show a gradual transition to the crisis, starting in 2005 and preceded by an even earlier period during which anomalous debt loops could have led to the underestimation of counter-party risk. These early-warning signals are undetectable if the network is reconstructed from partial bank-specific data, as routinely done. We discuss important implications for bank regulatory policies. PMID:24285089

  9. Early-warning signals of topological collapse in interbank networks

    NASA Astrophysics Data System (ADS)

    Squartini, Tiziano; van Lelyveld, Iman; Garlaschelli, Diego

    2013-11-01

    The financial crisis clearly illustrated the importance of characterizing the level of `systemic' risk associated with an entire credit network, rather than with single institutions. However, the interplay between financial distress and topological changes is still poorly understood. Here we analyze the quarterly interbank exposures among Dutch banks over the period 1998-2008, ending with the crisis. After controlling for the link density, many topological properties display an abrupt change in 2008, providing a clear - but unpredictable - signature of the crisis. By contrast, if the heterogeneity of banks' connectivity is controlled for, the same properties show a gradual transition to the crisis, starting in 2005 and preceded by an even earlier period during which anomalous debt loops could have led to the underestimation of counter-party risk. These early-warning signals are undetectable if the network is reconstructed from partial bank-specific data, as routinely done. We discuss important implications for bank regulatory policies.

  10. Polymorphism of Cross-Linked Actin Networks in Giant Vesicles

    NASA Astrophysics Data System (ADS)

    Limozin, Laurent; Sackmann, Erich

    2002-09-01

    Actin networks cross-linked by natural linkers α-actinin and filamin are generated in giant vesicles by polymerization through ionophore-mediated influx of Mg2+. α-actinin induces the formation of randomly linked networks at 25 °C which transform at <15 °C into spiderweblike gels or ringlike bundles depending on the vesicle size. Muscle filamin forms ringlike structures under all experimental conditions which can supercoil by subsequent Mg2+ addition. The polymorphism is rationalized in terms of recent models of bivalent ion coupled semiflexible polyelectrolytes and by considering the topology of the linkers.

  11. Prediction of Links and Weights in Networks by Reliable Routes

    PubMed Central

    Zhao, Jing; Miao, Lili; Yang, Jian; Fang, Haiyang; Zhang, Qian-Ming; Nie, Min; Holme, Petter; Zhou, Tao

    2015-01-01

    Link prediction aims to uncover missing links or predict the emergence of future relationships from the current network structure. Plenty of algorithms have been developed for link prediction in unweighted networks, but only a few have been extended to weighted networks. In this paper, we present what we call a “reliable-route method” to extend unweighted local similarity indices to weighted ones. Using these indices, we can predict both the existence of links and their weights. Experiments on various real-world networks suggest that our reliable-route weighted resource-allocation index performs noticeably better than others with respect to weight prediction. For existence prediction it is either the highest or very close to the highest. Further analysis shows a strong positive correlation between the clustering coefficient and prediction accuracy. Finally, we apply our method to the prediction of missing protein-protein interactions and their confidence scores from known PPI networks. Once again, our reliable-route method shows the highest accuracy. PMID:26198206

  12. Porous Cross-Linked Polyimide-Urea Networks

    NASA Technical Reports Server (NTRS)

    Meador, Mary Ann B. (Inventor); Nguyen, Baochau N. (Inventor)

    2015-01-01

    Porous cross-linked polyimide-urea networks are provided. The networks comprise a subunit comprising two anhydride end-capped polyamic acid oligomers in direct connection via a urea linkage. The oligomers (a) each comprise a repeating unit of a dianhydride and a diamine and a terminal anhydride group and (b) are formulated with 2 to 15 of the repeating units. The subunit was formed by reaction of the diamine and a diisocyanate to form a diamine-urea linkage-diamine group, followed by reaction of the diamine-urea linkage-diamine group with the dianhydride and the diamine to form the subunit. The subunit has been cross-linked via a cross-linking agent, comprising three or more amine groups, at a balanced stoichiometry of the amine groups to the terminal anhydride groups. The subunit has been chemically imidized to yield the porous cross-linked polyimide-urea network. Also provided are wet gels, aerogels, and thin films comprising the networks, and methods of making the networks.

  13. Text mining for metabolic pathways, signaling cascades, and protein networks.

    PubMed

    Hoffmann, Robert; Krallinger, Martin; Andres, Eduardo; Tamames, Javier; Blaschke, Christian; Valencia, Alfonso

    2005-05-10

    The complexity of the information stored in databases and publications on metabolic and signaling pathways, the high throughput of experimental data, and the growing number of publications make it imperative to provide systems to help the researcher navigate through these interrelated information resources. Text-mining methods have started to play a key role in the creation and maintenance of links between the information stored in biological databases and its original sources in the literature. These links will be extremely useful for database updating and curation, especially if a number of technical problems can be solved satisfactorily, including the identification of protein and gene names (entities in general) and the characterization of their types of interactions. The first generation of openly accessible text-mining systems, such as iHOP (Information Hyperlinked over Proteins), provides additional functions to facilitate the reconstruction of protein interaction networks, combine database and text information, and support the scientist in the formulation of novel hypotheses. The next challenge is the generation of comprehensive information regarding the general function of signaling pathways and protein interaction networks. PMID:15886388

  14. Cascaded optical link on a telecommunication fiber network for ultra-stable frequency dissemination

    NASA Astrophysics Data System (ADS)

    Lopez, Olivier; Chiodo, Nicola; Stefani, Fabio; Wiotte, Fabrice; Quintin, Nicolas; Bercy, Anthony; Chardonnet, Christian; Santarelli, Giorgio; Pottie, Paul-Eric; Amy-Klein, Anne

    2015-03-01

    The transfer of ultra-stable frequencies between distant laboratories is required by many applications in time and frequency metrology, fundamental physics, particle accelerators and astrophysics. Optical fiber links have been intensively studied for a decade and brought the potential to transfer frequency with a very high accuracy and stability thanks to an active compensation of the propagation noise. We are currently developing an optical metrological network using the fibers of the French National Research and Education Network. Using the so-called dark-channel approach, the ultrastable signal is copropagating with data traffic using wavelength division multiplexing. Due to significant reflections and losses along the fibers, which cannot be compensated with amplifiers, we have developed some repeater stations for the metrological signal. These remotely-operated stations amplify the ultrastable signal and compensate the propagation noise. The link is thus composed of a few cascaded spans. It gives the possibility to increase the noise correction bandwidth, which is proportional to the inverse of the fiber length for each span. These stations are a key element for the deployment of a reliable and large scale metrological network. We report here on the implementation of a two-spans cascaded link of 740 km reaching a relative stability of a few 10-20 after 103 s averaging time. Extension to longer links and alternative transfer methods will be discussed.

  15. Deciphering the link between salicylic acid signaling and sphingolipid metabolism

    PubMed Central

    Sánchez-Rangel, Diana; Rivas-San Vicente, Mariana; de la Torre-Hernández, M. Eugenia; Nájera-Martínez, Manuela; Plasencia, Javier

    2015-01-01

    The field of plant sphingolipid biology has evolved in recent years. Sphingolipids are abundant in cell membranes, and genetic analyses revealed essential roles for these lipids in plant growth, development, and responses to abiotic and biotic stress. Salicylic acid (SA) is a key signaling molecule that is required for induction of defense-related genes and rapid and localized cell death at the site of pathogen infection (hypersensitive response) during incompatible host–pathogen interactions. Conceivably, while levels of SA rapidly increase upon pathogen infection for defense activation, they must be tightly regulated during plant growth and development in the absence of pathogens. Genetic and biochemical evidence suggest that the sphingolipid intermediates, long-chain sphingoid bases, and ceramides, play a role in regulating SA accumulation in plant cells. However, how signals generated from the perturbation of these key sphingolipid intermediates are transduced into the activation of the SA pathway has long remained to be an interesting open question. At least four types of molecules – MAP kinase 6, reactive oxygen species, free calcium, and nitric oxide – could constitute a mechanistic link between sphingolipid metabolism and SA accumulation and signaling. PMID:25806037

  16. MSAT signalling and network management architectures

    NASA Technical Reports Server (NTRS)

    Garland, Peter; Keelty, J. Malcolm

    1989-01-01

    Spar Aerospace has been active in the design and definition of Mobile Satellite Systems since the mid 1970's. In work sponsored by the Canadian Department of Communications, various payload configurations have evolved. In addressing the payload configuration, the requirements of the mobile user, the service provider and the satellite operator have always been the most important consideration. The current Spar 11 beam satellite design is reviewed, and its capabilities to provide flexibility and potential for network growth within the WARC87 allocations are explored. To enable the full capabilities of the payload to be realized, a large amount of ground based Switching and Network Management infrastructure will be required, when space segment becomes available. Early indications were that a single custom designed Demand Assignment Multiple Access (DAMA) switch should be implemented to provide efficient use of the space segment. As MSAT has evolved into a multiple service concept, supporting many service providers, this architecture should be reviewed. Some possible signalling and Network Management solutions are explored.

  17. Collective Calcium Signaling of Defective Multicellular Networks

    NASA Astrophysics Data System (ADS)

    Potter, Garrett; Sun, Bo

    2015-03-01

    A communicating multicellular network processes environmental cues into collective cellular dynamics. We have previously demonstrated that, when excited by extracellular ATP, fibroblast monolayers generate correlated calcium dynamics modulated by both the stimuli and gap junction communication between the cells. However, just as a well-connected neural network may be compromised by abnormal neurons, a tissue monolayer can also be defective with cancer cells, which typically have down regulated gap junctions. To understand the collective cellular dynamics in a defective multicellular network we have studied the calcium signaling of co-cultured breast cancer cells and fibroblast cells in various concentrations of ATP delivered through microfluidic devices. Our results demonstrate that cancer cells respond faster, generate singular spikes, and are more synchronous across all stimuli concentrations. Additionally, fibroblast cells exhibit persistent calcium oscillations that increase in regularity with greater stimuli. To interpret these results we quantitatively analyzed the immunostaining of purigenic receptors and gap junction channels. The results confirm our hypothesis that collective dynamics are mainly determined by the availability of gap junction communications.

  18. Neural Networks for Signal Processing and Control

    NASA Astrophysics Data System (ADS)

    Hesselroth, Ted Daniel

    cortex by the application of lateral interactions during the learning phase. The organization of the mature network is compared to that found in the macaque monkey by several analytical tests. The capacity of the network to process images is investigated. By a method of reconstructing the input images in terms of V1 activities, the simulations show that images can be faithfully represented in V1 by the proposed network. The signal-to-noise ratio of the image is improved by the representation, and compression ratios of well over two-hundred are possible. Lateral interactions between V1 neurons sharpen their orientational tuning. We further study the dynamics of the processing, showing that the rate of decrease of the error of the reconstruction is maximized for the receptive fields used. Lastly, we employ a Fokker-Planck equation for a more detailed prediction of the error value vs. time. The Fokker-Planck equation for an underdamped system with a driving force is derived, yielding an energy-dependent diffusion coefficient which is the integral of the spectral densities of the force and the velocity of the system. The theory is applied to correlated noise activation and resonant activation. Simulation results for the error of the network vs time are compared to the solution of the Fokker-Planck equation.

  19. Microglia Control Neuronal Network Excitability via BDNF Signalling

    PubMed Central

    2013-01-01

    Microglia-neuron interactions play a crucial role in several neurological disorders characterized by altered neural network excitability, such as epilepsy and neuropathic pain. While a series of potential messengers have been postulated as substrates of the communication between microglia and neurons, including cytokines, purines, prostaglandins, and nitric oxide, the specific links between messengers, microglia, neuronal networks, and diseases have remained elusive. Brain-derived neurotrophic factor (BDNF) released by microglia emerges as an exception in this riddle. Here, we review the current knowledge on the role played by microglial BDNF in controlling neuronal excitability by causing disinhibition. The efforts made by different laboratories during the last decade have collectively provided a robust mechanistic paradigm which elucidates the mechanisms involved in the synthesis and release of BDNF from microglia, the downstream TrkB-mediated signals in neurons, and the biophysical mechanism by which disinhibition occurs, via the downregulation of the K+-Cl− cotransporter KCC2, dysrupting Cl−homeostasis, and hence the strength of GABAA- and glycine receptor-mediated inhibition. The resulting altered network activity appears to explain several features of the associated pathologies. Targeting the molecular players involved in this canonical signaling pathway may lead to novel therapeutic approach for ameliorating a wide array of neural dysfunctions. PMID:24089642

  20. Locating inefficient links in a large-scale transportation network

    NASA Astrophysics Data System (ADS)

    Sun, Li; Liu, Like; Xu, Zhongzhi; Jie, Yang; Wei, Dong; Wang, Pu

    2015-02-01

    Based on data from geographical information system (GIS) and daily commuting origin destination (OD) matrices, we estimated the distribution of traffic flow in the San Francisco road network and studied Braess's paradox in a large-scale transportation network with realistic travel demand. We measured the variation of total travel time Δ T when a road segment is closed, and found that | Δ T | follows a power-law distribution if Δ T < 0 or Δ T > 0. This implies that most roads have a negligible effect on the efficiency of the road network, while the failure of a few crucial links would result in severe travel delays, and closure of a few inefficient links would counter-intuitively reduce travel costs considerably. Generating three theoretical networks, we discovered that the heterogeneously distributed travel demand may be the origin of the observed power-law distributions of | Δ T | . Finally, a genetic algorithm was used to pinpoint inefficient link clusters in the road network. We found that closing specific road clusters would further improve the transportation efficiency.

  1. TCP flow control using link layer information in mobile networks

    NASA Astrophysics Data System (ADS)

    Koga, Hiroyuki; Kawahara, Kenji; Oie, Yuji

    2002-07-01

    Mobile Networks have been expanding and IMT-2000 further increases their available bandwidth over wireless links. However, TCP, which is a reliable end-to-end transport protocol, is tuned to perform well in wired networks where bit error rates are very low and packet loss occurs mostly because of congestion. Although a TCP sender can execute flow control to utilize as much available bandwidth as possible in wired networks, it cannot work well in wireless networks characterized by high bit error rates. In the next generation mobile systems, sophisticated error recovery technologies of FEC and ARQ are indeed employed over wireless links, i.e., over Layer 2, to avoid performance degradation of upper layers. However, multiple retransmissions by Layer 2 ARQ can adversely increase transmission delay of TCP segments, which will further make TCP unnecessarily increase RTO (Retransmission TimeOut). Furthermore, a link bandwidth assigned to TCP flows can change in response to changing air conditions to use wireless links efficiently. TCP thus has to adapt its transmission rate according to the changing available bandwidth. The major goal of this study is to develop a receiver-based effective TCP flow control without any modification on TCP senders, which are probably connected with wired networks. For this end, we propose a TCP flow control employing some Layer 2 information on a wireless link at the mobile station. Our performance evaluation of the proposed TCP shows that the receiver-based TCP flow control can moderate the performance degradation very well even if FER on Layer 2 is high.

  2. Rainfall retrieval in urban areas using commercial microwave links from mobile networks: A modelling feasibility study

    NASA Astrophysics Data System (ADS)

    Zohidov, Bahtiyor; Andrieu, Hervé; Servières, Myriam; Normand, Nicolas

    2014-05-01

    Rainfall is usually measured by networks of rain gauges and weather radars. Many cities worldwide are not supplied with these devices; however, they are generally equipped with mobile telecommunication networks. Mobile networks use atmospheric Hyper-Frequency (HF) links whose transmitted signal power is attenuated by rainfall. Measuring that signal attenuation along each link could allow the measurement of path-averaged rainfall [Leijnse et al 2007, Overeem et al 2013, Messer et al 2006, Guili et al 1991, Zinevich et al 2008, Cuccoli et al 2011]. As HF links are concentrated in cities, these networks could constitute a self-sufficient approach to monitoring rainfall in urban areas. We adopt a simulation approach in order to study the feasibility of mapping rainfall fields at the city scale by means of existing HF links. Our domain of study is the central part of the city of Nantes, France, where the density of cellular networks is greatest. As a basis, we use a data set consisting of hundreds of weather radar images recorded by the Météo-France C band weather radar at high spatial (250m x 250m) and temporal (5 minute) resolutions located about 10 km north of the center of Nantes. We convert these images into rainfall maps using the Z-R relation and consider them as reference rainfall fields. The simulation is performed as follows. First, we simulate the measurement of total attenuation along each HF link using a rain-attenuation model based on Mie theory and a known drop size distribution in a continental temperate climate. This procedure is applied for 256 real radio links operating at different frequencies (18, 23, 38 GHz) with lengths ranging from 0.4 to 16 km. This helps us to substitute the attenuation data for the signal power received from microwave links. Error sources affecting measurement accuracy are introduced as a zero-mean Gaussian distributed random variable with variance of 10% of total attenuation. The retrieval of the rainfield is performed by a

  3. Linking Individual and Collective Behavior in Adaptive Social Networks

    NASA Astrophysics Data System (ADS)

    Pinheiro, Flávio L.; Santos, Francisco C.; Pacheco, Jorge M.

    2016-03-01

    Adaptive social structures are known to promote the evolution of cooperation. However, up to now the characterization of the collective, population-wide dynamics resulting from the self-organization of individual strategies on a coevolving, adaptive network has remained unfeasible. Here we establish a (reversible) link between individual (micro)behavior and collective (macro)behavior for coevolutionary processes. We demonstrate that an adaptive network transforms a two-person social dilemma locally faced by individuals into a collective dynamics that resembles that associated with an N -person coordination game, whose characterization depends sensitively on the relative time scales between the entangled behavioral and network evolutions. In particular, we show that the faster the relative rate of adaptation of the network, the smaller the critical fraction of cooperators required for cooperation to prevail, thus establishing a direct link between network adaptation and the evolution of cooperation. The framework developed here is general and may be readily applied to other dynamical processes occurring on adaptive networks, notably, the spreading of contagious diseases or the diffusion of innovations.

  4. Neural network-based sensor signal accelerator.

    SciTech Connect

    Vogt, M. C.

    2000-10-16

    A strategy has been developed to computationally accelerate the response time of a generic electronic sensor. The strategy can be deployed as an algorithm in a control system or as a physical interface (on an embedded microcontroller) between a slower responding external sensor and a higher-speed control system. Optional code implementations are available to adjust algorithm performance when computational capability is limited. In one option, the actual sensor signal can be sampled at the slower rate with adaptive linear neural networks predicting the sensor's future output and interpolating intermediate synthetic output values. In another option, a synchronized collection of predictors sequentially controls the corresponding synthetic output voltage. Error is adaptively corrected in both options. The core strategy has been demonstrated with automotive oxygen sensor data. A prototype interface device is under construction. The response speed increase afforded by this strategy could greatly offset the cost of developing a replacement sensor with a faster physical response time.

  5. Predicting top-L missing links with node and link clustering information in large-scale networks

    NASA Astrophysics Data System (ADS)

    Wu, Zhihao; Lin, Youfang; Wan, Huaiyu; Jamil, Waleed

    2016-08-01

    Networks are mathematical structures that are universally used to describe a large variety of complex systems, such as social, biological, and technological systems. The prediction of missing links in incomplete complex networks aims to estimate the likelihood of the existence of a link between a pair of nodes. Various topological features of networks have been applied to develop link prediction methods. However, the exploration of features of links is still limited. In this paper, we demonstrate the power of node and link clustering information in predicting top -L missing links. In the existing literature, link prediction algorithms have only been tested on small-scale and middle-scale networks. The network scale factor has not attracted the same level of attention. In our experiments, we test the proposed method on three groups of networks. For small-scale networks, since the structures are not very complex, advanced methods cannot perform significantly better than classical methods. For middle-scale networks, the proposed index, combining both node and link clustering information, starts to demonstrate its advantages. In many networks, combining both node and link clustering information can improve the link prediction accuracy a great deal. Large-scale networks with more than 100 000 links have rarely been tested previously. Our experiments on three large-scale networks show that local clustering information based methods outperform other methods, and link clustering information can further improve the accuracy of node clustering information based methods, in particular for networks with a broad distribution of the link clustering coefficient.

  6. A Survey of Link Prediction in Social Networks

    NASA Astrophysics Data System (ADS)

    Hasan, Mohammad Al; Zaki, Mohammed J.

    Link prediction is an important task for analying social networks which also has applications in other domains like, information retrieval, bioinformatics and e-commerce. There exist a variety of techniques for link prediction, ranging from feature-based classification and kernel-based method to matrix factorization and probabilistic graphical models. These methods differ from each other with respect to model complexity, prediction performance, scalability, and generalization ability. In this article, we survey some representative link prediction methods by categorizing them by the type of the models. We largely consider three types of models: first, the traditional (non-Bayesian) models which extract a set of features to train a binary classification model. Second, the probabilistic approaches which model the joint-probability among the entities in a network by Bayesian graphical models. And, finally the linear algebraic approach which computes the similarity between the nodes in a network by rank-reduced similarity matrices. We discuss various existing link prediction models that fall in these broad categories and analyze their strength and weakness. We conclude the survey with a discussion on recent developments and future research direction.

  7. Asynchronous transfer mode link performance over ground networks

    NASA Technical Reports Server (NTRS)

    Chow, E. T.; Markley, R. W.

    1993-01-01

    The results of an experiment to determine the feasibility of using asynchronous transfer mode (ATM) technology to support advanced spacecraft missions that require high-rate ground communications and, in particular, full-motion video are reported. Potential nodes in such a ground network include Deep Space Network (DSN) antenna stations, the Jet Propulsion Laboratory, and a set of national and international end users. The experiment simulated a lunar microrover, lunar lander, the DSN ground communications system, and distributed science users. The users were equipped with video-capable workstations. A key feature was an optical fiber link between two high-performance workstations equipped with ATM interfaces. Video was also transmitted through JPL's institutional network to a user 8 km from the experiment. Variations in video depending on the networks and computers were observed, the results are reported.

  8. Linking the levels: network and relational perspectives for community psychology.

    PubMed

    Neal, Jennifer Watling; Christens, Brian D

    2014-06-01

    In this article, we assert that relationships and networks are of paramount importance for understanding and improving settings, neighborhoods, communities, and larger social systems. Despite previous acknowledgements of their relevance, relational and social network perspectives and analyses remain underrepresented in community psychological research and action. Here, we claim that network and relational perspectives can provide conceptual and empirical 'links' between levels of analysis, more fully reflecting a transactional view. We also describe some of the sophisticated methodologies that can be employed in empirical studies drawing on these perspectives. Additionally, we contend that core concepts in community psychology such as health promotion, empowerment, coalition building, and dissemination and implementation can be better understood when employing relational and network perspectives. As an introduction to this special issue of American Journal of Community Psychology, we draw out themes and key points from the articles in the issue, and offer recommendations for future advancement of these perspectives in the field. PMID:24752731

  9. Viscoelastic Nanomechanics of Ionically Cross-linked Polyelectrolyte Networks

    NASA Astrophysics Data System (ADS)

    Han, Biao; Lee, Daeyeon; Han, Lin

    2015-03-01

    Understanding the mechanics of ionic polyelectrolyte networks is critical for applications where nm-to-um mechanics is the key to success. This study aims to reveal the roles of ionic cross-links and fixed charges in the viscoelasticity of layer-by-layer poly(allylamine hydrochloride)/poly(acrylic acid) microfilms, PAH/PAA, a complex held by pH-sensitive amine-carboxyl links. AFM-nanoindentation and force relaxation (tip R =12.5um) was performed at ionic strength(IS) =0.01-1.0M, pH =5.5-2.0 (pKa of PAA =2.3). When pH changes from 5.5 to 2.0, the films swell for 4x from densely linked, net neutral state to loosely linked, positively charged one. A >100x reduction in indentation modulus was observed at all IS, suggesting the dominance of decrease in cross-link density. In most states, more than 90% force relaxation was observed, where cross-link breaking/reformation likely dominates viscoelasticity. However, at pH =2.5 and IS =0.01M, when electrical double layer repulsion is important (Debye length =3nm), relaxation was about 60%, highlighting the contribution of fixed charges. In summary, this study revealed unique viscoelastic behaviors of PAH/PAA due to the pH- and IS-dependent cross-link and charge densities.

  10. Statistical signal processing in sensor networks

    NASA Astrophysics Data System (ADS)

    Guerriero, Marco

    In this dissertation we focus on decentralized signal processing in Sensor Networks (SN). Four topics are studied: (i) Direction of Arrival (DOA) estimation using a Wireless Sensor network (WSN), (ii) multiple target tracking in large SN, (iii) decentralized target detection in SN and (iv) decentralized sequential detection in SN with communication constraints. The first topic of this thesis addresses the problem of estimating the DOA of an acoustic wavefront using a a WSN made of isotropic (hence individually useless) sensors. The WSN was designed according to the SENMA (SEnsor Network with Mobile Agents) architecture with a mobile agent (MA) that successively queries the sensors lying inside its field of view. We propose both fast/simple and optimal DOA-estimation schemes, and an optimization of the MAs observation management is also carried out, with the surprising finding that the MA ought to orient itself at an oblique angle to the expected DOA, rather than directly toward it. We also consider the extension to multiple sources; intriguingly, per-source DOA accuracy is higher when there is more than one source. In all cases, performance is investigated by simulation and compared, when appropriate, with asymptotic bounds; these latter are usually met after a moderate number of MA dwells. In the second topic, we study the problem of tracking multiple targets in large SN. While these networks hold significant potential for surveillance, it is of interest to address fundamental limitations in large-scale implementations. We first introduce a simple analytical tracker performance model. Analysis of this model suggests that scan-based tracking performance improves with increasing numbers of sensors, but only to a certain point beyond which degradation is observed. Correspondingly, we address model-based optimization of the local sensor detection threshold and the number of sensors. Next, we propose a two-stage tracking approach (fuse-before-track) as a possible

  11. RMOD: a tool for regulatory motif detection in signaling network.

    PubMed

    Kim, Jinki; Yi, Gwan-Su

    2013-01-01

    Regulatory motifs are patterns of activation and inhibition that appear repeatedly in various signaling networks and that show specific regulatory properties. However, the network structures of regulatory motifs are highly diverse and complex, rendering their identification difficult. Here, we present a RMOD, a web-based system for the identification of regulatory motifs and their properties in signaling networks. RMOD finds various network structures of regulatory motifs by compressing the signaling network and detecting the compressed forms of regulatory motifs. To apply it into a large-scale signaling network, it adopts a new subgraph search algorithm using a novel data structure called path-tree, which is a tree structure composed of isomorphic graphs of query regulatory motifs. This algorithm was evaluated using various sizes of signaling networks generated from the integration of various human signaling pathways and it showed that the speed and scalability of this algorithm outperforms those of other algorithms. RMOD includes interactive analysis and auxiliary tools that make it possible to manipulate the whole processes from building signaling network and query regulatory motifs to analyzing regulatory motifs with graphical illustration and summarized descriptions. As a result, RMOD provides an integrated view of the regulatory motifs and mechanism underlying their regulatory motif activities within the signaling network. RMOD is freely accessible online at the following URL: http://pks.kaist.ac.kr/rmod. PMID:23874612

  12. Effects of adaptive dynamical linking in networked games.

    PubMed

    Yang, Zhihu; Li, Zhi; Wu, Te; Wang, Long

    2013-10-01

    The role of dynamical topologies in the evolution of cooperation has received considerable attention, as some studies have demonstrated that dynamical networks are much better than static networks in terms of boosting cooperation. Here we study a dynamical model of evolution of cooperation on stochastic dynamical networks in which there are no permanent partners to each agent. Whenever a new link is created, its duration is randomly assigned without any bias or preference. We allow the agent to adaptively adjust the duration of each link during the evolution in accordance with the feedback from game interactions. By Monte Carlo simulations, we find that cooperation can be remarkably promoted by this adaptive dynamical linking mechanism both for the game of pairwise interactions, such as the Prisoner's Dilemma game (PDG), and for the game of group interactions, illustrated by the public goods game (PGG). And the faster the adjusting rate, the more successful the evolution of cooperation. We also show that in this context weak selection favors cooperation much more than strong selection does. What is particularly meaningful is that the prosperity of cooperation in this study indicates that the rationality and selfishness of a single agent in adjusting social ties can lead to the progress of altruism of the whole population. PMID:24229137

  13. Effects of adaptive dynamical linking in networked games

    NASA Astrophysics Data System (ADS)

    Yang, Zhihu; Li, Zhi; Wu, Te; Wang, Long

    2013-10-01

    The role of dynamical topologies in the evolution of cooperation has received considerable attention, as some studies have demonstrated that dynamical networks are much better than static networks in terms of boosting cooperation. Here we study a dynamical model of evolution of cooperation on stochastic dynamical networks in which there are no permanent partners to each agent. Whenever a new link is created, its duration is randomly assigned without any bias or preference. We allow the agent to adaptively adjust the duration of each link during the evolution in accordance with the feedback from game interactions. By Monte Carlo simulations, we find that cooperation can be remarkably promoted by this adaptive dynamical linking mechanism both for the game of pairwise interactions, such as the Prisoner's Dilemma game (PDG), and for the game of group interactions, illustrated by the public goods game (PGG). And the faster the adjusting rate, the more successful the evolution of cooperation. We also show that in this context weak selection favors cooperation much more than strong selection does. What is particularly meaningful is that the prosperity of cooperation in this study indicates that the rationality and selfishness of a single agent in adjusting social ties can lead to the progress of altruism of the whole population.

  14. CD-Based Indices for Link Prediction in Complex Network.

    PubMed

    Wang, Tao; Wang, Hongjue; Wang, Xiaoxia

    2016-01-01

    Lots of similarity-based algorithms have been designed to deal with the problem of link prediction in the past decade. In order to improve prediction accuracy, a novel cosine similarity index CD based on distance between nodes and cosine value between vectors is proposed in this paper. Firstly, node coordinate matrix can be obtained by node distances which are different from distance matrix and row vectors of the matrix are regarded as coordinates of nodes. Then, cosine value between node coordinates is used as their similarity index. A local community density index LD is also proposed. Then, a series of CD-based indices include CD-LD-k, CD*LD-k, CD-k and CDI are presented and applied in ten real networks. Experimental results demonstrate the effectiveness of CD-based indices. The effects of network clustering coefficient and assortative coefficient on prediction accuracy of indices are analyzed. CD-LD-k and CD*LD-k can improve prediction accuracy without considering the assortative coefficient of network is negative or positive. According to analysis of relative precision of each method on each network, CD-LD-k and CD*LD-k indices have excellent average performance and robustness. CD and CD-k indices perform better on positive assortative networks than on negative assortative networks. For negative assortative networks, we improve and refine CD index, referred as CDI index, combining the advantages of CD index and evolutionary mechanism of the network model BA. Experimental results reveal that CDI index can increase prediction accuracy of CD on negative assortative networks. PMID:26752405

  15. CD-Based Indices for Link Prediction in Complex Network

    PubMed Central

    Wang, Tao; Wang, Hongjue; Wang, Xiaoxia

    2016-01-01

    Lots of similarity-based algorithms have been designed to deal with the problem of link prediction in the past decade. In order to improve prediction accuracy, a novel cosine similarity index CD based on distance between nodes and cosine value between vectors is proposed in this paper. Firstly, node coordinate matrix can be obtained by node distances which are different from distance matrix and row vectors of the matrix are regarded as coordinates of nodes. Then, cosine value between node coordinates is used as their similarity index. A local community density index LD is also proposed. Then, a series of CD-based indices include CD-LD-k, CD*LD-k, CD-k and CDI are presented and applied in ten real networks. Experimental results demonstrate the effectiveness of CD-based indices. The effects of network clustering coefficient and assortative coefficient on prediction accuracy of indices are analyzed. CD-LD-k and CD*LD-k can improve prediction accuracy without considering the assortative coefficient of network is negative or positive. According to analysis of relative precision of each method on each network, CD-LD-k and CD*LD-k indices have excellent average performance and robustness. CD and CD-k indices perform better on positive assortative networks than on negative assortative networks. For negative assortative networks, we improve and refine CD index, referred as CDI index, combining the advantages of CD index and evolutionary mechanism of the network model BA. Experimental results reveal that CDI index can increase prediction accuracy of CD on negative assortative networks. PMID:26752405

  16. Spatial signals link exit from mitosis to spindle position

    PubMed Central

    Falk, Jill Elaine; Tsuchiya, Dai; Verdaasdonk, Jolien; Lacefield, Soni; Bloom, Kerry; Amon, Angelika

    2016-01-01

    In budding yeast, if the spindle becomes mispositioned, cells prevent exit from mitosis by inhibiting the mitotic exit network (MEN). The MEN is a signaling cascade that localizes to spindle pole bodies (SPBs) and activates the phosphatase Cdc14. There are two competing models that explain MEN regulation by spindle position. In the 'zone model', exit from mitosis occurs when a MEN-bearing SPB enters the bud. The 'cMT-bud neck model' posits that cytoplasmic microtubule (cMT)-bud neck interactions prevent MEN activity. Here we find that 1) eliminating cMT– bud neck interactions does not trigger exit from mitosis and 2) loss of these interactions does not precede Cdc14 activation. Furthermore, using binucleate cells, we show that exit from mitosis occurs when one SPB enters the bud despite the presence of a mispositioned spindle. We conclude that exit from mitosis is triggered by a correctly positioned spindle rather than inhibited by improper spindle position. DOI: http://dx.doi.org/10.7554/eLife.14036.001 PMID:27166637

  17. Spatial signals link exit from mitosis to spindle position.

    PubMed

    Falk, Jill Elaine; Tsuchiya, Dai; Verdaasdonk, Jolien; Lacefield, Soni; Bloom, Kerry; Amon, Angelika

    2016-01-01

    In budding yeast, if the spindle becomes mispositioned, cells prevent exit from mitosis by inhibiting the mitotic exit network (MEN). The MEN is a signaling cascade that localizes to spindle pole bodies (SPBs) and activates the phosphatase Cdc14. There are two competing models that explain MEN regulation by spindle position. In the 'zone model', exit from mitosis occurs when a MEN-bearing SPB enters the bud. The 'cMT-bud neck model' posits that cytoplasmic microtubule (cMT)-bud neck interactions prevent MEN activity. Here we find that 1) eliminating cMT- bud neck interactions does not trigger exit from mitosis and 2) loss of these interactions does not precede Cdc14 activation. Furthermore, using binucleate cells, we show that exit from mitosis occurs when one SPB enters the bud despite the presence of a mispositioned spindle. We conclude that exit from mitosis is triggered by a correctly positioned spindle rather than inhibited by improper spindle position. PMID:27166637

  18. Network modeling links breast cancer susceptibility and centrosome dysfunction.

    PubMed

    Pujana, Miguel Angel; Han, Jing-Dong J; Starita, Lea M; Stevens, Kristen N; Tewari, Muneesh; Ahn, Jin Sook; Rennert, Gad; Moreno, Víctor; Kirchhoff, Tomas; Gold, Bert; Assmann, Volker; Elshamy, Wael M; Rual, Jean-François; Levine, Douglas; Rozek, Laura S; Gelman, Rebecca S; Gunsalus, Kristin C; Greenberg, Roger A; Sobhian, Bijan; Bertin, Nicolas; Venkatesan, Kavitha; Ayivi-Guedehoussou, Nono; Solé, Xavier; Hernández, Pilar; Lázaro, Conxi; Nathanson, Katherine L; Weber, Barbara L; Cusick, Michael E; Hill, David E; Offit, Kenneth; Livingston, David M; Gruber, Stephen B; Parvin, Jeffrey D; Vidal, Marc

    2007-11-01

    Many cancer-associated genes remain to be identified to clarify the underlying molecular mechanisms of cancer susceptibility and progression. Better understanding is also required of how mutations in cancer genes affect their products in the context of complex cellular networks. Here we have used a network modeling strategy to identify genes potentially associated with higher risk of breast cancer. Starting with four known genes encoding tumor suppressors of breast cancer, we combined gene expression profiling with functional genomic and proteomic (or 'omic') data from various species to generate a network containing 118 genes linked by 866 potential functional associations. This network shows higher connectivity than expected by chance, suggesting that its components function in biologically related pathways. One of the components of the network is HMMR, encoding a centrosome subunit, for which we demonstrate previously unknown functional associations with the breast cancer-associated gene BRCA1. Two case-control studies of incident breast cancer indicate that the HMMR locus is associated with higher risk of breast cancer in humans. Our network modeling strategy should be useful for the discovery of additional cancer-associated genes. PMID:17922014

  19. The cost and capacity of signaling in the Escherichia coli protein reaction network

    NASA Astrophysics Data System (ADS)

    Axelsen, Jacob Bock; Krishna, Sandeep; Sneppen, Kim

    2008-01-01

    In systems biology new ways are required to analyze the large amount of existing data on regulation of cellular processes. Recent work can be roughly classified into either dynamical models of well-described subsystems, or coarse-grained descriptions of the topology of the molecular networks at the scale of the whole organism. In order to bridge these two disparate approaches one needs to develop simplified descriptions of dynamics and topological measures which address the propagation of signals in molecular networks. Transmission of a signal across a reaction node depends on the presence of other reactants. It will typically be more demanding to transmit a signal across a reaction node with more input links. Sending signals along a path with several subsequent reaction nodes also increases the constraints on the presence of other proteins in the overall network. Therefore counting in and out links along reactions of a potential pathway can give insight into the signaling properties of a particular molecular network. Here, we consider the directed network of protein regulation in E. coli, characterizing its modularity in terms of its potential to transmit signals. We demonstrate that the simplest measure based on identifying subnetworks of strong components, within which each node could send a signal to every other node, does indeed partition the network into functional modules. We suggest that the total number of reactants needed to send a signal between two nodes in the network can be considered as the cost associated with transmitting this signal. Similarly we define spread as the number of reaction products that could be influenced by transmission of a successful signal. Our considerations open for a new class of network measures that implicitly utilize the constrained repertoire of chemical modifications of any biological molecule. The counting of cost and spread connects the topology of networks to the specificity of signaling across the network. Thereby, we

  20. Stretching and bending in cross-linked biopolymer networks

    NASA Astrophysics Data System (ADS)

    Heussinger, Claus; Frey, Erwin

    2007-03-01

    The elastic response of cross-linked biopolymer networks is usually interpreted in terms of affine stretching models, adopted from the theory of rubber-elasticity valid for flexible polymer gels. Unlike flexible polymers, however, stiff polymers have a highly anisotropic elastic response, where the low-energy elastic excitations are actually of bending nature. As a consequence, similar to springs connected in series, one would expect the softer bending mode to dominate the elastic energy rather than the stiff stretching mode. We propose a theory that, unlike recent affine models, properly accounts for the soft bending response of stiff polymers. It allows calculating the macroscopic elastic moduli starting from a microscopic characterization of the (non-affine) deformation field. The calculated scaling properties for the shear modulus are in excellent agreement with the results of recent simulations obtained in simple two-dimensional model networks, and can also be applied to rationalize bulk rheological data in reconstituted actin networks.

  1. Using Distributed Sensor Network Architecture to Link Heterogeneous Astronomical Assets

    NASA Astrophysics Data System (ADS)

    White, R.; Evans, S.; Pergande, J.; Vestrand, W.; Wozniak, P.; Wren, J.

    The internet has brought about great change in the astronomical community, but this interconnectivity is just starting to be exploited for use in this type of instrumentation. Here we present the Telescope ALert Operations Network System (TALONS), a network software suite that allows intercommunication between external and internal astronomical resources and controls the distribution of information to each of the resources. TALONS is an fundamental element of the Thinking Telescopes System, in operation at Los Alamos National Laboratory, and has been enabling great science for the past four years. The system allows a distributed network of telescopes to perform more efficiently in synchronous operation than as individual instruments. TALONS is designed as a merger between a standard server/client architecture and a Distributed Sensor Network (DSN). It can dynamically regulate its client base, allowing any number of heterogeneous resources to be linked together and communicate. TALONS couples that capability with collaborative analysis and maintenance modules so that it can respond quickly to external requests and changing network environments. TALONS clients connect via an intelligent agent, which acts in proxy for the scientist, allowing the telescope to analyze incoming information and respond autonomously. TALONS has a proven track record of effectively supporting the instruments at Los Alamos and other astronomical resources around the world.

  2. Topology and dynamics of signaling networks: in search of transcriptional control of the inflammatory response.

    PubMed

    Androulakis, Ioannis P; Kamisoglu, Kubra; Mattick, John S

    2013-01-01

    Over the past several decades, to develop a fundamental understanding of inflammation's progression, research has focused on extracellular mediators, such as cytokines, as characteristic components of inflammatory response. These efforts have recently been complemented by advances in proteomics that allow analysis of multiple signaling proteins in parallel, to provide more complete mechanistic models of inflammation. In this review, we discuss various techniques for assessing protein activity, as well as computational techniques that are well suited for interpreting large amounts of proteomic data to generate signaling networks or for modeling the dynamics of known network interactions. We also discuss examples that explore these experimental and computational techniques in tandem to generate signaling networks under various conditions and that link those networks to transcriptional activity. Further advancements in this field will likely provide an explicit description of inflammatory response, paving the way for better diagnostics and therapies in clinic. PMID:23862674

  3. Distribution of Link Distances in a Wireless Network

    PubMed Central

    Miller, Leonard E.

    2001-01-01

    The probability distribution is found for the link distance between two randomly positioned mobile radios in a wireless network for two representative deployment scenarios: (1) the mobile locations are uniformly distributed over a rectangular area and (2) the x and y coordinates of the mobile locations have Gaussian distributions. It is shown that the shapes of the link distance distributions for these scenarios are very similar when the width of the rectangular area in the first scenario is taken to be about three times the standard deviation of the location distribution in the second scenario. Thus the choice of mobile location distribution is not critical, but can be selected for the convenience of other aspects of the analysis or simulation of the mobile system.

  4. Early-warning signals of topological collapse in interbank networks

    PubMed Central

    Squartini, Tiziano; van Lelyveld, Iman; Garlaschelli, Diego

    2013-01-01

    The financial crisis clearly illustrated the importance of characterizing the level of ‘systemic’ risk associated with an entire credit network, rather than with single institutions. However, the interplay between financial distress and topological changes is still poorly understood. Here we analyze the quarterly interbank exposures among Dutch banks over the period 1998–2008, ending with the crisis. After controlling for the link density, many topological properties display an abrupt change in 2008, providing a clear – but unpredictable – signature of the crisis. By contrast, if the heterogeneity of banks' connectivity is controlled for, the same properties show a gradual transition to the crisis, starting in 2005 and preceded by an even earlier period during which anomalous debt loops could have led to the underestimation of counter-party risk. These early-warning signals are undetectable if the network is reconstructed from partial bank-specific data, as routinely done. We discuss important implications for bank regulatory policies. PMID:24285089

  5. Establishing a Statistical Link between Network Oscillations and Neural Synchrony.

    PubMed

    Zhou, Pengcheng; Burton, Shawn D; Snyder, Adam C; Smith, Matthew A; Urban, Nathaniel N; Kass, Robert E

    2015-10-01

    Pairs of active neurons frequently fire action potentials or "spikes" nearly synchronously (i.e., within 5 ms of each other). This spike synchrony may occur by chance, based solely on the neurons' fluctuating firing patterns, or it may occur too frequently to be explicable by chance alone. When spike synchrony above chances levels is present, it may subserve computation for a specific cognitive process, or it could be an irrelevant byproduct of such computation. Either way, spike synchrony is a feature of neural data that should be explained. A point process regression framework has been developed previously for this purpose, using generalized linear models (GLMs). In this framework, the observed number of synchronous spikes is compared to the number predicted by chance under varying assumptions about the factors that affect each of the individual neuron's firing-rate functions. An important possible source of spike synchrony is network-wide oscillations, which may provide an essential mechanism of network information flow. To establish the statistical link between spike synchrony and network-wide oscillations, we have integrated oscillatory field potentials into our point process regression framework. We first extended a previously-published model of spike-field association and showed that we could recover phase relationships between oscillatory field potentials and firing rates. We then used this new framework to demonstrate the statistical relationship between oscillatory field potentials and spike synchrony in: 1) simulated neurons, 2) in vitro recordings of hippocampal CA1 pyramidal cells, and 3) in vivo recordings of neocortical V4 neurons. Our results provide a rigorous method for establishing a statistical link between network oscillations and neural synchrony. PMID:26465621

  6. Establishing a Statistical Link between Network Oscillations and Neural Synchrony

    PubMed Central

    Zhou, Pengcheng; Burton, Shawn D.; Snyder, Adam C.; Smith, Matthew A.; Urban, Nathaniel N.; Kass, Robert E.

    2015-01-01

    Pairs of active neurons frequently fire action potentials or “spikes” nearly synchronously (i.e., within 5 ms of each other). This spike synchrony may occur by chance, based solely on the neurons’ fluctuating firing patterns, or it may occur too frequently to be explicable by chance alone. When spike synchrony above chances levels is present, it may subserve computation for a specific cognitive process, or it could be an irrelevant byproduct of such computation. Either way, spike synchrony is a feature of neural data that should be explained. A point process regression framework has been developed previously for this purpose, using generalized linear models (GLMs). In this framework, the observed number of synchronous spikes is compared to the number predicted by chance under varying assumptions about the factors that affect each of the individual neuron’s firing-rate functions. An important possible source of spike synchrony is network-wide oscillations, which may provide an essential mechanism of network information flow. To establish the statistical link between spike synchrony and network-wide oscillations, we have integrated oscillatory field potentials into our point process regression framework. We first extended a previously-published model of spike-field association and showed that we could recover phase relationships between oscillatory field potentials and firing rates. We then used this new framework to demonstrate the statistical relationship between oscillatory field potentials and spike synchrony in: 1) simulated neurons, 2) in vitro recordings of hippocampal CA1 pyramidal cells, and 3) in vivo recordings of neocortical V4 neurons. Our results provide a rigorous method for establishing a statistical link between network oscillations and neural synchrony. PMID:26465621

  7. Radar signal categorization using a neural network

    NASA Technical Reports Server (NTRS)

    Anderson, James A.; Gately, Michael T.; Penz, P. Andrew; Collins, Dean R.

    1991-01-01

    Neural networks were used to analyze a complex simulated radar environment which contains noisy radar pulses generated by many different emitters. The neural network used is an energy minimizing network (the BSB model) which forms energy minima - attractors in the network dynamical system - based on learned input data. The system first determines how many emitters are present (the deinterleaving problem). Pulses from individual simulated emitters give rise to separate stable attractors in the network. Once individual emitters are characterized, it is possible to make tentative identifications of them based on their observed parameters. As a test of this idea, a neural network was used to form a small data base that potentially could make emitter identifications.

  8. Assessing the weather monitoring capabilities of cellular microwave link networks

    NASA Astrophysics Data System (ADS)

    Fencl, Martin; Vrzba, Miroslav; Rieckermann, Jörg; Bareš, Vojtěch

    2016-04-01

    Using of microwave links for rainfall monitoring was suggested already by (Atlas and Ulbrich, 1977). However, this technique attracted broader attention of scientific community only in the recent decade, with the extensive growth of cellular microwave link (CML) networks, which form the backbone of today's cellular telecommunication infrastructure. Several studies have already shown that CMLs can be conveniently used as weather sensors and have potential to provide near-ground path-integrated observations of rainfall but also humidity or fog. However, although research is still focusing on algorithms to improve the weather sensing capabilities (Fencl et al., 2015), it is not clear how to convince cellular operators to provide the power levels of their network. One step in this direction is to show in which regions or municipalities the networks are sufficiently dense to provide/develop good services. In this contribution we suggest a standardized approach to evaluate CML networks in terms of rainfall observation and to identify suitable regions for CML rainfall monitoring. We estimate precision of single CML based on its sensitivity to rainfall, i.e. as a function of frequency, polarization and path length. Capability of a network to capture rainfall spatial patterns is estimated from the CML coverage and path lengths considering that single CML provides path-integrated rain rates. We also search for suitable predictors for regions where no network topologies are available. We test our approach on several European networks and discuss the results. Our results show that CMLs are very dense in urban areas (> 1 CML/km2), but less in rural areas (< 0.02 CML/km2). We found a strong correlation between a population and CML network density (e.g. R2 = 0.97 in Czech Republic), thus population could be a simple proxy to identify suitable regions for CML weather monitoring. To enable a simple and efficient assessment of the CML monitoring potential for any region worldwide

  9. Responses to olfactory signals reflect network structure of flower-visitor interactions.

    PubMed

    Junker, Robert R; Höcherl, Nicole; Blüthgen, Nico

    2010-07-01

    1. Network analyses provide insights into the diversity and complexity of ecological interactions and have motivated conclusions about community stability and co-evolution. However, biological traits and mechanisms such as chemical signals regulating the interactions between individual species--the microstructure of a network--are poorly understood. 2. We linked the responses of receivers (flower visitors) towards signals (flower scent) to the structure of a highly diverse natural flower-insect network. For each interaction, we define link temperature--a newly developed metric--as the deviation of the observed interaction strength from neutrality, assuming that animals randomly interact with flowers. 3. Link temperature was positively correlated to the specific visitors' responses to floral scents, experimentally examined in a mobile olfactometer. Thus, communication between plants and consumers via phytochemical signals reflects a significant part of the microstructure in a complex network. Negative as well as positive responses towards floral scents contributed to these results, where individual experience was important apart from innate behaviour. 4. Our results indicate that: (1) biological mechanisms have a profound impact on the microstructure of complex networks that underlies the outcome of aggregate statistics, and (2) floral scents act as a filter, promoting the visitation of some flower visitors, but also inhibiting the visitation of others. PMID:20412348

  10. SP-NET: A draft signal processor network protocol

    NASA Astrophysics Data System (ADS)

    Burns, David M.

    SP-net, a synchronous high-speed switched network that has been designed for signal processor backplanes, is discussed. The network uses bit-slicing to improve fault tolerance and to allow growth in the width of the data path. In addition, single-bit error detection has been included in the protocol. Although no company at present is building a network to the draft SP-net specifications, SP-net has several similarities to signal processor network designs by major defense contractors.

  11. An extended signal control strategy for urban network traffic flow

    NASA Astrophysics Data System (ADS)

    Yan, Fei; Tian, Fuli; Shi, Zhongke

    2016-03-01

    Traffic flow patterns are in general repeated on a daily or weekly basis. To improve the traffic conditions by using the inherent repeatability of traffic flow, a novel signal control strategy for urban networks was developed via iterative learning control (ILC) approach. Rigorous analysis shows that the proposed learning control method can guarantee the asymptotic convergence. The impacts of the ILC-based signal control strategy on the macroscopic fundamental diagram (MFD) were analyzed by simulations on a test road network. The results show that the proposed ILC strategy can evenly distribute the accumulation in the network and improve the network mobility.

  12. Signaled and Unsignaled Terminal Links in Concurrent Chains I: Effects of Reinforcer Probability and Immediacy

    ERIC Educational Resources Information Center

    Mattson, Karla M.; Hucks, Andrew; Grace, Randolph C.; McLean, Anthony P.

    2010-01-01

    Eight pigeons responded in a three-component concurrent-chains procedure, with either independent or dependent initial links. Relative probability and immediacy of reinforcement in the terminal links were both varied, and outcomes on individual trials (reinforcement or nonreinforcement) were either signaled or unsignaled. Terminal-link fixed-time…

  13. Information routing driven by background chatter in a signaling network.

    PubMed

    Domedel-Puig, Núria; Rué, Pau; Pons, Antonio J; García-Ojalvo, Jordi

    2011-12-01

    Living systems are capable of processing multiple sources of information simultaneously. This is true even at the cellular level, where not only coexisting signals stimulate the cell, but also the presence of fluctuating conditions is significant. When information is received by a cell signaling network via one specific input, the existence of other stimuli can provide a background activity -or chatter- that may affect signal transmission through the network and, therefore, the response of the cell. Here we study the modulation of information processing by chatter in the signaling network of a human cell, specifically, in a Boolean model of the signal transduction network of a fibroblast. We observe that the level of external chatter shapes the response of the system to information carrying signals in a nontrivial manner, modulates the activity levels of the network outputs, and effectively determines the paths of information flow. Our results show that the interactions and node dynamics, far from being random, confer versatility to the signaling network and allow transitions between different information-processing scenarios. PMID:22174668

  14. Link-state-estimation-based transmission power control in wireless body area networks.

    PubMed

    Kim, Seungku; Eom, Doo-Seop

    2014-07-01

    This paper presents a novel transmission power control protocol to extend the lifetime of sensor nodes and to increase the link reliability in wireless body area networks (WBANs). We first experimentally investigate the properties of the link states using the received signal strength indicator (RSSI). We then propose a practical transmission power control protocol based on both short- and long-term link-state estimations. Both the short- and long-term link-state estimations enable the transceiver to adapt the transmission power level and target the RSSI threshold range, respectively, to simultaneously satisfy the requirements of energy efficiency and link reliability. Finally, the performance of the proposed protocol is experimentally evaluated in two experimental scenarios-body posture change and dynamic body motion-and compared with the typical WBAN transmission power control protocols, a real-time reactive scheme, and a dynamic postural position inference mechanism. From the experimental results, it is found that the proposed protocol increases the lifetime of the sensor nodes by a maximum of 9.86% and enhances the link reliability by reducing the packet loss by a maximum of 3.02%. PMID:24107988

  15. Predictors of the peak width for networks with exponential links

    USGS Publications Warehouse

    Troutman, B.M.; Karlinger, M.R.

    1989-01-01

    We investigate optimal predictors of the peak (S) and distance to peak (T) of the width function of drainage networks under the assumption that the networks are topologically random with independent and exponentially distributed link lengths. Analytical results are derived using the fact that, under these assumptions, the width function is a homogeneous Markov birth-death process. In particular, exact expressions are derived for the asymptotic conditional expectations of S and T given network magnitude N and given mainstream length H. In addition, a simulation study is performed to examine various predictors of S and T, including N, H, and basin morphometric properties; non-asymptotic conditional expectations and variances are estimated. The best single predictor of S is N, of T is H, and of the scaled peak (S divided by the area under the width function) is H. Finally, expressions tested on a set of drainage basins from the state of Wyoming perform reasonably well in predicting S and T despite probable violations of the original assumptions. ?? 1989 Springer-Verlag.

  16. Increasing link utilization in IP over WDM networks

    NASA Astrophysics Data System (ADS)

    Nucci, Antonio; Taft, Nina; Thiran, Patrick; Zang, Hui; Diot, Christophe

    2002-07-01

    In this paper we study an approach to Quality of Service that offers end-users the choice between two classes of service defined according to their level of transmission protection. The first class of service, called Fully Protected (FP), offers end-users a guarantee of survivability in the case of a single failure; all FP traffic is protected using either a 1:1 or 1+1 protection scheme at the WDM layer. The second class of service, called Best-Effort Protected (BEP), is not protected; when a failure occurs, the network does the best it can by restoring at the IP layer only as much BEP traffic as possible. The FP service class mimics what Internet users receive today. The motivation of this approach is to increase the amount of bandwidth used on backbone networks by offering a lower quality of service that does not affect the current QoS provided by the network. We design an ILP model, for finding primary and backup paths at the optical layer, that incorporates a number of carriers' common practices. Namely we allow the FP demand to be specified via a traffic matrix at the IP layer, we include an overprovisioning factor that specifies the portion of each link that must be left unused, and we incorporate a minimal fairness requirement on how the BEP traffic is allocated. Our goal is thus to quantify how much BEP traffic can be carried in addition to the FP traffic, without impacting the protection quality of the FP traffic even in the case of failure, and without impacting the FP load. We show that by having two such classes of service, the load on a network can be increased by a factor of 4 to 7 (depending upon the network). Even if carriers want to overprovision their networks by 50%, we can still triple the total network load. We illustrate that the location of the bottleneck can affect whether or not we see a difference in performance between 1:1 or 1+1 protection schemes. Finally we evaluate the tradeoff between the two carrier requirements of overprovisioning

  17. Time Score: A New Feature for Link Prediction in Social Networks

    NASA Astrophysics Data System (ADS)

    Munasinghe, Lankeshwara; Ichise, Ryutaro

    Link prediction in social networks, such as friendship networks and coauthorship networks, has recently attracted a great deal of attention. There have been numerous attempts to address the problem of link prediction through diverse approaches. In the present paper, we focus on the temporal behavior of the link strength, particularly the relationship between the time stamps of interactions or links and the temporal behavior of link strength and how link strength affects future link evolution. Most previous studies have not sufficiently discussed either the impact of time stamps of the interactions or time stamps of the links on link evolution. The gap between the current time and the time stamps of the interactions or links is also important to link evolution. In the present paper, we introduce a new time-aware feature, referred to as time score, that captures the important aspects of time stamps of interactions and the temporality of the link strengths. We also analyze the effectiveness of time score with different parameter settings for different network data sets. The results of the analysis revealed that the time score was sensitive to different networks and different time measures. We applied time score to two social network data sets, namely, Facebook friendship network data set and a coauthorship network data set. The results revealed a significant improvement in predicting future links.

  18. Cell cycle networks link gene expression dysregulation, mutation, and brain maldevelopment in autistic toddlers.

    PubMed

    Pramparo, Tiziano; Lombardo, Michael V; Campbell, Kathleen; Barnes, Cynthia Carter; Marinero, Steven; Solso, Stephanie; Young, Julia; Mayo, Maisi; Dale, Anders; Ahrens-Barbeau, Clelia; Murray, Sarah S; Lopez, Linda; Lewis, Nathan; Pierce, Karen; Courchesne, Eric

    2015-12-01

    Genetic mechanisms underlying abnormal early neural development in toddlers with Autism Spectrum Disorder (ASD) remain uncertain due to the impossibility of direct brain gene expression measurement during critical periods of early development. Recent findings from a multi-tissue study demonstrated high expression of many of the same gene networks between blood and brain tissues, in particular with cell cycle functions. We explored relationships between blood gene expression and total brain volume (TBV) in 142 ASD and control male toddlers. In control toddlers, TBV variation significantly correlated with cell cycle and protein folding gene networks, potentially impacting neuron number and synapse development. In ASD toddlers, their correlations with brain size were lost as a result of considerable changes in network organization, while cell adhesion gene networks significantly correlated with TBV variation. Cell cycle networks detected in blood are highly preserved in the human brain and are upregulated during prenatal states of development. Overall, alterations were more pronounced in bigger brains. We identified 23 candidate genes for brain maldevelopment linked to 32 genes frequently mutated in ASD. The integrated network includes genes that are dysregulated in leukocyte and/or postmortem brain tissue of ASD subjects and belong to signaling pathways regulating cell cycle G1/S and G2/M phase transition. Finally, analyses of the CHD8 subnetwork and altered transcript levels from an independent study of CHD8 suppression further confirmed the central role of genes regulating neurogenesis and cell adhesion processes in ASD brain maldevelopment. PMID:26668231

  19. Convergent, RIC-8-Dependent Gα Signaling Pathways in the Caenorhabditis elegans Synaptic Signaling Network

    PubMed Central

    Reynolds, Nicole K.; Schade, Michael A.; Miller, Kenneth G.

    2005-01-01

    We used gain-of-function and null synaptic signaling network mutants to investigate the relationship of the Gαq and Gαs pathways to synaptic vesicle priming and to each other. Genetic epistasis studies using Gαq gain-of-function and null mutations, along with a mutation that blocks synaptic vesicle priming and the synaptic vesicle priming stimulator phorbol ester, suggest that the Gαq pathway generates the core, obligatory signals for synaptic vesicle priming. In contrast, the Gαs pathway is not required for the core priming function, because steady-state levels of neurotransmitter release are not significantly altered in animals lacking a neuronal Gαs pathway, even though these animals are strongly paralyzed as a result of functional (nondevelopmental) defects. However, our genetic analysis indicates that these two functionally distinct pathways converge and that they do so downstream of DAG production. Further linking the two pathways, our epistasis analysis of a ric-8 null mutant suggests that RIC-8 (a receptor-independent Gα guanine nucleotide exchange factor) is required to maintain both the Gαq vesicle priming pathway and the neuronal Gαs pathway in a functional state. We propose that the neuronal Gαs pathway transduces critical positional information onto the core Gαq pathway to stabilize the priming of selected synapses that are optimal for locomotion. PMID:15489511

  20. Crosstalk between pathways enhances the controllability of signalling networks.

    PubMed

    Wang, Dingjie; Jin, Suoqin; Zou, Xiufen

    2016-02-01

    The control of complex networks is one of the most challenging problems in the fields of biology and engineering. In this study, the authors explored the controllability and control energy of several signalling networks, which consisted of many interconnected pathways, including networks with a bow-tie architecture. On the basis of the theory of structure controllability, they revealed that biological mechanisms, such as cross-pathway interactions, compartmentalisation and so on make the networks easier to fully control. Furthermore, using numerical simulations for two realistic examples, they demonstrated that the control energy of normal networks with crosstalk is lower than in networks without crosstalk. These results indicate that the biological networks are optimally designed to achieve their normal functions from the viewpoint of the control theory. The authors' work provides a comprehensive understanding of the impact of network structures and properties on controllability. PMID:26816393

  1. Signal propagation through feedforward neuronal networks with different operational modes

    NASA Astrophysics Data System (ADS)

    Li, Jie; Liu, Feng; Xu, Ding; Wang, Wei

    2009-02-01

    How neuronal activity is propagated across multiple layers of neurons is a fundamental issue in neuroscience. Using numerical simulations, we explored how the operational mode of neurons —coincidence detector or temporal integrator— could affect the propagation of rate signals through a 10-layer feedforward network with sparse connectivity. Our study was based on two kinds of neuron models. The Hodgkin-Huxley (HH) neuron can function as a coincidence detector, while the leaky integrate-and-fire (LIF) neuron can act as a temporal integrator. When white noise is afferent to the input layer, rate signals can be stably propagated through both networks, while neurons in deeper layers fire synchronously in the absence of background noise; but the underlying mechanism for the development of synchrony is different. When an aperiodic signal is presented, the network of HH neurons can represent the temporal structure of the signal in firing rate. Meanwhile, synchrony is well developed and is resistant to background noise. In contrast, rate signals are somewhat distorted during the propagation through the network of LIF neurons, and only weak synchrony occurs in deeper layers. That is, coincidence detectors have a performance advantage over temporal integrators in propagating rate signals. Therefore, given weak synaptic conductance and sparse connectivity between layers in both networks, synchrony does greatly subserve the propagation of rate signals with fidelity, and coincidence detection could be of considerable functional significance in cortical processing.

  2. A design concept for reliable mobile radio networks with frequency-hopping signaling

    NASA Astrophysics Data System (ADS)

    Ephremides, Anthony

    1988-09-01

    The design of a packet radio network must reflect the operational requirements and environmental constraints to which it is subject. In this report we outline those features that distinguish the High Frequency (HF) Intra Task Force (ITF) Network from other packet radio networks, and we present a design concept for this network that encompasses organizational structure, waveform design, and channel access. Network survivability is achieved through the use of distributed network control and frequency-hopping spread-spectrum signaling. We show how the execution of the fully distributed Linked Cluster Algorithm can enable a network to reconfigure itself when it is affected by connectivity changes such as those resulting from jamming. Additional resistance against jamming is provided by frequency hopping, which leads naturally to the use of Code Division Multiple Access (CDMA) techniques that permit the simultaneous successful transmission by several users. Distributed algorithms that exploit CDMA properties have been developed to schedule contention-free transmissions for much of the channel access in this network. Contention-based channel access protocols can also be implemented in conjunction with the Linked Cluster network structure. The design concept presented in this report provides a high degree of survivability and flexibility to accommodate changing environment conditions and user demands.

  3. Capacity Limit, Link Scheduling and Power Control in Wireless Networks

    ERIC Educational Resources Information Center

    Zhou, Shan

    2013-01-01

    The rapid advancement of wireless technology has instigated the broad deployment of wireless networks. Different types of networks have been developed, including wireless sensor networks, mobile ad hoc networks, wireless local area networks, and cellular networks. These networks have different structures and applications, and require different…

  4. Linking Metabolism to Membrane Signaling: The GABA-Malate Connection.

    PubMed

    Gilliham, Matthew; Tyerman, Stephen D

    2016-04-01

    γ-Aminobutyric acid (GABA) concentration increases rapidly in tissues when plants encounter abiotic or biotic stress, and GABA manipulation affects growth. This, coupled to GABA's well-described role as a neurotransmitter in mammals, led to over a decade of speculation that GABA is a signal in plants. The discovery of GABA-regulated anion channels in plants provides compelling mechanistic proof that GABA is a legitimate plant-signaling molecule. Here we examine research avenues unlocked by this finding and propose that these plant 'GABA receptors' possess novel properties ideally suited to translating changes in metabolic status into physiological responses. Specifically, we suggest they have a role in signaling altered cycling of tricarboxylic acid (TCA) intermediates during stress via eliciting changes in electrical potential differences across membranes. PMID:26723562

  5. Teleconnection Paths via Climate Network Direct Link Detection

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  6. Teleconnection Paths via Climate Network Direct Link Detection.

    PubMed

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

    2015-12-31

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

  7. Human Identification with Electrocardiogram Signals: a Neural Network Approach

    NASA Astrophysics Data System (ADS)

    Wan, Yongbo; Yao, Jianchu

    2009-05-01

    This paper presents a neural network developed to identify human subjects using electrocardiogram (ECG) signals collected from an "in-house" wearable electrocardiogram (ECG) sensor. In this project, noises were first removed from the raw signals with wavelet filters. ECG cycles were then extracted from the filtered signals and decomposed into wavelet coefficient structures. These coefficient structures were used as input vectors to a 3-layer feedforward neural network that generates the identification results. In the current study, 61 datasets collected from 23 subjects were utilized to train the neural network, which thereafter was tested with 15 new datasets from 15 different subjects. All the 15 subjects in the experiment were successfully identified. The testing results demonstrate that the neural network is effective.

  8. Structural permeability of complex networks to control signals

    NASA Astrophysics Data System (ADS)

    Lo Iudice, Francesco; Garofalo, Franco; Sorrentino, Francesco

    2015-09-01

    Many biological, social and technological systems can be described as complex networks. The goal of affecting their behaviour has motivated recent work focusing on the relationship between the network structure and its propensity to be controlled. While this work has provided insight into several relevant problems, a comprehensive approach to address partial and complete controllability of networks is still lacking. Here, we bridge this gap by developing a framework to maximize the diffusion of the control signals through a network, while taking into account physical and economic constraints that inevitably arise in applications. This approach allows us to introduce the network permeability, a unified metric of the propensity of a network to be controllable. The analysis of the permeability of several synthetic and real networks enables us to extract some structural features that deepen our quantitative understanding of the ease with which specific controllability requirements can be met.

  9. Structural permeability of complex networks to control signals

    PubMed Central

    Lo Iudice, Francesco; Garofalo, Franco; Sorrentino, Francesco

    2015-01-01

    Many biological, social and technological systems can be described as complex networks. The goal of affecting their behaviour has motivated recent work focusing on the relationship between the network structure and its propensity to be controlled. While this work has provided insight into several relevant problems, a comprehensive approach to address partial and complete controllability of networks is still lacking. Here, we bridge this gap by developing a framework to maximize the diffusion of the control signals through a network, while taking into account physical and economic constraints that inevitably arise in applications. This approach allows us to introduce the network permeability, a unified metric of the propensity of a network to be controllable. The analysis of the permeability of several synthetic and real networks enables us to extract some structural features that deepen our quantitative understanding of the ease with which specific controllability requirements can be met. PMID:26391186

  10. SIMULATING BIOCHEMICAL SIGNALING NETWORKS IN COMPLEX MOVING GEOMETRIES.

    PubMed

    Strychalski, Wanda; Adalsteinsson, David; Elston, Timothy C

    2010-01-01

    Signaling networks regulate cellular responses to environmental stimuli through cascades of protein interactions. External signals can trigger cells to polarize and move in a specific direction. During migration, spatially localized activity of proteins is maintained. To investigate the effects of morphological changes on intracellular signaling, we developed a numerical scheme consisting of a cut cell finite volume spatial discretization coupled with level set methods to simulate the resulting advection-reaction-diffusion system. We then apply the method to several biochemical reaction networks in changing geometries. We found that a Turing instability can develop exclusively by cell deformations that maintain constant area. For a Turing system with a geometry-dependent single or double peak solution, simulations in a dynamically changing geometry suggest that a single peak solution is the only stable one, independent of the oscillation frequency. The method is also applied to a model of a signaling network in a migrating fibroblast. PMID:24086102

  11. Fiber fault location utilizing traffic signal in optical network.

    PubMed

    Zhao, Tong; Wang, Anbang; Wang, Yuncai; Zhang, Mingjiang; Chang, Xiaoming; Xiong, Lijuan; Hao, Yi

    2013-10-01

    We propose and experimentally demonstrate a method for fault location in optical communication network. This method utilizes the traffic signal transmitted across the network as probe signal, and then locates the fault by correlation technique. Compared with conventional techniques, our method has a simple structure and low operation expenditure, because no additional device is used, such as light source, modulator and signal generator. The correlation detection in this method overcomes the tradeoff between spatial resolution and measurement range in pulse ranging technique. Moreover, signal extraction process can improve the location result considerably. Experimental results show that we achieve a spatial resolution of 8 cm and detection range of over 23 km with -8-dBm mean launched power in optical network based on synchronous digital hierarchy protocols. PMID:24104308

  12. Effectiveness of Link Prediction for Face-to-Face Behavioral Networks

    PubMed Central

    Tsugawa, Sho; Ohsaki, Hiroyuki

    2013-01-01

    Research on link prediction for social networks has been actively pursued. In link prediction for a given social network obtained from time-windowed observation, new link formation in the network is predicted from the topology of the obtained network. In contrast, recent advances in sensing technology have made it possible to obtain face-to-face behavioral networks, which are social networks representing face-to-face interactions among people. However, the effectiveness of link prediction techniques for face-to-face behavioral networks has not yet been explored in depth. To clarify this point, here we investigate the accuracy of conventional link prediction techniques for networks obtained from the history of face-to-face interactions among participants at an academic conference. Our findings were (1) that conventional link prediction techniques predict new link formation with a precision of 0.30–0.45 and a recall of 0.10–0.20, (2) that prolonged observation of social networks often degrades the prediction accuracy, (3) that the proposed decaying weight method leads to higher prediction accuracy than can be achieved by observing all records of communication and simply using them unmodified, and (4) that the prediction accuracy for face-to-face behavioral networks is relatively high compared to that for non-social networks, but not as high as for other types of social networks. PMID:24339956

  13. PD-1 Coinhibitory Signals: The Link Between Pathogenesis and Protection

    PubMed Central

    Kulpa, Deanna A.; Lawani, Mariam; Cooper, Anthony; Peretz, Yoav; Ahlers, Jeff; Sékaly, Rafick-Pierre

    2013-01-01

    In the majority of HIV-1 infected individuals, the adaptive immune response drives virus escape resulting in persistent viremia and a lack of immune-mediated control. The expression of negative regulatory molecules such as PD-1 during chronic HIV infection provides a useful marker to differentiate functional memory T cell subsets and the frequency of T cells with an exhausted phenotype. In addition, cell-based measurements of virus persistence equate with activation markers and the frequency of CD4 T cells expressing PD-1. High-level expression of PD-1 and its ligands PD-L1 and - L2 are found on hematopoietic and non-hematopoietic cells, which are regulated by chronic antigen stimulation, Type 1 and Type II interferons (IFNs), and homeostatic cytokines. In HIV infected subjects, PD-1 levels on CD4 and CD8 T cells continue to remain high following combination anti-retroviral therapy (cART). System biology approaches have begun to elucidate signal transduction pathways regulated by PD-1 expression in CD4 and CD8 T cell subsets that become dysfunctional through chronic TCR activation and PD-1 signaling. In this review, we summarize our current understanding of transcriptional signatures and signal transduction pathways associated with immune exhaustion with a focus on recent work in our laboratory characterizing the role of PD-1 in T cell dysfunction and HIV pathogenesis. We also highlight the therapeutic potential of blocking PD-1-PD-L1 and other immune checkpoints for activating potent cellular immune responses against chronic viral infections and cancer. PMID:23548749

  14. Comorbidities of Psoriasis - Exploring the Links by Network Approach

    PubMed Central

    Sundarrajan, Sudharsana; Arumugam, Mohanapriya

    2016-01-01

    Increasing epidemiological studies in patients with psoriasis report the frequent occurrence of one or more associated disorders. Psoriasis is associated with multiple comorbidities including autoimmune disease, neurological disorders, cardiometabolic diseases and inflammatory-bowel disease. An integrated system biology approach is utilized to decipher the molecular alliance of psoriasis with its comorbidities. An unbiased integrative network medicine methodology is adopted for the investigation of diseasome, biological process and pathways of five most common psoriasis associated comorbidities. A significant overlap was observed between genes acting in similar direction in psoriasis and its comorbidities proving the mandatory occurrence of either one of its comorbidities. The biological processes involved in inflammatory response and cell signaling formed a common basis between psoriasis and its associated comorbidities. The pathway analysis revealed the presence of few common pathways such as angiogenesis and few uncommon pathways which includes CCKR signaling map and gonadotrophin-realising hormone receptor pathway overlapping in all the comorbidities. The work shed light on few common genes and pathways that were previously overlooked. These fruitful targets may serve as a starting point for diagnosis and/or treatment of psoriasis comorbidities. The current research provides an evidence for the existence of shared component hypothesis between psoriasis and its comorbidities. PMID:26966903

  15. Protein S-glutathionlyation links energy metabolism to redox signaling in mitochondria.

    PubMed

    Mailloux, Ryan J; Treberg, Jason R

    2016-08-01

    At its core mitochondrial function relies on redox reactions. Electrons stripped from nutrients are used to form NADH and NADPH, electron carriers that are similar in structure but support different functions. NADH supports ATP production but also generates reactive oxygen species (ROS), superoxide (O2(·-)) and hydrogen peroxide (H2O2). NADH-driven ROS production is counterbalanced by NADPH which maintains antioxidants in an active state. Mitochondria rely on a redox buffering network composed of reduced glutathione (GSH) and peroxiredoxins (Prx) to quench ROS generated by nutrient metabolism. As H2O2 is quenched, NADPH is expended to reactivate antioxidant networks and reset the redox environment. Thus, the mitochondrial redox environment is in a constant state of flux reflecting changes in nutrient and ROS metabolism. Changes in redox environment can modulate protein function through oxidation of protein cysteine thiols. Typically cysteine oxidation is considered to be mediated by H2O2 which oxidizes protein thiols (SH) forming sulfenic acid (SOH). However, problems begin to emerge when one critically evaluates the regulatory function of SOH. Indeed SOH formation is slow, non-specific, and once formed SOH reacts rapidly with a variety of molecules. By contrast, protein S-glutathionylation (PGlu) reactions involve the conjugation and removal of glutathione moieties from modifiable cysteine residues. PGlu reactions are driven by fluctuations in the availability of GSH and oxidized glutathione (GSSG) and thus should be exquisitely sensitive to changes ROS flux due to shifts in the glutathione pool in response to varying H2O2 availability. Here, we propose that energy metabolism-linked redox signals originating from mitochondria are mediated indirectly by H2O2 through the GSH redox buffering network in and outside mitochondria. This proposal is based on several observations that have shown that unlike other redox modifications PGlu reactions fulfill the requisite

  16. Protein S-glutathionlyation links energy metabolism to redox signaling in mitochondria

    PubMed Central

    Mailloux, Ryan J.; Treberg, Jason R.

    2015-01-01

    At its core mitochondrial function relies on redox reactions. Electrons stripped from nutrients are used to form NADH and NADPH, electron carriers that are similar in structure but support different functions. NADH supports ATP production but also generates reactive oxygen species (ROS), superoxide (O2·-) and hydrogen peroxide (H2O2). NADH-driven ROS production is counterbalanced by NADPH which maintains antioxidants in an active state. Mitochondria rely on a redox buffering network composed of reduced glutathione (GSH) and peroxiredoxins (Prx) to quench ROS generated by nutrient metabolism. As H2O2 is quenched, NADPH is expended to reactivate antioxidant networks and reset the redox environment. Thus, the mitochondrial redox environment is in a constant state of flux reflecting changes in nutrient and ROS metabolism. Changes in redox environment can modulate protein function through oxidation of protein cysteine thiols. Typically cysteine oxidation is considered to be mediated by H2O2 which oxidizes protein thiols (SH) forming sulfenic acid (SOH). However, problems begin to emerge when one critically evaluates the regulatory function of SOH. Indeed SOH formation is slow, non-specific, and once formed SOH reacts rapidly with a variety of molecules. By contrast, protein S-glutathionylation (PGlu) reactions involve the conjugation and removal of glutathione moieties from modifiable cysteine residues. PGlu reactions are driven by fluctuations in the availability of GSH and oxidized glutathione (GSSG) and thus should be exquisitely sensitive to changes ROS flux due to shifts in the glutathione pool in response to varying H2O2 availability. Here, we propose that energy metabolism-linked redox signals originating from mitochondria are mediated indirectly by H2O2 through the GSH redox buffering network in and outside mitochondria. This proposal is based on several observations that have shown that unlike other redox modifications PGlu reactions fulfill the requisite

  17. Wavelet neural network for detection of signals in communications

    NASA Astrophysics Data System (ADS)

    Gomez-Sanchez, Raquel; Andina, Diego

    1998-03-01

    Our objective is the design and simulation of an efficient system for detection of signals in communications in terms of speed and computational complexity. The proposed scheme takes advantage of two powerful frameworks in signal processing: wavelets and neural networks. The decision system will take a decision based on the computation of the a prior probabilities of the input signal. For the estimation of such probability density functions, a wavelet neural network has been chosen. The election has risen under the following considerations: (a) neural networks have been established as a general approximation tool for fitting nonlinear models from input/output data and (b) the increasing popularity of the wavelet decomposition as a powerful tool for approximation. The integration of the above factors leads to the wavelet neural network concept. This network preserves the universal approximation property of wavelet series, with the advantage of the speed and efficient computation of a neural network architecture. The topology and learning algorithm of the network will provide an efficient approximation to the required probability density functions.

  18. Network Features and Pathway Analyses of a Signal Transduction Cascade

    PubMed Central

    Yanashima, Ryoji; Kitagawa, Noriyuki; Matsubara, Yoshiya; Weatheritt, Robert; Oka, Kotaro; Kikuchi, Shinichi; Tomita, Masaru; Ishizaki, Shun

    2008-01-01

    The scale-free and small-world network models reflect the functional units of networks. However, when we investigated the network properties of a signaling pathway using these models, no significant differences were found between the original undirected graphs and the graphs in which inactive proteins were eliminated from the gene expression data. We analyzed signaling networks by focusing on those pathways that best reflected cellular function. Therefore, our analysis of pathways started from the ligands and progressed to transcription factors and cytoskeletal proteins. We employed the Python module to assess the target network. This involved comparing the original and restricted signaling cascades as a directed graph using microarray gene expression profiles of late onset Alzheimer's disease. The most commonly used method of shortest-path analysis neglects to consider the influences of alternative pathways that can affect the activation of transcription factors or cytoskeletal proteins. We therefore introduced included k-shortest paths and k-cycles in our network analysis using the Python modules, which allowed us to attain a reasonable computational time and identify k-shortest paths. This technique reflected results found in vivo and identified pathways not found when shortest path or degree analysis was applied. Our module enabled us to comprehensively analyse the characteristics of biomolecular networks and also enabled analysis of the effects of diseases considering the feedback loop and feedforward loop control structures as an alternative path. PMID:19543432

  19. Add/drop multiplexing and TDM signal transmission in an optical CDMA ring network

    NASA Astrophysics Data System (ADS)

    Chen, Biao; Guo, Changjian; Chen, Jiajia; Zhang, Linjian; Jiang, Qiong; He, Sailing

    2007-08-01

    It is shown that a ring topology is better than a star topology for an optical-code-division multiple access (OCDMA) network as an optical metropolitan or local area network in terms of security and capacity. Each node in an OCDMA ring network requires an OCDMA add/drop multiplexer. We present what we believe to be a novel OCDMA add/drop multiplexer that can simultaneously add and drop multiple code channels, and a proof-of-feasibility experiment is demonstrated. An OCDMA ring may also adapt code channels for time domain multiplexing and other digital signal transmission systems. An experiment for the synchronized digital hierarchy (SDH) signal over a OCDMA link is demonstrated.

  20. Efficient Mobility Management Signalling in Network Mobility Supported PMIPV6.

    PubMed

    Samuelraj, Ananthi Jebaseeli; Jayapal, Sundararajan

    2015-01-01

    Proxy Mobile IPV6 (PMIPV6) is a network based mobility management protocol which supports node's mobility without the contribution from the respective mobile node. PMIPV6 is initially designed to support individual node mobility and it should be enhanced to support mobile network movement. NEMO-BSP is an existing protocol to support network mobility (NEMO) in PMIPV6 network. Due to the underlying differences in basic protocols, NEMO-BSP cannot be directly applied to PMIPV6 network. Mobility management signaling and data structures used for individual node's mobility should be modified to support group nodes' mobility management efficiently. Though a lot of research work is in progress to implement mobile network movement in PMIPV6, it is not yet standardized and each suffers with different shortcomings. This research work proposes modifications in NEMO-BSP and PMIPV6 to achieve NEMO support in PMIPV6. It mainly concentrates on optimizing the number and size of mobility signaling exchanged while mobile network or mobile network node changes its access point. PMID:26366431

  1. Efficient Mobility Management Signalling in Network Mobility Supported PMIPV6

    PubMed Central

    Jebaseeli Samuelraj, Ananthi; Jayapal, Sundararajan

    2015-01-01

    Proxy Mobile IPV6 (PMIPV6) is a network based mobility management protocol which supports node's mobility without the contribution from the respective mobile node. PMIPV6 is initially designed to support individual node mobility and it should be enhanced to support mobile network movement. NEMO-BSP is an existing protocol to support network mobility (NEMO) in PMIPV6 network. Due to the underlying differences in basic protocols, NEMO-BSP cannot be directly applied to PMIPV6 network. Mobility management signaling and data structures used for individual node's mobility should be modified to support group nodes' mobility management efficiently. Though a lot of research work is in progress to implement mobile network movement in PMIPV6, it is not yet standardized and each suffers with different shortcomings. This research work proposes modifications in NEMO-BSP and PMIPV6 to achieve NEMO support in PMIPV6. It mainly concentrates on optimizing the number and size of mobility signaling exchanged while mobile network or mobile network node changes its access point. PMID:26366431

  2. Dictyostelium uses ether-linked inositol phospholipids for intracellular signalling

    PubMed Central

    Clark, Jonathan; Kay, Robert R; Kielkowska, Anna; Niewczas, Izabella; Fets, Louise; Oxley, David; Stephens, Len R; Hawkins, Phillip T

    2014-01-01

    Inositol phospholipids are critical regulators of membrane biology throughout eukaryotes. The general principle by which they perform these roles is conserved across species and involves binding of differentially phosphorylated inositol head groups to specific protein domains. This interaction serves to both recruit and regulate the activity of several different classes of protein which act on membrane surfaces. In mammalian cells, these phosphorylated inositol head groups are predominantly borne by a C38:4 diacylglycerol backbone. We show here that the inositol phospholipids of Dictyostelium are different, being highly enriched in an unusual C34:1e lipid backbone, 1-hexadecyl-2-(11Z-octadecenoyl)-sn-glycero-3-phospho-(1'-myo-inositol), in which the sn-1 position contains an ether-linked C16:0 chain; they are thus plasmanylinositols. These plasmanylinositols respond acutely to stimulation of cells with chemoattractants, and their levels are regulated by PIPKs, PI3Ks and PTEN. In mammals and now in Dictyostelium, the hydrocarbon chains of inositol phospholipids are a highly selected subset of those available to other phospholipids, suggesting that different molecular selectors are at play in these organisms but serve a common, evolutionarily conserved purpose. PMID:25180230

  3. Irregularity and asynchrony in biologic network signals.

    PubMed

    Pincus, S M

    2000-01-01

    ; "r" is chosen as a fixed percentage (often 20%) of the subject's SD. This version of ApEn has the property that it is decorrelated from process SD--it remains unchanged under uniform process magnification, reduction, and translation (shift by a constant). Cross-ApEn is generally applied to compare sequences from two distinct yet interwined variables in a network. Thus we can directly assess network, and not just nodal, evolution, under different settings--e.g., to directly evaluate uncoupling and/or changes in feedback and control. Hence, cross-ApEn facilitates analyses of output from myriad complicated networks, avoiding the requirement to fully model the underlying system. This is especially important, since accurate modeling of (biological) networks is often nearly impossible. Algorithmically and insofar as implementation and reproducibility properties are concerned, cross-ApEn is thematically similar to ApEn. Furthermore, cross-ApEn is shown to be complementary to the two most prominent statistical means of assessing multivariate series, correlation and power spectral methodologies. In particular, we highlight, both theoretically and by case study examples, the many physiological feedback and/or control systems and models for which cross-ApEn can detect significant changes in bivariate asynchrony, yet for which cross-correlation and cross-spectral methods fail to clearly highlight markedly changing features of the data sets under consideration. Finally, we introduce spatial ApEn, which appears to have considerable potential, both theoretically and empirically, in evaluating multidimensional lattice structures, to discern and quantify the extent of changing patterns, and for the emergence and dissolution of traveling waves, throughout multiple contexts within biology and chemistry. PMID:10909056

  4. Multi-entity Bayesian network for the handling of uncertainties in SATCOM links

    NASA Astrophysics Data System (ADS)

    Tian, Xin; Chen, Genshe; Chang, K. C.; Martin, Todd; Nguyen, Tien; Pham, Khanh; Blasch, Erik

    2015-05-01

    Accurate prediction of satellite communications (SATCOM) data link loss is critical for SATCOM systems to effectively achieve required Quality of Service (QoS) and link availability. A major challenge is to account for various sources of uncertainties (such as atmospheric loss, rain loss, depolarization loss, pointing offset loss, etc.,) and their impacts on the aggregated link loss. This paper investigates the use of Bayesian Network (BN) for acquiring accurate SATCOM link loss estimation and link budget analysis over various modulation and coding schemes. Based on the proposed BN models, a SATCOM Bayesian Network Analysis toolbox has been developed to support link budget analysis and decision making for robust SATCOM applications.

  5. On the propagation of diel signals in river networks using analytic solutions of flow equations

    NASA Astrophysics Data System (ADS)

    Fonley, Morgan; Mantilla, Ricardo; Small, Scott J.; Curtu, Rodica

    2016-07-01

    Several authors have reported diel oscillations in streamflow records and have hypothesized that these oscillations are linked to evapotranspiration cycles in the watershed. The timing of oscillations in rivers, however, lags behind those of temperature and evapotranspiration in hillslopes. Two hypotheses have been put forth to explain the magnitude and timing of diel streamflow oscillations during low-flow conditions. The first suggests that delays between the peaks and troughs of streamflow and daily evapotranspiration are due to processes occurring in the soil as water moves toward the channels in the river network. The second posits that they are due to the propagation of the signal through the channels as water makes its way to the outlet of the basin. In this paper, we design and implement a theoretical model to test these hypotheses. We impose a baseflow signal entering the river network and use a linear transport equation to represent flow along the network. We develop analytic streamflow solutions for the case of uniform velocities in space over all river links. We then use our analytic solution to simulate streamflows along a self-similar river network for different flow velocities. Our results show that the amplitude and time delay of the streamflow solution are heavily influenced by transport in the river network. Moreover, our equations show that the geomorphology and topology of the river network play important roles in determining how amplitude and signal delay are reflected in streamflow signals. Finally, we have tested our theoretical formulation in the Dry Creek Experimental Watershed, where oscillations are clearly observed in streamflow records. We find that our solution produces streamflow values and fluctuations that are similar to those observed in the summer of 2011.

  6. Stable transmission of radio frequency signals on fiber links using interferomectric delay sensing

    SciTech Connect

    Wilcox, Russell B.; Byrd, J.M.; Doolittle, Lawrence; Huang, Gang; Staples, J.W.

    2009-07-29

    The authors demonstrate distribution of a 2850 MHz rf signal over stabilized optical fiber links. For a 2.2 km link they measure an rms drift of 19.4 fs over 60 h, and for a 200 m link an rms drift of 8.4 fs over 20 h. The rf signals are transmitted as amplitude modulation on a continuous optical carrier. Variations in the delay length are sensed using heterodyne interferometry and used to correct the rf phase. The system uses standard fiber telecommunications components.

  7. Neural Networks For Demodulation Of Phase-Modulated Signals

    NASA Technical Reports Server (NTRS)

    Altes, Richard A.

    1995-01-01

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

  8. Distributed Estimation for Vector Signal in Linear Coherent Sensor Networks

    NASA Astrophysics Data System (ADS)

    Wu, Chien-Hsien; Lin, Ching-An

    We introduce the distributed estimation of a random vector signal in wireless sensor networks that follow coherent multiple access channel model. We adopt the linear minimum mean squared error fusion rule. The problem of interest is to design linear coding matrices for those sensors in the network so as to minimize mean squared error of the estimated vector signal under a total power constraint. We show that the problem can be formulated as a convex optimization problem and we obtain closed form expressions of the coding matrices. Numerical results are used to illustrate the performance of the proposed method.

  9. Cellular Signaling Networks Function as Generalized Wiener-Kolmogorov Filters to Suppress Noise

    NASA Astrophysics Data System (ADS)

    Hinczewski, Michael; Thirumalai, D.

    2014-10-01

    Cellular signaling involves the transmission of environmental information through cascades of stochastic biochemical reactions, inevitably introducing noise that compromises signal fidelity. Each stage of the cascade often takes the form of a kinase-phosphatase push-pull network, a basic unit of signaling pathways whose malfunction is linked with a host of cancers. We show that this ubiquitous enzymatic network motif effectively behaves as a Wiener-Kolmogorov optimal noise filter. Using concepts from umbral calculus, we generalize the linear Wiener-Kolmogorov theory, originally introduced in the context of communication and control engineering, to take nonlinear signal transduction and discrete molecule populations into account. This allows us to derive rigorous constraints for efficient noise reduction in this biochemical system. Our mathematical formalism yields bounds on filter performance in cases important to cellular function—such as ultrasensitive response to stimuli. We highlight features of the system relevant for optimizing filter efficiency, encoded in a single, measurable, dimensionless parameter. Our theory, which describes noise control in a large class of signal transduction networks, is also useful both for the design of synthetic biochemical signaling pathways and the manipulation of pathways through experimental probes such as oscillatory input.

  10. Signal processing techniques for synchronization of wireless sensor networks

    NASA Astrophysics Data System (ADS)

    Lee, Jaehan; Wu, Yik-Chung; Chaudhari, Qasim; Qaraqe, Khalid; Serpedin, Erchin

    2010-11-01

    Clock synchronization is a critical component in wireless sensor networks, as it provides a common time frame to different nodes. It supports functions such as fusing voice and video data from different sensor nodes, time-based channel sharing, and sleep wake-up scheduling, etc. Early studies on clock synchronization for wireless sensor networks mainly focus on protocol design. However, clock synchronization problem is inherently related to parameter estimation, and recently, studies of clock synchronization from the signal processing viewpoint started to emerge. In this article, a survey of latest advances on clock synchronization is provided by adopting a signal processing viewpoint. We demonstrate that many existing and intuitive clock synchronization protocols can be interpreted by common statistical signal processing methods. Furthermore, the use of advanced signal processing techniques for deriving optimal clock synchronization algorithms under challenging scenarios will be illustrated.

  11. Structural link prediction based on ant colony approach in social networks

    NASA Astrophysics Data System (ADS)

    Sherkat, Ehsan; Rahgozar, Maseud; Asadpour, Masoud

    2015-02-01

    As the size and number of online social networks are increasing day by day, social network analysis has become a popular issue in many branches of science. The link prediction is one of the key rolling issues in the analysis of social network's evolution. As the size of social networks is increasing, the necessity for scalable link prediction algorithms is being felt more. The aim of this paper is to introduce a new unsupervised structural link prediction algorithm based on the ant colony approach. Recently, ant colony approach has been used for solving some graph problems. Different kinds of networks are used for testing the proposed approach. In some networks, the proposed scalable algorithm has the best result in comparison to other structural unsupervised link prediction algorithms. In order to evaluate the algorithm results, methods like the top- n precision, area under the Receiver Operating Characteristic (ROC) and Precision-Recall curves are carried out on real-world networks.

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

    PubMed Central

    Xu, Jianfeng; Lan, Yueheng

    2015-01-01

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

  13. Neuroplasticity Signaling Pathways Linked to the Pathophysiology of Schizophrenia

    PubMed Central

    Balu, Darrick T.; Coyle, Joseph T.

    2010-01-01

    Schizophrenia is a severe mental illness that afflicts nearly 1% of the world's population. One of the cardinal pathological features of schizophrenia is perturbation in synaptic connectivity. Although the etiology of schizophrenia is unknown, it appears to be a developmental disorder involving the interaction of a potentially large number of risk genes, with no one gene producing a strong effect except rare, highly penetrant copy number variants. The purpose of this review is to detail how putative schizophrenia risk genes (DISC-1, neuregulin/ErbB4, dysbindin, Akt1, BDNF, and NMDA receptor) are involved in regulating neuroplasticity and how alterations in their expression may contribute to the disconnectivity observed in schizophrenia. Moreover, this review highlights how many of these risk genes converge to regulate common neurotransmitter systems and signaling pathways. Future studies aimed at elucidating the functions of these risk genes will provide new insights into the pathophysiology of schizophrenia and will likely lead to the nomination of novel therapeutic targets for restoring proper synaptic connectivity in the brain in schizophrenia and related disorders. PMID:20951727

  14. Bacterial signal transduction network in a genomic perspective†

    PubMed Central

    Galperin, Michael Y.

    2005-01-01

    Summary Bacterial signalling network includes an array of numerous interacting components that monitor environmental and intracellular parameters and effect cellular response to changes in these parameters. The complexity of bacterial signalling systems makes comparative genome analysis a particularly valuable tool for their studies. Comparative studies revealed certain general trends in the organization of diverse signalling systems. These include (i) modular structure of signalling proteins; (ii) common organization of signalling components with the flow of information from N-terminal sensory domains to the C-terminal transmitter or signal output domains (N-to-C flow); (iii) use of common conserved sensory domains by different membrane receptors; (iv) ability of some organisms to respond to one environmental signal by activating several regulatory circuits; (v) abundance of intracellular signalling proteins, typically consisting of a PAS or GAF sensor domains and various output domains; (vi) importance of secondary messengers, cAMP and cyclic diguanylate; and (vii) crosstalk between components of different signalling pathways. Experimental characterization of the novel domains and domain combinations would be needed for achieving a better understanding of the mechanisms of signalling response and the intracellular hierarchy of different signalling pathways. PMID:15142243

  15. VLSI Neural Networks Help To Compress Video Signals

    NASA Technical Reports Server (NTRS)

    Fang, Wai-Chi; Sheu, Bing J.

    1996-01-01

    Advanced analog/digital electronic system for compression of video signals incorporates artificial neural networks. Performs motion-estimation and image-data-compression processing. Effectively eliminates temporal and spatial redundancies of sequences of video images; processes video image data, retaining only nonredundant parts to be transmitted, then transmits resulting data stream in form of efficient code. Reduces bandwidth and storage requirements for transmission and recording of video signal.

  16. Plant gravitropic signal transduction: A network analysis leads to gene discovery

    NASA Astrophysics Data System (ADS)

    Wyatt, Sarah

    Gravity plays a fundamental role in plant growth and development. Although a significant body of research has helped define the events of gravity perception, the role of the plant growth regulator auxin, and the mechanisms resulting in the gravity response, the events of signal transduction, those that link the biophysical action of perception to a biochemical signal that results in auxin redistribution, those that regulate the gravitropic effects on plant growth, remain, for the most part, a “black box.” Using a cold affect, dubbed the gravity persistent signal (GPS) response, we developed a mutant screen to specifically identify components of the signal transduction pathway. Cloning of the GPS genes have identified new proteins involved in gravitropic signaling. We have further exploited the GPS response using a multi-faceted approach including gene expression microarrays, proteomics analysis, and bioinformatics analysis and continued mutant analysis to identified additional genes, physiological and biochemical processes. Gene expression data provided the foundation of a regulatory network for gravitropic signaling. Based on these gene expression data and related data sets/information from the literature/repositories, we constructed a gravitropic signaling network for Arabidopsis inflorescence stems. To generate the network, both a dynamic Bayesian network approach and a time-lagged correlation coefficient approach were used. The dynamic Bayesian network added existing information of protein-protein interaction while the time-lagged correlation coefficient allowed incorporation of temporal regulation and thus could incorporate the time-course metric from the data set. Thus the methods complemented each other and provided us with a more comprehensive evaluation of connections. Each method generated a list of possible interactions associated with a statistical significance value. The two networks were then overlaid to generate a more rigorous, intersected

  17. A molecular mechanism that links Hippo signalling to the inhibition of Wnt/β-catenin signalling

    PubMed Central

    Imajo, Masamichi; Miyatake, Koichi; Iimura, Akira; Miyamoto, Atsumu; Nishida, Eisuke

    2012-01-01

    The Hippo signalling pathway has emerged as a key regulator of organ size, tissue homeostasis, and patterning. Recent studies have shown that two effectors in this pathway, YAP/TAZ, modulate Wnt/β-catenin signalling through their interaction with β-catenin or Dishevelled, depending on biological contexts. Here, we identify a novel mechanism through which Hippo signalling inhibits Wnt/β-catenin signalling. We show that YAP and TAZ, the transcriptional co-activators in the Hippo pathway, suppress Wnt signalling without suppressing the stability of β-catenin but through preventing its nuclear translocation. Our results show that YAP/TAZ binds to β-catenin, thereby suppressing Wnt-target gene expression, and that the Hippo pathway-stimulated phosphorylation of YAP, which induces cytoplasmic translocation of YAP, is required for the YAP-mediated inhibition of Wnt/β-catenin signalling. We also find that downregulation of Hippo signalling correlates with upregulation of β-catenin signalling in colorectal cancers. Remarkably, our analysis demonstrates that phosphorylated YAP suppresses nuclear translocation of β-catenin by directly binding to it in the cytoplasm. These results provide a novel mechanism, in which Hippo signalling antagonizes Wnt signalling by regulating nuclear translocation of β-catenin. PMID:22234184

  18. Functional Divergence in the Role of N-Linked Glycosylation in Smoothened Signaling

    PubMed Central

    Marada, Suresh; Navarro, Gemma; Truong, Ashley; Stewart, Daniel P.; Arensdorf, Angela M.; Nachtergaele, Sigrid; Angelats, Edgar; Opferman, Joseph T.; Rohatgi, Rajat; McCormick, Peter J.; Ogden, Stacey K.

    2015-01-01

    The G protein-coupled receptor (GPCR) Smoothened (Smo) is the requisite signal transducer of the evolutionarily conserved Hedgehog (Hh) pathway. Although aspects of Smo signaling are conserved from Drosophila to vertebrates, significant differences have evolved. These include changes in its active sub-cellular localization, and the ability of vertebrate Smo to induce distinct G protein-dependent and independent signals in response to ligand. Whereas the canonical Smo signal to Gli transcriptional effectors occurs in a G protein-independent manner, its non-canonical signal employs Gαi. Whether vertebrate Smo can selectively bias its signal between these routes is not yet known. N-linked glycosylation is a post-translational modification that can influence GPCR trafficking, ligand responsiveness and signal output. Smo proteins in Drosophila and vertebrate systems harbor N-linked glycans, but their role in Smo signaling has not been established. Herein, we present a comprehensive analysis of Drosophila and murine Smo glycosylation that supports a functional divergence in the contribution of N-linked glycans to signaling. Of the seven predicted glycan acceptor sites in Drosophila Smo, one is essential. Loss of N-glycosylation at this site disrupted Smo trafficking and attenuated its signaling capability. In stark contrast, we found that all four predicted N-glycosylation sites on murine Smo were dispensable for proper trafficking, agonist binding and canonical signal induction. However, the under-glycosylated protein was compromised in its ability to induce a non-canonical signal through Gαi, providing for the first time evidence that Smo can bias its signal and that a post-translational modification can impact this process. As such, we postulate a profound shift in N-glycan function from affecting Smo ER exit in flies to influencing its signal output in mice. PMID:26291458

  19. Ultrasensitive response motifs: basic amplifiers in molecular signalling networks

    PubMed Central

    Zhang, Qiang; Bhattacharya, Sudin; Andersen, Melvin E.

    2013-01-01

    Multi-component signal transduction pathways and gene regulatory circuits underpin integrated cellular responses to perturbations. A recurring set of network motifs serve as the basic building blocks of these molecular signalling networks. This review focuses on ultrasensitive response motifs (URMs) that amplify small percentage changes in the input signal into larger percentage changes in the output response. URMs generally possess a sigmoid input–output relationship that is steeper than the Michaelis–Menten type of response and is often approximated by the Hill function. Six types of URMs can be commonly found in intracellular molecular networks and each has a distinct kinetic mechanism for signal amplification. These URMs are: (i) positive cooperative binding, (ii) homo-multimerization, (iii) multistep signalling, (iv) molecular titration, (v) zero-order covalent modification cycle and (vi) positive feedback. Multiple URMs can be combined to generate highly switch-like responses. Serving as basic signal amplifiers, these URMs are essential for molecular circuits to produce complex nonlinear dynamics, including multistability, robust adaptation and oscillation. These dynamic properties are in turn responsible for higher-level cellular behaviours, such as cell fate determination, homeostasis and biological rhythm. PMID:23615029

  20. Full-duplex radio over fiber link with colorless source-free base station based on single sideband optical mm-wave signal with polarization rotated optical carrier

    NASA Astrophysics Data System (ADS)

    Ma, Jianxin

    2016-07-01

    A full-duplex radio-over fiber (RoF) link scheme based on single sideband (SSB) optical millimeter (mm)-wave signal with polarization-rotated optical carrier is proposed to realize the source-free colorless base station (BS), in which a polarization beam splitter (PBS) is used to abstract part of the optical carrier for conveying the uplink data. Since the optical carrier for the uplink does not bear the downlink signal, no cross-talk from the downlink contaminates the uplink signal. The simulation results demonstrate that both down- and up-links maintain good performance. The mm-wave signal distribution network based on the proposed full duplex fiber link scheme can use the uniform source-free colorless BSs, which makes the access system very simpler.

  1. Efficient network disintegration under incomplete information: the comic effect of link prediction

    NASA Astrophysics Data System (ADS)

    Tan, Suo-Yi; Wu, Jun; Lü, Linyuan; Li, Meng-Jun; Lu, Xin

    2016-03-01

    The study of network disintegration has attracted much attention due to its wide applications, including suppressing the epidemic spreading, destabilizing terrorist network, preventing financial contagion, controlling the rumor diffusion and perturbing cancer networks. The crux of this matter is to find the critical nodes whose removal will lead to network collapse. This paper studies the disintegration of networks with incomplete link information. An effective method is proposed to find the critical nodes by the assistance of link prediction techniques. Extensive experiments in both synthetic and real networks suggest that, by using link prediction method to recover partial missing links in advance, the method can largely improve the network disintegration performance. Besides, to our surprise, we find that when the size of missing information is relatively small, our method even outperforms than the results based on complete information. We refer to this phenomenon as the “comic effect” of link prediction, which means that the network is reshaped through the addition of some links that identified by link prediction algorithms, and the reshaped network is like an exaggerated but characteristic comic of the original one, where the important parts are emphasized.

  2. Efficient network disintegration under incomplete information: the comic effect of link prediction

    PubMed Central

    Tan, Suo-Yi; Wu, Jun; Lü, Linyuan; Li, Meng-Jun; Lu, Xin

    2016-01-01

    The study of network disintegration has attracted much attention due to its wide applications, including suppressing the epidemic spreading, destabilizing terrorist network, preventing financial contagion, controlling the rumor diffusion and perturbing cancer networks. The crux of this matter is to find the critical nodes whose removal will lead to network collapse. This paper studies the disintegration of networks with incomplete link information. An effective method is proposed to find the critical nodes by the assistance of link prediction techniques. Extensive experiments in both synthetic and real networks suggest that, by using link prediction method to recover partial missing links in advance, the method can largely improve the network disintegration performance. Besides, to our surprise, we find that when the size of missing information is relatively small, our method even outperforms than the results based on complete information. We refer to this phenomenon as the “comic effect” of link prediction, which means that the network is reshaped through the addition of some links that identified by link prediction algorithms, and the reshaped network is like an exaggerated but characteristic comic of the original one, where the important parts are emphasized. PMID:26960247

  3. Efficient network disintegration under incomplete information: the comic effect of link prediction.

    PubMed

    Tan, Suo-Yi; Wu, Jun; Lü, Linyuan; Li, Meng-Jun; Lu, Xin

    2016-01-01

    The study of network disintegration has attracted much attention due to its wide applications, including suppressing the epidemic spreading, destabilizing terrorist network, preventing financial contagion, controlling the rumor diffusion and perturbing cancer networks. The crux of this matter is to find the critical nodes whose removal will lead to network collapse. This paper studies the disintegration of networks with incomplete link information. An effective method is proposed to find the critical nodes by the assistance of link prediction techniques. Extensive experiments in both synthetic and real networks suggest that, by using link prediction method to recover partial missing links in advance, the method can largely improve the network disintegration performance. Besides, to our surprise, we find that when the size of missing information is relatively small, our method even outperforms than the results based on complete information. We refer to this phenomenon as the "comic effect" of link prediction, which means that the network is reshaped through the addition of some links that identified by link prediction algorithms, and the reshaped network is like an exaggerated but characteristic comic of the original one, where the important parts are emphasized. PMID:26960247

  4. Modeling of cell signaling pathways in macrophages by semantic networks

    PubMed Central

    Hsing, Michael; Bellenson, Joel L; Shankey, Conor; Cherkasov, Artem

    2004-01-01

    Background Substantial amounts of data on cell signaling, metabolic, gene regulatory and other biological pathways have been accumulated in literature and electronic databases. Conventionally, this information is stored in the form of pathway diagrams and can be characterized as highly "compartmental" (i.e. individual pathways are not connected into more general networks). Current approaches for representing pathways are limited in their capacity to model molecular interactions in their spatial and temporal context. Moreover, the critical knowledge of cause-effect relationships among signaling events is not reflected by most conventional approaches for manipulating pathways. Results We have applied a semantic network (SN) approach to develop and implement a model for cell signaling pathways. The semantic model has mapped biological concepts to a set of semantic agents and relationships, and characterized cell signaling events and their participants in the hierarchical and spatial context. In particular, the available information on the behaviors and interactions of the PI3K enzyme family has been integrated into the SN environment and a cell signaling network in human macrophages has been constructed. A SN-application has been developed to manipulate the locations and the states of molecules and to observe their actions under different biological scenarios. The approach allowed qualitative simulation of cell signaling events involving PI3Ks and identified pathways of molecular interactions that led to known cellular responses as well as other potential responses during bacterial invasions in macrophages. Conclusions We concluded from our results that the semantic network is an effective method to model cell signaling pathways. The semantic model allows proper representation and integration of information on biological structures and their interactions at different levels. The reconstruction of the cell signaling network in the macrophage allowed detailed

  5. Discrete dynamic modeling of T cell survival signaling networks

    NASA Astrophysics Data System (ADS)

    Zhang, Ranran

    2009-03-01

    Biochemistry-based frameworks are often not applicable for the modeling of heterogeneous regulatory systems that are sparsely documented in terms of quantitative information. As an alternative, qualitative models assuming a small set of discrete states are gaining acceptance. This talk will present a discrete dynamic model of the signaling network responsible for the survival and long-term competence of cytotoxic T cells in the blood cancer T-LGL leukemia. We integrated the signaling pathways involved in normal T cell activation and the known deregulations of survival signaling in leukemic T-LGL, and formulated the regulation of each network element as a Boolean (logic) rule. Our model suggests that the persistence of two signals is sufficient to reproduce all known deregulations in leukemic T-LGL. It also indicates the nodes whose inactivity is necessary and sufficient for the reversal of the T-LGL state. We have experimentally validated several model predictions, including: (i) Inhibiting PDGF signaling induces apoptosis in leukemic T-LGL. (ii) Sphingosine kinase 1 and NFκB are essential for the long-term survival of T cells in T-LGL leukemia. (iii) T box expressed in T cells (T-bet) is constitutively activated in the T-LGL state. The model has identified potential therapeutic targets for T-LGL leukemia and can be used for generating long-term competent CTL necessary for tumor and cancer vaccine development. The success of this model, and of other discrete dynamic models, suggests that the organization of signaling networks has an determining role in their dynamics. Reference: R. Zhang, M. V. Shah, J. Yang, S. B. Nyland, X. Liu, J. K. Yun, R. Albert, T. P. Loughran, Jr., Network Model of Survival Signaling in LGL Leukemia, PNAS 105, 16308-16313 (2008).

  6. Subsurface event detection and classification using Wireless Signal Networks.

    PubMed

    Yoon, Suk-Un; Ghazanfari, Ehsan; Cheng, Liang; Pamukcu, Sibel; Suleiman, Muhannad T

    2012-01-01

    Subsurface environment sensing and monitoring applications such as detection of water intrusion or a landslide, which could significantly change the physical properties of the host soil, can be accomplished using a novel concept, Wireless Signal Networks (WSiNs). The wireless signal networks take advantage of the variations of radio signal strength on the distributed underground sensor nodes of WSiNs to monitor and characterize the sensed area. To characterize subsurface environments for event detection and classification, this paper provides a detailed list and experimental data of soil properties on how radio propagation is affected by soil properties in subsurface communication environments. Experiments demonstrated that calibrated wireless signal strength variations can be used as indicators to sense changes in the subsurface environment. The concept of WSiNs for the subsurface event detection is evaluated with applications such as detection of water intrusion, relative density change, and relative motion using actual underground sensor nodes. To classify geo-events using the measured signal strength as a main indicator of geo-events, we propose a window-based minimum distance classifier based on Bayesian decision theory. The window-based classifier for wireless signal networks has two steps: event detection and event classification. With the event detection, the window-based classifier classifies geo-events on the event occurring regions that are called a classification window. The proposed window-based classification method is evaluated with a water leakage experiment in which the data has been measured in laboratory experiments. In these experiments, the proposed detection and classification method based on wireless signal network can detect and classify subsurface events. PMID:23202191

  7. Subsurface Event Detection and Classification Using Wireless Signal Networks

    PubMed Central

    Yoon, Suk-Un; Ghazanfari, Ehsan; Cheng, Liang; Pamukcu, Sibel; Suleiman, Muhannad T.

    2012-01-01

    Subsurface environment sensing and monitoring applications such as detection of water intrusion or a landslide, which could significantly change the physical properties of the host soil, can be accomplished using a novel concept, Wireless Signal Networks (WSiNs). The wireless signal networks take advantage of the variations of radio signal strength on the distributed underground sensor nodes of WSiNs to monitor and characterize the sensed area. To characterize subsurface environments for event detection and classification, this paper provides a detailed list and experimental data of soil properties on how radio propagation is affected by soil properties in subsurface communication environments. Experiments demonstrated that calibrated wireless signal strength variations can be used as indicators to sense changes in the subsurface environment. The concept of WSiNs for the subsurface event detection is evaluated with applications such as detection of water intrusion, relative density change, and relative motion using actual underground sensor nodes. To classify geo-events using the measured signal strength as a main indicator of geo-events, we propose a window-based minimum distance classifier based on Bayesian decision theory. The window-based classifier for wireless signal networks has two steps: event detection and event classification. With the event detection, the window-based classifier classifies geo-events on the event occurring regions that are called a classification window. The proposed window-based classification method is evaluated with a water leakage experiment in which the data has been measured in laboratory experiments. In these experiments, the proposed detection and classification method based on wireless signal network can detect and classify subsurface events. PMID:23202191

  8. Signal-Response Modeling of Partial Hormone Feedback Networks

    PubMed Central

    Johnson, Michael L.; Veldhuis, Paula P.; Evans, William S.

    2009-01-01

    Background Endocrine feedback control networks are typically complex and contain multiple hormones, pools, and compartments. The hormones themselves commonly interact via multiple pathways and targets within the networks, and a complete description of such relationships may involve hundreds of parameters. In addition, it is often difficult, if not impossible, to collect experimental data pertaining to every component within the network. Therefore, the complete simultaneous analysis of such networks is challenging. Nevertheless, an understanding of these networks is critical for furthering our knowledge of hormonal regulation in both physiologic and pathophysiologic conditions. Methods We propose a novel approach for the analysis of dose-response relationships of subsets of hormonal feedback networks. The algorithm and signal-response quantification (SRQuant) software is based on convolution integrals, and tests whether several discretely measured input signals can be individually delayed, spread in time, transformed, combined, and discretely convolved with an elimination function to predict the time course of the concentration of an output hormone. Signal-response quantification is applied to examples from the endocrine literature to demonstrate its applicability to the analysis of the different endocrine networks. Results In one example, SRQuant determines the dose-response relationship by which one hormone regulates another, highlighting its advantages over other traditional methods. In a second example, for the first time (to the best of our knowledge), we show that the secretion of glucagon may be jointly controlled by the β and the δ cells. Conclusion We have developed a novel convolution integral-based approach, algorithm, and software (SRQuant) for the analysis of dose-response relationships within subsets of complex endocrine feedback control networks. PMID:20046649

  9. A Noise-Filtering Method for Link Prediction in Complex Networks

    PubMed Central

    Ouyang, Bo

    2016-01-01

    Link prediction plays an important role in both finding missing links in networked systems and complementing our understanding of the evolution of networks. Much attention from the network science community are paid to figure out how to efficiently predict the missing/future links based on the observed topology. Real-world information always contain noise, which is also the case in an observed network. This problem is rarely considered in existing methods. In this paper, we treat the existence of observed links as known information. By filtering out noises in this information, the underlying regularity of the connection information is retrieved and then used to predict missing or future links. Experiments on various empirical networks show that our method performs noticeably better than baseline algorithms. PMID:26788737

  10. Neural network approach to classification of infrasound signals

    NASA Astrophysics Data System (ADS)

    Lee, Dong-Chang

    As part of the International Monitoring Systems of the Preparatory Commissions for the Comprehensive Nuclear Test-Ban Treaty Organization, the Infrasound Group at the University of Alaska Fairbanks maintains and operates two infrasound stations to monitor global nuclear activity. In addition, the group specializes in detecting and classifying the man-made and naturally produced signals recorded at both stations by computing various characterization parameters (e.g. mean of the cross correlation maxima, trace velocity, direction of arrival, and planarity values) using the in-house developed weighted least-squares algorithm. Classifying commonly observed low-frequency (0.015--0.1 Hz) signals at out stations, namely mountain associated waves and high trace-velocity signals, using traditional approach (e.g. analysis of power spectral density) presents a problem. Such signals can be separated statistically by setting a window to the trace-velocity estimate for each signal types, and the feasibility of such technique is demonstrated by displaying and comparing various summary plots (e.g. universal, seasonal and azimuthal variations) produced by analyzing infrasound data (2004--2007) from the Fairbanks and Antarctic arrays. Such plots with the availability of magnetic activity information (from the College International Geophysical Observatory located at Fairbanks, Alaska) leads to possible physical sources of the two signal types. Throughout this thesis a newly developed robust algorithm (sum of squares of variance ratios) with improved detection quality (under low signal to noise ratios) over two well-known detection algorithms (mean of the cross correlation maxima and Fisher Statistics) are investigated for its efficacy as a new detector. A neural network is examined for its ability to automatically classify the two signals described above against clutter (spurious signals with common characteristics). Four identical perceptron networks are trained and validated (with

  11. SSL: Signal Similarity-Based Localization for Ocean Sensor Networks

    PubMed Central

    Chen, Pengpeng; Ma, Honglu; Gao, Shouwan; Huang, Yan

    2015-01-01

    Nowadays, wireless sensor networks are often deployed on the sea surface for ocean scientific monitoring. One of the important challenges is to localize the nodes’ positions. Existing localization schemes can be roughly divided into two types: range-based and range-free. The range-based localization approaches heavily depend on extra hardware capabilities, while range-free ones often suffer from poor accuracy and low scalability, far from the practical ocean monitoring applications. In response to the above limitations, this paper proposes a novel signal similarity-based localization (SSL) technology, which localizes the nodes’ positions by fully utilizing the similarity of received signal strength and the open-air characteristics of the sea surface. In the localization process, we first estimate the relative distance between neighboring nodes through comparing the similarity of received signal strength and then calculate the relative distance for non-neighboring nodes with the shortest path algorithm. After that, the nodes’ relative relation map of the whole network can be obtained. Given at least three anchors, the physical locations of nodes can be finally determined based on the multi-dimensional scaling (MDS) technology. The design is evaluated by two types of ocean experiments: a zonal network and a non-regular network using 28 nodes. Results show that the proposed design improves the localization accuracy compared to typical connectivity-based approaches and also confirm its effectiveness for large-scale ocean sensor networks. PMID:26610520

  12. SSL: Signal Similarity-Based Localization for Ocean Sensor Networks.

    PubMed

    Chen, Pengpeng; Ma, Honglu; Gao, Shouwan; Huang, Yan

    2015-01-01

    Nowadays, wireless sensor networks are often deployed on the sea surface for ocean scientific monitoring. One of the important challenges is to localize the nodes' positions. Existing localization schemes can be roughly divided into two types: range-based and range-free. The range-based localization approaches heavily depend on extra hardware capabilities, while range-free ones often suffer from poor accuracy and low scalability, far from the practical ocean monitoring applications. In response to the above limitations, this paper proposes a novel signal similarity-based localization (SSL) technology, which localizes the nodes' positions by fully utilizing the similarity of received signal strength and the open-air characteristics of the sea surface. In the localization process, we first estimate the relative distance between neighboring nodes through comparing the similarity of received signal strength and then calculate the relative distance for non-neighboring nodes with the shortest path algorithm. After that, the nodes' relative relation map of the whole network can be obtained. Given at least three anchors, the physical locations of nodes can be finally determined based on the multi-dimensional scaling (MDS) technology. The design is evaluated by two types of ocean experiments: a zonal network and a non-regular network using 28 nodes. Results show that the proposed design improves the localization accuracy compared to typical connectivity-based approaches and also confirm its effectiveness for large-scale ocean sensor networks. PMID:26610520

  13. Robust allocation of weighted dependency links in cyber-physical networks

    NASA Astrophysics Data System (ADS)

    Li, Xin; Wu, Haotian; Scoglio, Caterina; Gruenbacher, Don

    2015-09-01

    Interdependent network models are often used to show how one network has an effect on another network through dependencies. In this paper, we propose a novel interdependent network model which consists of two individual networks with unequal numbers of nodes and one-to-multiple weighted dependency links between the two networks. Based on realistic assumptions, this model differs from previous works that considered equal numbers of nodes in the two networks and identical dependency links. We formulate an optimization problem to allocate dependency links using least resources. This novel model enhances the practicability of traditional cyber-physical system structures, but it makes the dependency link deployment problem more complex and the optimization problem cannot be solved in large networks. To overcome this problem, we propose a new algorithm based on a revised network flow method. Extensive simulations on random networks and real networks show that our deployment method produces topologies that are more robust than the ones obtained by other deployment techniques. Results indicate that our algorithm is efficient and cost-effective in designing robust interdependent networks, and our deployment method is suitable for networks of any size.

  14. Signal bi-amplification in networks of unidirectionally coupled MEMS

    NASA Astrophysics Data System (ADS)

    Tchakui, Murielle Vanessa; Woafo, Paul; Colet, Pere

    2016-01-01

    The purpose of this paper is to analyze the propagation and the amplification of an input signal in networks of unidirectionally coupled micro-electro-mechanical systems (MEMS). Two types of external excitations are considered: sinusoidal and stochastic signals. We show that sinusoidal signals are amplified up to a saturation level which depends on the transmission rate and despite MEMS being nonlinear the sinusoidal shape is well preserved if the number of MEMS is not too large. However, increasing the number of MEMS, there is an instability that leads to chaotic behavior and which is triggered by the amplification of the harmonics generated by the nonlinearities. We also show that for stochastic input signals, the MEMS array acts as a band-pass filter and after just a few elements the signal has a narrow power spectra.

  15. Emerging roles of microRNAs in the Wnt signaling network.

    PubMed

    Schepeler, Troels

    2013-01-01

    The Wnt signaling network is known to regulate many cellular processes and is of crucial importance during development and in pathological conditions, including cancer. Small noncoding RNAs from the microRNA family (miRNAs) are important elements in the post-transcriptional control of gene expression. In this work, I review the cross talk between miRNAs and the canonical Wnt signaling pathway in various biological processes with particular emphasis on carcinogenesis. Because alterations of miRNA activity and aberrant Wnt signaling are each intimately linked to tumor biology, deciphering the complex interplay between these two regulatory modules is essential to advance our understanding of the integrated functions of miRNAs in signal transduction cascades and develop rational treatment regimens against cancer. PMID:23614621

  16. The aryl hydrocarbon receptor links integrin signaling to the TGF-β pathway.

    PubMed

    Silginer, M; Burghardt, I; Gramatzki, D; Bunse, L; Leske, H; Rushing, E J; Hao, N; Platten, M; Weller, M; Roth, P

    2016-06-23

    Glioblastoma is the most common and aggressive form of intrinsic brain tumor. Transforming growth factor (TGF)-β represents a central mediator of the malignant phenotype of these tumors by promoting invasiveness and angiogenesis, maintaining tumor cell stemness and inducing profound immunosuppression. Integrins, which are highly expressed in glioma cells, interact with the TGF-β pathway. Furthermore, a link has been described between activity of the transcription factor aryl hydrocarbon receptor (AhR) and TGF-β expression. Here we demonstrate that integrin inhibition, using αv, β3 or β5 neutralizing antibodies, RNA interference-mediated integrin gene silencing or pharmacological inhibition by the cyclic RGD peptide EMD 121974 (cilengitide) or the non-peptidic molecule GLPG0187, inhibits AhR activity. These effects are independent of cell detachment or cell density. While AhR mRNA expression was not affected by integrin inhibition, AhR total and nuclear protein levels were reduced, suggesting that integrin inhibition-mediated regulation of AhR may occur at a post-transcriptional level. AhR-null astrocytes, AhR-null hepatocytes or glioblastoma cells with a transiently silenced AhR gene showed reduced sensitivity to integrin inhibition-mediated alterations in TGF-β signaling, indicating that AhR mediates integrin control of the TGF-β pathway. Accordingly, there was a significant correlation of αv integrin levels with nuclear AhR and pSmad2 levels as determined by immunohistochemistry in human glioblastoma in vivo. In summary, this study identifies a signaling network comprising integrins, AhR and TGF-β and validates integrin inhibition as a promising strategy not only to inhibit angiogenesis, but also to block AhR- and TGF-β-controlled features of malignancy in human glioblastoma. PMID:26500056

  17. Effects of link-orientation methods on robustness against cascading failures in complex networks

    NASA Astrophysics Data System (ADS)

    Jiang, Zhong-Yuan; Ma, Jian-Feng; Shen, Yu-Long; Zeng, Yong

    2016-09-01

    Unidirectional and bidirectional links may coexist in many realistic networked complex systems such as the city transportation networks. Even more, for some considerations, several bidirectional links are shifted to unidirectional ones. Many link-orientation strategies might be employed, including High-to-Low, Low-to-High and Random direction-determining methods, abbreviated as HTLDD, LTHDD and RDD respectively. Traffic passing through a unidirectional link is restricted to one-side direction. In real complex systems, nodes are correlated with each other. The failure from an initial node may be propagated iteratively, resulting in a large scale of failures of other nodes, called cascade phenomenon which may damage the safety or security of the networked system. Assuming that traffic load on any failed node can be redistributed to its non-failed neighbors, in this work, we try to reveal the effects of unidirectional links on network robustness against cascades. Extensive simulations have been implemented on kinds of networks including Scale-Free networks, Small-World networks, and Erdös-Rényi random networks. The results showed that all of the above three direction-determining methods decrease the robustness of the original networks against cascading failure. This work can help network designers and managers understand the robustness of network well and efficiently prevent the safety events.

  18. Multiplexed Signal Distribution Using Fiber Network For Radar Applications

    NASA Astrophysics Data System (ADS)

    Meena, D.; Prakasam, L. G. M.; Pandey, D. C.; Shivaleela, E. S.; Srinivas, T.

    2011-10-01

    Most of the modern Active phased Array Radars consist of multiple receive modules in an Antenna array. This demands the distribution of various Local Oscillator Signals (LOs) for the down conversion of received signals to the Intermediate Frequency (IF) band signals. This is normally achieved through Radio Frequency (RF) cables with Complex distribution networks which adds additional weight to the Arrays. Similarly these kinds of receivers require Control/Clock signals which are digital in nature, for the synchronization of all receive modules of the radar system which are also distributed through electrical cables. In addition some of the control messages (Digital in nature) are distributed through Optical interfaces. During Transmit operation, the RF transmit Signal is also distributed through the same receiver modules which will in turn distribute to all the elements of the Array which require RF cables which are bulky in nature. So it is very essential to have a multiplexed Signal distribution scheme through the existing Optical Interface for distribution of these signals which are RF and Digital in nature. This paper discusses about various distribution schemes for the realization in detail. We propose a distribution network architecture where existing fibers can be further extended for the distribution of other types of signals also. In addition, it also briefs about a comparative analysis done on these schemes by considering the complexity and space constraint factors. Thus we bring out an optimum scheme which will lead to the reduction in both hardware complexity and weight of the array systems. In addition, being an Optical network it is free from Electromagnetic interference which is a crucial requirement in an array environment.

  19. Reverse engineering GTPase programming languages with reconstituted signaling networks.

    PubMed

    Coyle, Scott M

    2016-07-01

    The Ras superfamily GTPases represent one of the most prolific signaling currencies used in Eukaryotes. With these remarkable molecules, evolution has built GTPase networks that control diverse cellular processes such as growth, morphology, motility and trafficking. (1-4) Our knowledge of the individual players that underlie the function of these networks is deep; decades of biochemical and structural data has provided a mechanistic understanding of the molecules that turn GTPases ON and OFF, as well as how those GTPase states signal by controlling the assembly of downstream effectors. However, we know less about how these different activities work together as a system to specify complex dynamic signaling outcomes. Decoding this molecular "programming language" would help us understand how different species and cell types have used the same GTPase machinery in different ways to accomplish different tasks, and would also provide new insights as to how mutations to these networks can cause disease. We recently developed a bead-based microscopy assay to watch reconstituted H-Ras signaling systems at work under arbitrary configurations of regulators and effectors. (5) Here we highlight key observations and insights from this study and propose extensions to our method to further study this and other GTPase signaling systems. PMID:27128855

  20. Structural and functional protein network analyses predict novel signaling functions for rhodopsin

    PubMed Central

    Kiel, Christina; Vogt, Andreas; Campagna, Anne; Chatr-aryamontri, Andrew; Swiatek-de Lange, Magdalena; Beer, Monika; Bolz, Sylvia; Mack, Andreas F; Kinkl, Norbert; Cesareni, Gianni; Serrano, Luis; Ueffing, Marius

    2011-01-01

    Orchestration of signaling, photoreceptor structural integrity, and maintenance needed for mammalian vision remain enigmatic. By integrating three proteomic data sets, literature mining, computational analyses, and structural information, we have generated a multiscale signal transduction network linked to the visual G protein-coupled receptor (GPCR) rhodopsin, the major protein component of rod outer segments. This network was complemented by domain decomposition of protein–protein interactions and then qualified for mutually exclusive or mutually compatible interactions and ternary complex formation using structural data. The resulting information not only offers a comprehensive view of signal transduction induced by this GPCR but also suggests novel signaling routes to cytoskeleton dynamics and vesicular trafficking, predicting an important level of regulation through small GTPases. Further, it demonstrates a specific disease susceptibility of the core visual pathway due to the uniqueness of its components present mainly in the eye. As a comprehensive multiscale network, it can serve as a basis to elucidate the physiological principles of photoreceptor function, identify potential disease-associated genes and proteins, and guide the development of therapies that target specific branches of the signaling pathway. PMID:22108793

  1. Model calibration and uncertainty analysis in signaling networks.

    PubMed

    Heinemann, Tim; Raue, Andreas

    2016-06-01

    For a long time the biggest challenges in modeling cellular signal transduction networks has been the inference of crucial pathway components and the qualitative description of their interactions. As a result of the emergence of powerful high-throughput experiments, it is now possible to measure data of high temporal and spatial resolution and to analyze signaling dynamics quantitatively. In addition, this increase of high-quality data is the basis for a better understanding of model limitations and their influence on the predictive power of models. We review established approaches in signal transduction network modeling with a focus on ordinary differential equation models as well as related developments in model calibration. As central aspects of the calibration process we discuss possibilities of model adaptation based on data-driven parameter optimization and the concomitant objective of reducing model uncertainties. PMID:27085224

  2. Hedgehog signaling: networking to nurture a promalignant tumor microenvironment.

    PubMed

    Harris, Lillianne G; Samant, Rajeev S; Shevde, Lalita A

    2011-09-01

    In addition to its role in embryonic development, the Hedgehog pathway has been shown to be an active participant in cancer development, progression, and metastasis. Although this pathway is activated by autocrine signaling by Hedgehog ligands, it can also initiate paracrine signaling with cells in the microenvironment. This creates a network of Hedgehog signaling that determines the malignant behavior of the tumor cells. As a result of paracrine signal transmission, the effects of Hedgehog signaling most profoundly influence the stromal cells that constitute the tumor microenvironment. The stromal cells in turn produce factors that nurture the tumor. Thus, such a resonating cross-talk can amplify Hedgehog signaling, resulting in molecular chatter that overall promotes tumor progression. Inhibitors of Hedgehog signaling have been the subject of intense research. Several of these inhibitors are currently being evaluated in clinical trials. Here, we review the role of the Hedgehog pathway in the signature characteristics of cancer cells that determine tumor development, progression, and metastasis. This review condenses the latest findings on the signaling pathways that are activated and/or regulated by molecules generated from Hedgehog signaling in cancer and cites promising clinical interventions. Finally, we discuss future directions for identifying the appropriate patients for therapy, developing reliable markers of efficacy of treatment, and combating resistance to Hedgehog pathway inhibitors. PMID:21775419

  3. Fragmentation transition in a coevolving network with link-state dynamics.

    PubMed

    Carro, A; Vazquez, F; Toral, R; San Miguel, M

    2014-06-01

    We study a network model that couples the dynamics of link states with the evolution of the network topology. The state of each link, either A or B, is updated according to the majority rule or zero-temperature Glauber dynamics, in which links adopt the state of the majority of their neighboring links in the network. Additionally, a link that is in a local minority is rewired to a randomly chosen node. While large systems evolving under the majority rule alone always fall into disordered topological traps composed by frustrated links, any amount of rewiring is able to drive the network to complete order, by relinking frustrated links and so releasing the system from traps. However, depending on the relative rate of the majority rule and the rewiring processes, the system evolves towards different ordered absorbing configurations: either a one-component network with all links in the same state or a network fragmented in two components with opposite states. For low rewiring rates and finite-size networks there is a domain of bistability between fragmented and nonfragmented final states. Finite-size scaling indicates that fragmentation is the only possible scenario for large systems and any nonzero rate of rewiring. PMID:25019828

  4. Dynamic Analysis of Integrated Signaling, Metabolic, and Regulatory Networks

    PubMed Central

    Eddy, James A.; Papin, Jason A.

    2008-01-01

    Extracellular cues affect signaling, metabolic, and regulatory processes to elicit cellular responses. Although intracellular signaling, metabolic, and regulatory networks are highly integrated, previous analyses have largely focused on independent processes (e.g., metabolism) without considering the interplay that exists among them. However, there is evidence that many diseases arise from multifunctional components with roles throughout signaling, metabolic, and regulatory networks. Therefore, in this study, we propose a flux balance analysis (FBA)–based strategy, referred to as integrated dynamic FBA (idFBA), that dynamically simulates cellular phenotypes arising from integrated networks. The idFBA framework requires an integrated stoichiometric reconstruction of signaling, metabolic, and regulatory processes. It assumes quasi-steady-state conditions for “fast” reactions and incorporates “slow” reactions into the stoichiometric formalism in a time-delayed manner. To assess the efficacy of idFBA, we developed a prototypic integrated system comprising signaling, metabolic, and regulatory processes with network features characteristic of actual systems and incorporating kinetic parameters based on typical time scales observed in literature. idFBA was applied to the prototypic system, which was evaluated for different environments and gene regulatory rules. In addition, we applied the idFBA framework in a similar manner to a representative module of the single-cell eukaryotic organism Saccharomyces cerevisiae. Ultimately, idFBA facilitated quantitative, dynamic analysis of systemic effects of extracellular cues on cellular phenotypes and generated comparable time-course predictions when contrasted with an equivalent kinetic model. Since idFBA solves a linear programming problem and does not require an exhaustive list of detailed kinetic parameters, it may be efficiently scaled to integrated intracellular systems that incorporate signaling, metabolic, and

  5. Signalling Network Construction for Modelling Plant Defence Response

    PubMed Central

    Miljkovic, Dragana; Stare, Tjaša; Mozetič, Igor; Podpečan, Vid; Petek, Marko; Witek, Kamil; Dermastia, Marina; Lavrač, Nada; Gruden, Kristina

    2012-01-01

    Plant defence signalling response against various pathogens, including viruses, is a complex phenomenon. In resistant interaction a plant cell perceives the pathogen signal, transduces it within the cell and performs a reprogramming of the cell metabolism leading to the pathogen replication arrest. This work focuses on signalling pathways crucial for the plant defence response, i.e., the salicylic acid, jasmonic acid and ethylene signal transduction pathways, in the Arabidopsis thaliana model plant. The initial signalling network topology was constructed manually by defining the representation formalism, encoding the information from public databases and literature, and composing a pathway diagram. The manually constructed network structure consists of 175 components and 387 reactions. In order to complement the network topology with possibly missing relations, a new approach to automated information extraction from biological literature was developed. This approach, named Bio3graph, allows for automated extraction of biological relations from the literature, resulting in a set of (component1, reaction, component2) triplets and composing a graph structure which can be visualised, compared to the manually constructed topology and examined by the experts. Using a plant defence response vocabulary of components and reaction types, Bio3graph was applied to a set of 9,586 relevant full text articles, resulting in 137 newly detected reactions between the components. Finally, the manually constructed topology and the new reactions were merged to form a network structure consisting of 175 components and 524 reactions. The resulting pathway diagram of plant defence signalling represents a valuable source for further computational modelling and interpretation of omics data. The developed Bio3graph approach, implemented as an executable language processing and graph visualisation workflow, is publically available at http://ropot.ijs.si/bio3graph/and can be utilised for

  6. Topic Models for Link Prediction in Document Networks

    ERIC Educational Resources Information Center

    Kataria, Saurabh

    2012-01-01

    Recent explosive growth of interconnected document collections such as citation networks, network of web pages, content generated by crowd-sourcing in collaborative environments, etc., has posed several challenging problems for data mining and machine learning community. One central problem in the domain of document networks is that of "link…

  7. Teaming Up: Linking Collaboration Networks, Collective Efficacy, and Student Achievement

    ERIC Educational Resources Information Center

    Moolenaar, Nienke M.; Sleegers, Peter J. C.; Daly, Alan J.

    2012-01-01

    Improving student achievement through teacher collaboration networks is a current focus of schools in many countries. Yet, empirical evidence on the relationship between teacher networks and student achievement and mechanisms that may explain this relationship is limited. This study examined the relationship between teacher networks and student…

  8. Reducing the Spectral Radius of a Torus Network by Link Removal

    PubMed Central

    Yang, Xiaofan; Li, Pengdeng; Yang, Lu-Xing; Wu, Yingbo

    2016-01-01

    The optimal link removal (OLR) problem aims at removing a given number of links of a network so that the spectral radius of the residue network obtained by removing the links from the network attains the minimum. Torus networks are a class of regular networks that have witnessed widespread applications. This paper addresses three subproblems of the OLR problem for torus networks, where two or three or four edges are removed. For either of the three subproblems, a link-removing scheme is described. Exhaustive searches show that, for small-sized tori, each of the proposed schemes produces an optimal solution to the corresponding subproblem. Monte-Carlo simulations demonstrate that, for medium-sized tori, each of the three schemes produces a solution to the corresponding subproblem, which is optimal when compared to a large set of randomly produced link-removing schemes. Consequently, it is speculated that each of the three schemes produces an optimal solution to the corresponding subproblem for all torus networks. The set of links produced by each of our schemes is evenly distributed over a network, which may be a common feature of an optimal solution to the OLR problem for regular networks. PMID:27171372

  9. Reducing the Spectral Radius of a Torus Network by Link Removal.

    PubMed

    Yang, Xiaofan; Li, Pengdeng; Yang, Lu-Xing; Wu, Yingbo

    2016-01-01

    The optimal link removal (OLR) problem aims at removing a given number of links of a network so that the spectral radius of the residue network obtained by removing the links from the network attains the minimum. Torus networks are a class of regular networks that have witnessed widespread applications. This paper addresses three subproblems of the OLR problem for torus networks, where two or three or four edges are removed. For either of the three subproblems, a link-removing scheme is described. Exhaustive searches show that, for small-sized tori, each of the proposed schemes produces an optimal solution to the corresponding subproblem. Monte-Carlo simulations demonstrate that, for medium-sized tori, each of the three schemes produces a solution to the corresponding subproblem, which is optimal when compared to a large set of randomly produced link-removing schemes. Consequently, it is speculated that each of the three schemes produces an optimal solution to the corresponding subproblem for all torus networks. The set of links produced by each of our schemes is evenly distributed over a network, which may be a common feature of an optimal solution to the OLR problem for regular networks. PMID:27171372

  10. NASA 60 GHz intersatellite communication link definition study. Addendum A: Mixed baseband and IF signals

    NASA Technical Reports Server (NTRS)

    1986-01-01

    As part of a definition study for a 60 GHz intersatellite communications link system (ICLS), baseline design concepts for a channelized crosslink were identified. The crosslink would allow communications between geostationary satellites of the planned Tracking and Data Acquisition System (TDAS) and would accommodate a mixture of frequency translation coherent links (bent pipe links) and baseband-in/baseband-out links (mod/demod links). A 60 GHz communication system was developed for sizing and analyzing the crosslink. For the coherent links this system translates incoming signals directly up to the 60 GHz band; trunks the signals across from one satellite to a second satellite at 60 GHz then down converts to the proper frequency for re-transmission from the second satellite without converting to any intermediate frequencies. For the baseband-in/baseband-out links the baseband data is modulated on to the 60 GHz carrier at the transmitting satellite and demodulated at the receiving satellite. The frequency plan, equipment diagrams, and link calculations are presented along with results from sizing and reliability analyses.

  11. Technique for stabilizing the phase of the reference signals in analog fiber-optic links.

    PubMed

    Shadaram, M; Medrano, J; Pappert, S A; Berry, M H; Gookin, D M

    1995-12-20

    The effects of temperature and longitudinal stress on the phase delay of reference signals in a fiber-optic link are discussed. A feedback system that uses a fiber-optic phase modulator is used to compensate for the phase fluctuations of a reference signal in the link. The phase deviations of a 50-MHz reference frequency that are caused by temperature variations of the link is reduced by more than 95% on optimization of the correction system. The advantages of this technique are that the fiber-optic phase modulator has a greater stability compared with the electronic phase modulators, and signal conversions from electric to optic and optic to electric are avoided. PMID:21068946

  12. EGFR Signal-Network Reconstruction Demonstrates Metabolic Crosstalk in EMT

    PubMed Central

    Choudhary, Kumari Sonal; Rohatgi, Neha; Briem, Eirikur; Gudjonsson, Thorarinn; Gudmundsson, Steinn; Rolfsson, Ottar

    2016-01-01

    Epithelial to mesenchymal transition (EMT) is an important event during development and cancer metastasis. There is limited understanding of the metabolic alterations that give rise to and take place during EMT. Dysregulation of signalling pathways that impact metabolism, including epidermal growth factor receptor (EGFR), are however a hallmark of EMT and metastasis. In this study, we report the investigation into EGFR signalling and metabolic crosstalk of EMT through constraint-based modelling and analysis of the breast epithelial EMT cell model D492 and its mesenchymal counterpart D492M. We built an EGFR signalling network for EMT based on stoichiometric coefficients and constrained the network with gene expression data to build epithelial (EGFR_E) and mesenchymal (EGFR_M) networks. Metabolic alterations arising from differential expression of EGFR genes was derived from a literature review of AKT regulated metabolic genes. Signaling flux differences between EGFR_E and EGFR_M models subsequently allowed metabolism in D492 and D492M cells to be assessed. Higher flux within AKT pathway in the D492 cells compared to D492M suggested higher glycolytic activity in D492 that we confirmed experimentally through measurements of glucose uptake and lactate secretion rates. The signaling genes from the AKT, RAS/MAPK and CaM pathways were predicted to revert D492M to D492 phenotype. Follow-up analysis of EGFR signaling metabolic crosstalk in three additional breast epithelial cell lines highlighted variability in in vitro cell models of EMT. This study shows that the metabolic phenotype may be predicted by in silico analyses of gene expression data of EGFR signaling genes, but this phenomenon is cell-specific and does not follow a simple trend. PMID:27253373

  13. EGFR Signal-Network Reconstruction Demonstrates Metabolic Crosstalk in EMT.

    PubMed

    Choudhary, Kumari Sonal; Rohatgi, Neha; Halldorsson, Skarphedinn; Briem, Eirikur; Gudjonsson, Thorarinn; Gudmundsson, Steinn; Rolfsson, Ottar

    2016-06-01

    Epithelial to mesenchymal transition (EMT) is an important event during development and cancer metastasis. There is limited understanding of the metabolic alterations that give rise to and take place during EMT. Dysregulation of signalling pathways that impact metabolism, including epidermal growth factor receptor (EGFR), are however a hallmark of EMT and metastasis. In this study, we report the investigation into EGFR signalling and metabolic crosstalk of EMT through constraint-based modelling and analysis of the breast epithelial EMT cell model D492 and its mesenchymal counterpart D492M. We built an EGFR signalling network for EMT based on stoichiometric coefficients and constrained the network with gene expression data to build epithelial (EGFR_E) and mesenchymal (EGFR_M) networks. Metabolic alterations arising from differential expression of EGFR genes was derived from a literature review of AKT regulated metabolic genes. Signaling flux differences between EGFR_E and EGFR_M models subsequently allowed metabolism in D492 and D492M cells to be assessed. Higher flux within AKT pathway in the D492 cells compared to D492M suggested higher glycolytic activity in D492 that we confirmed experimentally through measurements of glucose uptake and lactate secretion rates. The signaling genes from the AKT, RAS/MAPK and CaM pathways were predicted to revert D492M to D492 phenotype. Follow-up analysis of EGFR signaling metabolic crosstalk in three additional breast epithelial cell lines highlighted variability in in vitro cell models of EMT. This study shows that the metabolic phenotype may be predicted by in silico analyses of gene expression data of EGFR signaling genes, but this phenomenon is cell-specific and does not follow a simple trend. PMID:27253373

  14. Nonlinear signal processing using neural networks: Prediction and system modelling

    SciTech Connect

    Lapedes, A.; Farber, R.

    1987-06-01

    The backpropagation learning algorithm for neural networks is developed into a formalism for nonlinear signal processing. We illustrate the method by selecting two common topics in signal processing, prediction and system modelling, and show that nonlinear applications can be handled extremely well by using neural networks. The formalism is a natural, nonlinear extension of the linear Least Mean Squares algorithm commonly used in adaptive signal processing. Simulations are presented that document the additional performance achieved by using nonlinear neural networks. First, we demonstrate that the formalism may be used to predict points in a highly chaotic time series with orders of magnitude increase in accuracy over conventional methods including the Linear Predictive Method and the Gabor-Volterra-Weiner Polynomial Method. Deterministic chaos is thought to be involved in many physical situations including the onset of turbulence in fluids, chemical reactions and plasma physics. Secondly, we demonstrate the use of the formalism in nonlinear system modelling by providing a graphic example in which it is clear that the neural network has accurately modelled the nonlinear transfer function. It is interesting to note that the formalism provides explicit, analytic, global, approximations to the nonlinear maps underlying the various time series. Furthermore, the neural net seems to be extremely parsimonious in its requirements for data points from the time series. We show that the neural net is able to perform well because it globally approximates the relevant maps by performing a kind of generalized mode decomposition of the maps. 24 refs., 13 figs.

  15. Signal Processing in Periodically Forced Gradient Frequency Neural Networks

    PubMed Central

    Kim, Ji Chul; Large, Edward W.

    2015-01-01

    Oscillatory instability at the Hopf bifurcation is a dynamical phenomenon that has been suggested to characterize active non-linear processes observed in the auditory system. Networks of oscillators poised near Hopf bifurcation points and tuned to tonotopically distributed frequencies have been used as models of auditory processing at various levels, but systematic investigation of the dynamical properties of such oscillatory networks is still lacking. Here we provide a dynamical systems analysis of a canonical model for gradient frequency neural networks driven by a periodic signal. We use linear stability analysis to identify various driven behaviors of canonical oscillators for all possible ranges of model and forcing parameters. The analysis shows that canonical oscillators exhibit qualitatively different sets of driven states and transitions for different regimes of model parameters. We classify the parameter regimes into four main categories based on their distinct signal processing capabilities. This analysis will lead to deeper understanding of the diverse behaviors of neural systems under periodic forcing and can inform the design of oscillatory network models of auditory signal processing. PMID:26733858

  16. Efficient Sparse Signal Transmission over a Lossy Link Using Compressive Sensing

    PubMed Central

    Wu, Liantao; Yu, Kai; Cao, Dongyu; Hu, Yuhen; Wang, Zhi

    2015-01-01

    Reliable data transmission over lossy communication link is expensive due to overheads for error protection. For signals that have inherent sparse structures, compressive sensing (CS) is applied to facilitate efficient sparse signal transmissions over lossy communication links without data compression or error protection. The natural packet loss in the lossy link is modeled as a random sampling process of the transmitted data, and the original signal will be reconstructed from the lossy transmission results using the CS-based reconstruction method at the receiving end. The impacts of packet lengths on transmission efficiency under different channel conditions have been discussed, and interleaving is incorporated to mitigate the impact of burst data loss. Extensive simulations and experiments have been conducted and compared to the traditional automatic repeat request (ARQ) interpolation technique, and very favorable results have been observed in terms of both accuracy of the reconstructed signals and the transmission energy consumption. Furthermore, the packet length effect provides useful insights for using compressed sensing for efficient sparse signal transmission via lossy links. PMID:26287195

  17. Link prediction based on hyperbolic mapping with community structure for complex networks

    NASA Astrophysics Data System (ADS)

    Wang, Zuxi; Wu, Yao; Li, Qingguang; Jin, Fengdong; Xiong, Wei

    2016-05-01

    Link prediction is becoming a concerned topic in the complex network field in recent years. However, the existing link prediction methods are unsatisfactory for processing topological information and have high time complexity. This paper presents a novel method of Link Prediction with Community Structure (LPCS) based on hyperbolic mapping. Different from the existing link prediction methods, to utilize global structure information of the network, LPCS deals with the network from an overall perspective. LPCS takes full advantage of the community structure and its hierarchical organization to map networks into hyperbolic space, and obtains the hyperbolic coordinates which depict the global structure information of the network, then uses hyperbolic distance to describe the similarity between the nodes, finally predicts missing links according to the degree of the similarity between unconnected node pairs. The combination of the hyperbolic geometry framework and the community structure makes LPCS perform well in predicting missing links, and the time complexity of LPCS is linear, which makes LPCS can be applied to handle large scale networks in acceptable time. LPCS outperforms many state-of-the-art link prediction methods in the networks obeying power-law degree distribution.

  18. On-Board Fiber-Optic Network Architectures for Radar and Avionics Signal Distribution

    NASA Technical Reports Server (NTRS)

    Alam, Mohammad F.; Atiquzzaman, Mohammed; Duncan, Bradley B.; Nguyen, Hung; Kunath, Richard

    2000-01-01

    Continued progress in both civil and military avionics applications is overstressing the capabilities of existing radio-frequency (RF) communication networks based on coaxial cables on board modem aircrafts. Future avionics systems will require high-bandwidth on- board communication links that are lightweight, immune to electromagnetic interference, and highly reliable. Fiber optic communication technology can meet all these challenges in a cost-effective manner. Recently, digital fiber-optic communication systems, where a fiber-optic network acts like a local area network (LAN) for digital data communications, have become a topic of extensive research and development. Although a fiber-optic system can be designed to transport radio-frequency (RF) signals, the digital fiber-optic systems under development today are not capable of transporting microwave and millimeter-wave RF signals used in radar and avionics systems on board an aircraft. Recent advances in fiber optic technology, especially wavelength division multiplexing (WDM), has opened a number of possibilities for designing on-board fiber optic networks, including all-optical networks for radar and avionics RF signal distribution. In this paper, we investigate a number of different novel approaches for fiber-optic transmission of on-board VHF and UHF RF signals using commercial off-the-shelf (COTS) components. The relative merits and demerits of each architecture are discussed, and the suitability of each architecture for particular applications is pointed out. All-optical approaches show better performance than other traditional approaches in terms of signal-to-noise ratio, power consumption, and weight requirements.

  19. From Cellular Attractor Selection to Adaptive Signal Control for Traffic Networks.

    PubMed

    Tian, Daxin; Zhou, Jianshan; Sheng, Zhengguo; Wang, Yunpeng; Ma, Jianming

    2016-01-01

    The management of varying traffic flows essentially depends on signal controls at intersections. However, design an optimal control that considers the dynamic nature of a traffic network and coordinates all intersections simultaneously in a centralized manner is computationally challenging. Inspired by the stable gene expressions of Escherichia coli in response to environmental changes, we explore the robustness and adaptability performance of signalized intersections by incorporating a biological mechanism in their control policies, specifically, the evolution of each intersection is induced by the dynamics governing an adaptive attractor selection in cells. We employ a mathematical model to capture such biological attractor selection and derive a generic, adaptive and distributed control algorithm which is capable of dynamically adapting signal operations for the entire dynamical traffic network. We show that the proposed scheme based on attractor selection can not only promote the balance of traffic loads on each link of the network but also allows the global network to accommodate dynamical traffic demands. Our work demonstrates the potential of bio-inspired intelligence emerging from cells and provides a deep understanding of adaptive attractor selection-based control formation that is useful to support the designs of adaptive optimization and control in other domains. PMID:26972968

  20. From Cellular Attractor Selection to Adaptive Signal Control for Traffic Networks

    PubMed Central

    Tian, Daxin; Zhou, Jianshan; Sheng, Zhengguo; Wang, Yunpeng; Ma, Jianming

    2016-01-01

    The management of varying traffic flows essentially depends on signal controls at intersections. However, design an optimal control that considers the dynamic nature of a traffic network and coordinates all intersections simultaneously in a centralized manner is computationally challenging. Inspired by the stable gene expressions of Escherichia coli in response to environmental changes, we explore the robustness and adaptability performance of signalized intersections by incorporating a biological mechanism in their control policies, specifically, the evolution of each intersection is induced by the dynamics governing an adaptive attractor selection in cells. We employ a mathematical model to capture such biological attractor selection and derive a generic, adaptive and distributed control algorithm which is capable of dynamically adapting signal operations for the entire dynamical traffic network. We show that the proposed scheme based on attractor selection can not only promote the balance of traffic loads on each link of the network but also allows the global network to accommodate dynamical traffic demands. Our work demonstrates the potential of bio-inspired intelligence emerging from cells and provides a deep understanding of adaptive attractor selection-based control formation that is useful to support the designs of adaptive optimization and control in other domains. PMID:26972968

  1. From Cellular Attractor Selection to Adaptive Signal Control for Traffic Networks

    NASA Astrophysics Data System (ADS)

    Tian, Daxin; Zhou, Jianshan; Sheng, Zhengguo; Wang, Yunpeng; Ma, Jianming

    2016-03-01

    The management of varying traffic flows essentially depends on signal controls at intersections. However, design an optimal control that considers the dynamic nature of a traffic network and coordinates all intersections simultaneously in a centralized manner is computationally challenging. Inspired by the stable gene expressions of Escherichia coli in response to environmental changes, we explore the robustness and adaptability performance of signalized intersections by incorporating a biological mechanism in their control policies, specifically, the evolution of each intersection is induced by the dynamics governing an adaptive attractor selection in cells. We employ a mathematical model to capture such biological attractor selection and derive a generic, adaptive and distributed control algorithm which is capable of dynamically adapting signal operations for the entire dynamical traffic network. We show that the proposed scheme based on attractor selection can not only promote the balance of traffic loads on each link of the network but also allows the global network to accommodate dynamical traffic demands. Our work demonstrates the potential of bio-inspired intelligence emerging from cells and provides a deep understanding of adaptive attractor selection-based control formation that is useful to support the designs of adaptive optimization and control in other domains.

  2. An Improved Network Strain Filter for Detecting Transient Deformation Signals

    NASA Astrophysics Data System (ADS)

    Ohtani, R.; McGuire, J.; Segall, P.

    2008-12-01

    We have developed a tool to detect transient signals such as aseismic fault slip and magmatic intrusion automatically from large-scale (principally GPS) geodetic arrays, referred to as a Network Strain Filter (NSF). The NSF is capable of detecting transient signals in large data sets which may be difficult to identify by visual inspection of individual time series. The underlying principle is to exploit the spatially coherent nature of tectonic signals. The NSF models GPS displacement time series as a sum of contributions from tectonic transients, steady motion due to secular deformation, site-specific local benchmark motion, reference frame errors, and white noise. Transient deformation is represented by a spatial wavelet basis with time varying coefficients estimated using Kalman filtering techniques. A "hyperparameter" is also estimated to constrain the amount of temporal smoothness of the tectonic deformation. As station distribution is irregular and wavelets have local support (non-zero only over a localized domain), the design matrix is generally ill-conditioned. We investigate two strategies for regularizing the problem. The first is explicit spatial smoothing of the transient deformation. The second is to simply exclude wavelet bases that don't span some minimum number of stations. In this case, the smallest wavelet scale is determined such that the residual variance is consistent with the a priori errors of the data. Similarly the degree of spatial smoothing is determined by a priori knowledge of the data errors. To test the performance of the NSF, we carried out numerical tests using the southern California Integrated GPS Network (SCIGN) station distribution with synthetic transients of variable signal to noise ratio. We tested a six-year-long time series with a slow slip event with a duration of three years. Due to the long duration of the transient event, the contributions from secular motion and benchmark wobble make it difficult to identify the

  3. Distributed Signal Processing for Wireless EEG Sensor Networks.

    PubMed

    Bertrand, Alexander

    2015-11-01

    Inspired by ongoing evolutions in the field of wireless body area networks (WBANs), this tutorial paper presents a conceptual and exploratory study of wireless electroencephalography (EEG) sensor networks (WESNs), with an emphasis on distributed signal processing aspects. A WESN is conceived as a modular neuromonitoring platform for high-density EEG recordings, in which each node is equipped with an electrode array, a signal processing unit, and facilities for wireless communication. We first address the advantages of such a modular approach, and we explain how distributed signal processing algorithms make WESNs more power-efficient, in particular by avoiding data centralization. We provide an overview of distributed signal processing algorithms that are potentially applicable in WESNs, and for illustration purposes, we also provide a more detailed case study of a distributed eye blink artifact removal algorithm. Finally, we study the power efficiency of these distributed algorithms in comparison to their centralized counterparts in which all the raw sensor signals are centralized in a near-end or far-end fusion center. PMID:25850092

  4. Oma1 Links Mitochondrial Protein Quality Control and TOR Signaling To Modulate Physiological Plasticity and Cellular Stress Responses.

    PubMed

    Bohovych, Iryna; Kastora, Stavroula; Christianson, Sara; Topil, Danelle; Kim, Heejeong; Fangman, Teresa; Zhou, You J; Barrientos, Antoni; Lee, Jaekwon; Brown, Alistair J P; Khalimonchuk, Oleh

    2016-09-01

    A network of conserved proteases known as the intramitochondrial quality control (IMQC) system is central to mitochondrial protein homeostasis and cellular health. IMQC proteases also appear to participate in establishment of signaling cues for mitochondrion-to-nucleus communication. However, little is known about this process. Here, we show that in Saccharomyces cerevisiae, inactivation of the membrane-bound IMQC protease Oma1 interferes with oxidative-stress responses through enhanced production of reactive oxygen species (ROS) during logarithmic growth and reduced stress signaling via the TORC1-Rim15-Msn2/Msn4 axis. Pharmacological or genetic prevention of ROS accumulation in Oma1-deficient cells restores this defective TOR signaling. Additionally, inactivation of the Oma1 ortholog in the human fungal pathogen Candida albicans also alters TOR signaling and, unexpectedly, leads to increased resistance to neutrophil killing and virulence in the invertebrate animal model Galleria mellonella Our findings reveal a novel and evolutionarily conserved link between IMQC and TOR-mediated signaling that regulates physiological plasticity and pancellular oxidative-stress responses. PMID:27325672

  5. Full duplex fiber link for alternative wired and wireless access based on SSB optical millimeter-wave with 4-PAM signal

    NASA Astrophysics Data System (ADS)

    Ma, Jianxin; Zhang, Junjie

    2015-03-01

    A novel full-duplex fiber-wireless link based on single sideband (SSB) optical millimeter (mm)-wave with 10 Gbit/s 4-pulse amplitude modulation (PAM) signal is proposed to provide alternative wired and 40 GHz wireless accesses for the user terminals. The SSB optical mm-wave with 4-PAM signal consists of two tones: one bears the 4-PAM signal and the other is unmodulated with high power. After transmission over the fiber to the hybrid optical network unit (HONU), the SSB optical mm-wave signal can be decomposed by fiber Bragg gratings (FBGs) as the SSB optical mm-wave signal with reduced carrier-to-sideband ratio (the baseband 4-PAM optical signal) and the uplink optical carrier for the wireless (wired) access. This makes the HONU free from the laser source. For the uplink, since the wireless access signal is converted to the baseband by power detection, both the transmitter in the HONU and the receiver in optical line terminal (OLT) are co-shared for both wireless and wired accesses, which makes the full duplex link much simpler. In our scheme, the optical electrical field of the square-root increment level 4-PAM signal assures an equal level spacing receiving for both the downlink wired and wireless accesses. Since the downlink wireless signal is down-converted to the baseband by power detection, RF local oscillator is unnecessary. To confirm the feasibility of our proposed scheme, a simulation full duplex link with 40 GHz SSB optical mm-wave with 10 Gbit/s 4-PAM signal is built. The simulation results show that both down- and up-links for either wired or wireless access can keep good performance even if the link length of the SSMF is extended to 40 km.

  6. Integration and Analysis of Neighbor Discovery and Link Quality Estimation in Wireless Sensor Networks

    PubMed Central

    Radi, Marjan; Dezfouli, Behnam; Abu Bakar, Kamalrulnizam; Abd Razak, Shukor

    2014-01-01

    Network connectivity and link quality information are the fundamental requirements of wireless sensor network protocols to perform their desired functionality. Most of the existing discovery protocols have only focused on the neighbor discovery problem, while a few number of them provide an integrated neighbor search and link estimation. As these protocols require a careful parameter adjustment before network deployment, they cannot provide scalable and accurate network initialization in large-scale dense wireless sensor networks with random topology. Furthermore, performance of these protocols has not entirely been evaluated yet. In this paper, we perform a comprehensive simulation study on the efficiency of employing adaptive protocols compared to the existing nonadaptive protocols for initializing sensor networks with random topology. In this regard, we propose adaptive network initialization protocols which integrate the initial neighbor discovery with link quality estimation process to initialize large-scale dense wireless sensor networks without requiring any parameter adjustment before network deployment. To the best of our knowledge, this work is the first attempt to provide a detailed simulation study on the performance of integrated neighbor discovery and link quality estimation protocols for initializing sensor networks. This study can help system designers to determine the most appropriate approach for different applications. PMID:24678277

  7. Visualizing weighted networks: a performance comparison of adjacency matrices versus node-link diagrams

    NASA Astrophysics Data System (ADS)

    McIntire, John P.; Osesina, O. Isaac; Bartley, Cecilia; Tudoreanu, M. Eduard; Havig, Paul R.; Geiselman, Eric E.

    2012-06-01

    Ensuring the proper and effective ways to visualize network data is important for many areas of academia, applied sciences, the military, and the public. Fields such as social network analysis, genetics, biochemistry, intelligence, cybersecurity, neural network modeling, transit systems, communications, etc. often deal with large, complex network datasets that can be difficult to interact with, study, and use. There have been surprisingly few human factors performance studies on the relative effectiveness of different graph drawings or network diagram techniques to convey information to a viewer. This is particularly true for weighted networks which include the strength of connections between nodes, not just information about which nodes are linked to other nodes. We describe a human factors study in which participants performed four separate network analysis tasks (finding a direct link between given nodes, finding an interconnected node between given nodes, estimating link strengths, and estimating the most densely interconnected nodes) on two different network visualizations: an adjacency matrix with a heat-map versus a node-link diagram. The results should help shed light on effective methods of visualizing network data for some representative analysis tasks, with the ultimate goal of improving usability and performance for viewers of network data displays.

  8. Traffic Management in ATM Networks Over Satellite Links

    NASA Technical Reports Server (NTRS)

    Goyal, Rohit; Jain, Raj; Goyal, Mukul; Fahmy, Sonia; Vandalore, Bobby; vonDeak, Thomas

    1999-01-01

    This report presents a survey of the traffic management Issues in the design and implementation of satellite Asynchronous Transfer Mode (ATM) networks. The report focuses on the efficient transport of Transmission Control Protocol (TCP) traffic over satellite ATM. First, a reference satellite ATM network architecture is presented along with an overview of the service categories available in ATM networks. A delay model for satellite networks and the major components of delay and delay variation are described. A survey of design options for TCP over Unspecified Bit Rate (UBR), Guaranteed Frame Rate (GFR) and Available Bit Rate (ABR) services in ATM is presented. The main focus is on traffic management issues. Several recommendations on the design options for efficiently carrying data services over satellite ATM networks are presented. Most of the results are based on experiments performed on Geosynchronous (GEO) latencies. Some results for Low Earth Orbits (LEO) and Medium Earth Orbit (MEO) latencies are also provided.

  9. Wireless sensor networks for monitoring physiological signals of multiple patients.

    PubMed

    Dilmaghani, R S; Bobarshad, H; Ghavami, M; Choobkar, S; Wolfe, C

    2011-08-01

    This paper presents the design of a novel wireless sensor network structure to monitor patients with chronic diseases in their own homes through a remote monitoring system of physiological signals. Currently, most of the monitoring systems send patients' data to a hospital with the aid of personal computers (PC) located in the patients' home. Here, we present a new design which eliminates the need for a PC. The proposed remote monitoring system is a wireless sensor network with the nodes of the network installed in the patients' homes. These nodes are then connected to a central node located at a hospital through an Internet connection. The nodes of the proposed wireless sensor network are created by using a combination of ECG sensors, MSP430 microcontrollers, a CC2500 low-power wireless radio, and a network protocol called the SimpliciTI protocol. ECG signals are first sampled by a small portable device which each patient carries. The captured signals are then wirelessly transmitted to an access point located within the patients' home. This connectivity is based on wireless data transmission at 2.4-GHz frequency. The access point is also a small box attached to the Internet through a home asynchronous digital subscriber line router. Afterwards, the data are sent to the hospital via the Internet in real time for analysis and/or storage. The benefits of this remote monitoring are wide ranging: the patients can continue their normal lives, they do not need a PC all of the time, their risk of infection is reduced, costs significantly decrease for the hospital, and clinicians can check data in a short time. PMID:23851949

  10. Linking autophagy with inflammation through IRF1 signaling in ER+ breast cancer

    PubMed Central

    Cook, Katherine L; Schwartz-Roberts, Jessica L; Baumann, William T; Clarke, Robert

    2016-01-01

    Resistance to antiestrogen therapy remains a critical determinant of mortality in patients affected by ER+ breast cancer. Our previous work identified autophagy and interferon regulatory factor 1 (IRF1) signaling as key regulators of this process. We have recently demonstrated a novel reciprocal interaction between IRF1 and ATG7, linking inflammation and autophagy. PMID:27308537

  11. Multi-Hop Link Capacity of Multi-Route Multi-Hop MRC Diversity for a Virtual Cellular Network

    NASA Astrophysics Data System (ADS)

    Daou, Imane; Kudoh, Eisuke; Adachi, Fumiyuki

    In virtual cellular network (VCN), proposed for high-speed mobile communications, the signal transmitted from a mobile terminal is received by some wireless ports distributed in each virtual cell and relayed to the central port that acts as a gateway to the core network. In this paper, we apply the multi-route MHMRC diversity in order to decrease the transmit power and increase the multi-hop link capacity. The transmit power, the interference power and the link capacity are evaluated for DS-CDMA multi-hop VCN by computer simulation. The multi-route MHMRC diversity can be applied to not only DS-CDMA but also other access schemes (i. e. MC-CDMA, OFDM, etc.).

  12. Modeling of cortical signals using echo state networks

    NASA Astrophysics Data System (ADS)

    Zhou, Hanying; Wang, Yongji; Huang, Jiangshuai

    2009-10-01

    Diverse modeling frameworks have been utilized with the ultimate goal of translating brain cortical signals into prediction of visible behavior. The inputs to these models are usually multidimensional neural recordings collected from relevant regions of a monkey's brain while the outputs are the associated behavior which is typically the 2-D or 3-D hand position of a primate. Here our task is to set up a proper model in order to figure out the move trajectories by input the neural signals which are simultaneously collected in the experiment. In this paper, we propose to use Echo State Networks (ESN) to map the neural firing activities into hand positions. ESN is a newly developed recurrent neural network(RNN) model. Besides its dynamic property and short term memory just as other recurrent neural networks have, it has a special echo state property which endows it with the ability to model nonlinear dynamic systems powerfully. What distinguished it from transitional recurrent neural networks most significantly is its special learning method. In this paper we train this net with a refined version of its typical training method and get a better model.

  13. Common neighbours and the local-community-paradigm for topological link prediction in bipartite networks

    NASA Astrophysics Data System (ADS)

    Daminelli, Simone; Thomas, Josephine Maria; Durán, Claudio; Vittorio Cannistraci, Carlo

    2015-11-01

    Bipartite networks are powerful descriptions of complex systems characterized by two different classes of nodes and connections allowed only across but not within the two classes. Unveiling physical principles, building theories and suggesting physical models to predict bipartite links such as product-consumer connections in recommendation systems or drug-target interactions in molecular networks can provide priceless information to improve e-commerce or to accelerate pharmaceutical research. The prediction of nonobserved connections starting from those already present in the topology of a network is known as the link-prediction problem. It represents an important subject both in many-body interaction theory in physics and in new algorithms for applied tools in computer science. The rationale is that the existing connectivity structure of a network can suggest where new connections can appear with higher likelihood in an evolving network, or where nonobserved connections are missing in a partially known network. Surprisingly, current complex network theory presents a theoretical bottle-neck: a general framework for local-based link prediction directly in the bipartite domain is missing. Here, we overcome this theoretical obstacle and present a formal definition of common neighbour index and local-community-paradigm (LCP) for bipartite networks. As a consequence, we are able to introduce the first node-neighbourhood-based and LCP-based models for topological link prediction that utilize the bipartite domain. We performed link prediction evaluations in several networks of different size and of disparate origin, including technological, social and biological systems. Our models significantly improve topological prediction in many bipartite networks because they exploit local physical driving-forces that participate in the formation and organization of many real-world bipartite networks. Furthermore, we present a local-based formalism that allows to intuitively

  14. Pathway connectivity and signaling coordination in the yeast stress-activated signaling network

    PubMed Central

    Chasman, Deborah; Ho, Yi-Hsuan; Berry, David B; Nemec, Corey M; MacGilvray, Matthew E; Hose, James; Merrill, Anna E; Lee, M Violet; Will, Jessica L; Coon, Joshua J; Ansari, Aseem Z; Craven, Mark; Gasch, Audrey P

    2014-01-01

    Stressed cells coordinate a multi-faceted response spanning many levels of physiology. Yet knowledge of the complete stress-activated regulatory network as well as design principles for signal integration remains incomplete. We developed an experimental and computational approach to integrate available protein interaction data with gene fitness contributions, mutant transcriptome profiles, and phospho-proteome changes in cells responding to salt stress, to infer the salt-responsive signaling network in yeast. The inferred subnetwork presented many novel predictions by implicating new regulators, uncovering unrecognized crosstalk between known pathways, and pointing to previously unknown ‘hubs’ of signal integration. We exploited these predictions to show that Cdc14 phosphatase is a central hub in the network and that modification of RNA polymerase II coordinates induction of stress-defense genes with reduction of growth-related transcripts. We find that the orthologous human network is enriched for cancer-causing genes, underscoring the importance of the subnetwork's predictions in understanding stress biology. PMID:25411400

  15. An information-theoretic model for link prediction in complex networks

    NASA Astrophysics Data System (ADS)

    Zhu, Boyao; Xia, Yongxiang

    2015-09-01

    Various structural features of networks have been applied to develop link prediction methods. However, because different features highlight different aspects of network structural properties, it is very difficult to benefit from all of the features that might be available. In this paper, we investigate the role of network topology in predicting missing links from the perspective of information theory. In this way, the contributions of different structural features to link prediction are measured in terms of their values of information. Then, an information-theoretic model is proposed that is applicable to multiple structural features. Furthermore, we design a novel link prediction index, called Neighbor Set Information (NSI), based on the information-theoretic model. According to our experimental results, the NSI index performs well in real-world networks, compared with other typical proximity indices.

  16. An information-theoretic model for link prediction in complex networks

    PubMed Central

    Zhu, Boyao; Xia, Yongxiang

    2015-01-01

    Various structural features of networks have been applied to develop link prediction methods. However, because different features highlight different aspects of network structural properties, it is very difficult to benefit from all of the features that might be available. In this paper, we investigate the role of network topology in predicting missing links from the perspective of information theory. In this way, the contributions of different structural features to link prediction are measured in terms of their values of information. Then, an information-theoretic model is proposed that is applicable to multiple structural features. Furthermore, we design a novel link prediction index, called Neighbor Set Information (NSI), based on the information-theoretic model. According to our experimental results, the NSI index performs well in real-world networks, compared with other typical proximity indices. PMID:26335758

  17. Wnt-signalling pathways and microRNAs network in carcinogenesis: experimental and bioinformatics approaches.

    PubMed

    Onyido, Emenike K; Sweeney, Eloise; Nateri, Abdolrahman Shams

    2016-01-01

    Over the past few years, microRNAs (miRNAs) have not only emerged as integral regulators of gene expression at the post-transcriptional level but also respond to signalling molecules to affect cell function(s). miRNAs crosstalk with a variety of the key cellular signalling networks such as Wnt, transforming growth factor-β and Notch, control stem cell activity in maintaining tissue homeostasis, while if dysregulated contributes to the initiation and progression of cancer. Herein, we overview the molecular mechanism(s) underlying the crosstalk between Wnt-signalling components (canonical and non-canonical) and miRNAs, as well as changes in the miRNA/Wnt-signalling components observed in the different forms of cancer. Furthermore, the fundamental understanding of miRNA-mediated regulation of Wnt-signalling pathway and vice versa has been significantly improved by high-throughput genomics and bioinformatics technologies. Whilst, these approaches have identified a number of specific miRNA(s) that function as oncogenes or tumour suppressors, additional analyses will be necessary to fully unravel the links among conserved cellular signalling pathways and miRNAs and their potential associated components in cancer, thereby creating therapeutic avenues against tumours. Hence, we also discuss the current challenges associated with Wnt-signalling/miRNAs complex and the analysis using the biomedical experimental and bioinformatics approaches. PMID:27590724

  18. Sweet Taste Receptor Signaling Network: Possible Implication for Cognitive Functioning

    PubMed Central

    Welcome, Menizibeya O.; Mastorakis, Nikos E.; Pereverzev, Vladimir A.

    2015-01-01

    Sweet taste receptors are transmembrane protein network specialized in the transmission of information from special “sweet” molecules into the intracellular domain. These receptors can sense the taste of a range of molecules and transmit the information downstream to several acceptors, modulate cell specific functions and metabolism, and mediate cell-to-cell coupling through paracrine mechanism. Recent reports indicate that sweet taste receptors are widely distributed in the body and serves specific function relative to their localization. Due to their pleiotropic signaling properties and multisubstrate ligand affinity, sweet taste receptors are able to cooperatively bind multiple substances and mediate signaling by other receptors. Based on increasing evidence about the role of these receptors in the initiation and control of absorption and metabolism, and the pivotal role of metabolic (glucose) regulation in the central nervous system functioning, we propose a possible implication of sweet taste receptor signaling in modulating cognitive functioning. PMID:25653876

  19. Calcium/calmodulin-mediated signal network in plants

    NASA Technical Reports Server (NTRS)

    Yang, Tianbao; Poovaiah, B. W.

    2003-01-01

    Various extracellular stimuli elicit specific calcium signatures that can be recognized by different calcium sensors. Calmodulin, the predominant calcium receptor, is one of the best-characterized calcium sensors in eukaryotes. In recent years, completion of the Arabidopsis genome project and advances in functional genomics have helped to identify and characterize numerous calmodulin-binding proteins in plants. There are some similarities in Ca(2+)/calmodulin-mediated signaling in plants and animals. However, plants possess multiple calmodulin genes and many calmodulin target proteins, including unique protein kinases and transcription factors. Some of these proteins are likely to act as "hubs" during calcium signal transduction. Hence, a better understanding of the function of these calmodulin target proteins should help in deciphering the Ca(2+)/calmodulin-mediated signal network and its role in plant growth, development and response to environmental stimuli.

  20. Linking species functional roles to their network roles.

    PubMed

    Coux, Camille; Rader, Romina; Bartomeus, Ignasi; Tylianakis, Jason M

    2016-07-01

    Species roles in ecological networks combine to generate their architecture, which contributes to their stability. Species trait diversity also affects ecosystem functioning and resilience, yet it remains unknown whether species' contributions to functional diversity relate to their network roles. Here, we use 21 empirical pollen transport networks to characterise this relationship. We found that, apart from a few abundant species, pollinators with original traits either had few interaction partners or interacted most frequently with a subset of these partners. This suggests that narrowing of interactions to a subset of the plant community accompanies pollinator niche specialisation, congruent with our hypothesised trade-off between having unique traits vs. being able to interact with many mutualist partners. Conversely, these effects were not detected in plants, potentially because key aspects of their flowering traits are conserved at a family level. Relating functional and network roles can provide further insight into mechanisms underlying ecosystem functioning. PMID:27169359

  1. Reverse engineering of linking preferences from network restructuring

    NASA Astrophysics Data System (ADS)

    Palla, Gergely; Farkas, Illés; Derényi, Imre; Barabási, Albert-László; Vicsek, Tamás

    2004-10-01

    We provide a method to deduce the preferences governing the restructuring dynamics of a network from the observed rewiring of the edges. Our approach is applicable for systems in which the preferences can be formulated in terms of a single-vertex energy function with f(k) being the contribution of a node of degree k to the total energy, and the dynamics obeys the detailed balance. The method is first tested by Monte Carlo simulations of restructuring graphs with known energies; then it is used to study variations of real network systems ranging from the coauthorship network of scientific publications to the asset graphs of the New York Stock Exchange. The empirical energies obtained from the restructuring can be described by a universal function f(k)˜-klnk , which is consistent with and justifies the validity of the preferential attachment rule proposed for growing networks.

  2. FORUM: Ecological networks: the missing links in biomonitoring science

    PubMed Central

    Gray, Clare; Baird, Donald J; Baumgartner, Simone; Jacob, Ute; Jenkins, Gareth B; O'Gorman, Eoin J; Lu, Xueke; Ma, Athen; Pocock, Michael J O; Schuwirth, Nele; Thompson, Murray; Woodward, Guy

    2014-01-01

    Monitoring anthropogenic impacts is essential for managing and conserving ecosystems, yet current biomonitoring approaches lack the tools required to deal with the effects of stressors on species and their interactions in complex natural systems. Ecological networks (trophic or mutualistic) can offer new insights into ecosystem degradation, adding value to current taxonomically constrained schemes. We highlight some examples to show how new network approaches can be used to interpret ecological responses. Synthesis and applications. Augmenting routine biomonitoring data with interaction data derived from the literature, complemented with ground-truthed data from direct observations where feasible, allows us to begin to characterise large numbers of ecological networks across environmental gradients. This process can be accelerated by adopting emerging technologies and novel analytical approaches, enabling biomonitoring to move beyond simple pass/fail schemes and to address the many ecological responses that can only be understood from a network-based perspective. PMID:25558087

  3. Similarity index based on local paths for link prediction of complex networks

    NASA Astrophysics Data System (ADS)

    Lü, Linyuan; Jin, Ci-Hang; Zhou, Tao

    2009-10-01

    Predictions of missing links of incomplete networks, such as protein-protein interaction networks or very likely but not yet existent links in evolutionary networks like friendship networks in web society, can be considered as a guideline for further experiments or valuable information for web users. In this paper, we present a local path index to estimate the likelihood of the existence of a link between two nodes. We propose a network model with controllable density and noise strength in generating links, as well as collect data of six real networks. Extensive numerical simulations on both modeled networks and real networks demonstrated the high effectiveness and efficiency of the local path index compared with two well-known and widely used indices: the common neighbors and the Katz index. Indeed, the local path index provides competitively accurate predictions as the Katz index while requires much less CPU time and memory space than the Katz index, which is therefore a strong candidate for potential practical applications in data mining of huge-size networks.

  4. Energy Efficient Link Aware Routing with Power Control in Wireless Ad Hoc Networks

    PubMed Central

    Katiravan, Jeevaa; Sylvia, D.; Rao, D. Srinivasa

    2015-01-01

    In wireless ad hoc networks, the traditional routing protocols make the route selection based on minimum distance between the nodes and the minimum number of hop counts. Most of the routing decisions do not consider the condition of the network such as link quality and residual energy of the nodes. Also, when a link failure occurs, a route discovery mechanism is initiated which incurs high routing overhead. If the broadcast nature and the spatial diversity of the wireless communication are utilized efficiently it becomes possible to achieve improvement in the performance of the wireless networks. In contrast to the traditional routing scheme which makes use of a predetermined route for packet transmission, such an opportunistic routing scheme defines a predefined forwarding candidate list formed by using single network metrics. In this paper, a protocol is proposed which uses multiple metrics such as residual energy and link quality for route selection and also includes a monitoring mechanism which initiates a route discovery for a poor link, thereby reducing the overhead involved and improving the throughput of the network while maintaining network connectivity. Power control is also implemented not only to save energy but also to improve the network performance. Using simulations, we show the performance improvement attained in the network in terms of packet delivery ratio, routing overhead, and residual energy of the network. PMID:26167529

  5. K-Lysine acetyltransferase 2a regulates a hippocampal gene expression network linked to memory formation

    PubMed Central

    Stilling, Roman M; Rönicke, Raik; Benito, Eva; Urbanke, Hendrik; Capece, Vincenzo; Burkhardt, Susanne; Bahari-Javan, Sanaz; Barth, Jonas; Sananbenesi, Farahnaz; Schütz, Anna L; Dyczkowski, Jerzy; Martinez-Hernandez, Ana; Kerimoglu, Cemil; Dent, Sharon YR; Bonn, Stefan; Reymann, Klaus G; Fischer, Andre

    2014-01-01

    Neuronal histone acetylation has been linked to memory consolidation, and targeting histone acetylation has emerged as a promising therapeutic strategy for neuropsychiatric diseases. However, the role of histone-modifying enzymes in the adult brain is still far from being understood. Here we use RNA sequencing to screen the levels of all known histone acetyltransferases (HATs) in the hippocampal CA1 region and find that K-acetyltransferase 2a (Kat2a)—a HAT that has not been studied for its role in memory function so far—shows highest expression. Mice that lack Kat2a show impaired hippocampal synaptic plasticity and long-term memory consolidation. We furthermore show that Kat2a regulates a highly interconnected hippocampal gene expression network linked to neuroactive receptor signaling via a mechanism that involves nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB). In conclusion, our data establish Kat2a as a novel and essential regulator of hippocampal memory consolidation. PMID:25024434

  6. Real time data acquisition of commercial microwave link networks for hydrometeorological applications

    NASA Astrophysics Data System (ADS)

    Chwala, C.; Keis, F.; Kunstmann, H.

    2015-11-01

    The usage of data from commercial microwave link (CML) networks for scientific purposes is becoming increasingly popular, in particular for rain rate estimation. However, data acquisition and availability is still a crucial problem and limits research possibilities. To overcome this issue, we have developed an open source data acquisition system based on the Simple Network Management Protocol (SNMP). It is able to record transmitted- and received signal levels of a large number of CMLs simultaneously with a temporal resolution of up to one second. We operate this system at Ericsson Germany, acquiring data from 450 CMLs with minutely real time transfer to our data base. Our data acquisition system is not limited to a particular CML hardware model or manufacturer, though. We demonstrate this by running the same system for CMLs of a different manufacturer, operated by an alpine skiing resort in Germany. There, the data acquisition is running simultaneously for four CMLs with a temporal resolution of one second. We present an overview of our system, describe the details of the necessary SNMP requests and show results from its operational application.

  7. Real-time data acquisition of commercial microwave link networks for hydrometeorological applications

    NASA Astrophysics Data System (ADS)

    Chwala, Christian; Keis, Felix; Kunstmann, Harald

    2016-03-01

    The usage of data from commercial microwave link (CML) networks for scientific purposes is becoming increasingly popular, in particular for rain rate estimation. However, data acquisition and availability is still a crucial problem and limits research possibilities. To overcome this issue, we have developed an open-source data acquisition system based on the Simple Network Management Protocol (SNMP). It is able to record transmitted and received signal levels of a large number of CMLs simultaneously with a temporal resolution of up to 1 s. We operate this system at Ericsson Germany, acquiring data from 450 CMLs with minutely real-time transfer to our database. Our data acquisition system is not limited to a particular CML hardware model or manufacturer, though. We demonstrate this by running the same system for CMLs of a different manufacturer, operated by an alpine ski resort in Germany. There, the data acquisition is running simultaneously for four CMLs with a temporal resolution of 1 s. We present an overview of our system, describe the details of the necessary SNMP requests and show results from its operational application.

  8. Phosphatase Specificity and Pathway Insulation in Signaling Networks

    PubMed Central

    Rowland, Michael A.; Harrison, Brian; Deeds, Eric J.

    2015-01-01

    Phosphatases play an important role in cellular signaling networks by regulating the phosphorylation state of proteins. Phosphatases are classically considered to be promiscuous, acting on tens to hundreds of different substrates. We recently demonstrated that a shared phosphatase can couple the responses of two proteins to incoming signals, even if those two substrates are from otherwise isolated areas of the network. This finding raises a potential paradox: if phosphatases are indeed highly promiscuous, how do cells insulate themselves against unwanted crosstalk? Here, we use mathematical models to explore three possible insulation mechanisms. One approach involves evolving phosphatase KM values that are large enough to prevent saturation by the phosphatase’s substrates. Although this is an effective method for generating isolation, the phosphatase becomes a highly inefficient enzyme, which prevents the system from achieving switch-like responses and can result in slow response kinetics. We also explore the idea that substrate degradation can serve as an effective phosphatase. Assuming that degradation is unsaturatable, this mechanism could insulate substrates from crosstalk, but it would also preclude ultrasensitive responses and would require very high substrate turnover to achieve rapid dephosphorylation kinetics. Finally, we show that adaptor subunits, such as those found on phosphatases like PP2A, can provide effective insulation against phosphatase crosstalk, but only if their binding to substrates is uncoupled from their binding to the catalytic core. Analysis of the interaction network of PP2A’s adaptor domains reveals that although its adaptors may isolate subsets of targets from one another, there is still a strong potential for phosphatase crosstalk within those subsets. Understanding how phosphatase crosstalk and the insulation mechanisms described here impact the function and evolution of signaling networks represents a major challenge for

  9. Dexras1 links glucocorticoids to insulin-like growth factor-1 signaling in adipogenesis.

    PubMed

    Kim, Hyo Jung; Cha, Jiyoung Y; Seok, Jo Woon; Choi, Yoonjeong; Yoon, Bo Kyung; Choi, Hyeonjin; Yu, Jung Hwan; Song, Su Jin; Kim, Ara; Lee, Hyemin; Kim, Daeun; Han, Ji Yoon; Kim, Jae-Woo

    2016-01-01

    Glucocorticoids are associated with obesity, but the underlying mechanism by which they function remains poorly understood. Previously, we showed that small G protein Dexras1 is expressed by glucocorticoids and leads to adipocyte differentiation. In this study, we explored the mechanism by which Dexras1 mediates adipogenesis and show a link to the insulin-like growth factor-1 (IGF-1) signaling pathway. Without Dexras1, the activation of MAPK and subsequent phosphorylation of CCAAT/enhancer binding protein β (C/EBPβ) is abolished, thereby inhibiting mitotic clonal expansion and further adipocyte differentiation. Dexras1 translocates to the plasma membrane upon insulin or IGF-1 treatment, for which the unique C-terminal domain (amino acids 223-276) is essential. Dexras1-dependent MAPK activation is selectively involved in the IGF-1 signaling, because another Ras protein, H-ras localized to the plasma membrane independently of insulin treatment. Moreover, neither epidermal growth factor nor other cell types shows Dexras1-dependent MAPK activation, indicating the importance of Dexras1 in IGF-1 signaling in adipogenesis. Dexras1 interacts with Shc and Raf, indicating that Dexras1-induced activation of MAPK is largely dependent on the Shc-Grb2-Raf complex. These results suggest that Dexras1 is a critical mediator of the IGF-1 signal to activate MAPK, linking glucocorticoid signaling to IGF-1 signaling in adipogenesis. PMID:27345868

  10. Dexras1 links glucocorticoids to insulin-like growth factor-1 signaling in adipogenesis

    PubMed Central

    Kim, Hyo Jung; Cha, Jiyoung Y.; Seok, Jo Woon; Choi, Yoonjeong; Yoon, Bo Kyung; Choi, Hyeonjin; Yu, Jung Hwan; Song, Su Jin; Kim, Ara; Lee, Hyemin; Kim, Daeun; Han, Ji Yoon; Kim, Jae-woo

    2016-01-01

    Glucocorticoids are associated with obesity, but the underlying mechanism by which they function remains poorly understood. Previously, we showed that small G protein Dexras1 is expressed by glucocorticoids and leads to adipocyte differentiation. In this study, we explored the mechanism by which Dexras1 mediates adipogenesis and show a link to the insulin-like growth factor-1 (IGF-1) signaling pathway. Without Dexras1, the activation of MAPK and subsequent phosphorylation of CCAAT/enhancer binding protein β (C/EBPβ) is abolished, thereby inhibiting mitotic clonal expansion and further adipocyte differentiation. Dexras1 translocates to the plasma membrane upon insulin or IGF-1 treatment, for which the unique C-terminal domain (amino acids 223–276) is essential. Dexras1-dependent MAPK activation is selectively involved in the IGF-1 signaling, because another Ras protein, H-ras localized to the plasma membrane independently of insulin treatment. Moreover, neither epidermal growth factor nor other cell types shows Dexras1-dependent MAPK activation, indicating the importance of Dexras1 in IGF-1 signaling in adipogenesis. Dexras1 interacts with Shc and Raf, indicating that Dexras1-induced activation of MAPK is largely dependent on the Shc-Grb2-Raf complex. These results suggest that Dexras1 is a critical mediator of the IGF-1 signal to activate MAPK, linking glucocorticoid signaling to IGF-1 signaling in adipogenesis. PMID:27345868

  11. Phytochrome and retrograde signalling pathways coverage to antogonistically regulate a light-induced transcription network

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Plastid-to-nucleus retrograde signals emitted by dysfunctional chloroplasts impact photomorphogenic development, but the molecular link between retrograde and photosensory-receptor signaling has remained undefined. Here, we show that the phytochrome (phy) and retrograde signaling pathways converge a...

  12. Redox signalling directly regulates TDP-43 via cysteine oxidation and disulphide cross-linking.

    PubMed

    Cohen, Todd J; Hwang, Andrew W; Unger, Travis; Trojanowski, John Q; Lee, Virginia M Y

    2012-03-01

    TDP-43 is the major disease protein in ubiquitin-positive inclusions of amyotrophic lateral sclerosis and frontotemporal lobar degeneration (FTLD) characterized by TDP-43 pathology (FTLD-TDP). Accumulation of insoluble TDP-43 aggregates could impair normal TDP-43 functions and initiate disease progression. Thus, it is critical to define the signalling mechanisms regulating TDP-43 since this could open up new avenues for therapeutic interventions. Here, we have identified a redox-mediated signalling mechanism directly regulating TDP-43. Using in vitro and cell-based studies, we demonstrate that oxidative stress promotes TDP-43 cross-linking via cysteine oxidation and disulphide bond formation leading to decreased TDP-43 solubility. Biochemical analysis identified several cysteine residues located within and adjacent to the second RNA-recognition motif that contribute to both intra- and inter-molecular interactions, supporting TDP-43 as a target of redox signalling. Moreover, increased levels of cross-linked TDP-43 species are found in FTLD-TDP brains, indicating that aberrant TDP-43 cross-linking is a prominent pathological feature of this disease. Thus, TDP-43 is dynamically regulated by a redox regulatory switch that links oxidative stress to the modulation of TDP-43 and its downstream targets. PMID:22193716

  13. Redox signalling directly regulates TDP-43 via cysteine oxidation and disulphide cross-linking

    PubMed Central

    Cohen, Todd J; Hwang, Andrew W; Unger, Travis; Trojanowski, John Q; Lee, Virginia M Y

    2012-01-01

    TDP-43 is the major disease protein in ubiquitin-positive inclusions of amyotrophic lateral sclerosis and frontotemporal lobar degeneration (FTLD) characterized by TDP-43 pathology (FTLD-TDP). Accumulation of insoluble TDP-43 aggregates could impair normal TDP-43 functions and initiate disease progression. Thus, it is critical to define the signalling mechanisms regulating TDP-43 since this could open up new avenues for therapeutic interventions. Here, we have identified a redox-mediated signalling mechanism directly regulating TDP-43. Using in vitro and cell-based studies, we demonstrate that oxidative stress promotes TDP-43 cross-linking via cysteine oxidation and disulphide bond formation leading to decreased TDP-43 solubility. Biochemical analysis identified several cysteine residues located within and adjacent to the second RNA-recognition motif that contribute to both intra- and inter-molecular interactions, supporting TDP-43 as a target of redox signalling. Moreover, increased levels of cross-linked TDP-43 species are found in FTLD-TDP brains, indicating that aberrant TDP-43 cross-linking is a prominent pathological feature of this disease. Thus, TDP-43 is dynamically regulated by a redox regulatory switch that links oxidative stress to the modulation of TDP-43 and its downstream targets. PMID:22193716

  14. Private link between signal and response in Bacillus subtilis quorum sensing

    PubMed Central

    Oslizlo, Anna; Stefanic, Polonca; Dogsa, Iztok; Mandic-Mulec, Ines

    2014-01-01

    Bacteria coordinate their behavior using quorum sensing (QS), whereby cells secrete diffusible signals that generate phenotypic responses associated with group living. The canonical model of QS is one of extracellular signaling, where signal molecules bind to cognate receptors and cause a coordinated response across many cells. Here we study the link between QS input (signaling) and QS output (response) in the ComQXPA QS system of Bacillus subtilis by characterizing the phenotype and fitness of comQ null mutants. These lack the enzyme to produce the ComX signal and do not activate the ComQXPA QS system in other cells. In addition to the activation effect of the signal, however, we find evidence of a second, repressive effect of signal production on the QS system. Unlike activation, which can affect other cells, repression acts privately: the de-repression of QS in comQ cells is intracellular and only affects mutant cells lacking ComQ. As a result, the QS signal mutants have an overly responsive QS system and overproduce the secondary metabolite surfactin in the presence of the signal. This surfactin overproduction is associated with a strong fitness cost, as resources are diverted away from primary metabolism. Therefore, by acting as a private QS repressor, ComQ may be protected against evolutionary competition from loss-of-function mutations. Additionally, we find that surfactin participates in a social selection mechanism that targets signal null mutants in coculture with signal producers. Our study shows that by pleiotropically combining intracellular and extracellular signaling, bacteria may generate evolutionarily stable QS systems. PMID:24425772

  15. Leveraging Social Links for Trust and Privacy in Networks

    NASA Astrophysics Data System (ADS)

    Cutillo, Leucio Antonio; Molva, Refik; Strufe, Thorsten

    Existing on-line social networks (OSN) such as Facebook suffer from several weaknesses regarding privacy and security due to their inherent handling of personal data. As pointed out in [4], a preliminary analysis of existing OSNs shows that they are subject to a number of vulnerabilities, ranging from cloning legitimate users to sybil attacks through privacy violations. Starting from these OSN vulnerabilities as the first step of a broader research activity, we came up with a new approach that is very promising in re-visiting security and privacy problems in distributed systems and networks. We suggest a solution that both aims at avoiding any centralized control and leverages on the real life trust between users, that is part of the social network application itself. An anonymization technique based on multi-hop routing among trusted nodes guarantees privacy in data access and, generally speaking, in all the OSN operations.

  16. LINKEDIN TRILOGY: Part 1. Top 10 Reasons You Should NOT Join LinkedIn Professional Network!

    ERIC Educational Resources Information Center

    Berk, Ronald A.

    2013-01-01

    Disclaimer: I have been an active "free" user of LinkedIn for 5.463 years with more than 3000 (1st degree) connections from all over the world. I have no vested interest in LinkedIn other than as a user of the services it provides. Despite the fact that LinkedIn was originally designed as a network for business professionals, not…

  17. Biasing vector network analyzers using variable frequency and amplitude signals

    NASA Astrophysics Data System (ADS)

    Nobles, J. E.; Zagorodnii, V.; Hutchison, A.; Celinski, Z.

    2016-08-01

    We report the development of a test setup designed to provide a variable frequency biasing signal to a vector network analyzer (VNA). The test setup is currently used for the testing of liquid crystal (LC) based devices in the microwave region. The use of an AC bias for LC based devices minimizes the negative effects associated with ionic impurities in the media encountered with DC biasing. The test setup utilizes bias tees on the VNA test station to inject the bias signal. The square wave biasing signal is variable from 0.5 to 36.0 V peak-to-peak (VPP) with a frequency range of DC to 10 kHz. The test setup protects the VNA from transient processes, voltage spikes, and high-frequency leakage. Additionally, the signals to the VNA are fused to ½ amp and clipped to a maximum of 36 VPP based on bias tee limitations. This setup allows us to measure S-parameters as a function of both the voltage and the frequency of the applied bias signal.

  18. Biasing vector network analyzers using variable frequency and amplitude signals.

    PubMed

    Nobles, J E; Zagorodnii, V; Hutchison, A; Celinski, Z

    2016-08-01

    We report the development of a test setup designed to provide a variable frequency biasing signal to a vector network analyzer (VNA). The test setup is currently used for the testing of liquid crystal (LC) based devices in the microwave region. The use of an AC bias for LC based devices minimizes the negative effects associated with ionic impurities in the media encountered with DC biasing. The test setup utilizes bias tees on the VNA test station to inject the bias signal. The square wave biasing signal is variable from 0.5 to 36.0 V peak-to-peak (VPP) with a frequency range of DC to 10 kHz. The test setup protects the VNA from transient processes, voltage spikes, and high-frequency leakage. Additionally, the signals to the VNA are fused to ½ amp and clipped to a maximum of 36 VPP based on bias tee limitations. This setup allows us to measure S-parameters as a function of both the voltage and the frequency of the applied bias signal. PMID:27587141

  19. Building Student Networks with LinkedIn: The Potential for Connections, Internships, and Jobs

    ERIC Educational Resources Information Center

    Peterson, Robert M.; Dover, Howard F.

    2014-01-01

    Networking is a chance to interact with people, build friendships or business partners, identify opportunities, and create value. Technology has made this process easier, since individuals can readily contact others who were previously unknown. In the professional world, LinkedIn has become the standard way to build virtual and personal networks.…

  20. Analysis and research on technology system of space broadband network based on laser link

    NASA Astrophysics Data System (ADS)

    Chang, Chengwu; Fei, Ligang; Chen, Erhu; Kou, Baohua; Cheng, Liyu

    2015-10-01

    Space broadband network based on laser link represents the future development direction, Europe, the United States, Japan and other space powers have been researching the theory of space laser communication and the key technology constantly, and have carried out the key technology test of inter-satellite laser communication and satellite-ground laser communication on orbit. However, what is the technology system of space broadband network based on laser link? up to now, it is still controversial, such as wavelength, coding, and modulation mode, exchange mode and so on. Here, by analyzing all kinds of space laser communication test and its technology parameters, combined with the application requirement of space broadband network, a set of technology system for space broadband network based on laser link is put forward, although just a preliminary research result. At first, this paper introduces the basic conception of space broadband network based on laser link, defines the space laser broadband network technology system and its research scope. Then analyze the main contents of space laser broadband network technology system, especially the technical route choice involved, and by studying, the related suggestions are given. Finally, with the development of space broadband network, the issue of standardization in space laser communication technology system is put forward, in order to cause attaches great importance to scientific research institutes and relevant experts.

  1. 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.

  2. Rheology and nonlinear mechanics of transiently cross linked semiflexible networks: Bundling, ripping, healing, and mechnomemory

    NASA Astrophysics Data System (ADS)

    Levine, Alex

    Transiently cross linked networks of semiflexible filaments make up the principal structural component of the cell -- the cytoskeleton. This intracellular network, along with molecular motors, forms the basis for cellular control of morphology and force generation. In this talk, I report on investigations of the effect of transiently bound cross linkers on the structure and mechanics of semiflexible networks. Specifically, I address the role of Casimir or fluctuation-induced interactions between cross linkers in the formation of filament bundles. I report on the linear viscoelasticity of transiently cross-linked networks of bundles. Finally, I discuss the nonlinear mechanical response of such networks, where applied stress induces a persistent structural rearrangement of the network that can dramatically alter its nonlinear response to stresses subsequently applied.

  3. Signalling design and architecture for a proposed mobile satellite network

    NASA Technical Reports Server (NTRS)

    Yan, T.-Y.; Cheng, U.; Wang, C.

    1990-01-01

    In a frequency-division/demand-assigned multiple-access (FD/DAMA) architecture, each mobile subscriber must make a connection request to the Network Management Center before transmission for either open-end or closed-end services. Open-end services are for voice calls and long file transfer and are processed on a blocked-call-cleared basis. Closed-end services are for transmitting burst data and are processed on a first-come first-served basis. This paper presents the signalling design and architecture for non-voice services of an FD/DAMA mobile satellite network. The connection requests are made through the recently proposed multiple channel collision resolution scheme which provides a significantly higher throughput than the traditional slotted ALOHA scheme. For non-voice services, it is well known that retransmissions are necessary to ensure the delivery of a message in its entirety from the source to destination. Retransmission protocols for open-end and closed-end data transfer are investigated. The signal structure for the proposed network is derived from X-25 standards with appropriate modifications. The packet types and their usages are described in this paper.

  4. Query and Visualization of extremely large network datasets over the web using Quadtree based KML Regional Network Links

    SciTech Connect

    Dadi, Upendra; Liu, Cheng; Vatsavai, Raju

    2009-01-01

    Geographic data sets are often very large in size. Interactive visualization of such data at all scales is not easy because of the limited resolution of the monitors and inability of visualization applications to handle the volume of data. This is especially true for large vector datasets. The end user s experience is frequently unsatisfactory when exploring such data over the web using a naive application. Network bandwidth is another contributing factor to the low performance. In this paper, a Quadtree based technique to visualize extremely large spatial network datasets over the web is described. It involves using custom developed algorithms leveraging a PostGIS database as the data source and Google Earth as the visualization client. This methodology supports both point and range queries along with non-spatial queries. This methodology is demonstrated using a network dataset consisting of several million links. The methodology is based on using some of the powerful features of KML (Keyhole Markup Language). Keyhole Markup Language (KML) is an Open Geospatial Consortium (OGC) standard for displaying geospatial data on Earth browsers. One of the features of KML is the notion of Network Links. Using network links, a wide range of geospatial data sources such as geodatabases, static files and geospatial data services can be simultaneously accessed and visualized seamlessly. Using the network links combined with Level of Detail principle, view based rendering and intelligent server and client-side caching, scalability in visualizing extremely large spatial datasets can be achieved.

  5. Exploiting the yeast stress-activated signaling network to inform on stress biology and disease signaling

    PubMed Central

    Ho, Yi-Hsuan

    2016-01-01

    Healthy cells utilize intricate systems to monitor their environment and mount robust responses in the event of cellular stress. Whether stress arises from external insults or defects due to mutation and disease, cells must be able to respond precisely to mount the appropriate defenses. Multi-faceted stress responses are generally coupled with arrest of growth and cell-cycle progression, which both limits the transmission of damaged materials and serves to reallocate limited cellular resources toward defense. Therefore, stress defense versus rapid growth represent competing interests in the cell. How eukaryotic cells set the balance between defense versus proliferation, and in particular knowledge of the regulatory networks that control this decision, are poorly understood. In this perspective, we expand upon our recent work inferring the stress-activated signaling network in budding yeast, which captures pathways controlling stress defense and regulators of growth and cell-cycle progression. We highlight similarities between the yeast and mammalian stress responses and explore how stress-activated signaling networks in yeast can inform on signaling defects in human cancers. PMID:25957506

  6. Linking Data and Learning - The Grow Network Study: Summary Report

    ERIC Educational Resources Information Center

    Light, Daniel; Honey, Margaret; Heinze, Juliet; Brunner, Cornelia; Wexler, Dara; Mandinach, Ellen; Fasca, Chad

    2005-01-01

    With funding from the Carnegie Corporation, in the spring of 2002, EDC's Center for Children and Technology began a two-year exploratory study that examined how educators and administrators within the New York City public school system are using data?made available to them through the print and web-based reporting system of the Grow Network to…

  7. Transcription factor and microRNA-regulated network motifs for cancer and signal transduction networks

    PubMed Central

    2015-01-01

    Abstract Background Molecular networks are the basis of biological processes. Such networks can be decomposed into smaller modules, also known as network motifs. These motifs show interesting dynamical behaviors, in which co-operativity effects between the motif components play a critical role in human diseases. We have developed a motif-searching algorithm, which is able to identify common motif types from the cancer networks and signal transduction networks (STNs). Some of the network motifs are interconnected which can be merged together and form more complex structures, the so-called coupled motif structures (CMS). These structures exhibit mixed dynamical behavior, which may lead biological organisms to perform specific functions. Results In this study, we integrate transcription factors (TFs), microRNAs (miRNAs), miRNA targets and network motifs information to build the cancer-related TF-miRNA-motif networks (TMMN). This allows us to examine the role of network motifs in cancer formation at different levels of regulation, i.e. transcription initiation (TF → miRNA), gene-gene interaction (CMS), and post-transcriptional regulation (miRNA → target genes). Among the cancer networks and STNs we considered, it is found that there is a substantial amount of crosstalking through motif interconnections, in particular, the crosstalk between prostate cancer network and PI3K-Akt STN. Conclusions To validate the role of network motifs in cancer formation, several examples are presented which demonstrated the effectiveness of the present approach. A web-based platform has been set up which can be accessed at: http://ppi.bioinfo.asia.edu.tw/pathway/. It is very likely that our results can supply very specific CMS missing information for certain cancer types, it is an indispensable tool for cancer biology research. PMID:25707690

  8. Neurodegenerative and Inflammatory Pathway Components Linked to TNF-α/TNFR1 Signaling in the Glaucomatous Human Retina

    PubMed Central

    Yang, Xiangjun; Luo, Cheng; Cai, Jian; Powell, David W.; Yu, Dahai; Kuehn, Markus H.

    2011-01-01

    Purpose. This study aimed to determine retinal proteomic alterations in human glaucoma, with particular focus on links to TNF-α/TNFR1 signaling. Methods. Human retinal protein samples were obtained from 20 donors with (n = 10) or without (n = 10) glaucoma. Alterations in protein expression were individually analyzed by quantitative LC-MS/MS. Quantitative Western blot analysis with cleavage or phosphorylation site-specific antibodies was used for data validation, and cellular localization of selected proteins was determined by immunohistochemical analysis of the retina in an additional group of glaucomatous human donor eyes (n = 38) and nonglaucomatous controls (n = 30). Results. Upregulated retinal proteins in human glaucoma included a number of downstream adaptor/interacting proteins and protein kinases involved in TNF-α/TNFR1 signaling. Bioinformatic analysis of the high-throughput data established extended networks of diverse functional interactions with death-promoting and survival-promoting pathways and mediation of immune response. Upregulated pathways included death receptor-mediated caspase cascade, mitochondrial dysfunction, endoplasmic reticulum stress, calpains leading to apoptotic cell death, NF-κB and JAK/STAT pathways, and inflammasome-assembly mediating inflammation. Interestingly, retinal expression pattern of a regulator molecule, TNFAIP3, exhibited prominent variability between individual samples, and methylation of cytosine nucleotides in the TNFAIP3 promoter was found to be correlated with this variability among glaucomatous donors. Conclusions. Findings of this study reveal a number of proteins upregulated in the glaucomatous human retina that exhibit many links to TNF-α/TNFR1 signaling. By highlighting various signaling molecules and regulators involved in cell death and immune response pathways and by correlating proteomic findings with epigenetic alterations, these findings provide a framework motivating further research. PMID:21917936

  9. A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models.

    PubMed

    Ryll, A; Bucher, J; Bonin, A; Bongard, S; Gonçalves, E; Saez-Rodriguez, J; Niklas, J; Klamt, S

    2014-10-01

    Systems biology has to increasingly cope with large- and multi-scale biological systems. Many successful in silico representations and simulations of various cellular modules proved mathematical modelling to be an important tool in gaining a solid understanding of biological phenomena. However, models spanning different functional layers (e.g. metabolism, signalling and gene regulation) are still scarce. Consequently, model integration methods capable of fusing different types of biological networks and various model formalisms become a key methodology to increase the scope of cellular processes covered by mathematical models. Here we propose a new integration approach to couple logical models of signalling or/and gene-regulatory networks with kinetic models of metabolic processes. The procedure ends up with an integrated dynamic model of both layers relying on differential equations. The feasibility of the approach is shown in an illustrative case study integrating a kinetic model of central metabolic pathways in hepatocytes with a Boolean logical network depicting the hormonally induced signal transduction and gene regulation events involved. In silico simulations demonstrate the integrated model to qualitatively describe the physiological switch-like behaviour of hepatocytes in response to nutritionally regulated changes in extracellular glucagon and insulin levels. A simulated failure mode scenario addressing insulin resistance furthermore illustrates the pharmacological potential of a model covering interactions between signalling, gene regulation and metabolism. PMID:25063553

  10. Real time data acquisition of a countrywide commercial microwave link network

    NASA Astrophysics Data System (ADS)

    Chwala, Christian; Keis, Felix; Kunstmann, Harald

    2015-04-01

    Research in recent years has shown that data from commercial microwave link networks can provide very valuable precipitation information. Since these networks comprise the backbone of the cell phone network, they provide countrywide coverage. However acquiring the necessary data from the network operators is still difficult. Data is usually made available for researchers with a large time delay and often at irregular basis. This of course hinders the exploitation of commercial microwave link data in operational applications like QPE forecasts running at national meteorological services. To overcome this, we have developed a custom software in joint cooperation with our industry partner Ericsson. The software is installed on a dedicated server at Ericsson and is capable of acquiring data from the countrywide microwave link network in Germany. In its current first operational testing phase, data from several hundred microwave links in southern Germany is recorded. All data is instantaneously sent to our server where it is stored and organized in an emerging database. Time resolution for the Ericsson data is one minute. The custom acquisition software, however, is capable of processing higher sampling rates. Additionally we acquire and manage 1 Hz data from four microwave links operated by the skiing resort in Garmisch-Partenkirchen. We will present the concept of the data acquisition and show details of the custom-built software. Additionally we will showcase the accessibility and basic processing of real time microwave link data via our database web frontend.

  11. Cascading failures in coupled networks with both inner-dependency and inter-dependency links

    NASA Astrophysics Data System (ADS)

    Liu, Run-Ran; Li, Ming; Jia, Chun-Xiao; Wang, Bing-Hong

    2016-05-01

    We study the percolation in coupled networks with both inner-dependency and inter-dependency links, where the inner- and inter-dependency links represent the dependencies between nodes in the same or different networks, respectively. We find that when most of dependency links are inner- or inter-ones, the coupled networks system is fragile and makes a discontinuous percolation transition. However, when the numbers of two types of dependency links are close to each other, the system is robust and makes a continuous percolation transition. This indicates that the high density of dependency links could not always lead to a discontinuous percolation transition as the previous studies. More interestingly, although the robustness of the system can be optimized by adjusting the ratio of the two types of dependency links, there exists a critical average degree of the networks for coupled random networks, below which the crossover of the two types of percolation transitions disappears, and the system will always demonstrate a discontinuous percolation transition. We also develop an approach to analyze this model, which is agreement with the simulation results well.

  12. Cascading failures in coupled networks with both inner-dependency and inter-dependency links

    PubMed Central

    Liu, Run-Ran; Li, Ming; Jia, Chun-Xiao; Wang, Bing-Hong

    2016-01-01

    We study the percolation in coupled networks with both inner-dependency and inter-dependency links, where the inner- and inter-dependency links represent the dependencies between nodes in the same or different networks, respectively. We find that when most of dependency links are inner- or inter-ones, the coupled networks system is fragile and makes a discontinuous percolation transition. However, when the numbers of two types of dependency links are close to each other, the system is robust and makes a continuous percolation transition. This indicates that the high density of dependency links could not always lead to a discontinuous percolation transition as the previous studies. More interestingly, although the robustness of the system can be optimized by adjusting the ratio of the two types of dependency links, there exists a critical average degree of the networks for coupled random networks, below which the crossover of the two types of percolation transitions disappears, and the system will always demonstrate a discontinuous percolation transition. We also develop an approach to analyze this model, which is agreement with the simulation results well. PMID:27142883

  13. Cascading failures in coupled networks with both inner-dependency and inter-dependency links.

    PubMed

    Liu, Run-Ran; Li, Ming; Jia, Chun-Xiao; Wang, Bing-Hong

    2016-01-01

    We study the percolation in coupled networks with both inner-dependency and inter-dependency links, where the inner- and inter-dependency links represent the dependencies between nodes in the same or different networks, respectively. We find that when most of dependency links are inner- or inter-ones, the coupled networks system is fragile and makes a discontinuous percolation transition. However, when the numbers of two types of dependency links are close to each other, the system is robust and makes a continuous percolation transition. This indicates that the high density of dependency links could not always lead to a discontinuous percolation transition as the previous studies. More interestingly, although the robustness of the system can be optimized by adjusting the ratio of the two types of dependency links, there exists a critical average degree of the networks for coupled random networks, below which the crossover of the two types of percolation transitions disappears, and the system will always demonstrate a discontinuous percolation transition. We also develop an approach to analyze this model, which is agreement with the simulation results well. PMID:27142883

  14. Simulation study of communication link for Pioneer Saturn/Uranus atmospheric entry probe. [signal acquisition by candidate modem for radio link

    NASA Technical Reports Server (NTRS)

    Hinrichs, C. A.

    1974-01-01

    A digital simulation is presented for a candidate modem in a modeled atmospheric scintillation environment with Doppler, Doppler rate, and signal attenuation typical of the radio link conditions for an outer planets atmospheric entry probe. The results indicate that the signal acquisition characteristics and the channel error rate are acceptable for the system requirements of the radio link. The simulation also outputs data for calculating other error statistics and a quantized symbol stream from which error correction decoding can be analyzed.

  15. Model for a neural network structure and signal transmission

    NASA Astrophysics Data System (ADS)

    Kotsavasiloglou, C.; Kalampokis, A.; Argyrakis, P.; Baloyannis, S.

    1997-10-01

    We present a model of a neural network that is based on the diffusion-limited-aggregation (DLA) structure from fractal physics. A single neuron is one DLA cluster, while a large number of clusters, in an interconnected fashion, make up the neural network. Using simulation techniques, a signal is randomly generated and traced through its transmission inside the neuron and from neuron to neuron through the synapses. The activity of the entire neural network is monitored as a function of time. The characteristics included in the model contain, among others, the threshold for firing, the excitatory or inhibitory character of the synapse, the synaptic delay, and the refractory period. The system activity results in ``noisy'' time series that exhibit an oscillatory character. Standard power spectra are evaluated and fractal analyses performed, showing that the system is not chaotic, but the varying parameters can be associated with specific values of fractal dimensions. It is found that the network activity is not linear with the system parameters, e.g., with the numbers of active synapses. The details of this behavior may have interesting repercussions from the neurological point of view.

  16. Signal integration in the galactose network of Escherichia coli.

    PubMed

    Semsey, Szabolcs; Krishna, Sandeep; Sneppen, Kim; Adhya, Sankar

    2007-07-01

    The gal regulon of Escherichia coli contains genes involved in galactose transport and metabolism. Transcription of the gal regulon genes is regulated in different ways by two iso-regulatory proteins, Gal repressor (GalR) and Gal isorepressor (GalS), which recognize the same binding sites in the absence of d-galactose. DNA binding by both GalR and GalS is inhibited in the presence of d-galactose. Many of the gal regulon genes are activated in the presence of the adenosine cyclic-3',5'-monophosphate (cAMP)-cAMP receptor protein (CRP) complex. We studied transcriptional regulation of the gal regulon promoters simultaneously in a purified system and attempted to integrate the two small molecule signals, d-galactose and cAMP, that modulate the isoregulators and CRP respectively, at each promoter, using Boolean logic. Results show that similarly organized promoters can have different input functions. We also found that in some cases the activity of the promoter and the cognate gene can be described by different logic gates. We combined the transcriptional network of the galactose regulon, obtained from our experiments, with literature data to construct an integrated map of the galactose network. Structural analysis of the network shows that at the interface of the genetic and metabolic network, feedback loops are by far the most common motif. PMID:17630975

  17. Controlling self-sustained spiking activity by adding or removing one network link

    NASA Astrophysics Data System (ADS)

    Xu, Kesheng; Huang, Wenwen; Li, Baowen; Dhamala, Mukesh; Liu, Zonghua

    2013-06-01

    Being able to control the neuronal spiking activity in specific brain regions is central to a treatment scheme in several brain disorders such as epileptic seizures, mental depression, and Parkinson's diseases. Here, we present an approach for controlling self-sustained oscillations by adding or removing one directed network link in coupled neuronal oscillators, in contrast to previous approaches of adding stimuli or noise. We find that such networks can exhibit a variety of activity patterns such as on-off switch, sustained spikes, and short-term spikes. We derive the condition for a specific link to be the controller of the on-off effect. A qualitative analysis is provided to facilitate the understanding of the mechanism for spiking activity by adding one link. Our findings represent the first report on generating spike activity with the addition of only one directed link to a network and provide a deeper understanding of the microscopic roots of self-sustained spiking.

  18. Diol-linked microporous networks of cubic siloxane cages.

    PubMed

    Wada, Yuko; Iyoki, Kenta; Sugawara-Narutaki, Ayae; Okubo, Tatsuya; Shimojima, Atsushi

    2013-01-28

    A new class of inorganic-organic hybrid porous materials has been synthesized by a reaction between octa(hydridosilsesquioxane) (H(8)Si(8)O(12)), which has a double-four-ring (D4R) structure, and various diols, such as 1,3-propanediol (PD), 1,4-cyclohexanediol (CHD), and 1,3-adamantanediol (AD). Solid-state (29) Si magic-angle-spinning NMR spectroscopic analysis confirmed that most of the corner Si-H groups reacted with diols to form Si-O-C bonds with retention of the D4R cage. Nitrogen adsorption-desorption studies showed that the products are microporous solids with high BET surface areas (up to ≈580 m(2) g(-1) for CHD- and AD-linked products). If n-alkanediols are used as linkers, the surface area becomes smaller as the number of carbon atoms is increased. The thermal and hydrolytic stability of the products strongly depend on the type of diol linkers. The highest stabilities are found for the AD-linked products, which are thermally stable up to around 400 °C and remain intact even after being soaked in water for 1 day. In contrast, the PD-linked product is easily hydrolyzed in water to give microporous silica. These results offer a new route toward a series of silica-based porous materials with unique structures and properties. PMID:23203900

  19. Space Network Time Distribution and Synchronization Protocol Development for Mars Proximity Link

    NASA Technical Reports Server (NTRS)

    Woo, Simon S.; Gao, Jay L.; Mills, David

    2010-01-01

    Time distribution and synchronization in deep space network are challenging due to long propagation delays, spacecraft movements, and relativistic effects. Further, the Network Time Protocol (NTP) designed for terrestrial networks may not work properly in space. In this work, we consider the time distribution protocol based on time message exchanges similar to Network Time Protocol (NTP). We present the Proximity-1 Space Link Interleaved Time Synchronization (PITS) algorithm that can work with the CCSDS Proximity-1 Space Data Link Protocol. The PITS algorithm provides faster time synchronization via two-way time transfer over proximity links, improves scalability as the number of spacecraft increase, lowers storage space requirement for collecting time samples, and is robust against packet loss and duplication which underlying protocol mechanisms provide.

  20. The structural role of weak and strong links in a financial market network

    NASA Astrophysics Data System (ADS)

    Garas, A.; Argyrakis, P.; Havlin, S.

    2008-05-01

    We investigate the properties of correlation based networks originating from economic complex systems, such as the network of stocks traded at the New York Stock Exchange (NYSE). The weaker links (low correlation) of the system are found to contribute to the overall connectivity of the network significantly more than the strong links (high correlation). We find that nodes connected through strong links form well defined communities. These communities are clustered together in more complex ways compared to the widely used classification according to the economic activity. We find that some companies, such as General Electric (GE), Coca Cola (KO), and others, can be involved in different communities. The communities are found to be quite stable over time. Similar results were obtained by investigating markets completely different in size and properties, such as the Athens Stock Exchange (ASE). The present method may be also useful for other networks generated through correlations.

  1. Deep Space Network Capabilities for Receiving Weak Probe Signals

    NASA Technical Reports Server (NTRS)

    Asmar, Sami; Johnston, Doug; Preston, Robert

    2005-01-01

    Planetary probes can encounter mission scenarios where communication is not favorable during critical maneuvers or emergencies. Launch, initial acquisition, landing, trajectory corrections, safing. Communication challenges due to sub-optimum antenna pointing or transmitted power, amplitude/frequency dynamics, etc. Prevent lock-up on signal and extraction of telemetry. Examples: loss of Mars Observer, nutation of Ulysses, Galileo antenna, Mars Pathfinder and Mars Exploration Rovers Entry, Descent, and Landing, and the Cassini Saturn Orbit Insertion. A Deep Space Network capability to handle such cases has been used successfully to receive signals to characterize the scenario. This paper will describe the capability and highlight the cases of the critical communications for the Mars rovers and Saturn Orbit Insertion and preparation radio tracking of the Huygens probe at (non-DSN) radio telescopes.

  2. Mesoscopic simulations of hydrophilic cross-linked polycarbonate polyurethane networks: structure and morphology.

    PubMed

    Iype, E; Esteves, A C C; de With, G

    2016-06-14

    Polyurethane (PU) cross-linked networks are frequently used in biomedical and marine applications, e.g., as hydrophilic polymer coatings with antifouling or low-friction properties and have been reported to exhibit characteristic phase separation between soft and hard segments. Understanding this phase-separation behavior is critical to design novel hydrophilic polymer coatings. However, most of the studies on the structure and morphology of cross-linked coatings are experimental, which only assess the phase separation via indirect methods. Herein we present a mesoscopic simulation study of the network characteristics of model hydrophilic polymer networks, consisting of PU with and without methyl-polyethylene glycol (mPEG) dangling chains. The systems are analyzed using a number of tools, such as the radial distribution function, the cross-link point density distribution and the Voronoi volume distribution (of the cross-linking points). The combined results show that the cross-linked networks without dangling chains are rather homogeneous but contain a small amount of clustering of cross-linker molecules. A clear phase separation is observed when introducing the dangling chains. In spite of that, the amount of cross-linker molecules connected to dangling chains only, i.e., not connected to the main network, is relatively small, leading to about 3 wt% extractables. Thus, these cross-linked polymers consist of a phase-separated, yet highly connected network. This study provides valuable guidelines towards new self-healing hydrophilic coatings based on the molecular design of cross-linked networks in direct contact with water or aqueous fluids, e.g., as anti-fouling self-repairing coatings for marine applications. PMID:27174657

  3. Matching-centrality decomposition and the forecasting of new links in networks.

    PubMed

    Rohr, Rudolf P; Naisbit, Russell E; Mazza, Christian; Bersier, Louis-Félix

    2016-02-10

    Networks play a prominent role in the study of complex systems of interacting entities in biology, sociology, and economics. Despite this diversity, we demonstrate here that a statistical model decomposing networks into matching and centrality components provides a comprehensive and unifying quantification of their architecture. The matching term quantifies the assortative structure in which node makes links with which other node, whereas the centrality term quantifies the number of links that nodes make. We show, for a diverse set of networks, that this decomposition can provide a tight fit to observed networks. Then we provide three applications. First, we show that the model allows very accurate prediction of missing links in partially known networks. Second, when node characteristics are known, we show how the matching-centrality decomposition can be related to this external information. Consequently, it offers us a simple and versatile tool to explore how node characteristics explain network architecture. Finally, we demonstrate the efficiency and flexibility of the model to forecast the links that a novel node would create if it were to join an existing network. PMID:26842568

  4. A Modular Analysis of the Auxin Signalling Network

    PubMed Central

    Farcot, Etienne; Lavedrine, Cyril; Vernoux, Teva

    2015-01-01

    Auxin is essential for plant development from embryogenesis onwards. Auxin acts in large part through regulation of transcription. The proteins acting in the signalling pathway regulating transcription downstream of auxin have been identified as well as the interactions between these proteins, thus identifying the topology of this network implicating 54 Auxin Response Factor (ARF) and Aux/IAA (IAA) transcriptional regulators. Here, we study the auxin signalling pathway by means of mathematical modeling at the single cell level. We proceed analytically, by considering the role played by five functional modules into which the auxin pathway can be decomposed: the sequestration of ARF by IAA, the transcriptional repression by IAA, the dimer formation amongst ARFs and IAAs, the feedback loop on IAA and the auxin induced degradation of IAA proteins. Focusing on these modules allows assessing their function within the dynamics of auxin signalling. One key outcome of this analysis is that there are both specific and overlapping functions between all the major modules of the signaling pathway. This suggests a combinatorial function of the modules in optimizing the speed and amplitude of auxin-induced transcription. Our work allows identifying potential functions for homo- and hetero-dimerization of transcriptional regulators, with ARF:IAA, IAA:IAA and ARF:ARF dimerization respectively controlling the amplitude, speed and sensitivity of the response and a synergistic effect of the interaction of IAA with transcriptional repressors on these characteristics of the signaling pathway. Finally, we also suggest experiments which might allow disentangling the structure of the auxin signaling pathway and analysing further its function in plants. PMID:25807071

  5. ATR inhibition rewires cellular signaling networks induced by replication stress.

    PubMed

    Wagner, Sebastian A; Oehler, Hannah; Voigt, Andrea; Dalic, Denis; Freiwald, Anja; Serve, Hubert; Beli, Petra

    2016-02-01

    The slowing down or stalling of replication forks is commonly known as replication stress and arises from multiple causes such as DNA lesions, nucleotide depletion, RNA-DNA hybrids, and oncogene activation. The ataxia telangiectasia and Rad3-related kinase (ATR) plays an essential role in the cellular response to replication stress and inhibition of ATR has emerged as therapeutic strategy for the treatment of cancers that exhibit high levels of replication stress. However, the cellular signaling induced by replication stress and the substrate spectrum of ATR has not been systematically investigated. In this study, we employed quantitative MS-based proteomics to define the cellular signaling after nucleotide depletion-induced replication stress and replication fork collapse following ATR inhibition. We demonstrate that replication stress results in increased phosphorylation of a subset of proteins, many of which are involved in RNA splicing and transcription and have previously not been associated with the cellular replication stress response. Furthermore, our data reveal the ATR-dependent phosphorylation following replication stress and discover novel putative ATR target sites on MCM6, TOPBP1, RAD51AP1, and PSMD4. We establish that ATR inhibition rewires cellular signaling networks induced by replication stress and leads to the activation of the ATM-driven double-strand break repair signaling. PMID:26572502

  6. Enhanced Mechanical Properties of Nanoparticle Networks Cross-Linked by Biomimetic Catch Bonds

    NASA Astrophysics Data System (ADS)

    Mbanga, Badel L.; Iyer, Balaji V. S.; Yashin, Victor V.; Balazs, Anna C.

    2015-03-01

    The tunable behavior of cross-linked networks of Polymer-Grafted Nanoparticles (PGNs) makes them excellent candidates for designing novel materials with enhanced mechanical properties. The building block of a PGN network is a nanoparticle with grafted polymer chains whose free ends' reactive groups can form bonds with the end chains on the nearby particles. We use computer modeling to study the tensile behavior of 3D samples, in which some fraction of cross-links is formed through the biomimetic ``catch'' bonds. In contrast to conventional ``slip'' bonds, the catch bonds might become stronger under an applied force due to transitions between two conformational states. The mechanical properties of the PGN networks are shown to exhibit a drastic improvement upon introduction of the catch bonds into the network. We discuss how ductility, toughness, and rate of strain recovery of the network depend on the catch bond content.

  7. Criteria for Evaluating Alternative Network and Link Layer Protocols for the NASA Constellation Program Communication Architecture

    NASA Technical Reports Server (NTRS)

    Benbenek, Daniel; Soloff, Jason; Lieb, Erica

    2010-01-01

    Selecting a communications and network architecture for future manned space flight requires an evaluation of the varying goals and objectives of the program, development of communications and network architecture evaluation criteria, and assessment of critical architecture trades. This paper uses Cx Program proposed exploration activities as a guideline; lunar sortie, outpost, Mars, and flexible path options are described. A set of proposed communications network architecture criteria are proposed and described. They include: interoperability, security, reliability, and ease of automating topology changes. Finally a key set of architecture options are traded including (1) multiplexing data at a common network layer vs. at the data link layer, (2) implementing multiple network layers vs. a single network layer, and (3) the use of a particular network layer protocol, primarily IPv6 vs. Delay Tolerant Networking (DTN). In summary, the protocol options are evaluated against the proposed exploration activities and their relative performance with respect to the criteria are assessed. An architectural approach which includes (a) the capability of multiplexing at both the network layer and the data link layer and (b) a single network layer for operations at each program phase, as these solutions are best suited to respond to the widest array of program needs and meet each of the evaluation criteria.

  8. Link removal for the control of stochastically evolving epidemics over networks: a comparison of approaches.

    PubMed

    Enns, Eva A; Brandeau, Margaret L

    2015-04-21

    For many communicable diseases, knowledge of the underlying contact network through which the disease spreads is essential to determining appropriate control measures. When behavior change is the primary intervention for disease prevention, it is important to understand how to best modify network connectivity using the limited resources available to control disease spread. We describe and compare four algorithms for selecting a limited number of links to remove from a network: two "preventive" approaches (edge centrality, R0 minimization), where the decision of which links to remove is made prior to any disease outbreak and depends only on the network structure; and two "reactive" approaches (S-I edge centrality, optimal quarantining), where information about the initial disease states of the nodes is incorporated into the decision of which links to remove. We evaluate the performance of these algorithms in minimizing the total number of infections that occur over the course of an acute outbreak of disease. We consider different network structures, including both static and dynamic Erdös-Rényi random networks with varying levels of connectivity, a real-world network of residential hotels connected through injection drug use, and a network exhibiting community structure. We show that reactive approaches outperform preventive approaches in averting infections. Among reactive approaches, removing links in order of S-I edge centrality is favored when the link removal budget is small, while optimal quarantining performs best when the link removal budget is sufficiently large. The budget threshold above which optimal quarantining outperforms the S-I edge centrality algorithm is a function of both network structure (higher for unstructured Erdös-Rényi random networks compared to networks with community structure or the real-world network) and disease infectiousness (lower for highly infectious diseases). We conduct a value-of-information analysis of knowing which

  9. Link removal for the control of stochastically evolving epidemics over networks: A comparison of approaches

    PubMed Central

    Brandeau, Margaret L.

    2015-01-01

    For many communicable diseases, knowledge of the underlying contact network through which the disease spreads is essential to determining appropriate control measures. When behavior change is the primary intervention for disease prevention, it is important to understand how to best modify network connectivity using the limited resources available to control disease spread. We describe and compare four algorithms for selecting a limited number of links to remove from a network: two “preventive” approaches (edge centrality, R0 minimization), where the decision of which links to remove is made prior to any disease outbreak and depends only on the network structure; and two “reactive” approaches (S-I edge centrality, optimal quarantining), where information about the initial disease states of the nodes is incorporated into the decision of which links to remove. We evaluate the performance of these algorithms in minimizing the total number of infections that occur over the course of an acute outbreak of disease. We consider different network structures, including both static and dynamic Erdős-Rényi random networks with varying levels of connectivity, a real-world network of residential hotels connected through injection drug use, and a network exhibiting community structure. We show that reactive approaches outperform preventive approaches in averting infections. Among reactive approaches, removing links in order of S-I edge centrality is favored when the link removal budget is small, while optimal quarantining performs best when the link removal budget is sufficiently large. The budget threshold above which optimal quarantining outperforms the S-I edge centrality algorithm is a function of both network structure (higher for unstructured Erdős-Rényi random networks compared to networks with community structure or the real-world network) and disease infectiousness (lower for highly infectious diseases). We conduct a value-of-information analysis of knowing

  10. Value Co-creation and Co-innovation: Linking Networked Organisations and Customer Communities

    NASA Astrophysics Data System (ADS)

    Romero, David; Molina, Arturo

    Strategic networks such as Collaborative Networked Organisations (CNOs) and Virtual Customer Communities (VCCs) show a high potential as drivers of value co-creation and collaborative innovation in today’s Networking Era. Both look at the network structures as a source of jointly value creation and open innovation through access to new skills, knowledge, markets and technologies by sharing risk and integrating complementary competencies. This collaborative endeavour has proven to be able to enhance the adaptability and flexibility of CNOs and VCCs value creating systems in order to react in response to external drivers such as collaborative (business) opportunities. This paper presents a reference framework for creating interface networks, also known as ‘experience-centric networks’, as enablers for linking networked organisations and customer communities in order to support the establishment of user-driven and collaborative innovation networks.

  11. Autophagy links β-catenin and Smad signaling to promote epithelial-mesenchymal transition via upregulation of integrin linked kinase.

    PubMed

    Pang, Min; Wang, Hailong; Rao, Padmashree; Zhao, Ye; Xie, Jun; Cao, Qi; Wang, Yiping; Wang, Yuan Min; Lee, Vincent W; Alexander, Stephen I; Harris, David C H; Zheng, Guoping

    2016-07-01

    TGF-β1 induces epithelial-mesenchymal transition (EMT) and autophagy in a variety of cells. However, the role of autophagy in TGF-β1-induced EMT has not been clearly elucidated and the underlying mechanisms are unclear. In the present study, we found that TGF-β1 induced both autophagy and EMT in mouse tubular epithelial C1.1 cells. Inhibition of autophagy by 3-methyladenine or siRNA knockdown of Beclin 1 reduced TGF-β1-induced increase of vimentin and decreased E-cadherin expression. In contrast, rapamycin-associated enhancement of TGF-β1-induced autophagy increased EMT of C1.1 cells. Serum rescue inhibited autophagy followed by reversal of EMT. Blocking of autophagosome-lysosomal but not proteosomal degradation reduced the decrease of E-cadherin, demonstrating a role for autophagy in degradation of E-cadherin during EMT. Autophagy promoted the activation of Src and Src-associated phosphorylation of β-catenin at Y-654 leading to pY654-β-catenin/p-Smad2 complex formation. Chromatin immunoprecipitation assay demonstrated binding by the pY654-β-catenin/p-Smad2 complex to ILK promoter thus increasing ILK expression. Taken together, our results demonstrate that TGF-β1-induced autophagy links β-catenin and Smad signaling to promote EMT in C1.1 cells through a novel pY654-β-catenin/p-Smad2/ILK pathway. The pathway delineated links disruption of E-cadherin/β-catenin-mediated cell-cell contact to induction of EMT via upregulation of ILK. PMID:27177845

  12. Time Development in the Early History of Social Networks: Link Stabilization, Group Dynamics, and Segregation

    PubMed Central

    Bruun, Jesper; Bearden, Ian G.

    2014-01-01

    Studies of the time development of empirical networks usually investigate late stages where lasting connections have already stabilized. Empirical data on early network history are rare but needed for a better understanding of how social network topology develops in real life. Studying students who are beginning their studies at a university with no or few prior connections to each other offers a unique opportunity to investigate the formation and early development of link patterns and community structure in social networks. During a nine week introductory physics course, first year physics students were asked to identify those with whom they communicated about problem solving in physics during the preceding week. We use these students' self reports to produce time dependent student interaction networks. We investigate these networks to elucidate possible effects of different student attributes in early network formation. Changes in the weekly number of links show that while roughly half of all links change from week to week, students also reestablish a growing number of links as they progress through their first weeks of study. Using the Infomap community detection algorithm, we show that the networks exhibit community structure, and we use non-network student attributes, such as gender and end-of-course grade to characterize communities during their formation. Specifically, we develop a segregation measure and show that students structure themselves according to gender and pre-organized sections (in which students engage in problem solving and laboratory work), but not according to end-of-coure grade. Alluvial diagrams of consecutive weeks' communities show that while student movement between groups are erratic in the beginnning of their studies, they stabilize somewhat towards the end of the course. Taken together, the analyses imply that student interaction networks stabilize quickly and that students establish collaborations based on who is immediately

  13. RANK-mediated signaling network and cancer metastasis

    PubMed Central

    Chu, Chia-Yi Gina; Chung, Leland W. K.

    2014-01-01

    Cancer metastasis is highly inefficient and complex. Common features of metastatic cancer cells have been observed using cancer cell lines and genetically reconstituted mouse and human tumor xenograft models. These include cancer cell interaction with the tumor microenvironment, and the ability of cancer cells to sense extracellular stimuli and adapt to adverse growth conditions. This review summarizes the coordinated response of cancer cells to soluble growth factors, such as RANKL, by a unique forward feedback mechanism employing coordinated upregulation of RANKL and c-Met with downregulation of androgen receptor. The RANK-mediated signal network was found to drive epithelial to mesenchymal transition in prostate cancer cells, promote osteomimicry and the ability of prostate cancer cells to assume stem cell and neuroendocrine phenotypes, and confer the ability of prostate cancer cells to home to bone. Prostate cancer cells with activated RANK-mediated signal network were observed to recruit and even transform the non-tumorigenic prostate cancer cells to participate in bone and soft tissue colonization. The coordinated regulation of cancer cell invasion and metastasis by the forward feedback mechanism involving RANKL, c-Met, transcription factors and VEGF-neuropilin could offer new therapeutic opportunities to target prostate cancer bone and soft tissue metastases. PMID:24398859

  14. Control of cancer-related signal transduction networks

    NASA Astrophysics Data System (ADS)

    Albert, Reka

    2013-03-01

    Intra-cellular signaling networks are crucial to the maintenance of cellular homeostasis and for cell behavior (growth, survival, apoptosis, movement). Mutations or alterations in the expression of elements of cellular signaling networks can lead to incorrect behavioral decisions that could result in tumor development and/or the promotion of cell migration and metastasis. Thus, mitigation of the cascading effects of such dysregulations is an important control objective. My group at Penn State is collaborating with wet-bench biologists to develop and validate predictive models of various biological systems. Over the years we found that discrete dynamic modeling is very useful in molding qualitative interaction information into a predictive model. We recently demonstrated the effectiveness of network-based targeted manipulations on mitigating the disease T cell large granular lymphocyte (T-LGL) leukemia. The root of this disease is the abnormal survival of T cells which, after successfully fighting an infection, should undergo programmed cell death. We synthesized the relevant network of within-T-cell interactions from the literature, integrated it with qualitative knowledge of the dysregulated (abnormal) states of several network components, and formulated a Boolean dynamic model. The model indicated that the system possesses a steady state corresponding to the normal cell death state and a T-LGL steady state corresponding to the abnormal survival state. For each node, we evaluated the restorative manipulation consisting of maintaining the node in the state that is the opposite of its T-LGL state, e.g. knocking it out if it is overexpressed in the T-LGL state. We found that such control of any of 15 nodes led to the disappearance of the T-LGL steady state, leaving cell death as the only potential outcome from any initial condition. In four additional cases the probability of reaching the T-LGL state decreased dramatically, thus these nodes are also possible control

  15. Automated Measurement and Signaling Systems for the Transactional Network

    SciTech Connect

    Piette, Mary Ann; Brown, Richard; Price, Phillip; Page, Janie; Granderson, Jessica; Riess, David; Czarnecki, Stephen; Ghatikar, Girish; Lanzisera, Steven

    2013-12-31

    The Transactional Network Project is a multi-lab activity funded by the US Department of Energy?s Building Technologies Office. The project team included staff from Lawrence Berkeley National Laboratory, Pacific Northwest National Laboratory and Oak Ridge National Laboratory. The team designed, prototyped and tested a transactional network (TN) platform to support energy, operational and financial transactions between any networked entities (equipment, organizations, buildings, grid, etc.). PNNL was responsible for the development of the TN platform, with agents for this platform developed by each of the three labs. LBNL contributed applications to measure the whole-building electric load response to various changes in building operations, particularly energy efficiency improvements and demand response events. We also provide a demand response signaling agent and an agent for cost savings analysis. LBNL and PNNL demonstrated actual transactions between packaged rooftop units and the electric grid using the platform and selected agents. This document describes the agents and applications developed by the LBNL team, and associated tests of the applications.

  16. Joint transfer of time and frequency signals and multi-point synchronization via fiber network

    NASA Astrophysics Data System (ADS)

    Nan, Cheng; Wei, Chen; Qin, Liu; Dan, Xu; Fei, Yang; You-Zhen, Gui; Hai-Wen, Cai

    2016-01-01

    A system of jointly transferring time signals with a rate of 1 pulse per second (PPS) and frequency signals of 10 MHz via a dense wavelength division multiplex-based (DWDM) fiber is demonstrated in this paper. The noises of the fiber links are suppressed and compensated for by a controlled fiber delay line. A method of calibrating and characterizing time is described. The 1PPS is synchronized by feed-forward calibrating the fiber delays precisely. The system is experimentally examined via a 110 km spooled fiber in laboratory. The frequency stabilities of the user end with compensation are 1.8×10-14 at 1 s and 2.0×10-17 at 104 s average time. The calculated uncertainty of time synchronization is 13.1 ps, whereas the direct measurement of the uncertainty is 12 ps. Next, the frequency and 1PPS are transferred via a metropolitan area optical fiber network from one central site to two remote sites with distances of 14 km and 110 km. The frequency stabilities of 14 km link reach 3.0×10-14 averaged in 1 s and 1.4×10-17 in 104 s respectively; and the stabilities of 110 km link are 8.3×10-14 and 1.7×10-17, respectively. The accuracies of synchronization are estimated to be 12.3 ps for the 14 km link and 13.1 ps for the 110 km link, respectively. Project supported by the National Natural Science Foundation of China (Grant No. 61405227).

  17. Pattern recognition for electroencephalographic signals based on continuous neural networks.

    PubMed

    Alfaro-Ponce, M; Argüelles, A; Chairez, I

    2016-07-01

    This study reports the design and implementation of a pattern recognition algorithm to classify electroencephalographic (EEG) signals based on artificial neural networks (NN) described by ordinary differential equations (ODEs). The training method for this kind of continuous NN (CNN) was developed according to the Lyapunov theory stability analysis. A parallel structure with fixed weights was proposed to perform the classification stage. The pattern recognition efficiency was validated by two methods, a generalization-regularization and a k-fold cross validation (k=5). The classifier was applied on two different databases. The first one was made up by signals collected from patients suffering of epilepsy and it is divided in five different classes. The second database was made up by 90 single EEG trials, divided in three classes. Each class corresponds to a different visual evoked potential. The pattern recognition algorithm achieved a maximum correct classification percentage of 97.2% using the information of the entire database. This value was similar to some results previously reported when this database was used for testing pattern classification. However, these results were obtained when only two classes were considered for the testing. The result reported in this study used the whole set of signals (five different classes). In comparison with similar pattern recognition methods that even considered less number of classes, the proposed CNN proved to achieve the same or even better correct classification results. PMID:27131469

  18. The RalGEF-Ral Effector Signaling Network

    PubMed Central

    Neel, Nicole F.; Martin, Timothy D.; Stratford, Jeran K.; Zand, Tanya P.; Reiner, David J.; Der, Channing J.

    2011-01-01

    The high frequency of RAS mutations in human cancers (33%) has stimulated intense interest in the development of anti-Ras inhibitors for cancer therapy. Currently, the major focus of these efforts is centered on inhibitors of components involved in Ras downstream effector signaling. In particular, more than 40 inhibitors of the Raf-MEK-ERK mitogen-activated protein kinase cascade and phosphoinositide 3-kinase-AKT-mTOR effector signaling networks are currently under clinical evaluation. However, these efforts are complicated by the fact that Ras can utilize at least 9 additional functionally distinct effectors, with at least 3 additional effectors with validated roles in Ras-mediated oncogenesis. Of these, the guanine nucleotide exchange factors of the Ras-like (Ral) small GTPases (RalGEFs) have emerged as important effectors of mutant Ras in pancreatic, colon, and other cancers. In this review, we summarize the evidence for the importance of this effector pathway in cancer and discuss possible directions for therapeutic inhibition of aberrant Ral activation and signaling. PMID:21779498

  19. The optical antenna system design research on earth integrative network laser link in the future

    NASA Astrophysics Data System (ADS)

    Liu, Xianzhu; Fu, Qiang; He, Jingyi

    2014-11-01

    Earth integrated information network can be real-time acquisition, transmission and processing the spatial information with the carrier based on space platforms, such as geostationary satellites or in low-orbit satellites, stratospheric balloons or unmanned and manned aircraft, etc. It is an essential infrastructure for China to constructed earth integrated information network. Earth integrated information network can not only support the highly dynamic and the real-time transmission of broadband down to earth observation, but the reliable transmission of the ultra remote and the large delay up to the deep space exploration, as well as provide services for the significant application of the ocean voyage, emergency rescue, navigation and positioning, air transportation, aerospace measurement or control and other fields.Thus the earth integrated information network can expand the human science, culture and productive activities to the space, ocean and even deep space, so it is the global research focus. The network of the laser communication link is an important component and the mean of communication in the earth integrated information network. Optimize the structure and design the system of the optical antenna is considered one of the difficulty key technologies for the space laser communication link network. Therefore, this paper presents an optical antenna system that it can be used in space laser communication link network.The antenna system was consisted by the plurality mirrors stitched with the rotational paraboloid as a substrate. The optical system structure of the multi-mirror stitched was simulated and emulated by the light tools software. Cassegrain form to be used in a relay optical system. The structural parameters of the relay optical system was optimized and designed by the optical design software of zemax. The results of the optimal design and simulation or emulation indicated that the antenna system had a good optical performance and a certain

  20. Space Link Extension Protocol Emulation for High-Throughput, High-Latency Network Connections

    NASA Technical Reports Server (NTRS)

    Tchorowski, Nicole; Murawski, Robert

    2014-01-01

    New space missions require higher data rates and new protocols to meet these requirements. These high data rate space communication links push the limitations of not only the space communication links, but of the ground communication networks and protocols which forward user data to remote ground stations (GS) for transmission. The Consultative Committee for Space Data Systems, (CCSDS) Space Link Extension (SLE) standard protocol is one protocol that has been proposed for use by the NASA Space Network (SN) Ground Segment Sustainment (SGSS) program. New protocol implementations must be carefully tested to ensure that they provide the required functionality, especially because of the remote nature of spacecraft. The SLE protocol standard has been tested in the NASA Glenn Research Center's SCENIC Emulation Lab in order to observe its operation under realistic network delay conditions. More specifically, the delay between then NASA Integrated Services Network (NISN) and spacecraft has been emulated. The round trip time (RTT) delay for the continental NISN network has been shown to be up to 120ms; as such the SLE protocol was tested with network delays ranging from 0ms to 200ms. Both a base network condition and an SLE connection were tested with these RTT delays, and the reaction of both network tests to the delay conditions were recorded. Throughput for both of these links was set at 1.2Gbps. The results will show that, in the presence of realistic network delay, the SLE link throughput is significantly reduced while the base network throughput however remained at the 1.2Gbps specification. The decrease in SLE throughput has been attributed to the implementation's use of blocking calls. The decrease in throughput is not acceptable for high data rate links, as the link requires constant data a flow in order for spacecraft and ground radios to stay synchronized, unless significant data is queued a the ground station. In cases where queuing the data is not an option

  1. Microphase-separated structures within randomly end-linked copolymer networks

    NASA Astrophysics Data System (ADS)

    Zeng, Di; Hayward, Ryan

    Self-assembly within randomly cross-linked or end-linked copolymer networks provides a robust method to generate co-continuous nanometer-scale structures. Here, we investigate self-assembly within copolymer networks prepared by end linking of several different pairs of telechelic polymers in a common solvent. For sufficiently high levels of immiscibility between the constituent polymers, removal of solvent leads to microphase separation into disordered nanoscale structures. Using a variety of characterization methods, including transmission electron microscopy, small-angle X-ray scattering, differential scanning calorimetry, and dynamic mechanical analysis, we find that these networks exhibit co-continuous morphologies over a wide range of volume fraction of the two components, with a characteristic length scale that can be tuned by adjusting the molecular weight of the starting polymers.

  2. Remote facility sharing with ATM networks [PC based ATM Link Delay Simulator (LDS)]. Final report

    SciTech Connect

    Kung, H. T.

    2001-06-01

    The ATM Link Delay Simulator (LDS) adds propagation delay to the ATM link on which it is installed, to allow control of link propagation delay in network protocol experiments simulating an adjustable piece of optical fiber. Our LDS simulates a delay of between 1.5 and 500 milliseconds and is built with commodity PC hardware, only the ATM network interface card is not generally available. Our implementation is special in that it preserves the exact spacing of ATM data cells a feature that requires sustained high performance. Our implementation shows that applications demanding sustained high performance are possible on commodity PC hardware. This illustrates the promise that PC hardware has for adaptability to demanding specialized testing of high speed network.

  3. TNF-insulin crosstalk at the transcription factor GATA6 is revealed by a model that links signaling and transcriptomic data tensors.

    PubMed

    Chitforoushzadeh, Zeinab; Ye, Zi; Sheng, Ziran; LaRue, Silvia; Fry, Rebecca C; Lauffenburger, Douglas A; Janes, Kevin A

    2016-01-01

    Signal transduction networks coordinate transcriptional programs activated by diverse extracellular stimuli, such as growth factors and cytokines. Cells receive multiple stimuli simultaneously, and mapping how activation of the integrated signaling network affects gene expression is a challenge. We stimulated colon adenocarcinoma cells with various combinations of the cytokine tumor necrosis factor (TNF) and the growth factors insulin and epidermal growth factor (EGF) to investigate signal integration and transcriptional crosstalk. We quantitatively linked the proteomic and transcriptomic data sets by implementing a structured computational approach called tensor partial least squares regression. This statistical model accurately predicted transcriptional signatures from signaling arising from single and combined stimuli and also predicted time-dependent contributions of signaling events. Specifically, the model predicted that an early-phase, AKT-associated signal downstream of insulin repressed a set of transcripts induced by TNF. Through bioinformatics and cell-based experiments, we identified the AKT-repressed signal as glycogen synthase kinase 3 (GSK3)-catalyzed phosphorylation of Ser(37) on the long form of the transcription factor GATA6. Phosphorylation of GATA6 on Ser(37) promoted its degradation, thereby preventing GATA6 from repressing transcripts that are induced by TNF and attenuated by insulin. Our analysis showed that predictive tensor modeling of proteomic and transcriptomic data sets can uncover pathway crosstalk that produces specific patterns of gene expression in cells receiving multiple stimuli. PMID:27273097

  4. Full-duplex fiber-wireless link with 40 Gbit/s 16-QAM signals for alternative wired and wireless accesses based on homodyne/heterodyne coherent detection

    NASA Astrophysics Data System (ADS)

    Zhang, Ruijiao; Ma, Jianxin; Wang, Zhao; Zhang, Junjie; Li, Yanjie; Zheng, Guoli; Liu, Wen; Yu, Jianguo; Zhang, Qi; Wang, Qin; Liu, Renhao

    2014-06-01

    A novel full-duplex fiber-wireless link with 40 Gbit/s 16-ary quadrature amplitude modulation (QAM) signals is proposed to provide alternative wired and wireless accesses for the user terminals. In the central station (CS), the downstream signal for wired and wireless accesses is beared onto the CW laser source via an optical I/Q modulator to realize the QAM modulation. At the hybrid optical network unit (HONU), a tunable laser is used to provide coherent optical local oscillator for homo-/heterodyne beating to coherently down-convert the baseband optical signal to the baseband electrical one for wired access or to the mm-wave one for wireless access according to the requirement of the user terminals. Simultaneously, the lightwave from the tunable laser is also used as the uplink optical carrier for either wired or wireless access, and is modulated colorlessly by the baseband or mm-wave signal of the uplink alternatively. After filtering, only one tone carrying the uplink signal is transmitted back to the CS even for the wireless access. The theoretical analysis and simulation results show that our proposed full-duplex link for the alternative wired and wireless accesses maintains good performance even when the transmission link with standard single mode fiber (SSMF) is extended to 30 km.

  5. Design principles of nuclear receptor signaling: how complex networking improves signal transduction

    PubMed Central

    Kolodkin, Alexey N; Bruggeman, Frank J; Plant, Nick; Moné, Martijn J; Bakker, Barbara M; Campbell, Moray J; van Leeuwen, Johannes P T M; Carlberg, Carsten; Snoep, Jacky L; Westerhoff, Hans V

    2010-01-01

    The topology of nuclear receptor (NR) signaling is captured in a systems biological graphical notation. This enables us to identify a number of ‘design' aspects of the topology of these networks that might appear unnecessarily complex or even functionally paradoxical. In realistic kinetic models of increasing complexity, calculations show how these features correspond to potentially important design principles, e.g.: (i) cytosolic ‘nuclear' receptor may shuttle signal molecules to the nucleus, (ii) the active export of NRs may ensure that there is sufficient receptor protein to capture ligand at the cytoplasmic membrane, (iii) a three conveyor belts design dissipating GTP-free energy, greatly aids response, (iv) the active export of importins may prevent sequestration of NRs by importins in the nucleus and (v) the unspecific nature of the nuclear pore may ensure signal-flux robustness. In addition, the models developed are suitable for implementation in specific cases of NR-mediated signaling, to predict individual receptor functions and differential sensitivity toward physiological and pharmacological ligands. PMID:21179018

  6. Signaling network of lipids as a comprehensive scaffold for omics data integration in sputum of COPD patients.

    PubMed

    Azimzadeh Jamalkandi, Sadegh; Mirzaie, Mehdi; Jafari, Mohieddin; Mehrani, Hossein; Shariati, Parvin; Khodabandeh, Mahvash

    2015-10-01

    Chronic obstructive pulmonary disease (COPD) is a heterogeneous and progressive inflammatory condition that has been linked to the dysregulation of many metabolic pathways including lipid biosynthesis. How lipid metabolism could affect disease progression in smokers with COPD remains unclear. We cross-examined the transcriptomics, proteomics, metabolomics, and phenomics data available on the public domain to elucidate the mechanisms by which lipid metabolism is perturbed in COPD. We reconstructed a sputum lipid COPD (SpLiCO) signaling network utilizing active/inactive, and functional/dysfunctional lipid-mediated signaling pathways to explore how lipid-metabolism could promote COPD pathogenesis in smokers. SpLiCO was further utilized to investigate signal amplifiers, distributers, propagators, feed-forward and/or -back loops that link COPD disease severity and hypoxia to disruption in the metabolism of sphingolipids, fatty acids and energy. Also, hypergraph analysis and calculations for dependency of molecules identified several important nodes in the network with modular regulatory and signal distribution activities. Our systems-based analyses indicate that arachidonic acid is a critical and early signal distributer that is upregulated by the sphingolipid signaling pathway in COPD, while hypoxia plays a critical role in the elevated dependency to glucose as a major energy source. Integration of SpLiCo and clinical data shows a strong association between hypoxia and the upregulation of sphingolipids in smokers with emphysema, vascular disease, hypertension and those with increased risk of lung cancer. PMID:26215076

  7. Linking social and pathogen transmission networks using microbial genetics in giraffe (Giraffa camelopardalis).

    PubMed

    VanderWaal, Kimberly L; Atwill, Edward R; Isbell, Lynne A; McCowan, Brenda

    2014-03-01

    Although network analysis has drawn considerable attention as a promising tool for disease ecology, empirical research has been hindered by limitations in detecting the occurrence of pathogen transmission (who transmitted to whom) within social networks. Using a novel approach, we utilize the genetics of a diverse microbe, Escherichia coli, to infer where direct or indirect transmission has occurred and use these data to construct transmission networks for a wild giraffe population (Giraffe camelopardalis). Individuals were considered to be a part of the same transmission chain and were interlinked in the transmission network if they shared genetic subtypes of E. coli. By using microbial genetics to quantify who transmits to whom independently from the behavioural data on who is in contact with whom, we were able to directly investigate how the structure of contact networks influences the structure of the transmission network. To distinguish between the effects of social and environmental contact on transmission dynamics, the transmission network was compared with two separate contact networks defined from the behavioural data: a social network based on association patterns, and a spatial network based on patterns of home-range overlap among individuals. We found that links in the transmission network were more likely to occur between individuals that were strongly linked in the social network. Furthermore, individuals that had more numerous connections or that occupied 'bottleneck' positions in the social network tended to occupy similar positions in the transmission network. No similar correlations were observed between the spatial and transmission networks. This indicates that an individual's social network position is predictive of transmission network position, which has implications for identifying individuals that function as super-spreaders or transmission bottlenecks in the population. These results emphasize the importance of association patterns in

  8. Network Analysis of Epidermal Growth Factor Signaling using Integrated Genomic, Proteomic and Phosphorylation Data

    SciTech Connect

    Waters, Katrina M.; Liu, Tao; Quesenberry, Ryan D.; Willse, Alan R.; Bandyopadhyay, Somnath; Kathmann, Loel E.; Weber, Thomas J.; Smith, Richard D.; Wiley, H. S.; Thrall, Brian D.

    2012-03-29

    To understand how integration of multiple data types can help decipher cellular responses at the systems level, we analyzed the mitogenic response of human mammary epithelial cells to epidermal growth factor (EGF) using whole genome microarrays, mass spectrometry-based proteomics and large-scale western blots with over 1000 antibodies. A time course analysis revealed significant differences in the expression of 3172 genes and 596 proteins, including protein phosphorylation changes measured by western blot. Integration of these disparate data types showed that each contributed qualitatively different components to the observed cell response to EGF and that varying degrees of concordance in gene expression and protein abundance measurements could be linked to specific biological processes. Networks inferred from individual data types were relatively limited, whereas networks derived from the integrated data recapitulated the known major cellular responses to EGF and exhibited more highly connected signaling nodes than networks derived from any individual dataset. While cell cycle regulatory pathways were altered as anticipated, we found the most robust response to mitogenic concentrations of EGF was induction of matrix metalloprotease cascades, highlighting the importance of the EGFR system as a regulator of the extracellular environment. These results demonstrate the value of integrating multiple levels of biological information to more accurately reconstruct networks of cellular response.

  9. Disruption of O-linked N-Acetylglucosamine Signaling Induces ER Stress and β Cell Failure.

    PubMed

    Alejandro, Emilyn U; Bozadjieva, Nadejda; Kumusoglu, Doga; Abdulhamid, Sarah; Levine, Hannah; Haataja, Leena; Vadrevu, Suryakiran; Satin, Leslie S; Arvan, Peter; Bernal-Mizrachi, Ernesto

    2015-12-22

    Nutrient levels dictate the activity of O-linked N-acetylglucosamine transferase (OGT) to regulate O-GlcNAcylation, a post-translational modification mechanism to "fine-tune" intracellular signaling and metabolic status. However, the requirement of O-GlcNAcylation for maintaining glucose homeostasis by regulating pancreatic β cell mass and function is unclear. Here, we reveal that mice lacking β cell OGT (βOGT-KO) develop diabetes and β cell failure. βOGT-KO mice demonstrated increased ER stress and distended ER architecture, and these changes ultimately caused the loss of β cell mass due to ER-stress-induced apoptosis and decreased proliferation. Akt1/2 signaling was also dampened in βOGT-KO islets. The mechanistic role of these processes was demonstrated by rescuing the phenotype of βOGT-KO mice with concomitant Chop gene deletion or genetic reconstitution of Akt2. These findings identify OGT as a regulator of β cell mass and function and provide a direct link between O-GlcNAcylation and β cell survival by regulation of ER stress responses and modulation of Akt1/2 signaling. PMID:26673325

  10. The expanding regulatory network of STING-mediated signaling.

    PubMed

    Surpris, Guy; Poltorak, Alexander

    2016-08-01

    The identification and characterization of DNA-sensing pathways has been a subject of intensive investigation for the last decade. This interest, in part, is supported by the fact that the main outcome of DNA-responses is production of type I interferon (IFN-I), which, if produced in excessive amounts, leads to various pathologies. STING (stimulator of interferon genes) is positioned in the center of these responses and is activated either via direct sensing of second messengers or via interaction with upstream sensors of dsDNA. STING mediates responses to pathogens as well as host-derived DNA and is, therefore, linked to various autoimmune diseases, cancer predisposition and ageing. Recent mouse models of DNA damage showed the adaptor STING to be crucial for heightened resting levels of IFN-I. In this review, we will focus on recent advances in understanding the regulation of STING-signaling and identification of its novel components. PMID:27414485

  11. Is the kinetoplast DNA a percolating network of linked rings at its critical point?

    NASA Astrophysics Data System (ADS)

    Michieletto, Davide; Marenduzzo, Davide; Orlandini, Enzo

    2015-05-01

    In this work we present a computational study of the kinetoplast genome, modelled as a large number of semiflexible unknotted loops, which are allowed to link with each other. As the DNA density increases, the systems shows a percolation transition between a gas of unlinked rings and a network of linked loops which spans the whole system. Close to the percolation transition, we find that the mean valency of the network, i.e. the average number of loops which are linked to any one loop, is around three, as found experimentally for the kinetoplast DNA (kDNA). Even more importantly, by simulating the digestion of the network by a restriction enzyme, we show that the distribution of oligomers, i.e. structures formed by a few loops which remain linked after digestion, quantitatively matches experimental data obtained from gel electrophoresis, provided that the density is, once again, close to the percolation transition. With respect to previous work, our analysis builds on a reduced number of assumptions, yet can still fully explain the experimental data. Our findings suggest that the kDNA can be viewed as a network of linked loops positioned very close to the percolation transition, and we discuss the possible biological implications of this remarkable fact.

  12. Maintaining communication link based on AODV routing protocol in mobile robot networks

    NASA Astrophysics Data System (ADS)

    Hu, Hui; Jiang, Hong

    2007-12-01

    Wired computer networks are vital in modern life. However, these networks are extremely vulnerable to disaster or attack in emergency situations. Therefore, how to maintain communication link under emergency situations is very important. In this paper, we utilize a series of autonomous mobile slave robots which follow behind the lead robot and automatically stop where needed to maintain an ad hoc network for guaranteeing a link between the lead robot and its remote monitor/control station. To accomplish this target, an efficient communication protocol limitation mobile robots broadcast based on AODV (LMRB-AODV) is proposed for deployment in multi-robot system. After then the lead robot could carry service traffics to the monitor station under emergency situations through the communication link. At any instance, the lead robot has the ability to reclaim the relay robot(s) which are unneeded in the network to rejoin the convoy behind the lead robot and use it to extend the range of wireless communication when the radio frequency (RF) shortcuts are detected by the lead robot. All relay deployment and reclaiming strategy functions occur without the operator's involvement. Finally, we provide a comparative study of their performance in a number of different simulation environments. The results show that the proposed scheme is very efficient in maintaining communication link in wireless network.

  13. Space Link Extension (SLE) Emulation for High-Throughput Network Communication

    NASA Technical Reports Server (NTRS)

    Murawski, Robert W.; Tchorowski, Nicole; Golden, Bert

    2014-01-01

    As the data rate requirements for space communications increases, significant stress is placed not only on the wireless satellite communication links, but also on the ground networks which forward data from end-users to remote ground stations. These wide area network (WAN) connections add delay and jitter to the end-to-end satellite communication link, effects which can have significant impacts on the wireless communication link. It is imperative that any ground communication protocol can react to these effects such that the ground network does not become a bottleneck in the communication path to the satellite. In this paper, we present our SCENIC Emulation Lab testbed which was developed to test the CCSDS SLE protocol implementations proposed for use on future NASA communication networks. Our results show that in the presence of realistic levels of network delay, high-throughput SLE communication links can experience significant data rate throttling. Based on our observations, we present some insight into why this data throttling happens, and trace the probable issue back to non-optimal blocking communication which is sup-ported by the CCSDS SLE API recommended practices. These issues were presented as well to the SLE implementation developers which, based on our reports, developed a new release for SLE which we show fixes the SLE blocking issue and greatly improves the protocol throughput. In this paper, we also discuss future developments for our end-to-end emulation lab and how these improvements can be used to develop and test future space communication technologies.

  14. Link Prediction in Criminal Networks: A Tool for Criminal Intelligence Analysis

    PubMed Central

    Berlusconi, Giulia; Calderoni, Francesco; Parolini, Nicola; Verani, Marco; Piccardi, Carlo

    2016-01-01

    The problem of link prediction has recently received increasing attention from scholars in network science. In social network analysis, one of its aims is to recover missing links, namely connections among actors which are likely to exist but have not been reported because data are incomplete or subject to various types of uncertainty. In the field of criminal investigations, problems of incomplete information are encountered almost by definition, given the obvious anti-detection strategies set up by criminals and the limited investigative resources. In this paper, we work on a specific dataset obtained from a real investigation, and we propose a strategy to identify missing links in a criminal network on the basis of the topological analysis of the links classified as marginal, i.e. removed during the investigation procedure. The main assumption is that missing links should have opposite features with respect to marginal ones. Measures of node similarity turn out to provide the best characterization in this sense. The inspection of the judicial source documents confirms that the predicted links, in most instances, do relate actors with large likelihood of co-participation in illicit activities. PMID:27104948

  15. Link Prediction in Criminal Networks: A Tool for Criminal Intelligence Analysis.

    PubMed

    Berlusconi, Giulia; Calderoni, Francesco; Parolini, Nicola; Verani, Marco; Piccardi, Carlo

    2016-01-01

    The problem of link prediction has recently received increasing attention from scholars in network science. In social network analysis, one of its aims is to recover missing links, namely connections among actors which are likely to exist but have not been reported because data are incomplete or subject to various types of uncertainty. In the field of criminal investigations, problems of incomplete information are encountered almost by definition, given the obvious anti-detection strategies set up by criminals and the limited investigative resources. In this paper, we work on a specific dataset obtained from a real investigation, and we propose a strategy to identify missing links in a criminal network on the basis of the topological analysis of the links classified as marginal, i.e. removed during the investigation procedure. The main assumption is that missing links should have opposite features with respect to marginal ones. Measures of node similarity turn out to provide the best characterization in this sense. The inspection of the judicial source documents confirms that the predicted links, in most instances, do relate actors with large likelihood of co-participation in illicit activities. PMID:27104948

  16. The Yeast Sks1p Kinase Signaling Network Regulates Pseudohyphal Growth and Glucose Response

    PubMed Central

    Johnson, Cole; Kweon, Hye Kyong; Sheidy, Daniel; Shively, Christian A.; Mellacheruvu, Dattatreya; Nesvizhskii, Alexey I.; Andrews, Philip C.; Kumar, Anuj

    2014-01-01

    The yeast Saccharomyces cerevisiae undergoes a dramatic growth transition from its unicellular form to a filamentous state, marked by the formation of pseudohyphal filaments of elongated and connected cells. Yeast pseudohyphal growth is regulated by signaling pathways responsive to reductions in the availability of nitrogen and glucose, but the molecular link between pseudohyphal filamentation and glucose signaling is not fully understood. Here, we identify the glucose-responsive Sks1p kinase as a signaling protein required for pseudohyphal growth induced by nitrogen limitation and coupled nitrogen/glucose limitation. To identify the Sks1p signaling network, we applied mass spectrometry-based quantitative phosphoproteomics, profiling over 900 phosphosites for phosphorylation changes dependent upon Sks1p kinase activity. From this analysis, we report a set of novel phosphorylation sites and highlight Sks1p-dependent phosphorylation in Bud6p, Itr1p, Lrg1p, Npr3p, and Pda1p. In particular, we analyzed the Y309 and S313 phosphosites in the pyruvate dehydrogenase subunit Pda1p; these residues are required for pseudohyphal growth, and Y309A mutants exhibit phenotypes indicative of impaired aerobic respiration and decreased mitochondrial number. Epistasis studies place SKS1 downstream of the G-protein coupled receptor GPR1 and the G-protein RAS2 but upstream of or at the level of cAMP-dependent PKA. The pseudohyphal growth and glucose signaling transcription factors Flo8p, Mss11p, and Rgt1p are required to achieve wild-type SKS1 transcript levels. SKS1 is conserved, and deletion of the SKS1 ortholog SHA3 in the pathogenic fungus Candida albicans results in abnormal colony morphology. Collectively, these results identify Sks1p as an important regulator of filamentation and glucose signaling, with additional relevance towards understanding stress-responsive signaling in C. albicans. PMID:24603354

  17. A More Accurate Characterization of UH-60A Pitch Link Loads Using Neural Networks

    NASA Technical Reports Server (NTRS)

    Kottapalli, Sesi; Aiken, Ed (Technical Monitor)

    1998-01-01

    A more accurate, neural-network-based characterization of the full-scale UH-60A maximum, vibratory pitch link loads (MXVPLL) was obtained. The MXVPLL data were taken from the NASA/Army UH-60A Airloads Program flight test database. This database includes data from level flights, and both simple and "complex" maneuvers. In the present context, a complex maneuver was defined as one which involved simultaneous, non-zero aircraft angle-of-bank (associated with turns) and aircraft pitch-rate (associated with a pull-up or a push-over). The present approach combines physical insight followed by the neural networks application. Since existing load factors do not represent the above-defined complex maneuver, a new, combined load factor ('p resent-load-factor') was introduced. A back-propagation type of neural network with five inputs and one output was used to characterize the UH-60A MXVPLL. The neural network inputs were as follows: rotor advance ratio, aircraft gross weight, rotor RPM, air density ratio, and the present-load-factor. The neural network output was the maximum, vibratory pitch link load (MXVPLL). It was shown that a more accurate characterization of the full-scale flight test pitch link loads can be obtained by combining physical insight with a neural-network-based approach.

  18. Seismic Signal Classification with Offshore/Amphibious Networks Using an Artificial Neural Network

    NASA Astrophysics Data System (ADS)

    Williams, M. C.; Trehu, A. M.

    2011-12-01

    The amphibious Central Oregon Locked Zone Array (COLZA) of seismic stations was deployed from 2007-2009 to record earthquakes occurring in the seismogenic zone offshore central Oregon. This array included two year-long deployments of ocean bottom seismometers (OBS's) from the NSF OBSIP. In addition to local and distant earthquakes, the OBS array recorded thousands of impulsive local signals, which are not easily filtered out by a standard STA/LTA detection algorithm. Many of these signals are likely of biological origin (informally referred to as "bio-bumps"). These signals have a wide range of amplitudes, can mask local earthquake phase arrivals, and make automatic detection more difficult. We show that signal characteristics derived from 3-component seismic data at each station can be used to filter out event detections that are unlikely to be earthquake-generated. A decision-making algorithm is run using a joint set of signal characteristics to identify possible local events and classify detections that are likely to be "bumps". We present results on the effectiveness of this classification technique using various combinations of input parameters applied to the onshore/offshore COLZA array dataset. The classification algorithm is a multilayer perceptron (MLP) artificial neural network, trained through backpropagation using human-identified examples of both earthquake phases and impulsive "bumps". The effectiveness of a neural network is highly dependent on the data space consisting of the inputs calculated for each signal, which represent its main characteristics and differentiate it from other events. As inputs to the neural network, for each event detection, in addition to the STA/LTA value, we determine three signal characteristics from 3-component waveform data: the variance of the power cepstrum calculated from a portion of the signal spectrum, the rectilinearity of particle motion, and the ratio of particle motion orthogonal to the principle direction of

  19. Network coding based joint signaling and dynamic bandwidth allocation scheme for inter optical network unit communication in passive optical networks

    NASA Astrophysics Data System (ADS)

    Wei, Pei; Gu, Rentao; Ji, Yuefeng

    2014-06-01

    As an innovative and promising technology, network coding has been introduced to passive optical networks (PON) in recent years to support inter optical network unit (ONU) communication, yet the signaling process and dynamic bandwidth allocation (DBA) in PON with network coding (NC-PON) still need further study. Thus, we propose a joint signaling and DBA scheme for efficiently supporting differentiated services of inter ONU communication in NC-PON. In the proposed joint scheme, the signaling process lays the foundation to fulfill network coding in PON, and it can not only avoid the potential threat to downstream security in previous schemes but also be suitable for the proposed hybrid dynamic bandwidth allocation (HDBA) scheme. In HDBA, a DBA cycle is divided into two sub-cycles for applying different coding, scheduling and bandwidth allocation strategies to differentiated classes of services. Besides, as network traffic load varies, the entire upstream transmission window for all REPORT messages slides accordingly, leaving the transmission time of one or two sub-cycles to overlap with the bandwidth allocation calculation time at the optical line terminal (the OLT), so that the upstream idle time can be efficiently eliminated. Performance evaluation results validate that compared with the existing two DBA algorithms deployed in NC-PON, HDBA demonstrates the best quality of service (QoS) support in terms of delay for all classes of services, especially guarantees the end-to-end delay bound of high class services. Specifically, HDBA can eliminate queuing delay and scheduling delay of high class services, reduce those of lower class services by at least 20%, and reduce the average end-to-end delay of all services over 50%. Moreover, HDBA also achieves the maximum delay fairness between coded and uncoded lower class services, and medium delay fairness for high class services.

  20. Phytochrome and retrograde signalling pathways converge to antagonistically regulate a light-induced transcriptional network

    PubMed Central

    Martín, Guiomar; Leivar, Pablo; Ludevid, Dolores; Tepperman, James M.; Quail, Peter H.; Monte, Elena

    2016-01-01

    Plastid-to-nucleus retrograde signals emitted by dysfunctional chloroplasts impact photomorphogenic development, but the molecular link between retrograde- and photosensory-receptor signalling has remained unclear. Here, we show that the phytochrome and retrograde signalling (RS) pathways converge antagonistically to regulate the expression of the nuclear-encoded transcription factor GLK1, a key regulator of a light-induced transcriptional network central to photomorphogenesis. GLK1 gene transcription is directly repressed by PHYTOCHROME-INTERACTING FACTOR (PIF)-class bHLH transcription factors in darkness, but light-activated phytochrome reverses this activity, thereby inducing expression. Conversely, we show that retrograde signals repress this induction by a mechanism independent of PIF mediation. Collectively, our data indicate that light at moderate levels acts through the plant's nuclear-localized sensory-photoreceptor system to induce appropriate photomorphogenic development, but at excessive levels, sensed through the separate plastid-localized RS system, acts to suppress such development, thus providing a mechanism for protection against photo-oxidative damage by minimizing the tissue exposure to deleterious radiation. PMID:27150909

  1. Phytochrome and retrograde signalling pathways converge to antagonistically regulate a light-induced transcriptional network.

    PubMed

    Martín, Guiomar; Leivar, Pablo; Ludevid, Dolores; Tepperman, James M; Quail, Peter H; Monte, Elena

    2016-01-01

    Plastid-to-nucleus retrograde signals emitted by dysfunctional chloroplasts impact photomorphogenic development, but the molecular link between retrograde- and photosensory-receptor signalling has remained unclear. Here, we show that the phytochrome and retrograde signalling (RS) pathways converge antagonistically to regulate the expression of the nuclear-encoded transcription factor GLK1, a key regulator of a light-induced transcriptional network central to photomorphogenesis. GLK1 gene transcription is directly repressed by PHYTOCHROME-INTERACTING FACTOR (PIF)-class bHLH transcription factors in darkness, but light-activated phytochrome reverses this activity, thereby inducing expression. Conversely, we show that retrograde signals repress this induction by a mechanism independent of PIF mediation. Collectively, our data indicate that light at moderate levels acts through the plant's nuclear-localized sensory-photoreceptor system to induce appropriate photomorphogenic development, but at excessive levels, sensed through the separate plastid-localized RS system, acts to suppress such development, thus providing a mechanism for protection against photo-oxidative damage by minimizing the tissue exposure to deleterious radiation. PMID:27150909

  2. Evaluating link-state update triggers in wavelength-routed networks

    NASA Astrophysics Data System (ADS)

    Shen, Shu; Xiao, Gaoxi; Cheng, Tee Hiang

    2005-02-01

    In this paper, we evaluate link-state update triggers in wavelength-routed networks. We consider two popular triggers, namely the Absolute Threshold Trigger and the Relative Threshold Trigger. The blocking performance of the two triggers is confirmed to be highly dependent on traffic load. Moreover, it is observed that under light traffic load, blocking performance degrades significantly once the threshold is shifted away from advertising every single link state change immediately. We expect that the above observation would be of significant importance and would impose a critical challenge to the future development of link-state update methods.

  3. Linking MLL and the HGF-MET signaling pathway in liver cancer.

    PubMed

    Marquardt, Jens U; Thorgeirsson, Snorri S

    2013-07-01

    Mixed-lineage leukemia (MLL; also known as myeloid/lymphoid), the human homolog of trithorax in Drosophila, is a transcriptional coactivator that plays an essential role during early development and hematopoiesis. Furthermore, MLL is critically involved in the epigenetic regulation of cell cycle, senescence, DNA damage, and stem cell self-renewal. Chromosomal aberrations of MLL in acute leukemias are well documented, but the role of this gene in solid malignancies remains unclear. In this issue of the JCI, Takeda et al. describe a novel epigenetic link between MLL and the HGF-MET signaling pathway conferring invasive and metastatic properties to hepatocellular carcinoma cells. PMID:23934122

  4. An intimate link: two-component signal transduction systems and metal transport systems in bacteria

    PubMed Central

    Singh, Kamna; Senadheera, Dilani B; Cvitkovitch, Dennis G

    2014-01-01

    Bacteria have evolved various strategies to contend with high concentrations of environmental heavy metal ions for rapid, adaptive responses to maintain cell viability. Evidence gathered in the past two decades suggests that bacterial two-component signal transduction systems (TCSTSs) are intimately involved in monitoring cation accumulation, and can regulate the expression of related metabolic and virulence genes to elicit adaptive responses to changes in the concentration of these ions. Using examples garnered from recent studies, we summarize the cross-regulatory relationships between metal ions and TCSTSs. We present evidence of how bacterial TCSTSs modulate metal ion homeostasis and also how metal ions, in turn, function to control the activities of these signaling systems linked with bacterial survival and virulence. PMID:25437189

  5. The BK channel: a vital link between cellular calcium and electrical signaling.

    PubMed

    Rothberg, Brad S

    2012-12-01

    Large-conductance Ca²⁺-activated K⁺ channels (BK channels) constitute an key physiological link between cellular Ca²⁺ signaling and electrical signaling at the plasma membrane. Thus these channels are critical to the control of action potential firing and neurotransmitter release in several types of neurons, as well as the dynamic control of smooth muscle tone in resistance arteries, airway, and bladder. Recent advances in our understanding of K⁺ channel structure and function have led to new insight toward the molecular mechanisms of opening and closing (gating) of these channels. Here we will focus on mechanisms of BK channel gating by Ca²⁺, transmembrane voltage, and auxiliary subunit proteins. PMID:22996175

  6. Effect of link margin and frequency granularity on the performance of a flexgrid optical network.

    PubMed

    Mitra, Abhijit; Lord, Andrew; Kar, Subrat; Wright, Paul

    2014-01-13

    We show how dynamically adjustable modulation formats can be used to reduce link margins in flexgrid networks, reverting to lower order QAM due to reduced OSNR, if ageing occurs. Spectral savings amount to as much as 63% gain in capacity across a network using 64QAM with a fine frequency granularity of 6.25 GHz, with variable baud rate transponder. Further, a fixed baud rate, demand multiplexed transponder with adaptive modulation has been suggested. These transponders provide twice as much network capacity as compared to widely used fixed baud rate transponders operating at fixed grid of 50 GHz. PMID:24514963

  7. Suppression of optical beat interference-noise in orthogonal frequency division multiple access-passive optical network link using self-homodyne balanced detection

    NASA Astrophysics Data System (ADS)

    Won, Yong-Yuk; Jung, Sang-Min; Han, Sang-Kook

    2014-08-01

    A new technique, which reduces optical beat interference (OBI) noise in orthogonal frequency division multiple access-passive optical network (OFDMA-PON) links, is proposed. A self-homodyne balanced detection, which uses a single laser for the optical line terminal (OLT) as well as for the optical network unit (ONU), reduces OBI noise and also improves the signal to noise ratio (SNR) of the discrete multi-tone (DMT) signal. The proposed scheme is verified by transmitting quadrature phase shift keying (QPSK)-modulated DMT signal over a 20-km single mode fiber. The optical signal to noise ratio (OSNR), that is required for BER of 10-5, is reduced by 2 dB in the balanced detection compared with a single channel due to the cancellation of OBI noise in conjunction with the local laser.

  8. Dominant Enhancers of Egfr in Drosophila Melanogaster: Genetic Links between the Notch and Egfr Signaling Pathways

    PubMed Central

    Price, J. V.; Savenye, E. D.; Lum, D.; Breitkreutz, A.

    1997-01-01

    The Drosophila epidermal growth factor receptor (EGFR) is a key component of a complex signaling pathway that participates in multiple developmental processes. We have performed an F(1) screen for mutations that cause dominant enhancement of wing vein phenotypes associated with mutations in Egfr. With this screen, we have recovered mutations in Hairless (H), vein, groucho (gro), and three apparently novel loci. All of the E(Egfr)s we have identified show dominant interactions in transheterozygous combinations with each other and with alleles of N or Su(H), suggesting that they are involved in cross-talk between the N and EGFR signaling pathways. Further examination of the phenotypic interactions between Egfr, H, and gro revealed that reductions in Egfr activity enhanced both the bristle loss associated with H mutations, and the bristle hyperplasia and ocellar hypertrophy associated with gro mutations. Double mutant combinations of Egfr and gro hypomorphic alleles led to the formation of ectopic compound eyes in a dosage sensitive manner. Our findings suggest that these E(Egfr)s represent links between the Egfr and Notch signaling pathways, and that Egfr activity can either promote or suppress Notch signaling, depending on its developmental context. PMID:9383058

  9. Analysis of the congestion effects of link failures in wide area networks

    NASA Astrophysics Data System (ADS)

    Tipper, David; Hammond, Joseph L.; Sharma, Sandeep; Khetan, Archana; Balakrishnan, Krishnan; Menon, Sunil

    1994-01-01

    In this paper, we present the results of a study to determine the effects of link failures on the performance of a network in terms of the occurrence of congestion due to traffic restoration after a failure. The network studied is a virtual circuit based packet switched wide area network. A generic queueing framework is developed to study the effect of failures and the subsequent traffic restoration on network performance. In general, the congestion resulting after a failure is a transient phenomenon. Hence, a numerical methods based nonstationary queueing analysis is conducted in order to quantify the effects of failures in terms of the transient behavior of queue lengths and packet loss probabilities. A bounding relationship is developed whereby a network node can determine whether or not congestion will occur as the result of traffic restoration after a failure.

  10. A local-world heterogeneous model of wireless sensor networks with node and link diversity

    NASA Astrophysics Data System (ADS)

    Li, Shudong; Li, Lixiang; Yang, Yixian

    2011-03-01

    In this paper, we present a novel local-world model of wireless sensor networks (WSN) with two kinds of nodes: sensor nodes and sink nodes, which is different from other models with identical nodes and links. The model balances energy consumption by limiting the connectivity of sink nodes to prolong the life of the network. How the proportion of sink nodes, different energy distribution and the local-world scale would affect the topological structure and network performance are investigated. We find that, using mean-field theory, the degree distribution is obtained as an integral with respect to the proportion of sink nodes and energy distribution. We also show that, the model exhibits a mixed connectivity correlation which is greatly distinct from general networks. Moreover, from the perspective of the efficiency and the average hops for data processing, we find some suitable range of the proportion p of sink nodes would make the network model have optimal performance for data processing.

  11. Linking Transnational Logics: A Feminist Rhetorical Analysis of Public Policy Networks

    ERIC Educational Resources Information Center

    Dingo, Rebecca

    2008-01-01

    In this article, the author investigates the circulation and appropriation of representations of women in public policy. The author effectively mobilizes the metaphor of the network to examine the discursive intersections and transnational links between U.S. welfare programs and the World Bank gender mainstreaming policies. Her analysis reveals…

  12. Computational modeling of mechanical response of dual cross-linked polymer grafted nanoparticle networks

    NASA Astrophysics Data System (ADS)

    v S, Balaji; Yashin, Victor; Salib, Isaac; Kowalewski, Tomasz; Matyjaszewski, Krzystof; Balazs, Anna; Anna Balazs Collaboration; Krzystof Matyjaszewski Collaboration

    2013-03-01

    We develop a hybrid computational model for the behavior of a network of cross-linked polymer-grafted nanoparticles (PGNs). The individual nanoparticles are composed of a rigid core and a corona of grafted polymers that encompass reactive end groups. With the overlap of the coronas on adjacent particles, the reactive end groups can form permanent or labile bonds, which lead to the formation of a ``dual cross-linked'' network. To capture these multi-scale interactions, our approach integrates the essential structural features of the polymer grafted nanoparticles, the interactions between the overlapping coronas, and the kinetics of bond formation and rupture between the reactive groups on the chain ends. We investigate the mechanical response of the dual-cross linked network to an applied tensile deformation. We find that the response depends on the bond energies of the labile bonds, the fraction of permanent bonds in the network, and thickness of the corona. This model provides a powerful tool for the computational design of dual cross-linked PGN's by predicting how the structural features of the system affect the mechanical performance.

  13. The Impact of the OhioLINK Network on Traditional Interlibrary Loan.

    ERIC Educational Resources Information Center

    Van Dam, Scott; Block, Jennifer; Pettitt, Richard N., Jr.

    1997-01-01

    Summarizes the effects OhioLINK, a networked patron self-initiated interlibrary borrowing system, has had on the traditional interlibrary loan (ILL) department at Miami University (OH). Finds Miami's lending to 11 other schools decreased 13% and filled photocopy requests increased 17% while Miami's borrowing increased less than 2%, filled loan…

  14. Wnt Signaling Translocates Lys48-Linked Polyubiquitinated Proteins to the Lysosomal Pathway.

    PubMed

    Kim, Hyunjoon; Vick, Philipp; Hedtke, Joshua; Ploper, Diego; De Robertis, Edward M

    2015-05-26

    Cellular proteins are degraded in either proteasomes or lysosomes depending on the types of ubiquitin chains that covalently modify them. It is not known whether the choice between these two pathways is physiologically regulated. The Lys48-polyubiquitin chain is the major signal directing proteins for degradation in proteasomes. Here, we report the unexpected finding that canonical Wnt signaling translocates some K48-linked polyubiquitinated proteins to the endolysosomal pathway. Proteasomal target proteins, such as b-catenin, Smad1, and Smad4, were targeted into endolysosomes in a process dependent on GSK3 activity. Relocalization was also dependent on Axin1 and the multivesicular body (MVB) proteins HRS/Vps27 and Vps4. The Wnt-induced accumulation of K48-linked polyubiquitinated proteins in endolysosomal organelles was accompanied by a transient decrease in cellular levels of free mono-ubiquitin, which may contribute to Wnt-regulated stabilization of proteins (Wnt/ STOP). We conclude that Wnt redirects Lys48-polyubiquitinated proteins that are normally degraded in proteasomes to endolysosomes. PMID:26004177

  15. Effective-medium approach for stiff polymer networks with flexible cross-links

    NASA Astrophysics Data System (ADS)

    Broedersz, C. P.; Storm, C.; Mackintosh, F. C.

    2009-06-01

    Recent experiments have demonstrated that the nonlinear elasticity of in vitro networks of the biopolymer actin is dramatically altered in the presence of a flexible cross-linker such as the abundant cytoskeletal protein filamin. The basic principles of such networks remain poorly understood. Here we describe an effective-medium theory of flexibly cross-linked stiff polymer networks. We argue that the response of the cross-links can be fully attributed to entropic stiffening, while softening due to domain unfolding can be ignored. The network is modeled as a collection of randomly oriented rods connected by flexible cross-links to an elastic continuum. This effective medium is treated in a linear elastic limit as well as in a more general framework, in which the medium self-consistently represents the nonlinear network behavior. This model predicts that the nonlinear elastic response sets in at strains proportional to cross-linker length and inversely proportional to filament length. Furthermore, we find that the differential modulus scales linearly with the stress in the stiffening regime. These results are in excellent agreement with bulk rheology data.

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

    NASA Technical Reports Server (NTRS)

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

    2011-01-01

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

  17. Link and subgraph likelihoods in random undirected networks with fixed and partially fixed degree sequences

    NASA Astrophysics Data System (ADS)

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

    2007-10-01

    The simplest null models for networks, used to distinguish significant features of a particular network from a priori expected features, are random ensembles with the degree sequence fixed by the specific network of interest. These “fixed degree sequence” (FDS) ensembles are, however, famously resistant to analytic attack. In this paper we introduce ensembles with partially-fixed degree sequences (PFDS) and compare analytic results obtained for them with Monte Carlo results for the FDS ensemble. These results include link likelihoods, subgraph likelihoods, and degree correlations. We find that local structural features in the FDS ensemble can be reasonably well estimated by simultaneously fixing only the degrees of a few nodes, in addition to the total number of nodes and links. As test cases we use two protein interaction networks (Escherichia coli, Saccharomyces cerevisiae), the internet on the autonomous system (AS) level, and the World Wide Web. Fixing just the degrees of two nodes gives the mean neighbor degree as a function of node degree, ⟨k'⟩k , in agreement with results explicitly obtained from rewiring. For power law degree distributions, we derive the disassortativity analytically. In the PFDS ensemble the partition function can be expanded diagrammatically. We obtain an explicit expression for the link likelihood to lowest order, which reduces in the limit of large, sparse undirected networks with L links and with kmax≪L to the simple formula P(k,k')=kk'/(2L+kk') . In a similar limit, the probability for three nodes to be linked into a triangle reduces to the factorized expression PΔ(k1,k2,k3)=P(k1,k2)P(k1,k3)P(k2,k3) .

  18. The Obesity-Linked Gene Nudt3 Drosophila Homolog Aps Is Associated With Insulin Signaling.

    PubMed

    Williams, Michael J; Eriksson, Anders; Shaik, Muksheed; Voisin, Sarah; Yamskova, Olga; Paulsson, Johan; Thombare, Ketan; Fredriksson, Robert; Schiöth, Helgi B

    2015-09-01

    Several genome-wide association studies have linked the Nudix hydrolase family member nucleoside diphosphate-linked moiety X motif 3 (NUDT3) to obesity. However, the manner of NUDT3 involvement in obesity is unknown, and NUDT3 expression, regulation, and signaling in the central nervous system has not been studied. We performed an extensive expression analysis in mice, as well as knocked down the Drosophila NUDT3 homolog Aps in the nervous system, to determine its effect on metabolism. Detailed in situ hybridization studies in the mouse brain revealed abundant Nudt3 mRNA and protein expression throughout the brain, including reward- and feeding-related regions of the hypothalamus and amygdala, whereas Nudt3 mRNA expression was significantly up-regulated in the hypothalamus and brainstem of food-deprived mice. Knocking down Aps in the Drosophila central nervous system, or a subset of median neurosecretory cells, known as the insulin-producing cells (IPCs), induces hyperinsulinemia-like phenotypes, including a decrease in circulating trehalose levels as well as significantly decreasing all carbohydrate levels under starvation conditions. Moreover, lowering Aps IPC expression leads to a decreased ability to recruit these lipids during starvation. Also, loss of neuronal Aps expression caused a starvation susceptibility phenotype while inducing hyperphagia. Finally, the loss of IPC Aps lowered the expression of Akh, Ilp6, and Ilp3, genes known to be inhibited by insulin signaling. These results point toward a role for this gene in the regulation of insulin signaling, which could explain the robust association with obesity in humans. PMID:26168034

  19. Plasticity of the MAPK Signaling Network in Response to Mechanical Stress

    PubMed Central

    Shekhar, Shashank; Kanger, Johannes S.; Subramaniam, Vinod; Martín-Blanco, Enrique

    2014-01-01

    Cells display versatile responses to mechanical inputs and recent studies have identified the mitogen-activated protein kinase (MAPK) cascades mediating the biological effects observed upon mechanical stimulation. Although, MAPK pathways can act insulated from each other, several mechanisms facilitate the crosstalk between the components of these cascades. Yet, the combinatorial complexity of potential molecular interactions between these elements have prevented the understanding of their concerted functions. To analyze the plasticity of the MAPK signaling network in response to mechanical stress we performed a non-saturating epistatic screen in resting and stretched conditions employing as readout a JNK responsive dJun-FRET biosensor. By knocking down MAPKs, and JNK pathway regulators, singly or in pairs in Drosophila S2R+ cells, we have uncovered unexpected regulatory links between JNK cascade kinases, Rho GTPases, MAPKs and the JNK phosphatase Puc. These relationships have been integrated in a system network model at equilibrium accounting for all experimentally validated interactions. This model allows predicting the global reaction of the network to its modulation in response to mechanical stress. It also highlights its context-dependent sensitivity. PMID:25025279

  20. Probing Rubber Cross-Linking Generation of Industrial Polymer Networks at Nanometer Scale.

    PubMed

    Gabrielle, Brice; Gomez, Emmanuel; Korb, Jean-Pierre

    2016-06-23

    We present improved analyses of rheometric torque measurements as well as (1)H double-quantum (DQ) nuclear magnetic resonance (NMR) buildup data on polymer networks of industrial compounds. This latter DQ NMR analysis allows finding the distribution of an orientation order parameter (Dres) resulting from the noncomplete averaging of proton dipole-dipole couplings within the cross-linked polymer chains. We investigate the influence of the formulation (filler and vulcanization systems) as well as the process (curing temperature) ending to the final polymer network. We show that DQ NMR follows the generation of the polymer network during the vulcanization process from a heterogeneous network to a very homogeneous one. The time variations of microscopic Dres and macroscopic rheometric torques present power-law behaviors above a threshold time scale with characteristic exponents of the percolation theory. We observe also a very good linear correlation between the kinetics of Dres and rheometric data routinely performed in industry. All these observations confirm the description of the polymer network generation as a critical phenomenon. On the basis of all these results, we believe that DQ NMR could become a valuable tool for investigating in situ the cross-linking of industrial polymer networks at the nanometer scale. PMID:27254797

  1. Linking EEG signals, brain functions and mental operations: Advantages of the Laplacian transformation.

    PubMed

    Vidal, Franck; Burle, Boris; Spieser, Laure; Carbonnell, Laurence; Meckler, Cédric; Casini, Laurence; Hasbroucq, Thierry

    2015-09-01

    Electroencephalography (EEG) is a very popular technique for investigating brain functions and/or mental processes. To this aim, EEG activities must be interpreted in terms of brain and/or mental processes. EEG signals being a direct manifestation of neuronal activity it is often assumed that such interpretations are quite obvious or, at least, straightforward. However, they often rely on (explicit or even implicit) assumptions regarding the structures supposed to generate the EEG activities of interest. For these assumptions to be used appropriately, reliable links between EEG activities and the underlying brain structures must be established. Because of volume conduction effects and the mixture of activities they induce, these links are difficult to establish with scalp potential recordings. We present different examples showing how the Laplacian transformation, acting as an efficient source separation method, allowed to establish more reliable links between EEG activities and brain generators and, ultimately, with mental operations. The nature of those links depends on the depth of inferences that can vary from weak to strong. Along this continuum, we show that 1) while the effects of experimental manipulation can appear widely distributed with scalp potentials, Laplacian transformation allows to reveal several generators contributing (in different manners) to these modulations, 2) amplitude variations within the same set of generators can generate spurious differences in scalp potential topographies, often interpreted as reflecting different source configurations. In such a case, Laplacian transformation provides much more similar topographies, evidencing the same generator(s) set, and 3) using the LRP as an index of response activation most often produces ambiguous results, Laplacian-transformed response-locked ERPs obtained over motor areas allow resolving these ambiguities. PMID:25958789

  2. Age-dependent homeostatic plasticity of GABAergic signaling in developing retinal networks.

    PubMed

    Hennig, Matthias H; Grady, John; van Coppenhagen, James; Sernagor, Evelyne

    2011-08-24

    Developing retinal ganglion cells fire in correlated spontaneous bursts, resulting in propagating waves with robust spatiotemporal features preserved across development and species. Here we investigate the effects of homeostatic adaptation on the circuits controlling retinal waves. Mouse retinal waves were recorded in vitro for up to 35 h with a multielectrode array in presence of the GABA(A) antagonist bicuculline, allowing us to obtain a precise, time-resolved characterization of homeostatic effects in this preparation. Experiments were performed at P4-P6, when GABA(A) signaling is depolarizing in ganglion cells, and at P7-P10, when GABA(A) signaling is hyperpolarizing. At all ages, bicuculline initially increased the wave sizes and other activity metrics. At P5-P6, wave sizes decreased toward control levels within a few hours while firing remained strong, but this ability to compensate disappeared entirely from P7 onwards. This demonstrates that homeostatic control of spontaneous retinal activity maintains specific network dynamic properties in an age-dependent manner, and suggests that the underlying mechanism is linked to GABA(A) signaling. PMID:21865458

  3. Hijacking common mycorrhizal networks for herbivore-induced defence signal transfer between tomato plants

    PubMed Central

    Song, Yuan Yuan; Ye, Mao; Li, Chuanyou; He, Xinhua; Zhu-Salzman, Keyan; Wang, Rui Long; Su, Yi Juan; Luo, Shi Ming; Zeng, Ren Sen

    2014-01-01

    Common mycorrhizal networks (CMNs) link multiple plants together. We hypothesized that CMNs can serve as an underground conduit for transferring herbivore-induced defence signals. We established CMN between two tomato plants in pots with mycorrhizal fungus Funneliformis mosseae, challenged a ‘donor' plant with caterpillar Spodoptera litura, and investigated defence responses and insect resistance in neighbouring CMN-connected ‘receiver' plants. After CMN establishment caterpillar infestation on ‘donor' plant led to increased insect resistance and activities of putative defensive enzymes, induction of defence-related genes and activation of jasmonate (JA) pathway in the ‘receiver' plant. However, use of a JA biosynthesis defective mutant spr2 as ‘donor' plants resulted in no induction of defence responses and no change in insect resistance in ‘receiver' plants, suggesting that JA signalling is required for CMN-mediated interplant communication. These results indicate that plants are able to hijack CMNs for herbivore-induced defence signal transfer and interplant defence communication. PMID:24468912

  4. Age-dependent Homeostatic Plasticity of GABAergic Signaling in Developing Retinal Networks

    PubMed Central

    Hennig, Matthias H.; Grady, John; van Coppenhagen, James; Sernagor, Evelyne

    2013-01-01

    Developing retinal ganglion cells fire in correlated spontaneous bursts, resulting in propagating waves with robust spatiotemporal features preserved across development and species. Here we investigate the effects of homeostatic adaptation on the circuits controlling retinal waves. Mouse retinal waves were recorded in vitro for up to 35 h with a multielectrode array in presence of the GABAA antagonist bicuculline, allowing us to obtain a precise, time-resolved characterization of homeostatic effects in this preparation. Experiments were performed at P4–P6, when GABAA signaling is depolarizing in ganglion cells, and at P7–P10, when GABAA signaling is hyperpolarizing. At all ages, bicuculline initially increased the wave sizes and other activity metrics. At P5–P6, wave sizes decreased toward control levels within a few hours while firing remained strong, but this ability to compensate disappeared entirely from P7 onwards. This demonstrates that homeostatic control of spontaneous retinal activity maintains specific network dynamic properties in an age-dependent manner, and suggests that the underlying mechanism is linked to GABAA signaling. PMID:21865458

  5. Integrative Phosphoproteomics Links IL-23R Signaling with Metabolic Adaptation in Lymphocytes.

    PubMed

    Lochmatter, Corinne; Fischer, Roman; Charles, Philip D; Yu, Zhanru; Powrie, Fiona; Kessler, Benedikt M

    2016-01-01

    Interleukin (IL)-23 mediated signal transduction represents a major molecular mechanism underlying the pathology of inflammatory bowel disease, Crohn's disease and ulcerative colitis. In addition, emerging evidence supports the role of IL-23-driven Th17 cells in inflammation. Components of the IL-23 signaling pathway, such as IL-23R, JAK2 and STAT3, have been characterized, but elements unique to this network as compared to other interleukins have not been readily explored. In this study, we have undertaken an integrative phosphoproteomics approach to better characterise downstream signaling events. To this end, we performed and compared phosphopeptide and phosphoprotein enrichment methodologies after activation of T lymphocytes by IL-23. We demonstrate the complementary nature of the two phosphoenrichment approaches by maximizing the capture of phosphorylation events. A total of 8202 unique phosphopeptides, and 4317 unique proteins were identified, amongst which STAT3, PKM2, CDK6 and LASP-1 showed induction of specific phosphorylation not readily observed after IL-2 stimulation. Interestingly, quantitative analysis revealed predominant phosphorylation of pre-existing STAT3 nuclear subsets in addition to translocation of phosphorylated STAT3 within 30 min after IL-23 stimulation. After IL-23R activation, a small subset of PKM2 also translocates to the nucleus and may contribute to STAT3 phosphorylation, suggesting multiple cellular responses including metabolic adaptation. PMID:27080861

  6. Integrative Phosphoproteomics Links IL-23R Signaling with Metabolic Adaptation in Lymphocytes

    PubMed Central

    Lochmatter, Corinne; Fischer, Roman; Charles, Philip D.; Yu, Zhanru; Powrie, Fiona; Kessler, Benedikt M.

    2016-01-01

    Interleukin (IL)-23 mediated signal transduction represents a major molecular mechanism underlying the pathology of inflammatory bowel disease, Crohn’s disease and ulcerative colitis. In addition, emerging evidence supports the role of IL-23-driven Th17 cells in inflammation. Components of the IL-23 signaling pathway, such as IL-23R, JAK2 and STAT3, have been characterized, but elements unique to this network as compared to other interleukins have not been readily explored. In this study, we have undertaken an integrative phosphoproteomics approach to better characterise downstream signaling events. To this end, we performed and compared phosphopeptide and phosphoprotein enrichment methodologies after activation of T lymphocytes by IL-23. We demonstrate the complementary nature of the two phosphoenrichment approaches by maximizing the capture of phosphorylation events. A total of 8202 unique phosphopeptides, and 4317 unique proteins were identified, amongst which STAT3, PKM2, CDK6 and LASP-1 showed induction of specific phosphorylation not readily observed after IL-2 stimulation. Interestingly, quantitative analysis revealed predominant phosphorylation of pre-existing STAT3 nuclear subsets in addition to translocation of phosphorylated STAT3 within 30 min after IL-23 stimulation. After IL-23R activation, a small subset of PKM2 also translocates to the nucleus and may contribute to STAT3 phosphorylation, suggesting multiple cellular responses including metabolic adaptation. PMID:27080861

  7. 47 CFR 73.4157 - Network signals which adversely affect affiliate broadcast service.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 4 2010-10-01 2010-10-01 false Network signals which adversely affect affiliate broadcast service. 73.4157 Section 73.4157 Telecommunication FEDERAL COMMUNICATIONS COMMISSION....4157 Network signals which adversely affect affiliate broadcast service. See Public Notice, FCC...

  8. 47 CFR 73.4157 - Network signals which adversely affect affiliate broadcast service.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 47 Telecommunication 4 2011-10-01 2011-10-01 false Network signals which adversely affect affiliate broadcast service. 73.4157 Section 73.4157 Telecommunication FEDERAL COMMUNICATIONS COMMISSION....4157 Network signals which adversely affect affiliate broadcast service. See Public Notice, FCC...

  9. 47 CFR 73.4157 - Network signals which adversely affect affiliate broadcast service.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 47 Telecommunication 4 2014-10-01 2014-10-01 false Network signals which adversely affect affiliate broadcast service. 73.4157 Section 73.4157 Telecommunication FEDERAL COMMUNICATIONS COMMISSION....4157 Network signals which adversely affect affiliate broadcast service. See Public Notice, FCC...

  10. 47 CFR 73.4157 - Network signals which adversely affect affiliate broadcast service.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 47 Telecommunication 4 2013-10-01 2013-10-01 false Network signals which adversely affect affiliate broadcast service. 73.4157 Section 73.4157 Telecommunication FEDERAL COMMUNICATIONS COMMISSION....4157 Network signals which adversely affect affiliate broadcast service. See Public Notice, FCC...

  11. 47 CFR 73.4157 - Network signals which adversely affect affiliate broadcast service.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 47 Telecommunication 4 2012-10-01 2012-10-01 false Network signals which adversely affect affiliate broadcast service. 73.4157 Section 73.4157 Telecommunication FEDERAL COMMUNICATIONS COMMISSION....4157 Network signals which adversely affect affiliate broadcast service. See Public Notice, FCC...

  12. Mapping edge-based traffic measurements onto the internal links in MPLS network

    NASA Astrophysics Data System (ADS)

    Zhao, Guofeng; Tang, Hong; Zhang, Yi

    2004-09-01

    Applying multi-protocol label switching techniques to IP-based backbone for traffic engineering goals has shown advantageous. Obtaining a volume of load on each internal link of the network is crucial for traffic engineering applying. Though collecting can be available for each link, such as applying traditional SNMP scheme, the approach may cause heavy processing load and sharply degrade the throughput of the core routers. Then monitoring merely at the edge of the network and mapping the measurements onto the core provides a good alternative way. In this paper, we explore a scheme for traffic mapping with edge-based measurements in MPLS network. It is supposed that the volume of traffic on each internal link over the domain would be mapped onto by measurements available only at ingress nodes. We apply path-based measurements at ingress nodes without enabling measurements in the core of the network. We propose a method that can infer a path from the ingress to the egress node using label distribution protocol without collecting routing data from core routers. Based on flow theory and queuing theory, we prove that our approach is effective and present the algorithm for traffic mapping. We also show performance simulation results that indicate potential of our approach.

  13. Motion in partially and fully cross-linked F-actin networks

    NASA Astrophysics Data System (ADS)

    Morris, Eliza; Ehrlicher, Allen; Weitz, David

    2012-02-01

    Single molecule experiments have measured stall forces and procession rates of molecular motors on isolated cytoskeletal fibers in Newtonian fluids. But in the cell, these motors are transporting cargo through a highly complex cytoskeletal network. To compare these single molecule results to the forces exerted by motors within the cell, an evaluation of the response of the cytoskeletal network is needed. Using magnetic tweezers and fluorescence confocal microscopy we observe and quantify the relationship between bead motion and filament response in F-actin networks both partially and fully cross-linked with filamin We find that when the transition from full to partial cross-linking is brought about by a decrease in cross-linker concentration there is a simultaneous decline in the elasticity of the network, but the response of the bead remains qualitatively similar. However, when the cross-linking is reduced through a shortening of the F-actin filaments the bead response is completely altered. The characteristics of the altered bead response will be discussed here.

  14. Microwave analog fiber-optic link for use in the deep space network

    NASA Technical Reports Server (NTRS)

    Logan, R. T., Jr.; Lutes, G. F.; Maleki, L.

    1990-01-01

    A novel fiber-optic system with dynamic range of up to 150 dB-Hz for transmission of microwave analog signals is described. The design, analysis, and laboratory evaluations of this system are reported, and potential applications in the NASA/JPL Deep Space Network are discussed.

  15. Nonlinear dynamic system identification using Chebyshev functional link artificial neural networks.

    PubMed

    Patra, J C; Kot, A C

    2002-01-01

    A computationally efficient artificial neural network (ANN) for the purpose of dynamic nonlinear system identification is proposed. The major drawback of feedforward neural networks, such as multilayer perceptrons (MLPs) trained with the backpropagation (BP) algorithm, is that they require a large amount of computation for learning. We propose a single-layer functional-link ANN (FLANN) in which the need for a hidden layer is eliminated by expanding the input pattern by Chebyshev polynomials. The novelty of this network is that it requires much less computation than that of a MLP. We have shown its effectiveness in the problem of nonlinear dynamic system identification. In the presence of additive Gaussian noise, the performance of the proposed network is found to be similar or superior to that of a MLP. A performance comparison in terms of computational complexity has also been carried out. PMID:18238146

  16. Signal processing using artificial neural network for BOTDA sensor system.

    PubMed

    Azad, Abul Kalam; Wang, Liang; Guo, Nan; Tam, Hwa-Yaw; Lu, Chao

    2016-03-21

    We experimentally demonstrate the use of artificial neural network (ANN) to process sensing signals obtained from Brillouin optical time domain analyzer (BOTDA). The distributed temperature information is extracted directly from the local Brillouin gain spectra (BGSs) along the fiber under test without the process of determination of Brillouin frequency shift (BFS) and hence conversion from BFS to temperature. Unlike our previous work for short sensing distance where ANN is trained by measured BGSs, here we employ ideal BGSs with different linewidths to train the ANN in order to take the linewidth variation due to different conditions from the training and testing phases into account, making it feasible for long distance sensing. Moreover, the performance of ANN is compared with other two techniques, Lorentzian curve fitting and cross-correlation method, and our results show that ANN has higher accuracy and larger tolerance to measurement error, especially at large frequency scanning step. We also show that the temperature extraction from BOTDA measurements employing ANN is significantly faster than the other two approaches. Hence ANN can be an excellent alternative tool to process BGSs measured by BOTDA and obtain temperature distribution along the fiber, especially when large frequency scanning step is adopted to significantly reduce the measurement time but without sacrifice of sensing accuracy. PMID:27136863

  17. Network Signal Processor No. 2 after removal from Columbia

    NASA Technical Reports Server (NTRS)

    1998-01-01

    Two USA employees, Tim Seymour (at left) and Danny Brown (at right), look at the network signal processor (NSP) that was responsible for postponement of the launch of STS-90 on Apr. 16. The Space Shuttle Columbia's liftoff from Launch Pad 39B was postponed 24 hours due to difficulty with NSP No. 2 on the orbiter. This device formats data and voice communications between the ground and the Space Shuttle. The unit, which is located in the orbiter's mid-deck, was removed and replaced on Apr. 16. Mission managers first noticed the problem at about 3 a.m. during normal communications systems activation prior to tanking operations. As a result, work to load the external tank with the cryogenic propellants did not begin and launch postponement was made official at about 8:15 a.m. STS-90 is slated to be the launch of Neurolab, a nearly 17-day mission to examine the effects of spaceflight on the brain, spinal cord, peripheral nerves and sensory organs in the human body.

  18. G protein-linked signaling pathways in bipolar and major depressive disorders.

    PubMed

    Tomita, Hiroaki; Ziegler, Mary E; Kim, Helen B; Evans, Simon J; Choudary, Prabhakara V; Li, Jun Z; Meng, Fan; Dai, Manhong; Myers, Richard M; Neal, Charles R; Speed, Terry P; Barchas, Jack D; Schatzberg, Alan F; Watson, Stanley J; Akil, Huda; Jones, Edward G; Bunney, William E; Vawter, Marquis P

    2013-01-01

    The G-protein linked signaling system (GPLS) comprises a large number of G-proteins, G protein-coupled receptors (GPCRs), GPCR ligands, and downstream effector molecules. G-proteins interact with both GPCRs and downstream effectors such as cyclic adenosine monophosphate (cAMP), phosphatidylinositols, and ion channels. The GPLS is implicated in the pathophysiology and pharmacology of both major depressive disorder (MDD) and bipolar disorder (BPD). This study evaluated whether GPLS is altered at the transcript level. The gene expression in the dorsolateral prefrontal (DLPFC) and anterior cingulate (ACC) were compared from MDD, BPD, and control subjects using Affymetrix Gene Chips and real time quantitative PCR. High quality brain tissue was used in the study to control for confounding effects of agonal events, tissue pH, RNA integrity, gender, and age. GPLS signaling transcripts were altered especially in the ACC of BPD and MDD subjects. Transcript levels of molecules which repress cAMP activity were increased in BPD and decreased in MDD. Two orphan GPCRs, GPRC5B and GPR37, showed significantly decreased expression levels in MDD, and significantly increased expression levels in BPD. Our results suggest opposite changes in BPD and MDD in the GPLS, "activated" cAMP signaling activity in BPD and "blunted" cAMP signaling activity in MDD. GPRC5B and GPR37 both appear to have behavioral effects, and are also candidate genes for neurodegenerative disorders. In the context of the opposite changes observed in BPD and MDD, these GPCRs warrant further study of their brain effects. PMID:24391664

  19. G-Protein/β-Arrestin-Linked Fluctuating Network of G-Protein-Coupled Receptors for Predicting Drug Efficacy and Bias Using Short-Term Molecular Dynamics Simulation

    PubMed Central

    Ichikawa, Osamu; Fujimoto, Kazushi; Yamada, Atsushi; Okazaki, Susumu; Yamazaki, Kazuto

    2016-01-01

    The efficacy and bias of signal transduction induced by a drug at a target protein are closely associated with the benefits and side effects of the drug. In particular, partial agonist activity and G-protein/β-arrestin-biased agonist activity for the G-protein-coupled receptor (GPCR) family, the family with the most target proteins of launched drugs, are key issues in drug discovery. However, designing GPCR drugs with appropriate efficacy and bias is challenging because the dynamic mechanism of signal transduction induced by ligand—receptor interactions is complicated. Here, we identified the G-protein/β-arrestin-linked fluctuating network, which initiates large-scale conformational changes, using sub-microsecond molecular dynamics (MD) simulations of the β2-adrenergic receptor (β2AR) with a diverse collection of ligands and correlation analysis of their G protein/β-arrestin efficacy. The G-protein-linked fluctuating network extends from the ligand-binding site to the G-protein-binding site through the connector region, and the β-arrestin-linked fluctuating network consists of the NPxxY motif and adjacent regions. We confirmed that the averaged values of fluctuation in the fluctuating network detected are good quantitative indexes for explaining G protein/β-arrestin efficacy. These results indicate that short-term MD simulation is a practical method to predict the efficacy and bias of any compound for GPCRs. PMID:27187591

  20. G-Protein/β-Arrestin-Linked Fluctuating Network of G-Protein-Coupled Receptors for Predicting Drug Efficacy and Bias Using Short-Term Molecular Dynamics Simulation.

    PubMed

    Ichikawa, Osamu; Fujimoto, Kazushi; Yamada, Atsushi; Okazaki, Susumu; Yamazaki, Kazuto

    2016-01-01

    The efficacy and bias of signal transduction induced by a drug at a target protein are closely associated with the benefits and side effects of the drug. In particular, partial agonist activity and G-protein/β-arrestin-biased agonist activity for the G-protein-coupled receptor (GPCR) family, the family with the most target proteins of launched drugs, are key issues in drug discovery. However, designing GPCR drugs with appropriate efficacy and bias is challenging because the dynamic mechanism of signal transduction induced by ligand-receptor interactions is complicated. Here, we identified the G-protein/β-arrestin-linked fluctuating network, which initiates large-scale conformational changes, using sub-microsecond molecular dynamics (MD) simulations of the β2-adrenergic receptor (β2AR) with a diverse collection of ligands and correlation analysis of their G protein/β-arrestin efficacy. The G-protein-linked fluctuating network extends from the ligand-binding site to the G-protein-binding site through the connector region, and the β-arrestin-linked fluctuating network consists of the NPxxY motif and adjacent regions. We confirmed that the averaged values of fluctuation in the fluctuating network detected are good quantitative indexes for explaining G protein/β-arrestin efficacy. These results indicate that short-term MD simulation is a practical method to predict the efficacy and bias of any compound for GPCRs. PMID:27187591

  1. Echo state property linked to an input: exploring a fundamental characteristic of recurrent neural networks.

    PubMed

    Manjunath, G; Jaeger, H

    2013-03-01

    The echo state property is a key for the design and training of recurrent neural networks within the paradigm of reservoir computing. In intuitive terms, this is a passivity condition: a network having this property, when driven by an input signal, will become entrained by the input and develop an internal response signal. This excited internal dynamics can be seen as a high-dimensional, nonlinear, unique transform of the input with a rich memory content. This view has implications for understanding neural dynamics beyond the field of reservoir computing. Available definitions and theorems concerning the echo state property, however, are of little practical use because they do not relate the network response to temporal or statistical properties of the driving input. Here we present a new definition of the echo state property that directly connects it to such properties. We derive a fundamental 0-1 law: if the input comes from an ergodic source, the network response has the echo state property with probability one or zero, independent of the given network. Furthermore, we give a sufficient condition for the echo state property that connects statistical characteristics of the input to algebraic properties of the network connection matrix. The mathematical methods that we employ are freshly imported from the young field of nonautonomous dynamical systems theory. Since these methods are not yet well known in neural computation research, we introduce them in some detail. As a side story, we hope to demonstrate the eminent usefulness of these methods. PMID:23272918

  2. Broadband nanophotonic wireless links and networks using on-chip integrated plasmonic antennas.

    PubMed

    Yang, Yuanqing; Li, Qiang; Qiu, Min

    2016-01-01

    Owing to their high capacity and flexibility, broadband wireless communications have been widely employed in radio and microwave regimes, playing indispensable roles in our daily life. Their optical analogs, however, have not been demonstrated at the nanoscale. In this paper, by exploiting plasmonic nanoantennas, we demonstrate the complete design of broadband wireless links and networks in the realm of nanophotonics. With a 100-fold enhancement in power transfer superior to previous designs as well as an ultrawide bandwidth that covers the entire telecommunication wavelength range, such broadband nanolinks and networks are expected to pave the way for future optical integrated nanocircuits. PMID:26783033

  3. Broadband nanophotonic wireless links and networks using on-chip integrated plasmonic antennas

    NASA Astrophysics Data System (ADS)

    Yang, Yuanqing; Li, Qiang; Qiu, Min

    2016-01-01

    Owing to their high capacity and flexibility, broadband wireless communications have been widely employed in radio and microwave regimes, playing indispensable roles in our daily life. Their optical analogs, however, have not been demonstrated at the nanoscale. In this paper, by exploiting plasmonic nanoantennas, we demonstrate the complete design of broadband wireless links and networks in the realm of nanophotonics. With a 100-fold enhancement in power transfer superior to previous designs as well as an ultrawide bandwidth that covers the entire telecommunication wavelength range, such broadband nanolinks and networks are expected to pave the way for future optical integrated nanocircuits.

  4. Broadband nanophotonic wireless links and networks using on-chip integrated plasmonic antennas

    PubMed Central

    Yang, Yuanqing; Li, Qiang; Qiu, Min

    2016-01-01

    Owing to their high capacity and flexibility, broadband wireless communications have been widely employed in radio and microwave regimes, playing indispensable roles in our daily life. Their optical analogs, however, have not been demonstrated at the nanoscale. In this paper, by exploiting plasmonic nanoantennas, we demonstrate the complete design of broadband wireless links and networks in the realm of nanophotonics. With a 100-fold enhancement in power transfer superior to previous designs as well as an ultrawide bandwidth that covers the entire telecommunication wavelength range, such broadband nanolinks and networks are expected to pave the way for future optical integrated nanocircuits. PMID:26783033

  5. Impaired Generation Of 12-Hydroxylated Bile Acids Links Hepatic Insulin Signaling With Dyslipidemia

    PubMed Central

    Haeusler, Rebecca A.; Pratt-Hyatt, Matthew; Welch, Carrie L.; Klaassen, Curtis D.; Accili, Domenico

    2011-01-01

    Summary The association of type 2 diabetes with elevated plasma triglyceride (TG) and very low-density lipoproteins (VLDL), and intrahepatic lipid accumulation represents a pathophysiological enigma and an unmet therapeutic challenge. Here we uncover a link between insulin action through FoxO1, bile acid (BA) composition, and altered lipid homeostasis that brings new insight to this longstanding conundrum. FoxO1 ablation brings about two signature lipid abnormalities of diabetes and the metabolic syndrome, elevated liver and plasma TG. These changes are associated with deficiency of 12α-hydroxylated BAs and their synthetic enzyme, Cyp8b1, that hinders the TG-lowering effects of the BA receptor, Fxr. Accordingly, pharmacological activation of Fxr with GW4064 overcomes the BA imbalance, restoring hepatic and plasma TG levels of FoxO1-deficient mice to normal levels. We propose that generation of 12α-hydroxylated products of BA metabolism represents a signaling mechanism linking hepatic lipid abnormalities with type 2 diabetes, and a treatment target for this condition. PMID:22197325

  6. Using LinkedIn in the Marketing Classroom: Exploratory Insights and Recommendations for Teaching Social Media/Networking

    ERIC Educational Resources Information Center

    McCorkle, Denny E.; McCorkle, Yuhua Li

    2012-01-01

    With the rapid growth of social networking and media comes their consideration for use in the marketing classroom. Social networking skills are becoming essential for personal branding (e.g., networking, self-marketing) and corporate/product branding (e.g., marketing communication). This paper addresses the use of LinkedIn (i.e., an online…

  7. R4 regulators of G protein signaling (RGS) identify an ancient MHC-linked synteny group

    PubMed Central

    Suurväli, Jaanus; Robert, Jacques; Boudinot, Pierre; Boudinot, Sirje Rüütel

    2012-01-01

    Regulators of G Protein Signaling (RGS) are key regulators of G protein signaling. RGS proteins of the R4 RGS group are composed of a mere RGS domain and are mainly involved in immune response modulation. In both human and mouse, most genes encoding the R4 RGS proteins are located in the same region of chromosome 1. We show here that the RGS1/RGS16 neighborhood constitutes a synteny group well conserved across tetrapods, and closely linked to the MHC paralogon of chromosome 1. Genes located in the RGS1/RGS16 region have paralogs close to the MHC on chromosome 6 or close to the other MHC paralogons. In amphioxus, a cephalochordate, these genes possess orthologs that are located in the same scaffolds as a number of markers defining the proto-MHC in this species (Abi-Rached et al. 2002). We therefore propose that the RGS1/RGS16 region provides useful markers to investigate the origins and the evolution of the MHC. In addition, we show that some genes of the region appear to have immune functions not only in human, but also in Xenopus. PMID:23129146

  8. Droplet-Free Digital Enzyme-Linked Immunosorbent Assay Based on a Tyramide Signal Amplification System.

    PubMed

    Akama, Kenji; Shirai, Kentaro; Suzuki, Seigo

    2016-07-19

    Digital enzyme-linked immunosorbent assay (ELISA) is a single molecule counting technology and is one of the most sensitive immunoassay methods. The key aspect of this technology is to concentrate enzyme reaction products from a single target molecule in femtoliter droplets. This study presents a novel Digital ELISA that does not require droplets; instead, enzyme reaction products are concentrated using a tyramide signal amplification system. In our method, tyramide substrate reacts with horseradish peroxidase (HRP) labeled with an immunocomplex on beads, and the substrate is converted into short-lived radical intermediates. By adjusting the bead concentration in the HRP-tyramide reaction and conducting the reaction using freely moving beads, tyramide radicals are deposited only on beads labeled with HRP and there is no diffusion to other beads. Consequently, the fluorescence signal is localized on a portion of the beads, making it possible to count the number of labeled beads digitally. The performance of our method was demonstrated by detecting hepatitis B surface antigen with a limit of detection of 0.09 mIU/mL (139 aM) and a dynamic range of over 4 orders of magnitude. The obtained limit of detection represents a >20-fold higher sensitivity than conventional ELISA. Our method has potential applications in simple in vitro diagnostic systems for detecting ultralow concentrations of protein biomarkers. PMID:27322525

  9. Ghrelin signalling on food reward: a salient link between the gut and the mesolimbic system.

    PubMed

    Perello, M; Dickson, S L

    2015-06-01

    'Hunger is the best spice' is an old and wise saying that acknowledges the fact that almost any food tastes better when we are hungry. The neurobiological underpinnings of this lore include activation of the brain's reward system and the stimulation of this system by the hunger-promoting hormone ghrelin. Ghrelin is produced largely from the stomach and levels are higher preprandially. The ghrelin receptor is expressed in many brain areas important for feeding control, including not only the hypothalamic nuclei involved in energy balance regulation, but also reward-linked areas such as the ventral tegmental area. By targeting the mesoaccumbal dopamine neurones of the ventral tegmental area, ghrelin recruits pathways important for food reward-related behaviours that show overlap with but are also distinct from those important for food intake. We review a variety of studies that support the notion that ghrelin signalling at the level of the mesolimbic system is one of the key molecular substrates that provides a physiological signal connecting gut and reward pathways. PMID:25377898

  10. Cdc42/N-WASP signaling links actin dynamics to pancreatic β cell delamination and differentiation

    PubMed Central

    Kesavan, Gokul; Lieven, Oliver; Mamidi, Anant; Öhlin, Zarah Löf; Johansson, Jenny Kristina; Li, Wan-Chun; Lommel, Silvia; Greiner, Thomas Uwe; Semb, Henrik

    2014-01-01

    Delamination plays a pivotal role during normal development and cancer. Previous work has demonstrated that delamination and epithelial cell movement within the plane of an epithelium are associated with a change in cellular phenotype. However, how this positional change is linked to differentiation remains unknown. Using the developing mouse pancreas as a model system, we show that β cell delamination and differentiation are two independent events, which are controlled by Cdc42/N-WASP signaling. Specifically, we show that expression of constitutively active Cdc42 in β cells inhibits β cell delamination and differentiation. These processes are normally associated with junctional actin and cell-cell junction disassembly and the expression of fate-determining transcription factors, such as Isl1 and MafA. Mechanistically, we demonstrate that genetic ablation of N-WASP in β cells expressing constitutively active Cdc42 partially restores both delamination and β cell differentiation. These findings elucidate how junctional actin dynamics via Cdc42/N-WASP signaling cell-autonomously control not only epithelial delamination but also cell differentiation during mammalian organogenesis. PMID:24449844

  11. Multi-stimulus-responsive shape-memory polymer nanocomposite network cross-linked by cellulose nanocrystals.

    PubMed

    Liu, Ye; Li, Ying; Yang, Guang; Zheng, Xiaotong; Zhou, Shaobing

    2015-02-25

    In this study, we developed a thermoresponsive and water-responsive shape-memory polymer nanocomposite network by chemically cross-linking cellulose nanocrystals (CNCs) with polycaprolactone (PCL) and polyethylene glycol (PEG). The nanocomposite network was fully characterized, including the microstructure, cross-link density, water contact angle, water uptake, crystallinity, thermal properties, and static and dynamic mechanical properties. We found that the PEG[60]-PCL[40]-CNC[10] nanocomposite exhibited excellent thermo-induced and water-induced shape-memory effects in water at 37 °C (close to body temperature), and the introduction of CNC clearly improved the mechanical properties of the mixture of both PEG and PCL polymers with low molecular weights. In addition, Alamar blue assays based on osteoblasts indicated that the nanocomposites possessed good cytocompatibility. Therefore, this thermoresponsive and water-responsive shape-memory nanocomposite could be potentially developed into a new smart biomaterial. PMID:25647407

  12. Linking Semiconductor Nanocrystals into Gel Networks through All-Inorganic Bridges.

    PubMed

    Singh, Amita; Lindquist, Beth A; Ong, Gary K; Jadrich, Ryan B; Singh, Ajay; Ha, Heonjoo; Ellison, Christopher J; Truskett, Thomas M; Milliron, Delia J

    2015-12-01

    For colloidal semiconductor nanocrystals (NCs), replacement of insulating organic capping ligands with chemically diverse inorganic clusters enables the development of functional solids in which adjacent NCs are strongly coupled. Yet controlled assembly methods are lacking to direct the arrangement of charged, inorganic cluster-capped NCs into open networks. Herein, we introduce coordination bonds between the clusters capping the NCs thus linking the NCs into highly open gel networks. As linking cations (Pt(2+)) are added to dilute (under 1 vol %) chalcogenidometallate-capped CdSe NC dispersions, the NCs first form clusters, then gels with viscoelastic properties. The phase behavior of the gels for variable [Pt(2+)] suggests they may represent nanoscale analogues of bridged particle gels, which have been observed to form in certain polymer colloidal suspensions. PMID:26474402

  13. Signal recognition efficiencies of artificial neural-network pulse-shape discrimination in HPGe -decay searches

    NASA Astrophysics Data System (ADS)

    Caldwell, A.; Cossavella, F.; Majorovits, B.; Palioselitis, D.; Volynets, O.

    2015-07-01

    A pulse-shape discrimination method based on artificial neural networks was applied to pulses simulated for different background, signal and signal-like interactions inside a germanium detector. The simulated pulses were used to investigate variations of efficiencies as a function of used training set. It is verified that neural networks are well-suited to identify background pulses in true-coaxial high-purity germanium detectors. The systematic uncertainty on the signal recognition efficiency derived using signal-like evaluation samples from calibration measurements is estimated to be 5 %. This uncertainty is due to differences between signal and calibration samples.

  14. Structural Analysis and Mechanical Characterization of Hyaluronic Acid-Based Doubly Cross-Linked Networks

    PubMed Central

    Jha, Amit K.; Hule, Rohan A.; Jiao, Tong; Teller, Sean S.; Clifton, Rodney J.; Duncan, Randall L.; Pochan, Darrin J.; Jia, Xinqiao

    2009-01-01

    We have created a new class of hyaluronic acid (HA)-based hydrogel materials with HA hydrogel particles (HGPs) embedded in and covalently cross-linked to a secondary network. HA HGPs with an average diameter of ∼900 nm and narrow particle size distribution were synthesized using a refined reverse micelle polymerization technique. The average mesh size of the HGPs was estimated to be approximately 5.5 to 7.0 nm by a protein uptake experiment. Sodium periodate oxidation not only introduced aldehyde groups to the particles but also reduced the average particle size. The aldehyde groups generated were used as reactive handles for subsequent cross-linking with an HA derivative containing hydrazide groups. The resulting macroscopic gels contain two distinct hierarchical networks (doubly cross-linked networks, DXNs): one within individual particles and another among different particles. Bulk gels (BGs) formed by direct mixing of HA derivatives with mutually reactive groups were included for comparison. The hydrogel microstructures were collectively characterized by microscopy and neutron scattering techniques. Their viscoelasticity was quantified at low frequencies (0.1−10 Hz) using a controlled stress rheometer and at high frequencies (up to 200 Hz) with a home-built torsional wave apparatus. Both BGs and DXNs are stable elastic gels that become stiffer at higher frequencies. The HA-based DXN offers unique structural hierarchy and mechanical properties that are suitable for soft tissue regeneration. PMID:20046226

  15. Structural Analysis and Mechanical Characterization of Hyaluronic Acid-Based Doubly Cross-Linked Networks.

    PubMed

    Jha, Amit K; Hule, Rohan A; Jiao, Tong; Teller, Sean S; Clifton, Rodney J; Duncan, Randall L; Pochan, Darrin J; Jia, Xinqiao

    2009-01-01

    We have created a new class of hyaluronic acid (HA)-based hydrogel materials with HA hydrogel particles (HGPs) embedded in and covalently cross-linked to a secondary network. HA HGPs with an average diameter of ∼900 nm and narrow particle size distribution were synthesized using a refined reverse micelle polymerization technique. The average mesh size of the HGPs was estimated to be approximately 5.5 to 7.0 nm by a protein uptake experiment. Sodium periodate oxidation not only introduced aldehyde groups to the particles but also reduced the average particle size. The aldehyde groups generated were used as reactive handles for subsequent cross-linking with an HA derivative containing hydrazide groups. The resulting macroscopic gels contain two distinct hierarchical networks (doubly cross-linked networks, DXNs): one within individual particles and another among different particles. Bulk gels (BGs) formed by direct mixing of HA derivatives with mutually reactive groups were included for comparison. The hydrogel microstructures were collectively characterized by microscopy and neutron scattering techniques. Their viscoelasticity was quantified at low frequencies (0.1-10 Hz) using a controlled stress rheometer and at high frequencies (up to 200 Hz) with a home-built torsional wave apparatus. Both BGs and DXNs are stable elastic gels that become stiffer at higher frequencies. The HA-based DXN offers unique structural hierarchy and mechanical properties that are suitable for soft tissue regeneration. PMID:20046226

  16. Space Link Extension (SLE) Emulation for High-Throughput Network Communication

    NASA Technical Reports Server (NTRS)

    Murawski, Robert; Tchorowski, Nicole; Golden, Bert

    2014-01-01

    As the data rate requirements for space communications increases, signicant stressis placed not only on the wireless satellite communication links, but also on the groundnetworks which forward data from end-users to remote ground stations. These wide areanetwork (WAN) connections add delay and jitter to the end-to-end satellite communicationlink, eects which can have signicant impacts on the wireless communication link. It isimperative that any ground communication protocol can react to these eects such that theground network does not become a bottleneck in the communication path to the satellite.In this paper, we present our SCENIC Emulation Lab testbed which was developed to testthe CCSDS SLE protocol implementations proposed for use on future NASA communica-tion networks. Our results show that in the presence of realistic levels of network delay,high-throughput SLE communication links can experience signicant data rate throttling.Based on our observations, we present some insight into why this data throttling happens,and trace the probable issue back to non-optimal blocking communication which is sup-ported by the CCSDS SLE API recommended practices. These issues were presented aswell to the SLE implementation developers which, based on our reports, developed a newrelease for SLE which we show xes the SLE blocking issue and greatly improves the pro-tocol throughput. In this paper, we also discuss future developments for our end-to-endemulation lab and how these improvements can be used to develop and test future spacecommunication technologies.

  17. Summarizing scale-free networks based on virtual and real links

    NASA Astrophysics Data System (ADS)

    Bei, Yijun; Lin, Zhen; Chen, Deren

    2016-02-01

    Techniques to summarize and cluster graphs are indispensable to understand the internal characteristics of large complex networks. However, existing methods that analyze graphs mainly focus on aggregating strong-interaction vertices into the same group without considering the node properties, particularly multi-valued attributes. This study aims to develop a unified framework based on the concept of a virtual graph by integrating attributes and structural similarities. We propose a summarizing graph based on virtual and real links (SGVR) approach to aggregate similar nodes in a scale-free graph into k non-overlapping groups based on user-selected attributes considering both virtual links (attributes) and real links (graph structures). An effective data structure called HB-Graph is adopted to adjust the subgroups and optimize the grouping results. Extensive experiments are carried out on actual and synthetic datasets. Results indicate that our proposed method is both effective and efficient.

  18. Network and atomistic simulations unveil the structural determinants of mutations linked to retinal diseases.

    PubMed

    Mariani, Simona; Dell'Orco, Daniele; Felline, Angelo; Raimondi, Francesco; Fanelli, Francesca

    2013-01-01

    A number of incurable retinal diseases causing vision impairments derive from alterations in visual phototransduction. Unraveling the structural determinants of even monogenic retinal diseases would require network-centered approaches combined with atomistic simulations. The transducin G38D mutant associated with the Nougaret Congenital Night Blindness (NCNB) was thoroughly investigated by both mathematical modeling of visual phototransduction and atomistic simulations on the major targets of the mutational effect. Mathematical modeling, in line with electrophysiological recordings, indicates reduction of phosphodiesterase 6 (PDE) recognition and activation as the main determinants of the pathological phenotype. Sub-microsecond molecular dynamics (MD) simulations coupled with Functional Mode Analysis improve the resolution of information, showing that such impairment is likely due to disruption of the PDEγ binding cavity in transducin. Protein Structure Network analyses additionally suggest that the observed slight reduction of theRGS9-catalyzed GTPase activity of transducin depends on perturbed communication between RGS9 and GTP binding site. These findings provide insights into the structural fundamentals of abnormal functioning of visual phototransduction caused by a missense mutation in one component of the signaling network. This combination of network-centered modeling with atomistic simulations represents a paradigm for future studies aimed at thoroughly deciphering the structural determinants of genetic retinal diseases. Analogous approaches are suitable to unveil the mechanism of information transfer in any signaling network either in physiological or pathological conditions. PMID:24009494

  19. Transport link scanner: simulating geographic transport network expansion through individual investments

    NASA Astrophysics Data System (ADS)

    Jacobs-Crisioni, C.; Koopmans, C. C.

    2016-07-01

    This paper introduces a GIS-based model that simulates the geographic expansion of transport networks by several decision-makers with varying objectives. The model progressively adds extensions to a growing network by choosing the most attractive investments from a limited choice set. Attractiveness is defined as a function of variables in which revenue and broader societal benefits may play a role and can be based on empirically underpinned parameters that may differ according to private or public interests. The choice set is selected from an exhaustive set of links and presumably contains those investment options that best meet private operator's objectives by balancing the revenues of additional fare against construction costs. The investment options consist of geographically plausible routes with potential detours. These routes are generated using a fine-meshed regularly latticed network and shortest path finding methods. Additionally, two indicators of the geographic accuracy of the simulated networks are introduced. A historical case study is presented to demonstrate the model's first results. These results show that the modelled networks reproduce relevant results of the historically built network with reasonable accuracy.

  20. Transport link scanner: simulating geographic transport network expansion through individual investments

    NASA Astrophysics Data System (ADS)

    Jacobs-Crisioni, C.; Koopmans, C. C.

    2016-06-01

    This paper introduces a GIS-based model that simulates the geographic expansion of transport networks by several decision-makers with varying objectives. The model progressively adds extensions to a growing network by choosing the most attractive investments from a limited choice set. Attractiveness is defined as a function of variables in which revenue and broader societal benefits may play a role and can be based on empirically underpinned parameters that may differ according to private or public interests. The choice set is selected from an exhaustive set of links and presumably contains those investment options that best meet private operator's objectives by balancing the revenues of additional fare against construction costs. The investment options consist of geographically plausible routes with potential detours. These routes are generated using a fine-meshed regularly latticed network and shortest path finding methods. Additionally, two indicators of the geographic accuracy of the simulated networks are introduced. A historical case study is presented to demonstrate the model's first results. These results show that the modelled networks reproduce relevant results of the historically built network with reasonable accuracy.

  1. Linking Climate Risk, Policy Networks and Adaptation Planning in Public Lands

    NASA Astrophysics Data System (ADS)

    Lubell, M.; Schwartz, M.; Peters, C.

    2014-12-01

    Federal public land management agencies in the United States have engaged a variety of planning efforts to address climate adaptation. A major goal of these efforts is to build policy networks that enable land managers to access information and expertise needed for responding to local climate risks. This paper investigates whether the perceived and modeled climate risk faced by different land managers is leading to larger networks or more participating in climate adaptation. In theory, the benefits of climate planning networks are larger when land managers are facing more potential changes. The basic hypothesis is tested with a survey of public land managers from hundreds of local and regional public lands management units in the Southwestern United States, as well as other stakeholders involved with climate adaptation planning. All survey respondents report their perceptions of climate risk along a variety of dimensions, as well as their participation in climate adaptation planning and information sharing networks. For a subset of respondents, we have spatially explicity GIS data about their location, which will be linked with downscaled climate model data. With the focus on climate change, the analysis is a subset of the overall idea of linking social and ecological systems.

  2. Prestressed F-actin networks cross-linked by hinged filamins replicate mechanical properties of cells

    NASA Astrophysics Data System (ADS)

    Gardel, M. L.; Nakamura, F.; Hartwig, J. H.; Crocker, J. C.; Stossel, T. P.; Weitz, D. A.

    2006-02-01

    We show that actin filaments, shortened to physiological lengths by gelsolin and cross-linked with recombinant human filamins (FLNs), exhibit dynamic elastic properties similar to those reported for live cells. To achieve elasticity values of comparable magnitude to those of cells, the in vitro network must be subjected to external prestress, which directly controls network elasticity. A molecular requirement for the strain-related behavior at physiological conditionsis a flexible hinge found in FLNa and some FLNb molecules. Basic physical properties of the in vitro filamin-F-actin network replicate the essential mechanical properties of living cells. This physical behavior could accommodate passive deformation and internal organelle trafficking at low strains yet resist externally or internally generated high shear forces. cytoskeleton | cell mechanics | nonlinear rheology

  3. Impulse-induced optimum signal amplification in scale-free networks.

    PubMed

    Martínez, Pedro J; Chacón, Ricardo

    2016-04-01

    Optimizing information transmission across a network is an essential task for controlling and manipulating generic information-processing systems. Here, we show how topological amplification effects in scale-free networks of signaling devices are optimally enhanced when the impulse transmitted by periodic external signals (time integral over two consecutive zeros) is maximum. This is demonstrated theoretically by means of a star-like network of overdamped bistable systems subjected to generic zero-mean periodic signals and confirmed numerically by simulations of scale-free networks of such systems. Our results show that the enhancer effect of increasing values of the signal's impulse is due to a correlative increase of the energy transmitted by the periodic signals, while it is found to be resonant-like with respect to the topology-induced amplification mechanism. PMID:27176316

  4. Impulse-induced optimum signal amplification in scale-free networks

    NASA Astrophysics Data System (ADS)

    Martínez, Pedro J.; Chacón, Ricardo

    2016-04-01

    Optimizing information transmission across a network is an essential task for controlling and manipulating generic information-processing systems. Here, we show how topological amplification effects in scale-free networks of signaling devices are optimally enhanced when the impulse transmitted by periodic external signals (time integral over two consecutive zeros) is maximum. This is demonstrated theoretically by means of a star-like network of overdamped bistable systems subjected to generic zero-mean periodic signals and confirmed numerically by simulations of scale-free networks of such systems. Our results show that the enhancer effect of increasing values of the signal's impulse is due to a correlative increase of the energy transmitted by the periodic signals, while it is found to be resonant-like with respect to the topology-induced amplification mechanism.

  5. Energy Efficiency of Distributed Signal Processing in Wireless Networks: A Cross-Layer Analysis

    NASA Astrophysics Data System (ADS)

    Geraci, Giovanni; Wildemeersch, Matthias; Quek, Tony Q. S.

    2016-02-01

    In order to meet the growing mobile data demand, future wireless networks will be equipped with a multitude of access points (APs). Besides the important implications for the energy consumption, the trend towards densification requires the development of decentralized and sustainable radio resource management techniques. It is critically important to understand how the distribution of signal processing operations affects the energy efficiency of wireless networks. In this paper, we provide a cross-layer framework to evaluate and compare the energy efficiency of wireless networks under different levels of distribution of the signal processing load: (i) hybrid, where the signal processing operations are shared between nodes and APs, (ii) centralized, where signal processing is entirely implemented at the APs, and (iii) fully distributed, where all operations are performed by the nodes. We find that in practical wireless networks, hybrid signal processing exhibits a significant energy efficiency gain over both centralized and fully distributed approaches.

  6. Self-Organized Link State Aware Routing for Multiple Mobile Agents in Wireless Network

    NASA Astrophysics Data System (ADS)

    Oda, Akihiro; Nishi, Hiroaki

    Recently, the importance of data sharing structures in autonomous distributed networks has been increasing. A wireless sensor network is used for managing distributed data. This type of distributed network requires effective information exchanging methods for data sharing. To reduce the traffic of broadcasted messages, reduction of the amount of redundant information is indispensable. In order to reduce packet loss in mobile ad-hoc networks, QoS-sensitive routing algorithm have been frequently discussed. The topology of a wireless network is likely to change frequently according to the movement of mobile nodes, radio disturbance, or fading due to the continuous changes in the environment. Therefore, a packet routing algorithm should guarantee QoS by using some quality indicators of the wireless network. In this paper, a novel information exchanging algorithm developed using a hash function and a Boolean operation is proposed. This algorithm achieves efficient information exchanges by reducing the overhead of broadcasting messages, and it can guarantee QoS in a wireless network environment. It can be applied to a routing algorithm in a mobile ad-hoc network. In the proposed routing algorithm, a routing table is constructed by using the received signal strength indicator (RSSI), and the neighborhood information is periodically broadcasted depending on this table. The proposed hash-based routing entry management by using an extended MAC address can eliminate the overhead of message flooding. An analysis of the collision of hash values contributes to the determination of the length of the hash values, which is minimally required. Based on the verification of a mathematical theory, an optimum hash function for determining the length of hash values can be given. Simulations are carried out to evaluate the effectiveness of the proposed algorithm and to validate the theory in a general wireless network routing algorithm.

  7. Ionically Cross-Linked Polymer Networks for the Multiple-Month Release of Small Molecules.

    PubMed

    Lawrence, Patrick G; Patil, Pritam S; Leipzig, Nic D; Lapitsky, Yakov

    2016-02-01

    Long-term (multiple-week or -month) release of small, water-soluble molecules from hydrogels remains a significant pharmaceutical challenge, which is typically overcome at the expense of more-complicated drug carrier designs. Such approaches are payload-specific and include covalent conjugation of drugs to base materials or incorporation of micro- and nanoparticles. As a simpler alternative, here we report a mild and simple method for achieving multiple-month release of small molecules from gel-like polymer networks. Densely cross-linked matrices were prepared through ionotropic gelation of poly(allylamine hydrochloride) (PAH) with either pyrophosphate (PPi) or tripolyphosphate (TPP), all of which are commonly available commercial molecules. The loading of model small molecules (Fast Green FCF and Rhodamine B dyes) within these polymer networks increases with the payload/network binding strength and with the PAH and payload concentrations used during encapsulation. Once loaded into the PAH/PPi and PAH/TPP ionic networks, only a few percent of the payload is released over multiple months. This extended release is achieved regardless of the payload/network binding strength and likely reflects the small hydrodynamic mesh size within the gel-like matrices. Furthermore, the PAH/TPP networks show promising in vitro cytocompatibility with model cells (human dermal fibroblasts), though slight cytotoxic effects were exhibited by the PAH/PPi networks. Taken together, the above findings suggest that PAH/PPi and (especially) PAH/TPP networks might be attractive materials for the multiple-month delivery of drugs and other active molecules (e.g., fragrances or disinfectants). PMID:26811936

  8. Digital Signal Processing and Control for the Study of Gene Networks

    PubMed Central

    Shin, Yong-Jun

    2016-01-01

    Thanks to the digital revolution, digital signal processing and control has been widely used in many areas of science and engineering today. It provides practical and powerful tools to model, simulate, analyze, design, measure, and control complex and dynamic systems such as robots and aircrafts. Gene networks are also complex dynamic systems which can be studied via digital signal processing and control. Unlike conventional computational methods, this approach is capable of not only modeling but also controlling gene networks since the experimental environment is mostly digital today. The overall aim of this article is to introduce digital signal processing and control as a useful tool for the study of gene networks. PMID:27102828

  9. Digital Signal Processing and Control for the Study of Gene Networks.

    PubMed

    Shin, Yong-Jun

    2016-01-01

    Thanks to the digital revolution, digital signal processing and control has been widely used in many areas of science and engineering today. It provides practical and powerful tools to model, simulate, analyze, design, measure, and control complex and dynamic systems such as robots and aircrafts. Gene networks are also complex dynamic systems which can be studied via digital signal processing and control. Unlike conventional computational methods, this approach is capable of not only modeling but also controlling gene networks since the experimental environment is mostly digital today. The overall aim of this article is to introduce digital signal processing and control as a useful tool for the study of gene networks. PMID:27102828

  10. Broadband local service offerings using free-space optical links: a network business perspective

    NASA Astrophysics Data System (ADS)

    Britz, David M.; Dodley, J. P.; Barnickel, D. J.

    2001-02-01

    12 This paper describes a promising optical wireless broadband technology that will provide low cost broadband services to the local access `last mile' market. This paper examines the application, advantages and limitations of utilizing Free Space Optical Communications (FSOC) systems for broadband access markets. The service markets that would fully utilize FSOC technologies include metropolitan areas, BLECs (multi- tenant dwellings/business apartments), campuses, industrial parks and `pole-to-hole' neighborhood deployments. This paper will identify weather dependent link availability as being the primary consideration in defining and selecting suitable locations for FSOC-based systems. Link availability in turn determines link range, type of service, and the need for transmission diversity. This paper will describe the implications of telecom `five nines' last-mile access availability and its effect on the transparent integration of FSOC technologies into the existing fiber optic networks. This paper will also describe propagation losses and link budget requirements for broadband FSOC-based local service. During adverse weather conditions, stand-alone, FSOC-based optical wireless links typically offer path lengths of less than 200 meters while still meeting the `five nines' availability criteria. This paper will also consider `availability limited' services. These services may prove to be attractive to customers who are willing to accept broadband service on an `as available basis'. The use of availability-enhancing transmission diversity and the use of intelligent `roof-top' routing and optical wireless cross connects between buildings will also be discussed.

  11. A mixed connection recovery strategy for surviving dual link failure in WDM networks

    NASA Astrophysics Data System (ADS)

    Yadav, Dharmendra Singh; Rana, Santosh; Prakash, Shashi

    2013-03-01

    As the size and complexity of a network increases, the probability of a dual link failure also increases. For recovering the dual link failures, two strategies have been presented in past. As per the first strategy, SPP-MAS (Shared Path Protection-Maximum Allowable Sharing), the sharing of backup lightpaths in SPP (Shared Path Protection) has been reduced, and in the second strategy TBPS (Two Backup Path Shared), the reservation of two backup lightpaths for each primary lightpath has been undertaken. The main flaw of these strategies is the requirement of redundant network resources towards the establishment of backup lightpaths, and the occurrence of trap problem after the second link fails. To minimize the redundant backup resources and the trap problem, a mixed connection recovery algorithm namely Adaptive Backup Routing over Reserved Resources (ABRRR) has been proposed. The design of ABRRR takes leverage of both, the pre-planned, and the post-failure connection recovery mechanisms. In ABRRR, the failed connections are re-provisioned adaptively over the pre-allocated backup network resources. Adaptive re-provisioning of the failed connection minimizes the trap problem. Using simulation experiments, we undertake a comparative study of the proposed strategy with the existing strategies (i.e. SPP-MAS and TBPS) under the network parameters of Blocking Probability, Dual Restorability, and Resource Utilization Ratio (RUR). Detailed investigations establish that the use of ABRRR leads to lower Blocking Probability, higher Dual Restorability, and minimized RUR compared to the existing strategies. Results also show that the proposed strategy not only survives more connections but also utilizes fewer numbers of resources compared to the existing strategies.

  12. Ether-linked diglycerides inhibit vascular smooth muscle cell growth via decreased MAPK and PI3K/Akt signaling.

    PubMed

    Houck, Kristy L; Fox, Todd E; Sandirasegarane, Lakshman; Kester, Mark

    2008-10-01

    Diglycerides (DGs) are phospholipid-derived second messengers that regulate PKC-dependent signaling pathways. Distinct species of DGs are generated from inflammatory cytokines and growth factors. Growth factors increase diacyl- but not ether-linked DG species, whereas inflammatory cytokines predominately generate alkyl, acyl- and alkenyl, acyl-linked DG species in rat mesenchymal cells. These DG species have been shown to differentially regulate protein kinase C (PKC) isotypes. Ester-linked diacylglycerols activate PKC-epsilon and cellular proliferation in contrast to ether-linked DGs, which lead to growth arrest through the inactivation of PKC-epsilon. It is now hypothesized that ether-linked DGs inhibit mitogenesis through the inactivation of ERK and/or Akt signaling cascades. We demonstrate that cell-permeable ether-linked DGs reduce vascular smooth muscle cell growth by inhibiting platelet-derived growth factor-stimulated ERK in a PKC-epsilon-dependent manner. This inhibition is specific to the ERK pathway, since ether-linked DGs do not affect growth factor-induced activation of other family members of the MAPKs, including p38 MAPK and c-Jun NH(2)-terminal kinases. We also demonstrate that ether-linked DGs reduce prosurvival phosphatidylinositol 3-kinase (PI3K)/Akt signaling, independent of PKC-epsilon, by diminishing an interaction between the subunits of PI3K and not by affecting protein phosphatase 2A or lipid (phosphatase and tensin homologue deleted in chromosome 10) phosphatases. Taken together, our studies identify ether-linked DGs as potential adjuvant therapies to limit vascular smooth muscle migration and mitogenesis in atherosclerotic and restenotic models. PMID:18723771

  13. Newly Constructed Network Models of Different WNT Signaling Cascades Applied to Breast Cancer Expression Data

    PubMed Central

    Kramer, Frank; Pukrop, Tobias; Beißbarth, Tim; Bleckmann, Annalen

    2015-01-01

    Introduction WNT signaling is a complex process comprising multiple pathways: the canonical β-catenin-dependent pathway and several alternative non-canonical pathways that act in a β-catenin-independent manner. Representing these intricate signaling mechanisms through bioinformatic approaches is challenging. Nevertheless, a simplified but reliable bioinformatic WNT pathway model is needed, which can be further utilized to decipher specific WNT activation states within e.g. high-throughput data. Results In order to build such a model, we collected, parsed, and curated available WNT signaling knowledge from different pathway databases. The data were assembled to construct computationally suitable models of different WNT signaling cascades in the form of directed signaling graphs. This resulted in four networks representing canonical WNT signaling, non-canonical WNT signaling, the inhibition of canonical WNT signaling and the regulation of WNT signaling pathways, respectively. Furthermore, these networks were integrated with microarray and RNA sequencing data to gain deeper insight into the underlying biology of gene expression differences between MCF-7 and MDA-MB-231 breast cancer cell lines, representing weakly and highly invasive breast carcinomas, respectively. Differential genes up-regulated in the MDA-MB-231 compared to the MCF-7 cell line were found to display enrichment in the gene set originating from the non-canonical network. Moreover, we identified and validated differentially regulated modules representing canonical and non-canonical WNT pathway components specific for the aggressive basal-like breast cancer subtype. Conclusions In conclusion, we demonstrated that these newly constructed WNT networks reliably reflect distinct WNT signaling processes. Using transcriptomic data, we shaped these networks into comprehensive modules of the genes implicated in the aggressive basal-like breast cancer subtype and demonstrated that non-canonical WNT signaling is

  14. Cerebral Networks Linked to Itch-related Sensations Induced by Histamine and Capsaicin.

    PubMed

    Vierow, Verena; Forster, Clemens; Vogelgsang, Rebekka; Dörfler, Arnd; Handwerker, Herman O

    2015-07-01

    This functional magnetic resonance imaging (fMRI) study explored the central nervous processing of itch induced by histamine and capsaicin, delivered via inactivated cowhage spicules, and the influence of low-dose naltrexone. Scratch bouts were delivered at regular intervals after spicule insertion in order temporarily to suppress the itch. At the end of each trial the subjects rated their itch and scratch-related sensations. Stepwise multiple regression analyses were employed for identifying cerebral networks contributing to the intensities of "itching", "burning", "stinging", "pricking" and "itch relief by scratching". In the capsaicin experiments a network for "burning" was identified, which included the posterior insula, caudate and putamen. In the histamine experiments networks for "itching" and "itch relief" were found, which included operculum, hippocampus and amygdala. Naltrexone generally reduced fMRI activation and the correlations between fMRI signal and ratings. Furthermore, scratching was significantly less pleasant under naltrexone. PMID:25387448

  15. Reconstruction of the temporal signaling network in Salmonella-infected human cells

    PubMed Central

    Budak, Gungor; Eren Ozsoy, Oyku; Aydin Son, Yesim; Can, Tolga; Tuncbag, Nurcan

    2015-01-01

    Salmonella enterica is a bacterial pathogen that usually infects its host through food sources. Translocation of the pathogen proteins into the host cells leads to changes in the signaling mechanism either by activating or inhibiting the host proteins. Given that the bacterial infection modifies the response network of the host, a more coherent view of the underlying biological processes and the signaling networks can be obtained by using a network modeling approach based on the reverse engineering principles. In this work, we have used a published temporal phosphoproteomic dataset of Salmonella-infected human cells and reconstructed the temporal signaling network of the human host by integrating the interactome and the phosphoproteomic dataset. We have combined two well-established network modeling frameworks, the Prize-collecting Steiner Forest (PCSF) approach and the Integer Linear Programming (ILP) based edge inference approach. The resulting network conserves the information on temporality, direction of interactions, while revealing hidden entities in the signaling, such as the SNARE binding, mTOR signaling, immune response, cytoskeleton organization, and apoptosis pathways. Targets of the Salmonella effectors in the host cells such as CDC42, RHOA, 14-3-3δ, Syntaxin family, Oxysterol-binding proteins were included in the reconstructed signaling network although they were not present in the initial phosphoproteomic data. We believe that integrated approaches, such as the one presented here, have a high potential for the identification of clinical targets in infectious diseases, especially in the Salmonella infections. PMID:26257716

  16. Promoting Wired Links in Wireless Mesh Networks: An Efficient Engineering Solution

    PubMed Central

    Barekatain, Behrang; Raahemifar, Kaamran; Ariza Quintana, Alfonso; Triviño Cabrera, Alicia

    2015-01-01

    Wireless Mesh Networks (WMNs) cannot completely guarantee good performance of traffic sources such as video streaming. To improve the network performance, this study proposes an efficient engineering solution named Wireless-to-Ethernet-Mesh-Portal-Passageway (WEMPP) that allows effective use of wired communication in WMNs. WEMPP permits transmitting data through wired and stable paths even when the destination is in the same network as the source (Intra-traffic). Tested with four popular routing protocols (Optimized Link State Routing or OLSR as a proactive protocol, Dynamic MANET On-demand or DYMO as a reactive protocol, DYMO with spanning tree ability and HWMP), WEMPP considerably decreases the end-to-end delay, jitter, contentions and interferences on nodes, even when the network size or density varies. WEMPP is also cost-effective and increases the network throughput. Moreover, in contrast to solutions proposed by previous studies, WEMPP is easily implemented by modifying the firmware of the actual Ethernet hardware without altering the routing protocols and/or the functionality of the IP/MAC/Upper layers. In fact, there is no need for modifying the functionalities of other mesh components in order to work with WEMPPs. The results of this study show that WEMPP significantly increases the performance of all routing protocols, thus leading to better video quality on nodes. PMID:25793516

  17. A Systems Approach Identifies Networks and Genes Linking Sleep and Stress: Implications for Neuropsychiatric Disorders

    PubMed Central

    Jiang, Peng; Scarpa, Joseph R.; Fitzpatrick, Karrie; Losic, Bojan; Gao, Vance D.; Hao, Ke; Summa, Keith C.; Yang, He S.; Zhang, Bin; Allada, Ravi; Vitaterna, Martha H.; Turek, Fred W.; Kasarskis, Andrew

    2016-01-01

    SUMMARY Sleep dysfunction and stress susceptibility are co-morbid complex traits, which often precede and predispose patients to a variety of neuropsychiatric diseases. Here, we demonstrate multi-level organizations of genetic landscape, candidate genes, and molecular networks associated with 328 stress and sleep traits in a chronically stressed population of 338 (C57BL/6J×A/J) F2 mice. We constructed striatal gene co-expression networks, revealing functionally and cell-type specific gene co-regulations important for stress and sleep. Using a composite ranking system, we identified network modules most relevant for 15 independent phenotypic categories, highlighting a mitochondria/synaptic module that links sleep and stress. The key network regulators of this module are overrepresented with genes implicated in neuropsychiatric diseases. Our work suggests the interplay between sleep, stress, and neuropathology emerge from genetic influences on gene expression and their collective organization through complex molecular networks, providing a framework to interrogate the mechanisms underlying sleep, stress susceptibility, and related neuropsychiatric disorders. PMID:25921536

  18. The Structure of Gold-Nanoparticle Networks Cross-Linked by Di- and Multifunctional RAFT Oligomers.

    PubMed

    Rossner, Christian; Glatter, Otto; Saldanha, Oliva; Köster, Sarah; Vana, Philipp

    2015-09-29

    Gold nanoparticle (AuNP) network structures featuring particles from the two-phase Brust-Schiffrin synthesis and linear RAFT oligomers of styrene with two and multiple trithiocarbonate (TTC) groups along their backbone have been investigated in detail. Insights into the internal structures of these particle networks could be obtained from small-angle X-ray scattering experiments, showing that primary AuNPs are cross-linked by the employed molecular linker. The extent of AuNP network formation was investigated by means of dynamic light scattering and UV/visible extinction spectroscopy, showing an abrupt attenuation of network formation after a critical degree of polymerization of the cross-linker is exceeded. Analysis of transmission electron micrographs indicated a three-dimensional shape of the particle superstructures, which is evenly filled with the primary AuNPs. From the results obtained in this study, guidelines for the fabrication of nanoparticle networks from the self-assembly with macromolecular cross-linkers are suggested. PMID:26340689

  19. Promoting wired links in wireless mesh networks: an efficient engineering solution.

    PubMed

    Barekatain, Behrang; Raahemifar, Kaamran; Ariza Quintana, Alfonso; Triviño Cabrera, Alicia

    2015-01-01

    Wireless Mesh Networks (WMNs) cannot completely guarantee good performance of traffic sources such as video streaming. To improve the network performance, this study proposes an efficient engineering solution named Wireless-to-Ethernet-Mesh-Portal-Passageway (WEMPP) that allows effective use of wired communication in WMNs. WEMPP permits transmitting data through wired and stable paths even when the destination is in the same network as the source (Intra-traffic). Tested with four popular routing protocols (Optimized Link State Routing or OLSR as a proactive protocol, Dynamic MANET On-demand or DYMO as a reactive protocol, DYMO with spanning tree ability and HWMP), WEMPP considerably decreases the end-to-end delay, jitter, contentions and interferences on nodes, even when the network size or density varies. WEMPP is also cost-effective and increases the network throughput. Moreover, in contrast to solutions proposed by previous studies, WEMPP is easily implemented by modifying the firmware of the actual Ethernet hardware without altering the routing protocols and/or the functionality of the IP/MAC/Upper layers. In fact, there is no need for modifying the functionalities of other mesh components in order to work with WEMPPs. The results of this study show that WEMPP significantly increases the performance of all routing protocols, thus leading to better video quality on nodes. PMID:25793516

  20. An integrated signal transduction network of macrophage migration inhibitory factor.

    PubMed

    Subbannayya, Tejaswini; Variar, Prathyaksha; Advani, Jayshree; Nair, Bipin; Shankar, Subramanian; Gowda, Harsha; Saussez, Sven; Chatterjee, Aditi; Prasad, T S Keshava

    2016-06-01

    Macrophage migration inhibitory factor (MIF) is a glycosylated multi-functional protein that acts as an enzyme as well as a cytokine. MIF mediates its actions through a cell surface class II major histocompatibility chaperone, CD74 and co-receptors such as CD44, CXCR2, CXCR4 or CXCR7. MIF has been implicated in the pathogenesis of several acute and chronic inflammatory diseases. Although MIF is a molecule of biomedical importance, a public resource of MIF signaling pathway is currently lacking. In view of this, we carried out detailed data mining and documentation of the signaling events pertaining to MIF from published literature and developed an integrated reaction map of MIF signaling. This resulted in the cataloguing of 68 molecules belonging to MIF signaling pathway, which includes 24 protein-protein interactions, 44 post-translational modifications, 11 protein translocation events and 8 activation/inhibition events. In addition, 65 gene regulation events at the mRNA levels induced by MIF signaling have also been catalogued. This signaling pathway has been integrated into NetPath ( http://www.netpath.org ), a freely available human signaling pathway resource developed previously by our group. The MIF pathway data is freely available online in various community standard data exchange formats. We expect that data on signaling events and a detailed signaling map of MIF will provide the scientific community with an improved platform to facilitate further molecular as well as biomedical investigations on MIF. PMID:27139435

  1. Fascin links Btl/FGFR signalling to the actin cytoskeleton during Drosophila tracheal morphogenesis.

    PubMed

    Okenve-Ramos, Pilar; Llimargas, Marta

    2014-02-01

    A key challenge in normal development and in disease is to elucidate the mechanisms of cell migration. Here we approach this question using the tracheal system of Drosophila as a model. Tracheal cell migration requires the Breathless/FGFR pathway; however, how the pathway induces migration remains poorly understood. We find that the Breathless pathway upregulates singed at the tip of tracheal branches, and that this regulation is functionally relevant. singed encodes Drosophila Fascin, which belongs to a conserved family of actin-bundling proteins involved in cancer progression and metastasis upon misregulation. We show that singed is required for filopodia stiffness and proper morphology of tracheal tip cells, defects that correlate with an abnormal actin organisation. We propose that singed-regulated filopodia and cell fronts are required for timely and guided branch migration and for terminal branching and branch fusion. We find that singed requirements rely on its actin-bundling activity controlled by phosphorylation, and that active Singed can promote tip cell features. Furthermore, we find that singed acts in concert with forked, another actin cross-linker. The absence of both cross-linkers further stresses the relevance of tip cell morphology and filopodia for tracheal development. In summary, our results on the one hand reveal a previously undescribed role for forked in the organisation of transient actin structures such as filopodia, and on the other hand identify singed as a new target of Breathless signal, establishing a link between guidance cues, the actin cytoskeleton and tracheal morphogenesis. PMID:24496629

  2. Hippo signaling regulates Microprocessor and links cell density-dependent miRNA biogenesis to cancer

    PubMed Central

    Mori, Masaki; Triboulet, Robinson; Mohseni, Morvarid; Schlegelmilch, Karin; Shrestha, Kriti; Camargo, Fernando D.; Gregory, Richard I.

    2014-01-01

    SUMMARY Global downregulation of microRNAs (miRNAs) is commonly observed in human cancers and can have a causative role in tumorigenesis. The mechanisms responsible for this phenomenon remain poorly understood. Here we show that YAP, the downstream target of the tumor-suppressive Hippo signaling pathway regulates miRNA biogenesis in a cell density-dependent manner. At low cell density, nuclear YAP binds and sequesters p72 (DDX17), a regulatory component of the miRNA processing machinery. At high cell density, Hippo-mediated cytoplasmic retention of YAP facilitates p72 association with Microprocessor and binding to a specific sequence motif in pri-miRNAs. Inactivation of the Hippo pathway or expression of constitutively active YAP causes widespread miRNA suppression in cells and tumors and a corresponding post-transcriptional induction of MYC expression. Thus, the Hippo pathway links contact-inhibition regulation to miRNA biogenesis and may be responsible for the widespread miRNA repression observed in cancer. PMID:24581491

  3. 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. PMID:22745503

  4. Methods for the Analysis of Protein Phosphorylation-Mediated Cellular Signaling Networks.

    PubMed

    White, Forest M; Wolf-Yadlin, Alejandro

    2016-06-12

    Protein phosphorylation-mediated cellular signaling networks regulate almost all aspects of cell biology, including the responses to cellular stimulation and environmental alterations. These networks are highly complex and comprise hundreds of proteins and potentially thousands of phosphorylation sites. Multiple analytical methods have been developed over the past several decades to identify proteins and protein phosphorylation sites regulating cellular signaling, and to quantify the dynamic response of these sites to different cellular stimulation. Here we provide an overview of these methods, including the fundamental principles governing each method, their relative strengths and weaknesses, and some examples of how each method has been applied to the analysis of complex signaling networks. When applied correctly, each of these techniques can provide insight into the topology, dynamics, and regulation of protein phosphorylation signaling networks. PMID:27049636

  5. Methods for the Analysis of Protein Phosphorylation–Mediated Cellular Signaling Networks

    NASA Astrophysics Data System (ADS)

    White, Forest M.; Wolf-Yadlin, Alejandro

    2016-06-01

    Protein phosphorylation–mediated cellular signaling networks regulate almost all aspects of cell biology, including the responses to cellular stimulation and environmental alterations. These networks are highly complex and comprise hundreds of proteins and potentially thousands of phosphorylation sites. Multiple analytical methods have been developed over the past several decades to identify proteins and protein phosphorylation sites regulating cellular signaling, and to quantify the dynamic response of these sites to different cellular stimulation. Here we provide an overview of these methods, including the fundamental principles governing each method, their relative strengths and weaknesses, and some examples of how each method has been applied to the analysis of complex signaling networks. When applied correctly, each of these techniques can provide insight into the topology, dynamics, and regulation of protein phosphorylation signaling networks.

  6. Concentric Archimedean polyhedra: Mn(III)12Mn(II)9 aggregates linked into a cubic network.

    PubMed

    Nayak, Sanjit; Lan, Yanhua; Clérac, Rodolphe; Anson, Christopher E; Powell, Annie K

    2008-11-30

    A Mn(III)(12)Mn(II)(9) aggregate has a structure built up of concentric polyhedra with these units linked into a cubic network to give a remarkably pleasing structure isotypic with iron pyrites. PMID:19009052

  7. Networks.

    ERIC Educational Resources Information Center

    Maughan, George R.; Petitto, Karen R.; McLaughlin, Don

    2001-01-01

    Describes the connectivity features and options of modern campus communication and information system networks, including signal transmission (wire-based and wireless), signal switching, convergence of networks, and network assessment variables, to enable campus leaders to make sound future-oriented decisions. (EV)

  8. Beyond the wiring diagram: signalling through complex neuromodulator networks

    PubMed Central

    Brezina, Vladimir

    2010-01-01

    During the computations performed by the nervous system, its ‘wiring diagram’—the map of its neurons and synaptic connections—is dynamically modified and supplemented by multiple actions of neuromodulators that can be so complex that they can be thought of as constituting a biochemical network that combines with the neuronal network to perform the computation. Thus, the neuronal wiring diagram alone is not sufficient to specify, and permit us to understand, the computation that underlies behaviour. Here I review how such modulatory networks operate, the problems that their existence poses for the experimental study and conceptual understanding of the computations performed by the nervous system, and how these problems may perhaps be solved and the computations understood by considering the structural and functional ‘logic’ of the modulatory networks. PMID:20603357

  9. A Novel Clustering Algorithm for Mobile Ad Hoc Networks Based on Determination of Virtual Links' Weight to Increase Network Stability

    PubMed Central

    Karimi, Abbas; Afsharfarnia, Abbas; Zarafshan, Faraneh; Al-Haddad, S. A. R.

    2014-01-01

    The stability of clusters is a serious issue in mobile ad hoc networks. Low stability of clusters may lead to rapid failure of clusters, high energy consumption for reclustering, and decrease in the overall network stability in mobile ad hoc network. In order to improve the stability of clusters, weight-based clustering algorithms are utilized. However, these algorithms only use limited features of the nodes. Thus, they decrease the weight accuracy in determining node's competency and lead to incorrect selection of cluster heads. A new weight-based algorithm presented in this paper not only determines node's weight using its own features, but also considers the direct effect of feature of adjacent nodes. It determines the weight of virtual links between nodes and the effect of the weights on determining node's final weight. By using this strategy, the highest weight is assigned to the best choices for being the cluster heads and the accuracy of nodes selection increases. The performance of new algorithm is analyzed by using computer simulation. The results show that produced clusters have longer lifetime and higher stability. Mathematical simulation shows that this algorithm has high availability in case of failure. PMID:25114965

  10. How rapid is aphid-induced signal transfer between plants via common mycelial networks?

    PubMed

    Babikova, Zdenka; Johnson, David; Bruce, Toby; Pickett, John A; Gilbert, Lucy

    2013-11-01

    Arbuscular mycorrhizal (AM) fungi are important plant mutualists that can connect roots of neighboring plants to form common mycelial networks. A recent study demonstrated that these networks can act as conduits for aphid-induced signals between plants, activating chemical defenses in uninfested neighboring plants so that they become unattractive to aphids but attractive to their enemies (parasitoids). The benefit to the neighboring plants will increase if the signal speed is rapid, enabling them to respond before aphids attack. Here, we determine the speed of aphid-induced signal transfer between plants infested with aphids ("donor") and neighboring aphid-free plants that were either connected or unconnected to the donor via a common mycelial network. Induced changes in plant volatiles from neighbors connected to donors started within 24 h of aphid infestation of donors. This demonstrates a rapid signal, implying potential benefit to plants receiving the signal, and raises intriguing ecological and evolutionary questions. PMID:24563703

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

    NASA Technical Reports Server (NTRS)

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

    2011-01-01

    A lunar surface systems study explores the application of optical communications to support a high bandwidth data link from a lunar relay satellite and from fixed lunar assets. The results show that existing 1-m ground stations could provide more than 99% coverage of the lunar terminal at 100Mb/s data rates from a lunar relay satellite and in excess of 200Mb/s from a fixed terminal on the lunar surface. We have looked at the effects of the lunar regolith and its removal on optical samples. Our results indicate that under repeated dust removal episodes sapphire rather than fused silica would be a more durable material for optical surfaces. Disruption tolerant network protocols can minimize the data loss due to link dropouts. We report on the preliminary results of the DTN protocol implemented over the optical carrier.

  12. Probing the protein interaction network of Pseudomonas aeruginosa cells by chemical cross-linking mass spectrometry

    PubMed Central

    Navare, Arti T.; Chavez, Juan D.; Zheng, Chunxiang; Weisbrod, Chad R.; Eng, Jimmy K.; Siehnel, Richard; Singh, Pradeep K.; Manoil, Colin; Bruce, James E.

    2015-01-01

    SUMMARY In pathogenic Gram-negative bacteria, interactions among membrane proteins are key mediators of host cell attachment, invasion, pathogenesis, and antibiotic resistance. Membrane protein interactions are highly dependent upon local properties and environment, warranting direct measurements on native protein complex structures as they exist in cells. Here we apply in vivo chemical cross-linking mass spectrometry, to reveal the first large-scale protein interaction network in the Pseudomonas aeruginosa, an opportunistic human pathogen, by covalently linking interacting protein partners, thereby fixing protein complexes in vivo. A total of 626 cross-linked peptide pairs, including previously unknown interactions of many membrane proteins are reported. These pairs not only define the existence of these interactions in cells, but also provide linkage constraints for complex structure predictions. Structures of three membrane proteins, namely, SecD-SecF, OprF, and OprI are predicted using in vivo cross-linked sites. These findings improve understanding of membrane protein interactions and structures in cells. PMID:25800553

  13. Gelatin hydrogels cross-linked with bis(vinylsulfonyl)methane (BVSM): 1. The chemical networks.

    PubMed

    Hellio-Serughetti, Dominique; Djabourov, Madeleine

    2006-09-26

    This paper deals with chemical gelation of gelatin in the presence of a cross-linker, bis(vinylsulfonyl)methane (BVSM), which is able to create covalent C-N bonds with amine groups. The investigation is performed at 40 degrees C, where no triple helices are present. Gelatin is in random coil conformation. The influence of various parameters (gelatin concentration, cross-linker concentration, and pH (number of reacting sites along the gelatin chain)) was examined. Gel formation was followed by rheological and thermodynamic measurements (microcalorimetry) versus time (kinetic measurements). Furthermore, the storage moduli were compared to the number of links formed in the course of gelation. The experiments show that, within the experimental range investigated, a fully homogeneous network is not reached; the chemical gels, even upon completion of the reactions, are still in the critical domain, near the threshold. A power law behavior was put in evidence for the shear modulus versus the distance to the gel point, expressed as the concentration of links per gelatin chain. The exponent (f = 3.4 +/- 0.3) is close to that expected for the vulcanization of long chains. The storage moduli can be superposed on a single curve where the abscissa is the product of the number of C-N links per unit volume and the gelatin concentration at an exponent equal to -0.76 +/- 0.03. This exponent suggests the role of entanglements for interchain cross-linking. PMID:16981770

  14. A novel progressive signal association algorithm for detecting teleseismic/network-outside events using regional seismic networks

    NASA Astrophysics Data System (ADS)

    Jin, Ping; Pan, Changzhou; Zhang, Chengliu; Shen, Xufeng; Wang, Hongchun; Lu, Na

    2015-06-01

    Regional seismic networks may and in some cases need to be used to monitor teleseismic or network-outside events. For detecting and localizing teleseismic events automatically and reliably in this case, in this paper we present a novel progressive association algorithm for teleseismic signals recorded by a regional seismic network. The algorithm takes triangle station arrays as the starting point to search for P waves of teleseismic events progressively by that, as detections from different stations actually are from the same teleseismic event, their arrival times should be linearly related to the average slowness vector with which the signal propagates across the network, and the slowness of direct teleseismic P wave basically is different from other major seismic phases. We have tested this algorithm using data recorded by Xinjiang Seismic Network of China (XJSN) for 16 d. The results show that the algorithm can effectively and reliably detect and localize earthquakes outside of the network. For the period of the test data, as all mb 4.0+ events with Δc < 30° and all mb 4.5+ events with Δc < 60° referring to the International Data Center-Reviewed Event Bulletin (IDC REB) were detected, where Δc is the epicentral distance relative to the network's geographical centre, the rate of false events only accounted for 2.4 per cent, suggesting that the new association algorithm has good application prospect for situations when regional seismic networks need to be used to monitor teleseismic events.

  15. Reduction of resting state network segregation is linked to disorders of consciousness

    NASA Astrophysics Data System (ADS)

    Rudas, Jorge; Martínez, Darwin; Guaje, Javier; Demertzi, Athena; Heine, Lizette; Tshibanda, Luaba; Soddu, Andrea; Laureys, Steven; Gómez, Francisco

    2015-12-01

    Recent evidence suggests that healthy brain is organized on large-scale in regions spatially distant and partially temporally synchronized. These regions commonly are called Resting State Networks (RSNs). Many RSNs has been identified in multiples spatial scales in healthy subjects and their interactions has been used to define the functional network connectivity (FNC). The main idea in FNC is that the dynamic shown in the interactions among RSNs in control subjects, can change in pathological and pharmacological conditions. However, this hypothesis assumes that functional structure of healthy brain, remains in other brain states or conditions. In this work, we proposed a novel methodology in order to find the new brain functional structure for disorders of consciousness conditions, based on multi-objective optimization approach. Particularly, we find the best partition of RSNs set, that maximize two modularity measures (Kapur and Otsu measures). Our results suggest that the brain segregation level, may be linked to consciousness level.

  16. Finite-time synchronization of complex dynamical networks with multi-links via intermittent controls

    NASA Astrophysics Data System (ADS)

    Zheng, Mingwen; Li, Lixiang; Peng, Haipeng; Xiao, Jinghua; Yang, Yixian; Zhao, Hui; Ren, Jingfeng

    2016-02-01

    This paper considers finite-time synchronization of complex multi-links dynamical networks with or without internal time delays via intermittent controls. Two simple intermittent feedback controllers are designed to achieve finite-time synchronization between the drive and response system. Some novel and effective finite-time synchronization criteria are derived based on finite-time stability analysis techniques. By constructing suitable Lyapunov functions, we theoretically prove its correctness. Finally, two numerical simulation examples are given to show the effectiveness of proposed method in this paper.

  17. Identification of nonlinear dynamic systems using functional link artificial neural networks.

    PubMed

    Patra, J C; Pal, R N; Chatterji, B N; Panda, G

    1999-01-01

    We have presented an alternate ANN structure called functional link ANN (FLANN) for nonlinear dynamic system identification using the popular backpropagation algorithm. In contrast to a feedforward ANN structure, i.e., a multilayer perceptron (MLP), the FLANN is basically a single layer structure in which nonlinearity is introduced by enhancing the input pattern with nonlinear functional expansion. With proper choice of functional expansion in a FLANN, this network performs as good as and in some cases even better than the MLP structure for the problem of nonlinear system identification. PMID:18252296

  18. The Linked System Project : a network interconnection project between three major bibliographic utilities and LC

    NASA Astrophysics Data System (ADS)

    Kurihara, Shin'ichi

    The Linked Systems Project (LSP) is the first network project based on the Open Systems Interconnection (OSI) in the world. The purpose of the project is to interconnect between three major bibliographic utilities and LC, and to perform as one system on the whole. The first application developed for the LSP is the sharing of name authority data based on the Name Authority Cooperative (NACO) Project. In 1985, LC began to send name authority records to RLG/RLIN. Since 1987, RLG/RLIN and OCLC send name authority records to LC. Bibliographic records will be sent mutually between three major bibliographic utilities and LC near future.

  19. Response of biopolymer networks governed by the physical properties of cross-linking molecules.

    PubMed

    Wei, Xi; Zhu, Qian; Qian, Jin; Lin, Yuan; Shenoy, V B

    2016-02-23

    In this study, we examine how the physical properties of cross-linking molecules affect the bulk response of bio-filament networks, an outstanding question in the study of biological gels and the cytoskeleton. We show that the stress-strain relationship of such networks typically undergoes linear increase - strain hardening - stress serration - total fracture transitions due to the interplay between the bending and stretching of individual filaments and the deformation and breakage of cross-linkers. Interestingly, the apparent network modulus is found to scale with the linear and rotational stiffness of the crosslinks to a power exponent of 0.78 and 0.13, respectively. In addition, the network fracture energy will reach its minimum at intermediate rotational compliance values, reflecting the fact that most of the strain energy will be stored in the distorted filaments with rigid cross-linkers while the imposed deformation will be "evenly" distributed among significantly more crosslinking molecules with high rotational compliance. PMID:26760315

  20. Stress Enhanced Gelation in α-Actinin-4 Cross-linked Actin Networks

    NASA Astrophysics Data System (ADS)

    Yao, Norman; Broedersz, Chase; Depken, Martin; Becker, Daniel; Pollak, Martin; Mackintosh, Frederick; Weitz, David

    2012-02-01

    A hallmark of biopolymer networks is their exquisite sensitivity to stress, demonstrated for example, by pronounced nonlinear elastic stiffening. Typically, they also yield under increased static load, providing a mechanism to achieve fluid-like behavior. In this talk, I will demonstrate an unexpected dynamical behavior in biopolymer networks consisting of F-actin cross-linked by a physiological actin binding protein, α-Actinin-4. Applied stress actually enhances gelation of these networks by delaying the onset of structural relaxation and network flow, thereby extending the regime of solid-like behavior to much lower frequencies. By using human kidney disease-associated mutant cross-linkers with varying binding affinities, we propose a molecular origin for this stress-enhanced gelation: It arises from the increased binding affinity of the cross-linker under load, characteristic of catch-bond-like behavior. This property may have important biological implications for intracellular mechanics, representing as it does a qualitatively new class of material behavior.

  1. F-actin cross-linking enhances the stability of force generation in disordered actomyosin networks

    NASA Astrophysics Data System (ADS)

    Jung, Wonyeong; Murrell, Michael P.; Kim, Taeyoon

    2015-12-01

    Myosin molecular motors and actin cross-linking proteins (ACPs) are known to mediate the generation and transmission of mechanical forces within the cortical F-actin cytoskeleton that drive major cellular processes such as cell division and migration. However, how motors and ACPs interact collectively over diverse timescales to modulate the time-dependent mechanical properties of the cytoskeleton remains unclear. In this study, we present a three-dimensional agent-based computational model of the cortical actomyosin network to quantitatively determine the effects of motor activity and the density and kinetics of ACPs on the accumulation and maintenance of mechanical tension within a disordered actomyosin network. We found that motors accumulate large stress quickly by behaving as temporary cross-linkers although this stress is relaxed over time unless there are sufficient passive ACPs to stabilize the network. Stabilization by ACPs helps motors to generate forces up to their maximum potential, leading to significant enhancement of the efficiency and stability of stress generation. Thus, we demonstrated that the force-dependent kinetics of ACP dissociation plays a critical role for the accumulation and sustainment of stress and the structural remodeling of networks.

  2. TALON - The Telescope Alert Operation Network System : intelligent linking of distributed autonomous robotic telescopes

    SciTech Connect

    White, R. R.; Wren, J.; Davis, H. R.; Galassi, M. C.; Starr, D. L.; Vestrand, W. T.; Wozniak, P. R.

    2004-01-01

    The internet has brought about great change in the astronomical community, but this interconnectivity is just starting to be exploited for use in instrumentation. Utilizing the internet for communicating between distributed astronomical systems is still in its infancy, but it already shows great potential. Here we present an example of a distributed network of telescopes that performs more efficienfiy in synchronous operation than as individual instruments. RAPid Telescopes for Optical Response (RAPTOR) is a system of telescopes at LANL that has intelligent intercommunication, combined with wide-field optics, temporal monitoring software, and deep-field follow-up capability all working in closed-loop real-time operation. The Telescope ALert Operations Network (TALON) is a network server that allows intercommunication of alert triggers from external and internal resources and controls the distribution of these to each of the telescopes on the network. TALON is designed to grow, allowing any number of telescopes to be linked together and communicate. Coupled with an intelligent alert client at each telescope, it can analyze and respond to each distributed TALON alert based on the telescopes needs and schedule.

  3. Preparation of single or double-network chitosan/poly(vinyl alcohol) gel films through selective cross-linking method

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A selective cross-linking method was developed to create single or double network chitosan/poly(vinyl alcohol) gel films. The cross-linking is based on the hydrogen bonding between PVA and borate and the strong electrostatic interaction between chitosan and tripolyphosphate. The resultant gel films ...

  4. Array signal processing in the NASA Deep Space Network

    NASA Technical Reports Server (NTRS)

    Pham, Timothy T.; Jongeling, Andre P.

    2004-01-01

    In this paper, we will describe the benefits of arraying and past as well as expected future use of this application. The signal processing aspects of array system are described. Field measurements via actual tracking spacecraft are also presented.

  5. Neuronal activity in primate dorsal anterior cingulate cortex signals task conflict and predicts adjustments in pupil-linked arousal

    PubMed Central

    Ebitz, R. Becket; Platt, Michael L.

    2014-01-01

    Summary Whether driving a car, shopping for food, or paying attention in a classroom of boisterous teenagers, it’s often hard to maintain focus on goals in the face of distraction. Brain imaging studies in humans implicate the dorsal anterior cingulate cortex (dACC) in regulating the conflict between goals and distractors. Here we show for the first time that single dACC neurons signal conflict between task goals and distractors in the rhesus macaque, particularly for biologically-relevant social stimuli. For some neurons, task conflict signals predicted subsequent changes in pupil size—a peripheral index of arousal linked to noradrenergic tone—associated with reduced distractor interference. dACC neurons also responded to errors and these signals predicted adjustments in pupil size. These findings provide the first neurophysiological endorsement of the hypothesis that dACC regulates conflict, in part, via modulation of pupil-linked processes such as arousal. PMID:25654259

  6. The Private User Network Interface--a GMPLS-compliant signaling

    NASA Astrophysics Data System (ADS)

    Papadimitriou, Dimitri; Rousseau, Bart; Körber, Wolfgang; Brockmann, Steffen; Verchère, Dominique

    2004-03-01

    To address the integration of [IP/MPLS (multiprotocol label-switching)] packet and (optical) transport networks, the Optical Internetworking Forum (OIF) has defined a user-to-network interface (UNI) for overlay networks: the OIF UNI version 1.0, also referred to as the Public UNI. However, since its implementation agreement specification, it has become clear that this UNI--based on OIF-specific extensions to the generalized MPLS (GMPLS) protocols--will not be able to meet the future requirements of some operational environments. Hence a flexible, extensible, and fully GMPLS-compliant UNI is being defined at the Internet Engineering Task Force (IETF): the Private UNI (aka GMPLS for overlay networks). The Private UNI enhances the interaction between the packet and transport network control planes of a multilayer network architecture. This interface is particularly suitable for a control-plane interconnection model in which the equipment belongs to a common administrative entity (i.e., a single carrier environment). Signaling sessions through the Private UNI are used to invoke two main services that require constructive coordination between the network layers: provisioning and network recovery. Here we present the Private UNI specific GMPLS resource reservation protocol-traffic engineering (RSVP-TE) extensions in support of these services in IP/MPLS over SONET/SDH (synchronous optical network/synchronous digital hierarchy) GMPLS multilayer networks and illustrate how Private UNI signaling enhances coordination in multilayer network recovery.

  7. Network Evolution: Rewiring and Signatures of Conservation in Signaling

    PubMed Central

    Costanzo, Michael; Boone, Charles; Kim, Philip M.

    2012-01-01

    The analysis of network evolution has been hampered by limited availability of protein interaction data for different organisms. In this study, we investigate evolutionary mechanisms in Src Homology 3 (SH3) domain and kinase interaction networks using high-resolution specificity profiles. We constructed and examined networks for 23 fungal species ranging from Saccharomyces cerevisiae to Schizosaccharomyces pombe. We quantify rates of different rewiring mechanisms and show that interaction change through binding site evolution is faster than through gene gain or loss. We found that SH3 interactions evolve swiftly, at rates similar to those found in phosphoregulation evolution. Importantly, we show that interaction changes are sufficiently rapid to exhibit saturation phenomena at the observed timescales. Finally, focusing on the SH3 interaction network, we observe extensive clustering of binding sites on target proteins by SH3 domains and a strong correlation between the number of domains that bind a target protein (target in-degree) and interaction conservation. The relationship between in-degree and interaction conservation is driven by two different effects, namely the number of clusters that correspond to interaction interfaces and the number of domains that bind to each cluster leads to sequence specific conservation, which in turn results in interaction conservation. In summary, we uncover several network evolution mechanisms likely to generalize across peptide recognition modules. PMID:22438796

  8. cAMP-dependent proteolysis of GATA-6 is linked to JNK-signaling pathway

    SciTech Connect

    Ushijima, Hironori; Maeda, Masatomo

    2012-07-13

    Highlights: Black-Right-Pointing-Pointer A JNK inhibitor SP600125 inhibited cAMP-dependent proteolysis of GATA-6. Black-Right-Pointing-Pointer Effect of a JNK activator anisomycin on the proteolysis was examined. Black-Right-Pointing-Pointer Anisomycin stimulated the export of nuclear GATA-6 into the cytoplasm. Black-Right-Pointing-Pointer JNK activated the CRM1 mediated nuclear export of GATA-6. Black-Right-Pointing-Pointer JNK further stimulated slowly the degradation of GATA-6 by cytoplasmic proteasomes. -- Abstract: A JNK inhibitor SP600125 inhibited cAMP-dependent proteolysis of GATA-6 by proteasomes around its IC50. We further examined the effects of SP600125 on the degradation of GATA-6 in detail, since an activator of JNK (anisomycin) is available. Interestingly, anisomycin immediately stimulated the export of nuclear GATA-6 into the cytoplasm, and then the cytoplasmic content of GATA-6 decreased slowly through degradation by proteasomes. Such an effect of anisomycin was inhibited by SP600125, indicating that the observed phenomenon might be linked to the JNK signaling pathway. The inhibitory effect of SP600125 could not be ascribed to the inhibition of PKA, since phosphorylation of CREB occurred in the presence of dbcAMP and SP600125. The nuclear export of GATA-6 was inhibited by leptomycin B, suggesting that CRM1-mediated export could be activated by anisomycin. Furthermore, it seems likely that the JNK activated by anisomycin may stimulate not only the nuclear export of GATA-6 through CRM1 but also the degradation of GATA-6 by cytoplasmic proteasomes. In contrast, A-kinase might activate only the latter process through JNK.

  9. Echistatin prevents posterior capsule opacification in diabetic rabbit model via integrin linked kinase signaling pathway

    PubMed Central

    Lin, Fengbin; Chen, Yingying; Liang, Hao; Tan, Shaojian

    2015-01-01

    Purpose: To investigate the effect of disintegrin echistatin on integrin linked kinase (ILK) and subsequent PI3-K/Akt and ERK1/2 signaling pathways in the posterior capsule opacification (PCO) model of diabetic rabbit. Methods: 56 rabbits were injected alloxan to model diabetic. Then they accepted lens extraction surgery and randomly and intraoperatively injected distilled water (control group; n = 28) or 10.0 mg·L-1 echistatin (echistatin-treated group; n = 28) into the anterior chamber. Each group was subdivided into ten days group (n = 14) and six weeks group (n = 14) respectively. The PCO severity was evaluated with a slit lamp microscope and light microscope for 10 days and 6 weeks postoperatively. The levels of ILK in the posterior capsule were determined by Q-PCR, Western blotting and Immunohistochemistry. Akt and ERK1/2 phosphorylation were analyzed by Western blotting. Results: 10 days and 6 weeks after surgery, the grades of PCO in the echistatin-treated group were lower than the control group. The lens epithelial cells (LECs) in the posterior capsule of echistatin-treated eyes had decreased degrees of proliferation and migration than the control group. And no significant side effects appeared after treated with echistatin. Echistatin could significantly reduce the expression of ILK in terms of both mRNA and protein levels. The phosphorylation levels of Akt and ERK1/2 were decreased in the echistatin-treated group compared with the control group. Conclusions: Echistatin could inhibit postoperative PCO occurrence and development in diabetic rabbit eyes, which may be related to down-regulation the expression of ILK and inhibition the PI3-K/Akt and ERK1/2 pathways. PMID:26823745

  10. NOD1 and NOD2 signalling links ER stress with inflammation.

    PubMed

    Keestra-Gounder, A Marijke; Byndloss, Mariana X; Seyffert, Núbia; Young, Briana M; Chávez-Arroyo, Alfredo; Tsai, April Y; Cevallos, Stephanie A; Winter, Maria G; Pham, Oanh H; Tiffany, Connor R; de Jong, Maarten F; Kerrinnes, Tobias; Ravindran, Resmi; Luciw, Paul A; McSorley, Stephen J; Bäumler, Andreas J; Tsolis, Renée M

    2016-04-21

    Endoplasmic reticulum (ER) stress is a major contributor to inflammatory diseases, such as Crohn disease and type 2 diabetes. ER stress induces the unfolded protein response, which involves activation of three transmembrane receptors, ATF6, PERK and IRE1α. Once activated, IRE1α recruits TRAF2 to the ER membrane to initiate inflammatory responses via the NF-κB pathway. Inflammation is commonly triggered when pattern recognition receptors (PRRs), such as Toll-like receptors or nucleotide-binding oligomerization domain (NOD)-like receptors, detect tissue damage or microbial infection. However, it is not clear which PRRs have a major role in inducing inflammation during ER stress. Here we show that NOD1 and NOD2, two members of the NOD-like receptor family of PRRs, are important mediators of ER-stress-induced inflammation in mouse and human cells. The ER stress inducers thapsigargin and dithiothreitol trigger production of the pro-inflammatory cytokine IL-6 in a NOD1/2-dependent fashion. Inflammation and IL-6 production triggered by infection with Brucella abortus, which induces ER stress by injecting the type IV secretion system effector protein VceC into host cells, is TRAF2, NOD1/2 and RIP2-dependent and can be reduced by treatment with the ER stress inhibitor tauroursodeoxycholate or an IRE1α kinase inhibitor. The association of NOD1 and NOD2 with pro-inflammatory responses induced by the IRE1α/TRAF2 signalling pathway provides a novel link between innate immunity and ER-stress-induced inflammation. PMID:27007849

  11. Probabilistic neural networks employing Lyapunov exponents for analysis of Doppler ultrasound signals.

    PubMed

    Ubeyli, Elif Derya

    2008-01-01

    The implementation of probabilistic neural networks (PNNs) with the Lyapunov exponents for Doppler ultrasound signals classification is presented. This study is directly based on the consideration that Doppler ultrasound signals are chaotic signals. This consideration was tested successfully using the nonlinear dynamics tools, like the computation of Lyapunov exponents. Decision making was performed in two stages: computation of Lyapunov exponents as representative features of the Doppler ultrasound signals and classification using the PNNs trained on the extracted features. The present research demonstrated that the Lyapunov exponents are the features which well represent the Doppler ultrasound signals and the PNNs trained on these features achieved high classification accuracies. PMID:17709103

  12. Signal Decompostion and Diagnostic Classification of the Electromyogram Using a Novel Neural Network Technique

    PubMed Central

    Spitzer, A.R.; Hassoun, M.; Wang, C.; Bearden, F.

    1990-01-01

    Interpretation of physiologic signals to assist medical diagnosis requires human expertise. Success in automating this process has been limited. We present a three-step method for automated interpretation of the EMG. Signal decomposition and classification steps, which have not been automated using traditional computer methods, utilize neural networks. To deal with poorly described signals, a novel decomposition method, pseudoun-supervised learning, has been developed. The resulting method is considerably more robust than prior methods.

  13. Insight into the crystallization of amorphous imine-linked polymer networks to 2D covalent organic frameworks.

    PubMed

    Smith, Brian J; Overholts, Anna C; Hwang, Nicky; Dichtel, William R

    2016-03-01

    We explore the crystallization of a high surface area imine-linked two-dimensional covalent organic framework (2D COF). The growth process reveals rapid initial formation of an amorphous network that subsequently crystallizes into the layered 2D network. The metastable amorphous polymer may be isolated and resubjected to growth conditions to form the COF. These experiments provide the first mechanistic insight into the mechanism of imine-linked 2D COF formation, which is distinct from that of boronate-ester linked COFs. PMID:26857035

  14. Surface sensing and signaling networks in plant pathogenic fungi.

    PubMed

    Kou, Yanjun; Naqvi, Naweed I

    2016-09-01

    Pathogenic fungi have evolved highly varied and remarkable strategies to invade and infect their plant hosts. Typically, such fungal pathogens utilize highly specialized infection structures, morphologies or cell types produced from conidia or ascospores on the cognate host surfaces to gain entry therein. Such diverse infection strategies require intricate coordination in cell signaling and differentiation in phytopathogenic fungi. Here, we present an overview of our current understanding of cell signaling and infection-associated development that primes host penetration in the top ten plant pathogenic fungi, which utilize specific receptors to sense and respond to different surface cues, such as topographic features, hydrophobicity, hardness, plant lipids, phytohormones, and/or secreted enzymes. Subsequently, diverse signaling components such as G proteins, cyclic AMP/Protein Kinase A and MAP kinases are activated to enable the differentiation of infection structures. Recent studies have also provided fascinating insights into the spatio-temporal dynamics and specialized sequestration and trafficking of signaling moieties required for proper development of infection structures in phytopathogenic fungi. Molecular insight in such infection-related morphogenesis and cell signaling holds promise for identifying novel strategies for intervention of fungal diseases in plants. PMID:27133541

  15. A network map of Interleukin-10 signaling pathway.

    PubMed

    Verma, Renu; Balakrishnan, Lavanya; Sharma, Kusum; Khan, Aafaque Ahmad; Advani, Jayshree; Gowda, Harsha; Tripathy, Srikanth Prasad; Suar, Mrutyunjay; Pandey, Akhilesh; Gandotra, Sheetal; Prasad, T S Keshava; Shankar, Subramanian

    2016-03-01

    Interleukin-10 (IL-10) is an anti-inflammatory cytokine with important immunoregulatory functions. It is primarily secreted by antigen-presenting cells such as activated T-cells, monocytes, B-cells and macrophages. In biologically functional form, it exists as a homodimer that binds to tetrameric heterodimer IL-10 receptor and induces downstream signaling. IL-10 is associated with survival, proliferation and anti-apoptotic activities of various cancers such as Burkitt lymphoma, non-Hodgkins lymphoma and non-small scell lung cancer. In addition, it plays a central role in survival and persistence of intracellular pathogens such as Leishmania donovani, Mycobacterium tuberculosis and Trypanosoma cruzi inside the host. The signaling mechanisms of IL-10 cytokine are not well explored and a well annotated pathway map has been lacking. To this end, we developed a pathway resource by manually annotating the IL-10 induced signaling molecules derived from literature. The reactions were categorized under molecular associations, activation/inhibition, catalysis, transport and gene regulation. In all, 37 molecules and 76 reactions were annotated. The IL-10 signaling pathway can be freely accessed through NetPath, a resource of signal transduction pathways previously developed by our group. PMID:26253919

  16. A new traffic control design method for large networks with signalized intersections

    NASA Technical Reports Server (NTRS)

    Leininger, G. G.; Colony, D. C.; Seldner, K.

    1979-01-01

    The paper presents a traffic control design technique for application to large traffic networks with signalized intersections. It is shown that the design method adopts a macroscopic viewpoint to establish a new traffic modelling procedure in which vehicle platoons are subdivided into main stream queues and turning queues. Optimization of the signal splits minimizes queue lengths in the steady state condition and improves traffic flow conditions, from the viewpoint of the traveling public. Finally, an application of the design method to a traffic network with thirty-three signalized intersections is used to demonstrate the effectiveness of the proposed technique.

  17. Neural network committees for finger joint angle estimation from surface EMG signals

    PubMed Central

    Shrirao, Nikhil A; Reddy, Narender P; Kosuri, Durga R

    2009-01-01

    Background In virtual reality (VR) systems, the user's finger and hand positions are sensed and used to control the virtual environments. Direct biocontrol of VR environments using surface electromyography (SEMG) signals may be more synergistic and unconstraining to the user. The purpose of the present investigation was to develop a technique to predict the finger joint angle from the surface EMG measurements of the extensor muscle using neural network models. Methodology SEMG together with the actual joint angle measurements were obtained while the subject was performing flexion-extension rotation of the index finger at three speeds. Several neural networks were trained to predict the joint angle from the parameters extracted from the SEMG signals. The best networks were selected to form six committees. The neural network committees were evaluated using data from new subjects. Results There was hysteresis in the measured SMEG signals during the flexion-extension cycle. However, neural network committees were able to predict the joint angle with reasonable accuracy. RMS errors ranged from 0.085 ± 0.036 for fast speed finger-extension to 0.147 ± 0.026 for slow speed finger extension, and from 0.098 ± 0.023 for the fast speed finger flexion to 0.163 ± 0.054 for slow speed finger flexion. Conclusion Although hysteresis was observed in the measured SEMG signals, the committees of neural networks were able to predict the finger joint angle from SEMG signals. PMID:19154615

  18. Strain recovery in dual cross-linked polymer grafted nanoparticle networks

    NASA Astrophysics Data System (ADS)

    v S, Balaji; Yashin, Victor; Salib, Isaac; Kowalewski, Tomasz; Matyjaszewski, Krzystof; Balazs, Anna; Anna Balazs Collaboration; Krzystof Matyjaszewski Collaboration

    2013-03-01

    Via computational modeling, we investigate the mechanism of strain-recovery in dual cross-linked polymer grafted nanoparticle networks. The individual nanoparticles are composed of a rigid core and a corona of grafted polymers that encompass reactive end groups. With the overlap of the coronas on adjacent particles, the reactive end groups form permanent or labile bonds, and thus form a ``dual cross-linked'' network. We consider the strain recovery of the material after it is allowed to relax from the application of the tensile force. We apply multiple cycles of tension and relaxation and determine how the stress-strain curves change in the course of these repetitive deformations. Notably, the existing labile bonds can break and new bonds can form in the course of deformation. Hence, a damaged material could be ``rejuvenated'' both in terms of the recovery of strain and the number of bonds, if the relaxation occurs over a sufficiently long time. We show that this rejuvenation depends on the fraction of permanent bonds, strength of labile bonds, and maximal strain.

  19. MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks.

    PubMed

    Cottret, Ludovic; Wildridge, David; Vinson, Florence; Barrett, Michael P; Charles, Hubert; Sagot, Marie-France; Jourdan, Fabien

    2010-07-01

    High-throughput metabolomic experiments aim at identifying and ultimately quantifying all metabolites present in biological systems. The metabolites are interconnected through metabolic reactions, generally grouped into metabolic pathways. Classical metabolic maps provide a relational context to help interpret metabolomics experiments and a wide range of tools have been developed to help place metabolites within metabolic pathways. However, the representation of metabolites within separate disconnected pathways overlooks most of the connectivity of the metabolome. By definition, reference pathways cannot integrate novel pathways nor show relationships between metabolites that may be linked by common neighbours without being considered as joint members of a classical biochemical pathway. MetExplore is a web server that offers the possibility to link metabolites identified in untargeted metabolomics experiments within the context of genome-scale reconstructed metabolic networks. The analysis pipeline comprises mapping metabolomics data onto the specific metabolic network of an organism, then applying graph-based methods and advanced visualization tools to enhance data analysis. The MetExplore web server is freely accessible at http://metexplore.toulouse.inra.fr. PMID:20444866

  20. Thermally Reversible Physically Cross-Linked Hybrid Network Hydrogels Formed by Thermosensitive Hairy Nanoparticles.

    PubMed

    Wright, Roger A E; Henn, Daniel M; Zhao, Bin

    2016-08-18

    This Article reports on thermally induced reversible formation of physically cross-linked, three-dimensional network hydrogels from aqueous dispersions of thermosensitive diblock copolymer brush-grafted silica nanoparticles (hairy NPs). The hairy NPs consisted of a silica core, a water-soluble polyelectrolyte inner block of poly(2-(methacryloyloxy)ethyltrimethylammonium iodide), and a thermosensitive poly(methoxydi(ethylene glycol) methacrylate) (PDEGMMA) outer block synthesized by sequential surface-initiated atom transfer radical polymerizations and postpolymerization quaternization of tertiary amine moieties. Moderately concentrated dispersions of these hairy nanoparticles in water underwent thermally induced reversible transitions between flowing liquids to self-supporting gels upon heating. The gelation was driven by the lower critical solution temperature (LCST) transition of the PDEGMMA outer block, which upon heating self-associated into hydrophobic domains acting as physical cross-linking points for the gel network. Rheological studies showed that the sol-gel transition temperature decreased with increasing hairy NP concentration, and the gelation was achieved at concentrations as low as 3 wt %. PMID:27455167

  1. Integrating in silico resources to map a signaling network.

    PubMed

    Liu, Hanqing; Beck, Tim N; Golemis, Erica A; Serebriiskii, Ilya G

    2014-01-01

    The abundance of publicly available life science databases offers a wealth of information that can support interpretation of experimentally derived data and greatly enhance hypothesis generation. Protein interaction and functional networks are not simply new renditions of existing data: they provide the opportunity to gain insights into the specific physical and functional role a protein plays as part of the biological system. In this chapter, we describe different in silico tools that can quickly and conveniently retrieve data from existing data repositories and we discuss how the available tools are best utilized for different purposes. While emphasizing protein-protein interaction databases (e.g., BioGrid and IntAct), we also introduce metasearch platforms such as STRING and GeneMANIA, pathway databases (e.g., BioCarta and Pathway Commons), text mining approaches (e.g., PubMed and Chilibot), and resources for drug-protein interactions, genetic information for model organisms and gene expression information based on microarray data mining. Furthermore, we provide a simple step-by-step protocol for building customized protein-protein interaction networks in Cytoscape, a powerful network assembly and visualization program, integrating data retrieved from these various databases. As we illustrate, generation of composite interaction networks enables investigators to extract significantly more information about a given biological system than utilization of a single database or sole reliance on primary literature. PMID:24233784

  2. Integrating In Silico Resources to Map a Signaling Network

    PubMed Central

    Liu, Hanqing; Beck, Tim N.; Golemis, Erica A.; Serebriiskii, Ilya G.

    2013-01-01

    The abundance of publicly available life science databases offer a wealth of information that can support interpretation of experimentally derived data and greatly enhance hypothesis generation. Protein interaction and functional networks are not simply new renditions of existing data: they provide the opportunity to gain insights into the specific physical and functional role a protein plays as part of the biological system. In this chapter, we describe different in silico tools that can quickly and conveniently retrieve data from existing data repositories and discuss how the available tools are best utilized for different purposes. While emphasizing protein-protein interaction databases (e.g., BioGrid and IntAct), we also introduce metasearch platforms such as STRING and GeneMANIA, pathway databases (e.g., BioCarta and Pathway Commons), text mining approaches (e.g., PubMed and Chilibot), and resources for drug-protein interactions, genetic information for model organisms and gene expression information based on microarray data mining. Furthermore, we provide a simple step-by-step protocol to building customized protein-protein interaction networks in Cytoscape, a powerful network assembly and visualization program, integrating data retrieved from these various databases. As we illustrate, generation of composite interaction networks enables investigators to extract significantly more information about a given biological system than utilization of a single database or sole reliance on primary literature. PMID:24233784

  3. Imbalanced functional link between executive control network and reward network explain the online-game seeking behaviors in Internet gaming disorder.

    PubMed

    Dong, Guangheng; Lin, Xiao; Hu, Yanbo; Xie, Chunming; Du, Xiaoxia

    2015-01-01

    Literatures have shown that Internet gaming disorder (IGD) subjects show impaired executive control and enhanced reward sensitivities than healthy controls. However, how these two networks jointly affect the valuation process and drive IGD subjects' online-game-seeking behaviors remains unknown. Thirty-five IGD and 36 healthy controls underwent a resting-states scan in the MRI scanner. Functional connectivity (FC) was examined within control and reward network seeds regions, respectively. Nucleus accumbens (NAcc) was selected as the node to find the interactions between these two networks. IGD subjects show decreased FC in the executive control network and increased FC in the reward network when comparing with the healthy controls. When examining the correlations between the NAcc and the executive control/reward networks, the link between the NAcc - executive control network is negatively related with the link between NAcc - reward network. The changes (decrease/increase) in IGD subjects' brain synchrony in control/reward networks suggest the inefficient/overly processing within neural circuitry underlying these processes. The inverse proportion between control network and reward network in IGD suggest that impairments in executive control lead to inefficient inhibition of enhanced cravings to excessive online game playing. This might shed light on the mechanistic understanding of IGD. PMID:25779894

  4. Imbalanced functional link between executive control network and reward network explain the online-game seeking behaviors in Internet gaming disorder

    PubMed Central

    Dong, Guangheng; Lin, Xiao; Hu, Yanbo; Xie, Chunming; Du, Xiaoxia

    2015-01-01

    Literatures have shown that Internet gaming disorder (IGD) subjects show impaired executive control and enhanced reward sensitivities than healthy controls. However, how these two networks jointly affect the valuation process and drive IGD subjects' online-game-seeking behaviors remains unknown. Thirty-five IGD and 36 healthy controls underwent a resting-states scan in the MRI scanner. Functional connectivity (FC) was examined within control and reward network seeds regions, respectively. Nucleus accumbens (NAcc) was selected as the node to find the interactions between these two networks. IGD subjects show decreased FC in the executive control network and increased FC in the reward network when comparing with the healthy controls. When examining the correlations between the NAcc and the executive control/reward networks, the link between the NAcc - executive control network is negatively related with the link between NAcc - reward network. The changes (decrease/increase) in IGD subjects' brain synchrony in control/reward networks suggest the inefficient/overly processing within neural circuitry underlying these processes. The inverse proportion between control network and reward network in IGD suggest that impairments in executive control lead to inefficient inhibition of enhanced cravings to excessive online game playing. This might shed light on the mechanistic understanding of IGD. PMID:25779894

  5. Increased signaling entropy in cancer requires the scale-free property of protein interaction networks.

    PubMed

    Teschendorff, Andrew E; Banerji, Christopher R S; Severini, Simone; Kuehn, Reimer; Sollich, Peter

    2015-01-01

    One of the key characteristics of cancer cells is an increased phenotypic plasticity, driven by underlying genetic and epigenetic perturbations. However, at a systems-level it is unclear how these perturbations give rise to the observed increased plasticity. Elucidating such systems-level principles is key for an improved understanding of cancer. Recently, it has been shown that signaling entropy, an overall measure of signaling pathway promiscuity, and computable from integrating a sample's gene expression profile with a protein interaction network, correlates with phenotypic plasticity and is increased in cancer compared to normal tissue. Here we develop a computational framework for studying the effects of network perturbations on signaling entropy. We demonstrate that the increased signaling entropy of cancer is driven by two factors: (i) the scale-free (or near scale-free) topology of the interaction network, and (ii) a subtle positive correlation between differential gene expression and node connectivity. Indeed, we show that if protein interaction networks were random graphs, described by Poisson degree distributions, that cancer would generally not exhibit an increased signaling entropy. In summary, this work exposes a deep connection between cancer, signaling entropy and interaction network topology. PMID:25919796

  6. Increased signaling entropy in cancer requires the scale-free property of protein interaction networks

    PubMed Central

    Teschendorff, Andrew E.; Banerji, Christopher R. S.; Severini, Simone; Kuehn, Reimer; Sollich, Peter

    2015-01-01

    One of the key characteristics of cancer cells is an increased phenotypic plasticity, driven by underlying genetic and epigenetic perturbations. However, at a systems-level it is unclear how these perturbations give rise to the observed increased plasticity. Elucidating such systems-level principles is key for an improved understanding of cancer. Recently, it has been shown that signaling entropy, an overall measure of signaling pathway promiscuity, and computable from integrating a sample's gene expression profile with a protein interaction network, correlates with phenotypic plasticity and is increased in cancer compared to normal tissue. Here we develop a computational framework for studying the effects of network perturbations on signaling entropy. We demonstrate that the increased signaling entropy of cancer is driven by two factors: (i) the scale-free (or near scale-free) topology of the interaction network, and (ii) a subtle positive correlation between differential gene expression and node connectivity. Indeed, we show that if protein interaction networks were random graphs, described by Poisson degree distributions, that cancer would generally not exhibit an increased signaling entropy. In summary, this work exposes a deep connection between cancer, signaling entropy and interaction network topology. PMID:25919796

  7. Signaling networks regulating leukocyte podosome dynamics and function

    PubMed Central

    Dovas, Athanassios; Cox, Dianne

    2011-01-01

    Podosomes are ventral adhesion structures prominent in cells of the myeloid lineage. A common aspect of these cells is that they are highly motile and are required to traverse multiple tissue barriers in order to perform their functions. Recently podosomes have gathered attention from researchers as important cellular structures that can influence cell adhesion, motility and matrix remodeling. Adhesive and soluble ligands act via transmembrane receptors and propagate signals to the leukocyte cytoskeleton via small G proteins of the Rho family, tyrosine kinases and scaffold proteins and are able to induce podosome formation and rearrangements. Manipulation of the signals that regulate podosome formation and dynamics can therefore be a strategy to interfere with leukocyte functions in a multitude of pathological settings, such as infections, atherosclerosis and arthritis. Here, we review the major signaling molecules that act in the formation and regulation of podosomes. PMID:21342664

  8. The LINK-A lncRNA activates normoxic HIF1α signalling in triple-negative breast cancer.

    PubMed

    Lin, Aifu; Li, Chunlai; Xing, Zhen; Hu, Qingsong; Liang, Ke; Han, Leng; Wang, Cheng; Hawke, David H; Wang, Shouyu; Zhang, Yanyan; Wei, Yongkun; Ma, Guolin; Park, Peter K; Zhou, Jianwei; Zhou, Yan; Hu, Zhibin; Zhou, Yubin; Marks, Jeffery R; Liang, Han; Hung, Mien-Chie; Lin, Chunru; Yang, Liuqing

    2016-02-01

    Although long non-coding RNAs (lncRNAs) predominately reside in the nucleus and exert their functions in many biological processes, their potential involvement in cytoplasmic signal transduction remains unexplored. Here, we identify a cytoplasmic lncRNA, LINK-A (long intergenic non-coding RNA for kinase activation), which mediates HB-EGF-triggered, EGFR:GPNMB heterodimer-dependent HIF1α phosphorylation at Tyr 565 and Ser 797 by BRK and LRRK2, respectively. These events cause HIF1α stabilization, HIF1α-p300 interaction, and activation of HIF1α transcriptional programs under normoxic conditions. Mechanistically, LINK-A facilitates the recruitment of BRK to the EGFR:GPNMB complex and BRK kinase activation. The BRK-dependent HIF1α Tyr 565 phosphorylation interferes with Pro 564 hydroxylation, leading to normoxic HIF1α stabilization. Both LINK-A expression and LINK-A-dependent signalling pathway activation correlate with triple-negative breast cancer (TNBC), promoting breast cancer glycolysis reprogramming and tumorigenesis. Our findings illustrate the magnitude and diversity of cytoplasmic lncRNAs in signal transduction and highlight the important roles of lncRNAs in cancer. PMID:26751287

  9. Neural networks for automated classification of ionospheric irregularities in HF radar backscattered signals

    NASA Astrophysics Data System (ADS)

    Wing, S.; Greenwald, R. A.; Meng, C.-I.; Sigillito, V. G.; Hutton, L. V.

    2003-08-01

    The classification of high frequency (HF) radar backscattered signals from the ionospheric irregularities (clutters) into those suitable, or not, for further analysis, is a time-consuming task even by experts in the field. We tested several different feedforward neural networks on this task, investigating the effects of network type (single layer versus multilayer) and number of hidden nodes upon performance. As expected, the multilayer feedforward networks (MLFNs) outperformed the single-layer networks. The MLFNs achieved performance levels of 100% correct on the training set and up to 98% correct on the testing set. Comparable figures for the single-layer networks were 94.5% and 92%, respectively. When measures of sensitivity, specificity, and proportion of variance accounted for by the model are considered, the superiority of the MLFNs over the single-layer networks is much more striking. Our results suggest that such neural networks could aid many HF radar operations such as frequency search, space weather, etc.

  10. Real-time in Situ Signal-to-noise Ratio Estimation for the Assessment of Operational Communications Links

    NASA Technical Reports Server (NTRS)

    Manning, Robert M.

    2002-01-01

    The work presented here formulates the rigorous statistical basis for the correct estimation of communication link SNR of a BPSK, QPSK, and for that matter, any M-ary phase-modulated digital signal from what is known about its statistical behavior at the output of the receiver demodulator. Many methods to accomplish this have been proposed and implemented in the past but all of them are based on tacit and unwarranted assumptions and are thus defective. However, the basic idea is well founded, i.e., the signal at the output of a communications demodulator has convolved within it the prevailing SNR characteristic of the link. The acquisition of the SNR characteristic is of the utmost importance to a communications system that must remain reliable in adverse propagation conditions. This work provides a correct and consistent mathematical basis for the proper statistical 'deconvolution' of the output of a demodulator to yield a measure of the SNR. The use of such techniques will alleviate the need and expense for a separate propagation link to assess the propagation conditions prevailing on the communications link. Furthermore, they are applicable for every situation involving the digital transmission of data over planetary and space communications links.

  11. Birth and death of links control disease spreading in empirical contact networks

    NASA Astrophysics Data System (ADS)

    Holme, Petter; Liljeros, Fredrik

    2014-05-01

    We investigate what structural aspects of a collection of twelve empirical temporal networks of human contacts are important to disease spreading. We scan the entire parameter spaces of the two canonical models of infectious disease epidemiology--the Susceptible-Infectious-Susceptible (SIS) and Susceptible-Infectious-Removed (SIR) models. The results from these simulations are compared to reference data where we eliminate structures in the interevent intervals, the time to the first contact in the data, or the time from the last contact to the end of the sampling. The picture we find is that the birth and death of links, and the total number of contacts over a link, are essential to predict outbreaks. On the other hand, the exact times of contacts between the beginning and end, or the interevent interval distribution, do not matter much. In other words, a simplified picture of these empirical data sets that suffices for epidemiological purposes is that links are born, is active with some intensity, and die.

  12. Equipment Management for Sensor Networks: Linking Physical Infrastructure and Actions to Observational Data

    NASA Astrophysics Data System (ADS)

    Jones, A. S.; Horsburgh, J. S.; Matos, M.; Caraballo, J.

    2015-12-01

    Networks conducting long term monitoring using in situ sensors need the functionality to track physical equipment as well as deployments, calibrations, and other actions related to site and equipment maintenance. The observational data being generated by sensors are enhanced if direct linkages to equipment details and actions can be made. This type of information is typically recorded in field notebooks or in static files, which are rarely linked to observations in a way that could be used to interpret results. However, the record of field activities is often relevant to analysis or post-processing of the observational data. We have developed an underlying database schema and deployed a web interface for recording and retrieving information on physical infrastructure and related actions for observational networks. The database schema for equipment was designed as an extension to the Observations Data Model 2 (ODM2), a community-developed information model for spatially discrete, feature based earth observations. The core entities of ODM2 describe location, observed variable, and timing of observations, and the equipment extension contains entities to provide additional metadata specific to the inventory of physical infrastructure and associated actions. The schema is implemented in a relational database system for storage and management with an associated web interface. We designed the web-based tools for technicians to enter and query information on the physical equipment and actions such as site visits, equipment deployments, maintenance, and calibrations. These tools were implemented for the iUTAH (innovative Urban Transitions and Aridregion Hydrosustainability) ecohydrologic observatory, and we anticipate that they will be useful for similar large-scale monitoring networks desiring to link observing infrastructure to observational data to increase the quality of sensor-based data products.

  13. Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming

    PubMed Central

    Guziolowski, Carito; Videla, Santiago; Eduati, Federica; Thiele, Sven; Cokelaer, Thomas; Siegel, Anne; Saez-Rodriguez, Julio

    2013-01-01

    Motivation: Logic modeling is a useful tool to study signal transduction across multiple pathways. Logic models can be generated by training a network containing the prior knowledge to phospho-proteomics data. The training can be performed using stochastic optimization procedures, but these are unable to guarantee a global optima or to report the complete family of feasible models. This, however, is essential to provide precise insight in the mechanisms underlaying signal transduction and generate reliable predictions. Results: We propose the use of Answer Set Programming to explore exhaustively the space of feasible logic models. Toward this end, we have developed caspo, an open-source Python package that provides a powerful platform to learn and characterize logic models by leveraging the rich modeling language and solving technologies of Answer Set Programming. We illustrate the usefulness of caspo by revisiting a model of pro-growth and inflammatory pathways in liver cells. We show that, if experimental error is taken into account, there are thousands (11 700) of models compatible with the data. Despite the large number, we can extract structural features from the models, such as links that are always (or never) present or modules that appear in a mutual exclusive fashion. To further characterize this family of models, we investigate the input–output behavior of the models. We find 91 behaviors across the 11 700 models and we suggest new experiments to discriminate among them. Our results underscore the importance of characterizing in a global and exhaustive manner the family of feasible models, with important implications for experimental design. Availability: caspo is freely available for download (license GPLv3) and as a web service at http://caspo.genouest.org/. Supplementary information: Supplementary materials are available at Bioinformatics online. Contact: santiago.videla@irisa.fr PMID:23853063

  14. Differentially Expressed Transcripts and Dysregulated Signaling Pathways and Networks in African American Breast Cancer

    PubMed Central

    Stewart, Paul A.; Luks, Jennifer; Roycik, Mark D.; Sang, Qing-Xiang Amy; Zhang, Jinfeng

    2013-01-01

    African Americans (AAs) have higher mortality rate from breast cancer than that of Caucasian Americans (CAs) even when socioeconomic factors are accounted for. To better understand the driving biological factors of this health disparity, we performed a comprehensive differential gene expression analysis, including subtype- and stage-specific analysis, using the breast cancer data in the Cancer Genome Atlas (TCGA). In total, 674 unique genes and other transcripts were found differentially expressed between these two populations. The numbers of differentially expressed genes between AA and CA patients increased in each stage of tumor progression: there were 26 in stage I, 161 in stage II, and 223 in stage III. Resistin, a gene that is linked to obesity, insulin resistance, and breast cancer, was expressed more than four times higher in AA tumors. An uncharacterized, long, non-coding RNA, LOC90784, was down-regulated in AA tumors, and its expression was inversely related to cancer stage and was the lowest in triple negative AA breast tumors. Network analysis showed increased expression of a majority of components in p53 and BRCA1 subnetworks in AA breast tumor samples, and members of the aurora B and polo-like kinase signaling pathways were also highly expressed. Higher gene expression diversity was observed in more advanced stage breast tumors suggesting increased genomic instability during tumor progression. Amplified resistin expression may indicate insulin-resistant type II diabetes and obesity are associated with AA breast cancer. Expression of LOC90784 may have a protective effect on breast cancer patients, and its loss, particularly in triple negative breast cancer, could be having detrimental effects. This work helps elucidate molecular mechanisms of breast cancer health disparity and identifies putative biomarkers and therapeutic targets such as resistin, and the aurora B and polo-like kinase signaling pathways for treating AA breast cancer patients. PMID

  15. Linking in with LinkedIn[R]: Three Exercises That Enhance Professional Social Networking and Career Building

    ERIC Educational Resources Information Center

    Gerard, Joseph G.

    2012-01-01

    Getting students to network with one another can be one of the biggest challenges in college courses, despite being a highly important function of higher education. Networking can, in fact, lead to that first job or to professional advancement, and technology can improve the success of individual and institutional efforts. This article describes…

  16. Linking the sender to the receiver: vocal adjustments by bats to maintain signal detection in noise

    PubMed Central

    Luo, Jinhong; Goerlitz, Holger R.; Brumm, Henrik; Wiegrebe, Lutz

    2015-01-01

    Short-term adjustments of signal characteristics allow animals to maintain reliable communication in noise. Noise-dependent vocal plasticity often involves simultaneous changes in multiple parameters. Here, we quantified for the first time the relative contributions of signal amplitude, duration, and redundancy for improving signal detectability in noise. To this end, we used a combination of behavioural experiments on pale spear-nosed bats (Phyllostomus discolor) and signal detection models. In response to increasing noise levels, all bats raised the amplitude of their echolocation calls by 1.8–7.9 dB (the Lombard effect). Bats also increased signal duration by 13%–85%, corresponding to an increase in detectability of 1.0–5.3 dB. Finally, in some noise conditions, bats increased signal redundancy by producing more call groups. Assuming optimal cognitive integration, this could result in a further detectability improvement by up to 4 dB. Our data show that while the main improvement in signal detectability was due to the Lombard effect, increasing signal duration and redundancy can also contribute markedly to improving signal detectability. Overall, our findings demonstrate that the observed adjustments of signal parameters in noise are matched to how these parameters are processed in the receiver’s sensory system, thereby facilitating signal transmission in fluctuating environments. PMID:26692325

  17. A High-Temporal and Spatial Resolution Soil Moisture and Soil Temperature Network In Iowa Using Wireless Links

    NASA Astrophysics Data System (ADS)

    Niemeier, J. J.; Kruger, A.; Krajewki, W. F.; Eichinger, W. E.; Hornbuckle, B. K.; Cunha, L.

    2007-12-01

    Over the past year we have created an in-situ soil moisture and soil temperature network in a 200 acre agricultural plot at Ames, Iowa. This work is part of a collaborative effort between researchers at The University of Iowa, and Iowa State University. The purpose of the network is to provide high temporal and spatial resolution soil moisture and soil temperature data to validate remotely-sensed observations of the terrestrial water cycle. This is part of a larger effort by the authors and collaborators to improve the quantitative value of remotely-sensed observations of the water cycle. In addition to the soil moisture and soil temperature measurements, detailed precipitation data, and atmospheric data such as air temperature, humidity, pressure, wind direction and velocity, and solar radiation data are collected. The current soil moisture network consists of 10 Iowa and Iowa State stations, each equipped with seven pairs of soil moisture and soil temperature sensors. In the future, the network will be expanded to 15 stations. At each of the 10 station the sensors pairs are deployed at depths of 1.5, 4.5, 15, 30, and 60 cm to provide a vertical profile of soil moisture and soil temperature. Prior to installation we calibrated the soil temperature sensors to within 0.1 degree Celsius. The time-domain reflectometry soil moisture measurements are adjusted for local soil conditions. At each of the 10 stations, data are collected every 10 minutes. The data are transmitted wirelessly with low power radio links to a central location. The system started collecting data at the beginning of July, 2007. One of the challenges we faced is how to provide reliable solar power to the wireless nodes, since the current crop, corn, grows up to 3 m tall, and casts dense shadows. The corn also significantly attenuates the radios signals, and the radios fell far short of their advertized ranges. Consequently, we had to use high-gain antennas, and robust retransmit communication modes

  18. Automated and comprehensive link engineering supporting branched, ring, and mesh network topologies

    NASA Astrophysics Data System (ADS)

    Farina, J.; Khomchenko, D.; Yevseyenko, D.; Meester, J.; Richter, A.

    2016-02-01

    Link design, while relatively easy in the past, can become quite cumbersome with complex channel plans and equipment configurations. The task of designing optical transport systems and selecting equipment is often performed by an applications or sales engineer using simple tools, such as custom Excel spreadsheets. Eventually, every individual has their own version of the spreadsheet as well as their own methodology for building the network. This approach becomes unmanageable very quickly and leads to mistakes, bending of the engineering rules and installations that do not perform as expected. We demonstrate a comprehensive planning environment, which offers an efficient approach to unify, control and expedite the design process by controlling libraries of equipment and engineering methodologies, automating the process and providing the analysis tools necessary to predict system performance throughout the system and for all channels. In addition to the placement of EDFAs and DCEs, performance analysis metrics are provided at every step of the way. Metrics that can be tracked include power, CD and OSNR, SPM, XPM, FWM and SBS. Automated routine steps assist in design aspects such as equalization, padding and gain setting for EDFAs, the placement of ROADMs and transceivers, and creating regeneration points. DWDM networks consisting of a large number of nodes and repeater huts, interconnected in linear, branched, mesh and ring network topologies, can be designed much faster when compared with conventional design methods. Using flexible templates for all major optical components, our technology-agnostic planning approach supports the constant advances in optical communications.

  19. Condensation transitions in a model for a directed network with weighted links

    NASA Astrophysics Data System (ADS)

    Angel, A. G.; Hanney, T.; Evans, M. R.

    2006-01-01

    An exactly solvable model for the rewiring dynamics of weighted, directed networks is introduced. Simulations indicate that the model exhibits two types of condensation: (i) a phase in which, for each node, a finite fraction of its total out-strength condenses onto a single link; (ii) a phase in which a finite fraction of the total weight in the system is directed into a single node. A virtue of the model is that its dynamics can be mapped onto those of a zero-range process with many species of interacting particles—an exactly solvable model of particles hopping between the sites of a lattice. This mapping, which is described in detail, guides the analysis of the steady state of the network model and leads to theoretical predictions for the conditions under which the different types of condensation may be observed. A further advantage of the mapping is that, by exploiting what is known about exactly solvable generalizations of the zero-range process, one can infer a number of generalizations of the network model and dynamics which remain exactly solvable.

  20. Application of Radial Basis Functional Link Networks to Exploration for Proterozoic Mineral Deposits in Central Iran

    SciTech Connect

    Behnia, Pouran

    2007-06-15

    The metallogeny of Central Iran is characterized mainly by the presence of several iron, apatite, and uranium deposits of Proterozoic age. Radial Basis Function Link Networks (RBFLN) were used as a data-driven method for GIS-based predictive mapping of Proterozoic mineralization in this area. To generate the input data for RBFLN, the evidential maps comprising stratigraphic, structural, geophysical, and geochemical data were used. Fifty-eight deposits and 58 'nondeposits' were used to train the network. The operations for the application of neural networks employed in this study involve both multiclass and binary representation of evidential maps. Running RBFLN on different input data showed that an increase in the number of evidential maps and classes leads to a larger classification sum of squared error (SSE). As a whole, an increase in the number of iterations resulted in the improvement of training SSE. The results of applying RBFLN showed that a successful classification depends on the existence of spatially well distributed deposits and nondeposits throughout the study area.

  1. Research on Shore-Ship Photonic Link Performance for Two- Frequency-Band Signals

    NASA Astrophysics Data System (ADS)

    Zuo, Yanqin; Cong, Bo

    2016-02-01

    Ka and Ku bands links for shore-ship communications suffer limited bandwidth and high loss. In this paper, photonics-based links are proposed and modeled. The principle of phase modulation (PM) is elaborated and analyzed. It is showed that PM can effectively suppress high-order inter-modulation distortion (IMD), reduce the insert loss and improve the reliability of the system.

  2. An Alzheimer Disease-linked Rare Mutation Potentiates Netrin Receptor Uncoordinated-5C-induced Signaling That Merges with Amyloid β Precursor Protein Signaling.

    PubMed

    Hashimoto, Yuichi; Toyama, Yuka; Kusakari, Shinya; Nawa, Mikiro; Matsuoka, Masaaki

    2016-06-01

    A missense mutation (T835M) in the uncoordinated-5C (UNC5C) netrin receptor gene increases the risk of late-onset Alzheimer disease (AD) and also the vulnerability of neurons harboring the mutation to various insults. The molecular mechanisms underlying T835M-UNC5C-induced death remain to be elucidated. In this study, we show that overexpression of wild-type UNC5C causes low-grade death, which is intensified by an AD-linked mutation T835M. An AD-linked survival factor, calmodulin-like skin protein (CLSP), and a natural ligand of UNC5C, netrin1, inhibit this death. T835M-UNC5C-induced neuronal cell death is mediated by an intracellular death-signaling cascade, consisting of death-associated protein kinase 1/protein kinase D/apoptosis signal-regulating kinase 1 (ASK1)/JNK/NADPH oxidase/caspases, which merges at ASK1 with a death-signaling cascade, mediated by amyloid β precursor protein (APP). Notably, netrin1 also binds to APP and partially inhibits the death-signaling cascade, induced by APP. These results may provide new insight into the amyloid β-independent pathomechanism of AD. PMID:27068745

  3. Processes entangling interactions in communities: forbidden links are more important than abundance in a hummingbird–plant network

    PubMed Central

    Vizentin-Bugoni, Jeferson; Maruyama, Pietro Kiyoshi; Sazima, Marlies

    2014-01-01

    Understanding the relative importance of multiple processes on structuring species interactions within communities is one of the major challenges in ecology. Here, we evaluated the relative importance of species abundance and forbidden links in structuring a hummingbird–plant interaction network from the Atlantic rainforest in Brazil. Our results show that models incorporating phenological overlapping and morphological matches were more accurate in predicting the observed interactions than models considering species abundance. This means that forbidden links, by imposing constraints on species interactions, play a greater role than species abundance in structuring the ecological network. We also show that using the frequency of interaction as a proxy for species abundance and network metrics to describe the detailed network structure might lead to biased conclusions regarding mechanisms generating network structure. Together, our findings suggest that species abundance can be a less important driver of species interactions in communities than previously thought. PMID:24552835

  4. Processes entangling interactions in communities: forbidden links are more important than abundance in a hummingbird-plant network.

    PubMed

    Vizentin-Bugoni, Jeferson; Maruyama, Pietro Kiyoshi; Sazima, Marlies

    2014-04-01

    Understanding the relative importance of multiple processes on structuring species interactions within communities is one of the major challenges in ecology. Here, we evaluated the relative importance of species abundance and forbidden links in structuring a hummingbird-plant interaction network from the Atlantic rainforest in Brazil. Our results show that models incorporating phenological overlapping and morphological matches were more accurate in predicting the observed interactions than models considering species abundance. This means that forbidden links, by imposing constraints on species interactions, play a greater role than species abundance in structuring the ecological network. We also show that using the frequency of interaction as a proxy for species abundance and network metrics to describe the detailed network structure might lead to biased conclusions regarding mechanisms generating network structure. Together, our findings suggest that species abundance can be a less important driver of species interactions in communities than previously thought. PMID:24552835

  5. Transmission of three-polarization-multiplexed 25-Gb/s DPSK signals over 300-km fiber link.

    PubMed

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

    2016-04-01

    Polarization is one of the key parameters to be utilized for large capacity and high spectral-efficient optical communication systems, especially the widely deployed polarization-division-multiplexing (PDM) scheme. To break the limitation of only two orthogonal polarization states that could be used for carrying data signals over the same wavelength, we experimentally demonstrate the first transmission of three-polarization-division-multiplexed DPSK signals at a rate up to 3×25  Gb/s over 300-km fiber link by using a single-carrier. PMID:27192302

  6. Chemical approaches for investigating phosphorylation in signal transduction networks.

    PubMed

    Rothman, Deborah M; Shults, Melissa D; Imperiali, Barbara

    2005-09-01

    The power and scope of chemical synthesis offer considerable opportunities to broaden the lexicon of chemical tools that can be implemented for the study of complex biological systems. To investigate individual signaling proteins and pathways, chemical tools provide a powerful complement to existing genetic, chemical genetic and immunologic methods. In particular, understanding phosphorylation-mediated signaling in real time yields important information about the regulation of cellular function and insights into the origin of disease. Recent advances in the development of photolabile caged analogs of bioactive species and fluorescence-based sensors of protein kinase activities are useful for investigating protein phosphorylation and the roles of phosphoproteins. Photolabile caged analogs allow spatial and temporal control over the release of a compound, while fluorescence-based sensors allow the real-time visualization of kinase activity. Here, we discuss recent advances that have increased the specificity and availability of these tools. PMID:16084095

  7. Detection and identification of seismic signals recorded at Krakatau volcano (Indonesia) using artificial neural networks

    NASA Astrophysics Data System (ADS)

    Ibs-von Seht, M.

    2008-10-01

    The Anak Krakatau volcano (Indonesia) has been monitored by a multi-parametric system since 2005. A variety of signal types can be observed in the records of the seismic stations installed on the island volcano. These include volcano-induced signals such as LP, VT, and tremor-type events as well as signals not originating from the volcano such as regional tectonic earthquakes and transient noise signals. The work presented here aims at the realization of a system that automatically detects and identifies the signals in order to estimate and monitor current activity states of the volcano. An artificial neural network approach was chosen for the identification task. A set of parameters was defined, describing waveform and spectrogram properties of events detected by an amplitude-ratio-based (STA/LTA) algorithm. The parameters are fed into a neural network which is, after a training phase, able to generalize input data and identify corresponding event types. The success of the identification depends on the network architecture and training strategy. Several tests have been performed in order to determine appropriate network layout and training for the given problem. The performance of the final system is found to be well suited to get an overview of the seismic activity recorded at the volcano. The reliability of the network classifier, as well as general drawbacks of the methods used, are discussed.

  8. The ATM signaling network in development and disease

    PubMed Central

    Stracker, Travis H.; Roig, Ignasi; Knobel, Philip A.; Marjanović, Marko

    2013-01-01

    The DNA damage response (DDR) rapidly recognizes DNA lesions and initiates the appropriate cellular programs to maintain genome integrity. This includes the coordination of cell cycle checkpoints, transcription, translation, DNA repair, metabolism, and cell fate decisions, such as apoptosis or senescence (Jackson and Bartek, 2009). DNA double-strand breaks (DSBs) represent one of the most cytotoxic DNA lesions and defects in their metabolism underlie many human hereditary diseases characterized by genomic instability (Stracker and Petrini, 2011; McKinnon, 2012). Patients with hereditary defects in the DDR display defects in development, particularly affecting the central nervous system, the immune system and the germline, as well as aberrant metabolic regulation and cancer predisposition. Central to the DDR to DSBs is the ataxia-telangiectasia mutated (ATM) kinase, a master controller of signal transduction. Understanding how ATM signaling regulates various aspects of the DDR and its roles in vivo is critical for our understanding of human disease, its diagnosis and its treatment. This review will describe the general roles of ATM signaling and highlight some recent advances that have shed light on the diverse roles of ATM and related proteins in human disease. PMID:23532176

  9. Constitutive and ligand-induced EGFR signaling triggers distinct and mutually exclusive downstream signaling networks

    PubMed Central

    Chakraborty, Sharmistha; Li, Li; Puliyappadamba, VineshkumarThidil; Guo, Gao; Hatanpaa, Kimmo J.; Mickey, Bruce; Souza, Rhonda F.; Vo, Peggy; Herz, Joachim; Chen, Mei-Ru; Boothman, David A.; Pandita, Tej K.; Wang, David H.; Sen, Ganes C.; Habib, Amyn A.

    2014-01-01

    EGFR overexpression plays an important oncogenic role in cancer. Regular EGFR protein levels are increased in cancer cells and the receptor then becomes constitutively active. However, downstream signals generated by constitutively activated EGFR are unknown. Here we report that the overexpressed EGFR oscillates between two distinct and mutually exclusive modes of signaling. Constitutive or non-canonical EGFR signaling activates the transcription factor IRF3 leading to expression of IFI27, IFIT1, and TRAIL. Ligand-mediated activation of EGFR switches off IRF3 dependent transcription, activates canonical ERK and Akt signals, and confers sensitivity to chemotherapy and virus-induced cell death. Mechanistically, the distinct downstream signals result from a switch of EGFR associated proteins. EGFR constitutively complexes with IRF3 and TBK1 leading to TBK1 and IRF3 phosphorylation. Addition of EGF dissociates TBK1, IRF3, and EGFR leading to a loss of IRF3 activity, Shc-EGFR association and ERK activation. Finally, we provide evidence for non-canonical EGFR signaling in glioblastoma. PMID:25503978

  10. Emotional stress recognition using a new fusion link between electroencephalogram and peripheral signals

    PubMed Central

    Hosseini, Seyyed Abed; Khalilzadeh, Mohammad Ali; Naghibi-Sistani, Mohammad Bagher; Homam, Seyyed Mehran

    2015-01-01

    Background: This paper proposes a new emotional stress assessment system using multi-modal bio-signals. Electroencephalogram (EEG) is the reflection of brain activity and is widely used in clinical diagnosis and biomedical research. Methods: We design an efficient acquisition protocol to acquire the EEG signals in five channels (FP1, FP2, T3, T4 and Pz) and peripheral signals such as blood volume pulse, skin conductance (SC) and respiration, under images induction (calm-neutral and negatively excited) for the participants. The visual stimuli images are selected from the subset International Affective Picture System database. The qualitative and quantitative evaluation of peripheral signals are used to select suitable segments of EEG signals for improving the accuracy of signal labeling according to emotional stress states. After pre-processing, wavelet coefficients, fractal dimension, and Lempel-Ziv complexity are used to extract the features of the EEG signals. The vast number of features leads to the problem of dimensionality, which is solved using the genetic algorithm as a feature selection method. Results: The results show that the average classification accuracy is 89.6% for two categories of emotional stress states using the support vector machine (SVM). Conclusion: This is a great improvement in results compared to other similar researches. We achieve a noticeable improvement of 11.3% in accuracy using SVM classifier, in compared to previous studies. Therefore, a new fusion between EEG and peripheral signals are more robust in comparison to the separate signals. PMID:26622979

  11. Dynamical system modeling via signal reduction and neural network simulation

    SciTech Connect

    Paez, T.L.; Hunter, N.F.

    1997-11-01

    Many dynamical systems tested in the field and the laboratory display significant nonlinear behavior. Accurate characterization of such systems requires modeling in a nonlinear framework. One construct forming a basis for nonlinear modeling is that of the artificial neural network (ANN). However, when system behavior is complex, the amount of data required to perform training can become unreasonable. The authors reduce